Center for Global Health Faculty

Associate Professor

Genetic Medicine, Biological Chemistry, Oncology and Pathology

Academic Degrees

• MD
• PHD

Departmental Affiliation

• Name:

  Molecular Microbiology and Immunology

  Affiliation Type:

  Primary

  Division:

  School of Medicine

Departmental Address

Contact Information

Email:

pandey+jhmi.edu

Phone:

410-502-6662

Link:

Personal Website

Research and Professional Experience

The Pandey Lab is a systems biology lab that integrates molecular and cellular biology, genomics, proteomics and bioinformatics.

Signal Transduction and Cancer Biology: Cell surface receptors transmit signals to the interior of the cell upon binding to a ligand. We have cloned a number of signaling molecules that are involved in signal transduction through receptor tyrosine kinases and cytokine receptors. Combining molecular biology and quantitative proteomics including SILAC and iTRAQ, our laboratory is dissecting these signaling pathways in various malignancies including lung cancer, breast cancer, pancreatic cancer, gastric cancer, cholangiocarcinoma and leukemias.

MiRNA Biology: microRNAs have been shown to be critical for post-transcriptional regulation of the genome. By binding to mRNAs, miRNAs can modulate translation through mechanisms that are not yet fully elucidated. Using quantitative proteomics, our laboratory has successfully identified potential targets of microRNAs miR-21 and miR-143. We also generated SILAC mice to study the function of Dicer and its impact on global proteomic changes.

Mass Spectrometry: High resolution mass spectrometry has become a core technology for large scale analysis of the proteome, lipidome and metabolome. Targeted analysis of molecules of interest is an emerging technology for accurate quantitative analyses by applying MRM (multiple reaction monitoring) on triple quadrupole mass spectrometer. The Pandey lab has a special interest in developing mass spectrometric methods for highly sensitive and accurate detection of molecules.

Human Genome Analysis and Bioinformatics: Our research in bioinformatics mainly involves functional annotation of genomes, creation of databases, comparative genomics and experimental approaches for validating computational predictions. In collaboration with the Institute of Bioinformatics in Bangalore, India, we have developed several resources focusing on human proteins and pathways: Human Protein Reference Database catalogs all human proteins, their modular domain structures and interaction partners. NetPath is a curated resource of signal transduction pathways in humans. We have also initiated a community resource, Human Proteinpedia, to share and integrate protein data in humans.

Keywords

Proteomics, bioinformatics, signal transduction, biomarkers, databases, systems biology, cancer, microRNA

Honors and Awards

Experimental Pathologist-in-training Award, American Society for Investigative Pathology, 1996
Howard Temin Award, National Cancer Institute, 1997
Sidney Kimmel Scholar Award, 2003
Beckman Young Investigator Award, 2004
DOD Era of Hope Scholar Award, 2006

Selected Publications

Chen H, Pimienta G, Gu Y, Sun X, Hu J, Kim MS, Chaerkady R, Gucek M, Cole RN, Sukumar S, Pandey A. (2010) Proteomic characterization of Her2/neu-overexpressing breast cancer cells. Proteomics. 10, 3800-3810.

Zhong J, Krawczyk SA, Chaerkady R, Huang H, Goel R, Bader JS, Wong GW, Corkey BE, Pandey A. (2010) Temporal profiling of the secretome during adipogenesis in humans. Journal of Proteome Research. 9, 5228-5238.

Yang Y, Chaerkady R, Kandasamy K, Huang TC, Selvan LD, Dwivedi SB, Kent OA, Mendell JT, Pandey A. (2010) Identifying targets of miR-143 using a SILAC-based proteomic approach. Molecular Biosystems. 6,1873-1882.

Kim MS, Kandasamy K, Chaerkady R, Pandey A.(2010) Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer. Journal of American Society of Mass Spectrometry. 21,1606-1611.

Zhong J, Pandey A. (2010) Site-directed mutagenesis reveals a unique requirement for tyrosine residues in IL-7Ralpha and TSLPR cytoplasmic domains in TSLP-dependent cell proliferation. BMC Immunology. 11, 5.

Chaerkady R, Kerr CL, Kandasamy K, Marimuthu A, Gearhart JD, Pandey A. (2010) Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics. 10,1359-1373.

Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu SN, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A. (2010) NetPath: a public resource of curated signal transduction pathways. Genome Biology. 11, R3.

Yang Y, Chaerkady R, Beer MA, Mendell JT, Pandey A.(2009) Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics. 9,1374-1384.

Harsha HC, Kandasamy K, Ranganathan P, Rani S, Ramabadran S, Gollapudi S, Balakrishnan L, Dwivedi SB, Telikicherla D, Selvan LDN, Goel R, Mathivanan S, Marimuthu A, Kashyap MK, Vizza RF, Mayer RJ, DeCaprio JA, Srivastava S, Hanash SM, Hruban RH, Pandey A. (2009) A compendium of potential biomarkers of pancreatic cancer. PLoS Medicine. 6, e1000046.

Chaerkady R, Kerr CL, Marimuthu A, Kelkar DS, Kashyap MK, Gucek M, Gearhart JD, Pandey A. (2009) Temporal analysis of neural differentiation using quantitative proteomics. Journal of Proteome Research. 8, 1315-1326.

Molina, H, Yang Y, Ruch T, Kim JW, Mortensen P, Otto T, Nalli A, Tang QQ, Lane MD, Chaerkady R, Pandey A. (2009) Temporal profiling of the adipocyte proteome during differentiation using a 5-plex SILAC based strategy. Journal of Proteome Research. 8, 48-58.

Mathivanan S, 158 coauthors, Pandey A. (2008) Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26, 164-167.

Guha U, Chaerkady R, Marimuthu A, Patterson AS, Kashyap MK, Harsha HC, Sato M, Bader JS, Lash AE, Minna JD, Pandey A, Varmus HE. (2008) Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proceedings of National Academy of Sciences of the United States of America. 105, 14112-14117.

Harsha HC, Molina H, Pandey A. (2008) Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nature Protocols. 3, 505-516.

Molina H, Horn DM, Tang N, Mathivanan S, Pandey A. (2007) Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proceedings of National Academy of Sciences of the United States of America. 104, 2199-2204.

Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A. (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 38, 285-293.

Bose R, Molina H, Patterson AS, Bitok JK, Periaswamy B, Bader JS, Pandey A, Cole PA. (2006) Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proceedings of National Academy of Sciences of the United States of America. 103, 9773-9778.

Qiao Y, Molina H, Pandey A, Zhang J, Cole PA. (2006) Chemical rescue of a mutant enzyme in living cells. Science. 311, 1293-1297.

Harsha HC, Suresh S, Amanchy R, Deshpande N, Shanker K, Yatish AJ, Muthusamy B, Vrushabendra BM, Rashmi BP, Chandrika KN, Padma N, Sharma S, Badano JL, Ramya MA, Shivashankar HN, Peri S, Choudhury DR, Kavitha MP, Saravana R, Niranjan V, Gandhi TK, Ghosh N, Chandran S, Menezes M, Joy M, Mohan SS, Katsanis N, Deshpande KS, Raghothama C, Prasad CK, Pandey A. (2005) A manually curated functional annotation of the human X chromosome. Nature Genetics. 37, 331-332.

Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM. (2005) Probabilistic model of the human protein-protein interaction network. Nature Biotechnology. 23, 951-959.

Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. (2004) Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proceedings of National Academy of Sciences of the United States of America. 101, 9309-9314.

Pandey A, Blagoev B, Kratchmarova I, Fernandez M, Nielsen M, Kristiansen TZ, Ohara O, Podtelejnikov AV, Roche S, Lodish HF, Mann M. Cloning of a novel phosphotyrosine binding domain containing molecule, Odin, involved in signaling by receptor tyrosine kinases. Oncogene. 21, 8029-8036.

Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Molecular & Cellular Proteomics. 1, 376-386.