OhAinle Group

Virus

Dr. Molly Ohainle is a Senior Staff Scientist that directs her own NIH-funded research in the Emerman Lab. Dr. Ohainle created a novel CRISPR screening method to identify genes important for inhibiting or enhancing HIV infection in cells, HIV-CRISPR screening (Ohainle et al eLife 2018).

Current work in the Ohainle Group includes:

  1. Screens identify genes responsible for inhibiting the replication of HIV-1 and related primate lentiviruses
  2. Studies aimed at understanding the mechanism of restriction of lentiviral capsids by TRIM34, an HIV restriction factor identified through HIV-CRISPR screening
  3. Development of novel functional genomics tools to understand host restrictions and virus adaptation

The Ohainle Group’s research combines both high throughput functional genomics approaches and molecular virology approaches to understand basic mechanisms of viral replication, host antiviral effector function, virus transmission (intra- and inter-species transmission) and virus adaptation to host barriers.

(You can find us on Twitter @MollyOhainle)

Current Projects

HIV-CRISPR Screening: Restriction Factor Discovery

HIV-CRISPR image

To infect human cells transmitted viruses must adapt to counteract the arsenal of human restriction factors encoded in the genome. HIV has evolved to escape or antagonize restriction factor barriers, thereby allowing for adaptation for replication in human cells. These host-encoded restriction factors play a key role in limiting infection of HIV and SIVs. By studying HIV strains and mutants that are not well-adapted to human cells we can better understand important human restriction barriers. Currently we are using HIV-CRISPR screening to identify key host cell restrictions blocking infection by a diverse array of HIV and SIV variants. Restriction factors that target the HIV capsid, key to delivery of HIV genomes into the host cell and to/through nuclear pores, are a major focus of the lab. The high-throughput nature, adaptability to different CRISPR sgRNA libraries, assay of the complete HIV lifecycle inside a cell and portability to other cell and viral systems make HIV-CRISPR screening a major step forward in the study of HIV restriction factor biology.

Mechanism of restriction of HIV and other primate lentiviruses by TRIM34

The HIV capsid gene (p24 or CA) forms the core of the HIV virion and is key to effective uncoating and delivery of the HIV genome into the nucleus where integration into the host chromosome can occur. Through HIV-CRISPR Screening we’ve recently found that a single amino acid CA mutation leads to enhanced susceptibility of HIV to a novel cellular restriction mediated by TRIM34. Our initial studies of TRIM34 show that it inhibits HIV at reverse transcription, requires its close paralog, TRIM5alpha, for its antiviral activity and inhibits a broad range of primate lentiviruses. Understanding the evolution and function of TRIM34 are a major focus of the lab.

  • How does TRIM34 inhibit the replication of restricted capsids?
  • Did HIV evolve to evade TRIM34 restriction during adaptation from primates?
  • Does TRIM34 restrict HIV evolution in HIV-infected individuals? 
HIV CA
TRIM

Further Development of Functional Genomics Tools in host/virus biology

We are continuing to develop functional genomics methods to understand host cell restrictions and virus adaptation to these barriers. This work includes adapting HIV-CRISPR screening to more cell systems (including primary CD4+ T cells in collaboration with the Overbaugh Lab @ Fred Hutch) and the development of a Deep Mutational Scanning Method to probe the function of mutations in HIV Capsid on restriction factor sensitivity and resistance. In collaboration we are also exploring expanding our work to include other viral pathogens, including SARS-CoV-2. Watch this space for more to come…

Current and Past Trainees

Graduate Students

  • Joy Twentyman (UW Pathobiology Graduate Program) – joined June 2020

Research Technicians

  • Juliana Olliff – joined August 2020
  • Abby Felton

Alumni

  • Sydney Fine – research tech I
  • Louisa Pendergast – research tech I

*we are always looking for great people. We are particularly keen on supporting those from underrepresented groups on their scientific path. Wondering if this is you? Reach out by email and let’s find out.

News

September 2020: the HIV-CRISPR vector and ISG-specific library (PIKAHIV) are now available through the NIH AIDS Reagent Program.

August 2020: Juliana Olliff joins as a research tech I. Welcome Juliana!

Summer 2020: Isabella Vazquez joins for a virtual summer undergraduate research internship through NSURP from CalPoly Pomona. Welcome Isabella!

June 2020: Sydney Fine leaves to start her MPH at the University of Michigan School of Public Health. Good luck Sydney!

June 2020: Joy Twentyman joins the Ohainle Group, our first graduate student. Welcome Joy!

May 2020: HIV-CRISPR Screening protocol published in bioprotocol.

May 2020: ISG-specific Human CRISPR Knockout Library deposited and available @ Addgene.

April 2020: Our newest paper describing TRIM34 inhibition of HIV-1 and SIV capsids is published in PLoS Pathogens.

November 2019: TRIM34 paper is up on biorxiv.

August 2019: The Ohainle lab receives a Collaborative Development Award (CDA) from the CHEETAH (Center for the Structural Biology of Cellular Host Elements in Egress, Trafficking and Assembly of HIV)

June 2019: The Ohainle Lab is awarded an R01 to find and study CA-targeting HIV restriction factors.

May 2019: Molly is awarded the Andy Kaplan Prize at the Cold Spring Harbor Retroviruses meeting.

December 2018: The HIV-CRISPR screen is published in eLife.

Selected Publications

Selected publications are listed below. For a complete list of publications, see Molly’s NCBI bibliography.

2020:

Ohainle M.*, Kim K., Keceli S., Felton A., Luban J., Campbell E., Emerman M.* (2020) TRIM34 restricts HIV-1 and SIV capsids in a TRIM5alpha-dependent manner. PLOS Pathogens 16(4): e1008507. (BioRxiv preprint doi: https://doi.org/10.1101/820886).
*co-corresponding authors

Roesch, F. and Ohainle, M. (2020). HIV-CRISPR: A CRISPR/Cas9 Screening Method to Identify Genes Affecting HIV Replication. Bio-protocol 10(9):e3614. DOI: 10.21769/BioProtoc.3614.

2019:

Ohainle, M.*, Kim, K., Keceli, S., Felton, A., Campbell, E.M., Luban, J., and Emerman, M.* (2019). TRIM34 acts with TRIM5 to restrict HIV and SIV capsids. bioRxiv, 820886.
*co-corresponding authors

Sharma, A., McLaughlin, R.N., Jr., Basom, R.S., Kikawa, C., OhAinle, M., Yount, J.S., Emerman, M., and Overbaugh, J. (2019). Macaque interferon-induced transmembrane proteins limit replication of SHIV strains in an Envelope-dependent manner. PLoS Pathog 15, e1007925.

2018:

OhAinle, M.*, Helms, L., Vermeire, J., Roesch, F., Humes, D., Basom, R., Delrow, J.J., Overbaugh, J., and Emerman, M.* (2018). A virus-packageable CRISPR screen identifies host factors mediating interferon inhibition of HIV. Elife 7.
*co-corresponding authors

Roesch, F., OhAinle, M., and Emerman, M. (2018). A CRISPR screen for factors regulating SAMHD1 degradation identifies IFITMs as potent inhibitors of lentiviral particle delivery. Retrovirology 15, 26.

Reagents & Protocols

Addgene:
Human Interferon-Stimulated Gene CRISPR Knockout Library (Pooled Library #125753)

NIH AIDS Reference and Reagent Repository:
HIV-CRISPR Vector (Catalog #13567)
PIKAHIV library (Catalog #13566)

Bioprotocol
HIV-CRISPR Screening

Collaborations

Luban Lab – UMass

Pornillos/Ganser-Pornillos Labs – University of Virginia

Campbell Lab – Loyola University Chicago

Overbaugh Lab - Fred Hutch 

Hahn Lab – University of Pennsylvania, Perelman School of Medicine

Ferdinand Roesch – Pasteur Institute (Vignuzzi Lab)

SAGE Bionetworks