Department of Biological Chemistry - Johns Hopkins University

Akhilesh Pandey
Associate Professor of Biological Chemistry
Secondary Appointment: Other
Johns Hopkins University School of Medicine

527 Broadway Research Building
733 N. Broadway
Baltimore, MD 21205
office tel: 410-502-6662
lab tel: 410-502-6665
Fax: 410-502-7544
Email: pandey@jhmi.edu
Lab web site

CV

Signal transduction; Mass spectrometry; Bioinformatics; Cancer biomarkers

The Pandey Lab is comprised of an interdisciplinary group of molecular biologists, mass spectrometrists, and computational biologists who are interested in systems biology.

Signal Transduction: 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. Using a combination of molecular biology and proteomics-based approaches including mass spectrometry, our laboratory is dissecting these signaling pathways further. We are also using peptide and protein microarrays as well as computational methods for identification of tyrosine kinase substrates and phosphorylation sites.

Mass Spectrometry: We are using state-of-the-art mass spectrometric methods for identification of proteins, for characterizing post-translational modifications in signal transduction pathways and in the analysis of different cancers. Techniques that help us quantitate levels of protein as well as post-translational modifications are being applied to various biological projects. Computational methods that allow researchers to extract annotated information from existing databases, including genomic databases, while performing searches using mass spectrometry-derived data are being developed.

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 (http://www.ibioinformatics.org), we have recently developed a Human Protein Reference Database (http://www.hprd.org). Our other interests include analysis of protein interactions networks and application of signaling networks in the context of microarray data.

Cancer Biomarkers: We are using proteomic approaches to identify potential biomarkers for early diagnosis of cancers. We are using body fluids (e.g. nipple aspirate, bile, pancreatic juice, serum) as well as tissue for identification of differentially expressed proteins by mass spectrometry. We use immunohistochemistry on tissue microarrays and ELISA assays on serum for validation of the biomarkers identified using mass spectrometry.

Recent Publications

Molina, H., Horn, D. M., Tang, N., Mathivanan, S. and Pandey, A. (2007). Global Proteomic Profiling of Phosphopeptides using Electron Transfer Dissociation Tandem Mass Spectrometry. Proceedings of the National Academy of Sciences, USA. 104, 2199-2204.

Amanchy, R., Periaswamy, B., Mathivanan, S., Reddy, R., Tattikota, S. G. and Pandey, A. (2007). A compendium of curated phosphorylation-based substrate and binding motifs. Nature Biotechnology. 25, 285-286.

Gandhi, T. K. B., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Nagaraju, S., Periyaswamy, B., Mishra, G., Nandakumar, K., Shen, B., Deshpande, N., Nayak, R., Sarker, M., Boeke, J. D., Parmigiani, G., Schultz, J., Bader, J. S. and Pandey, A. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 3, 285-293.
PubMed Reference

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

Gronborg, M. Kristiansen, T. Z., Iwahori, A., Chang, R., Reddy, R., Sato, N., Molina, H., Jensen, O. N., Hruban, R. H., Goggins, M. G., Maitra, A. and Pandey, A. (2006). Biomarker discovery from pancreatic cancer secretome using a differential proteomics approach. Molecular and Cellular Proteomics. 5, 157-171.
PubMed Reference

Harsha, H. C., Suresh, S., Amanchy, R., Deshpande, N., Shanker, K., Yatish, A. J., Muthusamy, B., Vrushabendra, B. M., Rashmi, B. P., Chandrika, K. N., Padma, N., Sharma, S., Badano, J. L, Ramya, M. A., Shivashankar, H.N., Peri, S., Choudhury, D. R., Kavitha, M. P., Saravana, R., Niranjan, V., Gandhi, T. K. B., Ghosh, N., Chandran, S., Menezes, M., Joy, M., Mohan, S. S., Katsanis, N., Deshpande, K. S., Raghothama, C., Prasad, C. K., and Pandey, A. (2005) A manually curated functional annotation of the human X chromosome. Nature Genetics. 37, 322-323.
PubMed Reference

Amanchy, R., Kalume, D. E., Iwahori, A., Zhong, J. and Pandey, A. (2005) Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC). Journal of Proteome Research. 4, 1661-1671.
PubMed Reference

Amanchy, R., Kalume, D. E. and Pandey A. (2005) Stable isotope labeling with amino acids in cell culture (SILAC) for studying dynamics of protein abundance and post-translational modifications. Science's STKE 2005. pl2.
PubMed Reference

Molina, H., Parmigiani, G. and Pandey, A. (2005). Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry. Analytical Chemistry. 77, 2739-2744.
PubMed Reference

Kalume, D. E., Peri, S., Zhong, J., Okulate, M., Reddy, R., Kumar, N. and Pandey, A. (2005) Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics. 6:128.
PubMed Reference

Muthusamy, B., Hanumanthu, G., Reshmi, R., Sriranjini, S., Suresh, S., Rekha, B., Srinivas, D., Karthick, L., Vrushabendra, B. M., Sharma, S., Mishra, G., Rashmi, B. P., Kadekar, S., Chatterjee, P., Mangala, K. S., Shivashankar, H. N., Chandrika, K. N., Deshpande, N., Suresh, M., Kannabiran, N., Niranjan, V., Nalli, A., Prasad, T. S. K., Arun, K. S., Reddy, R., Chandran, S., Jadhav, T., Julie, D., Mahesh, M., John, S. L., Palvankar, K., Sudhir, D., P. Bala., Jithesh, M. K., Rashmi, N. S., Vishnupriya, G., Dhar, K., Reshma, S., Raghothama, C., Prasad, C. K. Gandhi, T. K. B., Harsha, H. C., Mohan, S. S., Deshpande, K. S., Sarker, M. and Pandey, A. (2005) Plasma proteome database as a resource for proteomics research. Proteomics. 5, 3531-3536.
PubMed Reference

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

Ibarrola, N., Molina, H., Iwahori, A. and Pandey, A. (2004) A novel proteomic approach for specific identification of tyrosine kinase substrates using ¹³C-labeled tyrosine. Journal of Biological Chemistry. 279, 15805-15813.
PubMed Reference

Kristiansen, T. Z., Bunkenborg, J., Gronborg, M., Molina, H., Thuluvath, P. J., Argani, P., Goggins, M. G., Maitra, A. and Pandey, A. (2004). A proteomic analysis of human bile. Molecular and Cellular Proteomics. 3, 715-728.
PubMed Reference