Genomic Characterization of Invasive Lobular Breast Carcinoma Michael L. Gatza, Ph.D. TCGA Breast Cancer AWG Invasive Breast Carcinoma Invasive Ductal Carcinoma (IDC) 50-80% Ductal Mixed IDC.ILC 4-5% webmd.com Lobular 2 Invasive Lobular Carcinoma (ILC) 10-15% Summary of Data Freeze Pathology centrally re-reviewed (Andy Beck, Harvard) 817 490 127 88 112 3 Identification of differentially expressed genes Ductal LumA Ductal N=663 genes 2 Class SAM FDR=0 Lobular LumA Lobular Normal ATM network Immune signaling (multiple) MAPK signaling MYC targets (multiple) E-cadherin stabilization Low 4 Mike Gatza, UNC High mRNA Expression CDH1 Development of Integrated MAF DNA Exome sequencing Integrated MAF UNCeqR (mRNAseq / DNAseq) Integrated MAF Integrated MAF ABRA (CDH1, TP53, GATA3, PTEN, RB1) DNA-based MAF Matt Wilkerson (UNC), Lisle Mose (UNC) Giovanni Ciriello (MSKCC), Cyriac Kandoth (MSKCC) 5 Mike McLellan (Wash U) DNA-based MAF Comparison of significant alterations: IDC vs. ILC 6 Giovanni Ciriello, MSKCC Identifying IDC LumA and ILC LumA-specific alterations IDC ILC GATA3 (p=0.0002) Low High Protein Expression 7 Giovanni Ciriello, MSKCC PARADIGM analysis identifies IDC and ILCassociated signaling pathways Blue: ILC DOWN Red: ILC UP CDH1 IDC ILC IDC Low ILC mRNA p53/DNA Damage Response MYC Protein High mRNA Expression Low High Protein Expression XBP1 Immune Related 8 Christina Yau, Buck Institute Development of mRNA-based ILC classes 2 3 Centroid classifier (90genes) 1 ConsensusClusterPlus to ID 3 ILC classes Identified samples with positive sil. width ClaNC developed centroid predictor TCGA ILC LumA (n=106) TCGA ILC LumA (n=89) TCGA ILC LumA (n=89) 9 Mike Gatza, UNC 2 Class SAM identifies differentially expressed genes in ILC classes 988 genes (FDR=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 Low High mRNA Expression 10 Mike Gatza, UNC LCK IFNG ILC class mRNA / miRNA expression patterns correspond with IDC and Adjacent Normal IDC Norm 988 genes (FDR=0) miRNA (SAMseq FDR<0.05) ILC Low ILC IDC High Normal mRNA Expression Class 1 61 49 94 Class 2 39 167 0 Low High miRNA Expression Class 3 11 27 Mike Gatza, UNC 274 P<0.0001 0 Reanne Bowlby, BC Cancer Agency ILC Class1 corresponds with RPPA Reactive Subtype ILC Class (n=127) Class1 Class2 Class3 Reactive Non-reactive Missing data P<0.0001 RPPA Subtype (n=70) RPPA Annexin1 Caveolin1 Collagen IV Myh11 RMB15 Low High Protein Expression Mike Gatza, UNC 12 Gordon Mills, MDACC ILC Class1 tumors exhibit altered PDGFR/ STAT3 and FoxM1 signaling PARAGIGM FOXM1 sub-network PDGFR FoxM1 RPPA pSRC Y527 pSTAT3 Y705 FoxM1 Low High Protein Expression Christina Yau, Buck Institute 13 Mike Gatza, UNC ILC class 2 defined by high immune signaling and proliferation Class1 Class2 Class3 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) Low High Proliferation Score (PAM50) Signature Score 14 Mike Gatza, UNC P=1.39e-10 Class 1 Class 2 Class 3 PARADIGM analysis identifies IFNG and FOXM1 as key pathways in ILC class 2 tumors 15 Christina Yau, Buck Institute 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 16 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 17 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