Transcript Molecular Genetics for the Practicing Physician

Molecular Genetics for the Practicing
Physician: Can the Cancer Genome Atlas
Impact How We Treat Patients?
Gabriel G. Malouf, MD, PhD
Assistant Professor
Pitié-Salpêtriètre Hospital
Assistance-Publique Hôpitaux de Paris
Paris, France
Outline
I. Cell of Origin of Kidney Tumors
II. Diagnostic Markers and Therapeutic Targets
III. Predictive Biomarkers
Renal Cell Carcinoma is NOT a Single Disease
Clear cell RCC
Papillary RCC
Type 1
Type 2
Chromophobe RCC
Translocation RCC
Collecting Duct RCC
Mucinous tubular &
spindle cell RCC
The Cancer Genome Atlas (TCGA) Project
(2006-2016)
Clear-cell RCC (n=417)
Papillary RCC (n=161)
Chromophobe (n=66)
TCGA, Nature Genetics, 2013
• Clear-cell RCC1
• Chromophobe RCC2
• Papillary RCC3
• Tumor biology
Molecular
Genetics
TCGA
Patients
Practicing
Physicians
• Pathologist
• Urologist
• Radiologist
• Medical Oncologist
• Radiation Oncologist
• Comorbidities
• Optimal therapy
to improve
survival and
quality of life
1TCGA,
Nature, 2013
2Davis
C et al, Cancer Cell, 2014
3Linehan
WM et al. NEJM, 2015
I. Cell of Origin of Kidney Tumors
Distal nephrons
Thick ascending limbs of
the loop of Henle
Glomeruli
Distal Convoluted tubules
Proximal tubules
Hierarchical Clustering of Gene Expression in Kidney Structure
cTAL = cortical TAL, mTAL =medullary TAL, DCT= distal convoluted tubules, CNT= connecting tubules, OMCD = outer medullary collecting ducts
Cheval L et al. Physiol. Genomics, 2010
DNA Methylation and Gene Expression Differences Between
ChrRCC and ccRCC
CCD = cortical collecting ducts; ccRCC = clear cell renal cell carcinoma; chRCC = chromophobe renal cell carcinoma; cTAL = cortical thick ascending limbs of the loop of Henle; DCT = distal convoluted tubules; Glom =
glomeruli; mTAL =medullary thick ascending limbs of the loop of Henle; OMCD = outer medullary collecting ducts; TCGA = The Cancer Genome Atlas.
Davis C et al, Cancer Cell, 2014
Survival Prediction of Clear-cell Renal Cell Carcinomas Based on
Gene Expression Similarity to the Proximal Tubule of the Nephron
Clustering of renal cell carcinoma (RCC) tumours by
means of gene expression correlation between
profiles
of
tumours
and
profiles
of
human nephron cell types
Clustering of renal Cancer-specific survival (CSS) of
clear cell renal cell carcinoma (ccRCC) tumours
predicted by the S3-score
Büttner et al, Eur Urol, 2015
DNA Methylation Establishes the Foundation of RCC Ontogeny
C1
C2
Malouf GG et al, ASCO GU 2016
II. Diagnostic Markers and Therapeutic Targets
Incidence of Fusion Transcripts Detected in TCGA Clear-cell RCC
TCGA KIRC
dataset
(n=460)
No Translocation*
(n=379)
MITF
family
RCC
(n=7)
(1.9%)
PRCC/TFE3 (n=5)
KHSRP/TFE3 (n=1)
KHDRBS2/TFEB (n=1)
Translocation
(n=81) (17.6%)
Previously
known
gene
fusions
(n=12)
FHIT (n=2), SLC9A9 (n=2),
AFF1 (n=1), MKL1 (n=1),
LHFP (n=1), JAK2 (n=1),
ELL (n=1), DCX (n=1),
EP300 (n=1) & LNP1
(n=1)
Novel
fusions
(n=62)
Malouf GG et al. Clin Cancer Res, 2014
Incidence of Fusion Transcripts Detected in TCGA Papillary RCC
TCGA KIRP
dataset
(n=161)
No Translocation*
(n=144)
Non MITF
family
RCC
(n=9)
Translocation
(n=17) (10.6%)
MITF
family RCC
(n=8)
7 out of 60 Papillary
Type II (11.6%)
1 out of 101 Papillary
type I (1%)
Linehan WM et al. NEJM, 2015
A Subgroup of Papillary RCC Manifests a CpG Island Methylator Phenotype (CIMP) and FH Mutations
Linehan WM et al. NEJM, 2015
ChRCC with Eosinophilic Variants Resemble Oncocytoma Type II
Davis C et al, Cancer Cell, 2014
Joshi et al, Cell Reports, 2015
Putative Therapeutic Targets in Clear-cell RCC
TCGA, Nature, 2013
Putative Therapeutic Targets in Papillary RCC
Linehan WM et al. NEJM, 2015
III. Predictive Biomarkers
TCGA Transcriptomic Classification of ccRCC
Four subgroups
Response to sunitinib
TCGA, Nature, 2013
Beuselinck, Clin Cancer Res, 2015
Overall Survival in Two Independent Datasets of ccRCC
HR= hasard ratio.
(A) UT South Western cohort
(B) TCGA cohort
Kapur P et al, Lancet Oncol, 2013
While Many Biomarkers Are Associated in Univariate Analysis with Outcome in
TCGA Clear-Cell RCC, only ccB Remains in Multivariate Analysis
• Clinical and
pathological
charecteristics
• Somatic mutations
• Somatic copy
number expression
• Gene expression
analysis
Gulati S et al, Eur Urol, 2014
Tumor-based Biomarkers Confounded by Intratumor Heterogeneity

63-69% of all mutations not detectable across regions in same tumor
Gerlinger et al. NEJM, 2012
Multi-Region Sequencing of Clear-cell Renal Cell Carcinoma
Multi-Region Sequencing of RCC with IVC Thrombus
Long-non coding RNA Classification of ccRCC Reveals Four
Subtypes Associated with Clinical Outcome
Malouf GG et al, Molecular Oncology , 2015
CIMP Defines a Subtype of Clear-cell Renal Cell Carcinomas with
Poor Outcome
Cluster 1: CpG Island Methylator Phenotype (CIMP) low; Cluster 2: CIMP negative; Cluster 3: CIMP positive
Malouf GG et al, Unpublished
Conclusions
• Understanding ontogeny of different RCC subtypes
will provide insights on tumorigenesis
• To date, there are no approved biomarkers to predict
recurrence after nephrectomy or response to therapy
• Frequent mutations in chromatin modifying genes in
both ccRCC and pRCC imply a role for epigenetic
therapy
Conclusions (continued)
• Inter- and intra-tumoral genetic heterogeneity might
hamper the development of predictive and prognostic
genetic biomarkers in RCC
• Mutational Convergence in chromatin modifying
genes highlights the importance of epigenetic drift in
the evolution of aggressive RCC clones
• Epigenetic biomarkers might be more stable and
therefore should be pursued for precision medicine
Acknowledgements
• Pitié-Salpêtrière Hospital, Paris, France
• Pr David Khayat (Oncology)
• Pr Jean-Philippe Spano (Oncology)
• Dr Haide Boostandoost (Oncology)
• Pr Eva Compérat (Pathology)
• Pr Morgan Rouprêt (Urology)
• Dr Jérôme Parra (Urology)
• Dr Christophe Vaessen (Urology)
• Fondation AVEC laboratory, Paris, France
• Dr Roger Mouawad, PhD
• Frédérick Allanick, Ms
• Dr Souheyla Bensalma, PhD
• Dr Linda Denaise, MD, PhDc
• Dr Marion Classe, MD, PhDc
• Dr Ronan Flippot, MD, MS
• Temple University, Philadelphia, USA
• Jaroslav Jelinek
• Jean-Pierre Issa
• MD Anderson Cancer Center, Houston, USA
• Pr Nizar M. Tannir (Medical Oncology)
• Dr Xiaoping Su (Bionformatics)
• Dr Hui Yao (Bionformatics)
• Dr Jose A. Karam (Urology)
• Pr Christopher G. Wood (Urology)
• The patients and their families