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

TLDR

The human liver’s critical functions depend on interactions between parenchymal and non‑parenchymal cells, and recent single‑cell transcriptional methods allow unprecedented resolution, though dissociation can limit profiling of parenchymal cells. We profiled 73,295 liver cells with matched scRNA‑seq and snRNA‑seq to map the organ’s transcriptional landscape. Spatial transcriptomics and immunohistochemistry confirmed the distinct localization of hepatocyte, cholangiocyte, and mesenchymal populations. Adding snRNA‑seq revealed interzonal hepatocytes, rare mesenchymal subtypes, and cholangiocyte progenitors, while scRNA‑seq uniquely identified T, B, and NK cells, demonstrating that both methods are required for a complete liver cell map.

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.