Sumanth Polikepahad, Ph.D.
Contact: **** ****** ** *** ****
Houston, TX - 77054
Visa Status: Permanent Resident
01/2002-02/2006 Ph.D. in Molecular Pharmacology (Veterinary Medical
Department of Comparative Biomedical Sciences
Louisiana State University, Baton Rouge, LA, USA
07/1996-11/2001 B.V.Sc (Bachelors in Veterinary Sciences)
magna cum laude
Acharya N.G. Ranga Agricultural University, Hyderabad,
10/2013 – Present Research Associate
Division of Molecular Oncology in the Department of
Investigative and Genomic Pathology, Texas Children’s
Hospital, Houston, TX, USA
Department of Pathology, Baylor College of Medicine,
Houston, TX, USA
03/2006-07/2012 Postdoctoral Research Associate
Department of Pathology and Immunology
Baylor College of Medicine, Houston, TX, USA
01/2002-02/2006 Graduate Research Assistant
Department of Comparative Biomedical Sciences
Louisiana State University, Baton Rouge, LA, USA
Summary of Research Experience:
Eight years of research experience in Next Generation Sequencing (NGS), Transcriptomics,
RNA biology and Genomics. During my first postdoctoral training, I employed Illumina
NGS technology, wide array of molecular biological techniques and cutting edge
bioinformatics approaches to study the unique biochemical properties of non-coding RNAs
in T-lymphocytes, and delineated the role of non-coding RNAs, particularly microRNAs in
the molecular pathogenesis of allergic diseases.
After procuring solid foundation in the NGS based research, I transitioned in to senior
postdoctoral program at Texas Children’s Hospital (TCH) to develop NGS based assays for
pediatric cancer diagnosis. By using Ion Torrent PGM, I have participated in the
advancement of novel cancer diagnostic assays and bioinformatics tools to analyze NGS
1. While working in a CAP certified (soon to be CLIA certified) molecular oncology
laboratory at TCH and with the collaboration of Fusion Genomics company
(www.fusiongenomics.com), I have optimized the Ion Torrent PGM work flow for
cancer fusion transcript detection in pediatric sarcoma clinical tumor samples by
using Targeted RNA Ion Ampliseq panels and probe based pull down of target
fusion gene transcripts.
2. Optimized high quality DNA and RNA extraction protocols from FFPE as well as
frozen tumor samples from pediatric cancer patients.
3. By using Illumina HiSeq Whole Transcriptome Sequencing (performed in the
Human Genome Research Center, Baylor College of Medicine) and cutting edge
bioinformatics programs such as Tophat-Fusion, ChimeraScan and defuse, I have
identified novel fusion genes in pediatric sarcoma patients.
4. Played crucial role in the development of Ion Torrent PGM targeted gene NGS
pediatric cancer mutation detection assay. This diagnostic assay contains a primer
panel of all vital mutations that are highly prevalent in most common pediatric
cancers. To develop this, we collaborated with Life Technologies to modify Ion
Ampliseq Cancer Hotspot panel v2. This assay as well as fusion genomics assay are
soon to be released as standard clinical diagnostic assays in Pediatric Clinical
Pathology department at TCH.
5. Using python programming language, I wrote several useful scripts that analyze
NGS data. Most notably I wrote PeCMAN (Pediatric Cancer Mutation Annotator)
program which intersects the PGM generated VCF files with relevant cancer
annotation databases including COSMIC, ANNOVAR, dbSNP and others, extracts
useful annotations and finally generates a clinical report that can be directly
communicated to the patient. This program is soon to be released in to clinical
pathology core facility where clinicians can plug-in the PGM generated data and
obtain all relevant annotations.
6. In collaboration with University of Houston Genomics Core facility, I profiled
Argonaute1 and 2 bound short-RNAs in mouse splenic CD4+T cells by employing
Illumina Next Generation Sequencing technology (Genome Analyzer IIx).
7. Identified potentially miRNA mediated regulatory pathways in the CD4+T cells
through expression profiling in murine Th1 and Th2 cells by utilizing Illumina
8. Co-investigated the determination of let-7 and miR-1266 regulation of Th1 and
Th17 immune responses in Human emphysema by using Illumina NGS and
9. Determined the pro-inflammatory role of murine let-7 group of miRNAs in the
experimental model of asthma, by employing Solexa Next Generation Sequencing
and nucleic acid transfection methods.
10. Co-investigated the role of matrix metalloproteinase 7 (mmp-7) and retinoic acid in
High quality RNA/DNA extraction from FFPE and frozen
Assessing RNA/DNA quality by using Bioanalyzer, nanodrop
and Qubit assays.
Long Range PCR, Nested PCR, qRTPCR, Westerns, Gel
Electrophoresis, Silver Staining, Molecular Cloning, and In
vivo and in vitro transfection of plasmids and oligos.
In vivo and in vitro knock down of miRNAs by using Locked
Nucleic Acids. miRNA target validation by dual luciferase
Microarray sample preparation and data analysis.
Next Generation Sequencing:
Ion Torrent: DNA/RNA Library preparation, template
preparation using Ion OneTouch 2 system, enrichment using
Ion OneTouch 2 ES system, initialization and operation of
Illumina: Sample/library preparation and data analysis.
Deep Sequencing Data analysis. Expert in installing, running and
troubleshooting several open source bioinformatics tools such as
Bowtie, Tophat, IGV, BLAST, BLAT etc.
Advanced level expertise in running fusion-gene detection
programs such as Tophat-Fusion, Chimerascan and defuse.
Advanced level expertise in Python and R languages. Wrote
several scripts to analyze the NGS data.
Expert Linux user. Advanced level of expertise in bash scripting
and command line usage.
Expertise in using online databases and genome browsers such
as UCSC, BLAST and ENSEMBL etc.
Immunology: ELISA, ELISPOT, Multiplex-Cytokine assays,
Immunohistochemistry, primary cell aseptic isolation/culture and Flow Cytometry.
Pharmacology: In vitro dose-response pharmacological studies in
physiobaths/organbaths to determine pharmacological affinity of receptor
Animal models: Extensive experience in working with mice.
Developed novel mouse model of allergic lung disease.
Supervision: Trained several graduate students, visiting scientists and postdoctoral
scientists in various techniques.
Communication skills: Excellent, both written and spoken, as demonstrated by
several publications and conference presentations.
1. Peters TL, Kumar V, Polikepahad S, Lin FY, Sarabia SF, Lopez-Terrada D, Plon SE,
Parsons DW, Roy A. The BCOR/CCNB3 Fusion Gene Is Present in a Subset of
Undifferentiated Pediatric Sarcomas. (Submitted) Modern Pathology
2. Polikepahad S, Kumar V, Lopez-Terrada D, Roy A. A clinical report of rare EWSR1-
ETV1 fusion gene in a case of Ewing’s Sarcoma. (In preparation) Cancer Genetics
3. Polikepahad S and Corry DB. Profiling of T Helper Cell-Derived Small RNAs Reveals
Unique Antisense Transcripts and Differential Association of miRNAs With Argonaute
Proteins 1 and 2. Nucleic Acids Res. 2012 Nov 26. [Epub ahead of print]
4. Polikepahad S, Knight JM, Naghavi OA, Creighton CJ, Harris RA, Coarfa C, Zariff
A, Milosavljevic A, Kheradmand F, Gunaratne PH, Corry DB. Pro-inflammatory role for
let-7 microRNAs in experimental asthma. J. Biol. Chem. 2010 Sep 24; 285 (39): 30139-
49. Epub 2010 Jul 14.
5. Polikepahad S, Barranco WT, Porter P, Anderson B, Kheradmand F, Corry DB.
A Reversible, Non-Invasive Method for Airway Resistance Measurements and
Bronchoalveolar Lavage Fluid Sampling in Mice. J Vis Exp. 2010 Apr 13;(38). pii: 1720.
6. Goswami S, Angkasekwinai P, Shan M, Greenlee KJ, Barranco WT, Polikepahad S,
Seryshev A, Song LZ, Redding D, Singh B, Sur S, Woodruff P, Dong C, Corry DB,
Kheradmand F. Divergent functions for airway epithelial matrix metalloproteinase 7 and
retinoic acid in experimental asthma. Nature Immunol. 2009 May; 10 (5): 496-503. Epub
2009 Mar 29.
7. Polikepahad S., Haque M., Francis J., Moore R.M., Venugopal C.S. Characterization
of endothelin receptors in the peripheral lung tissues of horses unaffected and affected with
recurrent airway obstruction. Can J Vet Res. 2008 Jul; 72(4):340-9.
8. Polikepahad S, Moore RM, Venugopal CS. Endothelins and airways--a short review.
Res Commun Mol Pathol Pharmacol. 2006; 119(1-6):3-51.
9. Polikepahad S, Paulsen DB, Moore RM, Costa LRR, Venugopal CS.
Immunohistochemical determination of the expression of endothelin receptors in bronchial
smooth muscle and epithelium of healthy horses and horses affected by summer pasture-
associated obstructive pulmonary disease. Am J Vet Res. 2006 Feb; 67(2): 348-357.
10. Venugopal CS, Christopher CL, Wilson SM, Polikepahad S, Dequeant E, Holmes EP.
Pharmacologic evaluation of neurokinin-2 receptor antagonists in the guinea pig respiratory
tract. Am J Vet Res. 2004 Jul;65(7):984-91
Manuscripts in Preparation or Review:
1. Polikepahad S, Batts LM, Coarfa C, Creighton CJ, Gunaratne PH, Corry DB.
MicroRNA Expression Profiling of CD4+ T Cells Suggests Novel Genetic Pathways
regulating Effector Differentiation and Survival. (In preparation, for submission to BMC
2. Liu S, Shan M, Polikepahad S, Creighton CJ, Zariff A, Zhang Y, Hilsenbeck SG,
Milosavljevic A, Soibam B, Gunaratne PH, You R, Song L, Kheradmand F, and Corry DB.
Transcriptome-Wide Profiling Reveals MicroRNAs Regulating T Helper Cell Type 1 and
17 Responses in Human Emphysema. (In review, Journal of Biological Chemistry).
Sigma Xi, the Scientific Research Society
ASBMB, American Society for Biochemistry and Molecular Biology
Journal of Biomolecular Screening
Scientific Journals International
1. Authored a chapter “Cytokines, chemokines and their receptors in allergy and
asthma” in the book “Recent trends in aerobiology, allergy and immunology; ISBN:
2. Pending patent (Clayton Foundation of Research): Mirna expression in allergic
disease. WIPO Patent application WO/2010/129919.
1. S. Polikepahad, CJ. Creighton, H. Zhu, A. Harris, C. Coarfa, D. Berel, A.
Milosavljevic, DB. Corry and PH. Gunaratne. Differentially Expressed MicroRNAs in
Allergic Asthma Target Genes underlying Airway Hyper-Responsiveness and Goblet Cell
Hyperplasia. AAI-2009, Seattle, WA. J. Immunol., Apr 2009; 182: 136.22. (Selected for
2. S. Goswami, P. Angkasekwinai, M. Shan, KJ. Greenlee, WT. Barranco, S.
Polikepahad, A. Seryshev, S. Sur, P. Woodruff, C. Dong, DB. Corry, and F. Kheradmand.
Divergent Roles for Airway Epithelial MMP7 and Retinoic Acid in Experimental Asthma.
AAI-2009, Seattle, WA. J. Immunol., Apr 2009; 182: 140.5.
3. S. Polikepahad, Jad El-Daye, A. Naghavi, J. Miller, P. Gunaratne and D.B. Corry.
Essential role for micro RNAs in regulation of allergic asthma. Keystone Symposium,
microRNAs and Biology, Whistler, British Columbia, Canada, 2008.
4. S. Polikepahad, Jad El-Daye, A. Naghavi, J. Miller, P. Gunaratne and D.B. Corry.
Lung RNA profiling suggests an essential role for micro RNAs in regulating allergic lung
disease. AAI-2007, Miami, FL. The Journal of Immunology, 2007, 178: 91.9.
5. S. Polikepahad, M. Haque, J. Francis, R.M. Moore and C.S. Venugopal.
Characterization of pulmonary endothelin receptors in healthy and recurrent airway
obstruction-affected horses. Experimental Biology, FASEB J. 2006 April, 429.13
6. C.S. Venugopal, S. Polikepahad, E. Holmes and R.M. Moore. Evidence for endothelin-
B receptor involvement in recurrent airway obstruction in horses. Experimental Biology
FASEB J. 2006 April, 429.12
7. C. Venugopal, S. Polikepahad, E.Holmes and R. Moore. Endothelin-B receptor
mediated response of equine bronchial rings in health and disease. Experimental Biology
FASEB J. 2005 April; 19 (4): A113.
8. C. Venugopal, E. Holmes, S. Polikepahad and R. Moore. Neurokinin- A induced
hyperreactivity of equine airways in health and disease. Experimental Biology FASEB J.
2005 April; 19 (4): A113.
9. S. Polikepahad, D. Paulsen, R. Moore, L. Costa and C. Venugopal.
Immunohistochemical studies on expression of endothelin A and B receptors in the lungs of
clinically healthy and SPAOPD-affected horses. Experimental Biology FASEB J. 2004
April; 18 (4): A234.
10. S. Polikepahad, R. Moore, C. Koch, E. Holmes and C. Venugopal. Effects of epithelial
denudation on endothelin-1 induced bronchoconstriction in clinically healthy and summer
pasture-associated obstructive pulmonary disease (SPAOPD) affected horses.
Experimental Biology FASEB J. 2004 April; 18 (4): A234.
11. C. Venugopal, S. Polikepahad, E. Holmes, J. Vanden Heuvel, T. Leas and R. Moore.
Evidence for involvement of endothelin-B receptors in equine summer pasture-associated
obstructive pulmonary disease (SPAOPD). Experimental Biology FASEB J. 2004 April;
18 (4): A234.
12. S. Polikepahad, R. Moore, S. Krishna Kumar, J. Vanden Heuvel and C. Venugopal.
Pharmacological characterization of endothelin receptor responses of bronchi in clinically
healthy horses and those affected with summer pasture-associated obstructive pulmonary
disease. Experimental Biology FASEB J. 2003 April; 17 (4): A1047.
13. C. Venugopal, S. Wilson, E. Dequeant, S. Polikepahad and R. Moore. Response of
bronchial smooth muscle to neurokinin-A in clinically healthy horses and those affected
with summer pasture-associated obstructive pulmonary disease. Experimental Biology
FASEB J. 2003 April; 17 (4): A1047.
Available upon request