Identifying Patters of Doxorubicin Sensitivity in Soft Tissue Sarcoma Using Next Generation Sequencing THESIS Presented in Partial Fulfillment of the Requirements for the Degree Master of Public Health in the Graduate School of The Ohio State University By Manojkumar Bupathi Graduate Program in Public Health The Ohio State University 2017 Thesis Committee: Professor James Chen – Advisor Professor Philip Binkley Professor Gregory Otterson Professor Brian Hilligoss Copyright by Manojkumar Bupathi 2017 Abstract Soft-tissue sarcomas account for less than 1% of new cancer diagnoses in both men and women in the United States. Surgery is offered for localized disease amenable to resection. However, less than 20% of patients present with initially resectable disease, and the 5-year survival rate for this locally advanced/metastatic population is abysmal (<25%). Sadly, our ability to systemically treat metastatic soft tissue sarcoma chemotherapy remains a case of trial-and-error. Indeed, the National Cancer Center Network guidelines list nine acceptable single agents and six different combination regimens. Doxorubicin serves as the backbone of most treatment regimens but induces significant tumor regression in only 15-30% of patients. We conducted a retrospective review of patients with leiomyosarcoma who were treated at our institution and had next generation sequencing with FoundationOne. Our aim was to determine if we could determine sensitivity to doxorubicin and other agents that are commonly used to treat STS based on p53 status. Our data indicates that the type of abnormality in p53 can have prognostic implications with doxorubicin and pazopanib. Further, we performed a cluster analysis to determine if there are any specific patterns in genetic pathways which could identify be used to group patients together. Using the leiomyosarcoma database in TCGA and GENIE, we generated the same clusters for those patients to compare the patients between the datasets. We found that there are similarities among along three datasets. For example, most male patients with leiomyosarcoma fall into cluster 3. The exact ii mechanism of why this happens is currently not known. In addition, patients in cluster 2 in TCGA perform worse compared to our dataset. However, patients in our dataset were treated with targeted therapy suggesting that molecular directed therapy could have better outcomes. Finally, we identified 10 patients with BRCA alterations. Four out of six patients with BRCA2 alterations had the same variance of unknown significance alteration at K33226x. This specific alteration has been associated with increased risk in breast, ovarian, pancreas and lung cancer. Given the high prevalence of this alteration in our cohort, it is important for this be evaluated in other datasets to get a better understanding of its prevalence so that patients can appropriately be screened or counseled regarding their risks. Though precision medicine focuses on individualized care success truly requires a population-based approach and understanding what interventions work on individual need to be compared with data from large, diverse numbers of people to identify population subgroups likely to respond differently to intervention. iii Dedication This document is dedicated to my family. iv Acknowledgments I would like to express my appreciation to my advisory committee: Dr. James Chen, Dr. John Hays, and Dr. Philip Binkley. Thanks for giving me the opportunity to be part of the clinical translational research team in the lab. A special thanks to Dr. Chen for his time, dedication, and patience to ensure that I am successful in completing this project and obtaining my degree. Dr. Hays, it has been an honor to work with you and thank you for your advice and for acting as a mentor to me. Also, thanks Dr. Binkley for taking the time to review and assisting in completing my thesis. Dr. Otterson, thank you so much for all of your support and encouragement in completing this Masters while in my fellowship as well as serving on my thesis committee. My gratitude also goes to everyone who works in the lab, there are not enough words to describe your excellent work. Special thanks to Nicholas Grosenbacher, you were there to help no matter time or day of the week with data analysis. The most special thanks goes to my best partner and friend, my wife. Maithreye, you gave me your unconditional support and love through all this long process. v Vita June 2002 ....................................................... East Brunswick High School January 2005 .................................................. B.A. Biology, Rutgers University May 2009 ....................................................... M.D. St. Georges University July 2009 ...................................................... Post Graduate Training, Department of Internal Medicine, Case Western University July 2013 ...................................................... Post Graduate Training, Investigational Therapeutics, MD Anderson Cancer Center July 2014 ...................................................... Post Graduate Training, Medical Oncology, The Ohio State University Publications Book Chapter: Bupathi, M. “Myelodysplastic/Myeloproliferative Neoplasms” in Myelodysplastic Syndromes, second edition, H.J Deeg, DT Brown, SD Gore, T Haferlach, MM LeBeau, C Niemeyer, Eds. New York. Springer Publishing, 2013 pp 116-131 vi Peer-Reviewed Publications 1. Chemotherapy options for Intrahepatic Cholangiocarcinoma. Bupathi M, Bekaii- Saab T. Hepatobiliary Surgery and Nutrition. 26th Dec 2016. 2. Incidence of infusion reactions to anti-neoplastic agents in early phase clinical trials: The MD Anderson Cancer Center experience. Bupathi M, Hajjar J, Bean S, Fu S, Hong D, Karp D, Stephen B, Hess K, Meric-Bernstam F, Naing A. Investigational New Drugs. 29 Sept 2016. doi:10.1007/s10637-016-0395-y 3. Spotlight on bevacizumab in metastatic colorectal cancer: patient selection and perspectives. Bupathi M, Ahn D, Bekaii-Saab T. Gastrointestinal Cancer: Targets and Therapy. 30 June 2016; doi https://dx.doi.org/10.2147/GICTT.S97740 4. Biomarkers for immune therapy in colorectal cancer: mismatch-repair deficiency and others. Bupathi M, Wu C. J Gastrointest Oncol. 2016;7(5):713-720. doi: 10.21037/ jgo.2016.07.03 5. Modified irinotecan and infusional 5-fluorouracil (mFOLFIRI) in patients with refractory advanced pancreas cancer (APC): a single-institution experience. Bupathi M, Ahn D, Wu C, Ciombor KK, Stephens JA, Reardon J, Goldstein DA, Bekaii-Saab T. Medical Oncology. 2016 April; 33(4):37. vii 6. Clinical next-generation sequencing reveals aggressive cancer biology in adolescent and young adult patients. Subbiah V, Bupathi M, Kato S, Livingston A, Slopis J, Anderson PM, Hong DS. Oncoscience. 2015 Jul 8; 2(7):646-58. 7. Hepatocellular carcinoma: Where there is unmet need. Bupathi M, Kaseb A, Meric-Bernstam F, Naing A. Molecular Oncology. Mol Oncol. 2015 Jun 25. pii: S1574- 7891(15)00129-5. doi: 10.1016/j.molonc.2015.06.005. 8. Angiopoietin-2 as a therapeutic target in hepatocellular carcinoma treatment: current perspectives. Bupathi M, Kaseb A, Janku F. OncoTargets and Therapy. 2014 Oct 20;7:1927-32. doi: 10.2147/OTT.S46457 9. SF3B1 haploinsufficiency leads to formation of ring sideroblasts in myelodysplastic syndromes. Visconte V, Rogers HJ, Visconte V, Rogers HJ, Singh J, Barnard J, Bupathi M, Traina F, McMahon J, Makishima H, Szpurka H, Jankowska A, Jerez A, Sekeres MA, Saunthararajah Y, Advani AS, Copelan E, Koseki H, Isono K, Padgett RA, Osman S, Koide K, O'Keefe C, Maciejewski JP, Tiu RV. Blood. 2012 Oct 18;120(16):3173-86. doi: 10.1182/blood-2012-05-430876 10. Mutations in the spliceosome machinery, a novel and ubiquitous pathway in leukemogenesis. Makishima H, Visconte V, Sakaguchi H, Jankowska AM, Abu Kar S, viii Jerez A, Przychodzen B, Bupathi M, Guinta K, Afable MG, Sekeres MA, Padgett RA, Tiu RV, Maciejewski JP. Blood. 2012 Apr 5;119(14):3203-10. doi: 10.1182/blood-2011- 12-399774 11. Esophageal and Gastric T-Cell Lymphoma: A Rare Entity. Sappati R, Bupathi M, Solomon A, Kyprianou A. Journal of Krishna Institute of Medical Sciences. Jan 2012 12. Aquired Erythrocytosis on Treatment with infliximab for Ankylosing spondyilits. Antonelli M, Bupathi M, Janakiram M, Hergenroeder P, Khan MA. Journal of Rheumatology 2011 Mar;38(3):581-3. doi: 10.3899 Fields of Study Major Field: Public Health ix Table of Contents Abstract ............................................................................................................................... ii Dedication ........................................................................................................................... iv Acknowledgments ............................................................................................................... v Vita ..................................................................................................................................... vi List of Tables .................................................................................................................... xii List of Figures .................................................................................................................. xiii Chapter 1: Background ....................................................................................................... 1 Leiomyosarcoma .............................................................................................................. 5 Uterine Leiomyosarcoma ..............................................................................................