Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ

Amy S Rosenberg MD Supervisory Medical Officer Office of Biotechnology

Products CDER FDA

Immunological tolerance bull Definition

ndash unresponsiveness to an antigen induced by exposure of lymphocytes to that antigen antigen-specific (unlike ldquoimmunosuppressionrdquo)

bull Significance ndash All individuals are tolerant of their own antigens to a greater or

lesser extent (self-tolerance) breakdown of self-tolerance results in autoimmunity

ndash Therapeutic potential Inducing tolerance may be exploited to prevent graft rejection treat autoimmune and allergic diseases and prevent immune responses in gene therapy and stem cell transplantation

2

How Self is Self

Self proteins can be immunogenic and tolerance to them broken (eg by administration of a therapeutic homolog) TolerogenicityImmunogenicity of self proteins depends largely on

ndash Abundance determines the degree to which developing potentially autoreactive T and B cells are tolerized

ndash Alteration in chemicalphysical structure aggregation post-translational modifications (PTMs) chemical degradation

ndash Adjuvants bull Extrinsic innate immune response modifiers

bull Intrinsic immunomodulatory properties of the protein

Expect Immunogenicity No tolerance

Neutralize Product Hypersensitivity

Rare Immunogenicity Autoimmunity

Foreign proteins Self Proteins

FOREIGN SELF

Expect Immunogenicity

No tolerance Neutralize Product

Hypersensitivity

Potential Immunogenicity

Incomplete tolerance Altered structure Antigen Present

Epitope spreading

Rare Immunogenicity

Robust tolerance Novel Route of Administration Adjuvants HLA Haplotype Specific

bull Low abundance self-protein bull Aggregates of self proteins bull Chemical degradationmodification of self proteins bull Adjuvants

Antibody Response to Proteins The Mediators

BCR

Short lived

Plasma cell

Antigen

DC

Peptide

Cytokines

MHCII TCR

Memory B cell

Antibodies Helper T cell Tfh

B cell

Antibodies

Long lived

Plasma cell

Cellular Interactions in Generation of T cell Mediated Responses

(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)

CD4+ T cell

TCR TCR TCR

APC

Uptake by APC

Necrotic and apoptotic

cell material

MHC class-II

Cell T cell help

MHC class-II MHC class-I

APC

CD4+ T cell CD8+ T cell

A B

T Cells More Robustly Tolerant than B Cells to Self Proteins

(Weigle 1980)

T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms

bull Negative selection ndash T cells with high affinity for thymicperipheral tissue antigens that

access thymus in sufficient quantities ndash T cells with high affinity for peripheral tissue antigens whose

expression in thymus is mediated by transcription factor AIRE bull Natural (thymically generated) regulatory T cells (Tregs)

ndash Lineage deviation of T cells with high affinity to proteins expressed in thymus to immune suppressive regulatory T cells (Tregs) distinguished by FOXP3 transcription factor neuropilin and helios

Consequences of Self Antigen Recognition in Thymus

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier 10

Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs

(Sakaguchi et al 2008)

Mother of IPEX patient

IPEX patient

Normal

Autoimmune disease

Inflammatory bowel disease

Allergy

X

Confidential 7172016 12

167

Figure described in Palomares O Martiacuten-Fontecha M Lauener R Traidl-Hoffmann C Cavkaytar O Akdis M Akdis CA Regulatory T cells and immune regulation of allergic diseases roles of IL-10 and TGF- β Genes Immun 2014 Dec15(8)511-20

Natural tTreg nTreg originate in the thymus positively selected Inducedperipheral (ip)Tregs generated in the periphery originate from CD4+ T cells in response to environmental antigens

Tregs Arise in the Periphery (ip Tregs) as well as in the Thymus (tnTregs)

Immunological tolerance bull Definition

ndash unresponsiveness to an antigen induced by exposure of lymphocytes to that antigen antigen-specific (unlike ldquoimmunosuppressionrdquo)

bull Significance ndash All individuals are tolerant of their own antigens to a greater or

lesser extent (self-tolerance) breakdown of self-tolerance results in autoimmunity

ndash Therapeutic potential Inducing tolerance may be exploited to prevent graft rejection treat autoimmune and allergic diseases and prevent immune responses in gene therapy and stem cell transplantation

2

How Self is Self

Self proteins can be immunogenic and tolerance to them broken (eg by administration of a therapeutic homolog) TolerogenicityImmunogenicity of self proteins depends largely on

ndash Abundance determines the degree to which developing potentially autoreactive T and B cells are tolerized

ndash Alteration in chemicalphysical structure aggregation post-translational modifications (PTMs) chemical degradation

ndash Adjuvants bull Extrinsic innate immune response modifiers

bull Intrinsic immunomodulatory properties of the protein

Expect Immunogenicity No tolerance

Neutralize Product Hypersensitivity

Rare Immunogenicity Autoimmunity

Foreign proteins Self Proteins

FOREIGN SELF

Expect Immunogenicity

No tolerance Neutralize Product

Hypersensitivity

Potential Immunogenicity

Incomplete tolerance Altered structure Antigen Present

Epitope spreading

Rare Immunogenicity

Robust tolerance Novel Route of Administration Adjuvants HLA Haplotype Specific

bull Low abundance self-protein bull Aggregates of self proteins bull Chemical degradationmodification of self proteins bull Adjuvants

Antibody Response to Proteins The Mediators

BCR

Short lived

Plasma cell

Antigen

DC

Peptide

Cytokines

MHCII TCR

Memory B cell

Antibodies Helper T cell Tfh

B cell

Antibodies

Long lived

Plasma cell

Cellular Interactions in Generation of T cell Mediated Responses

(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)

CD4+ T cell

TCR TCR TCR

APC

Uptake by APC

Necrotic and apoptotic

cell material

MHC class-II

Cell T cell help

MHC class-II MHC class-I

APC

CD4+ T cell CD8+ T cell

A B

T Cells More Robustly Tolerant than B Cells to Self Proteins

(Weigle 1980)

T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms

bull Negative selection ndash T cells with high affinity for thymicperipheral tissue antigens that

access thymus in sufficient quantities ndash T cells with high affinity for peripheral tissue antigens whose

expression in thymus is mediated by transcription factor AIRE bull Natural (thymically generated) regulatory T cells (Tregs)

ndash Lineage deviation of T cells with high affinity to proteins expressed in thymus to immune suppressive regulatory T cells (Tregs) distinguished by FOXP3 transcription factor neuropilin and helios

Consequences of Self Antigen Recognition in Thymus

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier 10

Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs

(Sakaguchi et al 2008)

Mother of IPEX patient

IPEX patient

Normal

Autoimmune disease

Inflammatory bowel disease

Allergy

X

Confidential 7172016 12

167

Figure described in Palomares O Martiacuten-Fontecha M Lauener R Traidl-Hoffmann C Cavkaytar O Akdis M Akdis CA Regulatory T cells and immune regulation of allergic diseases roles of IL-10 and TGF- β Genes Immun 2014 Dec15(8)511-20

Natural tTreg nTreg originate in the thymus positively selected Inducedperipheral (ip)Tregs generated in the periphery originate from CD4+ T cells in response to environmental antigens

Tregs Arise in the Periphery (ip Tregs) as well as in the Thymus (tnTregs)

How Self is Self

Self proteins can be immunogenic and tolerance to them broken (eg by administration of a therapeutic homolog) TolerogenicityImmunogenicity of self proteins depends largely on

ndash Abundance determines the degree to which developing potentially autoreactive T and B cells are tolerized

ndash Alteration in chemicalphysical structure aggregation post-translational modifications (PTMs) chemical degradation

ndash Adjuvants bull Extrinsic innate immune response modifiers

bull Intrinsic immunomodulatory properties of the protein

Expect Immunogenicity No tolerance

Neutralize Product Hypersensitivity

Rare Immunogenicity Autoimmunity

Foreign proteins Self Proteins

FOREIGN SELF

Expect Immunogenicity

No tolerance Neutralize Product

Hypersensitivity

Potential Immunogenicity

Incomplete tolerance Altered structure Antigen Present

Epitope spreading

Rare Immunogenicity

Robust tolerance Novel Route of Administration Adjuvants HLA Haplotype Specific

bull Low abundance self-protein bull Aggregates of self proteins bull Chemical degradationmodification of self proteins bull Adjuvants

Antibody Response to Proteins The Mediators

BCR

Short lived

Plasma cell

Antigen

DC

Peptide

Cytokines

MHCII TCR

Memory B cell

Antibodies Helper T cell Tfh

B cell

Antibodies

Long lived

Plasma cell

Cellular Interactions in Generation of T cell Mediated Responses

(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)

CD4+ T cell

TCR TCR TCR

APC

Uptake by APC

Necrotic and apoptotic

cell material

MHC class-II

Cell T cell help

MHC class-II MHC class-I

APC

CD4+ T cell CD8+ T cell

A B

T Cells More Robustly Tolerant than B Cells to Self Proteins

(Weigle 1980)

T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms

bull Negative selection ndash T cells with high affinity for thymicperipheral tissue antigens that

access thymus in sufficient quantities ndash T cells with high affinity for peripheral tissue antigens whose

expression in thymus is mediated by transcription factor AIRE bull Natural (thymically generated) regulatory T cells (Tregs)

ndash Lineage deviation of T cells with high affinity to proteins expressed in thymus to immune suppressive regulatory T cells (Tregs) distinguished by FOXP3 transcription factor neuropilin and helios

Consequences of Self Antigen Recognition in Thymus

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier 10

Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs

(Sakaguchi et al 2008)

Mother of IPEX patient

IPEX patient

Normal

Autoimmune disease

Inflammatory bowel disease

Allergy

X

Confidential 7172016 12

167

Figure described in Palomares O Martiacuten-Fontecha M Lauener R Traidl-Hoffmann C Cavkaytar O Akdis M Akdis CA Regulatory T cells and immune regulation of allergic diseases roles of IL-10 and TGF- β Genes Immun 2014 Dec15(8)511-20

Natural tTreg nTreg originate in the thymus positively selected Inducedperipheral (ip)Tregs generated in the periphery originate from CD4+ T cells in response to environmental antigens

Tregs Arise in the Periphery (ip Tregs) as well as in the Thymus (tnTregs)

Expect Immunogenicity No tolerance

Neutralize Product Hypersensitivity

Rare Immunogenicity Autoimmunity

Foreign proteins Self Proteins

FOREIGN SELF

Expect Immunogenicity

No tolerance Neutralize Product

Hypersensitivity

Potential Immunogenicity

Incomplete tolerance Altered structure Antigen Present

Epitope spreading

Rare Immunogenicity

Robust tolerance Novel Route of Administration Adjuvants HLA Haplotype Specific

bull Low abundance self-protein bull Aggregates of self proteins bull Chemical degradationmodification of self proteins bull Adjuvants

Antibody Response to Proteins The Mediators

BCR

Short lived

Plasma cell

Antigen

DC

Peptide

Cytokines

MHCII TCR

Memory B cell

Antibodies Helper T cell Tfh

B cell

Antibodies

Long lived

Plasma cell

Cellular Interactions in Generation of T cell Mediated Responses

(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)

CD4+ T cell

TCR TCR TCR

APC

Uptake by APC

Necrotic and apoptotic

cell material

MHC class-II

Cell T cell help

MHC class-II MHC class-I

APC

CD4+ T cell CD8+ T cell

A B

T Cells More Robustly Tolerant than B Cells to Self Proteins

(Weigle 1980)

T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms

bull Negative selection ndash T cells with high affinity for thymicperipheral tissue antigens that

access thymus in sufficient quantities ndash T cells with high affinity for peripheral tissue antigens whose

expression in thymus is mediated by transcription factor AIRE bull Natural (thymically generated) regulatory T cells (Tregs)

ndash Lineage deviation of T cells with high affinity to proteins expressed in thymus to immune suppressive regulatory T cells (Tregs) distinguished by FOXP3 transcription factor neuropilin and helios

Consequences of Self Antigen Recognition in Thymus

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier 10

Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs

(Sakaguchi et al 2008)

Mother of IPEX patient

IPEX patient

Normal

Autoimmune disease

Inflammatory bowel disease

Allergy

X

Confidential 7172016 12

167

Figure described in Palomares O Martiacuten-Fontecha M Lauener R Traidl-Hoffmann C Cavkaytar O Akdis M Akdis CA Regulatory T cells and immune regulation of allergic diseases roles of IL-10 and TGF- β Genes Immun 2014 Dec15(8)511-20

Natural tTreg nTreg originate in the thymus positively selected Inducedperipheral (ip)Tregs generated in the periphery originate from CD4+ T cells in response to environmental antigens

Tregs Arise in the Periphery (ip Tregs) as well as in the Thymus (tnTregs)

FOREIGN SELF

Expect Immunogenicity

No tolerance Neutralize Product

Hypersensitivity

Potential Immunogenicity

Incomplete tolerance Altered structure Antigen Present

Epitope spreading

Rare Immunogenicity

Robust tolerance Novel Route of Administration Adjuvants HLA Haplotype Specific

bull Low abundance self-protein bull Aggregates of self proteins bull Chemical degradationmodification of self proteins bull Adjuvants

Antibody Response to Proteins The Mediators

BCR

Short lived

Plasma cell

Antigen

DC

Peptide

Cytokines

MHCII TCR

Memory B cell

Antibodies Helper T cell Tfh

B cell

Antibodies

Long lived

Plasma cell

Cellular Interactions in Generation of T cell Mediated Responses

(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)

CD4+ T cell

TCR TCR TCR

APC

Uptake by APC

Necrotic and apoptotic

cell material

MHC class-II

Cell T cell help

MHC class-II MHC class-I

APC

CD4+ T cell CD8+ T cell

A B

T Cells More Robustly Tolerant than B Cells to Self Proteins

(Weigle 1980)

T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms

bull Negative selection ndash T cells with high affinity for thymicperipheral tissue antigens that

access thymus in sufficient quantities ndash T cells with high affinity for peripheral tissue antigens whose

expression in thymus is mediated by transcription factor AIRE bull Natural (thymically generated) regulatory T cells (Tregs)

ndash Lineage deviation of T cells with high affinity to proteins expressed in thymus to immune suppressive regulatory T cells (Tregs) distinguished by FOXP3 transcription factor neuropilin and helios

Consequences of Self Antigen Recognition in Thymus

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier 10

Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs

(Sakaguchi et al 2008)

Mother of IPEX patient

IPEX patient

Normal

Autoimmune disease

Inflammatory bowel disease

Allergy

X

Confidential 7172016 12

167

Figure described in Palomares O Martiacuten-Fontecha M Lauener R Traidl-Hoffmann C Cavkaytar O Akdis M Akdis CA Regulatory T cells and immune regulation of allergic diseases roles of IL-10 and TGF- β Genes Immun 2014 Dec15(8)511-20

Natural tTreg nTreg originate in the thymus positively selected Inducedperipheral (ip)Tregs generated in the periphery originate from CD4+ T cells in response to environmental antigens

Tregs Arise in the Periphery (ip Tregs) as well as in the Thymus (tnTregs)

Antibody Response to Proteins The Mediators

BCR

Short lived

Plasma cell

Antigen

DC

Peptide

Cytokines

MHCII TCR

Memory B cell

Antibodies Helper T cell Tfh

B cell

Antibodies

Long lived

Plasma cell

Cellular Interactions in Generation of T cell Mediated Responses

(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)

CD4+ T cell

TCR TCR TCR

APC

Uptake by APC

Necrotic and apoptotic

cell material

MHC class-II

Cell T cell help

MHC class-II MHC class-I

APC

CD4+ T cell CD8+ T cell

A B

T Cells More Robustly Tolerant than B Cells to Self Proteins

(Weigle 1980)

T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms

bull Negative selection ndash T cells with high affinity for thymicperipheral tissue antigens that

access thymus in sufficient quantities ndash T cells with high affinity for peripheral tissue antigens whose

expression in thymus is mediated by transcription factor AIRE bull Natural (thymically generated) regulatory T cells (Tregs)

ndash Lineage deviation of T cells with high affinity to proteins expressed in thymus to immune suppressive regulatory T cells (Tregs) distinguished by FOXP3 transcription factor neuropilin and helios

Consequences of Self Antigen Recognition in Thymus

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier 10

Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs

(Sakaguchi et al 2008)

Mother of IPEX patient

IPEX patient

Normal

Autoimmune disease

Inflammatory bowel disease

Allergy

X

Confidential 7172016 12

167

Figure described in Palomares O Martiacuten-Fontecha M Lauener R Traidl-Hoffmann C Cavkaytar O Akdis M Akdis CA Regulatory T cells and immune regulation of allergic diseases roles of IL-10 and TGF- β Genes Immun 2014 Dec15(8)511-20

Natural tTreg nTreg originate in the thymus positively selected Inducedperipheral (ip)Tregs generated in the periphery originate from CD4+ T cells in response to environmental antigens

Tregs Arise in the Periphery (ip Tregs) as well as in the Thymus (tnTregs)

Cellular Interactions in Generation of T cell Mediated Responses

(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)

CD4+ T cell

TCR TCR TCR

APC

Uptake by APC

Necrotic and apoptotic

cell material

MHC class-II

Cell T cell help

MHC class-II MHC class-I

APC

CD4+ T cell CD8+ T cell

A B

T Cells More Robustly Tolerant than B Cells to Self Proteins

(Weigle 1980)

T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms

bull Negative selection ndash T cells with high affinity for thymicperipheral tissue antigens that

access thymus in sufficient quantities ndash T cells with high affinity for peripheral tissue antigens whose

expression in thymus is mediated by transcription factor AIRE bull Natural (thymically generated) regulatory T cells (Tregs)

ndash Lineage deviation of T cells with high affinity to proteins expressed in thymus to immune suppressive regulatory T cells (Tregs) distinguished by FOXP3 transcription factor neuropilin and helios

Consequences of Self Antigen Recognition in Thymus

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier 10

Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs

(Sakaguchi et al 2008)

Mother of IPEX patient

IPEX patient

Normal

Autoimmune disease

Inflammatory bowel disease

Allergy

X

Confidential 7172016 12

167

Figure described in Palomares O Martiacuten-Fontecha M Lauener R Traidl-Hoffmann C Cavkaytar O Akdis M Akdis CA Regulatory T cells and immune regulation of allergic diseases roles of IL-10 and TGF- β Genes Immun 2014 Dec15(8)511-20

Natural tTreg nTreg originate in the thymus positively selected Inducedperipheral (ip)Tregs generated in the periphery originate from CD4+ T cells in response to environmental antigens

Tregs Arise in the Periphery (ip Tregs) as well as in the Thymus (tnTregs)

T Cells More Robustly Tolerant than B Cells to Self Proteins

(Weigle 1980)

T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms

bull Negative selection ndash T cells with high affinity for thymicperipheral tissue antigens that

access thymus in sufficient quantities ndash T cells with high affinity for peripheral tissue antigens whose

expression in thymus is mediated by transcription factor AIRE bull Natural (thymically generated) regulatory T cells (Tregs)

ndash Lineage deviation of T cells with high affinity to proteins expressed in thymus to immune suppressive regulatory T cells (Tregs) distinguished by FOXP3 transcription factor neuropilin and helios

Consequences of Self Antigen Recognition in Thymus

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier 10

Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs

(Sakaguchi et al 2008)

Mother of IPEX patient

IPEX patient

Normal

Autoimmune disease

Inflammatory bowel disease

Allergy

X

Confidential 7172016 12

167

Figure described in Palomares O Martiacuten-Fontecha M Lauener R Traidl-Hoffmann C Cavkaytar O Akdis M Akdis CA Regulatory T cells and immune regulation of allergic diseases roles of IL-10 and TGF- β Genes Immun 2014 Dec15(8)511-20

Natural tTreg nTreg originate in the thymus positively selected Inducedperipheral (ip)Tregs generated in the periphery originate from CD4+ T cells in response to environmental antigens

Tregs Arise in the Periphery (ip Tregs) as well as in the Thymus (tnTregs)

T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms

bull Negative selection ndash T cells with high affinity for thymicperipheral tissue antigens that

access thymus in sufficient quantities ndash T cells with high affinity for peripheral tissue antigens whose

expression in thymus is mediated by transcription factor AIRE bull Natural (thymically generated) regulatory T cells (Tregs)

ndash Lineage deviation of T cells with high affinity to proteins expressed in thymus to immune suppressive regulatory T cells (Tregs) distinguished by FOXP3 transcription factor neuropilin and helios

Consequences of Self Antigen Recognition in Thymus

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier 10

Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs

(Sakaguchi et al 2008)

Mother of IPEX patient

IPEX patient

Normal

Autoimmune disease

Inflammatory bowel disease

Allergy

X

Confidential 7172016 12

167

Figure described in Palomares O Martiacuten-Fontecha M Lauener R Traidl-Hoffmann C Cavkaytar O Akdis M Akdis CA Regulatory T cells and immune regulation of allergic diseases roles of IL-10 and TGF- β Genes Immun 2014 Dec15(8)511-20

Natural tTreg nTreg originate in the thymus positively selected Inducedperipheral (ip)Tregs generated in the periphery originate from CD4+ T cells in response to environmental antigens

Tregs Arise in the Periphery (ip Tregs) as well as in the Thymus (tnTregs)

Consequences of Self Antigen Recognition in Thymus

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier 10

Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs

(Sakaguchi et al 2008)

Mother of IPEX patient

IPEX patient

Normal

Autoimmune disease

Inflammatory bowel disease

Allergy

X

Confidential 7172016 12

167

Figure described in Palomares O Martiacuten-Fontecha M Lauener R Traidl-Hoffmann C Cavkaytar O Akdis M Akdis CA Regulatory T cells and immune regulation of allergic diseases roles of IL-10 and TGF- β Genes Immun 2014 Dec15(8)511-20

Natural tTreg nTreg originate in the thymus positively selected Inducedperipheral (ip)Tregs generated in the periphery originate from CD4+ T cells in response to environmental antigens

Tregs Arise in the Periphery (ip Tregs) as well as in the Thymus (tnTregs)

Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs

(Sakaguchi et al 2008)

Mother of IPEX patient

IPEX patient

Normal

Autoimmune disease

Inflammatory bowel disease

Allergy

X

Confidential 7172016 12

167

Figure described in Palomares O Martiacuten-Fontecha M Lauener R Traidl-Hoffmann C Cavkaytar O Akdis M Akdis CA Regulatory T cells and immune regulation of allergic diseases roles of IL-10 and TGF- β Genes Immun 2014 Dec15(8)511-20

Natural tTreg nTreg originate in the thymus positively selected Inducedperipheral (ip)Tregs generated in the periphery originate from CD4+ T cells in response to environmental antigens

Tregs Arise in the Periphery (ip Tregs) as well as in the Thymus (tnTregs)

Confidential 7172016 12

167

Figure described in Palomares O Martiacuten-Fontecha M Lauener R Traidl-Hoffmann C Cavkaytar O Akdis M Akdis CA Regulatory T cells and immune regulation of allergic diseases roles of IL-10 and TGF- β Genes Immun 2014 Dec15(8)511-20

Natural tTreg nTreg originate in the thymus positively selected Inducedperipheral (ip)Tregs generated in the periphery originate from CD4+ T cells in response to environmental antigens

Tregs Arise in the Periphery (ip Tregs) as well as in the Thymus (tnTregs)

13

What Self Antigens are Seen in the Thymus

bull Ubiquitous cell-associated and circulating proteins bull Peripheral tissue antigens expression mediated by

Autoimmune Regulator (AIRE) transcription factor in thymic medullary epithelial cells and extrathymic bone marrow derived APC (eTACs) bull signal self-reactive thymocytes for death or lineage

deviation to Tregs

AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells

(Mathis and Benoist 2007)

AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1

(Kampe et al 2008)

AIRE Mediated Expression of of Liver Proteins in the Thymus

Cyp1a2 Prg4 Apoa1 Fgg Tdo2 Ambp Gys2 Fgb Alb Itih4 Apoa2 Apoc2 Mat1a Orm1 Itih3 Hp Igfbp1 Reln Hal Cyp26a1 Hamp

Cytochrome P450 family 1 subfamily A polypeptide 2

Proteoglycan 4 Apolipoprotein A-I Fibrinogen gamma chain Tryptophan 23-dioxygenase Alpha-1-microglobulinbikunin precursor Glycogen synthase 2 (liver) Fibrinogen beta chain Albumin Inter-alpha-trypsin inhibitor heavy chain

family member 4 Apolipoprotein A-II Apolipoprotein C-II Methionine adenosyltransferase I alpha Orosomucoid 1 Inter-alpha-trypsin inhibitor heavy chain 3 Haptoglobin insulin-like growth factor binding protein 1 reelin Histidine ammonia-lyase cytochrome P450 family 26 subfamily a

polypeptide 1 Hepcidin antimicrobial peptide

2272 2631 6268 1749 1384 1392 922 1535 1465 191 3341 3456 995 2983 1448 1083 152 120 103 273 337

206 317 959 27 225 266 195 367 439 58 1118 1216 378 116 58 496 83 223 22786 714 9461

Gene ID Gene Annotation WT Aire KO

11 8 6 6 6 5 4 4 3 3 2 2 2 2 2 2 1 05 05 04 04

Fold Change

223 94 8043 5906 279 3641 52 6643 73775 681 11107 249 424 5651 300 15456 416 15 28 14 163

Liver Expression Protein atlas

The list is the combination of SI from PNAS 2012 by Matthieu Giraud and 02670 Table2 (Microarray data from Affymetrix MgU74Av2 gene chip by using 20040429 Affymetrix annotation FPKM values or number of Fragments Per Kilobase gene model and Million reads were calculated as the sum of all its protein-coding transcripts and the average FPKM value for replicate samples were used as abundance scores) from RNA-seq analysis

CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance

Thymus Periphery

Ubiquitous self-antigen

Tissue-restricted self-antigen (no thymic expression)

Tconv

Treg

No self-antigen

Deletion Pancreatic self antigen

Treg expansion Lung or

intestinal self antigen

R

R R

R

R

X Ignorance

Suppression

Legoux et al 2015 Immunity 43 896ndash908

CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation

Immunosuppression Engraftment

IL-23 IL-6 IL-21

TGFβ

IL-4

IL-12

Naiumlve CD4+ T cell

Th2 (IL-4 IL-5

IL-13)

Treg (IL-10 TGFβ)

TH17 (IL-17)

TH1 (IFNγ)

Liver graft rejection

Stat4 T-bet

Stat6 Gata3

Stat3 RORγ

Stat5 Foxp3

(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)

Autoimmunity is Suppressed by both Thymic and Peripheral Tregs

Local immune suppression Oral tolerance Fetal tolerance Mucosal tolerance

Nrp-1

APC

Thymus tTreg

Tnaive

Teff

pTreg

Teff Site of Inflammation

specialized APC

Immune homeostasis Autoimmune responses

Yadav M et al Frontiers in Immunology 2013

Mechanisms by which Tregs Suppress Immune Responses

20

Tolerance Mechanisms in the Liver bull 80 of the blood that passes through the liver sinusoids comes from the GI tract

carrying harmless dietary and commensal organism antigens the default immune response must be tolerancehellipmaintained by the myriad of tolerogenic APC in the liverrdquo hellipcontinuous exposure of liver cells to these entities leads to ldquoendotoxin tolerancerdquo ldquo

bull Antigen presentation within the liver mediated by a variety of cell types including plasmacytoid and myeloid dendritic cells (pmDC) Kupffer Cells sinusoidal endothelial cells hepatic stellate cells and hepatocytes generally leads to T cell tolerance and not immunity

ndash pDC-IL-27 secretion mediates expression of PDL-1 on pDC promoting activation and expansion of Tregs

ndash mDC express PDL-1 induce IDO

ndash KC- expression of Fas-L kills CD8T cells IDO IL-10 expression of PDL-1

ndash Hepatocytes induce apoptosis of CD4+ and CD8+ Tcells

ndash LSEC functional inactivation of CD8+ T cells and bias CD4+ T cells to Treg-dependent on a cell surface expressed lectin (LSEC lectin)

bull CD8+T cells transiently activated then undergo apoptosis or exhaustion bull Generating robust immune responses appears to hinge on full activation of CD4+ T

cells which provide help to CD8+ T cells

21

Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells

IL-10

TGF-β1

IDO

Cox2-gtPGE2

FasL

HEP

Dead HEP

ldquoMDSCrdquo

LSEC

pDC

mDC

HSC Kupffer

PD-L1

LSECtin

IL-10

IL-27

PD-L1

IDO PD-L1

TGF-β1 + retinol

PD-L1

kynurenine

IL-10 TGFβ1 other

IFN-γ

HGF

T reg

T reg

8+

4+

Crispe IN 2014 Hepatology

Generating Immune Responses in the Liver

bull NK NKT γδ and mucosal associated innate lT cell (MAIT) activation and responses may be critical in response to infectious organisms ndash Promote DC maturation into APCs activate CD4+ CD8+ T cells Bcells

PMNs and macrophages via contact and cytokine dependent interactions

bull However none of these populations uses HLA the single greatest risk factor for autoimmune disease as restriction element for immune response suggesting criticality for mediating response to infection but potentially only indirect mechanism of action in triggering AIH spectrum

23

Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of

Infection but not in the Context of HLA (Doherty D 2016 J Autoimmunity)

Type 1 NKT cell Type 2 NKT cell MAIT cell γδ T cell γδ T cell γδ T cell γδ T cell

Vα24Jα18 Diverse Vα72Jα33 Vδ1 Vδ1 Vγ9Vδ2 Vδ3

CD1d CD1d MR1 MICA MICB Rae1 CD1c CD1d Butyrophilin 3A1 CD1d

Glycolipids Glycolipids Riboflavin metabolites Stress-inducible proteins Glycolipids Pyrophosphates Glycolipids

Cell Type T Cell Receptor Antigen-presenting

Molecule Stimulatory

Ligands

Genetic Basis of ToleranceAutoimmunity

bull Genetic predisposition of autoimmune diseases bull HLA genes

ndash Major genetic association with autoimmune diseases ndash Disease-associated alleles are present in normal individuals

bull Non-HLA genes ndash Many loci identified by genomic methods (eg genome wide

association studies [GWAS]) ndash Examples include FoxP3 AIRE CD25 (IL2R-α) NOD (sensor of

microbes) PTPN22 (tyrosine phosphatase) bull Multiple genes are associated with autoimmunity

ndash No single mutation causes common autoimmune diseases

25

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells

(Mathis and Benoist 2007)

AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1

(Kampe et al 2008)

AIRE Mediated Expression of of Liver Proteins in the Thymus

Cyp1a2 Prg4 Apoa1 Fgg Tdo2 Ambp Gys2 Fgb Alb Itih4 Apoa2 Apoc2 Mat1a Orm1 Itih3 Hp Igfbp1 Reln Hal Cyp26a1 Hamp

Cytochrome P450 family 1 subfamily A polypeptide 2

Proteoglycan 4 Apolipoprotein A-I Fibrinogen gamma chain Tryptophan 23-dioxygenase Alpha-1-microglobulinbikunin precursor Glycogen synthase 2 (liver) Fibrinogen beta chain Albumin Inter-alpha-trypsin inhibitor heavy chain

family member 4 Apolipoprotein A-II Apolipoprotein C-II Methionine adenosyltransferase I alpha Orosomucoid 1 Inter-alpha-trypsin inhibitor heavy chain 3 Haptoglobin insulin-like growth factor binding protein 1 reelin Histidine ammonia-lyase cytochrome P450 family 26 subfamily a

polypeptide 1 Hepcidin antimicrobial peptide

2272 2631 6268 1749 1384 1392 922 1535 1465 191 3341 3456 995 2983 1448 1083 152 120 103 273 337

206 317 959 27 225 266 195 367 439 58 1118 1216 378 116 58 496 83 223 22786 714 9461

Gene ID Gene Annotation WT Aire KO

11 8 6 6 6 5 4 4 3 3 2 2 2 2 2 2 1 05 05 04 04

Fold Change

223 94 8043 5906 279 3641 52 6643 73775 681 11107 249 424 5651 300 15456 416 15 28 14 163

Liver Expression Protein atlas

The list is the combination of SI from PNAS 2012 by Matthieu Giraud and 02670 Table2 (Microarray data from Affymetrix MgU74Av2 gene chip by using 20040429 Affymetrix annotation FPKM values or number of Fragments Per Kilobase gene model and Million reads were calculated as the sum of all its protein-coding transcripts and the average FPKM value for replicate samples were used as abundance scores) from RNA-seq analysis

CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance

Thymus Periphery

Ubiquitous self-antigen

Tissue-restricted self-antigen (no thymic expression)

Tconv

Treg

No self-antigen

Deletion Pancreatic self antigen

Treg expansion Lung or

intestinal self antigen

R

R R

R

R

X Ignorance

Suppression

Legoux et al 2015 Immunity 43 896ndash908

CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation

Immunosuppression Engraftment

IL-23 IL-6 IL-21

TGFβ

IL-4

IL-12

Naiumlve CD4+ T cell

Th2 (IL-4 IL-5

IL-13)

Treg (IL-10 TGFβ)

TH17 (IL-17)

TH1 (IFNγ)

Liver graft rejection

Stat4 T-bet

Stat6 Gata3

Stat3 RORγ

Stat5 Foxp3

(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)

Autoimmunity is Suppressed by both Thymic and Peripheral Tregs

Local immune suppression Oral tolerance Fetal tolerance Mucosal tolerance

Nrp-1

APC

Thymus tTreg

Tnaive

Teff

pTreg

Teff Site of Inflammation

specialized APC

Immune homeostasis Autoimmune responses

Yadav M et al Frontiers in Immunology 2013

Mechanisms by which Tregs Suppress Immune Responses

20

Tolerance Mechanisms in the Liver bull 80 of the blood that passes through the liver sinusoids comes from the GI tract

carrying harmless dietary and commensal organism antigens the default immune response must be tolerancehellipmaintained by the myriad of tolerogenic APC in the liverrdquo hellipcontinuous exposure of liver cells to these entities leads to ldquoendotoxin tolerancerdquo ldquo

bull Antigen presentation within the liver mediated by a variety of cell types including plasmacytoid and myeloid dendritic cells (pmDC) Kupffer Cells sinusoidal endothelial cells hepatic stellate cells and hepatocytes generally leads to T cell tolerance and not immunity

ndash pDC-IL-27 secretion mediates expression of PDL-1 on pDC promoting activation and expansion of Tregs

ndash mDC express PDL-1 induce IDO

ndash KC- expression of Fas-L kills CD8T cells IDO IL-10 expression of PDL-1

ndash Hepatocytes induce apoptosis of CD4+ and CD8+ Tcells

ndash LSEC functional inactivation of CD8+ T cells and bias CD4+ T cells to Treg-dependent on a cell surface expressed lectin (LSEC lectin)

bull CD8+T cells transiently activated then undergo apoptosis or exhaustion bull Generating robust immune responses appears to hinge on full activation of CD4+ T

cells which provide help to CD8+ T cells

21

Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells

IL-10

TGF-β1

IDO

Cox2-gtPGE2

FasL

HEP

Dead HEP

ldquoMDSCrdquo

LSEC

pDC

mDC

HSC Kupffer

PD-L1

LSECtin

IL-10

IL-27

PD-L1

IDO PD-L1

TGF-β1 + retinol

PD-L1

kynurenine

IL-10 TGFβ1 other

IFN-γ

HGF

T reg

T reg

8+

4+

Crispe IN 2014 Hepatology

Generating Immune Responses in the Liver

bull NK NKT γδ and mucosal associated innate lT cell (MAIT) activation and responses may be critical in response to infectious organisms ndash Promote DC maturation into APCs activate CD4+ CD8+ T cells Bcells

PMNs and macrophages via contact and cytokine dependent interactions

bull However none of these populations uses HLA the single greatest risk factor for autoimmune disease as restriction element for immune response suggesting criticality for mediating response to infection but potentially only indirect mechanism of action in triggering AIH spectrum

23

Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of

Infection but not in the Context of HLA (Doherty D 2016 J Autoimmunity)

Type 1 NKT cell Type 2 NKT cell MAIT cell γδ T cell γδ T cell γδ T cell γδ T cell

Vα24Jα18 Diverse Vα72Jα33 Vδ1 Vδ1 Vγ9Vδ2 Vδ3

CD1d CD1d MR1 MICA MICB Rae1 CD1c CD1d Butyrophilin 3A1 CD1d

Glycolipids Glycolipids Riboflavin metabolites Stress-inducible proteins Glycolipids Pyrophosphates Glycolipids

Cell Type T Cell Receptor Antigen-presenting

Molecule Stimulatory

Ligands

Genetic Basis of ToleranceAutoimmunity

bull Genetic predisposition of autoimmune diseases bull HLA genes

ndash Major genetic association with autoimmune diseases ndash Disease-associated alleles are present in normal individuals

bull Non-HLA genes ndash Many loci identified by genomic methods (eg genome wide

association studies [GWAS]) ndash Examples include FoxP3 AIRE CD25 (IL2R-α) NOD (sensor of

microbes) PTPN22 (tyrosine phosphatase) bull Multiple genes are associated with autoimmunity

ndash No single mutation causes common autoimmune diseases

25

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1

(Kampe et al 2008)

AIRE Mediated Expression of of Liver Proteins in the Thymus

Cyp1a2 Prg4 Apoa1 Fgg Tdo2 Ambp Gys2 Fgb Alb Itih4 Apoa2 Apoc2 Mat1a Orm1 Itih3 Hp Igfbp1 Reln Hal Cyp26a1 Hamp

Cytochrome P450 family 1 subfamily A polypeptide 2

Proteoglycan 4 Apolipoprotein A-I Fibrinogen gamma chain Tryptophan 23-dioxygenase Alpha-1-microglobulinbikunin precursor Glycogen synthase 2 (liver) Fibrinogen beta chain Albumin Inter-alpha-trypsin inhibitor heavy chain

family member 4 Apolipoprotein A-II Apolipoprotein C-II Methionine adenosyltransferase I alpha Orosomucoid 1 Inter-alpha-trypsin inhibitor heavy chain 3 Haptoglobin insulin-like growth factor binding protein 1 reelin Histidine ammonia-lyase cytochrome P450 family 26 subfamily a

polypeptide 1 Hepcidin antimicrobial peptide

2272 2631 6268 1749 1384 1392 922 1535 1465 191 3341 3456 995 2983 1448 1083 152 120 103 273 337

206 317 959 27 225 266 195 367 439 58 1118 1216 378 116 58 496 83 223 22786 714 9461

Gene ID Gene Annotation WT Aire KO

11 8 6 6 6 5 4 4 3 3 2 2 2 2 2 2 1 05 05 04 04

Fold Change

223 94 8043 5906 279 3641 52 6643 73775 681 11107 249 424 5651 300 15456 416 15 28 14 163

Liver Expression Protein atlas

The list is the combination of SI from PNAS 2012 by Matthieu Giraud and 02670 Table2 (Microarray data from Affymetrix MgU74Av2 gene chip by using 20040429 Affymetrix annotation FPKM values or number of Fragments Per Kilobase gene model and Million reads were calculated as the sum of all its protein-coding transcripts and the average FPKM value for replicate samples were used as abundance scores) from RNA-seq analysis

CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance

Thymus Periphery

Ubiquitous self-antigen

Tissue-restricted self-antigen (no thymic expression)

Tconv

Treg

No self-antigen

Deletion Pancreatic self antigen

Treg expansion Lung or

intestinal self antigen

R

R R

R

R

X Ignorance

Suppression

Legoux et al 2015 Immunity 43 896ndash908

CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation

Immunosuppression Engraftment

IL-23 IL-6 IL-21

TGFβ

IL-4

IL-12

Naiumlve CD4+ T cell

Th2 (IL-4 IL-5

IL-13)

Treg (IL-10 TGFβ)

TH17 (IL-17)

TH1 (IFNγ)

Liver graft rejection

Stat4 T-bet

Stat6 Gata3

Stat3 RORγ

Stat5 Foxp3

(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)

Autoimmunity is Suppressed by both Thymic and Peripheral Tregs

Local immune suppression Oral tolerance Fetal tolerance Mucosal tolerance

Nrp-1

APC

Thymus tTreg

Tnaive

Teff

pTreg

Teff Site of Inflammation

specialized APC

Immune homeostasis Autoimmune responses

Yadav M et al Frontiers in Immunology 2013

Mechanisms by which Tregs Suppress Immune Responses

20

Tolerance Mechanisms in the Liver bull 80 of the blood that passes through the liver sinusoids comes from the GI tract

carrying harmless dietary and commensal organism antigens the default immune response must be tolerancehellipmaintained by the myriad of tolerogenic APC in the liverrdquo hellipcontinuous exposure of liver cells to these entities leads to ldquoendotoxin tolerancerdquo ldquo

bull Antigen presentation within the liver mediated by a variety of cell types including plasmacytoid and myeloid dendritic cells (pmDC) Kupffer Cells sinusoidal endothelial cells hepatic stellate cells and hepatocytes generally leads to T cell tolerance and not immunity

ndash pDC-IL-27 secretion mediates expression of PDL-1 on pDC promoting activation and expansion of Tregs

ndash mDC express PDL-1 induce IDO

ndash KC- expression of Fas-L kills CD8T cells IDO IL-10 expression of PDL-1

ndash Hepatocytes induce apoptosis of CD4+ and CD8+ Tcells

ndash LSEC functional inactivation of CD8+ T cells and bias CD4+ T cells to Treg-dependent on a cell surface expressed lectin (LSEC lectin)

bull CD8+T cells transiently activated then undergo apoptosis or exhaustion bull Generating robust immune responses appears to hinge on full activation of CD4+ T

cells which provide help to CD8+ T cells

21

Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells

IL-10

TGF-β1

IDO

Cox2-gtPGE2

FasL

HEP

Dead HEP

ldquoMDSCrdquo

LSEC

pDC

mDC

HSC Kupffer

PD-L1

LSECtin

IL-10

IL-27

PD-L1

IDO PD-L1

TGF-β1 + retinol

PD-L1

kynurenine

IL-10 TGFβ1 other

IFN-γ

HGF

T reg

T reg

8+

4+

Crispe IN 2014 Hepatology

Generating Immune Responses in the Liver

bull NK NKT γδ and mucosal associated innate lT cell (MAIT) activation and responses may be critical in response to infectious organisms ndash Promote DC maturation into APCs activate CD4+ CD8+ T cells Bcells

PMNs and macrophages via contact and cytokine dependent interactions

bull However none of these populations uses HLA the single greatest risk factor for autoimmune disease as restriction element for immune response suggesting criticality for mediating response to infection but potentially only indirect mechanism of action in triggering AIH spectrum

23

Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of

Infection but not in the Context of HLA (Doherty D 2016 J Autoimmunity)

Type 1 NKT cell Type 2 NKT cell MAIT cell γδ T cell γδ T cell γδ T cell γδ T cell

Vα24Jα18 Diverse Vα72Jα33 Vδ1 Vδ1 Vγ9Vδ2 Vδ3

CD1d CD1d MR1 MICA MICB Rae1 CD1c CD1d Butyrophilin 3A1 CD1d

Glycolipids Glycolipids Riboflavin metabolites Stress-inducible proteins Glycolipids Pyrophosphates Glycolipids

Cell Type T Cell Receptor Antigen-presenting

Molecule Stimulatory

Ligands

Genetic Basis of ToleranceAutoimmunity

bull Genetic predisposition of autoimmune diseases bull HLA genes

ndash Major genetic association with autoimmune diseases ndash Disease-associated alleles are present in normal individuals

bull Non-HLA genes ndash Many loci identified by genomic methods (eg genome wide

association studies [GWAS]) ndash Examples include FoxP3 AIRE CD25 (IL2R-α) NOD (sensor of

microbes) PTPN22 (tyrosine phosphatase) bull Multiple genes are associated with autoimmunity

ndash No single mutation causes common autoimmune diseases

25

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

AIRE Mediated Expression of of Liver Proteins in the Thymus

Cyp1a2 Prg4 Apoa1 Fgg Tdo2 Ambp Gys2 Fgb Alb Itih4 Apoa2 Apoc2 Mat1a Orm1 Itih3 Hp Igfbp1 Reln Hal Cyp26a1 Hamp

Cytochrome P450 family 1 subfamily A polypeptide 2

Proteoglycan 4 Apolipoprotein A-I Fibrinogen gamma chain Tryptophan 23-dioxygenase Alpha-1-microglobulinbikunin precursor Glycogen synthase 2 (liver) Fibrinogen beta chain Albumin Inter-alpha-trypsin inhibitor heavy chain

family member 4 Apolipoprotein A-II Apolipoprotein C-II Methionine adenosyltransferase I alpha Orosomucoid 1 Inter-alpha-trypsin inhibitor heavy chain 3 Haptoglobin insulin-like growth factor binding protein 1 reelin Histidine ammonia-lyase cytochrome P450 family 26 subfamily a

polypeptide 1 Hepcidin antimicrobial peptide

2272 2631 6268 1749 1384 1392 922 1535 1465 191 3341 3456 995 2983 1448 1083 152 120 103 273 337

206 317 959 27 225 266 195 367 439 58 1118 1216 378 116 58 496 83 223 22786 714 9461

Gene ID Gene Annotation WT Aire KO

11 8 6 6 6 5 4 4 3 3 2 2 2 2 2 2 1 05 05 04 04

Fold Change

223 94 8043 5906 279 3641 52 6643 73775 681 11107 249 424 5651 300 15456 416 15 28 14 163

Liver Expression Protein atlas

The list is the combination of SI from PNAS 2012 by Matthieu Giraud and 02670 Table2 (Microarray data from Affymetrix MgU74Av2 gene chip by using 20040429 Affymetrix annotation FPKM values or number of Fragments Per Kilobase gene model and Million reads were calculated as the sum of all its protein-coding transcripts and the average FPKM value for replicate samples were used as abundance scores) from RNA-seq analysis

CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance

Thymus Periphery

Ubiquitous self-antigen

Tissue-restricted self-antigen (no thymic expression)

Tconv

Treg

No self-antigen

Deletion Pancreatic self antigen

Treg expansion Lung or

intestinal self antigen

R

R R

R

R

X Ignorance

Suppression

Legoux et al 2015 Immunity 43 896ndash908

CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation

Immunosuppression Engraftment

IL-23 IL-6 IL-21

TGFβ

IL-4

IL-12

Naiumlve CD4+ T cell

Th2 (IL-4 IL-5

IL-13)

Treg (IL-10 TGFβ)

TH17 (IL-17)

TH1 (IFNγ)

Liver graft rejection

Stat4 T-bet

Stat6 Gata3

Stat3 RORγ

Stat5 Foxp3

(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)

Autoimmunity is Suppressed by both Thymic and Peripheral Tregs

Local immune suppression Oral tolerance Fetal tolerance Mucosal tolerance

Nrp-1

APC

Thymus tTreg

Tnaive

Teff

pTreg

Teff Site of Inflammation

specialized APC

Immune homeostasis Autoimmune responses

Yadav M et al Frontiers in Immunology 2013

Mechanisms by which Tregs Suppress Immune Responses

20

Tolerance Mechanisms in the Liver bull 80 of the blood that passes through the liver sinusoids comes from the GI tract

carrying harmless dietary and commensal organism antigens the default immune response must be tolerancehellipmaintained by the myriad of tolerogenic APC in the liverrdquo hellipcontinuous exposure of liver cells to these entities leads to ldquoendotoxin tolerancerdquo ldquo

bull Antigen presentation within the liver mediated by a variety of cell types including plasmacytoid and myeloid dendritic cells (pmDC) Kupffer Cells sinusoidal endothelial cells hepatic stellate cells and hepatocytes generally leads to T cell tolerance and not immunity

ndash pDC-IL-27 secretion mediates expression of PDL-1 on pDC promoting activation and expansion of Tregs

ndash mDC express PDL-1 induce IDO

ndash KC- expression of Fas-L kills CD8T cells IDO IL-10 expression of PDL-1

ndash Hepatocytes induce apoptosis of CD4+ and CD8+ Tcells

ndash LSEC functional inactivation of CD8+ T cells and bias CD4+ T cells to Treg-dependent on a cell surface expressed lectin (LSEC lectin)

bull CD8+T cells transiently activated then undergo apoptosis or exhaustion bull Generating robust immune responses appears to hinge on full activation of CD4+ T

cells which provide help to CD8+ T cells

21

Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells

IL-10

TGF-β1

IDO

Cox2-gtPGE2

FasL

HEP

Dead HEP

ldquoMDSCrdquo

LSEC

pDC

mDC

HSC Kupffer

PD-L1

LSECtin

IL-10

IL-27

PD-L1

IDO PD-L1

TGF-β1 + retinol

PD-L1

kynurenine

IL-10 TGFβ1 other

IFN-γ

HGF

T reg

T reg

8+

4+

Crispe IN 2014 Hepatology

Generating Immune Responses in the Liver

bull NK NKT γδ and mucosal associated innate lT cell (MAIT) activation and responses may be critical in response to infectious organisms ndash Promote DC maturation into APCs activate CD4+ CD8+ T cells Bcells

PMNs and macrophages via contact and cytokine dependent interactions

bull However none of these populations uses HLA the single greatest risk factor for autoimmune disease as restriction element for immune response suggesting criticality for mediating response to infection but potentially only indirect mechanism of action in triggering AIH spectrum

23

Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of

Infection but not in the Context of HLA (Doherty D 2016 J Autoimmunity)

Type 1 NKT cell Type 2 NKT cell MAIT cell γδ T cell γδ T cell γδ T cell γδ T cell

Vα24Jα18 Diverse Vα72Jα33 Vδ1 Vδ1 Vγ9Vδ2 Vδ3

CD1d CD1d MR1 MICA MICB Rae1 CD1c CD1d Butyrophilin 3A1 CD1d

Glycolipids Glycolipids Riboflavin metabolites Stress-inducible proteins Glycolipids Pyrophosphates Glycolipids

Cell Type T Cell Receptor Antigen-presenting

Molecule Stimulatory

Ligands

Genetic Basis of ToleranceAutoimmunity

bull Genetic predisposition of autoimmune diseases bull HLA genes

ndash Major genetic association with autoimmune diseases ndash Disease-associated alleles are present in normal individuals

bull Non-HLA genes ndash Many loci identified by genomic methods (eg genome wide

association studies [GWAS]) ndash Examples include FoxP3 AIRE CD25 (IL2R-α) NOD (sensor of

microbes) PTPN22 (tyrosine phosphatase) bull Multiple genes are associated with autoimmunity

ndash No single mutation causes common autoimmune diseases

25

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance

Thymus Periphery

Ubiquitous self-antigen

Tissue-restricted self-antigen (no thymic expression)

Tconv

Treg

No self-antigen

Deletion Pancreatic self antigen

Treg expansion Lung or

intestinal self antigen

R

R R

R

R

X Ignorance

Suppression

Legoux et al 2015 Immunity 43 896ndash908

CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation

Immunosuppression Engraftment

IL-23 IL-6 IL-21

TGFβ

IL-4

IL-12

Naiumlve CD4+ T cell

Th2 (IL-4 IL-5

IL-13)

Treg (IL-10 TGFβ)

TH17 (IL-17)

TH1 (IFNγ)

Liver graft rejection

Stat4 T-bet

Stat6 Gata3

Stat3 RORγ

Stat5 Foxp3

(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)

Autoimmunity is Suppressed by both Thymic and Peripheral Tregs

Local immune suppression Oral tolerance Fetal tolerance Mucosal tolerance

Nrp-1

APC

Thymus tTreg

Tnaive

Teff

pTreg

Teff Site of Inflammation

specialized APC

Immune homeostasis Autoimmune responses

Yadav M et al Frontiers in Immunology 2013

Mechanisms by which Tregs Suppress Immune Responses

20

Tolerance Mechanisms in the Liver bull 80 of the blood that passes through the liver sinusoids comes from the GI tract

carrying harmless dietary and commensal organism antigens the default immune response must be tolerancehellipmaintained by the myriad of tolerogenic APC in the liverrdquo hellipcontinuous exposure of liver cells to these entities leads to ldquoendotoxin tolerancerdquo ldquo

bull Antigen presentation within the liver mediated by a variety of cell types including plasmacytoid and myeloid dendritic cells (pmDC) Kupffer Cells sinusoidal endothelial cells hepatic stellate cells and hepatocytes generally leads to T cell tolerance and not immunity

ndash pDC-IL-27 secretion mediates expression of PDL-1 on pDC promoting activation and expansion of Tregs

ndash mDC express PDL-1 induce IDO

ndash KC- expression of Fas-L kills CD8T cells IDO IL-10 expression of PDL-1

ndash Hepatocytes induce apoptosis of CD4+ and CD8+ Tcells

ndash LSEC functional inactivation of CD8+ T cells and bias CD4+ T cells to Treg-dependent on a cell surface expressed lectin (LSEC lectin)

bull CD8+T cells transiently activated then undergo apoptosis or exhaustion bull Generating robust immune responses appears to hinge on full activation of CD4+ T

cells which provide help to CD8+ T cells

21

Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells

IL-10

TGF-β1

IDO

Cox2-gtPGE2

FasL

HEP

Dead HEP

ldquoMDSCrdquo

LSEC

pDC

mDC

HSC Kupffer

PD-L1

LSECtin

IL-10

IL-27

PD-L1

IDO PD-L1

TGF-β1 + retinol

PD-L1

kynurenine

IL-10 TGFβ1 other

IFN-γ

HGF

T reg

T reg

8+

4+

Crispe IN 2014 Hepatology

Generating Immune Responses in the Liver

bull NK NKT γδ and mucosal associated innate lT cell (MAIT) activation and responses may be critical in response to infectious organisms ndash Promote DC maturation into APCs activate CD4+ CD8+ T cells Bcells

PMNs and macrophages via contact and cytokine dependent interactions

bull However none of these populations uses HLA the single greatest risk factor for autoimmune disease as restriction element for immune response suggesting criticality for mediating response to infection but potentially only indirect mechanism of action in triggering AIH spectrum

23

Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of

Infection but not in the Context of HLA (Doherty D 2016 J Autoimmunity)

Type 1 NKT cell Type 2 NKT cell MAIT cell γδ T cell γδ T cell γδ T cell γδ T cell

Vα24Jα18 Diverse Vα72Jα33 Vδ1 Vδ1 Vγ9Vδ2 Vδ3

CD1d CD1d MR1 MICA MICB Rae1 CD1c CD1d Butyrophilin 3A1 CD1d

Glycolipids Glycolipids Riboflavin metabolites Stress-inducible proteins Glycolipids Pyrophosphates Glycolipids

Cell Type T Cell Receptor Antigen-presenting

Molecule Stimulatory

Ligands

Genetic Basis of ToleranceAutoimmunity

bull Genetic predisposition of autoimmune diseases bull HLA genes

ndash Major genetic association with autoimmune diseases ndash Disease-associated alleles are present in normal individuals

bull Non-HLA genes ndash Many loci identified by genomic methods (eg genome wide

association studies [GWAS]) ndash Examples include FoxP3 AIRE CD25 (IL2R-α) NOD (sensor of

microbes) PTPN22 (tyrosine phosphatase) bull Multiple genes are associated with autoimmunity

ndash No single mutation causes common autoimmune diseases

25

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation

Immunosuppression Engraftment

IL-23 IL-6 IL-21

TGFβ

IL-4

IL-12

Naiumlve CD4+ T cell

Th2 (IL-4 IL-5

IL-13)

Treg (IL-10 TGFβ)

TH17 (IL-17)

TH1 (IFNγ)

Liver graft rejection

Stat4 T-bet

Stat6 Gata3

Stat3 RORγ

Stat5 Foxp3

(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)

Autoimmunity is Suppressed by both Thymic and Peripheral Tregs

Local immune suppression Oral tolerance Fetal tolerance Mucosal tolerance

Nrp-1

APC

Thymus tTreg

Tnaive

Teff

pTreg

Teff Site of Inflammation

specialized APC

Immune homeostasis Autoimmune responses

Yadav M et al Frontiers in Immunology 2013

Mechanisms by which Tregs Suppress Immune Responses

20

Tolerance Mechanisms in the Liver bull 80 of the blood that passes through the liver sinusoids comes from the GI tract

carrying harmless dietary and commensal organism antigens the default immune response must be tolerancehellipmaintained by the myriad of tolerogenic APC in the liverrdquo hellipcontinuous exposure of liver cells to these entities leads to ldquoendotoxin tolerancerdquo ldquo

bull Antigen presentation within the liver mediated by a variety of cell types including plasmacytoid and myeloid dendritic cells (pmDC) Kupffer Cells sinusoidal endothelial cells hepatic stellate cells and hepatocytes generally leads to T cell tolerance and not immunity

ndash pDC-IL-27 secretion mediates expression of PDL-1 on pDC promoting activation and expansion of Tregs

ndash mDC express PDL-1 induce IDO

ndash KC- expression of Fas-L kills CD8T cells IDO IL-10 expression of PDL-1

ndash Hepatocytes induce apoptosis of CD4+ and CD8+ Tcells

ndash LSEC functional inactivation of CD8+ T cells and bias CD4+ T cells to Treg-dependent on a cell surface expressed lectin (LSEC lectin)

bull CD8+T cells transiently activated then undergo apoptosis or exhaustion bull Generating robust immune responses appears to hinge on full activation of CD4+ T

cells which provide help to CD8+ T cells

21

Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells

IL-10

TGF-β1

IDO

Cox2-gtPGE2

FasL

HEP

Dead HEP

ldquoMDSCrdquo

LSEC

pDC

mDC

HSC Kupffer

PD-L1

LSECtin

IL-10

IL-27

PD-L1

IDO PD-L1

TGF-β1 + retinol

PD-L1

kynurenine

IL-10 TGFβ1 other

IFN-γ

HGF

T reg

T reg

8+

4+

Crispe IN 2014 Hepatology

Generating Immune Responses in the Liver

bull NK NKT γδ and mucosal associated innate lT cell (MAIT) activation and responses may be critical in response to infectious organisms ndash Promote DC maturation into APCs activate CD4+ CD8+ T cells Bcells

PMNs and macrophages via contact and cytokine dependent interactions

bull However none of these populations uses HLA the single greatest risk factor for autoimmune disease as restriction element for immune response suggesting criticality for mediating response to infection but potentially only indirect mechanism of action in triggering AIH spectrum

23

Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of

Infection but not in the Context of HLA (Doherty D 2016 J Autoimmunity)

Type 1 NKT cell Type 2 NKT cell MAIT cell γδ T cell γδ T cell γδ T cell γδ T cell

Vα24Jα18 Diverse Vα72Jα33 Vδ1 Vδ1 Vγ9Vδ2 Vδ3

CD1d CD1d MR1 MICA MICB Rae1 CD1c CD1d Butyrophilin 3A1 CD1d

Glycolipids Glycolipids Riboflavin metabolites Stress-inducible proteins Glycolipids Pyrophosphates Glycolipids

Cell Type T Cell Receptor Antigen-presenting

Molecule Stimulatory

Ligands

Genetic Basis of ToleranceAutoimmunity

bull Genetic predisposition of autoimmune diseases bull HLA genes

ndash Major genetic association with autoimmune diseases ndash Disease-associated alleles are present in normal individuals

bull Non-HLA genes ndash Many loci identified by genomic methods (eg genome wide

association studies [GWAS]) ndash Examples include FoxP3 AIRE CD25 (IL2R-α) NOD (sensor of

microbes) PTPN22 (tyrosine phosphatase) bull Multiple genes are associated with autoimmunity

ndash No single mutation causes common autoimmune diseases

25

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

Autoimmunity is Suppressed by both Thymic and Peripheral Tregs

Local immune suppression Oral tolerance Fetal tolerance Mucosal tolerance

Nrp-1

APC

Thymus tTreg

Tnaive

Teff

pTreg

Teff Site of Inflammation

specialized APC

Immune homeostasis Autoimmune responses

Yadav M et al Frontiers in Immunology 2013

Mechanisms by which Tregs Suppress Immune Responses

20

Tolerance Mechanisms in the Liver bull 80 of the blood that passes through the liver sinusoids comes from the GI tract

carrying harmless dietary and commensal organism antigens the default immune response must be tolerancehellipmaintained by the myriad of tolerogenic APC in the liverrdquo hellipcontinuous exposure of liver cells to these entities leads to ldquoendotoxin tolerancerdquo ldquo

bull Antigen presentation within the liver mediated by a variety of cell types including plasmacytoid and myeloid dendritic cells (pmDC) Kupffer Cells sinusoidal endothelial cells hepatic stellate cells and hepatocytes generally leads to T cell tolerance and not immunity

ndash pDC-IL-27 secretion mediates expression of PDL-1 on pDC promoting activation and expansion of Tregs

ndash mDC express PDL-1 induce IDO

ndash KC- expression of Fas-L kills CD8T cells IDO IL-10 expression of PDL-1

ndash Hepatocytes induce apoptosis of CD4+ and CD8+ Tcells

ndash LSEC functional inactivation of CD8+ T cells and bias CD4+ T cells to Treg-dependent on a cell surface expressed lectin (LSEC lectin)

bull CD8+T cells transiently activated then undergo apoptosis or exhaustion bull Generating robust immune responses appears to hinge on full activation of CD4+ T

cells which provide help to CD8+ T cells

21

Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells

IL-10

TGF-β1

IDO

Cox2-gtPGE2

FasL

HEP

Dead HEP

ldquoMDSCrdquo

LSEC

pDC

mDC

HSC Kupffer

PD-L1

LSECtin

IL-10

IL-27

PD-L1

IDO PD-L1

TGF-β1 + retinol

PD-L1

kynurenine

IL-10 TGFβ1 other

IFN-γ

HGF

T reg

T reg

8+

4+

Crispe IN 2014 Hepatology

Generating Immune Responses in the Liver

bull NK NKT γδ and mucosal associated innate lT cell (MAIT) activation and responses may be critical in response to infectious organisms ndash Promote DC maturation into APCs activate CD4+ CD8+ T cells Bcells

PMNs and macrophages via contact and cytokine dependent interactions

bull However none of these populations uses HLA the single greatest risk factor for autoimmune disease as restriction element for immune response suggesting criticality for mediating response to infection but potentially only indirect mechanism of action in triggering AIH spectrum

23

Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of

Infection but not in the Context of HLA (Doherty D 2016 J Autoimmunity)

Type 1 NKT cell Type 2 NKT cell MAIT cell γδ T cell γδ T cell γδ T cell γδ T cell

Vα24Jα18 Diverse Vα72Jα33 Vδ1 Vδ1 Vγ9Vδ2 Vδ3

CD1d CD1d MR1 MICA MICB Rae1 CD1c CD1d Butyrophilin 3A1 CD1d

Glycolipids Glycolipids Riboflavin metabolites Stress-inducible proteins Glycolipids Pyrophosphates Glycolipids

Cell Type T Cell Receptor Antigen-presenting

Molecule Stimulatory

Ligands

Genetic Basis of ToleranceAutoimmunity

bull Genetic predisposition of autoimmune diseases bull HLA genes

ndash Major genetic association with autoimmune diseases ndash Disease-associated alleles are present in normal individuals

bull Non-HLA genes ndash Many loci identified by genomic methods (eg genome wide

association studies [GWAS]) ndash Examples include FoxP3 AIRE CD25 (IL2R-α) NOD (sensor of

microbes) PTPN22 (tyrosine phosphatase) bull Multiple genes are associated with autoimmunity

ndash No single mutation causes common autoimmune diseases

25

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

Mechanisms by which Tregs Suppress Immune Responses

20

Tolerance Mechanisms in the Liver bull 80 of the blood that passes through the liver sinusoids comes from the GI tract

carrying harmless dietary and commensal organism antigens the default immune response must be tolerancehellipmaintained by the myriad of tolerogenic APC in the liverrdquo hellipcontinuous exposure of liver cells to these entities leads to ldquoendotoxin tolerancerdquo ldquo

bull Antigen presentation within the liver mediated by a variety of cell types including plasmacytoid and myeloid dendritic cells (pmDC) Kupffer Cells sinusoidal endothelial cells hepatic stellate cells and hepatocytes generally leads to T cell tolerance and not immunity

ndash pDC-IL-27 secretion mediates expression of PDL-1 on pDC promoting activation and expansion of Tregs

ndash mDC express PDL-1 induce IDO

ndash KC- expression of Fas-L kills CD8T cells IDO IL-10 expression of PDL-1

ndash Hepatocytes induce apoptosis of CD4+ and CD8+ Tcells

ndash LSEC functional inactivation of CD8+ T cells and bias CD4+ T cells to Treg-dependent on a cell surface expressed lectin (LSEC lectin)

bull CD8+T cells transiently activated then undergo apoptosis or exhaustion bull Generating robust immune responses appears to hinge on full activation of CD4+ T

cells which provide help to CD8+ T cells

21

Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells

IL-10

TGF-β1

IDO

Cox2-gtPGE2

FasL

HEP

Dead HEP

ldquoMDSCrdquo

LSEC

pDC

mDC

HSC Kupffer

PD-L1

LSECtin

IL-10

IL-27

PD-L1

IDO PD-L1

TGF-β1 + retinol

PD-L1

kynurenine

IL-10 TGFβ1 other

IFN-γ

HGF

T reg

T reg

8+

4+

Crispe IN 2014 Hepatology

Generating Immune Responses in the Liver

bull NK NKT γδ and mucosal associated innate lT cell (MAIT) activation and responses may be critical in response to infectious organisms ndash Promote DC maturation into APCs activate CD4+ CD8+ T cells Bcells

PMNs and macrophages via contact and cytokine dependent interactions

bull However none of these populations uses HLA the single greatest risk factor for autoimmune disease as restriction element for immune response suggesting criticality for mediating response to infection but potentially only indirect mechanism of action in triggering AIH spectrum

23

Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of

Infection but not in the Context of HLA (Doherty D 2016 J Autoimmunity)

Type 1 NKT cell Type 2 NKT cell MAIT cell γδ T cell γδ T cell γδ T cell γδ T cell

Vα24Jα18 Diverse Vα72Jα33 Vδ1 Vδ1 Vγ9Vδ2 Vδ3

CD1d CD1d MR1 MICA MICB Rae1 CD1c CD1d Butyrophilin 3A1 CD1d

Glycolipids Glycolipids Riboflavin metabolites Stress-inducible proteins Glycolipids Pyrophosphates Glycolipids

Cell Type T Cell Receptor Antigen-presenting

Molecule Stimulatory

Ligands

Genetic Basis of ToleranceAutoimmunity

bull Genetic predisposition of autoimmune diseases bull HLA genes

ndash Major genetic association with autoimmune diseases ndash Disease-associated alleles are present in normal individuals

bull Non-HLA genes ndash Many loci identified by genomic methods (eg genome wide

association studies [GWAS]) ndash Examples include FoxP3 AIRE CD25 (IL2R-α) NOD (sensor of

microbes) PTPN22 (tyrosine phosphatase) bull Multiple genes are associated with autoimmunity

ndash No single mutation causes common autoimmune diseases

25

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

Tolerance Mechanisms in the Liver bull 80 of the blood that passes through the liver sinusoids comes from the GI tract

carrying harmless dietary and commensal organism antigens the default immune response must be tolerancehellipmaintained by the myriad of tolerogenic APC in the liverrdquo hellipcontinuous exposure of liver cells to these entities leads to ldquoendotoxin tolerancerdquo ldquo

bull Antigen presentation within the liver mediated by a variety of cell types including plasmacytoid and myeloid dendritic cells (pmDC) Kupffer Cells sinusoidal endothelial cells hepatic stellate cells and hepatocytes generally leads to T cell tolerance and not immunity

ndash pDC-IL-27 secretion mediates expression of PDL-1 on pDC promoting activation and expansion of Tregs

ndash mDC express PDL-1 induce IDO

ndash KC- expression of Fas-L kills CD8T cells IDO IL-10 expression of PDL-1

ndash Hepatocytes induce apoptosis of CD4+ and CD8+ Tcells

ndash LSEC functional inactivation of CD8+ T cells and bias CD4+ T cells to Treg-dependent on a cell surface expressed lectin (LSEC lectin)

bull CD8+T cells transiently activated then undergo apoptosis or exhaustion bull Generating robust immune responses appears to hinge on full activation of CD4+ T

cells which provide help to CD8+ T cells

21

Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells

IL-10

TGF-β1

IDO

Cox2-gtPGE2

FasL

HEP

Dead HEP

ldquoMDSCrdquo

LSEC

pDC

mDC

HSC Kupffer

PD-L1

LSECtin

IL-10

IL-27

PD-L1

IDO PD-L1

TGF-β1 + retinol

PD-L1

kynurenine

IL-10 TGFβ1 other

IFN-γ

HGF

T reg

T reg

8+

4+

Crispe IN 2014 Hepatology

Generating Immune Responses in the Liver

bull NK NKT γδ and mucosal associated innate lT cell (MAIT) activation and responses may be critical in response to infectious organisms ndash Promote DC maturation into APCs activate CD4+ CD8+ T cells Bcells

PMNs and macrophages via contact and cytokine dependent interactions

bull However none of these populations uses HLA the single greatest risk factor for autoimmune disease as restriction element for immune response suggesting criticality for mediating response to infection but potentially only indirect mechanism of action in triggering AIH spectrum

23

Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of

Infection but not in the Context of HLA (Doherty D 2016 J Autoimmunity)

Type 1 NKT cell Type 2 NKT cell MAIT cell γδ T cell γδ T cell γδ T cell γδ T cell

Vα24Jα18 Diverse Vα72Jα33 Vδ1 Vδ1 Vγ9Vδ2 Vδ3

CD1d CD1d MR1 MICA MICB Rae1 CD1c CD1d Butyrophilin 3A1 CD1d

Glycolipids Glycolipids Riboflavin metabolites Stress-inducible proteins Glycolipids Pyrophosphates Glycolipids

Cell Type T Cell Receptor Antigen-presenting

Molecule Stimulatory

Ligands

Genetic Basis of ToleranceAutoimmunity

bull Genetic predisposition of autoimmune diseases bull HLA genes

ndash Major genetic association with autoimmune diseases ndash Disease-associated alleles are present in normal individuals

bull Non-HLA genes ndash Many loci identified by genomic methods (eg genome wide

association studies [GWAS]) ndash Examples include FoxP3 AIRE CD25 (IL2R-α) NOD (sensor of

microbes) PTPN22 (tyrosine phosphatase) bull Multiple genes are associated with autoimmunity

ndash No single mutation causes common autoimmune diseases

25

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells

IL-10

TGF-β1

IDO

Cox2-gtPGE2

FasL

HEP

Dead HEP

ldquoMDSCrdquo

LSEC

pDC

mDC

HSC Kupffer

PD-L1

LSECtin

IL-10

IL-27

PD-L1

IDO PD-L1

TGF-β1 + retinol

PD-L1

kynurenine

IL-10 TGFβ1 other

IFN-γ

HGF

T reg

T reg

8+

4+

Crispe IN 2014 Hepatology

Generating Immune Responses in the Liver

bull NK NKT γδ and mucosal associated innate lT cell (MAIT) activation and responses may be critical in response to infectious organisms ndash Promote DC maturation into APCs activate CD4+ CD8+ T cells Bcells

PMNs and macrophages via contact and cytokine dependent interactions

bull However none of these populations uses HLA the single greatest risk factor for autoimmune disease as restriction element for immune response suggesting criticality for mediating response to infection but potentially only indirect mechanism of action in triggering AIH spectrum

23

Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of

Infection but not in the Context of HLA (Doherty D 2016 J Autoimmunity)

Type 1 NKT cell Type 2 NKT cell MAIT cell γδ T cell γδ T cell γδ T cell γδ T cell

Vα24Jα18 Diverse Vα72Jα33 Vδ1 Vδ1 Vγ9Vδ2 Vδ3

CD1d CD1d MR1 MICA MICB Rae1 CD1c CD1d Butyrophilin 3A1 CD1d

Glycolipids Glycolipids Riboflavin metabolites Stress-inducible proteins Glycolipids Pyrophosphates Glycolipids

Cell Type T Cell Receptor Antigen-presenting

Molecule Stimulatory

Ligands

Genetic Basis of ToleranceAutoimmunity

bull Genetic predisposition of autoimmune diseases bull HLA genes

ndash Major genetic association with autoimmune diseases ndash Disease-associated alleles are present in normal individuals

bull Non-HLA genes ndash Many loci identified by genomic methods (eg genome wide

association studies [GWAS]) ndash Examples include FoxP3 AIRE CD25 (IL2R-α) NOD (sensor of

microbes) PTPN22 (tyrosine phosphatase) bull Multiple genes are associated with autoimmunity

ndash No single mutation causes common autoimmune diseases

25

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

Generating Immune Responses in the Liver

bull NK NKT γδ and mucosal associated innate lT cell (MAIT) activation and responses may be critical in response to infectious organisms ndash Promote DC maturation into APCs activate CD4+ CD8+ T cells Bcells

PMNs and macrophages via contact and cytokine dependent interactions

bull However none of these populations uses HLA the single greatest risk factor for autoimmune disease as restriction element for immune response suggesting criticality for mediating response to infection but potentially only indirect mechanism of action in triggering AIH spectrum

23

Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of

Infection but not in the Context of HLA (Doherty D 2016 J Autoimmunity)

Type 1 NKT cell Type 2 NKT cell MAIT cell γδ T cell γδ T cell γδ T cell γδ T cell

Vα24Jα18 Diverse Vα72Jα33 Vδ1 Vδ1 Vγ9Vδ2 Vδ3

CD1d CD1d MR1 MICA MICB Rae1 CD1c CD1d Butyrophilin 3A1 CD1d

Glycolipids Glycolipids Riboflavin metabolites Stress-inducible proteins Glycolipids Pyrophosphates Glycolipids

Cell Type T Cell Receptor Antigen-presenting

Molecule Stimulatory

Ligands

Genetic Basis of ToleranceAutoimmunity

bull Genetic predisposition of autoimmune diseases bull HLA genes

ndash Major genetic association with autoimmune diseases ndash Disease-associated alleles are present in normal individuals

bull Non-HLA genes ndash Many loci identified by genomic methods (eg genome wide

association studies [GWAS]) ndash Examples include FoxP3 AIRE CD25 (IL2R-α) NOD (sensor of

microbes) PTPN22 (tyrosine phosphatase) bull Multiple genes are associated with autoimmunity

ndash No single mutation causes common autoimmune diseases

25

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of

Infection but not in the Context of HLA (Doherty D 2016 J Autoimmunity)

Type 1 NKT cell Type 2 NKT cell MAIT cell γδ T cell γδ T cell γδ T cell γδ T cell

Vα24Jα18 Diverse Vα72Jα33 Vδ1 Vδ1 Vγ9Vδ2 Vδ3

CD1d CD1d MR1 MICA MICB Rae1 CD1c CD1d Butyrophilin 3A1 CD1d

Glycolipids Glycolipids Riboflavin metabolites Stress-inducible proteins Glycolipids Pyrophosphates Glycolipids

Cell Type T Cell Receptor Antigen-presenting

Molecule Stimulatory

Ligands

Genetic Basis of ToleranceAutoimmunity

bull Genetic predisposition of autoimmune diseases bull HLA genes

ndash Major genetic association with autoimmune diseases ndash Disease-associated alleles are present in normal individuals

bull Non-HLA genes ndash Many loci identified by genomic methods (eg genome wide

association studies [GWAS]) ndash Examples include FoxP3 AIRE CD25 (IL2R-α) NOD (sensor of

microbes) PTPN22 (tyrosine phosphatase) bull Multiple genes are associated with autoimmunity

ndash No single mutation causes common autoimmune diseases

25

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

Genetic Basis of ToleranceAutoimmunity

bull Genetic predisposition of autoimmune diseases bull HLA genes

ndash Major genetic association with autoimmune diseases ndash Disease-associated alleles are present in normal individuals

bull Non-HLA genes ndash Many loci identified by genomic methods (eg genome wide

association studies [GWAS]) ndash Examples include FoxP3 AIRE CD25 (IL2R-α) NOD (sensor of

microbes) PTPN22 (tyrosine phosphatase) bull Multiple genes are associated with autoimmunity

ndash No single mutation causes common autoimmune diseases

25

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

HLA is the Strongest Genetic Factor for Susceptibility to Autoimmune Disease

26

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

Non-HLA Genes in Autoimmunity

27

Lymphadenopathy enteropathy eczema infection

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

HLA Association with AIH

DQB DQA DRB1 DRB1 DRB3 DRB3 Previous data DRB1 DRB1 DRB1

Locus Allele OR p Value n

603 103

1301 1302

101 202

13

13 + 3 3

218 455 680 016 149 055 69 106 53

ns 0013 000247 000845 ns ns 100E-06 100E-07 100E-04

66 33 39 39 84 95

111

111 33

Goldberg AC et al 2001 Human Immunology

Previous data refer to odds ratio (OR) observed when a larger cohort of patients was analyzed by low resolution PCR-SSP for the HLA-DRB1 locus

DRB11301 appears the major susceptibility factor its only amino acid different from DRB11302 is in position 86 corresponding to pocket 1 in the peptide-presenting groove-glycine for valine

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

Polymorphisms in TNF-α Gene Associated with AIH

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

TNFA2 + + ndash ndash

Phenotype Patients Comparison OR P

HLA-A1 + ndash + ndash

HLA-B8 + ndash + ndash

HLA-DRB10301 + ndash + ndash

(n = 83) 35 12 4 32

(n = 83) 43 4 0 36

(n = 85) 40 8 4 71

(n = 98) 15 11 9 63

(n = 98) 17 9 3 69

(n = 102) 15 12 3 4

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

+ + vs ndash ndash 36 + ndash vs ndash ndash NS ndash + vs ndash ndash NS

lt00004

lt00004

lt00003

Controls

Cookson S et al 1999 Hepatology

Of note is high degree of linkage disequilibrium between the TNFA locus and both HLA B8 and HLA DRB10301 within the extended haplotype B8-TNFA2- DRB10301

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

Pathogenesis of Organ-Specific Autoimmunity

Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011 c Elsevier

Failure of control mechanisms is the underlying cause of most autoimmune diseases

30 Abbas Lichtman and Pillai Cellular and Molecular Immunology 7th edition 2011

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

Deliberately Breaking Self Tolerance

bull Monoclonal antibodies to checkpoint inhibitors (PD-1 PDL-1)

bull Monoclonal antibodies to suppressive molecules (eg CTLA-4 IL-2Ra)

bull Chimeric Antigen Receptor T cells (CAR-T) bull Inhibitors of Indoleamine Diooxygenase (IDO)

31

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases

Cancer Chronic Infection

Autoimmunity Graft Rejection

Checkpoint Inhibitor

Antagonists

Checkpoint Inhibitor Agonists

Treg

Teff

Treg

Teff

Treg

Teff

Autoimmunity CancerChronic Infection

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

Acknowledgements

bull Mark Avigan and John Senior OSE FDA bull Michael Norcross OBP FDA bull Jeff Bluestone UCSF bull Abul Abbas UCSF bull Daniela Verthelyi OBP FDA bull Steven Kozlowski OBP FDA

33

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34

34

• Mechanisms of Immune Tolerance The Liver as Immunoprivileged Organ
• Slide Number 2
• How Self is Self
• Slide Number 4
• Slide Number 5
• Antibody Response to Proteins The Mediators
• Cellular Interactions in Generation of T cell Mediated Responses(Sanchez-Fueyo A and TB Strom Gastroenterology 2011)
• T Cells More Robustly Tolerant than B Cells to Self Proteins(Weigle 1980)
• T Cells More Robustly Tolerant to Self-ProteinsThymic Mechanisms
• Slide Number 10
• Mutations in Tregulatory cell Transcription Factor FoxP3 Confer Autoimmunity by Deficiency of Tregs(Sakaguchi et al 2008)
• Slide Number 13
• AIRE Promotes Expression of Peripheral Tissue Antigens in the Thymus DeletingDeviating High Affinity Autoreactive T cells(Mathis and Benoist 2007)
• AIRE Mutations are Associated with Autoimmune Polyendocrine Syndrome Type 1(Kampe et al 2008)
• AIRE Mediated Expression of of Liver Proteins in the Thymus
• CD4+ T cells Specific for Tissue Restricted Antigens do not Undergo Extensive Thymic Deletion Expanded Tregs Mediate Tolerance
• CD4+ T cell Fate Depends on Cytokine Milieu in Site of Activation
• Autoimmunity is Suppressed by both Thymic and Peripheral Tregs
• Slide Number 20
• Tolerance Mechanisms in the Liver
• Immunosuppressive Circuits in Liver Mediated Mainly Through Liver Resident Myeloid Cells
• Generating Immune Responses in the Liver
• Innate T Cells Present at High Levels in the Human Liver Recognize Microbial or Stress Induced Antigens Indicative of Infection but not in the Context of HLA(Doherty D 2016 J Autoimmunity)
• Slide Number 25
• Slide Number 26
• Slide Number 27
• HLA Association with AIH
• Polymorphisms in TNF-a Gene Associated with AIH
• Slide Number 30
• Deliberately Breaking Self Tolerance
• The Immune System on a Knifersquos Edge Tipping the Balance for Therapy of Serious Diseases
• Acknowledgements
• Slide Number 34