James Brugarolas, M.D., Ph.D.

Kidney Cancer Program Leader

Virginia Murchison Linthicum Endowed Scholar

Associate Professor of Internal Medicine

University of Texas Southwestern Medical Center

http://www.utsouthwestern.edu/kidneycancer

Molecular Patient Selection

KCA 2016

Relevant Disclosures

Peloton Therapeutics: Research Support

Patent (PCT/US2016/052118; U.S. Serial No. 62/221,527) “Biomarkers of Response to HIF-2-Alpha Inhibition in Cancer and Methods for the Use Thereof” by Brugarolas, et al.

Molecular Patient Selection

IL-2 (FDA approval 1992)

SELECT trial, PD-L1

Angiogenesis inhibitors (first FDA approval 2005)

Polymorphisms in VEGF/VEGFR genes

mTORC1 inhibitors (first FDA approval 2007)

Mutations MTOR, RHEB, TSC1, TSC2…

Checkpoint Inhibitors (Nivolumab)

PD-L1, mutation load, neoantigens

Emerging therapies:

HIF-2 inhibitor (PT2385)

Why: (i) Targets an early/truncal event; (ii) Highly specific, allosteric drug binding an uncommon feature; (iii) Variable dependency on target; (iv) Variable target expression in ccRCC; (v) Target itself may be a biomarker

– No

– No

– No

– No

Scheuermann et al.

PNAS 2009

B

A

B

A

HRE (DNA)

HIF-2a HIF-1b

HRE (DNA)

HIF-1bHIF-2a

Scheuermann et al.

Nat Chem Biol 2013

High-Throughput Screen

HIF2-I

Development of a HIF-2 inhibitor (HIF2-I)

UT Southwestern BioCenter

Sivanand et al., Sci Transl Med 2012

Unsupervised hierarchical clustering of gene expression shows similarities

between tumors and corresponding tumorgrafts

Tumorgrafts reproduce the mutations, gene expression and

drug responsiveness of human RCC

HIF2-I (PT2399) is active against

human ccRCC transplants in mice

Days

Tum

or

volu

me (

mm

3) Vehicle

Sunitinib

HIF2-I

HIF2-I is active in 50% of ccRCC

Inte

rmed

.S

en

sit

ive

Resis

tan

t

Vehicle

Sunitinib

HIF2-I

267 mice from 22 independently derived TG lines (18 ccRCC)

Chen et al., Nature 2016

HIF2-I (PT2399) has greater activity than sunitinib

and is better tolerated

Chen et al., Nature 2016EPO may serve as a PD biomarker

HIF2-I is active in 50% of ccRCC

Inte

rmed

.S

en

sit

ive

Resis

tan

t

Vehicle

Sunitinib

HIF2-I

267 mice from 22 independently derived TG lines (18 ccRCC)

Chen et al., Nature 2016

Sensitive ccRCC include tumors with rhabdoid/sarcomatoid features

Response PDX line HistologyFuhrman

GradeTissue

VHLstatus

BAP1 (IHC)

PBRM1 (IHC)

Relative GI%

(p value)

Sensitive XP26 ccRCC 2 Adrenal mut mut wt 87 (0.0003)

XP144 ccRCC 4 Kidney mut wt wt 98 (<0.0001)

XP164 ccRCC* 4 Kidney wt wt wt 134 (<0.0001)

XP165 ccRCC 3 Abd wall mut wt mut 112 (<0.0001)

XP373 ccRCC 4 Tu Thr wt¥ mut wt 103 (<0.0001)

XP374 ccRCC*# 4 Kidney mut wt wt 109 (<0.0001)

XP453 ccRCC 3 Tu Thr wt¥ wt wt 110 (<0.0001)

XP454 ccRCC 3 Kidney wt mut wt 156 (0.0032)

XP469 ccRCC 3 Kidney mut mut mut 91 (<0.0001)

XP534 ccRCC 4 Kidney mut mut n/a 129 (0.0007)

Intermediate XP237 tRCC n/a LN n/a wt wt 43 (0.0144)

XP391 ccRCC 4 Tu Thr mut wt mut 45 (0.0018)

XP426@ ccRCC# 4 Kidney mut wt wt 44 (0.0273)

XP427@ ccRCC# 4 LN mut wt wt 54 (0.0206)

XP466 ccRCC 3 Kidney wt mut n/a 67 (0.0030)

Resistant XP169 Unclassified n/a Kidney wt wt wt 0 (0.0119$)

XP258 ccRCC* 4 Kidney mut mut wt 39 (0.11)

XP296 ccRCC* 4 Kidney mut wt wt 29 (0.30)

XP462 Unclassified n/a Kidney wt wt mut 29 (0.11)

XP490 ccRCC*# 4 Kidney mut wt wt 39 (0.89)

XP506 ccRCC 3 Ascites wt wt wt 20 (0.76)

XP530 Unclassified n/a Kidney wt n/a n/a 2 (0.68)

@ Independent tumors from same patient, * Sarcomatoid differentiation, # Rhabdoid features, $ HIF2-I-treated mice

had greater relative growth than vehicle-treated mice, ¥ Promoter methylation

Chen et al., Nature 2016

HIF2-I (PT2399) inhibits proliferation &

angiogenesis in sensitive ccRCC

XP

16

4X

P4

69

XP

45

4X

P3

73

HIF2-Ivehicle

V4239 P4244

P3297V3294

V5407 P5399

V4921 P4924

HIF2-Iveh

XP

37

3X

P1

44

CD

31

H&

E

XP

37

3K

i67

veh HIF2-I

XP

16

4X

P4

90

XP

16

9X

P3

73

vehicle HIF2-I

V4237

V5239 V5229 P5231 P5240

V4236 V4241V4234

V3290 V3294 V3287 V3281

V3212 V3224 V3210 V3214

Vehicle

HIF2-I

Sunitinib

Chen et al., Nature 2016

HIF2-I (PT2399) dissociates HIF-2 in sensitive tumors

RE

SIS

TA

NT

S

EN

SIT

IVE

Chen et al., Nature 2016

Resistance mutations in HIF-2a and HIF-1b

validate HIF-2 as the drug target

P3283V3286

Fo

rwa

rdR

eve

rse

G323E

(HIF-2a)

V1849 P5123

Fo

rwa

rdR

eve

rse

F446L

(HIF-1b)

HIF-1b HIF-2a

0

500

1000

1500

2000

2500

3000

3500

4000

4500

5000

-20 0 20 40 60 80 100 120 140 160 180 200

Tu

mo

r V

olu

me

(m

m3)

XP164

3283

3288

3296

3295

3299

3286Veh

Sunitinib

HIF2-I

Input

IP HIF-1b

V3

29

0

V3

29

4

V3

29

8

P3

28

3

P3

28

8

P3

29

7

V3

29

0

V3

29

4

V3

29

8

P3

28

3

P3

29

7

Tubulin

post-

resistance

HIF-2a

HIF-1b

P3

28

8

pre-resistance

vehicle HIF2-I HIF2-I

Chen et al., Nature 2016

HIF-2a and HIF-1b mutations are sufficient to

preserve HIF-2 complexes despite PT2399

FLAG-HIF-1b

Input IP FLAG (HIF-1b)

Vehicle Vehicle PT2399PT2399

+

-

+

+

-

-

-

-

-

+

+ +

+

+

- -

Tubulin

HA

FLAG

FLAG-HIF-1b (F466L)

HA-HIF-2a

HA-HIF-2a (G323E)

+

-

+

+

-

-

-

-

-

+

+ +

+

+

- - +

-

+

+

-

-

-

-

-

+

+ +

+

+

- - +

-

+

+

-

-

-

-

-

+

+ +

+

+

- -

Chen et al., Nature 2016

HIF2-I is active in 50% of ccRCC

Inte

rmed

.S

en

sit

ive

Resis

tan

t

Vehicle

Sunitinib

HIF2-I

267 mice from 22 independently derived TG lines (18 ccRCC)

Chen et al., Nature 2016

HIF2-I (PT2399) dissociates HIF-2

also in resistant tumors

RE

SIS

TA

NT

S

EN

SIT

IVE

Chen et al., Nature 2016

HIF2-I is active in 50% of ccRCC

Inte

rmed

.S

en

sit

ive

Resis

tan

t

Vehicle

Sunitinib

HIF2-I

267 mice from 22 independently derived TG lines (18 ccRCC)

Chen et al., Nature 2016

Responsiveness does not correlate with BAP1 or PBRM1 status

Response PDX line HistologyFuhrman

GradeTissue

VHLstatus

BAP1 (IHC)

PBRM1 (IHC)

Relative GI%

(p value)

Sensitive XP26 ccRCC 2 Adrenal mut mut wt 87 (0.0003)

XP144 ccRCC 4 Kidney mut wt wt 98 (<0.0001)

XP164 ccRCC* 4 Kidney wt wt wt 134 (<0.0001)

XP165 ccRCC 3 Abd wall mut wt mut 112 (<0.0001)

XP373 ccRCC 4 Tu Thr wt¥ mut wt 103 (<0.0001)

XP374 ccRCC*# 4 Kidney mut wt wt 109 (<0.0001)

XP453 ccRCC 3 Tu Thr wt¥ wt wt 110 (<0.0001)

XP454 ccRCC 3 Kidney wt mut wt 156 (0.0032)

XP469 ccRCC 3 Kidney mut mut mut 91 (<0.0001)

XP534 ccRCC 4 Kidney mut mut n/a 129 (0.0007)

Intermediate XP237 tRCC n/a LN n/a wt wt 43 (0.0144)

XP391 ccRCC 4 Tu Thr mut wt mut 45 (0.0018)

XP426@ ccRCC# 4 Kidney mut wt wt 44 (0.0273)

XP427@ ccRCC# 4 LN mut wt wt 54 (0.0206)

XP466 ccRCC 3 Kidney wt mut n/a 67 (0.0030)

Resistant XP169 Unclassified n/a Kidney wt wt wt 0 (0.0119$)

XP258 ccRCC* 4 Kidney mut mut wt 39 (0.11)

XP296 ccRCC* 4 Kidney mut wt wt 29 (0.30)

XP462 Unclassified n/a Kidney wt wt mut 29 (0.11)

XP490 ccRCC*# 4 Kidney mut wt wt 39 (0.89)

XP506 ccRCC 3 Ascites wt wt wt 20 (0.76)

XP530 Unclassified n/a Kidney wt n/a n/a 2 (0.68)

@ Independent tumors from same patient, * Sarcomatoid differentiation, # Rhabdoid features, $ HIF2-I-treated mice

had greater relative growth than vehicle-treated mice, ¥ Promoter methylation

PBRM1+ BAP1+

PBRM1- BAP1+

PBRM1+ BAP1-

PBRM1- BAP1-

Joseph, R.* and Kapur, P.* et al., J. Urol. 2015

Kapur et al., Lancet Oncology 2013

Chen et al., Nature 2016

HIF2-I is active in 50% of ccRCC

Inte

rmed

.S

en

sit

ive

Resis

tan

t

Vehicle

Sunitinib

HIF2-I

267 mice from 22 independently derived TG lines (18 ccRCC)

Chen et al., Nature 2016

Inhibition of HIF-2-regulated genes

in sensitive but not resistant tumors

Veh HIF2-I Veh HIF2-I

Sensitive Resistant

Vehicle

HIF2-I

Sunitinib

Up 195 0

Down 297 0

Total 492 0

Differential Gene Expression

Sensitive Resistant

Veh v HIF2-I Veh v HIF2-I

pg

/ml

hVEGF

Rela

tive

mR

NA

ex

pre

ss

ion

Rela

tive

mR

NA

ex

pre

ss

ion

CCND1 TGFA

hVEGF SERPINE1 IGFBP3

SLC2A1

Chen et al., Nature 2016

Sensitive tumors have higher levels of HIF-2a

HIF-2α HIF-1αHIF-2αHIF-1α

XP

469

XP

374

XP

164

XP

490

XP

530

XP

462

HIF2-a

Pe

rce

nta

ge

po

sitiv

e c

ells

Chen et al., Nature 2016

Sensitive

Differential dependency on HIF-2 in ccRCC

HIF2-I

VEGF VEGF

Resistant

HIF2-I

?

Gene expression

Identification of biomarkers of HIF-2-dependencyRNAseq

Chen et al., Nature 2016

75-gene Nanostring signature distinguishes

sensitive & resistant tumorgrafts

(different tumors and cohorts)

75-gene Nanostring signature distinguishes also

samples from corresponding patients

Demographics and Baseline Treatment Characteristics

Escalation/Expansion

n = 51

Age, years, median (range) 65 (29-80)

Gender, n

Female

Male

15

36

ECOG PS, n (%)

0

1

16 (31%)

35 (69%)

Number of prior therapies, median (range) 4 (1-7)

Prior systemic therapies, n (%)

1

2

3

4

> 5

7 (14%)

9 (18%)

8 (16%)

12 (24%)

15 (29%)

Prior anti-cancer therapies, n (%)

VEGF / VEGFR inhibitor

mTORC1 inhibitor

Cytokine

Other Immunotherapy

Investigational/Other

51 (100%)

31 (61%)

9 (18%)

10 (20%)

13 (25%)

Adapted from Courtney

et al., ASCO 2016

Phase 1 Clinical Trial of HIF2-I (PT2385)

Pharmacodynamics: Decrease in

HIF-2a target EPO

• Rapid reduction of erythropoietin observed at all doses

• No further reduction observed above 800 mg b.i.d.

800 mg b.i.d. Recommended Phase 2 Dose

Adapted from Courtney et al., ASCO 2016

No DLT

002 041 016 035 026 047 001 028 020 036 055 033 034 054 048 043 004 003 012 049 045 029 053 023 021 010 007 019 022 027 005 030 038 046 042 037 009 057 013 011 015 018 052 025 039 040 017 008 006

-1 0 0

-9 0

-8 0

-7 0

-6 0

-5 0

-4 0

-3 0

-2 0

-1 0

0

1 0

2 0

3 0

4 0

5 0

Ma

xim

um

S

LD

R

ed

uc

tio

n fro

m B

as

eli

ne

(%

)

M a x im u m S L D - A ll P a tie n ts

Maximum Radiographic Response

PD

SD

PR

CR

Data cutoff: May 18, 2016

1 CR, 3 PR, and 16 pts with SD > 16 weeks

100 mg, b.i.d.200 mg, b.i.d.400 mg, b.i.d.800 mg, b.i.d.1,200 mg, b.i.d.1,800 mg, b.i.d.

Adapted from Courtney et al., ASCO 2016

Ongoing treatmentPartial ResponseComplete Response

Data cutoff: May 18, 2016

0 5 1 0 1 5 2 0 2 5 3 0 3 5 4 0 4 5 5 0 5 5 6 0 6 5

024

019

012

044

030

043

034

048

016

041

001

003

010

022

026

054

035

036

047

055

004

005

033

057

023

007

028

020

002

037

053

052

021

049

046

045

018

040

042

029

038

039

027

025

017

015

013

011

009

008

006

W e e k s o n T re a tm e n t

Pa

tie

nt

100 mg, b.i.d.200 mg, b.i.d.400 mg, b.i.d.800 mg, b.i.d.1,200 mg, b.i.d.1,800 mg, b.i.d.

Duration of Treatment

Adapted from Courtney et al., ASCO 2016

SPORE: Translating Discovery

& Innovation at UTSW

Project 1: Targeting HIF-2 for the Treatment of ccRCC (Brugarolas, Courtney, Pedrosa)

Project 2: Evaluation of the Functional and Clinical Significance of the Novel Tumor Suppressor Gene BAP1 (Kapur, Carroll, Yu)

Project 3: Clinically Actionable Biomarkers from RCC Metabolism and Imaging (DeBerardinis, Margulis, Pedrosa)

Project 4: Prognostic Significance and Therapeutic Potential of DROSHA Mutations in Wilms Tumor (Amatruda, Mendell)

Cores: Admin, Pathology (Kapur, Rakheja), Imaging (Pedrosa, Lenkiski), Data Analytics (Xie, Xie, Hwang).

30%55%

3%

12%

wt PBRM1 BAP1 & PBRM1 BAP1

30%

12%

55%3%

wt BAP1 PBRM1 BAP1/PBRM1

30%

12%

55%3%

wt BAP1 PBRM1 BAP1/PBRM1

30%

12%

55%3%

wt BAP1 PBRM1 BAP1/PBRM1

30%

12%

55%3%

wt BAP1 PBRM1 BAP1/PBRM1

VHL

HIF-2

ccRCC is not one tumor type – HIF-2 and BAP1/PBRM1 define distinct

subtypes with different dependencies and biology.

This may impact drug responsiveness, in particular to drugs targeting

pathways other than VEGF.

Molecular subtypes of ccRCC

Brugarolas Lab

Brinda Chellappan

Yifeng Gu

Allison Joyce

Meghan Konda

Eric Ma

Renee McKay

Tiffani McKenzie

Neville Wang

Nick C. Wolff

Juan Yang

Hui Ye

Anum Yousuf

Alana Christie

Min Kim

Tao Wang

Xian-Jin Xie

Yang Xie

Wenfang Chen

Shannon Cohn

Haley Hill

Eboni Holloman

Farrah Homayoun

Blanka Kucejova

Andrea Pavia-Jimenez

Samuel Peña-Llopis

Sharanya Sivanand

Vanina Toffessi

Tram Anh Tran

Silvia Vega-Rubin de Celis

Shanshan Wang

Toshinari Yamasaki

Jenny Chang

Deni Von Merveldt

Vincy Alex

Debbie Harvey

Funding

Virginia Murchison Linthicum Endowment

Cancer Prevention and Research Institute of Texas

NIH, National Cancer Institute

Kidney Cancer Program

Urology

Jeff Cadeddu

Jeff Gahan

Yair Lotan

Vitaly Margulis

Ganesh Raj

Arthur I. Sagalowsky

Medical Oncology

Yull Arriaga

Kevin Courtney

Eugene Frenkel

Hans Hammers

Radiation Oncology

Raquibul Hannan

Nathan Kim

David Pistenmaa

Robert Timmerman

Pathology

Payal Kapur

Dinesh Rakheja

Radiology

Ivan Pedrosa

Lori Watumull

Clinical Genetics

Megan Farley

Illumina Inc.

Arnold Liao

Nan Leng

Christian Haudenschild

Mark Ross

David Bentley

Mayo Clinic

Richard W. Joseph

Daniel J. Serie

Jeanette Eckel-Passow

Thai Ho

John C. Cheville

Alexander Parker

Genentech

Anwesha Dey

Steffen Durinck

Eric W. Stawiski

Zora Modrusan

Sekar Seshagiri

NCI

Laura Schmidt

Marston Linehan

Other Collaborators

Thomas Carroll

Ralph DeBerardinis

Robert E. Hammer

Bruce Posner

Dipti Ranganathan

Noelle Williams

Jin Ye

Yonghao Yu

Phase 1 Trial

Kevin Courtney

Jeffrey R. Infante

Elaine T. Lam

Robert A. Figlin

Brian I. Rini

Naseem J. Zojwalla

Keshi Wang

Eli M. Wallace

John A. Josey

Toni K. Choueiri

Bioniformatics

Min Kim

Dipti Ranganathan

Phillip Reeder

Tao Wang

Yang Xie

He Zhang