Uma Chandran, PhD, MSIS

Research Interests: 
  • Genomic data mining
  • Next Generation Sequencing data analysis
  • Integrative analysis of The Cancer Genome Atlas Project (TCGA)
  • Development of computing infrastructure for large genomics datasets
Research Associate Professor, Biomedical Informatics
Co-Director, Cancer Boinformatics Services, UPMC Hillman Cancer Center
Publications: 

Gau DM, Lesnock JL, Hood BL, Bhargava R, Sun M, Darcy K, Luthra S, Chandran U, Conrads TP, Edwards RP, Kelley JL, Krivak TC, Roy P. (2015). BRCA1 deficiency in ovarian cancer is associated with alteration in expression of several key regulators of cell motility – A proteomics study. Cell Cycle, 14(12), 1884–1892. http://doi.org/10.1080/15384101.2015.1036203 PMID: 25927284 PMCID: PMC4614952

Concha-Benavente F, Srivastava RM, Trivedi S, Lei Y, Chandran U, Seethala RR, Freeman GJ, Ferris RL. Identification of the Cell-Intrinsic and -Extrinsic Pathways Downstream of EGFR and IFNy That Induce PD-L1 Expression in Head and Neck Cancer. Cancer Research. 2016 Mar 1;76(5):1031-43. PMID:26676749.

Frahm KA, Peffer ME, Zhang JY, Luthra S, Chakka AB, Couger MB, Chandran UR, Monaghan AP, DeFranco DB. Research Resource: The Dexamethasone Transcriptome in Hypothalamic Embryonic Neural Stem Cells. Molecular Endocrinology (Baltimore, Md.). 2016 Jan;30(1):144-54. PMID: 26606517

Chandran, U. R., Luthra, S., Santana-Santos, L., Mao, P., Kim, S.-H., Minata, M., Li J, Benos PV, DeWang M, Hu B, Cheng SY, Nakano I, Sobol RW. (2015). Gene expression profiling distinguishes proneural glioma stem cells from mesenchymal glioma stem cells. Genomics Data, 5, 333–336. http://doi.org/10.1016/j.gdata.2015.07.007 PMID: 26251826 PMCID: PMC4523279

Liao S, Hartmaier RJ, McGuire KP, Puhalla SL, Luthra S, Chandran UR, Ma T, Bhargava R, Modugno F, Davidson NE, Benz S, Lee AV, Tseng GC, Oesterreich S. (2015). The molecular landscape of premenopausal breast cancer. Breast Cancer Research : BCR, 17(1), 104. http://doi.org/10.1186/s13058-015-0618-8 PMID: 26251034 PMCID: PMC4531812

Geskin A, Legowski E, Chakka A, Chandran UR, Barmada MM, LaFramboise WA, Berg J, Jacobson RS. (2015). Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center. PLoS ONE, 10(6), e0131166. http://doi.org/10.1371/journal.pone.0131166 PMID: 26115441 PMCID: PMC4483235

Manohar R, Li Y, Fohrer H, Guzik L, Stolz DB, Chandran UR, LaFramboise WA, Lagasse E.  (2015). Identification of a candidate stem cell in human gallbladder. Stem Cell Research, 14(3), 258–269. http://doi.org/10.1016/j.scr.2014.12.003  PMID:  25765520 PMCID: PMC4439375

McDade, K. K., Chandran, U., & Day, R. S. (2015). Improving Cancer Gene Expression Data Quality through a TCGA Data-Driven Evaluation of Identifier Filtering. Cancer Informatics, 14, 149–161.  PMID: 26715829 PMCID: PMC4686346 DOI: 10.4137/CIN.S33076

McDade KK, Chandran U, Day RS. Improving Cancer Gene Expression Data Quality through a TCGA Data-Driven Evaluation of Identifier Filtering. Cancer Informatics, 2015. PMID: 26715829 PMCID: PMC4686346

Sikora MJ, Cooper KL, Bahreini A, Luthra S, Wang G, Chandran UR, Davidson NE, Dabbs DJ, Welm AL, Oesterreich S. (2014). Invasive lobular carcinoma cell lines are characterized by unique estrogen-mediated gene expression patterns and altered tamoxifen response. Cancer Research, 74(5), 1463–1474. http://doi.org/10.1158/0008-5472.CAN-13-2779 PMID: 24425047 PMCID: PMC3955299

Maxwell GL, Allard J, Gadisetti CV, Litzi T, Casablanca Y, Chandran U, Darcy KM, Levine DA, Berchuck A, Hamilton CA, Conrads TP, Risinger JI. Transcript expression in endometrial cancers from Black and White patients. Gynecol Oncol. 2013 Jul; 130(1):169-73. PMID: 23603370. doi: 10.1016/j.ygyno.2013.04.017

Risinger JI, Allard J, Chandran U, Day R, Chandramouli GV, Miller C, Zahn C, Oliver J, Litzi T, Marcus C, Dubil E, Byrd K, Cassablanca Y, Becich M, Berchuck A, Darcy KM, Hamilton CA, Conrads TP, Maxwell GL. Gene expression analysis of early stage endometrial cancers reveals unique transcripts associated with grade and histology but not depth of invasion. Front Oncol. 2013 Jun 17; 3:139. PMID: 23785665. PMCID: PMC3683664. doi: 10.3389/fonc.2013.00139

Mao P, Joshi K, Li J, Kim SH, Li P, Santana-Santos L, Luthra S, Chandran UR, Benos PV, Smith L, Wang M, Hu B, Cheng SY, Sobol RW, Nakano I. Mesenchymal glioma stem cells are maintained by activated glycolytic metabolism involving aldehyde dehydrogenase 1A3. Proc Natl Acad Sci U S A. 2013 May 21;110(21):8644-9. PMID: 23650391. PMCID: PMC3666732. doi: 10.1073/pnas.1221478110

Krill-Burger JM, Lyons MA, Kelly LA, Sciulli CM, Petrosko P, Chandran UR, Kubal MD, Bastacky SI, Parwani AV, Dhir R, LaFramboise WA. Renal cell neoplasms contain shared tumor type-specific copy number variations. Am J Pathol. 2012 Jun; 180(6):2427-39. PMID: 22483639. PMCID: PMC3378847. doi: 10.1016/j.ajpath.2012.01.044

McDade K, Day RS, Chandran U, Lisovich A. Optimal Probeset Filtering Using Proteomic-Transcriptomic Correlations. In: Proceedings of the AMIA Joint Summit on Translational Science; 2012 Mar 19-21; San Francisco, CA.

Day RS, McDade K, Grover H, Luthra S, Chandran U, Lisovich A. Bioinformatic Data Integration to Assess Data Preprocessing. In: Proceedings of the AMIA Joint Summit on Translational Science; 2012 Mar 19-21; San Francisco, CA.

LaFramboise WA, Dhir R, Kelly LA, Petrosko P, Krill-Burger JM, Sciulli CM, Lyons-Weiler MA, Chandran UR, Lomakin A, Masterson RV, Marroquin OC, Mulukutla SR, McNamara DM. Serum protein profiles predict coronary artery disease in symptomatic patients referred for coronary angiography. BMC Med. 2012 Dec 5; 10:157. PMID: 23216991. PMCID: PMC3566965. doi: 10.1186/1741-7015-10-157

Li J, Luthra S, Wang XH, Chandran UR, Sobol RW. Transcriptional profiling reveals elevated Sox2 in DNA polymerase ß null mouse embryonic fibroblasts. Am J Cancer Res. 2012; 2(6):699-713. Epub 2012 Nov 20. PMID: 23226616. PMCID: PMC3512183

Maxwell GL, Hood BL, Day R, Chandran U, Kirchner D, Kolli VS, Bateman NW, Allard J, Miller C, Sun M, Flint MS, Zahn C, Oliver J, Banerjee S, Litzi T, Parwani A, Sandburg G, Rose S, Becich MJ, Berchuck A, Kohn E, Risinger JI, Conrads TP. Proteomic analysis of stage I endometrial cancer tissue: identification of proteins associated with oxidative processes and inflammation. Gynecologic oncology. 2011 Jun 1; 121 (3):586-94. Epub 2011 Apr 1. PMID: 21458040. doi: 10.1016/j.ygyno.2011.02.031

Boyd LB, Hunicke-Smith SP, Stafford GA, Freund ET, Ehlman M, Chandran U, Dennis R, Fernandez AT, Goldstein S, Steffen D, Tycko B, Klemm JD. The caBIG® Life Science Business Architecture Model. Bioinformatics. 2011 May 15; 27(10):1429-35. Epub 2011 Mar 29. PMID: 21450709. PMCID: PMC3087952. doi: 10.1093/bioinformatics/btr141.

Day RS, McDade KK, Chandran UR, Lisovich A, Conrads TP, Hood BL, Kolli VS, Kirchner D, Litzi T, Maxwell GL. (2011). Identifier mapping performance for integrating transcriptomics and proteomics experimental results. BMC Bioinformatics, 12, 213. http://doi.org/10.1186/1471-2105-12-213 PMID: 21619611 PMCID: PMC3124437

Manohar R, Komori J, Guzik L, Stolz DB, Chandran UR, LaFramboise WA, Lagasse E. Identification and expansion of a unique stem cell population from adult mouse gallbladder. Hepatology. 2011 Nov; 54(5):1830-41. PMID: 21793026. PMCID: PMC3205206 doi: 10.1002/hep.24568

Bartholow TL, Becich MJ, Chandran UR, Parwani AV. Immunohistochemical staining of slit2 in primary and metastatic prostatic adenocarcinoma. Translational oncology. 2011 Oct; 4(5):314-20. PMID: 21966548. PMCID: PMC3162306

Bartholow TL, Chandran UR, Becich MJ, Parwani AV. Immunohistochemical profiles of claudin-3 in primary and metastatic prostatic adenocarcinoma. Diagn Pathol. 2011 Jan 21;6:12. PMID: 21255442. PMCID: PMC3033791. doi: 10.1186/1746-1596-6-12

Bartholow TL, Chandran UR, Becich MJ, Parwani AV. Immunohistochemical staining of radixin and moesin in prostatic adenocarcinoma. BMC Clin Pathol. 2011 Jan 14;11:1. PMID: 21235778 PMCID: PMC3029218 doi: 10.1186/1472-6890-11-1

Lisovich A, Chandran UR, Lyons-Weiler MA, LaFramboise WA, Brown AR, Jakacki RI, Pollack IF, Sobol RW. (2011). A novel SNP analysis method to detect copy number alterations with an unbiased reference signal directly from tumor samples. BMC Medical Genomics, 4, 14. http://doi.org/10.1186/1755-8794-4-14 PMID: 21269491 PMCID: PMC3041647

Chang G, Xu S, Dhir R, Chandran U, O'Keefe DS, Greenberg NM, Gingrich JR. Hypoexpression and epigenetic regulation of candidate tumor suppressor gene CADM-2 in human prostate cancer. Clin Cancer Res. 2010 Nov 15; 16(22):5390-401. Epub 2010 Nov 9. PMID: 21062931. PMCID: PMC3541035. doi: 10.1158/1078-0432.CCR-10-1461.

AEscamilla-Hernandez, R., Little-Ihrig, L., Orwig, K. E., Yue, J., Chandran, U., & Zeleznik, A. J. (2008). Constitutively Active Protein Kinase A Qualitatively Mimics the Effects of Follicle-Stimulating Hormone on Granulosa Cell Differentiation. Molecular Endocrinology, 22(8), 1842–1852. http://doi.org/10.1210/me.2008-0103 PMID: 18535249 PMCID: PMC2725770

Monzon FA, Hagenkord JM, Lyons-Weiler MA, Balani JP, Parwani AV, Sciulli CM, Li J, Chandran UR, Bastacky SI, Dhir R. Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors. Modern Pathology : An Official JouCopyrnal of The United States and Canadian Academy of Pathology, Inc. 2008 May;21(5):599-608.  PMID: 18246049 DOI: 10.1038/modpathol.2008.20

Yin M, Bastacky S, Chandran U, Becich MJ, Dhir R. Prevalence of incidental prostate cancer in the general population: a study of healthy organ donors. The Journal of Urology. 2008 Mar;179(3):892-5; discussion 895. PMID: 18207193 DOI: 10.1016/j.juro.2007.10.057

Chandran UR, Lyons-Weiler J, Sciulli C, Monzon FA. Informatics requirements of a high throughput genomics laboratory. AMIA Summit on Translational Bioinformatics. 2008;(0).

Chandran UR, Ma C, Dhir R, Bisceglia M, Lyons-Weiler J, Liang W, Michalopoulos GK, Becich MJ, Monzon FA. Gene expression profiles of metastatic prostate cancer reveals disregulation of specific molecular pathways. BMC Cancer. 2007;7(0):64. PMID: 17430594 PMCID: PMC1865555

Chiosea S, Jelezcova E, Chandran U, Luo J, Mantha G, Sobol RW, Dacic S. Overexpression of Dicer in precursor lesions of lung adenocarcinoma. Cancer research. 2007 Mar 1;67(5):2345-50. PMID: 17332367 DOI: 10.1158/0008-5472.CAN-06-3533

Kelavkar UP, Harya NS, Hutzley J, Bacich DJ, Monzon FA, Chandran U, Dhir R, O'Keefe DS. DNA methylation paradigm shift: 15-lipoxygenase-1 upregulation in prostatic intraepithelial neoplasia and prostate cancer by atypical promoter hypermethylation. Prostaglandins & other lipid mediators. 2007 Jan;82(1):185-97. PMID: 17164146 DOI: 10.1016/j.prostaglandins.2006.05.015

Kelavkar, U., Lin, Y., Landsittel, D., Chandran, U., & Dhir, R. (2006). The yin and yang of 15-lipoxygenase-1 and delta-desaturases: Dietary omega-6 linoleic acid metabolic pathway in prostate. Journal of Carcinogenesis, 5, 9. http://doi.org/10.1186/1477-3163-5-9 PMID: 16566819 PMCID: PMC1440856

Chiosea S, Jelezcova E, Chandran U, Acquafondata M, McHale T, Sobol RW, Dhir R. Up-regulation of dicer, a component of the MicroRNA machinery, in prostate adenocarcinoma. The American journal of pathology. 2006 Nov;169(5):1812-20. PMID 17071602 PMCID: PMC1780192

Shah UZ, Dhir R, Gollin SM, Chandran UR, Lewis D, Acquafondata M, Pflug BR. Fatty Acid Synthase Gene Expression Amplification in Prostate Adenocarcinoma. Hum Pathol. 2006;4(0):401-409.

Chandran, U. R., Dhir, R., Ma, C., Michalopoulos, G., Becich, M., & Gilbertson, J. (2005). Differences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors. BMC Cancer, 5, 45. http://doi.org/10.1186/1471-2407-5-45 PMID: 15892885 PMCID: PMC1173092

Varambally S, Yu J, Laxman B, Rhodes DR, Mehra R, Tomlins SA, Shah RB, Chandran U, Monzon FA, Becich MJ, Wei JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM. Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer cell. 2005 Nov;8(5):393-406. PMID: 16286247

Chandran U, Monzon FA, Becich MJ, Gilbertson J. A new pathology biomarker laboratory. Proc. Medinfo. (CD). 2004;(0):1546.

Chandran UR, DeFranco DB. Regulation of gonadotropin-releasing hormone gene transcription. Behavioural Brain Research. 1999;105(0):29-36. PMID: 10553688

Chandran UR, Warren BS, Baumann CT, Hager GL, DeFranco DB. The glucocorticoid receptor is tethered to DNA-bound Oct-1 at the mouse GnRH distal negative glucocorticoid response element. J. Biol. Chem. 1999;274(0):2372-2378. PMID: 9891005

Attardi B, Tsujii T, Friedman R, Zeng Z, Roberts JL, Dellovade T, Pfaff D, Chandran UR, DeFranco DB. Glucocorticoid repression of gonadotropin-releasing hormone gene expression and secretion in morphologically distinct subpopulations of GT1-7 cells. Mol. Cell. Endocrinol. 1997;131(0):241-255. PMID: 9296383

Chandran UR, Attardi B, Friedman R, Zheng ZW, Roberts JL, DeFranco DB. Glucocorticoid repression of the mouse gonadotropin-releasing hormone gene is mediated by promoter elements that are recognized by heteromeric complexes containing glucocorticoid receptor. J. Biol. Chem.. 1996;271(0):20412-20420. PMID: 8702778

DeFranco DB, Madan AP, Tang Y, Chandran UR, Xiao N, Yang J. Nucleocytoplasmic shuttling of steroid receptors. In Vitamins and Hormones. Academic Press. 1994;51(0):315-338. PMID: 7483326

Chandran UR, Attardi B, Friedman R, Dong KW, Roberts JL, DeFranco DB. Glucocorticoid receptor-mediated repression of gonadotropin-releasing hormone promoter activity in GT1 hypothalamic cell lines. Endocrinol. 1994;134(0):1467-1474. PMID: 8119188

 DeFranco DB, Attardi B, Chandran UR. Glucocorticoid receptor-mediated repression of GnRH gene expression in a hypothalamic GnRH-secreting neuronal cell line. IN Brain Corticosteroid Receptors, Studies on the Mechanism Function, and Neurotoxicity of Corticosteroid Action. Annals of the New York Academy of Sciences. 1994;746(0):473-475.

Chandran UR, DeFranco DB. Internuclear migration of chicken progesterone receptor, but not SV40 large tumor antigen, in transient heterokaryons. Mol. Endocrinol. 1992;6(0):837-844.

Dr. Chandran's Summary of Research

Cancer Bioinformatics Services

Health Sciences Core Research Facilities

Biography:

I have extensive experience in both bench research and bioinformatics and co-direct the Cancer Bioinformatics Service (CBS), a translational core service at the UPMC Hillman Cancer Center. CBS is an interdisciplinary collaboration between my core team, the Department of Biomedical Informatics faculty, UPMC Hillman Cancer Center, the Institute for Personalized Medicine, the Pittsburgh Supercomputing Center and the University of Pittsburgh's Simulation and Modeling Center. The CBS aims are to 1) provide data analysis, 2) develop high performance computing (HPC) infrastructure and 3) develop research databases to integrate clinical and genomic data for biomarker discovery. I have deep experience working with all genomic platforms and applications including next generation sequencing (NGS) based RNA Seq, Whole Exome Seq (WXS) and Whole Genome Seq (WGS). I have also performed integrative analysis across multiple platforms and from large consortia datasets such as The Cancer Genome Atlas (TCGA) project. I am a key member of several data science projects in DBMI including the Pittsburgh Genome Resource Repository (PGRR), a regulatory, hardware and software infrastructure for TCGA data and the PACURE projects in breast and lung cancers. CBS supports all CCCG's disease specific programs and has performed somatic variant analysis in melanoma, lung, mesothelioma and renal cell cancers, copy number analysis to understand the differences and similarities between pediatric gliomas to adult gliomas, and RNA seq expression and integrative analysis of TCGA breast tumor samples. My team of analysts and I also support non-cancer genomic studies including development of methods for de novo transcriptome assembly. The combination of experience in bench science and bioinformatics allows me to not only provide data analysis services but also biological insight into the results of high throughput data such as integrative analysis of ChIP Seq and RNA seq data. We have partnered closely with the PSC and SaM to develop the HPC infrastructure to meet the computational demands of next generation sequencing analysis and have been awarded NSF's XSEDE award for computation and storage. With this team approach to bioinformatics, I have built a shared resource which can quickly meet the bioinformatics requirements of rapidly changing genomics landscape and a computing infrastructure which scales easily to terabytes of data.

Research Interests:
Genomic data mining
Next Generation Sequencing data analysis
Integrative analysis of The Cancer Genome Atlas Project (TCGA)
Development of computing infrastructure for large genomics datasets
Academic Appointments: 
12/2015 - present
Research Associate Professor, Department of Biomedical Informatics, University of Pittsburgh
12/2015 - present  
Co-director, Cancer Bioinformatics Services, UPMC Hillman Cancer Center, University of Pittsburgh
Director, Genomics Analysis Core (GAC), University of Pittsburgh
Grants & Contracts: 
02/1/2016 - 01/31/2017
NIH 5R01HD072189
Molecular Bases Committing Primate Spermatogonia to a Pathway of Differentiation
Role: Co-Investigator
06/1/2015 - 05/31/2018
PA DOH SAP4100070287
Big Data for Better Health (BD4BH) in Pennsylvania
Role: Co-Investigator
07/15/2013 - 06/30/2017
NIH 5R01DK099320
Regulation of HNF4 in Hepatic Failure in Cirrhosis
Role: Co-Investigator
07/1/2006 - 06/30/2018
NIH P50 CA121973
Spore in Skin Cancer
Role: Co-Investigator
09/1/1998 - 01/31/2017
NIH 5R01NS037704
Molecular Markers as Predictors of Outcome in Gliomas
Role: Research Associate
09/10/1997 - 07/31/2020
NIH/NCI 2P30CA047904
Cancer Center Support (CCSG)
Role: Core Lead
12/18/1996 - 02/28/2019
NIH 5R01CA186780
Roles of EAF2 in Androgen Action in the Prostate
Role: Co-Investigator
Teaching Activities: 
2013 - present   Intro to Bioinformatics
03/2007 - present   Introduction to Microarray Analysis
07/2002 - present   Introduction to Bioinformatics to Pathology Residents
Service Activities: 
Department
present Training Program Member, Training Program Committee
Other
present Reviewer, Pathology Informatics
present

Reviewer, AMIA conference on Translational Bioinformatics

Presentations: 
- Chandran U, Chakka A. Variant Analysis for Cancer Genomics. Presented at: AACR. San Diego, CA.
- Chandran U. PGRR - Intro to the Cancer Genome Atlas. Presented at: UPCI Annual Retreat 2014 2014 Jun 18 - 19. University of Pittsburgh Greensburg.
- Chandran U. The Cancer Genome Atlas. Presented at: Magee Women's Research Institute Annual Retreat 2013 Nov 15 - 16. Nemacolin Woods, PA.
- Chandran U. Bioinformatics - Practical Applications in Pathology. Presented at: APIII 2010 2010 Sep 19 - 22. Boston, MA.
Peer-reviewed Publications: 
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