Disclosures. Objectives 1/20/2016. Practical Molecular Diagnostics in Lung Cancer: Beyond the NCCN Guidelines. Genentech: Scientific Advisory Board

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1 Practical Molecular Diagnostics in Lung Cancer: Beyond the NCCN Guidelines Lynette M. Sholl, M.D. Department of Pathology Brigham and Women s Hospital Harvard Medical School Boston, MA Disclosures Genentech: Scientific Advisory Board Objectives Established and emerging molecular targets in lung cancer Applying advanced technologies in clinical practice Role of pathology in current lung cancer management Optimizing histologic diagnoses on small biopsies Application of predictive immunohistochemistry Accurate reporting of molecular results 1

2 Trends in lung cancer histology Carcinoma, Sarcoma, 0.2 NOS, 3.1 Other, 5.0 Small cell, 13.1 Large Cell, 2.1 NSCLC, 10.6 Squamous cell, 22.8 Adenocarcinoma, 43.2 Histologic Diagnoses, SEER data Meza et al. PLOSOne2015. Reasons for increased fraction of adenocarcinoma? Change in smoking habits Decline in tobacco use since the 1960s Increased use of filters requiring more vigorous inhalation Trends in lung cancer outcomes 27% of all cancer deaths in 2015 Significant downward trends in death rates among both men and women diagnosed with lung cancer between Edwards et al. Cancer

3 Reasons for decreasing mortality rates? Improved detection: Reasons for decreasing mortality rates? Improved therapy: Kris et al. JAMA2014. Lung adenocarcinoma TARGETED THERAPIES 3

4 EGFR an attractive therapeutic target Important pro-growth signaling protein in normal and neoplastic tissues Commonly overexpressedin multiple tumor types, including lung cancer EGFR TKIs the new wonder drugs in lung cancer?? Poor outcomes from clinical trials of erlotinib and gefitinib in unselected patients Occasional patients with exceptional response to therapy EGFR mutation is key biomarker 4

5 EGFR mutation vs. copy number? What s the relationship? In an EGFR-mutated tumor: Step 1: mutation Step 2: amplificationand protein overexpression Amplification/overexpression may occur in the absence of mutation. ALK translocations in NSCLC: 3 years (!) from bench to bedside 5

6 CAP/AMP/IASLC Clinical Practice Guidelines Any advanced stage (IV) patient with ACA or patient with progressive disease should receive EGFR and ALK testing Reflex testing may be appropriate in certain environments This testing is not recommended for lung tumors lacking evidence of ACA differentiation Avoid the term non small cell lung carcinoma whenever possible Prioritize tissue for EGFR and ALK testing ROS1 rearrangements in lung cancer Rare (1-2% of lung ACA) More common in never smokers Promising responses to crizotinib therapy Shaw AT et al. N Engl J Med 2014;371:

7 RET rearrangements in lung cancer Rare (1% of lung ACA) Results from small intrachromosomal rearrangement (inv (10)(p11.22q11.2) More common in never smokers Reported responses to: cabozantinib (c-met, VEGFR2 inhibitor) Vandetanib (VEGFR, EGFR, RET inhibitor) Takeuchi et al Nat Med year old woman with lung mass and numerous subcutaneous metastases: EGFR, ALK, ROS1 wild type Sequencing reveals METex14 mutation & MET amplification with Exon 14 skipping Efficacy of crizotinib in MET ex 14 splice tumors 7

8 64yo M, ~15 pack-year smoker, quit 1 year prior to diagnosis May 2014: diagnosed with stage IV lung adenocarcinoma Standard testing negative for EGFR, ALK, ROS1 Started on first-line carboplatin/pemetrexed, with mixed response BRAFc.1799T>A (p.v600e) detected by sequencing Dabrafenib(BRAFinhibitor) + Trametinib(MEK inhibitor)* October 2014 March 2015 *60% overall response rate in the phase 2 trial for patients with BRAFV600E mutations. Planchard et al. J Clin Oncol 33, 2015 (suppl; abstr 8006) Oncogenic drivers in non-squamous NSCLC (%) KRAS 33.8 No/unknown driver 29.9 HRAS 0.1 MAP2K1 0.3 AKT1 0.6 RET 1.0 ROS1 1.1 ERBB2 NRAS PIK3CA 2.9 MET 3.0 BRAF 3.8 ALK 3.9 EGFR

9 Reality check. Non small cell lung carcinoma Adenocarcinoma Squamous cell carcinoma Most common subtype in nonsmokers Unique chemosensitivity profile (pemetrexed) ~60% have a defined oncogenic driver - Targetable Smokers Use of antiangiogenic agents associated with massive pulmonary hemorrhage Minority with defined oncogenic driver -Limited targetability 9

10 IASLC algorithm for Small Biopsies Subclassificationof morphologic NSCLC-NOS IASLC classification of small biopsies, take home points: Distinguish ACA and SQC whenever possible The molecular profile of an ACA will dictate targeted therapy Judicious use of IHC is critical Two first-line markers: TTF1 and p63 or p40 Less established/less specific markers (napsin, mucin, CK7, CK5/6) should be considered second line 10

11 Make a diagnosis + EGFR, KRAS, HER2, BRAF, PIK3CA, ALK, ROS1, RET, MET, etc. mutations, copy number alterations, translocations EGFR mutation-specific antibodies (clones 43B2 and 6B6) Excellent specificity, limited sensitivity Study L858R Informative if positive-may be useful in scant specimens Ex19del Yu et al. Kawahara et al. Kato et al. Brevet et al. Fan et al. Bondgaard et al. Sensitivity Specificity Sensitivity Specificity 92% 99% 86% 100% (24 of 26) (193 of 195) (23 of 26) (196 of 196) 83% 100% 62% 100% (19 of 23) (16 of 16) (13 of 21) (16 of 16) 75% 97% 50% 100% (9 of 12) (56 of 58) (9 of 18) (52 of 52) 95% 99% 74% 99% (20 of 21) (171 of 173) (23 of 31) (161 of 163) 93% 100% 74% 99% (40 of 43) (126 of 126) (17 of 23) (145 of 146) 80% 98% 63% 99% (8 of 10) (152 of 155) (12 of 19) (153 of 155) ALK IHC % sensitive and specific as compared to FISH Ventana ALK(D5F3) CDxassay approved as a companion diagnostic for crizotinib Cutzet al. JTO

12 ROS1 IHC (D4D6 antibody) Ideal screening tool: Excellent sensitivity, good specificity Reference N Sensitivity Specificity Notes Sholl et al Focal expression in a KRASmutated tumor Strongexpression in a FISH negative tumor Mescam-Mancini et al Sholl et al. AJSP Expressed in two HER2- mutated tumors Cha et al * ROS1 expression seen in ROS1 WT tumors from ever-smokers Boyle et al As compared to FISH or RT-PCR Reference Clone IHCpattern vs. Tsutaet al EPR2871 Lee et al ab Sasaki et al Tsutaet al. Br. J. Cancer 2014 Any Any FISH or RTPCR Transcript profiling or FISH RET N WT N Sensitivity Specificity F8 Any RTPCR EPR2871 Any RTPCR EPR2871 Mod to strong only RET IHC Variable antibody performance Current evidence doesn t support routine clinical use RTPCR How has next gen sequencing (NGS) changed the game? Increased target coverage with decreased tissue requirements POPv2 GENE LIST SNV, INDELS, COPY NUMBER ALTERATIONS ABL1 BMPR1A CDKN1B EP300 FAS HRAS MDM2 NFKBIZ PRAME RPL26 STAG2 AKT1 BRAF CDKN1C EPHA3 FBXW7 ID3 MDM4 NKX2-1 PRDM1 RUNX1 STAT3 AKT2 BRCA1 CDKN2A EPHA5 FGFR1 IDH1 MECOM NOTCH1 PRF1 SBDS STAT6 AKT3 BRCA2 CDKN2B EPHA7 FGFR2 IDH2 MEF2B NOTCH2 PRKAR1A SDHA STK11 ALK BRD4 CDKN2C ERBB2 FGFR3 IGF1R MEN1 NPM1 PRKCI SDHAF2 SUFU ALOX12B BRIP1 CEBPA ERBB3 FGFR4 IKZF1 MET NPRL2 PRKCZ SDHB SUZ12 APC BUB1B CHEK2 ERBB4 FH IKZF3 MITF NPRL3 PRKDC SDHC SYK AR CADM2 CIITA ERCC2 FKBP9 INSIG1 MLH1 NRAS PRPF40B SDHD TCF3 ARAF CARD11 CREBBP ERCC3 FLCN JAK2 MLL NTRK1 PRPF8 SETBP1 TCF7L1 ARID1B CBLB CRLF2 ERCC5 FLT3 KCNIP1 MPL NTRK3 PTCH1 SF1 TERC ARID2 CCND1 CRTC1 ESR1 FLT4 KDM5C MSH2 PALB2 PTEN SF3B1 TERT ASXL1 CCND2 CRTC2 ETV1 FUS KDM6A MSH6 PARK2 PTK2 SH2B3 TET2 ATM CCND3 CSF1R ETV4 GATA3 KDM6B MTOR PAX5 PTPN11 SLITRK6 TLR4 ATRX CCNE1 CSF3R ETV5 GATA4 KDR MUTYH PBRM1 PTPRD SMAD2 TNFAIP3 AURKA CD274 CTNNB1 ETV6 GATA6 KEAP1 MYB PDCD1LG2 QKI SMAD4 TP53 AURKB CD58 CUX1 EWSR1 GLI1 KIT MYBL1 PDGFRA RAD21 SMARCA4 TSC1 AXL CD79B CYLD EXT1 GLI2 KRAS MYC PDGFRB RAF1 SMARCB1 TSC2 B2M CDC73 DDB2 EXT2 GLI3 LINC00894 MYCL1 PHF6 RARA SMC1A U2AF1 BAP1 CDH1 DDR2 EZH2 GNA11 LMO1 MYCN PHOX2B RB1 SMC3 VHL BCL2 CDK1 DEPDC5 FAM46C GNAQ LMO2 MYD88 PIK3C2B RBL2 SMO WRN BCL2L1 CDK2 DICER1 FANCA GNAS LMO3 NBN PIK3CA RECQL4 SOCS1 WT1 BCL2L12 CDK4 DIS3 FANCC GNB2L1 MAP2K1 NEGR1 PIK3R1 REL SOX2 XPA BCL6 CDK5 DMD FANCD2 GPC3 MAP2K4 NF1 PIM1 RET SOX9 XPC BCOR CDK6 DNMT3A FANCE GSTM5 MAP3K1 NF2 PMS1 RFWD2 SQSTM1 XPO1 BCORL1 CDK9 EED FANCF H3F3A MAPK1 NFE2L2 PMS2 RHEB SRC ZNF217 BLM CDKN1A EGFR FANCG HNF1A MCL1 NFKBIA PNRC1 RHPN2 SRSF2 ZNF708 ROS1 STAG1 ZRSR2 12

13 How has next gen sequencing (NGS) changed the game? Increased target coverage with decreased tissue requirements Less biased genomic analysis Detect novel variants in known oncogenes Detect variants outside of coding regions Detect variants in genes not typically included on clinical test menus Detect common variants in known oncogenes in unusual contexts NGSvs. IHCvs. FISH for ALK translocation detection ALK translocations in Lung Adenocarcinoma Clinical FISH and/or IHC ALK + ALK - ALK 25 0 Sensitivity Fusion + 96% Oncopanel ALK Specificity 1* 190 Fusion - 100% Total * 20% tumor in this specimen NGS as an arbiter in discrepant cases: FISH negative IHC positive ALK IHC (5A4 clone) 13

14 Fused Red only Green only CLIP4 From Vysis ALK FISH probe product insert NGS showed: CLIP4-ALK fusion AND EML4-ALK fusion FISH cannot detect cryptic EML4-ALK fusions. Unusual FISH results are considered negative but should be followed up. MET in tumorigenesis Exon 14 deletion removes the juxtamembrane domain of MET Tyr1003 phosphorylationsite necessary for Cbl binding Decreased ubiquitinationand impaired downregulation of the activated receptor Lai AZ, et al, Trends in Cell Bio, 2009 Identification of tumor-specific, intronic mutations in Met leading to exon 14 splicing. Monica Kong-Beltran et al. Cancer Res 2006;66: by American Association for Cancer Research 14

15 MET: Diverse Deletions & Point Mutations Awad et al. J Clin Oncol, MET juxtamembranesplice mutations: not uncommon in lung adenocarcinomas and predict response to MET inhibitors 2.4% in Kong-Beltran et al. Cancer Res, % in Onazatoet al. J Thor Oncol,2009 ~4.5% in TCGANature, % in Frampton et al. Cancer Discovery, % in Paik et al. Cancer Discovery, % in Awad et al. J Clin Oncol, 2016 Clinical Characteristics MET ex14 EGFR KRAS Clinical Characteristic (N = 28) (N = 99) (N = 169) Median age (range), years 72.5 (59-84) 61 (30-93) 65 (42-93) Sex, N (%) Male 9 (32%) 30 (30%) 62 (37%) Female 19 (68%) 69 (70%) 107 (63%) Smoking history, N (%) Never-smoker 10 (36%) 57 (58%) 6 (4%) 10 pack-years 3 (11%) 10 (10%) 11 (7%) >10 pack-years 15 (53%) 28 (28%) 152 (90%) Race, N (%) White, non-hispanic 28 (100%) 79 (80%) 157 (93%) Asian 0 (0%) 15 (15%) 0 (0%) Black 0 (0%) 1 (1%) 5 (3%) White, Hispanic 0 (0%) 3 (3%) 3 (2%) Unknown 0 (0%) 1 (1%) 4 (2%) Histology, N (%) Adenocarcinoma 18 (64%) 92 (93%) 150 (89%) Pleomorphic w/ adenocarcinoma component 4 (14%) 0 (0%) 3 (2%) NSCLC, poorly-differentiated 5 (18%) 4 (4%) 10 (6%) Squamous 0 (0%) 2 (2%) 5 (3%) Adenosquamous 1 (4%) 1 (1%) 1 (1%) Stage at diagnosis, N (%) I 13 (46%) 9 (9%) 12 (7%) II 2 (7%) 3 (3%) 12 (7%) III 4 (14%) 9 (9%) 44 (26%) IV 9 (32%) 78 (79%) 101 (60%) Awad et al. J Clin Oncol

16 Pulmonary sarcomatoid carcinoma Sarcomatoid carcinoma Pleomorphic carcinoma Giant cells or spindled cells comprise 10% of tumor Admixed adenocarcinoma, squamous, or undifferentiated carcinoma Carcinosarcoma Carcinoma + sarcoma with heterologous elements Pulmonary blastoma Fetal adenocarcinoma+ mesenchymal stroma 2-3% of lung cancers Predominantly smokers MET mutations in pulmonary pleomorphic/sarcomatoid carcinoma Luiet al, JCO2015: MET exon 14 splice mutations in 8/36 (22%) of pulmonary sarcomatoid carcinomas undergoing WES and targeted MET analysis BWH/DFCI: MET exon 14 splice mutations in 4/15 (27%) pulmonary pleomorphic carcinoma sequenced by NGS Other alterations include: KRAS(13%) NRAS (7%) no known driver (53%). Potential for NGS in diagnosis Distinguishing multiple primary lung tumors from metastases Defining site of origin for poorly differentiated carcinomas 16

17 74 year old woman, former smoker, incidental RUL mass and multiple GGOs RUL MET c t>c (p.d1010_splice) -in 34% of 449 reads RLL EGFR c.2573t>g (p.l858r), in 2.8% of 285 reads KRAS c.35g>a (p.g12d), in 15% of 438 reads Breast vs. Lung? 58 year old woman, h/o well differentiated T1aN0 invasive ductal carcinoma (ER+, PR+, HER2-) 5 years prior Now with lung left upper lobe mass and diaphragmatic implants Lung tumor: CK7+, TTF1-, GATA3 weak, ER weak, mammoglobin - The carcinoma in the lung is poorly differentiated with high grade nuclei, abundant cytoplasm, mucin production, and necrosis. The carcinoma does not resemble the breast carcinoma in the excision from The possibility that the patient has a different breast primary carcinoma should be considered. Back of the envelope: Gene KRAS mutation EGFR mutation ERBB2 amp Frequency in breast Frequency in Lung PPV 1% 25% 98% (for lung) 0 13% 100% (for lung) 16% 0.5% 91% (for breast) 17

18 Breast vs. Lung? KRAS c.34g>t (p.g12c), exon 1 STK11 c.206c>a (p.s69*), exon 1 TP53 c.499_501cag>g (p.q167fs), exon5 KEAP1 c.1016t>c (p.l339p), exon 3 KEAP1 c.382a>t (p.i128f), exon2 JAK2 c.3214c>t (p.q1072*), exon 24 BRIP1 c.434c>g (p.s145c), exon 5 CDC73 c.26g>t (p.r9l), exon 1 CHEK2 c.349a>g (p.r117g), exon 3 DMD c.10567g>a (p.e3523k), exon 75 JAK2 c.3214c>t (p.q1072*), exon 24 SMARCA4 c.2439_splice (p.s813_splice) TCF3 c.136g>a (p.g46r), exon 3 Genomic evidence supports a lung primary. Doganet al. Clin Cancer Res, Calles et al. Clin Cancer Res, NGS to explore new targets No/unknown driver 29.9 KRAS 33.8 Jamie Wyeth HRAS 0.1 MAP2K1 0.3 AKT1 0.6RET 1.0 ROS1 1.1 NRAS MET 1.0 ERBB PIK3CA 2.9 BRAF 3.8 ALK 3.9 EGFR 19.1 Targeted therapy is dead. -Anonymous PD-1/PD-L1 inhibitors Applicable across most tumor types 20-30% response rate on average 18 month response durability Mutation-targeted inhibitors Applicable to few tumors (lung, melanoma, GIST) 50-70% response rate Response durability 7-12 months From a population standpoint, immune checkpoint blockade outperforms mutation-targeted therapies. 18

19 PD-L1 IHC in practice Dako 28-8 pembrolizumab Roche SP142 E1L3N 22C3 pharmdx Roche SP263 nivolumab atezolizumab tremelimumab?? PD-L1 IHC: mass confusion. Drug Company FDA approval mab/platform Scoring criteria Comment Pembroluzimab (Keytruda) Nivolumab (Opdivo) Atezolizumab (MPDL3280) Durvalumab (MEDI4736) Merck Bristol-Myers Squibb FDA approved for NSCLC FDA approved for squamous and non squamous NSCLC 22C3 (DAKO pharmdx)/ Link 48 Autostainer 28-8 (DAKO pharmdx)/ Link 48 Autostainer 50% tumor cells Companion Roche Expected in 2016 SP142 (Ventana) Tumor cells and/or diagnostic 1 (as of Oct 2015) 1% tumor cells Complementary tumor infiltrating immune cells diagnostic (as of Oct 2015) Predictive only in non-squamous carcinomas In development Astra Zeneca Expected in 2016 SP263 (Ventana) 25% tumor cells In development Perhaps other biomarkers will be better Characteristics of immune infiltrate? Expression of other checkpoint inhibitors? Mutational load? Mutational signature? Biomarker reporting 19

20 Biomarker reporting Optional reporting template Available as CAP electronic cancer checklist (ecc) Focused on targets with accepted clinical significance Alteration type Methodology Updated version available in 2016 covers: EGFR KRAS BRAF ERBB2 ALK RET ROS1 MET Important topics given short shrift: Tumor types beyond adenocarcinoma Mechanisms of EGFR TKI resistance Mechanisms and significance of acquired resistance in patients receiving EGFR TKIs, MET/ALK/ROS1 inhibitors Liquid biopsy in solid tumor clinical management Sequist et al. SciTrans Med Thanks Questions? Acknowledgements: Mark Awad, DFCI Phil Cagle Pasi Janne, DFCI Neal Lindeman, BWH Geoff Oxnard, DFCI Members of the Pulmonary Pathology Society 20