Genomic Characterization of Invasive Lobular Breast Carcinoma

Michael L. Gatza, Ph.D.

TCGA Breast Cancer AWG

2

Invasive Breast Carcinoma

webmd.com

Invasive Ductal Carcinoma (IDC) 50-80%

Mixed IDC.ILC 4-5%

Ductal

Lobular

Invasive Lobular Carcinoma (ILC) 10-15%

3

Pathology centrally re-reviewed (Andy Beck, Harvard)

817

490

127

88

112

Summary of Data Freeze

4

Identification of differentially expressed genes

Ductal Lobular

2 C

lass

SA

M F

DR

=0

N=6

63 g

enes

LumA Ductal

LumA Lobular

ATM network Immune signaling (multiple) MAPK signaling

MYC targets (multiple) E-cadherin stabilization

Normal

CDH1

Mike Gatza, UNC

Low High

mRNA Expression

5

Development of Integrated MAF

Matt Wilkerson (UNC), Lisle Mose (UNC) Giovanni Ciriello (MSKCC), Cyriac Kandoth (MSKCC) Mike McLellan (Wash U)

DNA-based MAF

Inte

grat

ed M

AF

DNA Exome sequencing

UNCeqR (mRNAseq / DNAseq)

ABRA (CDH1, TP53, GATA3, PTEN, RB1)

Integrated MAF

DNA-based MAF

Inte

grat

ed M

AF

6

Comparison of significant alterations: IDC vs. ILC

Giovanni Ciriello, MSKCC

7

Identifying IDC LumA and ILC LumA-specific alterations

Giovanni Ciriello, MSKCC

IDC ILC GATA3 (p=0.0002)

Low High

Protein Expression

8

PARADIGM analysis identifies IDC and ILC-associated signaling pathways

XBP1

MYC p53/DNA Damage Response

Immune Related

CDH1

Blue: ILC DOWN Red: ILC UP

Christina Yau, Buck Institute

IDC ILC mRNA

IDC ILC Protein

Low High

mRNA Expression

Low High

Protein Expression

9

Development of mRNA-based ILC classes

1 2 3

Cen

troi

d cl

assi

fier (

90ge

nes)

ConsensusClusterPlus to ID 3 ILC classes

TCGA ILC LumA (n=106)

Identified samples with positive sil. width

TCGA ILC LumA (n=89)

ClaNC developed centroid predictor

TCGA ILC LumA (n=89)

Mike Gatza, UNC

10

2 Class SAM identifies differentially expressed genes in ILC classes

Mike Gatza, UNC

988

gene

s (F

DR

=0)

Class1 C2 C3

N= 722 genes EGFR MET GLI1 FGF17 WNT6 AREG KIT KRT 14, 15, 17, 32, 81 KRK 1, 6-8 CLDN 8,10,11, 19 PTCH2 TP63 VIT ID4

N= 268 genes Immune-related genes: >100 LCK IFNG

Low High

mRNA Expression

11

ILC class mRNA / miRNA expression patterns correspond with IDC and Adjacent Normal

ILC IDC Norm

988

gene

s (F

DR

=0)

P<0.0001

miR

NA

(SA

Mse

q FD

R<0

.05)

Mike Gatza, UNC Reanne Bowlby, BC Cancer Agency

Low High

miRNA Expression

Low High

mRNA Expression ILC IDC Normal

Class 1 61 49 94

Class 2 39 167 0

Class 3 27 274 0

12

ILC Class1 corresponds with RPPA Reactive Subtype

ILC Class (n=127)

RPPA Subtype (n=70)

Reactive Non-reactive Missing data

Class1 Class2 Class3

Mike Gatza, UNC Gordon Mills, MDACC

P<0.0001

Annexin1 Caveolin1 Collagen IV Myh11 RMB15

RPP

A

Low High

Protein Expression

13

ILC Class1 tumors exhibit altered PDGFR/ STAT3 and FoxM1 signaling

FOXM1 sub-network

PAR

AGIG

M

RPP

A

PDGFR

FoxM1

FoxM1

pSRC Y527 pSTAT3 Y705

Christina Yau, Buck Institute Mike Gatza, UNC

Low High

Protein Expression

14

ILC class 2 defined by high immune signaling and proliferation

Mike Gatza, UNC

Low High

Signature Score

B-cell BCR B-cell (CS) CD8 CD8 (CS) T-cell (CS) LCK T-cell (TNBC) NK T-cell (Teschendo) MΦ TH1 (CS) MΦ CSF1 TCR TCGA ILC (n=127)

Class1 Class2 Class3

P=1.39e-10

Prol

ifera

tion

Scor

e (P

AM50

)

Class 1 Class 2 Class 3

15

PARADIGM analysis identifies IFNG and FOXM1 as key pathways in ILC class 2 tumors

Christina Yau, Buck Institute

16

Summary

• Developed unique integrated MAF utilizing both DNA exome and mRNA sequencing

• ILC vs. IDC – FOXA1, CDH1 mutations associated with ILC – GATA3 mutation associated with IDC – Altered signaling: CDH1, Myc, p53/DNA damage, immune signaling – Identified differentially expressed miRNA and methylation

• ILC classes

– Class 1 associated with Reactive subtype – Class 2 immune component and highly proliferative

17

TCGA Breast Cancer Analysis Working Group Baylor College of Medicine Chad Creighton Xiaosong Wang

British Columbia Cancer Agency Andy Chu Elizabeth Chun Andy Mungall Gordon Robertson Dominik Stoll

Broad Institute Andrew Cherniack

Greater Poland Cancer Center Maciej Wiznerowicz

Harvard Medical School Terrence Wu Yonghong Xiao

Institute for Systems Biology Sheila Reynolds Ilya Shmulevich

Lawrence Berkeley National Laboratory Paul Spellman

Mayo Clinic Jim Ingle

The University of Texas MD Anderson Cancer Center Roel Verhaak Rehan Akbani Nancy Shih Gordon Mills

Memorial Sloan-Kettering Cancer Center Giovanni Ciriello Niki Schultz Ethan Cerami Arthur Goldberg Caitlin Byrne Anders Jacobsen Tari King Chris Sander

Nationwide Children’s Hospital Jay Bowen Julie Gastier-Foster

National Cancer Institute Chunhua Yan John Demchok Laura Dillon Margi Sheth Peter Good Jacqueline Palchik Heidi Sofia Kenna Shaw

University of California Santa Cruz Buck Institute Chris Benz David Haussler Christina Yau Sam Ng Ted Goldstein Kyle Ellrott Charlie Vaske Josh Stuart Jing Zhu

University of California, San Francisco Fred Waldman

University of Southern California Peter Laird Swapna Mahurkar Simeen Malik Dan Weisenberger Windber Research Institute Hai Hu Richard Mural

University of North Carolina Chuck Perou (co-chair) Katie Hoadley Mike Gatza Joel Parker Xiaping He Michael Iglesia Grace Silva Wei Zhao The Genome Institute at Washington University Matthew Ellis (co-chair) Li Ding Lucinda Fulton Daniel Koboldt Elaine Mardis