molecular biology, biomarkers, and tcga...molecular biology, biomarkers, and tcga jean-pascal...

MOLECULAR BIOLOGY, BIOMARKERS,

AND TCGA

Jean-Pascal Machiels

Department of medical oncology

Institut Roi Albert II

Cliniques universitaires Saint-Luc

Université catholique de Louvain, Brussels, Belgium

I

DISCLOSURE SLIDE

Advisory board member or speaker with honoraria (managed by my Institution): Pfizer,

Roche, Astra/Zeneca, Bayer, Innate, Merck Serono, Boerhinger, BMS, Novartis, Janssen,

Incyte, …

Travel expenses: Amgen, BMS, Pfizer, MSD, …

Data safety monitoring board with honoraria: Debio, Nanobiotix

Institutional conflict of interest (Funding to institution for research support): all companies

Uncompensated advisory role: MSD

EORTC: investigator and study coordinator

• Key molecular biology features of HPV-negative

and positive head and neck cancer

• Prognosis value of p16 and EGFR

• Predictive biomarkers: EGFR, p16 and PD-L1

Learning objectives

Squamous cell carcinoma of the head and neck

The seventh most common form of cancer

600 000 cases per year worldwide

➔Human Papillomavirus (HPV+)

(oropharynx)

➔Alcohol & tabacco(oral cavity, larynx and pharynx)

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0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0Years from RT

p16 posp16 neg

HR = 0.36, P = 0.0042-y OS: 74% & 91%

.125.25 .5 1 2 4

Hazard ratio 95% CI

• Key molecular features

• EGFR and p16 as prognosis biomarkers

• EGFR and p16 as predictive biomarkers

• Microenvironment: immunology

Presentation outline

Leemans R et al, Nature Reviews 2018

HPV-negative genomic alterations

Leemans R et al, Nature Reviews 2011

Amplified in 30%

Inactivated in 90%

Mutated

in 70%

HPV negative

Leemans R et al, Nature Reviews 2011

HPV positive

Leemans R et al, Nature Reviews 2011

Keck et al, Clin Cancer Res 2014

Gene expression profile

Leemans R et al, Nature Reviews 2018

HER family• EGFR amplification/mutation

in 15%• ERBB2 amplification/mutation

in 5%

FGFR pathway• FGFR1 amplification

in 10% HPV negdisease

• FGFR3 mutations in up to 10% HPV pos disease

PI3K pathway• PIK3CA

mutation/amplification in up to 56% HPV positive SCCHN

• PTEN loss in up to 12%

HRAS mutated in 4-5%

Homologours recombination deficiency in HPV+ or in HPV-platinum sensitive disease ?

Actionable genomic alterations

Leemans R et al, Nature Reviews 2011

Amplified in 30%

Inactivated in 90%

Mutated

in 70%

CDK inhibitors:

Palbociclib

LEE011,

LY2835219

HPV negative

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0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0Years from RT

p16 posp16 neg

HR = 0.36, P = 0.0042-y OS: 74% & 91%

.125.25 .5 1 2 4

Hazard ratio 95% CI

• Key molecular features

• EGFR and p16 as prognosis biomarkers

• EGFR and p16 as predictive biomarkers

• Microenvironment: immunology

Presentation outline

RTOG 0129 TROG 02.02

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0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0Years from RT

p16 posp16 neg

HR = 0.36, P = 0.0042-y OS: 74% & 91%

.125.25 .5 1 2 4

Hazard ratio 95% CI

• The gold standard to detect HPV infection is detection of E6/E7mRNA

• In Situ Hybridization for HPV DNA

• p16 is a good surrogate marker of HPV infection in oropharyngeal cancer:

sensitivity and specificity around 90%

• Diagnosis and prognosis value of p16 outside the oropharynx is controversial

• p16 positivity + HPV PCR DNA

RTOG 0129 TROG 02.02

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0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0Years from RT

p16 posp16 neg

HR = 0.36, P = 0.0042-y OS: 74% & 91%

.125.25 .5 1 2 4

Hazard ratio 95% CI

Ang KK NEJM 2015Rischin JCO 2010

Survival by HPV or p16 status for oropharyngeal cancer

Carole Fakhry et al. JCO 2014;32:3365-3373

©2014 by American Society of Clinical Oncology

Prognosis: p16 and recurrent disease

19

Locoregional relapse Distant metastases

Salvage surgery No salvage surgery

Fakhry et al. J Clin Oncol 2014

Prognosis: p16 and recurrent disease

Copyright © American Society of Clinical Oncology

Dannenberg, A. J. et al. J Clin Oncol; 23:254-266 2005

Ang, K. K. et al. Cancer Res 2002;62:7350-7356

Copyright ©2002 American Association for Cancer Research

Ang et al. Cancer Res 2002

EGFR expression and prognosis

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0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0Years from RT

p16 posp16 neg

HR = 0.36, P = 0.0042-y OS: 74% & 91%

.125.25 .5 1 2 4

Hazard ratio 95% CI

• Key molecular features

• EGFR and p16 as prognosis biomarkers

• EGFR and p16 as predictive biomarkers

• Microenvironment: immunology

Presentation outline

Tumor cell cytoplasmic membrane

Monoclonal

AntibodiesCetuximab

Panitumumab

Zalutumumab

Tyrosine kinase

InhibitorsGefitinib (EGFR)

Erlotinib (EGFR)

Lapatinib (EGFR + HER2)

Afatinib, dacomitinib (pan-HER)

Tumor proliferation

EGF receptor

HER1 or EGFR targeting

EGFR overexpression: NO

EGFR polysomy or amplification: NO

RAS mutations Rare in H&N

p16 or HPV ?

Who is going to response ?

Licitra et al, Annals of Oncology 2010

Penuel et al, AACR 2015

Courtesy of A. Pirzkall, Oncology Biomarker development, Genentech

Cetuximab versus MEHD after platinum ?

Months

Cetuximab + RT

(n=211)O

ve

rall

su

rviv

al (%

)

100

80

60

40

20

0

0 10 20 30 40 50 60 70

RT (n=213)29.3 49.0

Hazard ratio = 0.74 (95% CI: 0.57–0.97)

Log-rank p=0.03

Bonner J, et al. N Engl J Med 2006;354:567–578Bonner, Lancet Oncology 2010

Radiotherapy +/- cetuximab: stage 3 and 4

Bonner et al, Lancet Oncology 2011

p16 + : - 3-year LRC rate: 87% vs 65%- HR: 0.31 (95%, CI, 0.11-0.88)

p16 -: - 3-year LRC rate: 31 vs 19%- HR: 0.78 (95% CI, 0.49-1.25)

Rosenthal, J Clin Oncol 2016

p16 as a predictive marker

Study N N Population Benefit

RosenthalASCO 2014

Radiotherapy/cetuximab

Radiotherapy

p16+ = 44; p16- = 109

p16+ = 39; p16- = 120

Stage III/IV p16- : HR: 0.9(0S)

p16+: HR: 0.45

VermorkenAnn Oncol2014

Platin/5-FU/Cetuximab

Platin/5-FU

p16+ = 18; p16- = 178

p16+ = 23; p16- = 162

Recurrent/metastatic: first-line

p16- : HR: 0.82(0S)

p16+: HR: 0.63

Who is going to response ? HPV or p16 no clear answer

Study N N Population Benefit

RosenthalASCO 2014

Radiotherapy/cetuximab

Radiotherapy

p16+ = 44; p16- = 109

p16+ = 39; p16- = 120

Stage III/IV p16- : HR: 0.9(0S)

p16+: HR: 0.45

VermorkenAnn Oncol2014

Platin/5-FU/Cetuximab

Platin/5-FU

p16+ = 18; p16- = 178

p16+ = 23; p16- = 162

Recurrent/metastatic: first-line

p16- : HR: 0.82(0S)

p16+: HR: 0.63

VermorkenLancet Oncol2013

Platin/5-FU/Panitumumab

Platin/5-FU

p16+ = 57; p16- = 179

p16+ = 42; p16- = 165

Recurrent/metastatic first-line

p16- : HR: 0.73(0S)

p16+: HR: 1

MachielsLancet Oncol2015

Afatinib

Methotrexate

p16+ = 31; p16- =141

p16+ = 11; p16- = 42

Recurrent/metastatic second-line

p16- : HR: 0.69(PFS)p16+: HR: 0.95

Who is going to response ? HPV or p16 no clear answer

P P P P P P

EGFR HER-2 HER-3 HER-4

MEHD7945A

Lapatinib

Afatinib Dacomitimib

Study N N Population Benefit

RosenthalASCO 2014

Radiotherapy/cetuximab

Radiotherapy

p16+ = 44; p16- = 109

p16+ = 39; p16- = 120

Stage III/IV p16- : HR: 0.9(0S)

p16+: HR: .45

VermorkenAnn Oncol2014

Platin/5-FU/Cetuximab

Platin/5-FU

p16+ = 18; p16- = 178

p16+ = 23; p16- = 162

Recurrent/metastatic: first-line

p16- : HR: 0.82(0S)

p16+: HR: 0.63

VermorkenLancet Oncol2013

Platin/5-FU/Panitumumab

Platin/5-FU

p16+ = 57; p16- = 179

p16+ = 42; p16- = 165

Recurrent/metastatic first-line

p16- : HR: 0.73(0S)

p16+: HR: 1

MachielsLancet Oncol2015

Afatinib

Methotrexate

p16+ = 31; p16- =141

p16+ = 11; p16- = 42

Recurrent/metastatic second-line

p16- : HR: 0.69(PFS)p16+: HR: 0.95

Who is going to response ? HPV or p16 no clear answerWho is going to response ? HPV or p16 no clear answer

Study N N Population Benefit

RosenthalASCO 2014

Radiotherapy/cetuximab

Radiotherapy

p16+ = 44; p16- = 109

p16+ = 39; p16- = 120

Stage III/IV p16- : HR: 0.9(0S)

p16+: HR: .45

VermorkenAnn Oncol2014

Platin/5-FU/Cetuximab

Platin/5-FU

p16+ = 18; p16- = 178

p16+ = 23; p16- = 162

Recurrent/metastatic: first-line

p16- : HR: 0.82(0S)

p16+: HR: 0.63

VermorkenLancet Oncol2013

Platin/5-FU/Panitumumab

Platin/5-FU

p16+ = 57; p16- = 179

p16+ = 42; p16- = 165

Recurrent/metastatic first-line

p16- : HR: 0.73(0S)

p16+: HR: 1

MachielsLancet Oncol2015

Afatinib

Methotrexate

p16+ = 31; p16- =141

p16+ = 11; p16- = 42

Recurrent/metastatic second-line

p16- : HR: 0.69(PFS)p16+: HR: 0.95

- Very low number of patients in the p16

positive group

- p16 positive group included non-

oropharyngeal sites

- p16 cut-off different in the EXTREME (10%)

Who is going to response ? HPV or p16 no clear answer

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0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0Years from RT

p16 posp16 neg

HR = 0.36, P = 0.0042-y OS: 74% & 91%

.125.25 .5 1 2 4

Hazard ratio 95% CI

• Key molecular features

• EGFR and p16 as prognosis biomarkers

• EGFR and p16 as predictive biomarkers

• Microenvironment: immunology

Presentation outline

Courtesy of P. Coulie and S. LucasInstitut de Duve, UCLOUVAIN

Non-synonymous mutations result in amino acid change in a protein that can be recognizedby T-cells

Vogelstein et al. Science 2013

Antigens resulting from mutations

CTL = cytotoxic T cell.

Chen DS, Mellman I. Immunity 2013;39.

Release of cancer

cell antigens

(cancer cell death)

Cancer antigen

presentation

(dendritic cells/APCs)

Priming and activation

(APCs and T cells)

Trafficking of T cells

to tumours

Infiltration of T cells into tumours

(CTLs, endothelial cells)

Recognition of cancer cells

by T cells

(CTLs, cancer cells)

Killing of cancer cells

(immune and cancer cells)

Tumour

Lymph node

Blood vessel

◆ Antitumor T cells are present in patients with cancer prior to any treatment:

blood and tumor

◆ The T cell responses are insufficient

Spontaneous anti-tumor T cell responses exist in cancer

MHC = major histocompatibility complex; TGF-ß = tumor growth factor-ß.

Drake CG, et al. Adv Immunol. 2006;90:51–81; Vesely MD, et al. Annu Rev Immunol. 2011;29:235–271.

Inhibition of tumor antigen presentatione.g. down regulation of MHC I

1

APC

Inhibition of attack by immune cells

e.g. through T-cellcheckpoint pathways

3

Inactive T cell

Secretion ofimmunosuppressive factors

e.g. TGF-ß

2Tumor

cell

Recruitment of immunosuppressive cell typese.g. T-reg

4

ActivatedT cell

Mechanisms to evade or suppress the immune system

MHC TCR

B7 CD28

Activation signals

B7CD28

Antibody

Inhibitory signals

MHCTCR

PD-L1PD-1

Antibody Antibody

Negative signals

TCR = T-cell receptor; PD-L1 = programmed death-ligand 1.

Ribas A. N Engl J Med. 2012;366:2517‒2519.

Priming phase Effector phase

Dendriticcell

T cell

Lymphnode

Peripheraltissue

T cell Tumorcell

CTLA-4

56 29 20 16 14 12 10 9No. at Risk

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0 2 4 6 8 10 12 14

Time, mo

2.2 months

We have to learn how to fill this gap

Seiwert et al. Lancet Oncology 2016

This is only the beginning

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42

PD-L1+ immune cells PD-L1+ tumour cells

PD-L1 assessment

43

PD-L1 testing

HR (95% CI) P

Pembro alone 0.61 (0.45-0.83) 0.0007

EXTREME

Median (95% CI)

14.9 mo (11.6-21.5)

10.7 mo (8.8-12.8)

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

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1 0

2 0

3 0

4 0

5 0

6 0

7 0

8 0

9 0

1 0 0

M o n th s

OS

, %

N o . a t R is k

133 106 85 65 24

122 100 64 42 12

47

22

0

0

11

5

2

0

The benefit is clinically relevant in CPS > 20

45Data cutoff: 29 April, 2016.

Patients with PD-L1 high tumours

0 2 4 6 8 10 12 14 16 18 20 22 24

−100

−50

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50

100

Ch

ange

fro

m b

asel

ine

(%)

Time (months)

Subjects with confirmed CR/PROther subjectsNew lesion

Patients with PD-L1 low/negative tumours

0 2 4 6 8 10 12 14 16 18 20 22 24

−100

−50

0

50

100

Ch

ange

fro

m b

asel

ine

(%)

Time (months)

Subjects with confirmed CR/PROther subjectsNew lesion

Change in target lesion from baseline by PD-L1

Rizvi et al. Science 2015

Pembrolizumab in NSCLC

Also linked with:- Molecular smoking signature- Mutations in DNA repair mechanisms

THANK YOU !

Jean-pascal.machiels@uclouvain.be