Tumor Gene Sequencing: Ready for a Revolution?

Transcription

1 Tumor Gene Sequencing: Ready for a Revolution? Philippe Aftimos, M.D. Clinical Pharmacology Unit Institut Jules Bordet Brussels, Belgium ICBD Antwerp February 7 th, 2015

2 IHC: Historical Biomarkers Cold ischemic time Delay in fixation Different fixatives Duration of fixation Inter-observer variability Yildiz-Aktas IZ, Mod Pathol 2012 Apple S, Am J Clin Pathol 2011 Reisenbichler ES, Am J Clin Pathol 2013

3 The Molecular Shift

4 Endocrine therapy in the era of genomics 1960 Kirsten and Smith: clinical use of an anti-oestrogen for breast cancer 1971 Cole: use of tamoxifen as a anti-cancer drug 1986 Greene: 1 st DNA sequence of ER 1998: Letrozole FDA approved in the 2 nd line metastatic setting 1966: Tamoxifen synthesis as a fertility drug 1973 Jensen and De Sombre: 1 st description of ER 1998: Tamoxifen FDA approved in the adjuvant setting 2013 Toy: ESR1 mutations in the LBD and resistance to hormone therapy

5 ESR 1 Mutations Toy W, Nature Genetics 2013

6 538G-ERα confers resistance to 4HT and fulvestrant. Merenbakh-Lamin K et al. Cancer Res 2013;73: by American Association for Cancer Research

7 The Predictive Power of Genomics 13 patients with metastatic breast cancer were analyzed for mutations in cancer-related genes A mutation of A to G at position 1,613 of Erα in 5 patients with resistance to hormonal therapy Substitution of aspartic acid at position 538 to glycine (D538G) The mutation was not detected in the primary tumors obtained prior to endocrine treatment Merenbakh-Lamin K, Cancer Res 2013

8 GDC-0810 (ARN-810, RG6046) Selective estrogen receptor degrader (SERD) Designed to bind to the estrogen receptor to limit its function Change the shape of the receptor in such a way that the cell eliminates it by degradation ClinicalTrials.gov Identifier: NCT

9 Inhibition of Mutated, Activated BRAF in Metastatic Melanoma Flaherty KT et al, N Engl J Med 2010; 363:

10 Clinical Benefit Rate in Genomic-driven Clinical Trials Drug Tumor Type Molecular aberration Vemurafenib Melanoma BRAF V600E Response rate PFS Reference 81%* > 7 months NEJM 2010 Crizotinib NSCLC ALK translocatio n 61% 9.7 months Lancet Oncol 2012 Trametinib Melanoma BRAF 33%* 5.7 months Lancet 2012 Dabrafenib Melanoma BRAF 50%* 47% > 6 months Dabrafenib + Trametinib Lancet 2012 Melanoma BRAF V600 76%* 9.4 months NEJM 2012 LDK 378 NSCLC ALK translocatio n 70% 7.4 months ASCO 2013 * Dacarbazine: RR = 0 13%

11 Patient 2 Patient 1 ARAF mutation, NSCLC, sorafenib. Patient 3 TSC1 mutation, bladder cancer, everolimus. Iyer et al, Science 2013 Imielinski et al, J Clin Invest 2014 Wagle N et al. Cancer Discov 2014 mtor activating mutations, bladder cancer, pazopanib + everolimus

12 Comparisons of progression-free survival (PFS) on molecular profiling (MP) therapy (blue bars) versus PFS (time to progression [TTP]) on prior therapy (gold bars) for the 18 patients with a PFS 1.3. Von Hoff D D et al. JCO 2010;28: by American Society of Clinical Oncology

13 A, best response by RECIST of 175 patients with one molecular aberration treated with matched therapy: changes from baseline in tumor measurements (waterfall plot). Tsimberidou A et al. Clin Cancer Res 2012;18: by American Association for Cancer Research

14 Precision Medicine: the Obstacles Physician Education Inter and intra-tumor heterogeneity Serial tumor biopsies may be needed (± invasive) Evolving sequencing technologies Druggable targets Availability of drugs at the right time New (innovative) designs of clinical trials needed Ethical and legal challenges

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16 Participants: 57% medical oncologists, 29% surgeons, 14% radiation oncologists 22% percent of physicians reported low confidence in their genomic knowledge 18% of physicians anticipated testing patients infrequently ( 10%) Higher genomic confidence was associated with anticipating potentially actionable test results 42% of physicians endorsed disclosure of uncertain genomic findings to patients J Clin Oncol May 1;32(13):

17 Intra-tumour heterogeneity NSCLC: pathology and mutational discordance (BRAF) Wright GM et al. Oncotarget. 2014

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19 ROS 1 or ALK rearrangements and resistance mutations Bergethon K et al. J Clin Oncol 2012 Awad M et al. Clin Adv Hematol Oncol 2014

20 Thoughts after Talking to Elaine Mardis Is TGS a useful tool for Precision Medicine or should we perform WGS for all patients?

21 Integrative Sequencing Analysis ( 5500$) Courtesy C. Sotiriou

22 Successful sequencing in 70% of cases. Actionable mutations in 46%. Andre F et al. Lancet Oncol 2014

23 Small molecule inhibiting Ras? Maurer T el al. Proc Natl Acad Sci U S A. 2012

24 From common cancers to rare tumors Garraway L A JCO 2013;31:

25 PRECISION - Feasibility N=30 (metastatic colorectal, melanoma and NSCLC patients) Ion Torrent DNA-Seq OncoDNA JBI Meta Core Biospy 2 FFPE 1 Frozen 1 Blood Sections Real time on single patient basis JBI Path Histo And Cellularity Review JBI Tumor Sequencing Board JBI Clinicians Biobanking Illumina DNA-Seq ICF signature Biopsy + processing by central laboratory Results available to clinicians Weekly Tumor Sequencing Board 10 working days 15 working days

26 Biopsy Feasibility Biopsy Sites Number of Patients Liver 10 Lymph nodes 5 Skin 5 Lung (bronchoscopy) 4 Lung (CT) 3 Soft tissue 3 Rectal 2 Peritoneal 2 Success rate = molecular screening result 32/34 Adverse event 1 bronchial obstruction (bronchoscopy) Technical Turnaround Time 10 working days >20% tumor cells 27/34 (79%) >10 ng DNA 31/34 (91%)

27 Treatment Assignment Actionable mutations were found for 66% (21/32) of patients 76% (16/21) were treated with therapy according to the identified molecular alteration Reasons for non-targeted therapy were: non-eligibility (2) unavailable drugs (2) patient refusal (1)

28 BIG Feasibility MS Phase Set-up Molecular Advisory Board development phase blood Registration Result placed on MSPP Hospitals access MSPP 15 working days

29 Illustration of personalized medicine trial: SAFIR02 NGS Array CGH: 51 genomic alterations Therapeutic phase Targeted therapy according to genomic alteration (8 different therapies) Genomic alteration R mbc Her2-negative Standard of care No alteration: follow-up Sponsor: UNICANCER Partnership: ARC, AstraZeneca Sample size: 210 patients randomized Recruitment ongoing Courtesy F. Andre

30 The Belgian Molecular Profiling Program of Metastatic Cancer for Clinical Decision and Treatment Assignment A BSMO master protocol BSMO

31 PRECISION patients with metastatic solid tumours (first line preferred) Data sharing platform - Targeted gene sequencing - Select gene rearrangements - Select IHC Pharma PRECISION 2 * Clinical trials Standard of care Any molecular screening platform * Master protocol for basket trials

32 AURORA: Aiming to Understand the Molecular Aberration in Metastatic Breast Cancer Zardavas D et al. Br J Cancer. 2014

33 Selected alterations (TGS 400 genes) Somatic mutations CDH1 c.67c>t p.q23* Primary: 90.0 Metastasis: Not seen NOTCH1 c.4214c>a p.p1405h Primary: Not seen Metastasis: 23.6 PIK3CA c.3180c>g p.h1060q Primary: Not seen Metastasis: 13.7 Gene amplifications FGFR1 chr8: Primary: 24.0 Meta: 24.0 Germline mutations BRCA2 c.3274dela p.n1730ifs*11

34 What treatment choice? PF In Combination With Docetaxel In Patients With Advanced Breast Cancer: NCT A Phase I Pharmacodynamic Study of Copanlisib (BAY ) as Monotherapy in Patients With Non-Hodgkin's Lymphoma and Solid Tumors: NCT Lucitanib in Patients With FGFR1-amplified or Non-amplified Estrogen Receptor Positive Metastatic Breast Cancer (FINESSE):NCT Niraparib Versus Physician's Choice in Her2 Negative, Germline BRCA Mutation-positive Breast Cancer Patients (BRAVO): NCT

35 Questions 1. Can plasma be used as an alternative to metastatic biopsies in molecular screening programs using NGS? 2. Can the liquid biopsy more accurately capture tumor heterogeneity compared to the biopsy of a single metastatic site? Michail Ignatiadis, Institut Jules Bordet

36 Mutation analysis using the 50-cancer gene panel (Feasibility) Figure 1: Tumor Plasma Ion AmpliSeq TM Cancer Hotspot Panel v2 (50 genes) C G T T C A A T G A C G T DNA pol C A A H + H + T 70% had at least 1 mutation in either the p53, PIK3CA, 76% CONCORDANT PTEN, AKT1, IDH2 24% DISCORDANT or SMAD4 genes Tumor + / plasma + (n=9) Tumor + / plasma (n=2) Rothé et al. Annals of Oncology 2014 Tumor - / plasma +

37 Comparison between synchronous plasma and tumor lesions Figure 1: Tumor Plasma Ion AmpliSeq TM Cancer Hotspot Panel v2 (50 genes) C G T T C A A T G A C G T DNA pol C A A T H + H + 76% CONCORDANT 24% DISCORDANT Tumor + / plasma Tumor + / plasma + (n=2) (n=9) Tumor - / plasma + (n=2) Rothé et al. Annals of Oncology 2014

38 Plasma ctdna identifies subclone not detected in synchronous liver metastases F Rothe et al. Annals of Oncology 2014

39 Tumor Gene Sequencing: Ready for a Revolution? Tackling the obstacles Building the logistics Implementing quality control Building clinical trials Integrating Precision Immunotherapy We are not quite there but we are well on our way

40 Questions? Clinical trials: