Proliferation-based Enrichment of HIV-infected Cells Reveals Distinct Clonally Expanded Cell Populations

Abstract

Antiretroviral therapy (ART) effectively controls HIV-1 disease and prevents transmission through suppression of viral replication to clinically undetectable levels. Yet, ART is not curative due to integration of the virus into the host genome which is maintained as a long-lived reservoir of HIV-infected cells. HIV-1 infected cells can undergo clonal expansion over time on ART and this clonal expansion is thought to be driven by three non-mutually exclusive mechanisms: antigen-driven proliferation, homeostatic proliferation, and integration site (IS)-driven proliferation. By developing and using methods that support ex vivo homeostatic proliferation of cells from HIV-infected donors, I was able to enrich for infected cell populations with a proliferative advantage. I compared approximately 720 HIV IS from CD4+ T cells from individuals on ART to approximately 106 IS from ex vivo expanded CD4+ T cells from the same participants to determine if HIV IS might contribute to survival advantage by altering gene expression of the integrated gene. I demonstrate that distinct populations of clonal cells emerge as a consequence of proliferation-based enrichment indicating a preferred fitness of these cells to expand in homeostatic proliferation conditions. I demonstrate that HIV-host chimeric transcripts are formed between the HIV LTR and the major clone, CPNE1. I discovered that HIV integration into the CPNE1 gene disrupts normal cellular splicing pathways and results in a reading frame shift and intron retention of the CPNE1 gene. Intron retention may lead to altered gene expression, thus representing a novel mechanism of HIV-driven dysregulation of host gene expression.