Comparison of the single-cell and single-nucleus hepatic myeloid landscape within decompensated cirrhosis patients

Front Immunol. 2024 Feb 6:15:1346520. doi: 10.3389/fimmu.2024.1346520. eCollection 2024.

Abstract

Background and aims: A complete understanding of disease pathophysiology in advanced liver disease is hampered by the challenges posed by clinical specimen collection. Notably, in these patients, a transjugular liver biopsy (TJB) is the only safe way to obtain liver tissue. However, it remains unclear whether successful sequencing of this extremely small and fragile tissue can be achieved for downstream characterization of the hepatic landscape.

Methods: Here we leveraged in-house available single-cell RNA-sequencing (scRNA-seq) and single-nucleus (snRNA-seq) technologies and accompanying tissue processing protocols and performed an in-patient comparison on TJB's from decompensated cirrhosis patients (n = 3).

Results: We confirmed a high concordance between nuclear and whole cell transcriptomes and captured 31,410 single nuclei and 6,152 single cells, respectively. The two platforms revealed similar diversity since all 8 major cell types could be identified, albeit with different cellular proportions thereof. Most importantly, hepatocytes were most abundant in snRNA-seq, while lymphocyte frequencies were elevated in scRNA-seq. We next focused our attention on hepatic myeloid cells due to their key role in injury and repair during chronic liver disease. Comparison of their transcriptional signatures indicated that these were largely overlapping between the two platforms. However, the scRNA-seq platform failed to recover sufficient Kupffer cell numbers, and other monocytes/macrophages featured elevated expression of stress-related parameters.

Conclusion: Our results indicate that single-nucleus transcriptome sequencing provides an effective means to overcome complications associated with clinical specimen collection and could sufficiently profile all major hepatic cell types including all myeloid cell subsets.

Keywords: cirrhosis; decompensated; single cell sequence (scRNA-seq); single nucleus RNA sequencing; transjugular biopsy.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Profiling* / methods
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Liver Cirrhosis / genetics
  • Liver Diseases*
  • RNA, Small Nuclear
  • Sequence Analysis, RNA / methods

Substances

  • RNA, Small Nuclear

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was supported by a research grant from The Research Foundation – Flanders (FWO; Fonds voor Wetenschappelijk Onderzoek – Vlaanderen) (G082018N), LM (1110121N) received a junior research mandate and SM a senior research mandate from FWO. Additionally, our research was supported by internal funding from KU Leuven (C14/18/087, C14/23/135 & AKUL/19/039). Financial support was also received from the Belgian Association for the Study of the Liver and a research grant from the Belgian Week of Gastroenterology (BWGE) to LM and UZ Leuven (KOOR) to JV. The authors declare that this study also received funding from Gilead Sciences. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication.