Rahul M. Kohli, M.D., Ph.D.

Assistant Professor, Medicine and Biochemistry & Biophysics

Office Address:
Perelman School of Medicine
University of Pennsylvania
502B Johnson Pavilion
36th and Hamilton Walk
Philadelphia, PA 19104-6073

TEL 215-573-7523
FAX 215-349-5111
rkohli@upenn.edu

Kohli Lab Site

RESEARCH SUMMARY

Our laboratory focuses on the enzymatic generation of genomic diversity. We utilize a broad array of approaches, including biochemical characterization of enzyme mechanisms, chemical synthesis of enzyme probes, and biological assays spanning immunology and virology to study this central tactic in the constant battle between our immune system and pathogens.

From the host immune perspective, the generation of genomic diversity is used as both a defensive and an offensive weapon. On the one hand, host mutator enzymes such as Activation-Induced Cytidine Deaminase (AID) seed diversity in the adaptive immune system by introducing targeted mutations into the immunoglobulin locus that result in high affinity antibodies (somatic hypermutation) or altered isotypes (class switch recombination). Conversely, related deaminases of the innate immune system can directly attack retroviral threats by garbling the pathogen genome through mutation, as accomplished by the deaminase APOBEC3G, which restricts infection with HIV. Immune mutator enzymes, however, also pose a risk to the host, as overexpression or dysregulation have been associated with oncogenesis.

From the pathogen perspective, alteration in key antigenic determinants at a rate that outpaces immune responses is a potent means for evasion. Further, rapid mutation may allow for the development of resistance to antimicrobials.

Our research program aims to understand the enzymatic basis for diversity generation in the immune system and pathogens. We further aim to harness these diversity-generating systems for directed evolution and to chemically perturb these pathways to impede pathogen escape or prevent the neoplastic transformations that can result from genomic mutation.

Rotation students are welcome starting Fall 2010.

Projects of interest to the laboratory include:

1. Decipher the molecular basis for deamination by AID/APOBEC enzymes and perturb deaminase immunological functions. Members of the AID/APOBEC family are linked by the ability to bind nucleic acids, but distinguished from one another by targeting distinctions, at a global level (host vs. pathogen genome) and at a local level (targeting distinct DNA hotspots for deamination). We use a combination of chemical perturbation of substrates with site-directed mutagenesis to decipher the molecular determinants of deamination and targeting. We further posit that mechanism based chemical probes will offer needed insight into polynucleotide deaminase function and yield lead compounds for inhibition of potentially oncogenic AID/APOBEC activity. We aim to translate biochemical insights into immunologic and virologic studies that can reveal the enzymatic roles in HIV restriction, antibody diversity and unwanted chromosomal translocations.
2. Harness the enzymes of antibody diversity for directed evolution. The generation of antibody diversity is the most powerful natural example of protein evolution. In this process, the targeted introduction of DNA lesions into the immunoglobulin locus is coupled to error-prone, rather than error-free, repair. Our growing understanding of the pathway of antibody diversification offers an opportunity to harness the power of these enzymes for directed protein evolution. We aim to introduce the enzymatic machinery of B-cells into E. coli to yield a robust system for diversification and selection of proteins with new and improved functions. This system has the potential to offer a means to continuous, inducible evolution, overcoming limitations to existing methods for protein evolution.
3. Target pathogen pathways that promote evolution and resistance. Pathogens diversity allows for escape from immune pressures or resistance to antimicrobials. Diversity can be introduced by multiple means in pathogens: error prone replication by HIV reverse transcriptase, activation of the SOS pathways in bacteria and antigenic variation via gene conversion in trypanosomes represent a few remarkable examples. These pathways share a common thread of using DNA repair or replication enzymes in error prone manners and either revealing preexisting hidden genetic variations or newly introducing mutations. Targeting the enzymes that allow for the emergence of pathogen diversity offers an appealing, novel target to prevent the emergence of resistance and attenuate pathogen virulence. We initially aim to characterize the enzymes involved in the SOS pathway in Pseudomonas and develop small molecule inhibitors of these enzymes for evaluation as anti-infective agents with the ability to prevent the emergence of drug resistance.