CRISPR/Cas9-Mediated CCR5 Ablation in Human Hematopoietic Stem/Progenitor Cells Confers HIV-1 Resistance In Vivo

Abstract

Transplantation of hematopoietic stem cells (HSCs) with a naturally occurring CCR5 mutation confers a loss of detectable HIV-1 in the patient, making ablation of the CCR5 gene in HSCs an ideal therapy for an HIV-1 cure. Although CCR5 disruption has been attempted in CD4⁺ T cells and hematopoietic stem/progenitor cells (HSPCs), efficient gene editing with high specificity and long-term therapeutic potential remains a major challenge for clinical translation. Here, we established a CRISPR/Cas9 gene editing system in human CD34⁺ HSPCs and achieved efficient CCR5 ablation evaluated in long-term reconstituted NOD/Prkdc^scid/IL-2Rγ^null mice. The CCR5 disruption efficiency in our system remained robust in secondary transplanted repopulating hematopoietic cells. More importantly, an HIV-1 resistance effect was observed as indicated by significant reduction of virus titration and enrichment of human CD4⁺ T cells. Hence, we successfully established a CRISPR/Cas9 mediated CCR5 ablating system in long-term HSCs, which confers HIV-1 resistance in vivo. Our study provides evidence for translating CCR5 gene-edited HSC transplantation for an HIV cure to the clinic.

Keywords: CCR5; CRISPR; HIV-1/AIDS; gene editing; gene therapy; hematopoietic stem cell.

Graphical abstract

Figure 1

Efficient CCR5 Ablation In Vitro and In Vivo (A) Flowchart of sgRNA pair selection. The off-target effects of sgRNA pairs were predicted using multiple bioinformatic prediction tools, and high off-target pairs were eliminated. The remaining pairs were transfected with CRISPR/Cas9 into a cell line, and the cleavage efficiency was determined using T7 endonuclease I (T7EI) assay. (B) T7EI assay of CCR5 gene ablation in K562 cells and human CD34⁺ cells in a representative experiment. (C) Human CD34⁺ cells treated with the CRISPR/Cas9 system were analyzed in the CFU assay, and different types of colonies were presented. Scale bars, 200 μm. (D) Various types of colonies were counted for CRISPR/Cas9-treated or non-treated CD34⁺ cells. (E) Human CD45⁺ cell reconstitution was evaluated in peripheral blood in NPG mice transplanted with gene-edited HSPCs. Robust reconstitution was detected in mice from 6 to 12 weeks post-transplantation (mean values, 0.9%, 2.2%, 9.6%, and 9.9%; n = 9). (F) Human hematopoietic cell reconstitution of CCR5-disrupted or non-treated HSPCs in mouse peripheral blood lymphocytes collected at week 12 (mean ± SEM, n = 9). (G) Representative assay showing efficient human CCR5 disruption in peripheral blood of reconstituted mice 12 weeks after transplantation. The PCR products (647 bp) were digested into two fragments (465 and 182 bp), indicating effective CCR5 disruption. ΔCCR5, CCR5 gene ablation; Ctrl, non-treatment control.

Figure 2

Human Cell Chimerism and Feature of CCR5 Indels in Long-Term Reconstituted Mice (A) Chimerism and human T cell reconstitution of HSPCs after gene editing in multiple organs from representative reconstituted mice. Human CD3⁺ (huCD3), human CD4⁺ (huCD4), and human CD8⁺ (huCD8) cells were gated from human CD45⁺ (huCD45) cells. (B) Representative T7EI data from one long-term reconstituted mouse show multi-lineage activity of human HSPCs in multiple organs. B lymphocytes (CD19⁺), myeloid cells (CD33⁺), and NK cells (CD56⁺) were detected. (C) Features of CCR5 indels in long-term reconstituted mice. The PCR products of human CCR5 gene in long-term reconstitution mice were sequenced and analyzed (n = 12). The predictable indel (35-bp deletion) was present at a dominant rate (107/122, 87.7%).

Figure 3

CCR5 Ablation and Reconstitution in Secondary Transplanted Mice (A) Proportion of huCD45 in cells from bone marrow (BM), peripheral blood (PB), spleen, and thymus of four secondary transplanted mice after 12 weeks of reconstitution. Data from the same mouse were shown in the same color and shape. (B) Human CD34⁺/38⁻/45RA⁻/90⁺ HSPCs were detected in the bone marrow from secondary transplantation mice. (C) T7EI assay showing efficient CCR5 disruption of human hematopoietic cells in secondary transplantation mice after 12 weeks of reconstitution. (D) CCR5 indel efficiency was summarized from an in vitro experiment (in vitro, 27.0 ± 5, n = 3), primary transplanted mice of 12 weeks (primary, 32.2 ± 1.6, n = 5), long-term reconstituted mice (long-term, 31.2 ± 4.9, n = 12), and secondary transplanted mice (secondary, 24.7 ± 3.8, n = 9). Data are represented as mean ± SEM.

Figure 4

HIV-1 Resistance and the Selection Effect (A) HIV-1 RNA level was detected after Bal-1 virus strain infection in the peripheral blood plasma of NPG mice, which were transplanted with CCR5-disrupted (CCR5⁻) or non-treated control (Ctrl) HSPCs (mean ± SEM, n = 3). (B) The fold change of human CD4⁺ and human CD8⁺ cells in the peripheral blood of mice was evaluated based on the ratio of reconstitution from 6 to 8 weeks post-infection (mean ± SEM; p = 0.026, n = 3). (C) CCR5 locus of human cells in mouse peripheral blood was analyzed pre- and post-HIV challenge. Percentage of indel alleles significantly increased 8 weeks after Bal-1 HIV-1 infection, indicating the enrichment of CCR5 disruption. p = 0.042, n = 3.