Biology of Cancer and Omics

Etienne GC Brain, MD PhD

Institut Curie

Saint-Cloud, France

www.siog.org

etienne.brain@curie.fr 1

Tumour tissue vs normal tissue

2

*

Premalignant cells

Dysplasia

Adenoma

Cancer cells

Carcinoma

Invasive carcinoma

Normal cells

La carcinogenèse est un processus multi-étapes

*

*

*

Cell growth w/ increased proliferation and decreased apoptosis

Division = Apoptosis Division >> Apoptosis

1 g tumour = 212 cells = 10 years

3

Molecular abnormality

• Any modification of structure, function,

conformation or expression of a cellular

molecule

– DNA, RNA, proteins, lipids, saccharides

4

DNA

• Base

– Point mutation

– Methylation

• DNA sequence

– Insertion/deletion

– Repetition

– Fusion

• Chromosomes

– Fusion

– Deletion

– Modification of copy number 5

Proteins

• Expression

• Function (activation, inhibition or new function)

• Post translational

• Conformation (3D structure)

• Fusion

6

Somatic vs germinal

• Importance to make a distinction between

– Somatic mutation: acquired on tumour DNA only in specific

cells

– Germinal mutation: any detectable and heritable variation in the

lineage of germ cells in each cell

• BRCA 1 & 2: predisposition to breast & ovarian cancer

• DPD: pharmacogenomic and metabolism of 5-FU

• Cancer = genetic disease

– Succession of genome alterations 7

Passenger versus Driver Mutations

• Passenger no effect (genetic instability).

• Driver selection (proliferation, survival)

– Targetable: by a pharmacological agent

– Actionable: predicting sensitivity or resistance to

pharmacological agent

8

Type of Mutations

Meyerson Nat Rev Genet 2010 9

Hanahan & Weinberg Cell 201

IMMUNITY

ANGIOGENESIS

METABOLISM

MIGRATION

SURVIVAL

GENETIC INSTABILITY

TRANSDUCTION PATHWAYS

CELL CYLE

INFLAMMATION

IMMORTALITY

10

NGS Tools

Simon and Roychowdhury Nature Rev Drug Disc 2013 11

Mutations frequency vary across and within cancer types

Low mutational burden High mutational burden

12

Oncogenes & tumour suppressor genes

• Activation of cell growth

+ proliferation

- apoptosis

• Inhibition of cell growth

- proliferation

+ apoptosis

• Abnormal activation of activating

proteins

– Oncoproteins

• Abnormal inactivation of inhibitory

proteins

– Oncosuppressive proteins

• Oncogene activation

– Mutation

– Gene amplification

– Chromosome translocation

– Viral oncogene expression

≥ 1 event (dominant)

• Tumour suppressor gene

inactivation

– Double deletion

– Mutation and gene deletion

– Loss of gene expression

– Interaction w/ activated cell or virus

oncogene

≥ 2 events (recessive)

13

Definitions

• Oncogenes

– Signal transduction

• Tumour suppressor genes

– DNA repair (caretakers)

– Cell cycle control (gatekeepers)

14

Inactivation of tumour suppressor genes

& genetic predisposition Sporadic Inherited

Mut 1

Mut 2 Loss of

second allel

Constitutional

Germinal

mutation

Mut 2 Loss of

second allel

Somatic event

affecting

1 cell at the

origin of cancer

15

Accumulation of genetic alterations

Some yield selective advantage on growth 16

17

18

Pro-tumour effect Anti-tumour effect

Th1

Treg

Th17

T CD8+

Natural Killer T Lym

ph

oid

ce

lls

Myeloid derived

suppressor cells

Macrophage M2

Macrophage M1

Mye

loid

ce

lls

Carriani 2012 19

Alsaab Frontiers Pharmacol 2017 20

Alsaab Frontiers Pharmacol 2017 21

At least 6 Immune Subtypes In Cancer

Thorsson Cell 2018 22

Heterogeneity is multifactorial

1. Elderly – 75 yo vs 90 yo

– No comorbidity vs dementia

2. Cancers – Kidney cancer curative surgery

– M+ colorectal cancer surgery + chemotherapy

– High grade NHL intensive chemotherapy

3. An early stage breast tumour – ER- surgery + XRT + chemotherapy

– ER+ surgery + XRT + endocrine treatment ± chemotherapy

23

• HES stage, LN, immune infiltration

mucinous Poorly differenciation/medullar

TIL Peritumour Cohn-like reaction

CCR & Techniques - 1

24

• IHC

hMLH1 PMS2

hMSH2 hMLH6

HER2

CCR & Techniques - 2

25

CCR

MMR

Treatment strategy

Genetic

Lynch 5-10%

BRAF c.1799T>A (p.Val600Glu)

MSI Lynch Syndrome

26

Tumour DNA

• RAS mutations (KRAS & NRAS) & BRAF

Selection

Macrodissection

27

Illumina (Solexa)

PGM (LifeTech)

> 1 week, complex, compatibility with disease course

Analysis of a large number of sequences

Full or targeted sequencing (predfined genes)

High-depth sequencing to identify undererepresented clones (<10% cells)

High Through Put Sequencing

28

Liquid Biopsy

29

Monitoring Tumour Progression

30

Personalized Medicine

• Stratified/tailored medicine (precision)

Develop drug in a population

defined by a biomarker i.e

companion biomarker

• Personalized medicine Each patient is unique

• Precision & Personalized medicine

- Way that healthcare is moving in the future

- Model customizing healthcare based on the individual's and

tumour’s genetics

- Main goal = to make medicine predictive (precision),

preventive, personalized and participatory 31

Targets Targeted theapy Tumour type Biomarker

EGFR Erlotinib/Gefitinib Cetuximab/Panitumumab

Cetuximab

Lung Colon

H&N

Mutation EGFR Mutation KRAS

-

HER-2 Trastuzumab/TDM-1 Lapatinib/Pertuzumab

Trastuzumab

Breast Breast

Stomach

Amplification HER2 Amplification HER2

Amplification HER2

mTOR Temsirolimus/Everolimus Everolimus

Kidney Endocrine tumours

- -

c-Kit Imatinib GIST Over expression c-Kit

SMO Vismodegib Basocellular carcinoma -

VEGF(R) Bevacizumab Sunitinib

Sorafenib

Breast, kidney, colon, lung Kidney, endocrine tumours

Kidney, hepatocarcinoma

- -

-

HDAC Vorinostat Cutaneous lymphoa -

NF-κB Bortezomib Multiple myeloma -

CTLA4 Ipilumumab Melanoma -

RAF Vemurafenib Melanoma Mutation V600E BRAF

ALK Crizotinib Lung Translocation ALK

RET Vandetanib/Cabozantinib Thyroid medullary carcinoma - 32

> ?

Le Tourneau Lancet Oncol 2015 33

Cibles Altérations moléculaires Thérapies ciblées

KIT, ABL1/2, RET Mutation/Amplification Imatinib

PI3KCA, AKT1

AKT2/3, mTOR, RICTOR, RAPTOR

PTEN

STK11

INPP4B

Mutation/Amplification

Amplification

Délétion homozygote

Délétion Hétérozygote + mutation ou IHC

Délétion homozygote

Délétion Hétérozygote + mutation

Délétion homozygote

Everolimus

BRAF Mutation/Amplification Vemurafenib

PDGFRA/B, FLT3 Mutation/Amplification Sorafenib

EGFR Mutation/Amplification Erlotinib

HER-2 Mutation/Amplification Lapatinib + Trastuzumab

SRC

EPHA2, LCK, YES1

Mutation/Amplification

Amplification Dasatinib

RO, RP Expression protéique >10% en IHC Tamoxifen ou Letrozole

RA Expression protéique >10% en IHC Abiraterone

3 molecular pathways (hormone receptor, PI3K/AKT/mTOR, RAF/MEK)

Le Tourneau Lancet Oncol 2015 34

Oct 2012 to July 2014: 741 pts w/ any tumour type 293 (40%) pts w/ ≥ 1 molecular alteration matching 1 of 10 available regimens

Median FU 11.3 mo

Grade 3-4 AEs 43% vs 35% (p=0.30) Small study (n=195 randomized), heavily pretreated…

Multiple alterations and Rx groups

Supports caution

Le Tourneau Lancet Oncol 2015 35

Schematic representation of the five omics technologies, focusing on the accessed element (blue) and the methods used (orange).

Genomics: access to DNA sequences using gDNA-sequencing and bioinformatics for annotation. Transcriptomics: access to mRNA

sequence and level of expression using microarray hybridization or RNA-sequencing. Proteomics: access to protein sequence thanks to

liquid chromatography and mass spectrometry. Epigenomics: access to DNA methylation and histone modification (two of the most

characterized epigenetic modifications) using ChIP-sequencing or bisulfite sequencing. Cistromics: access to the genomic repertoire of

the binding sequences of a transcriptome factor (TF), using ChIP-sequencing.

5 Major Omics Technologies