Single-cell RNA sequencing of liver fine-needle aspirates captures immune diversity in the blood and liver in chronic hepatitis B patients

Alex S. Genshaft, Sonu Subudhi, Arlin Keo, Juan Diego Sanchez Vasquez, Nádia Conceição-Neto, Deeqa Mahamed, Lauke L. Boeijen, Nadia Alatrakchi, Chris Oetheimer, Mike Vilme, Riley Drake, Ira Fleming, Nancy Tran, Constantine Tzouanas, Jasmin Joseph-Chazan, Martin Arreola Villanueva, Harmen J.G. van de Werken, Gertine W. van Oord, Zwier M.A. Groothuismink, Boris J. BeudekerZgjim Osmani, Shirin Nkongolo, Aman Mehrotra, Kurt Spittaels, Jordan Feld, Raymond T. Chung, Robert J. de Knegt, Harry L.A. Janssen, Jeroen Aerssens, Jacques Bollekens, Nir Hacohen, Georg M. Lauer, Andre Boonstra, Alex K. Shalek, Adam J. Gehring*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

7 Citations (Scopus)
73 Downloads (Pure)


Background and Aims: HBV infection is restricted to the liver, where it drives exhaustion of virus-specific T and B cells and pathogenesis through dysregulation of intrahepatic immunity. Our understanding of liver-specific events related to viral control and liver damage has relied almost solely on animal models, and we lack useable peripheral biomarkers to quantify intrahepatic immune activation beyond cytokine measurement. Our objective was to overcome the practical obstacles of liver sampling using fine-needle aspiration and develop an optimized workflow to comprehensively compare the blood and liver compartments within patients with chronic hepatitis B using single-cell RNA sequencing. Approach and Results: We developed a workflow that enabled multi-site international studies and centralized single-cell RNA sequencing. Blood and liver fine-needle aspirations were collected, and cellular and molecular captures were compared between the Seq-Well S3 picowell-based and the 10× Chromium reverse-emulsion droplet–based single-cell RNA sequencing technologies. Both technologies captured the cellular diversity of the liver, but Seq-Well S3 effectively captured neutrophils, which were absent in the 10× dataset. CD8 T cells and neutrophils displayed distinct transcriptional profiles between blood and liver. In addition, liver fine-needle aspirations captured a heterogeneous liver macrophage population. Comparison between untreated patients with chronic hepatitis B and patients treated with nucleoside analogs showed that myeloid cells were highly sensitive to environmental changes while lymphocytes displayed minimal differences. Conclusions: The ability to electively sample and intensively profile the immune landscape of the liver, and generate high-resolution data, will enable multi-site clinical studies to identify biomarkers for intrahepatic immune activity in HBV and beyond.

Original languageEnglish
Pages (from-to)1525-1541
Number of pages17
Issue number5
Publication statusPublished - Nov 2023

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Copyright © 2023 The Author(s). Published by Wolters Kluwer Health, Inc.


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