The clinical applications of genome editing in HIV

Abstract

HIV/AIDS has long been at the forefront of the development of gene- and cell-based therapies. Although conventional gene therapy approaches typically involve the addition of anti-HIV genes to cells using semirandomly integrating viral vectors, newer genome editing technologies based on engineered nucleases are now allowing more precise genetic manipulations. The possible outcomes of genome editing include gene disruption, which has been most notably applied to the CCR5 coreceptor gene, or the introduction of small mutations or larger whole gene cassette insertions at a targeted locus. Disruption of CCR5 using zinc finger nucleases was the first-in-human application of genome editing and remains the most clinically advanced platform, with 7 completed or ongoing clinical trials in T cells and hematopoietic stem/progenitor cells (HSPCs). Here we review the laboratory and clinical findings of CCR5 editing in T cells and HSPCs for HIV therapy and summarize other promising genome editing approaches for future clinical development. In particular, recent advances in the delivery of genome editing reagents and the demonstration of highly efficient homology-directed editing in both T cells and HSPCs are expected to spur the development of even more sophisticated applications of this technology for HIV therapy.

Engineering HIV-Resistant, Anti-HIV Chimeric Antigen Receptor T Cells

“…[7][8][9][10][11] Because residual HIV expression continues despite effective ART [12][13][14][15][16] and is required for viral rebound, HIV-infected cells should theoretically be targetable by a T cell therapeutic agent. Several mechanisms are thought to be responsible for the apparent failure of autologous cytotoxic T lymphocytes (CTLs) to clear reactivated cells in HIV-infected individuals: HIV evolution prior to ART quickly selects for CTL escape mutations; [17][18][19] HIV Nef mediates downregulation of major histocompatibility complex class I (MHC-I), 20,21 protecting HIV-infected cells from T cell receptor (TCR)-dependent CTL killing; and HIV-specific CTL responses may be limited by exhaustion 22,23 or peripheral immune tolerance.…”

“…38 Hematopoietic stem cell transplant using a CCR5D32 donor led to the only known cure of HIV-1 infection, 39,40 and T cells treated with engineered nucleases that introduce mutations at the CCR5 locus are resistant to HIV, [41][42][43][44][45] accelerating ongoing efforts to develop gene editing-and cell-based therapeutic agents for HIV. 11,46 Using new gene-editing techniques, it has recently become possible to achieve high rates of homology-directed recombination (HDR) of therapeutic cassettes into targeted loci, including CCR5 in primary T cells. [47][48][49][50] We have previously shown introduction of cDNA expression cassettes at the CCR5 locus in primary human T cells using an mRNA-delivered megaTAL nuclease and a homologous AAV donor template at rates of up to 60%.…”

Recent advances in the use of ZFN-mediated gene editing for human gene therapy

“…CCR5 knockout via NHEJ was used in this strategy, since gene modification efficiency by HDR is relatively low. ZFN-in-duced genome editing of CCR5 is the most clinically advanced platform, with several ongoing clinical trials in T cells and HSPCs [22]. …”

“…The therapeutic effects of the ZFN treatment in five patients were monitored by a 12-week interruption of ART. The study established that the rate of decline of the CCR5-modified CD4 + T cells was slower than that of the unmodified cells, indicating a protective effect of CCR5 disruption [22]. One patient showed both delayed viral rebound and a peak viral count that was lower than the patient’s historical levels.…”

Clinical Applications of Genome Editing to HIV Cure

“…[26][27][28][29][30] Parameters being tested include the input T cell dose, number of infusions, inclusion of ZFNmodified CD8 T cells, a T cell depleting conditioning treatment using Cytoxan to improve engraftment of infused cells, and switching the method of ZFN delivery from adenoviral vectors to mRNA electroporation. 31 One trial is also evaluating the impact of CCR5D32 heterozygosity by recruiting a cohort of 10 heterozygous patients. 26 Eight weeks postinfusion, these patients underwent a 16-week ATI, during which three patients maintained markedly reduced viremia at low (<1000 copies/mL) or undetectable levels.…”