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Dr. Akhilesh Pandey

M.D., Ph.D.
Titles

Associate Professor of Biological Chemistry and Oncology

Schools\Degrees

M.D., Armed Forces Medical College Ph.D., University of Michigan, Ann Arbor

Training

Resident, Pathology, Brigham and Women's Hospital, Harvard Medical School
Postdoctoral research, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology

Research Summary

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

Signal TransductionCell-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 microarrays for identification of tyrosine kinase substrates. We are also using computational methods for prediction of phosphorylation sites.

Mass SpectrometryWe 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.

BioinformaticsOur 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 that is available at 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 BiomarkersWe 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.
 

Journal Citations

Bose, R., Molina, H., Patterson, A. S., Bitok, J. K., Periaswamy, B., Bader, J. S., Pandey, A. & Cole, P. A. (2006). Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proc Natl Acad Sci U S A 103, 9773-8.

Gandhi, T. K., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Nagaraju, S., Periaswamy, B., Mishra, G., Nandakumar, K., Shen, B., Deshpande, N., Nayak, R., Sarker, M., Boeke, J. D., Parmigiani, G., Schultz, J., Bader, J. S. & Pandey, A. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 38, 285-93.

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. & Pandey, A. (2006). Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Mol Cell Proteomics 5, 157-71.

Harsha, H.C., Jimeno, A., Molina, H., Mihalas, A.B., Goggins, M.G., Hruban, R.H., Schulick, R.D., Kamath, U., Maitra, A., Hidalgo, M., and Pandey, A. (2008). Activated epidermal growth factor receptor as a novel target in pancreatic cancer therapy. Journal of proteome research 7, 4651-4658.

Karanjawala, Z. E., P. B. Illei, R. Ashfaq, J. R. Infante, K. Murphy, A. Pandey, R. Schulick, J. Winter, R. Sharma, A. Maitra, M. Goggins, and R. H. Hruban. 2008. New Markers of Pancreatic Cancer Identified Through Differential Gene Expression Analyses: Claudin 18 and Annexin A8. Am J Surg Pathol 32:188-196.

Karanjawala, Z. F., P.B. Illei, R. Ashfaq, J.R. Infante, K. Murphy, A. Pandey, Schulick, R.D., J. Winter, R. Sharma, A. Maitra, M. Goggins and R.H. Hruban. 2008. New markers of pancreatic cancer identified through differential gene expression analyses: Claudin 18 and Annexin A8. Am J Surg Pathol 32:188-196.

Karanjawala, Z.E., Illei, P.B., Ashfaq, R., Infante, J.R., Murphy, K., Pandey, A., Schulick, R., Winter, J., Sharma, R., Maitra, A., Goggins, M., and Hruban, R.H. (2008). New markers of pancreatic cancer identified through differential gene expression analyses: claudin 18 and annexin A8. The American journal of surgical pathology 32, 188-196.

Lerin, C., Rodgers, J. T., Kalume, D. E., Kim, S. H., Pandey, A. & Puigserver, P. (2006). GCN5 acetyltransferase complex controls glucose metabolism through transcriptional repression of PGC-1alpha. Cell Metab 3, 429-38.

Lucito, R., S. Suresh, K. Walter, A. Pandey, B. Lakshmi, A. Krasnitz, J. Sebat, M. Wigler, A. P. Klein, K. Brune, E. Palmisano, A. Maitra, M. Goggins, and R. H. Hruban. 2007. Copy-Number Variants in Patients with a Strong Family History of Pancreatic Cancer. Cancer Biol Ther 6.

Luo, W., Slebos, R.J., Hill, S., Li, M., Brabek, J., Amanchy, R., Chaerkady, R., Pandey, A., Ham, A.J., and Hanks, S.K. (2008). Global impact of oncogenic Src on a phosphotyrosine proteome. J Proteome Res 7, 3447-3460.

Mathivanan, S., Ahmed, M., Ahn, N.G., Alexandre, H., Amanchy, R., Andrews, P.C., Bader, J.S., Balgley, B.M., Bantscheff, M., Bennett, K.L., Bjorling, E., Blagoev, B., Bose, R., Brahmachari, S.K., Burlingame, A.S., Bustelo, X.R., Cagney, G., Cantin, G.T., Cardasis, H.L., Celis, J.E., Chaerkady, R., Chu, F., Cole, P.A., Costello, C.E., Cotter, R.J., Crockett, D., DeLany, J.P., De Marzo, A.M., DeSouza, L.V., Deutsch, E.W., Dransfield, E., Drewes, G., Droit, A., Dunn, M.J., Elenitoba-Johnson, K., Ewing, R.M., Van Eyk, J., Faca, V., Falkner, J., Fang, X., Fenselau, C., Figeys, D., Gagne, P., Gelfi, C., Gevaert, K., Gimble, J.M., Gnad, F., Goel, R., Gromov, P., Hanash, S.M., Hancock, W.S., Harsha, H.C., Hart, G., Hays, F., He, F., Hebbar, P., Helsens, K., Hermeking, H., Hide, W., Hjerno, K., Hochstrasser, D.F., Hofmann, O., Horn, D.M., Hruban, R.H., Ibarrola, N., James, P., Jensen, O.N., Jensen, P.H., Jung, P., Kandasamy, K., Kheterpal, I., Kikuno, R.F., Korf, U., Korner, R., Kuster, B., Kwon, M.S., Lee, H.J., Lee, Y.J., Lefevre, M., Lehvas, Laiho, M., Lescuyer, P., Levander, F., Lim, M.S., Lobke, C., Loo, J.A., Mann, M., Martens, L., Martinez-Heredia, J., McComb, M., McRedmond, J., Mehrle, A., Menon, R., Miller, C.A., Mischak, H., Mohan, S.S., Mohmood, R., Molina, H., Moran, M.F., Morgan, J.D., Moritz, R., Morzel, M., Muddiman, D.C., Nalli, A., Navarro, J.D., Neubert, T.A., Ohara, O., Oliva, R., Omenn, G.S., Oyama, M., Paik, Y.K., Pennington, K., Pepperkok, R., Periaswamy, B., Petricoin, E.F., Poirier, G.G., Prasad, T.S., Purvine, S.O., Rahiman, B.A., Ramachandran, P., Ramachandra, Y.L., Rice, R.H., Rick, J., Ronnholm, R.H., Salonen, J., Sanchez, J.C., Sayd, T., Seshi, B., Shankari, K., Sheng, S.J., Shetty, V., Shivakumar, K., Simpson, R.J., Sirdeshmukh, R., Siu, K.W., Smith, J.C., Smith, R.D., States, D.J., Sugano, S., Sullivan, M., Superti-Furga, G., Takatalo, M., Thongboonkerd, V., Trinidad, J.C., Uhlen, M., Vandekerckhove, J., Vasilescu, J., Veenstra, T.D., Vidal-Taboada, J.M., Vihinen, M., Wait, R., Wang, X., Wiemann, S., Wu, B., Xu, T., Yates, J.R., Zhong, J., Zhou, M., Zhu, Y., Zurbig, P., and Pandey, A. (2008). Human Proteinpedia enables sharing of human protein data. Nature biotechnology 26, 164-167.

Qiao, Y., Molina, H., Pandey, A., Zhang, J. & Cole, P. A. (2006). Chemical rescue of a mutant enzyme in living cells. Science 311, 1293-7.

Song, D., Chaerkady, R., Tan, A.C., Garcia-Garcia, E., Nalli, A., Suarez-Gauthier, A., Lopez-Rios, F., Zhang, X.F., Solomon, A., Tong, J., Read, M., Fritz, C., Jimeno, A., Pandey, A., and Hidalgo, M. (2008). Antitumor activity and molecular effects of the novel heat shock protein 90 inhibitor, IPI-504, in pancreatic cancer. Molecular cancer therapeutics 7, 3275-3284.



Bose, R., Molina, H., Patterson, A. S., Bitok, J. K., Periaswamy, B., Bader, J. S., Pandey, A. & Cole, P. A. (2006). Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proc Natl Acad Sci U S A 103, 9773-8.

Gandhi, T. K., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Nagaraju, S., Periaswamy, B., Mishra, G., Nandakumar, K., Shen, B., Deshpande, N., Nayak, R., Sarker, M., Boeke, J. D., Parmigiani, G., Schultz, J., Bader, J. S. & Pandey, A. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 38, 285-93.

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. & Pandey, A. (2006). Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Mol Cell Proteomics 5, 157-71.

Harsha, H.C., Jimeno, A., Molina, H., Mihalas, A.B., Goggins, M.G., Hruban, R.H., Schulick, R.D., Kamath, U., Maitra, A., Hidalgo, M., and Pandey, A. (2008). Activated epidermal growth factor receptor as a novel target in pancreatic cancer therapy. Journal of proteome research 7, 4651-4658.

Karanjawala, Z. E., P. B. Illei, R. Ashfaq, J. R. Infante, K. Murphy, A. Pandey, R. Schulick, J. Winter, R. Sharma, A. Maitra, M. Goggins, and R. H. Hruban. 2008. New Markers of Pancreatic Cancer Identified Through Differential Gene Expression Analyses: Claudin 18 and Annexin A8. Am J Surg Pathol 32:188-196.

Karanjawala, Z. F., P.B. Illei, R. Ashfaq, J.R. Infante, K. Murphy, A. Pandey, Schulick, R.D., J. Winter, R. Sharma, A. Maitra, M. Goggins and R.H. Hruban. 2008. New markers of pancreatic cancer identified through differential gene expression analyses: Claudin 18 and Annexin A8. Am J Surg Pathol 32:188-196.

Karanjawala, Z.E., Illei, P.B., Ashfaq, R., Infante, J.R., Murphy, K., Pandey, A., Schulick, R., Winter, J., Sharma, R., Maitra, A., Goggins, M., and Hruban, R.H. (2008). New markers of pancreatic cancer identified through differential gene expression analyses: claudin 18 and annexin A8. The American journal of surgical pathology 32, 188-196.

Lerin, C., Rodgers, J. T., Kalume, D. E., Kim, S. H., Pandey, A. & Puigserver, P. (2006). GCN5 acetyltransferase complex controls glucose metabolism through transcriptional repression of PGC-1alpha. Cell Metab 3, 429-38.

Lucito, R., S. Suresh, K. Walter, A. Pandey, B. Lakshmi, A. Krasnitz, J. Sebat, M. Wigler, A. P. Klein, K. Brune, E. Palmisano, A. Maitra, M. Goggins, and R. H. Hruban. 2007. Copy-Number Variants in Patients with a Strong Family History of Pancreatic Cancer. Cancer Biol Ther 6.

Luo, W., Slebos, R.J., Hill, S., Li, M., Brabek, J., Amanchy, R., Chaerkady, R., Pandey, A., Ham, A.J., and Hanks, S.K. (2008). Global impact of oncogenic Src on a phosphotyrosine proteome. J Proteome Res 7, 3447-3460.

Mathivanan, S., Ahmed, M., Ahn, N.G., Alexandre, H., Amanchy, R., Andrews, P.C., Bader, J.S., Balgley, B.M., Bantscheff, M., Bennett, K.L., Bjorling, E., Blagoev, B., Bose, R., Brahmachari, S.K., Burlingame, A.S., Bustelo, X.R., Cagney, G., Cantin, G.T., Cardasis, H.L., Celis, J.E., Chaerkady, R., Chu, F., Cole, P.A., Costello, C.E., Cotter, R.J., Crockett, D., DeLany, J.P., De Marzo, A.M., DeSouza, L.V., Deutsch, E.W., Dransfield, E., Drewes, G., Droit, A., Dunn, M.J., Elenitoba-Johnson, K., Ewing, R.M., Van Eyk, J., Faca, V., Falkner, J., Fang, X., Fenselau, C., Figeys, D., Gagne, P., Gelfi, C., Gevaert, K., Gimble, J.M., Gnad, F., Goel, R., Gromov, P., Hanash, S.M., Hancock, W.S., Harsha, H.C., Hart, G., Hays, F., He, F., Hebbar, P., Helsens, K., Hermeking, H., Hide, W., Hjerno, K., Hochstrasser, D.F., Hofmann, O., Horn, D.M., Hruban, R.H., Ibarrola, N., James, P., Jensen, O.N., Jensen, P.H., Jung, P., Kandasamy, K., Kheterpal, I., Kikuno, R.F., Korf, U., Korner, R., Kuster, B., Kwon, M.S., Lee, H.J., Lee, Y.J., Lefevre, M., Lehvas, Laiho, M., Lescuyer, P., Levander, F., Lim, M.S., Lobke, C., Loo, J.A., Mann, M., Martens, L., Martinez-Heredia, J., McComb, M., McRedmond, J., Mehrle, A., Menon, R., Miller, C.A., Mischak, H., Mohan, S.S., Mohmood, R., Molina, H., Moran, M.F., Morgan, J.D., Moritz, R., Morzel, M., Muddiman, D.C., Nalli, A., Navarro, J.D., Neubert, T.A., Ohara, O., Oliva, R., Omenn, G.S., Oyama, M., Paik, Y.K., Pennington, K., Pepperkok, R., Periaswamy, B., Petricoin, E.F., Poirier, G.G., Prasad, T.S., Purvine, S.O., Rahiman, B.A., Ramachandran, P., Ramachandra, Y.L., Rice, R.H., Rick, J., Ronnholm, R.H., Salonen, J., Sanchez, J.C., Sayd, T., Seshi, B., Shankari, K., Sheng, S.J., Shetty, V., Shivakumar, K., Simpson, R.J., Sirdeshmukh, R., Siu, K.W., Smith, J.C., Smith, R.D., States, D.J., Sugano, S., Sullivan, M., Superti-Furga, G., Takatalo, M., Thongboonkerd, V., Trinidad, J.C., Uhlen, M., Vandekerckhove, J., Vasilescu, J., Veenstra, T.D., Vidal-Taboada, J.M., Vihinen, M., Wait, R., Wang, X., Wiemann, S., Wu, B., Xu, T., Yates, J.R., Zhong, J., Zhou, M., Zhu, Y., Zurbig, P., and Pandey, A. (2008). Human Proteinpedia enables sharing of human protein data. Nature biotechnology 26, 164-167.

Qiao, Y., Molina, H., Pandey, A., Zhang, J. & Cole, P. A. (2006). Chemical rescue of a mutant enzyme in living cells. Science 311, 1293-7.

Song, D., Chaerkady, R., Tan, A.C., Garcia-Garcia, E., Nalli, A., Suarez-Gauthier, A., Lopez-Rios, F., Zhang, X.F., Solomon, A., Tong, J., Read, M., Fritz, C., Jimeno, A., Pandey, A., and Hidalgo, M. (2008). Antitumor activity and molecular effects of the novel heat shock protein 90 inhibitor, IPI-504, in pancreatic cancer. Molecular cancer therapeutics 7, 3275-3284.

Amanchy, R., Kalume, D. E., Iwahori, A., Zhong, J., & Pandey, A. 2005. by amino acids in cell culture (SILAC). J. Proteome Res. 4:1661-1671.

Gronborg, M., Kristiansen, T. Z., Iwahori, A., Chang, R., Reddy, R., Sato, N., et al. 2005. Biomarker discovery from pancreatic cancer secretome using a differential proteomics approach. Mol. Cell. Proteomics. [Oct. Epub ahead of print].

Harsha, H. C., Suresh, S., Amanchy, R., Deshpande, N., Shanker, K., Yatish, A. J., et al. 2005. A manually curated functional annotation of the human X chromosome. Nat. Genet. 37:331-332.

Ibarrola, N., Molina, H., Iwahori, A., & Pandey, A. 2004. A novel proteomic approach for specific identification of tyrosine kinase substrates using [13C] tyrosine. J. Biol. Chem. 279:15805-15813.

Kalume, D. E., Peri, S., Zhong, J., Okulate, M., Surendranath, V., Kumar, N., et al. 2005. A proteomic analysis of salivary glands of female Anopheles gambiae mosquito. Proteomics. 5:3765-3777.

Molina, H., Bunkenborg, J., Reddy, G. H., Muthusamy, B., Scheel, P. J., & Pandey A. 2005. A proteomic analysis of human hemodialysis fluid. Mol. Cell. Proteomics. 4:637-650.

Muthusamy, B., Hanumanthu, G., Reshmi, R., Sriranjini, S., Rekha, B., Srinivas, D., et al. 2005. Plasma proteome database as a resource for proteomics. Proteomics. 5:3531-3536.

 

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