A Personal Antigen Selection Calculator (PASCal) for the...
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A Personal Antigen Selection Calculator (PASCal) for the design of personal cancer vaccines Eszter Somogyi 1 , Zsolt Csiszovszki 1 , Orsolya Lőrincz 1 , József Tóth 1 , Levente Molnár 1 , Wolfgang Schönharting 2 , Sybille Urban 2 , Tim Röhnisch 3 , Katalin Pántya 1 , Péter Páles 1 , Mónika Megyesi 1 , Enikő R. Tőke 1 1 Treos Bio Zrt., Veszprém, Hungary; 2 PMCR GmbH, Germany; 3 The Interdisciplinary Oncology Center Munich, Germany Background: The current challenge in developing effective cancer vaccines is the accurate prediction of epitopes that induce CD8+ cytotoxic T-cell responses. Recent technological advances have enabled development of patient-specific therapeutic vaccines. However, in these vaccines only about 10-20% of the predicted neoepitopes induced CD8+ T-cell responses in patients. To overcome this limitation, we developed PASCal for improved selection of peptides (epitopes) that induce T-cell responses. Methods: PASCal operates by 3 moduls: (1) a validated epitope database containing 10 8 true HLA-epitope pairs derived from 1300 tumor antigens and HLA class I and II molecules covering the HLA genotype of 26000 subjects. (2) Expression frequency-based shared tumor antigen database established for 19 indications based on >96000 tumor biopsies. (3) Algorithm for the identification of immunogenic peptides by the selection of personal epitopes (PEPIs) binding to ≥3 autologous HLA alleles. Using PASCal, personal 20mer peptide vaccines were designed for 3 HLA-genotyped cancer patients (with ovarian-, breast- and colorectal cancer). Immunogenicity of the vaccines was tested by ELISPOT and Intracellular Citokine Staining (ICS). Results: Personalized cancer vaccines contained PEPIs from 12 disease specific tumor-antigens most frequently expressed in the patients disease. T- cell responses were induced by 100% of peptides. An average of 11/12 PEPIs induced CD8+ T-cell responses and 12/12 induced CD4+ T-cell responses in each patient. Pre-existing antigen specific T-cell reactivities were detectable against 25% of vaccine antigens (demonstrating the expression of the target vaccine antigens by the patient’s tumor), the others were induced de novo. Both CD8+ and CD4+ T-cells were polyfunctional, as evident by secretion of multiple cytokines determined by ex vivo ICS. Conclusion: We used the largest validated database of tumor epitopes reported to-date along with an algorithm successfully selecting immunogenic peptides to develop personalized cancer vaccines. PEPIs outperform reported immunogenicity of personalized neoantigen vaccines and induced unprecedented immune responses in cancer patients. ABSTRACT # 1181PD P ERSONAL EPITOPES (PEPIs) Parameter Definition Retrospective validation n = 157* Clinical validation n = 70** PPV Positive Predictive Value The likelihood that an individual with a positive PEPI Test* result has antigen-specific T cell responses 84% 79% NPV Negative Predictive Value The likelihood that an individual with a negative PEPI Test result does not have antigen-specific T cell responses 42% 51% OPA Overall Percent Agreement The percentage of results that are true results, whether positive or negative 70% 64% Fisher’s exact probability test p-value of the hypothesis testing 0.01 0.01 PEPI VALIDATION • Analytical validation – prediction of HLA-epitope binding was determined with an established Reference Standard containing HLA-peptide pairs determined by experimental methods (direct binding assays) PROOF OF CONCEPT STUDIES USING PASCal *80 patients; 6 clinical trials; 157 dataset **10 patients; Treos phase I/II clinical trial; 70 dataset; PEPI Test CE-mark device Correspondence: [email protected] ; [email protected] Conflict of interest: ES, ZC, OL, JT, LM, KP, PP, MM and ET are employee of Treos Bio Zrt and hold shares of Treos Bio Ltd. LONG LASTING POLYFUNCTIONAL IMMUNE RESPONSES PEPI is an epitope restricted by ≥3 autologous HLA of the individual capable to mount T cell response against the cell expressing the same PEPI. References: 1 Toke ER et al, JCO, 37, 2019 (suppl; abstr e14295;) 2 Lorincz O et al, JCO, 37, 2019 (suppl; abstr e14298; 3 Hubbard JM et al. JCO, 37, 2019 (suppl; abstr 3557) SUMMARY • PASCal is a new platform for • the design of true immunogenic peptides - clinically validated • target selection without the need for tumor biopsy - confirmed by detected pre-existing immune responses • 19 cancer indications – including the ones with low mutational burden • PEPIs outperform reported immunogenicity of personalized mutation-based neoantigen vaccines and induced unprecedented immune responses in cancer patients. Parameter Definition Result Specificity Ability to identify true HLA-restricted human epitopes 93% Sensitivity Ability to exclude false HLA-restricted human epitopes 93% 11% 11% 58% 20% Binder set (#327) HIV Viral Tumor Other (fungi, bacteria, etc.) 17% 11% 34% 38% Non-binder set (#100) • Clinical validation – prediction of individuals’ antigen-specific immune responses A retrospective study was followed by our Phase I/II OBERTO101 trial: 10 metastatic CRC patients received PolyPEPI1018 vaccine designed by PASCal, optimized for CRC population 3 . Ex vivo detected polyfunctional T cell responses for PT1 measured by Intracellular staining (ICS) Reference Standard: Experimentally proven Binder and Non-binder HLA-epitope pairs ✓ High affinity epitopes (measured IC50 < 500nM) ✓ Broad antigen spectra ✓ Most frequent alleles Vaccine : 12/13 long peptides (PEPIs) derived from 12/13 shared cancer testis antigens frequently expressed in the patient’s tumor type Adjuvant : Montanide ISA 51VG Administration : subcutaneous injection into 2 arms and 2 tights Doses received : multiple doses (≥3 doses/patient) Patients were clinically monitored conform their standard-of-care and vaccinated under the “individuelle Heilversuche” regime in Germany as add-on to patient’s standard-of-care Pts. Tumor Safety #Patient - specific peptides included in the vaccine (#PEPIs) Tumor specific T cell responses (IFN - γ ELISpot) CD8+ CD4+ PT1 Metastatic Breast Cancer Safe and well tolerated* 12 11 12 PT2 Metastatic Ovarian Cancer Safe and well tolerated* 13 13 13 PT3 Metastatic Colorectal Cancer Safe and well tolerated* 13 13 7 Immunogenic peptides per patient : 12 Peptides (PEPIs) generating any T cell response : 100% *Flu like syndrome, Fatigue, palpitations and low fever, redness, itchiness at the site of the injections. DETAILED IMMUNOLOGICAL ANALYSIS P ASCAL TECHNOLOGY Key step: selection of validated Personal EPItopes (PEPIs) specific to the patient’s HLA genotype, not only to individual alleles 1,2 Tumor antigens ~1,300 HLA class I and II molecules ~26,000 patients HLA-epitope pairs ~100 million Validated Epitope Database Antigen expression frequency for 19 indications Antigen Expression Database Tumor Biopsies >96.000 PASCal Algorithm Clinical validation PEPI selection Ethnicities Cancer cohorts Model Population Analytical validation with Reference Standard Patients’ Tumor type Patients’ HLA genotype Immunogenic Vaccine peptides 71% 12% 11% 2% 3% 2% 18% 1% 65% 0% 16% 0% % CD8+ cells % CD4+ cells Memory CD8+ T cell responses were detected 14 months (436 days) after last vaccination against 4 tumor antigens Effector (Ex vivo) CD8+ T cell responses were detected 135 days (4.5 months) after last vaccination STANDARD-OF-CARE VACCINATION MATCHING VACCINE PEPTIDES WITH THE PATIENT’S UNIQUE GENETIC CODE Oncologist + Patient Oncologist + Patient VACCINE PREPARATION 12/13 Tumor & Patient- specific Peptides VACCINE DEVELOPMENT HLA Genotype & Tumor Type Sterile, endotoxin free ~6 weeks PERSONAL VACCINE SALIVA SAMPLE + TUMOR TYPE Pre-existing and de-novo induced immune responses against multiple antigens 0 50 100 150 200 250 300 350 135 days 321 days 436 days Spots per million PBMC AKAP4 (85%) BORIS (71%) FSIP1 (49%) Survivin (71%) MAGE-C1 (12%) after last vaccination *Antigen-specific immune responses (expression rates in breast cancer) * * * * * 0 100 200 300 400 500 600 700 135 days 321 days 436 days Spots per million PBMC IFN-ƴ Granzyme B TNF-α IFN-ƴ/Granzyme B IFN-ƴ/TNF-α Granzyme B/TNF-α IFN-ƴ/Granyzme B/TNF-α after last vaccination
Transcript of A Personal Antigen Selection Calculator (PASCal) for the...
A Personal Antigen Selection Calculator (PASCal) for the design of personal cancer vaccinesEszter Somogyi1, Zsolt Csiszovszki1, Orsolya Lőrincz1, József Tóth1, Levente Molnár1, Wolfgang Schönharting2, Sybille Urban2, Tim Röhnisch3, Katalin Pántya1, Péter Páles1, Mónika Megyesi1, Enikő R. Tőke1
1 Treos Bio Zrt., Veszprém, Hungary; 2 PMCR GmbH, Germany; 3 The Interdisciplinary Oncology Center Munich, Germany
Background: The current challenge in developing effective cancer vaccinesis the accurate prediction of epitopes that induce CD8+ cytotoxic T-cellresponses. Recent technological advances have enabled development ofpatient-specific therapeutic vaccines. However, in these vaccines only about10-20% of the predicted neoepitopes induced CD8+ T-cell responses inpatients. To overcome this limitation, we developed PASCal for improvedselection of peptides (epitopes) that induce T-cell responses.
Methods: PASCal operates by 3 moduls: (1) a validated epitope databasecontaining 108 true HLA-epitope pairs derived from 1300 tumor antigens andHLA class I and II molecules covering the HLA genotype of 26000 subjects.(2) Expression frequency-based shared tumor antigen database establishedfor 19 indications based on >96000 tumor biopsies. (3) Algorithm for theidentification of immunogenic peptides by the selection of personal epitopes(PEPIs) binding to ≥3 autologous HLA alleles. Using PASCal, personal20mer peptide vaccines were designed for 3 HLA-genotyped cancer patients(with ovarian-, breast- and colorectal cancer). Immunogenicity of thevaccines was tested by ELISPOT and Intracellular Citokine Staining (ICS).
Results: Personalized cancer vaccines contained PEPIs from 12 diseasespecific tumor-antigens most frequently expressed in the patients disease. T-cell responses were induced by 100% of peptides. An average of 11/12PEPIs induced CD8+ T-cell responses and 12/12 induced CD4+ T-cellresponses in each patient. Pre-existing antigen specific T-cell reactivitieswere detectable against 25% of vaccine antigens (demonstrating theexpression of the target vaccine antigens by the patient’s tumor), the otherswere induced de novo. Both CD8+ and CD4+ T-cells were polyfunctional, asevident by secretion of multiple cytokines determined by ex vivo ICS.
Conclusion: We used the largest validated database of tumor epitopesreported to-date along with an algorithm successfully selecting immunogenicpeptides to develop personalized cancer vaccines. PEPIs outperformreported immunogenicity of personalized neoantigen vaccines and inducedunprecedented immune responses in cancer patients.
ABSTRACT
#1181PD
PERSONAL EPITOPES (PEPIs)
Parameter DefinitionRetrospective
validationn = 157*
Clinicalvalidationn = 70**
PPVPositive Predictive Value
The likelihood that an individual with a positive PEPI Test* result has antigen-specific T cell responses 84% 79%
NPVNegative Predictive Value
The likelihood that an individual with a negative PEPI Test result does not have antigen-specific T
cell responses 42% 51%
OPAOverall Percent Agreement
The percentage of results that are true results, whether positive or negative 70% 64%
Fisher’s exact probability test
p-value of the hypothesis testing 0.01 0.01
PEPI VALIDATION • Analytical validation – prediction of HLA-epitope binding was determined
with an established Reference Standard containing HLA-peptide pairsdetermined by experimental methods (direct binding assays)
PROOF OF CONCEPT STUDIES USING PASCal
*80 patients; 6 clinical trials; 157 dataset **10 patients; Treos phase I/II clinical trial; 70 dataset; PEPI Test CE-mark device
Correspondence: [email protected]; [email protected] of interest: ES, ZC, OL, JT, LM, KP, PP, MM and ET are employee of Treos Bio Zrt and hold shares of Treos Bio Ltd.
LONG LASTING POLYFUNCTIONAL IMMUNE RESPONSESPEPI is an epitope restricted by ≥3 autologous HLA of the individual capable to mount T cell response against the cell expressing the same PEPI.
References: 1Toke ER et al, JCO, 37, 2019 (suppl; abstr e14295;) 2Lorincz O et al, JCO, 37, 2019 (suppl; abstr e14298;3Hubbard JM et al. JCO, 37, 2019 (suppl; abstr 3557)
SUMMARY• PASCal is a new platform for
• the design of true immunogenic peptides - clinically validated
• target selection without the need for tumor biopsy - confirmed by
detected pre-existing immune responses
• 19 cancer indications – including the ones with low mutational burden
• PEPIs outperform reported immunogenicity of personalized mutation-based
neoantigen vaccines and induced unprecedented immune responses in cancer
patients.
Parameter Definition Result Specificity Ability to identify true HLA-restricted human epitopes 93%Sensitivity Ability to exclude false HLA-restricted human epitopes 93%
11%
11%
58%
20%
Binder set (#327)HIV
Viral
Tumor
Other (fungi,bacteria, etc.)
17%
11%
34%
38%
Non-binder set (#100)
• Clinical validation – prediction of individuals’ antigen-specific immune responsesA retrospective study was followed by our Phase I/II OBERTO101 trial: 10metastatic CRC patients received PolyPEPI1018 vaccine designed by PASCal,optimized for CRC population3.
Ex vivo detectedpolyfunctional T cellresponses for PT1measured byIntracellular staining(ICS)
Reference Standard: Experimentally proven
Binder and Non-binderHLA-epitope pairs
✓ High affinity epitopes (measured IC50 < 500nM)
✓ Broad antigen spectra✓ Most frequent alleles
Vaccine: 12/13 long peptides (PEPIs) derived from 12/13 shared cancer testis antigens frequently expressed in the patient’s tumor typeAdjuvant: Montanide ISA 51VGAdministration: subcutaneous injection into 2 arms and 2 tightsDoses received: multiple doses (≥3 doses/patient)Patients were clinically monitored conform their standard-of-care and vaccinated under the “individuelle Heilversuche” regime in Germany as add-on to patient’s standard-of-care
Pts. Tumor Safety
#Patient-specific peptides included in
the vaccine (#PEPIs)
Tumor specific T cell responses (IFN-γ ELISpot)
CD8+ CD4+
PT1Metastatic Breast
CancerSafe and well
tolerated* 12 11 12
PT2Metastatic Ovarian
CancerSafe and well
tolerated* 13 13 13
PT3Metastatic
Colorectal CancerSafe and well
tolerated* 13 13 7
Immunogenic peptides per patient : 12
Peptides (PEPIs) generating any T cell response : 100%*Flu like syndrome, Fatigue, palpitations and low fever, redness, itchiness at the site of the injections.
DETAILED IMMUNOLOGICAL ANALYSIS
PASCAL TECHNOLOGYKey step: selection of validated Personal EPItopes (PEPIs) specific to thepatient’s HLA genotype, not only to individual alleles1,2
Tumor antigens~1,300
HLA class I and II molecules
~26,000 patients
HLA-epitope pairs~100 million
Validated Epitope Database
Antigen expression frequency for19 indications
Antigen Expression DatabaseTumor Biopsies >96.000
PASCal
AlgorithmClinical validation
PEPI selection
Ethnicities
Cancer cohorts
Model Population
Analytical validation with Reference Standard
Patients’ Tumor type
Patients’ HLA genotype
ImmunogenicVaccine peptides
71%
12%
11%
2% 3% 2%
18% 1%
65%
0% 16%
0%
% CD8+ cells % CD4+ cells
Memory CD8+ T cell responses were detected 14 months (436 days) after last
vaccination against 4 tumor antigens
Effector (Ex vivo) CD8+ T cell responses were detected 135 days (4.5 months) after last vaccination
STANDARD-OF-CARE VACCINATIONMATCHING VACCINE PEPTIDES
WITH THE PATIENT’S UNIQUE GENETIC CODE
Oncologist+
Patient
Oncologist+
Patient
VACCINE PREPARATION
12/13 Tumor & Patient-specific Peptides
VACCINE DEVELOPMENT
HLA Genotype
&Tumor Type Sterile,
endotoxin free
~6 weeks
PERSONALVACCINE
SALIVA SAMPLE
+TUMOR TYPE
Pre-existing and de-novo induced immune responses against multiple antigens
0
50
100
150
200
250
300
350
135 days 321 days 436 days
Spot
s per
mill
ion
PBM
CAKAP4 (85%) BORIS (71%)FSIP1 (49%) Survivin (71%)MAGE-C1 (12%)
after last vaccination
*Antigen-specific immune responses (expression rates in breast cancer)
*
*
***
0
100
200
300
400
500
600
700
135 days 321 days 436 days
Spot
s per
mill
ion
PBM
C
IFN-ƴ Granzyme BTNF-α IFN-ƴ/Granzyme BIFN-ƴ/TNF-α Granzyme B/TNF-αIFN-ƴ/Granyzme B/TNF-α
after last vaccination
