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

Heart Disease Cancer Stroke Years

1958 2010

Slow Improvements in Cancer Outcomes

Jan 30th, 2015

Precision Medicine Initiative – A Focus on Cancer

http://blogs.cdc.gov/genomics/2015/01/29/precision-medicine/

Clinical Trials – From Population to Precision

ER+ Tamoxifen HER2+ Herceptin

NCI MATCH

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

1990 2001 2013 Cost ~$1B ~$10-50M ~$3-5K Time ~6-8 yrs ~3-4mos ~1-2 days

100,000,000 (100M) bp “Old way” 500bp

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)

11 Total Samples: 10,480

University of Pittsburgh (784)

UT MD Anderson (621) Memorial Sloan Kettering (799)

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

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

ESR1 Frequency of mutated genes across primary tumors

Rare Events May be Important

Frampton & Yelensky, Nature Biotechnology 2013

0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 5 10 15

Breast (female) Melanoma of the skin Colon and rectum Oesophagus Liver and intrahepatic bile duct Pancreas Stomach Brain and other nervous system Oral cavity and pharynx Urinary bladder Thyroid Ovary Cervix uteri

Survival Rates of Difference Cancer Types

Adapted from Goss PE & Chambers AF Nature Reviews Cancer 10, 871-877. Based upon SEER data

Relative Survival Rates

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

• 1. Droplet formation & sample partitioning
• 2. PCR
• 3. Measurement of fluorescence from WT/

Mut probes in individual droplets - ABSOLUTE quantification

Mut WT

Digital PCR (ddPCR): Quantitation, and Detection of rare Events

Probes: Similar requirements as in qPCR (VIC and FAM) Partitions with both WT and Mut Background/no DNA

ESR1 Mutation Acquired After Endocrine Therapy

ESR1 (WT) ESR1 (Y537S)

Liver Met (autopsy)

Mutant ESR1

Lung Met Primary

Prior to endocrine therapy ESR1 Y537S undetectable (sensitivity 1 in 10,000)

5/1999 Primary Tumor ER+ IDC 3/2004 Lung Met ER+ IDC Chemo No Tam (declined) Chemo Tam AI Fulvestrant 12/2008 Liver Met Rapid Autopsy

ESR1 Y537S by:

• 1. Exome-seq
• 2. RNA-seq

CF27 CF28 CF23 CF16 CF14 CF08 CF04 BR19 BR17 BR11 BM14 PR28 PR21 PR03

Primary Bone met Brain met cfDNA

Allele frequency(%)

ESR1 Mutations in Breast Cancer

7.0% (3/43) 24.1% (7/29) 12.5% (3/24) 9.1% (1/11) (ER+ only) Wang et al. Clin Cancer Res. 2015 Oct 23. pii: clincanres.1534.2015.

Chemo

Month 39 Y537S Y537C

PARPi LU SERM AI Chemo mTORi LU Chemo Skin met

Y537C Y537S D538G

Time (months) Mutant allele frequency (%) CA 27.29 (U/ml)

Month 44

D538G

Polyclonal ESR1 Mutation Tracking

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

Women’s Cancer Research Center Ryan Hartmaier, PhD Steffi Oesterreich Ph.D. Amir Bahreini Nancy Davidson M.D. Adam Brufsky M.D., Ph.D. Aju Mathew M.D. Shannon Puhalla M.D. Peter Lucas M.D., Ph.D.

University of Pittsburgh School of Medicine Health Sciences Tissue Bank Christina Kline Merida Serrano Louise Mazur Michelle Bisceglia Magee-Womens Research Institute 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.