Chandan Kumar · Web viewCurriculum Vitae. Name: Chandan Kumar (Chandan Kumar-Sinha, in...

Curriculum Vitae

Name: Chandan Kumar (Chandan Kumar-Sinha, in publications)Present Title: Research Assistant ProfessorAddress: Michigan Center for Translational Pathology

1400 E Medical Center Drive, 5411 Cancer Center, Ann Arbor MI 48109

Telephone: Lab: 734 936 2592 Cell: 734 277 7096 Email: [email protected] Education 5/1987- 6/1990 B.Sc. (Honors) Zoology, Delhi University7/1990- 6/1992 M.Sc. Biotechnology, Madurai Kamaraj University, Madurai8/1992- 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 SitaInstitution: Indian Institute of Science, Bangalore, IndiaYear: 1999

Post-Doctoral Training

4/1999- 9/2003 Post-Doctoral Fellowship, Department of Pathology, University of Michigan, Ann Arbor, MIField: Cancer Genomics and Molecular BiologyMentor: Dr. Arul M Chinnaiyan, MD, PhDYears of Training: 4 years 4 months

Academic and Administrative Appointments

9/07/2003 Senior Research Scientist, Institute of Bioinformatics, Bangalore 2/17/2004 Scientific Officer E, Advanced Centre for Treatment, Research and

Education in Cancer (ACTREC), Navi Mumbai, India03/09/2007 Assistant Professor, Homi Bhabha National Institute, ACTREC, Navi

Mumbai, India08/06/2007 Research Lab Specialist Lead, Pathology Department, University of

Michigan10/01/2007 Research Assistant Professor, Pathology Department, University of

Michigan11/01/2007 Research Assistant Professor, Michigan Center for Translational

Pathology, University of Michigan

Chandan Kumar PhD 5/7/2023

mailto:[email protected]

Research Interests

I am interested in integrative functional-genomics of cancers using high-throughput genome and transcriptome analyses to develop cancer biomarkers and personalized therapeutic options. My scientific motto is that each cancer represents a unique genetic-environmental accident that shares hallmark molecular features with other cancers, as well as undergoes a private evolution- 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 mosNIH $202,602/yrHigh 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 Center 11/1/2011-10/31/2012 1.2 cal mosGI SPORE Career Development Program $50,000Targeting Tumor Specific Outlier Kinases through Kinome Profiling of Pancreatic Cancers- A Pilot Study for Personalized Treatment of Primary Human Tumor XenograftsGoals: 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/yrPersonalizing 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, triple negative. 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 mosDepartment of Defense $443,618/yrNational Functional Genomics CenterGoals: 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 mosDepartment of Defense $500,000/yrA Search for Gene Fusions/Translocations in Breast CancerSpecific 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 directsDiscovery of Recurrent Gene Fusions in Pancreatic Cancer using High-throughput SequencingGoals: 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- 2/2008Young 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 ofAssociation between HER2 and IGFBP2.Role: Principal Investigator

Department of Biotechnology, Govt. of India (PI: Kumar) 12/2005-12/2008INR 3,400,000 (~ USD 75,555) 100%Delineation of Prognostic Biomarkers of Progression of Cervical CancerRole: Principal Investigator

Department of Biotechnology, Govt. of India (PI: Dalal) 9/2006-9/2007INR 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) 6/2006-6/2007INR 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) 12/2005-2/2006Highthroughput Genotyping of Human Papillomaviruses in Cervical Cancer Biopsies of Patients at TMH using Type Specific Multiple Sequencing PrimersRole: Principal Investigator

PENDING

10/5/2011, 12-PAF01641 (PI: Chandan Kumar)Department of Health and Human Services, National Institutes of Health, RO1 MechanismRecurrent 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-USAMRAANational Functional Genomics Center-A Center for Genetic Origins of Cancer (CGOC) at the University of MichiganRole: 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-Investigator2/15/2011, 11-PAF04140 (PI: Ljungman, Radiation Oncology) Department of Health and Human Services, National Institutes of HealthMechanisms of Genotoxic Stress-regulated Gene Expression in Human Cells, Role: Co-Investigator

Honors and Awards

1990-1992 Department of Biotechnology (DBT, Govt. of India) Scholarship for MSc. Biotechnology

1992-1994 University Grants Commission (UGC), Government of India, Junior Research Fellowship for PhD

1994-1997 University Grants Commission (UGC), Government of India, Senior Research Fellowship for PhD

1997 International Society for Plant Molecular Biology (ISPMB) Travel Award2005-2008 Young Scientist Award, Science and Engineering Research Council, Department

of Science and Technology, Govt. of India2009-2010 Lustgarten Foundation Award for Pancreatic Cancer Research on “Discovery of

Recurrent Gene Fusions in Pancreatic Cancer using High-throughput Sequencing”2011 American 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 CommunicationLife Member: Indian Association of Cancer ResearchActive 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 of Cancer, 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

2009 Dan Robinson, University of California, San Diego2011 Vishal Kothari, Loma Linda Institute, California (from June 2011)

Thesis Committees

2007 Vishal 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

2010 Ming 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

2006-2010 Kavishwar 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

2010 Linda Ma, Medical Student, University of Michigan2011- Iris Wei, House Officer, Surgery, University of Michigan


Mentor, Graduate Students

2005-2007 Cheryl M. Travasso, Junior Research Fellow, ACTREC Fellowship, Cervical cancer gene expression profiling studies.

2005-2007 Aditi Galoda, Junior Research Fellow of Council for Scientific and Industrial Research, IGFBP2-HER2 signaling pathway in breast cancers.

2006-2007 Asha Thomas, Junior Research Fellow of Council for Scientific and Industrial Research, pursuing breast cancer microarray profiling using focused microarrays.

2009 Noah Wolfson PhD, University of Michigan2009 Joshua Regal MD PhD, University of Michigan

Mentor, Undergraduate Students

2004 Harshada Y Rane, Jawaharlal Nehru Centre for Advanced Scientific Research Summer Research (JNCASR) Fellow, MS Biotechnology, University of Mumbai

2005 Sukanya Suresh, M.S Applied Microbiology, PSG College of Arts and Science, Bharathiar University, Coimbatore.

2005 Krishna Kumar. S, B. Tech Biotechnology, Department of Biotechnology, Indian Institute Of Technology, Madras (IIT Madras), Tamilnadu.

2005 Chandrika N Deshpande, MS Biotechnology, Mysore. 2006 Rajiv Das Kangabam, MS Bioinformatics, Department of Bioinformatics, KSR

College of Arts and Science, Tamilnadu. 2006 Suchitra Venkatasubramani, MS Biotechnology, DY Patil Vidyapeeth. 2006 Sharath Poojary, MS Life Sciences. 2005-2006 Aditi Deshpande, MS Biotechnology, Project Assistant. 2008-2009 Aalisha Desai, University of Michigan Undergraduate Research Opportunity

Program (UROP)2008-2009 Haala Hai, University of Michigan Undergraduate Research Opportunity Program

(UROP)2008-2009 Balreet Kaur, University of Michigan Undergraduate Research Opportunity

Program (UROP)2008-2010 Han Li, University of Michigan Undergraduate Research Opportunity Program

(UROP)2008-2010 Peter Fullen, University of Michigan Undergraduate Research Opportunity

Program (UROP)2008-2009 Mah Jabeen Sidra, University of Michigan Undergraduate Research Opportunity

Program (UROP)2009-2010 Nikhil Patel, University of Michigan Undergraduate Research Opportunity

Program (UROP)2009-2010 Nikita Consul, University of Michigan Undergraduate Research Volunteer2009-2010 Chaitanya Malla, University of Michigan Undergraduate Research Volunteer2010-2011 Mei Mei, University of Michigan Undergraduate Research Opportunity Program

(UROP)2010-2011 Xin Cai, University of Michigan Undergraduate Research Opportunity Program

(UROP)


2010-2011 Joseph Mierzwa, University of Michigan Undergraduate Research Opportunity Program (UROP)

2010-2011 Cyril Mazhuvanchery, University of Michigan Undergraduate Research Opportunity Program (UROP)

2010-2011 Aditi Arora, University of Michigan Undergraduate Research Opportunity Program (UROP)

2010-2011 Tushar Shetty, University of Michigan Undergraduate Research Opportunity Program (UROP)

2010-2011 Julia Milton, University of Michigan Undergraduate Research Opportunity Program (UROP)

Course Lectures

2005 29th Annual Conference & CME of Mumbai Hematology Group, Tata Memorial Hospital, Faculty, Mumbai, India, March 19-20, 2005.

2006 Chairperson, Graduate Students Meeting, Session II, ACTREC, Tata Memorial Centre, Kharghar Navi Mumbai, India, September 23, 2006.

2006 Faculty and Member Scientific Committee, 4th Tata Memorial Hospital-Women’s Cancer Initiative (WCI) Conference, Mumbai, India, October 6-7, 2006.

2007 Junior Research Fellows Course Lecture: Gene Expression profiling by Microarrays

Host, International Visitors

August 2008 Nandan Deshpande, PhD student, Macquarie University, NSW, Australia, Analysis of Carbohydrate Metabolism Pathways by Microarrays. Aug 10- 28, 2008,

June-July 2009 Dr 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

2004-2007 Officer-in-Charge, Expression Profiling Committee, Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India

2004-2007 Advisor, DNA sequencing and Mutation Analysis Committee, Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India

2005-2006 Resource Person, Biology Olympiad Resource Generation Camp, Homi Bhabha Center for Science Education, Tata Institute of Fundamental Research

2005-2007 Member Secretary, Institutional Biosafety Committee Advanced 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

2006-2007 Convener “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 – present Member, Gastrointestinal Oncology program, Cancer Center, University of Michigan

2011- present Member, 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 Take Microarray 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 Cancer Multi-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 Medicine Translational Cancer Prevention and Biomarker Workshop, Mazumdar-Shaw Cancer Center, Bangalore, India, February 13-17, 2011.24. High-throughput Transcriptome Sequencing of Cancers: Ideas in Personalized Medicine 30th Annual Convention of Indian Association of Cancer Research Annual Meeting, Kolkata, India, February 4-6, 2011. 25. Personalized Cancer Genomics by High Throughput Sequencing: Challenges of Target Validation Qiagen Workshop, University of Michigan, June 1, 201126. Clinical High-Throughput Sequencing for Personalized Medicine: A Roadmap at Michigan Next-Generation Sequencing & Genomic Medicine Conference, IBC Drug Discovery & Diagnostic Development Week, August 1-3, 2011, San Francisco, CA.

Bibliography


(Name in publications, Chandan Kumar-Sinha,)

1. Chinnaiyan A.M., Huber-Lang M., Kumar-Sinha C., Barrette T.R., Shankar-Sinha S., Sarma V.J., Padgaonkar V.A., Ward P. A.. Molecular signatures of sepsis: multiorgan gene expression profiles of systemic inflammation. Am J Pathol. 2001; 159(4):1199-1209. PMID: 11583946 / PMCID: PMC1850525.2. Kumar-Sinha C., Varambally S., Sreekumar A., Chinnaiyan A. M.. Molecular cross-talk between the TRAIL and interferon signaling pathways. J Biol Chem. 2002; 277(1):575- 585. PMID: 11677236.3. Varambally S., Dhanasekaran S.M., Zhou M., Barrette T.R., Kumar-Sinha C., Sanda M.G.,

Ghosh D., Pienta K.J., Sewalt R.G., Otte A.P., Rubin M.A., Chinnaiyan A.M.. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature. 2002; 419(6907):624-629. PMID: 12374981.

4. Kumar-Sinha C., Ignatoski K.W., Lippman M.E., Ethier S.P., Chinnaiyan A. M.. Transcriptome analysis of HER2 reveals a molecular connection to fatty acid synthesis. Cancer Res. 2003 63(1):132-139. PMID: 12517789.

5. Kumar-Sinha C., Rhodes D.R., Yu J., Chinnaiyan A. M.. Prostate cancer biomarkers: a current perspective. Expert Rev Mol Diagn. 2003; 3(4):459-470. PMID: 12877385.6. Kumar-Sinha C., Chinnaiyan A. M.. Molecular markers to identify patients at risk for recurrence after primary treatment for prostate cancer. Urology 2003; 62 Suppl 1:19-35. PMID: 14747039.7. Peri S., Navarro J.D., Kristiansen T.Z., Amanchy R., Surendranath V., Muthusamy B., Gandhi T.K., Chandrika K.N., Deshpande N., Suresh S., Rashmi B.P., Shanker K., Padma N., Niranjan V., Harsha H.C., Talreja N., Vrushabendra B.M., Ramya M.A., Yatish A.J., Joy M., Shivashankar H.N., Kavitha M.P., Menezes M., Choudhury D.R., Ghosh N., Saravana R., Chandran S., Mohan S., Jonnalagadda C.K., Prasad C.K., Kumar-Sinha C., Deshpande K.S., Pandey A.. Human Protein Reference Database as a discovery resource for proteomics. Nucleic Acids Res. 2004; 32(Database issue):D497-501. PMID: 14681466 / PMCID: PMC308804.8. Kumar-Sinha C., Shah R.B., Laxman B., Tomlins S.A., Harwood J., Schmitz W., Conzelmann E., Sanda M.G., Wei J.T., Rubin M.A., Chinnaiyan A. M.. Elevated alpha- methylacyl-CoA racemase enzymatic activity in prostate cancer. Am J Pathol. 2004; 164(3):787-793. PMID: 14982833 / PMCID: PMC1613269.9. Albrecht E.A., Chinnaiyan A.M., Varambally S., Kumar-Sinha C., Barrette T.R., Sarma

J.V., Ward P. A.. C5a-induced gene expression in human umbilical vein endothelial cells. Am J. Pathol. 2004; 164(3):849-859. PMID: 14982839 / PMCID: PMC1613300.

10. Wu M., Wu Z.F., Kumar-Sinha C., Chinnaiyan A. M., Merajver S. D.. RhoC induces differential expression of genes involved in invasion and metastasis in MCF10A breast cells. Breast Cancer Res Treat. 2004; 84(1):3-12. PMID: 14999149.

11. Kumar-Sinha C., Chinnaiyan A.M.. A SLAMS dunk for cancer regulators. Nat Biotechnol. 2006; 24(5):524-526. PMID: 16680134.12. Kumar P.P., Purbey P.K., Sinha C.K., Notani D., Limaye A., Jayani R.S., Galande S.. Phosphorylation of SATB1, a global gene regulator, acts as a molecular switch regulating its transcriptional activity in vivo. Molecular Cell 2006; 22: 231–243. PMID: 16630892.13. Kumar-Sinha C., Tomlins S.A., Chinnaiyan A. M.. Evidence of recurrent gene fusions in common epithelial tumors. Trends Mol Med. 2006; 12(11):529-536. PMID: 17011825.


14. Hanauer D.A., Rhodes D.R., Sinha-Kumar C., Chinnaiyan AM. Bioinformatics approaches in the study of cancer. Curr Mol Med. 2007; 7(1):133-141. PMID: 17311538.15. Kim J.H., Dhanasekaran S.M., Mehra R., Tomlins S.A., Gu W., Yu J., Kumar-Sinha C., Cao X., Dash A., Wang L., Ghosh D., Shedden K., Montie J.E., Rubin M.A., Pienta K.J., Shah R.B., Chinnaiyan A. M.. Integrative analysis of genomic aberrations associated with prostate cancer progression. Cancer Res. 2007; 67(17):8229-8239. PMID: 17804737.16. Travasso C.M., Anand M., Samarth M., Deshpande A., Kumar-Sinha C.*. Human papillomavirus genotyping by multiplex pyrosequencing in cervical cancer patients from India. J Biosci. 2008; 33(1):73-80. PMID: 18376072.17. Kumar-Sinha C., Tomlins S.A., Chinnaiyan A.M.. Recurrent gene fusions in prostate cancer. Nat Rev Cancer. 2008; 8(7):497-511. PMID: 18563191 / PMCID: PMC2711688.18. Han B., Mehra R., Dhanasekaran S.M., Yu J., Menon A., Lonigro R.J., Wang X., Gong Y., Wang L., Shankar S., Laxman B., Shah R.B., Varambally S., Palanisamy N., Tomlins S.A., Kumar-Sinha C.*, Chinnaiyan A.M.*. A fluorescence in situ hybridization screen for E26 transformation-specific aberrations: identification of DDX5-ETV4 fusion protein in prostate cancer. Cancer Res. 2008; 68(18):7629-7637. PMID: 18794152 / PMCID: PMC2760292.*Shared Senior Authorship

19. Varambally S., Cao Q., Mani R.S., Shankar S., Wang X., Ateeq B., Laxman B., Cao X., Jing X., Ramnarayanan K., Brenner J.C., Yu J., Kim J.H., Han B., Tan P., Kumar-Sinha C., Lonigro R.J., Palanisamy N., Maher C.A., Chinnaiyan A. M.. Genomic loss of microRNA- 101 leads to overexpression of histone methyltransferase EZH2 in cancer. Science. 2008; 322(5908):1695-1699. PMID: 19008416 / PMCID: PMC2684823.20. Maher C.A.*, Kumar-Sinha C.*, Cao X., Kalyana-Sundaram S., Han B., Jing X., Sam L., Barrette T., Palanisamy N., Chinnaiyan A. M.. Transcriptome sequencing to detect gene fusions in cancer. Nature. 2009; 458(7234):97-101. PMID: 19136943 / PMCID: PMC2725402.*Equal contribution

21. Maher C.A., Palanisamy N., Brenner J.C., Cao X., Kalyana-Sundaram S., Luo S., Khrebtukova I., Barrette T.R., Grasso C., Yu J., Lonigro R.J., Schroth G., Kumar-Sinha C., Chinnaiyan A. M.. Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci USA. 2009; 106(30):12353-12358. PMID: 19592507 / PMCID: PMC2708976.22. Wagholikar K., Venkatraman P., Vijayaraghavan S. and Kumar-Sinha C.*. Sum-based meta-analytical enrichment of gene expression data to identify pathway signatures of cancers. J Cancer Therapy 2010; 1:36-42 doi:10.4236/jct.2010.11006 Published Online March 201023. Palanisamy N., Ateeq B., Kalyana-Sundaram S., Pflueger D., Ramnarayanan K., Shankar S., Han B., Cao Q., Cao X., Suleman K., Kumar-Sinha C., Dhanasekaran S., Chen Y., Esgueva R., Banerjee S., LaFargue C., Demichelis F., Moeller P., Bismar T., Kuefer R., Tomlins S.A., Varambally S., Rubin M. A., Maher C. A. & Chinnaiyan A.M.# Rearrangements of the RAF Kinase Pathway in Prostate Cancer. Nat Med. 2010; 16(7): 793-798. PMID: 20526349 / PMCID 2903732.


24. Sam L.T., Lipson D., Raz T., Cao X., Thompson J., Milos P.M., Robinson D., Chinnaiyan A.M. *, Kumar-Sinha C. *, Maher C. A.*. A Comparison of Single Molecule and Amplification Based Sequencing of Cancer Transcriptomes. PLoS One. 2011; 6(3):e17305. PMID: 21390249 / PMCID: 3046973.

*Shared Senior Authorship

25. Mehra R.*, Kumar-Sinha C.*, Shankar S.*, Lonigro R.J., Jing X., Philips N.E., Siddiqui J., Han B., Cao X., Smith D.C., Shah R.B., Chinnaiyan A.M., Pienta K.J., Characterization of bone metastases from rapid autopsies of prostate cancer patients. Clinical Cancer Research 2011 May 9. [Epub ahead of print] PMID: 21555375*Equal Contribution

26. Notani D., Ramanujam P.L., Kumar P.P., Gottimukkala K.P., Kumar-Sinha C., and Galande S. N-terminal PDZ-like domain of chromatin organizer SATB1 contributes towards its function as transcription regulator. J Biosci. 2011 Aug;36(3):461-9.27. Robinson D.R., Kalyana-Sundaram S., Wu Y.-M., Shankar S., Cao X., Asangani I.A., Ateeq

B., Maher C.A., Iyer M., Grasso C.S., Lonigro R.J., Quist M., Siddiqui J., Mehra R., Giordano T.J., Sabel M.S., Kleer C.G., Palanisamy N., Natrajan R., Lambros M.B., Reis-Filho J.S., Kumar-Sinha C*., and Arul M. Chinnaiyan*. Functionally Recurrent Rearrangements of the MAST Kinase and Notch Gene Families in Breast Cancer. Nature Medicine, 2011 Advance Online Publication doi:10.1038/nm.2580*Shared Senior Authorship

28. Kalyana-Sundaram S.*, Kumar-Sinha C.*, .Shankar S., Robinson D., Wu Y.-M., Cao X., Prensner J.R., Barrette T., Dhanasekaran S.M., Palanisamy N., and Chinnaiyan A. M.. Expression Profiling of Pseudogenes by Transcriptome Sequencing Reveals Tissue-Type and Cancer-Specific Signatures. Manuscript under review at Cell.*Equal Contribution

29. Kumar-Sinha C., Chinnaiyan A.M. Recurrent Gene Fusions in Epithelial Cancers: An Update. Annual Review of Pathology: Mechanisms of Disease, Volume 8. March 2012 Invited Review, Manuscript in preparation

30. Kumar-Sinha C. New technologies in Molecular Characterization of Pancreatic Cancer Molecular Genetics of Pancreatic Cancer, Eds. Diane Simeone and Anirban Maitra, March 2012. Book Chapter, Manuscript in preparation.

Abstracts

1. Chandan Kumar, Lakshmi Sita G. Cloning of Homeo-domain from Somatic Embryos of Sandalwood. International Plant & Animal Genome V Conference 1997, San Diego. International Society of Plant Molecular Biology (ISPMB) Travel Award.

2. Kumar-Sinha C., Ignatoski K.W., Lippman M. E., Ethier S.P., Chinnaiyan A. M.. Transcriptome Analysis of HER2 Reveals a Molecular Connection to Fatty Acid Synthesis. Proceedings of the AACR, Volume 43, March 2002, San Francisco, USA.


3. Albrecht E., Varambally S., Kumar-Sinha C., Barrette T.R., Sarma J.V.,Ward P.A.. Temporal endothelial gene expression in response to C5a. FASEB J 16 (4): A200-A200 Part 1 Mar 20, 2002

4. Kleer C.G., Zhang Y., Kumar-Sinha C, Chinnaiyan A.M., Merajver S.D.. Characterization of WISP3 expression, a novel tumor suppressor gene of inflammatory breast cancer, in normal breast and breast disease. Platform presentation, United States and Canadian Academy of Pathology (USCAP) Conference March 2003, Toronto, Canada.

5. Mei Wu, Zhi-Fen Wu, Kumar-Sinha C, Chinnaiyan AM, Sofia D. Merajver. RhoC over-expression induces differential expression of genes involved in invasion and metastasis in MCF10A breast cells. Proceedings of the AACR, Volume 45, March 2004

6. Bhagavathula N., Kumar-Sinha C, Kamalakar C. Nerusu, James Varani. Rosiglitazone- mechanism of action in hyperproliferative disorders of skin. Proceedings of the AACR, Volume 45, March 2004

7. Dimple Notani, Pawan Kumar, Kumar-Sinha C and Sanjeev Galande. PDZ like Signaling Domain dictates the regulatory function of SATB1, the Chromatin Organizer containing MAR binding domain and Homeodomain. Poster presentation at International EMBO Workshop, Center for Cellular and Molecular Biology (CCMB), Hyderabad, India, Dec 14, 2005

8. Kumar-Sinha C, Travasso C, Inamdar M, Tongaonkar HB, Chinoy RF, Parulekar S Gene expression patterns of cervical cancer: a preliminary assessment. 25th Annual Convention of the Indian Association for Cancer Research (IACR) & Silver jubilee symposium on ‘Molecular Profiling and Cancer Management’ Feb 15 - 18, 2006

9. Kumar-Sinha C*, Maher CA*, Cao X, Kalyana-Sundaram S, Bo Han B, Jing X, Sam L, Barrette T, Palanisamy N, & Chinnaiyan AM. Transcriptome sequencing to detect gene fusions in cancer. 2008 Cancer Research Symposium, University of Michigan, Nov 14, 2008

10. Kumar-Sinha C*, Maher CA*, Cao X, Kalyana-Sundaram S, Bo Han B, Jing X, Sam L, Barrette T, Palanisamy N, & Chinnaiyan AM. Integrative transcriptome sequencing to discover gene fusions in cancer. 10th annual Advances in Genome Biology and Technology (AGBT), Feb 4-7, 2009

11. Rohit Mehra, Bo Han, Kumar-Sinha C., Xiaojun Jing, Xuhong Cao, Jill Granger, Sunita Shanker, David C. Smith, Rajal B. Shah, Kenneth J. Pienta, Arul M. Chinnaiyan. Identification and characterization of viable bone metastases from rapid autopsies of prostate cancer patients. United States and Canadian Academy of Pathology (USCAP) 2010, Washington DC, March20-26, 2010

12. Ma L., Shankar S., Kalyana-Sundaram S., Robinson D., Cao X., Simeone D.M., Chinnaiyan A.M., Kumar-Sinha C.*. Identification of Therapeutic Targets in pancreatic Cancer through Highthroughput Transcriptome Sequencing Analysis. 22nd Annual Cancer Research Symposium, University of Michigan, Ann Arbor, Nov12, 2010

13. Kumar-Sinha C.*, Shankar S., Ma L., Robinson D., Kalyana-Sundaram S., Chinnaiyan A. M.. High-throughput Transcriptome Sequencing of Cancers: Ideas in Personalized Medicine. 30TH Annual Convention of Indian Association for Cancer Research and International Symposium on Signaling Network and Cancer, Feb6-9, 2011, Kolkata, India


14. Kumar-Sinha C.*, Shankar S., Ma L., Robinson D., Cao X., Kalyana-Sundaram S., Chinnaiyan A. M.. Kinome analysis of cancers by high-throughput transcriptome sequencing: Ideas in personalized medicine. 102nd Annual Meeting of American Association for Cancer Research, April 2-6, 2011, Orlando, Florida.

15. Kothari V., Wei I., Robinson D., Shankar S., Kalyana-Sundaram S., Simeone D.M, Chinnaiyan A.M., Kumar-Sinha C*. Inhibiting Polo-Like Kinases for the treatment of Pancreatic Cancer: Targeting Kinase Outliers for Personalized Therapy. University of Michigan Comprehensive Cancer Center, Fall Cancer Research Symposium, November 2011

16. Grasso C.S., Robinson D.R., Wu Y.-M., Dhanasekaran S.M., Quist M.J., Cao X., Jing X., Lonigro R.J., Brenner J.C., Chun S.Y., Prensner J.R., Siddiqui J., Sam L., Iyer M., Anstett M., Barrette T., Kumar-Sinha C., Varambally S., Mehra R., Palanisamy N., Rhodes D.R., Pienta K.J., Chinnaiyan A.M., Tomlins S.A. Exome sequencing and integrative mutational profiling of lethal castrate resistant prostate cancer. University of Michigan Comprehensive Cancer Center, Fall Cancer Research Symposium, November 2011

17. Robinson D.R., Kalyana-Sundaram S., Wu Y.-M., Shankar S., Cao X., Asangani I.A., Ateeq B., Maher C.A., Iyer M., Grasso C.S., Lonigro R.J., Quist M., Siddiqui J., Mehra R., Giordano T.J., Sabel M.S., Kleer C.G., Palanisamy N., Natrajan R., Lambros M.B., Reis-Filho J.S., Kumar-Sinha C*., and Arul M. Chinnaiyan*. Functionally Recurrent Rearrangements of the MAST Kinase and Notch Gene Families in Breast Cancer. University of Michigan Comprehensive Cancer Center, Fall Cancer Research Symposium, November 2011

18. Kalyana-Sundaram S.*, Kumar-Sinha C.*, .Shankar S., Robinson D., Wu Y.-M., Cao X., Prensner J.R., Barrette T., Dhanasekaran S.M., Palanisamy N., and Chinnaiyan A. M.. Expression profiling of pseudogenes by transcriptome sequencing reveals tissue-type and cancer-specific signatures. University of Michigan Comprehensive Cancer Center, Fall Cancer Research Symposium, November 2011


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