RUI: Transcriptional regulation of host-pathogen viral symbiosis at single-cell resolution

Many viruses infect hosts for a lifetime. In order to do so, viruses must balance opposing needs that affect timing of the life cycle. On one hand, active replication is required to make more copies and propagate.

On the other hand, inactive dormancy is required to avoid host detection and immune responses that could clear the virus. These oscillations in viral growth involve changes in viral gene expression. The infected host cell counters with subsequent changes in its own gene expression to perturb the viral life cycle.

This competition between host and pathogen has been well studied at the population level. Emerging data in the field, however, argues that individual viruses in a population do not act in unison. To balance the risk of active replication with the safety of inactive dormancy, subpopulations may express different genes.

This project aims to study how viruses generate diverse subpopulations during both active replication and inactivate dormancy. Data obtained by a research team will then be analyzed by an undergraduate computational biology class specifically designed to write code for this project. Barnard College, a liberal arts school for women, will support this effort through collaboration with established program cohorts that recruit underrepresented minorities.

The integrated goals of the project are to advance knowledge of fundamental questions at the interface of virology and computer science while simultaneously increasing participation of underrepresented women in computational biology.

Human herpesvirus-8 (HHV-8) is a double stranded DNA virus that persists in the host by establishing a lifelong symbiotic infection. Persistence over years strongly depends on the ability of the virus to shut down transcription to a quiescent latent state not detectable by the host. Equally important is also the ability to spontaneously replicate in response to cellular stress and generate new virions to replenish a depleted reservoir.

While much work has been done to understand the molecular basis of this lytic reactivation in a bulk population, studies at single-cell resolution have been lacking. Preliminary data demonstrates that HHV-8 populations display clear heterogeneity with multiple subpopulations. HHV-8 reactivation is also enriched in one specific subpopulation with a distinct host transcriptional signature.

Specific Aim 1 will test the effect of identified candidate host genes on HHV-8 reactivation. Specific Aim 2 will identify which subpopulations respond most readily to different stimuli of reactivation. Both aims build on a wide body of literature in the microbial world demonstrating a transcriptional basis to bet-hedging within a heterogeneous population.

The sum of experiments will advance our knowledge of the single-cell transcriptomes that control HHV-8 reactivation. The Department of Biology at Barnard College is establishing a new major in computational biology. This project will specifically contribute through the establishment of a new course-based undergraduate research experience, “Computational ViroSystOmics,” based on the experiments performed. The course will integrate strategies mindful of pedagogical studies of gender in computer science.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.