The John Coffin Lab

Research Publications Genetics Microbiology


 Retrovirus - Host Interaction 

Our research interests revolve around many different subjects relevant to obtaining a better understanding of the interaction of retroviruses with their host cells and organisms.  Over the past few decades, retroviruses have been remarkably rewarding objects for study, and have revealed and illuminated many aspects of biology, including evolution of host-pathogen relationships, mechanisms of disease, including cancer, AIDS, and others, cellular signaling and trafficking, and fundamental mechanisms of evolution. 

Avian Retroviruses and the Evolution of Retrovirus - Receptor Interaction

Avian retroviruses are remarkable in that they have been able to evolve fairly recently to use completely different cell surface proteins as receptors, a process which must involve changes in the hr 2 and 2 regions of the envelope protein necessary for binding and entry. Since there is considerable variation in receptor availability among the natural host (the chicken) of these viruses, such adaptability is crucial for their long-term survival.  To study the evolution of receptor usage, we have obtained numerous mutations in a small portion of hr1, all of which confer on the virus the ability to enter cells independent of receptor binding.  We are testing the mechanism of this effect, as well as the hypothesis that such mutations represent the first step in a complex evolutionary pathway toward use of a completely different receptor.

Mechanism and Specificity of Viral DNA Integration into the Host Genome

By data mining of large libraries of sequences flanking integrate HIV, MLV, and ALV proviruses, we uncovered a surprising preference for specific bases at specific positions relative to the integrated provirus, and an even more surprising symmetry of the base preferences relative to its ends.

Coffin Fig 1 

Figure 1. Distribution of specific bases relative to the sites of joining of the ends of HIV DNA to cell DNA (dotted lines).  The sequence of the two different strands is colored differently.  Note the striking symmetry around the midpoint of integration (arrow).

Mechanism of Retroviral Genetic Variation

We have been particularly interested in recombination which occurs when a cell is infected with a heterozygous virion that contains genomes derived from two different proviruses.  To study the potential of such virions to promote recombination we developed a tagging technique to label virus RNA with fluorescent dye fused to specific RNA binding proteins.  In collaboration with the laboratory of Wei-Shau Hu, at NCI-Frederick, we were able to visualize the genome RNA content of HIV virions made by cells with two different proviruses and show that distribution among virions was completely random, but could be strongly affected by a few specific base changes.

Coffin Fig 2

Figure 2. Each set of dots represents an HIV virion, with the two different genomes tagged red or green.  Arrows mark heterozygous virions containing both types of RNA, with wild-type (left) dimer linkage sequence, or simple mutations that suppress (middle) or enhance (right) dimer formation.

The "Fossil" Record of Endogenous Proviruses and Virus - Host Evolution

Endogenous proviruses are found in the normal DNA of all vertebrates and many other species.  Proviruses and fragments comprise more than 8% of the human genome, several fold more than genes.  When a relatively benign virus is transmitted to a new species, it can become much more virulent, leading to adaptation of both host and virus toward a more benign relationship.  During this process, some retroviruses can become established in the host genome as endogenous proviruses and transmitted to its descendant species, even long after the infectious virus has become extinct.

Coffin Fig 3 

Figure 3. The illustration depicts aspects of the relationship of endogenous retroviruses to their hosts.

We are pursuing the association of these viruses with human disease, such as the human endogenous virus HERV-K and breast cancer, as well as the newly described XMRV, a close relative of endogenous viruses of mice.  Finally, we are modeling the complex relationship between HIV and the infected host, with the goal of understanding the role of specific evolutionary forces in shaping the extraordinary genetic diversity of the virus, leading to important consequences such as resistance to antiviral drugs.



Apply to the Sackler School


The priority application deadlines are as follows:

December 1: Basic Science Division PhD Programs

February 15: Building Diversity in Biomedical Sciences

March 31: Post-Baccalaureate Research Program

May 1: Clinical & Translational Science, MS in Pharmacology & Drug Development

June 15: Online Certificate in Fundamentals of Clinical Care Research