Saleem A. Khan, PhD

Areas of research: Molecular biology and pathogenesis of human papillomaviruses (HPVs); Genomic, proteomic and microRNA analyses of HPV-associated cervical and oral cancers; Rolling-circle replication of drug resistance plasmids in Staphylococcus aureus; Role of the PcrA helicases of S. aureus and Bacillus anthracis in cellular DNA metabolism; Plasmid determinants of anthrax pathogenesis Human papillomaviruses (HPVs). Dr. Khan’s laboratory is studying the molecular mechanisms that regulate HPV gene expression during cellular differentiation, including the identification of cellular transcription factors that activate HPV gene expression. Another goal of the laboratory is to identify 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 are also carrying out proteomic studies to identify proteins that can serve as biomarkers for the progression of HPV-associated disease. 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 compared to the normal cervix. 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 also found that miR-218 expression parallels that of the tumor suppressor gene SLIT2 whose intron encodes miR-218. 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, including the biochemical activities associated with the plasmid-encoded initiator proteins. We are also studying the role of the PcrA helicase, which is essential for the growth and survival of Gram-positive organisms, in plasmid RC replication as well as in cellular DNA metabolism. We have purified the S. aureus and Bacillus anthracis PcrA helicases and shown that they 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 such as S. aureus and B. anthracis. We are also studying the replication mechanisms of the pXO1 and pXO2 virulence plasmids of B. anthracis that are involved in the pathogenesis of anthrax. We have identified the replication region of the pXO1 and pXO2 plasmids and studied the biochemical activities of the RepS replication initiator protein encoded by the pXO2 plasmid. We have also found that the RepX replication initiator protein of pXO1 has a GTPase domain and has similarity to the eubacterial FtsZ proteins that are involved in cell division. We have recently shown that, similar to FtsZ, the RepX protein 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.