Genomic Technologies and the New-era of Precision Cancer Medicine - PowerPoint PPT Presentation

UPCI and UPMC Cancer Centers Genomic Technologies and the New-era of Precision Cancer Medicine Adrian V. Lee, Ph.D. Professor of Pharmacology and Chemical Biology Professor of Human Genetics Director, Women’s Cancer Research Center Co-Leader, Breast and Ovarian Cancer Program

Outline 1) How can Precision Medicine improve cancer treatment and outcomes? 2) Sequencing technologies and applications 3) What does sequencing of tumor DNA tell us about cancer? 4) How can we use sequence information to guide patient care?

Cancer Incidence and Mortality

Slow Improvements in Cancer Outcomes Heart Disease Cancer Stroke 1958 Years 2010

Precision Medicine Initiative – A Focus on Cancer Jan 30th, 2015

Clinical Trials – From Population to Precision HER2+ Herceptin ER+ Tamoxifen NCI MATCH http://blogs.cdc.gov/genomics/2015/01/29/precision-medicine/

Outline 1) How can Precision Medicine improve cancer treatment and outcomes? 2) Sequencing technologies and applications 3) What does sequencing of tumor DNA tell us about cancer? 4) How can we use sequence information to guide patient care?

Revolution in DNA Sequencing “Old way” 500bp 100,000,000 (100M) bp 1990 2001 2013 Cost ~$1B ~$10-50M ~$3-5K Time ~6-8 yrs ~3-4mos ~1-2 days

Multiplexed In Situ Sequencing in FFPE Ke R. Nat Methods. 2013 Sep;10(9):857-60. In situ sequencing for RNA analysis in preserved tissue and cells.

Outline 1) How can Precision Medicine improve cancer treatment and outcomes? 2) Sequencing technologies and applications 3) What does sequencing of tumor DNA tell us about cancer? 4) How can we use sequence information to guide patient care?

The Cancer Genome Atlas (TCGA) University of Pittsburgh (784) Memorial Sloan Kettering (799) UT MD Anderson (621) Total Samples: 10,480 University of Pittsburgh: # 1 contributor in breast and prostate # 2 contributor in head and neck and renal # 3 contributor in ovarian # 4 contributor in melanoma and bladder 11

What we know about the cancer genome • Few genes are recurrently mutated • Different genes, in general, are mutated in different tumor types • Specific mutagens can impact mutation rate and can leave a ‘mutation signature’ • Heterogeneity is common and can lead to many genetically distinct subpopulations • Heterogeneity extends to each cell • ‘Long tail’ of many infrequently mutated genes with unknown relevance

Very Few Recurrent Mutations Kandoth & Ding, Nature 2013

Single Cell Heterogeneity Wang & Navin, Nature 2014

Rare Events May be Important Frequency of mutated genes across primary tumors ESR1 Frampton & Yelensky, Nature Biotechnology 2013

Survival Rates of Difference Cancer Types 1 0.9 Breast (female) 0.8 Melanoma of the skin Colon and rectum 0.7 Oesophagus Relative Survival Rates Liver and intrahepatic bile duct 0.6 Pancreas 0.5 Stomach Brain and other nervous system 0.4 Oral cavity and pharynx 0.3 Urinary bladder Thyroid 0.2 Ovary Cervix uteri 0.1 0 0 5 10 15 Adapted from Goss PE & Chambers AF Nature Reviews Cancer 10 , 871-877. Based upon SEER data

Outline 1) How can Precision Medicine improve cancer treatment and outcomes? 2) Sequencing technologies and applications 3) What does sequencing of tumor DNA tell us about cancer? 4) How can we use sequence information to guide patient care?

Release and extraction of cfDNA from blood Crowley, E. et al. (2013) Liquid biopsy: monitoring cancer-genetics in the blood Nat. Rev. Clin. Oncol. doi:10.1038/nrclinonc.2013.110 cfDNA

Liquid Biopsy – NYT 4/7/2014

European Label Approval for EGFR Mutation Test in cfDNA for Iressa

Digital PCR (ddPCR): Quantitation, and Detection of rare Events 2. PCR Probes: Similar requirements as in qPCR (VIC and FAM) 1. Droplet formation & sample partitioning Partitions with both WT and Mut Mut Background/no DNA WT 3. Measurement of fluorescence from WT/ Mut probes in individual droplets - ABSOLUTE quantification

ESR1 Mutation Acquired After Endocrine Therapy 5/1999 Primary Tumor ER+ IDC Primary Prior to endocrine Chemo therapy No Tam (declined) ESR1 Y537S undetectable ESR1 (Y537S) 3/2004 (sensitivity 1 in 10,000) Lung Met Lung Met ER+ IDC Chemo Tam Mutant AI ESR1 Fulvestrant Liver Met ESR1 Y537S by: (autopsy) 12/2008 1. Exome-seq Liver Met 2. RNA-seq Rapid Autopsy ESR1 (WT)

ESR1 Mutations in Breast Cancer Allele frequency(%) BM14 PR03 PR21 PR28 BR17 BR19 BR11 CF04 CF08 CF14 CF16 CF23 CF27 CF28 Primary Bone met Brain met cfDNA (ER+ only) 7.0% (3/43) 9.1% (1/11) 12.5% (3/24) 24.1% (7/29) Wang et al. Clin Cancer Res. 2015 Oct 23. pii: clincanres.1534.2015.

Polyclonal ESR1 Mutation Tracking Y537C Y537S D538G Month 39 Month 44 Y537C CA 27.29 (U/ml) Y537S Mutant allele frequency (%) D538G Skin met Time (months) AI Chemo PARPi SERM Chemo Chemo LU mTORi LU Wang et al. Clin Cancer Res. 2015 Oct 23. pii: clincanres.1534.2015.

Summary • DNA sequencing offer the opportunity to further personalize therapy • TCGA has shown that mutations in cancers are extremely heterogeneous • Seqeuncing of metastasis reveals mechanisms of evolution and new targets for therapy • ESR1 is mutated in metastasis – point mutatons and fusions • Liquid biopsies are being investigated as a non- invasive method to monitor tumors

Acknowledgements Patients and Clinicians University of Pittsburgh School of Medicine Health Sciences Tissue Bank Women’s Cancer Research Center Ryan Hartmaier, PhD Steffi Oesterreich Ph.D. Christina Kline Merida Serrano Louise Mazur Michelle Bisceglia Amir Bahreini Nancy Davidson M.D. Adam Brufsky M.D., Ph.D. Aju Mathew M.D. Magee-Womens Research Institute Shannon Puhalla M.D. Peter Lucas M.D., Ph.D. Kim Brunce Ph.D. Annie Shaw Dave Peters Ph.D. Center for Simulation and Modeling (SAM) Albert DeFrusco Ph.D. Tony Ferreira Ph.D. Mike Barmada Ph.D.