单细胞、单细胞核和空间 RNA 测序鉴定人类肝脏中的胆管细胞和间充质异质性。

Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity.

机构信息

Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada.

Department of Immunology, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto, ON, Canada.

出版信息

Hepatol Commun. 2022 Apr;6(4):821-840. doi: 10.1002/hep4.1854. Epub 2021 Nov 18.

Abstract

The critical functions of the human liver are coordinated through the interactions of hepatic parenchymal and non-parenchymal cells. Recent advances in single-cell transcriptional approaches have enabled an examination of the human liver with unprecedented resolution. However, dissociation-related cell perturbation can limit the ability to fully capture the human liver's parenchymal cell fraction, which limits the ability to comprehensively profile this organ. Here, we report the transcriptional landscape of 73,295 cells from the human liver using matched single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq). The addition of snRNA-seq enabled the characterization of interzonal hepatocytes at a single-cell resolution, revealed the presence of rare subtypes of liver mesenchymal cells, and facilitated the detection of cholangiocyte progenitors that had only been observed during in vitro differentiation experiments. However, T and B lymphocytes and natural killer cells were only distinguishable using scRNA-seq, highlighting the importance of applying both technologies to obtain a complete map of tissue-resident cell types. We validated the distinct spatial distribution of the hepatocyte, cholangiocyte, and mesenchymal cell populations by an independent spatial transcriptomics data set and immunohistochemistry. Conclusion: Our study provides a systematic comparison of the transcriptomes captured by scRNA-seq and snRNA-seq and delivers a high-resolution map of the parenchymal cell populations in the healthy human liver.

摘要

人类肝脏的关键功能是通过肝实质细胞和非实质细胞的相互作用来协调的。单细胞转录组学方法的最新进展使得人们能够以前所未有的分辨率来研究人类肝脏。然而,与分离相关的细胞扰动会限制全面捕获人类肝脏实质细胞部分的能力,从而限制了全面描绘该器官的能力。在这里,我们使用匹配的单细胞 RNA 测序(scRNA-seq)和单核 RNA 测序(snRNA-seq)报告了来自人类肝脏的 73295 个细胞的转录图谱。snRNA-seq 的加入使我们能够以单细胞分辨率描述区域间肝细胞,揭示了肝脏间充质细胞罕见亚型的存在,并有助于检测到仅在体外分化实验中观察到的胆管祖细胞。然而,T 和 B 淋巴细胞和自然杀伤细胞只能通过 scRNA-seq 区分,这突出了应用这两种技术获得组织驻留细胞类型完整图谱的重要性。我们通过独立的空间转录组学数据集和免疫组织化学验证了肝细胞、胆管细胞和间充质细胞群体的独特空间分布。结论:本研究对 scRNA-seq 和 snRNA-seq 捕获的转录组进行了系统比较,并提供了健康人类肝脏实质细胞群体的高分辨率图谱。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e93d/8948611/2281276792fd/HEP4-6-821-g001.jpg

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