Research Interests Human papillomaviruses (HPVs). Dr. Khan’s laboratory is identifying cellular pathways that are altered in HPV-associated cervical and oral cancers. Using GeneChips, we have identified a number of cellular genes involved in DNA repair, replication and recombination, apoptosis, signal transduction, transcription, etc. whose expression is altered in such cancers. We hope to classify HPV-induced cancers by molecular portrait of their gene expression and proteome profiles that can be of diagnostic and prognostic value. We are also investigating HPV-mediated changes in cellular microRNAs (miRNAs) that may play an important role in the progression of HPV-associated cancers. We have identified 3 miRNAs that are overexpressed and 24 that are underexpressed in HPV-16 positive cervical cancer cell lines and tissues and studies are in progress to identify the cellular targets and mechanism of action of these microRNAs. We have recently found that expression of the HPV-16 E6 oncogene reduces miR-218 expression, and conversely, RNA interference of E6/E7 oncogenes in an HPV-16 positive cell line increases miR-218 expression. We have identified LAMB3, which is involved in cell migration and tumorigenicity, as a target of miR-218. Our findings demonstrate specific regulation of cellular miRNAs in the presence of an HPV oncogene and may contribute to a better understanding of molecular mechanisms involved in cervical carcinogenesis. We are also investigating whether HPVs encode microRNAs and their potential role in HPV pathogenesis. In a collaborative study, we have identified miRNAs whose expression is altered in cell lines deficient in the Werner helicase or those containing mutations in DNA repair genes. The role of miRNAs in the aging process is currently being investigated. DNA helicases, replication of drug resistance and virulence plasmids, and bacterial pathogenesis. We are studying the rolling-circle (RC) replication of drug-resistance plasmids in Staphylococcus aureus. We are also studying the role of the PcrA helicase, which is essential for the growth and survival of Gram-positive organisms, in cellular DNA metabolism. We have shown that the S. aureus and Bacillus anthracis PcrA helicases are unusual in that they contain both 5’ to 3’ and 3’ to 5’ helicase activities. We have also shown that PcrA blocks DNA recombination in vitro by inhibiting RecA-catalyzed strand exchange reaction through displacement of RecA protein bound to the DNA. We are currently testing the hypothesis that the essential cellular function of PcrA involves the resolution of blocked recombination intermediates and/or stalled replication forks. In a collaborative study, we are also carrying out single-molecule studies dealing with the movement and interactions of the various PcrA domains during its translocation/helicase activities. Since PcrA is essential for cell survival, it may represent an important target for the development of novel antibacterial drugs against human pathogens. We are also studying the replication mechanisms of the pXO1 and pXO2 plasmids of B. anthracis that are involved in the pathogenesis of anthrax. We have identified the replication region of the pXO1 and pXO2 plasmids. We have found that the RepX replication initiator protein of pXO1 has similarity to the FtsZ and tubulin proteins. RepX is a GTPase that can polymerize in a GTP-dependent manner. We are currently studying the roles of RepX in pXO1 replication and segregation, including its possible co-localization with the cell division machinery. The eventual goal of these studies is to develop plasmid-specific drugs against B. anthracis and related organisms   Selected Publications Leuba SH, Anand SP, Harp JM, Khan SA. Expedient placement of two fluorescent dyes for investigating dynamic DNA protein interactions in real time. Chromosome Res. 2008;16(3):451-67. Anand SP, Akhtar P, Tinsley E, Watkins SC, Khan SA. GTP-dependent polymerization of the tubulin-like RepX replication protein encoded by the pXO1 plasmid of Bacillus anthracis. Mol Microbiol. 2008 Feb;67(4):881-90. Epub 2008 Jan 2. Tinsley E, Khan SA. A Bacillus anthracis-based in vitro system supports replication of plasmid pXO2 as well as rolling-circle-replicating plasmids. Appl Environ Microbiol. 2007 Aug;73(15):5005-10. Anand, S. P., Zheng, H., Bianco, P. R., Leuba, S. H. and Khan, S. A. DNA helicase activity of PcrA is not required for the displacement of RecA from DNA and inhibition of RecA-mediated strand exchange. J. Bacteriol. 2007 Jun;189, 4502-4509 (2007). Martinez, I., Wang, J., Hobson, K. F., Ferris, R. L. and Khan, S. A. Identification of differentially expressed genes in HPV-positive and HPV-negative squamous cell carcinomas of the head and neck. Eur. J. Cancer2007 Jan;43(2):415-32. Epub 2006 Oct 31. Complete Publication Listing   Grant Support NIH/NIDCR: Genomic and proteomic analysis of HPV-associated SCCHN. Principal Investigator NIH/NIGMS: Plasmid pT181 replication and PcrA helicase of S. aureus. Principal Investigator NIH/NIAID: Functions of the PcrA Helicase in Bacillus anthracis. Principal Investigator   Other Links MMG Faculty Webpage University of Pittsburgh

Saleem A Khan, Ph.D. Professor Office:  West 1243 Biomedical Science Tower Lab:West 1214A, West 1215, West 1216, West 1202 Biomedical Science Tower Phone:412-648-9025 Fax: 412-624-1401 khan@pitt.edu   Academic Affiliations Department of Microbiology and Molecular Genetics University of Pittsburgh School of Medicine Member, Biochemistry and Molecular Genetics Graduate Program University of Pittsburgh School of Medicine Pittsburgh Cancer Institute   Education 1970 - M. Sc. Biochemistry A. M. University, India 1975 - Ph.D. Biochemistry Indian Institute of Science Bangalore, India 1975-1977 - Postdoc Molecular Biology New York University School of Medicine Public Health Research Institute New York 1977-1982 - Postdoc Molecular Biology Public Health Research Institute New York   Lab Personnel Postdocs: Syam P. Anand Yugandhar Reddy Parvez Akhtar Jacobo Zuniga-Castillo Karen Thickman Graduate Students: Amy Gardiner Abigail Boster Technician: Katy Board