Single-nucleus RNA-seq reveals dysregulation of striatal cell identity due to Huntington's disease mutations

Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder caused by a trinucleotide expansion in exon 1 of the huntingtin (Htt) gene. Cell death in HD occurs primarily in striatal medium spiny neurons (MSNs), but the involvement of specific MSN subtypes and of other striatal cell types remains poorly understood. To gain insight into cell type-specific disease processes, we studied the nuclear transcriptomes of 4,524 cells from the striatum of a genetically precise knock-in mouse model of the HD mutation, HttQ175/+, and from wildtype controls. We used 14-15-month-old mice, a time point roughly equivalent to an early stage of symptomatic human disease. Cell count distributions indicated selective loss of D2 MSNs and increased microglia in aged HttQ175/+ mice. Thousands of differentially expressed genes were distributed across most striatal cell types, including transcriptional changes in glial populations that are not apparent from RNA-seq of bulk tissue. Reconstruction of cell type-specific transcriptional networks revealed a striking pattern of bidirectional dysregulation for many cell type-specific genes. Typically, these genes were repressed in their primary cell type, yet de-repressed in other striatal cell types. Integration with existing epigenomic and transcriptomic data suggest that partial loss-of-function of the Polycomb Repressive Complex 2 (PRC2) may underlie many of these transcriptional changes, leading to deficits in the maintenance of cell identity across virtually all cell types in the adult striatum. Single nucleus RNA sequencing of striatums of three wild type (WT) and four HttQ175/+ 14-15 month old mice亨廷顿舞蹈病（Huntington's disease, HD）是一种常染色体显性遗传性神经退行性疾病，由亨廷顿（huntingtin, Htt）基因第1外显子的三核苷酸重复扩增致病。HD的细胞死亡主要累及纹状体中型多棘神经元（medium spiny neurons, MSNs），但特定MSN亚型及其他纹状体细胞类型的参与机制仍未明确。为深入解析疾病的细胞类型特异性致病过程，本研究对HD突变精准基因敲入小鼠模型HttQ175/+以及野生型对照小鼠的纹状体共4524个细胞的核转录组开展了分析。实验选用14~15月龄的小鼠，该时间节点大致对应人类症状性疾病的早期阶段。细胞计数分布分析显示，老年HttQ175/+小鼠中D2型MSNs发生选择性丢失，小胶质细胞数量显著增加。数千个差异表达基因遍布绝大多数纹状体细胞类型，其中包括从整体组织RNA-seq中难以观测到的胶质细胞群体转录变化。细胞类型特异性转录网络重构揭示，众多细胞类型特异性基因呈现显著的双向失调模式：这类基因在其原发细胞类型中通常被抑制，却在其他纹状体细胞类型中发生去抑制。结合现有表观基因组与转录组数据的整合分析表明，多梳抑制复合体2（Polycomb Repressive Complex 2, PRC2）的部分功能缺失可能是此类多数转录变化的潜在机制，进而导致成年纹状体几乎所有细胞类型的细胞身份维持缺陷。本研究同时对3只野生型（wild type, WT）与4只14~15月龄HttQ175/+小鼠的纹状体进行了单细胞核RNA测序。