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Location:
Houston, TX
Posted:
April 26, 2014

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Resume:

Curriculum Vitae

Sumanth Polikepahad, Ph.D.

Contact: **** ****** ** *** ****

Houston, TX - 77054

Phone: 281-***-****

E-mail: acdvbr@r.postjobfree.com

Visa Status: Permanent Resident

Education:

01/2002-02/2006 Ph.D. in Molecular Pharmacology (Veterinary Medical

Sciences)

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,

India

Academic Appointments:

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

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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

data.

Research Projects:

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).

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7. Identified potentially miRNA mediated regulatory pathways in the CD4+T cells

through expression profiling in murine Th1 and Th2 cells by utilizing Illumina

NGS.

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

immunological methods.

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

experimental asthma.

Skills:

Molecular Biology:

High quality RNA/DNA extraction from FFPE and frozen

tissue samples.

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

assays.

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

PGM sequencer.

Illumina: Sample/library preparation and data analysis.

Bioinformatics:

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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

antagonists.

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.

Selected Publications:

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]

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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.

doi: 10.3791/1720.

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

Genomics)

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).

Professional Associations:

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Sigma Xi, the Scientific Research Society

ASBMB, American Society for Biochemistry and Molecular Biology

Peer Reviewer:

Journal of Biomolecular Screening

Scientific Journals International

Book chapters/Patents:

1. Authored a chapter “Cytokines, chemokines and their receptors in allergy and

asthma” in the book “Recent trends in aerobiology, allergy and immunology; ISBN:

978-81-308-0249-7 ”.

2. Pending patent (Clayton Foundation of Research): Mirna expression in allergic

disease. WIPO Patent application WO/2010/129919.

Conference Presentations:

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

Oral Presentation)

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

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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.

References:

Available upon request

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