Integrome signatures of lentiviral gene therapy for SCID-X1 patients. Integrome signatures of lentiviral gene therapy for SCID-X1 patients

Lentiviral vector (LV)-based gene therapy holds promise for a broad range of diseases. Analyzing more than 280,000 vector integration sites (VISs) in 273 samples from 10 patients with X-linked severe combined immunodeficiency (SCID-X1), we discovered shared LV integrome signatures in 9 out of 10 patients in relation to the genomics, epigenomics, and 3D structure of the human genome. VISs were enriched in the nuclear sub-compartment A1 and integrated into super-enhancers close to nuclear pore complexes. These signatures were validated in T cells transduced with an LV encoding a CD19-specific chimeric antigen receptor. Intriguingly, the one patient whose VISs deviated from the identified integrome signatures had a distinct clinical course. Comparison of LV and gamma retrovirus integromes regarding their 3D genome signatures, identified differences that might explain the lower risk of insertional mutagenesis in LV-based gene therapy. Our findings suggest that LV integrome signatures, shaped by common features such as genome organization, may impact the efficacy of LV-based cellular therapies. Overall design: To confirm VIS signatures, we performed single-cell profilng for bone marrow samples of two SCID-X1 patients 18 months after gene transfusion.

基于慢病毒载体（Lentiviral Vector, LV）的基因治疗在多种疾病的治疗中展现出可观的应用前景。我们对10名X连锁重症联合免疫缺陷（X-linked Severe Combined Immunodeficiency, SCID-X1）患者的273份样本中的28万余个载体整合位点（Vector Integration Site, VIS）进行分析后发现，在10名患者中的9名体内存在与人类基因组的基因组学、表观基因组学及三维结构相关的共通慢病毒整合组特征。载体整合位点富集于细胞核A1亚区，并整合至靠近核孔复合物的超级增强子区域。上述特征在转导了编码CD19特异性嵌合抗原受体（chimeric antigen receptor）的慢病毒载体的T细胞中得到了验证。值得注意的是，仅有1名患者的载体整合位点与上述整合组特征不符，其临床病程也独具特色。通过对比慢病毒载体与γ逆转录病毒（gamma retrovirus）的三维基因组整合组特征，我们鉴定出二者的差异，这或可解释基于慢病毒载体的基因治疗为何插入诱变（insertional mutagenesis）风险更低。本研究结果表明，由基因组组织等共性特征塑造的慢病毒整合组特征，或可影响基于慢病毒载体的细胞治疗的疗效。整体实验设计：为验证载体整合位点特征，我们对2名X连锁重症联合免疫缺陷患者在基因转导18个月后的骨髓样本进行了单细胞分析。