Curriculum Vitae
Name:Chandan Kumar(Chandan Kumar-Sinha, in publications)
Present Title:Research Assistant Professor
Address:Michigan Center for Translational Pathology
1400 E Medical Center Drive, 5411 Cancer Center,
Ann Arbor MI 48109
Telephone:Lab: 734 936 2592Cell: 734 277 7096
Email:
Education
5/1987- 6/1990B.Sc. (Honors) Zoology, Delhi University
7/1990- 6/1992M.Sc. Biotechnology, Madurai Kamaraj University, Madurai
8/1992- 3/1999 Ph.D. Faculty of Sciences
Dissertation Title: “Somatic Embryogenesis in Sandalwood (Santalum album L): A Study on the Molecular Basis of Meristem Induction”
Advisor: Prof. G. Lakshmi Sita
Institution: Indian Institute of Science, Bangalore, India
Year: 1999
Post-Doctoral Training
4/1999- 9/2003 Post-Doctoral Fellowship,
Department of Pathology, University of Michigan, Ann Arbor, MI
Field: Cancer Genomics and Molecular Biology
Mentor: Dr. Arul M Chinnaiyan, MD, PhD
Years of Training: 4 years 4 months
Academic and Administrative Appointments
9/07/2003Senior Research Scientist, Institute of Bioinformatics, Bangalore
2/17/2004Scientific Officer E, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai, India
03/09/2007Assistant Professor, Homi Bhabha National Institute, ACTREC, Navi Mumbai, India
08/06/2007 Research Lab Specialist Lead, Pathology Department, University of Michigan
10/01/2007Research Assistant Professor, Pathology Department, University of Michigan
11/01/2007Research Assistant Professor, Michigan Center for Translational Pathology, University of Michigan
Research Interests
I am interested in integrative functional-genomics of cancers using high-throughput genome and transcriptomeanalyses to develop cancer biomarkers and personalized therapeutic options. My scientific motto is that each cancerrepresents a unique genetic-environmental accident that shares hallmark molecular features with other cancers, as well as undergoes a privateevolution- and that both these common and private aberrations need to be integrated to improve diagnostic and therapeutic options. My work encompasses prostate, breast and pancreatic cancers using microarrays and more recently, next generation highthroughput sequencing platforms to identify cancer driving aberrations, including gene fusions, mutations and outlier gene expression signatures, with a special emphasis on therapeutically amenable genes to tailor and test combinatorial therapeutic regimens in experimental model systems. Specific current interests include discovery and characterization of gene fusions and sample specific outlier kinases driving the growth of pancreatic cancer cell lines and tumor tissues that may be targeted to achieve inhibition of tumor growth in cell culture and primary tumor xenograft models. Development and application of bioinformatic tools for analysis of diverse high throughput molecular data forms the core interest in all ongoing pursuits.
Grant Support:
ACTIVE
R21CA155992 (PI: Kumar) 04/1/2011 – 03/31/2013 2.4 cal mos
NIH$202,602/yr
High Throughput Transcriptome Sequencing for Systematic Detection of Recurrent Transcript Aberrations in Pancreatic Cancer
Goals:Using next generation highthroughput sequencing platforms to identify genomic and transcriptomic aberrations, including gene fusions, mutations and kinome signatures to tailor combinatorial therapeutic regimens in experimental model systems of Pancreatic Cancer.
Role: Principal Investigator
9/1/2011, (PI: Chandan Kumar)
University of Michigan Comprehensive Cancer Center11/1/2011-10/31/20121.2 cal mos
GI SPORECareer Development Program$50,000
Targeting Tumor Specific Outlier Kinases through Kinome Profiling of Pancreatic Cancers- A Pilot Study for Personalized Treatment of Primary Human Tumor Xenografts
Goals: To utilize gene expression profiles of individual pancreatic cancer cell lines and tissues to identify sample/ patient specific kinases that may be potentially targeted therapeutically.
Role: Principal Investigator
American Association for Cancer Research 10/01/09 – 9/30/12 1.2 cal mos
(Dream team leader: Gray)
Stand Up To Cancer Dream Team Translational Cancer Research$362,190/yr
Personalizing treatment of triple negative, metastatic breast cancer
Goals: Developing targeted molecular therapies for breast cancer treatment; test the efficacy of individualized treatment of drug-resistant, triplenegative.
Specific Aims: 1) Compare omic features of 100 drug resistant, TNBCs with those of untreated primary tumors to identify omic features associated with metastasis and/or drug resistance. 2.) Developed improved preclinical biological models of drug resistant, triple-negative breast cancer to facilitate identification of therapeutic approaches that will be effective against TNBC. 3) Identify omic features of metastatic, drug resistant TNBC subsets associated with response to approved and experimental therapeutic agents using novel computational and experimental approaches. 4) Develop and compare computational methods for selection of drugs/combinations for individualized treatment of TNBC patients based on the omic characteristics of their tumors. 5) Conduct an omic-marker-guided clinical trial of therapies predicted to be effective against TNBC subsets. 6) Develop a comprehensive public/patient education and awareness campaign to introduce the consumer community to the new “personalized medicine” concept.
Role: Co-Investigator
W81XWH-09-2-0014 (PI: Wicha) 03/01/09 – 04/24/11 3 cal mos
Department of Defense $443,618/yr
National Functional Genomics Center
Goals: To develop a comprehensive approach to genetics, proteomics and bioinformatics that can help elucidate the mechanisms driving tumorigenesis. This research investigates the notion that cancer stem cells are the key cell component driving tumorigenesis, metastasis and treatment resistance.
Specific Aims: 1) To isolate and achieve molecular characterization of cancer stem cells from human breast, prostate, colon, pancreas, head and neck, brain, ovarian and melanomas. 2) To better define pathways that regulate cancer we will utilize the integrative oncogenomics approaches including HIMAP to elucidate the interacting pathways regulating cancer stem cells. 3) To identify novel genes regulating cancer stem cells we propose to utilize a high throughput siRNA approach to screen for genes which play a functional role in stem cell self-renewal.
Role: Co-Investigator
W81XWH-08-0110 (PI: Chinnaiyan) 09/01/08 – 11/30/13 4.2 cal mos
Department of Defense $500,000/yr
A Search for Gene Fusions/Translocations in Breast Cancer
Specific Aims: 1) Develop high-throughput adaptations of existing methodologies such as fluorescence in situ hybridization (FISH), 2) employ bioinformatics and associated analytical tools to elucidate recurrent gene fusions in breast cancers, 3) employ next generation whole transcriptome sequencing of breast tumors.
Role: Co-Investigator
COMPLETED
Lustgarten Foundation(PI: Kumar)02/01/09- 01/31/2010
$100,000/yr directs
Discovery of Recurrent Gene Fusions in Pancreatic Cancer using High-throughput Sequencing
Goals: The goal of this project was to carry out a survey of pancreatic cancer transcriptome to identify recurrent gene fusions using high-throughput sequencing.
Role: Principal Investigator
Department of Science and Technology, Govt. of India (PI: Kumar) 2/2005- 2/2008
Young Scientist Award, Science and Engineering Research Council
INR 834,000 (~ USD 18, 533) 100%
HER2 Mediated Regulation of Gene Expression in Breast Cancer Cells: Characterization of
Association between HER2 and IGFBP2.
Role: Principal Investigator
Department of Biotechnology, Govt. of India (PI: Kumar) 12/2005-12/2008
INR 3,400,000 (~ USD 75,555) 100%
Delineation of Prognostic Biomarkers of Progression of Cervical Cancer
Role: Principal Investigator
Department of Biotechnology, Govt. of India (PI: Dalal) 9/2006-9/2007
INR 2,100,000 (~USD 44,444), 50%
Generation of Stem Cell Lines and Knockdown Mice that Lack Specific Gene products to study growth and Differentiation using RNA interference: Potential for the identification of Novel Therapeutic Strategies.
Role: Co-Investigator
Tata Memorial Hospital-Women’s Cancer Initiative (WCI) (PI: Badwe) 6/2006-6/2007
INR 420,000 (USD 9,333)
Assessing impact of exogenous progesterone on gene expressions in breast cancer: an exploratory study in postmenopausal women.
Role: Co-Investigator
Biotage (Sweden)-Chemito (India) (PI: Kumar) 12/2005-2/2006
Highthroughput Genotyping of Human Papillomaviruses in Cervical Cancer Biopsies of Patients at TMH using Type Specific Multiple Sequencing Primers
Role: Principal Investigator
PENDING
10/5/2011, 12-PAF01641(PI: Chandan Kumar)
Department of Health and Human Services, National Institutes of Health, RO1 Mechanism
Recurrent gene-fusions in breast cancer involving microtubule associated serine threonine (MAST) kinase genes.
Role: Principal Investigator
4/1/2011, 11-PAF01194 (PI: Max Wicha)
Department of the Army-USAMRAA
National Functional Genomics Center-A Center for Genetic Origins of Cancer (CGOC) at the University of Michigan
Role: Co-Investigator
3/2/2011, 11-PAF03759 (PI: Chinnaiyan, Center for Translational Pathology)
Department of Health and Human Services, National Institutes of Health
MI-ONCOSEQ: The Michigan Oncology Sequencing Center,
Role: Co-Investigator
2/15/2011, 11-PAF04140 (PI: Ljungman, Radiation Oncology)
Department of Health and Human Services, National Institutes of Health
Mechanisms of Genotoxic Stress-regulated Gene Expression in Human Cells,
Role: Co-Investigator
Honors and Awards
1990-1992Department of Biotechnology (DBT, Govt. of India) Scholarship for MSc. Biotechnology
1992-1994University Grants Commission (UGC), Government of India, Junior Research Fellowship for PhD
1994-1997University Grants Commission (UGC), Government of India, Senior Research Fellowship for PhD
1997International Society for Plant Molecular Biology (ISPMB) Travel Award
2005-2008Young Scientist Award, Science and Engineering Research Council, Department of Science and Technology, Govt. of India
2009-2010 Lustgarten Foundation Awardfor Pancreatic Cancer Research on “Discovery of
Recurrent Gene Fusions in Pancreatic Cancer using High-throughput Sequencing”
2011American Pancreatic Association Young Investigator Award, 42nd Annual Meeting of the American Pancreatic Association, Chicago, November 2-5, 2011
Memberships in Professional Societies
Invited member: Society for Cancer Research and Communication
Life Member: Indian Association of Cancer Research
Active Member: American Association for Cancer Research (AACR)
Minorities in Cancer Research (MICR)
Editorial Tasks
Reviewer, Pathobiology (PBY) Panel, Department of Defense Congressionally Directed Medical Research Program (CDMRP) in Prostate Cancer Research Program (PCRP), 2011
Standing Reviewer for:Cancer Research (AACR), Genome Medicine (Biomed Central), Journal of Biosciences (Indian Academy of Sciences)
Ad hoc reviewer for Nature, Science, Science Translational Medicine, Nature Genetics, Nature Medicine, Genome Biology, Genome Research, International Journal ofCancer, Nucleic Acid Research, Cancer Cell, PLOS One,PNAS (USA), Cancer Discovery
Patent/ Technology Transfer
1. U.S. Patent Application. University of Michigan, Identification of DDX5-ETV4 Fusion
Protein in Prostate Cancer.Filed July, 2008. Patent Number: UM-4126, Serial Number
61/187,776.
2. U.S. Patent Application. University of Michigan, Identification of Transcriptome Sequencing
to Detect Gene Fusions in Cancer. Filed September, 2008. Patent Number: UM-4166, Serial
Number 61/143,598.
3. U.S. Patent Application. University of Michigan, Functionally recurrent rearrangement of the
MAST Kinase and NOTCH gene families in breast cancer.Filed dated March 7, 2011. Patent
Number: UM-4958
4. U.S. Patent Application. University of Michigan, Analysis of Pseudogene Expression in the
Transcriptomic Landscape of Cancer.Filed dated June 15, 2011.Patent Number: UM-5067
Teaching Activities
Mentor, Post-Doctoral Fellows
2009Dan Robinson, University of California, San Diego
2011Vishal Kothari, Loma Linda Institute, California (from June 2011)
Thesis Committees
2007Vishal Kothari, Member, Thesis Committee, Advanced Center for Treatment, Research and Education in Cancer, Dissertation Proposal: Gene Therapy Studies for Head and Neck Squamous Cell Carcinoma: Use of RNAi to sensitize tumour cells to conventional therapy, 2009
2010Ming Hu, Member, Doctoral Committee, University of Michigan School of Public Health, Dissertation Proposal: Model Based Methods in High Throughput Genomic Data Analysis, April, 2010
Mentor, PhD co-Advisor
2006-2010Kavishwar Wagholikar, MBBS, PhD in Genetic Algorithm-Fuzzy Modeling for Medical Decision Support.
Currently a post-doctoral fellow at Mayo Clinic, Rochester, Minnesota
Mentor, Medical Students
2010Linda Ma, Medical Student, University of Michigan
2011-Iris Wei, House Officer, Surgery, University of Michigan
Mentor, Graduate Students
2005-2007Cheryl M. Travasso, Junior Research Fellow, ACTREC Fellowship, Cervical cancer gene expression profiling studies.
2005-2007Aditi Galoda, Junior Research Fellow of Council for Scientific and Industrial Research, IGFBP2-HER2 signaling pathway in breast cancers.
2006-2007Asha Thomas, Junior Research Fellow of Council for Scientific and Industrial Research, pursuing breast cancer microarray profiling using focused microarrays.
2009Noah Wolfson PhD, University of Michigan
2009Joshua Regal MD PhD, University of Michigan
Mentor, Undergraduate Students
2004Harshada Y Rane, Jawaharlal Nehru Centre for Advanced Scientific Research Summer Research (JNCASR) Fellow, MS Biotechnology, University of Mumbai
2005Sukanya Suresh, M.S Applied Microbiology, PSG College of Arts and Science, Bharathiar University, Coimbatore.
2005Krishna Kumar. S, B. Tech Biotechnology, Department of Biotechnology, Indian Institute Of Technology, Madras (IIT Madras), Tamilnadu.
2005Chandrika N Deshpande, MS Biotechnology, Mysore.
2006Rajiv Das Kangabam, MS Bioinformatics, Department of Bioinformatics, KSR College of Arts and Science, Tamilnadu.
2006Suchitra Venkatasubramani, MS Biotechnology, DY Patil Vidyapeeth.
2006Sharath Poojary, MS Life Sciences.
2005-2006Aditi Deshpande, MS Biotechnology, Project Assistant.
2008-2009Aalisha Desai, University of Michigan Undergraduate Research Opportunity Program (UROP)
2008-2009Haala Hai,University of Michigan Undergraduate Research Opportunity Program (UROP)
2008-2009Balreet Kaur, University of Michigan Undergraduate Research Opportunity Program (UROP)
2008-2010Han Li, University of Michigan Undergraduate Research Opportunity Program (UROP)
2008-2010Peter Fullen, University of Michigan Undergraduate Research Opportunity Program (UROP)
2008-2009Mah Jabeen Sidra, University of Michigan Undergraduate Research Opportunity Program (UROP)
2009-2010Nikhil Patel, University of Michigan Undergraduate Research Opportunity Program (UROP)
2009-2010Nikita Consul, University of Michigan Undergraduate Research Volunteer
2009-2010Chaitanya Malla,University of Michigan Undergraduate Research Volunteer
2010-2011Mei Mei, University of Michigan Undergraduate Research Opportunity Program (UROP)
2010-2011Xin Cai, University of Michigan Undergraduate Research Opportunity Program (UROP)
2010-2011Joseph Mierzwa,University of Michigan Undergraduate Research Opportunity Program (UROP)
2010-2011Cyril Mazhuvanchery,University of Michigan Undergraduate Research Opportunity Program (UROP)
2010-2011Aditi Arora,University of Michigan Undergraduate Research Opportunity Program (UROP)
2010-2011Tushar Shetty, University of Michigan Undergraduate Research Opportunity Program (UROP)
2010-2011Julia Milton,University of Michigan Undergraduate Research Opportunity Program (UROP)
Course Lectures
200529th Annual Conference & CME of Mumbai Hematology Group, Tata Memorial Hospital,Faculty, Mumbai, India, March 19-20, 2005.
2006Chairperson, Graduate Students Meeting, Session II, ACTREC, Tata Memorial
Centre, Kharghar Navi Mumbai, India, September 23, 2006.
2006Faculty and Member Scientific Committee, 4th Tata Memorial Hospital-Women’s
Cancer Initiative (WCI) Conference, Mumbai, India, October 6-7, 2006.
2007Junior Research Fellows Course Lecture: Gene Expression profiling by Microarrays
Host, International Visitors
August 2008Nandan Deshpande, PhD student, Macquarie University, NSW, Australia, Analysis of Carbohydrate Metabolism Pathways by Microarrays. Aug 10- 28, 2008,
June-July 2009Dr Kumar Prabhash, Associate Professor, Assistant Medico-Oncologist, TATA Memorial Hospital, Mumbai India: Provided Hands on Training in detection of gefitinib sensitizing EGFR mutations from formalin fixed paraffin embedded tissue sections.
Committee, Organizational, and Volunteer Service
2004-2007Officer-in-Charge,Expression Profiling Committee, Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
2004-2007Advisor, DNA sequencing and Mutation Analysis Committee, Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
2005-2006Resource Person, Biology Olympiad Resource Generation Camp, Homi Bhabha Center for Science Education, Tata Institute of Fundamental Research
2005-2007Member Secretary, Institutional Biosafety CommitteeAdvanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
Member, Academic Committee, Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
Member, Website Committee, Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
Member, Common Instrument Room Committee, Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
Member, Bioinformatics Committee, Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
Member, Library Committee, Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
2006-2007Convener“Crosstalk” A weekly journal club at, India to foster communication between clinical scientists and basic scientists. Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India -
2009 – presentMember, Gastrointestinal Oncology program, Cancer Center, University of Michigan
2011-presentMember, Sequencing Tumor Board, Michigan Center for Translational Pathology, University of Michigan.
Invited Presentations
1. Oncogeneic Connections of Fatty Acid Metabolism. University of Michigan Department of Pathology Research Seminar Series, Ann Arbor, MI, 2002.
2. Molecular Profiling of Cancer. DAE Collective Vision for the Future. Bhabha Atomic Research Centre, Mumbai, April 21, 2004
3. Increased Expression of Insulin like Growth Factor Binding Protein (IGFBP2) in HER2
Overexpressing Breast Cancer Cells: Evidence of a Novel Signaling Crosstalk 24th Annual
Convention of Indian Association for Cancer Research & International
Symposium on HPV and Cervical Cancer, February 9-12, 2005.
4. Molecular Profiling of Cancers: What about Gall Bladder Cancers? Cancer Gall Bladder
Workshop, Banaras Hindu University, Varanasi, India, April 2005.
5. Molecular Profiling of Cancers. Workshop on Trends in Oncology/ Human Genetics,
Moving Academy of Medicine and Biomedicine, Wardha, India, July 2005.
6. Genomics Applications in Diagnostics. Training Program in Specialized Aspects of
Biotechnology, UICT, Mumbai, India, August 2005.
7. Molecular Profiling of Cancers. Workshop on Trends in Oncology/ Human Genetics,
Moving Academy of Medicine and Biomedicine, Nagpur, India, September 2005.
8. Molecular Profiling of Cancers. Workshop on Trends in Oncology/ Human Genetics,
Moving Academy of Medicine and Biomedicine, Akole, India, January 2006.
9. Genome-wide search for Biomarkers in Cancer. Workshop on Recent Advances in
Medical, Plant and Enviro Biotechnologies, SIES-Indian Institute of Environment
Management, Navi Mumbai, India, January 2006.
10. Molecular Profiling of Cancers. Workshop on Trends in Oncology/ Human Genetics,
Moving Academy of Medicine and Biomedicine, Manipal, India, May, 2006.
11. Molecular Profiling of Cancers. Workshop on Trends in Oncology/ Human Genetics,
Moving Academy of Medicine and Biomedicine, Bhopal, India, June 2006.
12. Profiling for Prognosis: Working with Ores of Information? Seminar on Translational
Research, Tata Memorial Hospital, Mumbai, India, June 2006.
13. Microarrays in Prognosis: Signal or Noise? A Debate, 4th Tata Memorial Hospital-Women’s
Cancer Initiative (WCI) Conference, Tata Memorial Hospital, Mumbai, India, October 6-7,
2006.
14. Microarray data in Public Domain- a useful Give and TakeMicroarray Data Analysis
Workshop, Department of Bioinformatics, Sri Ramachandra Medical College, Chennai,
India, February 15-16, 2007.
15. Molecular Profiling of Cancers. Workshop on Trends in Oncology/ Human Genetics,
Moving Academy of Medicine and Biomedicine, Manipal, India, July 2007.
16. MCTP Representative,Advances in Genome Biology and Technology (AGBT),Marco
Island, FL, February 5-10, 2008.
17. Recurrent Gene Fusions in Prostate Cancer: A New Class of Biomarkers and
Therapeutic Targets.Roche,Branford, CT, May 19, 2008.
18. Detection of Gene Fusions in Cancer through the use of Transcriptome Sequencing- A New
Class of Mutations?Department of Pathology Research Seminar, University of Michigan
Ann Arbor, MI, September 11, 2008.
19. Transcriptome Sequencing to Detect Gene Fusions in CancerMulti-Institutional Prostate
SPORE Meeting, Baltimore, MD, February 3-, 2010.
20. Systematic Discovery of Cancer Gene Fusions using Paired End Transcriptome Sequencing
Cambridge Healthtech Institute’s 17th International Molecular Medicine Tri-Conference, San
Francisco, CA, February 3, 2010.
21. Oncomine to Oncoseq, Invited Presentation, Bioinformatics and Data mining,Stand up to
Cancer Meeting, Dallas, TX, February13, 2010.
22. Functional Genomics with High-Throughput Sequencing: Ideas for Personalized Medicine
Annual Research Summit, Michigan Center for Translational Pathology, Ann Arbor, MI,
May 18, 2010.
23. Clinical High throughput Sequencing to drive Personalized MedicineTranslational Cancer
Prevention and Biomarker Workshop,Mazumdar-Shaw Cancer Center, Bangalore, India,
February 13-17, 2011.