Genomic and functional fidelity of PDX models of small cell lung cancer Anna Farago, MD, PhD October 30, 2017
Disclosures Consulting for Pharmamar SA, Merrimack Pharmaceuticals, Takeda, Abbvie Honorarium from Foundation Medicine Travel expenses, food or lodging from Pharmamar SA, Abbvie Research funding (to institution) from AstraZeneca, Pharmamar SA, Abbvie, Loxo Oncology, Ignyta Inc., Bristol-Myers Squibb, Merck I will discuss off-label use of olaparib and temozolomide.
Molecular Classification of NSCLC SCLC ROS1 Squamous Non-squamous FGFR BRAF (adeno) RET HER2 NTRK1 MET amp PIK3CA MET Exon 14 ALK 4% No Known Genotype EGFR 13% KRAS 25%
Molecular Classification of SCLC SCLC
Molecular Classification of SCLC SCLC SCLC
Molecular Classification of SCLC SCLC
Small cell lung cancer: Summary • High-grade neuroendocrine tumor with high metastatic potential. • 15-20% of the estimated 1.6 million new lung cancer cases annually world-wide. • Metastatic SCLC has a median survival of 9-10 months and a 5-year overall survival of < 2%. • Most common genetic alterations: p53 & Rb1 inactivation. No clear targetable genetic drivers. • First-line treatment for metastatic disease is combination platinum plus etoposide or irinotecan. • Topotecan is the only FDA-approved second-line therapy, with response rates generally 10-30%. Noda et al., 2002; Hanna et al., 2006; Rossi et al., 2012; Seto et al., 2014; Slotman et al., 2015; Ardizzoni et al., 1997; O’Brien et al., 2006; Eckardt et al., 2007; Shepard et al., 2007; Pietanza et al., 2012; Owanikoko et al., 2012; NCCN Guidelines 7
SCLC in the clinic Initial Presentation Response to Therapy Relapse Why is SCLC so sensitive to chemotherapy initially? What is the best choice of therapy for relapsed SCLC?
Approaches to studying SCLC Tissue samples from patients Thunnissen et al., J Thor Oncol 2017, 12:334 Cell lines Calbo et al., Cancer Cell 2011; 19:244 Genetically engineered mouse models Gazdar et al., 1980; Carney et al., 1985; Gazdar et al., 2010; Meuwissen et al., 2003; Schaffer et al., 2010; McFadden et al., 2014
Approaches to studying SCLC Tissue samples from patients Patient-derived xenografts (PDX) P0 P1 P2 Thunnissen et al., J Thor Oncol 2017, 12:334 Cell lines Biopsy (if available) PDX Samples: • FFPE Calbo et al., Cancer Cell 2011; 19:244 • Snap freeze • Cryopreserve Genetically engineered mouse models Gazdar et al., 1980; Carney et al., 1985; Gazdar et al., 2010; Meuwissen et al., 2003; Schaffer et al., 2010; McFadden et al., 2014
SCLC PDX development • Patient-derived xenografts (PDXs) can model disease behavior in vivo without P0 P1 P2 an in vitro intermediate. Biopsy Rx (if available) PDX Samples: • FFPE • Snap freeze • Cryopreserve Repeat as above Relapse 11
SCLC PDX development • Patient-derived xenografts (PDXs) can model disease behavior in vivo without P0 P1 P2 an in vitro intermediate. • Dive and colleagues pioneered development of SCLC PDXs from circulating tumor cells (CTC-derived PDXs; CDXs). 1 Biopsy Rx (if available) PDX Samples: • FFPE • Snap freeze • Cryopreserve Repeat as above Relapse 1. Hodgkinson et al., Nat Med 2014; 20: 897-905. 12
SCLC PDX development • Patient-derived xenografts (PDXs) can model disease behavior in vivo without P0 P1 P2 an in vitro intermediate. iChip Neg • Dive and colleagues pioneered development of SCLC PDXs from circulating tumor cells (CTC-derived PDXs; CDXs). 1 • Biopsy The CTC iChip is a microfluidic device that can enrich for CTCs by depletion Rx (if available) of CD45+ leukocytes. 2,3 PDX Samples: • We utilized the CTC iChip to collect • FFPE • Snap freeze CTCs from SCLC patients and • Cryopreserve implanted the isolated cell pool into NSG mice. Repeat as above Relapse 1. Hodgkinson et al., Nat Med 2014; 20: 897-905. 2. Karabacak et al., Nat Protoc. 2014; 9: 694-710. 3. Ozkumur et al., Sci Transl Med. 2013; 5:179ra47. In collaboration with Haber/Maheswaran labs 13
SCLC PDX development P0 P1 P2 iChip Neg Biopsy Rx (if available) PDX Samples: • FFPE • Snap freeze • Cryopreserve Repeat as above Relapse 2. Karabacak et al., Nat Protoc. 2014; 9: 694-710. 3. Ozkumur et al., Sci Transl Med. 2013; 5:179ra47. In collaboration with Haber/Maheswaran labs 14
SCLC PDX development PDX summary statistics 31 SCLC models from 27 patients P0 P1 P2 iChip Neg PDX Take Rate (P0 / Attempts) CTC (iChip) 15 / 43 (35%) Biopsy 14 / 17 (82%) Biopsy CTC (RosetteSep/Ficoll) 1 / 4 Rx Effusions 1 / 3 (if available) PDX Samples: P0 latency (median ± st. dev.) • FFPE CTC 112 ± 65 days • Snap freeze • Cryopreserve Biopsy / Effusion 75 ± 31 days Repeat as above Model Establishment Passage success 32 / 32 models Relapse Cryopreservation 21 / 21 models PDX initiation cutoff: June 30, 2016 In collaboration with Haber/Maheswaran labs Data analysis cutoff: February 17, 2017 15
SCLC PDX development PDX summary statistics 31 SCLC models from 27 patients P0 P1 P2 iChip Neg PDX Take Rate (P0 / Attempts) CTC (iChip) 15 / 43 (35%) Biopsy 14 / 17 (82%) Biopsy CTC (RosetteSep/Ficoll) 1 / 4 Rx Effusions 1 / 3 (if available) PDX Samples: P0 latency (median ± st. dev.) • FFPE CTC 112 ± 65 days • Snap freeze • Cryopreserve Biopsy / Effusion 75 ± 31 days Repeat as above Model Establishment Passage success 31 / 31 models Relapse Cryopreservation 21 / 21 models PDX initiation cutoff: June 30, 2016 In collaboration with Haber/Maheswaran labs Data analysis cutoff: February 17, 2017 16
SCLC PDX development Model # Patient course PDX summary statistics CTC-derived 31 SCLC models from 27 patients Biopsy-derived PDX Take Rate (P0 / Attempts) Platinum/etoposide treatment CTC (iChip) 15 / 43 (35%) Other treatment Biopsy 14 / 17 (82%) CTC (RosetteSep/Ficoll) 1 / 4 Effusions 1 / 3 P0 latency (median ± st. dev.) CTC 112 ± 65 days Biopsy / Effusion 75 ± 31 days Model Establishment Passage success 31 / 31 models Cryopreservation 21 / 21 models PDX initiation cutoff: June 30, 2016 In collaboration with Haber/Maheswaran labs Data analysis cutoff: February 17, 2017 17
Assessing fidelity of models: Comparison back to patient tumor How well do PDXs model P0 P1 P2 the patient tumor? iChip Neg Histology Biopsy Genomics Rx (if available) PDX Samples: • FFPE Function • Snap freeze • Cryopreserve Repeat as above Relapse
Histology CTC MGH1504 Biopsy MGH1512 H&E SYP Chrg RB H&E SYP Chrg RB Pathologic Confirmation Model H&E + IHC: SCLC features 27 / 29 models* * 2 models had H&E consistent with SCLC but no NE marker expression All cases reviewed by Dr. Mari Mino-Kenudson
Histology CTC MGH1504 Biopsy MGH1512 H&E SYP Chrg RB H&E SYP Chrg RB Pathologic Confirmation Model H&E + IHC: SCLC features 27 / 29 models* Model H&E ≈ Patient 14 / 14 models Model IHC ≈ Patient 12 / 13 models * 2 models had H&E consistent with SCLC but no NE marker expression All cases reviewed by Dr. Mari Mino-Kenudson
Assessing fidelity of models: Comparison back to patient tumor How well do PDXs model P0 P1 P2 the patient tumor? iChip Neg Histology Biopsy Genomics Rx (if available) PDX Samples: • FFPE Function • Snap freeze • Cryopreserve Repeat as above Relapse
Cases selected for whole exome sequencing Time difference between biopsy Patient clinical Model number PDX type P0 latency (days) Patient prior therapies and model stage initiation (days) MGH1504-1 CTC 3 160 LS none MGH1514-1 CTC 4 130 ES none MGH1515-1 CTC 8 138 ES none MGH1518-1 biopsy 0 81 ES none MGH1525-1 CTC 1 45 ES none
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TP53 and RB1 alterations identified and consistent in FFPE biopsy, P0, P1/P2 MGH1504-1 MGH1512-1 MGH1514-1 MGH1515-1 MGH1518-1 MGH1525-1 MGH1528-1 Julie George Martin Peifer Roman Thomas
MGH1504: CTC-derived model Time difference Model number PDX type between biopsy and P0 latency (days) Patient clinical stage Patient prior therapies model initiation (days) MGH1504-1 CTC 3 160 LS none Patient Biopsy FFPE: - Tumor content: 97% - TP53 mutation p.S94* Patient biopsy PDX P0 PDX P2 Biopsy 281 mutations Julie George Martin Peifer Roman Thomas
MGH1504: CTC-derived model Time difference Model number PDX type between biopsy and P0 latency (days) Patient clinical stage Patient prior therapies model initiation (days) MGH1504-1 CTC 3 160 LS none Patient Biopsy FFPE: 10 - Tumor content: 97% - TP53 mutation p.S94* Patient biopsy PDX P0 P0 PDX: PDX P2 Biopsy - Tumor content: 99% PDX P0 - TP53 mutation p.S94* 14 Julie George Martin Peifer Roman Thomas
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