muscle invasive bladder cancer - comtecgroup€¦ · muscle invasive urothelial ... synon ymous m u...

Comprehensive characterization of 412 muscle invasive urothelial carcinomas – final analysis of the cancer genome atlas

(TCGA) project

AAGUS 2016

• Clinical trials

–Endo, FKD, JBL, Roche/Genentech, Viventia

• Advisory Board

– Ferring, Nucleix, OncoGeneX, Sitka, Taris

• Consultant

–Biocancell, Telesta, Theracoat, Vaxiion

• TCGA – volunteer > 6 years

Disclosures

Bladder Cancer Treatment Today

One size fits all – level I evidence

• NMIBC –

– Low risk – peri-op chemotx

– Intermediate risk – optimized MMC

– High risk – BCG

• MIBC

– Non-metastatic NAC

– Metastatic

SWOG 8507 BCG Maintenance

MMC

TCGA Initial vs. Newly Sequenced samples •54 significantly mutated genes (SMGs, prevalence as low as 2%) - increase from 32 in the original report

KRAS activating mutations in the new sample set (overall 4%) ERBB2 mutations were almost doubled in the new sample set RB1, ATM, STAG2, ELF3 mutations were significantly up in the new

sample set

NonsynonymousSynonymous

Mu

tatio

ns

0

500

1000

1500

2000

Sp

ectr

um

0.00.20.40.60.81.0

Paper New TCGA

SPN (2%)ZNF773 (2%)

TAF11 (2%)NUP93 (2%)

SF1 (3%)GNA13 (3%)

ZBTB7B (3%)MBD1 (3%)PTEN (3%)

CASP8 (4%)THRAP3 (4%)

KRAS (4%)METTL3 (4%)C3orf70 (4%)

ACTB (5%)RPTN (5%)CUL1 (5%)

RHOA (5%)HRAS (5%)

RBM10 (5%)PSIP1 (5%)

FAM47C (5%)KLF5 (6%)

RXRA (6%)PARD3 (6%)

NFE2L2 (6%)RHOB (6%)

CDKN2A (7%)ZFP36L1 (7%)

FBXW7 (8%)TSC1 (8%)

CDKN1A (9%)ERCC2 (9%)

ASXL2 (10%)ERBB3 (11%)

MLL (11%)SPTAN1 (12%)ERBB2 (12%)

ELF3 (12%)FAT1 (12%)

CREBBP (12%)ATM (14%)

STAG2 (14%)FGFR3 (14%)EP300 (15%)

RB1 (17%)MLL3 (19%)

PIK3CA (22%)ARID1A (25%)KDM6A (26%)

MLL2 (29%)TP53 (49%)

200 150 100 50 0# Mutations

In frame indel Other non syn. Missense Splice site Frame shift Nonsense

C>TC>AC>G

A>GA>CA>T

rank gene

1 TP53

2 PIK3CA

3 RB1

4 KDM6A

5 RHOB

6 TSC1

7 ELF3

8 MLL2

9 CDKN1A

10 FBXW7

11 CDKN2A

12 ZFP36L1

13 ARID1A

14 STAG2

15 CREBBP

16 EP300

17 HRAS

18 KRAS

19 ERCC2

20 NFE2L2

21 FGFR3

22 MLL

23 MLL3

24 ASXL2

25 C3orf70

26 RXRA

27 RHOA

28 PSIP1

29 KIAA1267

30 FAT1

31 ZBTB7B

32 PTEN

33 ATM

34 KLF5

35 SPTAN1

36 RBM10

37 PARD3

38 CUL1

39 RPTN

40 CASP8

41 FAM47C

42 TAF11

43 GNA13

44 ACTB

45 METTL3

46 SF1

47 ERBB2

48 ERBB3

49 ZNF773

50 NUP93

51 MBD1

52 THRAP3

53 SPN

54 C3orf59

First 131 tumors Additional 281 tumors

Kim, et al Clin Ca Res

RTK/Ras/PI3K pathways HER2/ERBB2 Activation as a potential

therapeutic target

• ERBB2 mutations doubled in expanded tumor set

• Her2 levels comparable to Her2+ breast cancer

Trastuzumab

Trastuzumab-DM1

Lapatinib [NCT00447226]

Neratinib [NCT01953926]

DN24-02 [NCT01353222]

Her2 – CAR (CAGT/BCM)

NB: Mutual exclusivity among many of the genes in these two pathways suggesting logical targets for therapy

Nature epub 1/29/14

Multiple Alterations in Kinase Signaling Pathways

Personalized Medicine in Urothelial Carcinoma mTOR/TSC1

• Patient treated on phase II trial of Everolimus – mTOR inhibitor

• Whole genome sequencing revealed TSC1 and NF2 inactivating mutations

• In vitro evaluation shows TSC1 sensitizes urothelial cancer cells to mTOR inhibition

Iyer et al. Science 2012;338:221

Study design, mutation rates, and aggregate significant somatic mutations

Eliezer M. Van Allen et al. Cancer Discovery 2014;4:1140-1153

©2014 by American Association for Cancer Research

COXEN prediction of treatment outcome in patients treated

with neoadjuvant MVAC

Takata (Japan)

COXEN

Gene Expression Model

Evaluation of Model on

Human Tumors

MSKCC & UVA Downstaging vs. COXEN Score

Downstaging defined as ≤pT1 or ≤T1 after two courses of MVAC

Downstaged NO Downstage

CO

XE

N S

co

re

NCI-60 Panel

Methotrexate

Vinblastine

Doxorubicin

Cisplatin

x

FL3Sensitive

1

1

11 1

2 2

2

2 2

33

3

3 3

x

VMCUB3Sensitive

11

11

1

2

2

22 2

3

3

33 3

x

T24TSensitive

1

1

1 1 1

22

22 2

33

33 3

x

SLT4Sensitive

1

1

11 1

2

2

2

2 2

3

3

3

3 3

x

RT4Sensitive

1 11

11

2 2

2

2 2

3 3

3

3 3

575ASensitive

1 1

1

1 1

2 2

2

2 2

3 3

3

3 3

x

y

VMCUB2Sensitive

1

1

11 1

22

22 2

33

33 3

x

y

JONSensitive

11

1

1 1

22

2

22

33

3

33

x

y

BC16.1Sensitive

1 1

1

1 1

2 2

2

2 2

x

y

HU456Sensitive

1 1

1

1 1

22

2

2 2

x

y

J82Sensitive

1 1

1

1

1

2 2

2

2 2

y

HTB9Sensitive

1 1

1

1 1

2 2

2

2 2

x

y

HT1197Sensitive

1 1

1

11

2 2

2

2 2

x

y

UMUC14Sensitive

11

11 1

2

2

22 2

x

y

MGH-U3Sensitive

1 1

1

1 1

22

22 2

x

y

MGH-U4Sensitive

1 1

1

1 1

22

22 2

x

y

UMUC3Sensitive

11

1

1 1

2 2

22 2

y

VMCUB1Sensitive

1 1

1

11

22

22 2

x

y

UMUC6Sensitive

1 1

11 1

2 2

22 2

x

y

TCCSUPSensitive

1 1 1

1 1

2 2

2

2 2

x

y

CUBIIISensitive

11

1

1 1

2 2

2

2 2

x

y

KU7Resistant

11

11 1

2 2

2

2 2

x

y

UMUC1Resistant

1 1

1

1 1

2 2

2

2 2

y

CRL2742Resistant

11

1

1 1

2 2

2

2 2

x

y

UMUC2Resistant

11

11 1

2 2

22 2

x

y

253JLavalResistant

1 1

1

11

2 2

2

2 2

x

y

UMUC13DResistant

1

1

1

1 1

2

2

22 2

x

y

253J-BVResistant

1 1

11 1

2 2

22 2

x

y

KK47Resistant

1 1

1

1 1

2 2

2

2 2

y

SW1710Resistant

1 1

1 11

2 2

2

2 2

x

y

UMUC9Resistant

1 1

1

1 1

2 2

2

22

x

y

T24Resistant

1 1

1

1 1

2 2

2

2 2

x

y

HT1376Resistant

1 1

1

1 1

22

2

2 2

x

y

253J-PResistant

1 1

1

1 1

2 2

2

2 2

x

y

CRL7833Resistant

1

1

11 1

2

2

22 2

y

CRL7193Resistant

1

1

1 11

2

2

2

2 2

Pro

po

rtio

n S

urv

ivin

g

Ref: Clin Can Res 2005;11(7): 2625

Tx: Neoadjuvant MVAC (N=45) + surgery or XRT

Outcome: Downstaging, Overall survival

SWOG S1314

COXEN Validation Neoadjuvant Chemotherapy Trial

Selection Criteria SWOG 8710

(T2-T4a N0M0, cisplatin eligible)

C

Y

S

T

E

C

T

O

M

Y

Randomize

to chemo

n=184

Gem-Cis

DD-MVAC

Assessment To characterize the

relationship of MVAC-

and GC-specific COXEN

scores in terms of pT0

rate

Biomarker validation and Biomarker discovery

Tumor

Sample

TURBT

Collection Tissue, blood, urine

Molecular Analysis Gene expression

Sequencing

microRNA

SNP

Collection Tissue (>P0), blood, urine

Molecular Analysis Gene expression

Sequencing

microRNA

SNP

Cystectomy

Pathology

Discovery

Activated July 1, 2014

RBM10 (5%)PSIP1 (5%)

FAM47C (5%)KLF5 (6%)

RXRA (6%)PARD3 (6%)

KIAA1267 (6%)ZFP36L1 (6%)NFE2L2 (6%)

RHOB (6%)CDKN2A (7%)

FBXW7 (8%)TSC1 (8%)

ASXL2 (9%)CDKN1A (9%)

ERCC2 (9%)ERBB3 (11%)

MLL (11%)SPTAN1 (12%)ERBB2 (12%)

ELF3 (12%)FAT1 (12%)


STAG2 (14%)FGFR3 (14%)EP300 (15%)

RB1 (17%)MLL3 (19%)


MLL2 (29%)TP53 (49%)

178

239

150 100 50 0

# mutations

Syn.

Non syn.

0

10

20

30

40

50

59

135

66

72

Muta

tion

s/M

b

Syn. In frame indel Other non syn. Missense Splice site Frame shift Nonsense

RB1 (16%)CDKN2A (43%)

KRAS (4%)EGFR (6%)

ERBB2 (5%)CCNE1 (8%)

GATA3 (11%)ZNF703 (10%)

MDM2 (9%)PPARG (13%)CCND1 (11%)YWHAZ (22%)PVRL4* (18%)

E2F3/SOX4 (17%)

200 150 100 50 0

# SCNA alterations

Copy Number < 1 1 < Copy Number < 1.5 3 < Copy Number < 5 Copy Number > 5

STAGEGENDER

SMOKINGSUBTYPE

Non−Papillary

Papillary

Non−smoker

Smoker

Male

Female

Stage I−II

Stage III

Stage IV

Marker paper I

Marker paper II

Marker paper III

Marker paper IV

Full Set(Nature 2014) Marker paper

SOX2DLX6MSI1

PLEKHG4B

TWIST1ZEB2ZEB1

SCELTGM1

HES2EGFR

MYCTP73TP63

KRT16KRT6AKRT6B

KRT5KRT14

UPK3AUPK1BUPK1A

UPK2KRT20FGFR3

GRHL3FOXA1

ELF3RXRA

PPARGKLF5

GATA3

CD274CTLA4

IL6IL2RACD44

CD4IRF1

FOXP3RELBIDO1

SNAI2SPI1

Neuroendocrine

EMT markers

Squamous cell differentation

Basal subtype markers

Luminal subtype markers

Urothelial differentiation

Immune

mRNA fold < 0.33 0.33 < mRNA fold < 0.67 1.5 < mRNA fold < 3 3 < mRNA fold

Squamous/basal

• Nearly all squamous differentiation clustered in this group

• Enriched with female gender • But also tumors without apparent

squamous differentiation

Immune

KRT5,6,14

Bladder Cancer 2:37, 2016

NAC with MVAC/Bevacizumab Phase II McConkey, et al Eur Urol, 2015, epub 9/3/2015

Sjodahl, et al Clin Cancer Res 18:3377, 2012

CNIO, 2015

RBM10 (5%)PSIP1 (5%)

FAM47C (5%)KLF5 (6%)

RXRA (6%)PARD3 (6%)

KIAA1267 (6%)ZFP36L1 (6%)NFE2L2 (6%)


FBXW7 (8%)TSC1 (8%)


ERCC2 (9%)ERBB3 (11%)

MLL (11%)SPTAN1 (12%)ERBB2 (12%)

ELF3 (12%)FAT1 (12%)


STAG2 (14%)FGFR3 (14%)EP300 (15%)

RB1 (17%)MLL3 (19%)


MLL2 (29%)TP53 (49%)

178

239

150 100 50 0

# mutations

Syn.

Non syn.

0

10

20

30

40

50

59

135

66

72

Muta

tion

s/M

b


RB1 (16%)CDKN2A (43%)

KRAS (4%)EGFR (6%)


GATA3 (11%)ZNF703 (10%)


E2F3/SOX4 (17%)

200 150 100 50 0

# SCNA alterations


STAGEGENDER

SMOKINGSUBTYPE

Non−Papillary

Papillary

Non−smoker

Smoker

Male

Female

Stage I−II

Stage III

Stage IV

Marker paper I

Marker paper II

Marker paper III

Marker paper IV


SOX2DLX6MSI1

PLEKHG4B

TWIST1ZEB2ZEB1

SCELTGM1

HES2EGFR

MYCTP73TP63

KRT16KRT6AKRT6B

KRT5KRT14

UPK3AUPK1BUPK1A

UPK2KRT20FGFR3

GRHL3FOXA1

ELF3RXRA

PPARGKLF5

GATA3

CD274CTLA4

IL6IL2RACD44

CD4IRF1

FOXP3RELBIDO1

SNAI2SPI1

Neuroendocrine

EMT markers





Immune


Luminal/urothelial

Enriched for tumors with papillary morphology

EMT

Immune

FGFR3, KRT20, Uroplakin

Papillary, Gata3, FOXA1

Uroplakin Immune Papillary

UP1-3, KRT 20

LN+ 56%

Rosenberg, et al Lancet epub 3/4/16

Atezolizumab - CDDP progressors



Both higher median mutation load and TCGA intrinsic molecular subtype (Luminal immune cluster II) independent predictors of overall survival

RBM10 (5%)PSIP1 (5%)

FAM47C (5%)KLF5 (6%)

RXRA (6%)PARD3 (6%)

KIAA1267 (6%)ZFP36L1 (6%)NFE2L2 (6%)


FBXW7 (8%)TSC1 (8%)


ERCC2 (9%)ERBB3 (11%)

MLL (11%)SPTAN1 (12%)ERBB2 (12%)

ELF3 (12%)FAT1 (12%)


STAG2 (14%)FGFR3 (14%)EP300 (15%)

RB1 (17%)MLL3 (19%)


MLL2 (29%)TP53 (49%)

178

239

150 100 50 0

# mutations

Syn.

Non syn.

0

10

20

30

40

50

59

135

66

72

Muta

tion

s/M

b


RB1 (16%)CDKN2A (43%)

KRAS (4%)EGFR (6%)


GATA3 (11%)ZNF703 (10%)


E2F3/SOX4 (17%)

200 150 100 50 0

# SCNA alterations


STAGEGENDER

SMOKINGSUBTYPE

Non−Papillary

Papillary

Non−smoker

Smoker

Male

Female

Stage I−II

Stage III

Stage IV

Marker paper I

Marker paper II

Marker paper III

Marker paper IV


SOX2DLX6MSI1

PLEKHG4B

TWIST1ZEB2ZEB1

SCELTGM1

HES2EGFR

MYCTP73TP63

KRT16KRT6AKRT6B

KRT5KRT14

UPK3AUPK1BUPK1A

UPK2KRT20FGFR3

GRHL3FOXA1

ELF3RXRA

PPARGKLF5

GATA3

CD274CTLA4

IL6IL2RACD44

CD4IRF1

FOXP3RELBIDO1

SNAI2SPI1

Neuroendocrine

EMT markers





Immune


Neuroendocrine

NE markers up

Immune markers down

Aine, et al Sci Rep 5:10957, 2015

Luminal immune NE

Papillary Basal/Scca Luminal uroplakin

Pts-deaths

Luminal KRT20+, GATA3+, FOXA1+

Basal/Squamous KRT5,6,14+, GATA3-, FOXA1-

Papillary Immune/EMT Uroplakin

Basal/SCCa Neuroendocrine

FGFR3mu Papillary histology

Low risk No NAC? FGFR3 inhibitors

ZEB 1,2 TWIST miR 200 CD270,CTLA-4 FOXP3

Anti-PDL1,PD-1 NAC

Chemoresistant? Targeted therapy?

Cisplatin-based NAC; PD-L1, PD-1

Etoposide/Cisplatin NAC

T2-4 Nx Mx Urothelial Bladder Cancer

Female SCCa differentiation Immune infiltrate

SOX2 DLX6 MSI1 PLEKHG4B E2F3/SOX4 amp

UP 1,2,3 KRT 20

muscle invasive bladder cancer - comtecgroup€¦ · muscle invasive urothelial ... synon ymous m u...

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