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Background  The CRISPR/Cas9 system has been widely used for genome editing in mammalian cells. CXCR4 is a co-receptor for human immunodeficiency virus type 1 (HIV-1) entry, and loss of  CXCR4  function can protect cells from CXCR4 (X4)-tropic HIV-1 infection, making  CXCR4  an important target for HIV-1 gene therapy. However, the large size of the CRISPR/SpCas9 system presents an obstacle to its efficient delivery into primary CD4 +  T cells. Recently, a small  Staphylococcus aureus  Cas9 (SaCas9) has been developed as a genome editing tool can address this question. Therefore, it provides a promising strategy for HIV-1 gene therapy if it is used to target CXCR4.    Results  Here, we employed a short version of Cas9 from  Staphylococcus aureus  (SaCas9) for targeting  CXCR4 . We demonstrated that transduction of lenti-virus expressing SaCas9 and selected single-guided RNAs of  CXCR4  in human CD4 +  T cell lines efficiently induced the editing of the  CXCR4  gene, making these cell lines resistant to X4-tropic HIV-1 infection. Moreover, we efficiently transduced primary human CD4 +  T cells using adeno-associated virus-delivered CRISPR/SaCas9 and disrupted CXCR4 expression. We also showed that  CXCR4 -edited primary CD4 +  T cells proliferated normally and were resistant to HIV-1 infection.    Conclusions  Our study provides a basis for possible application of  CXCR4 -targeted genome editing by CRISPR/SaCas9 in HIV-1 gene therapy.    Electronic supplementary material  The online version of this article (10.1186/s12977-017-0375-0) contains supplementary material, which is available to authorized users.

Genome modification of CXCR4 by Staphylococcus aureus Cas9 renders cells resistance to HIV-1 infection