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Genshaft AS, Subudhi S, Keo A, Sanchez Vasquez JD, Conceição-Neto N, Mahamed D, Boeijen LL, Alatrakchi N, Oetheimer C, Vilme M, Drake R, Fleming I, Tran N, Tzouanas C, Joseph-Chazan J, Arreola Villanueva M, van de Werken HJG, van Oord GW, Groothuismink ZMA, Beudeker BJ, Osmani Z, Nkongolo S, Mehrotra A, Spittaels K, Feld J, Chung RT, de Knegt RJ, Janssen HLA, Aerssens J, Bollekens J, Hacohen N, Lauer GM, Boonstra A, Shalek AK, Gehring AJ. Single-cell RNA sequencing of liver fine-needle aspirates captures immune diversity in the blood and liver in chronic hepatitis B patients. Hepatology 2023; 78:1525-1541. [PMID: 37158243 PMCID: PMC10581444 DOI: 10.1097/hep.0000000000000438] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 03/07/2023] [Accepted: 03/20/2023] [Indexed: 05/10/2023]
Abstract
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 S 3 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 S 3 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.
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Affiliation(s)
- Alex S. Genshaft
- Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Massachusetts, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sonu Subudhi
- Liver Center, Division of Gastroenterology and Liver Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Arlin Keo
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
| | - Juan Diego Sanchez Vasquez
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Nádia Conceição-Neto
- Infectious Diseases Biomarkers, Janssen Research and Development, Beerse, Belgium
| | - Deeqa Mahamed
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Lauke L. Boeijen
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Nadia Alatrakchi
- Liver Center, Division of Gastroenterology and Liver Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Chris Oetheimer
- Liver Center, Division of Gastroenterology and Liver Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Mike Vilme
- Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Massachusetts, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Riley Drake
- Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Massachusetts, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ira Fleming
- Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Massachusetts, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Nancy Tran
- Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Massachusetts, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Constantine Tzouanas
- Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Massachusetts, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jasmin Joseph-Chazan
- Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Massachusetts, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Martin Arreola Villanueva
- Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Massachusetts, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Harmen J. G. van de Werken
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
- Department of Immunology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
| | - Gertine W. van Oord
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Zwier M. A. Groothuismink
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Boris J. Beudeker
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Zgjim Osmani
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Shirin Nkongolo
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Aman Mehrotra
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Kurt Spittaels
- Infectious Diseases Biomarkers, Janssen Research and Development, Beerse, Belgium
| | - Jordan Feld
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Raymond T. Chung
- Liver Center, Division of Gastroenterology and Liver Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Robert J. de Knegt
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Harry L. A. Janssen
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Jeroen Aerssens
- Infectious Diseases Biomarkers, Janssen Research and Development, Beerse, Belgium
| | - Jacques Bollekens
- Infectious Diseases Biomarkers, Janssen Research and Development, Beerse, Belgium
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Georg M. Lauer
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, Massachusetts, USA
| | - Andre Boonstra
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Alex K. Shalek
- Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Massachusetts, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Adam J. Gehring
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
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Montanari NR, Ramírez R, Aggarwal A, van Buuren N, Doukas M, Moon C, Turner S, Diehl L, Li L, Debes JD, Feierbach B, Boonstra A. Multi-parametric analysis of human livers reveals variation in intrahepatic inflammation across phases of chronic hepatitis B infection. J Hepatol 2022; 77:332-343. [PMID: 35218813 DOI: 10.1016/j.jhep.2022.02.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/31/2022] [Accepted: 02/13/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Chronic HBV is clinically categorized into 4 phases by a combination of serum HBV DNA levels, HBeAg status and alanine aminotransferase (ALT): immunotolerant (IT), immune-active (IA), inactive carrier (IC) and HBeAg-negative hepatitis (ENEG). Immune and virological measurements in the blood have proven useful but are insufficient to explain the interrelation between the immune system and the virus since immune dynamics differ in the blood and liver. Furthermore, the inflammatory response in the liver and parenchymal cells cannot be fully captured in blood. METHODS Immunological composition and transcriptional profiles of core needle liver-biopsies in chronic HBV phases were compared to those of healthy controls by multiplex immunofluorescence and RNA-sequencing (n = 37 and 78, respectively) analyses. RESULTS Irrespective of the phase-specific serological profiles, increased immune-gene expression and frequency was observed in chronic HBV compared to healthy livers. Greater transcriptomic deregulation was seen in IA and ENEG (172 vs. 243 DEGs) than in IT and IC (13 vs. 35 DEGs) livers. Interferon-stimulated genes, immune-activation and exhaustion genes (ICOS, CTLA4, PDCD1) together with chemokine genes (CXCL10, CXCL9) were significantly induced in IA and ENEG livers. Moreover, distinct immune profiles associated with ALT elevation and a more accentuated immune-exhaustion profile (CTLA4, TOX, SLAMF6, FOXP3) were observed in ENEG, which set it apart from the IA phase (LGALS9, PDCD1). Interestingly, all HBV phases showed downregulation of metabolic pathways vs. healthy livers (fatty and bile acid metabolism). Finally, increased leukocyte infiltrate correlated with serum ALT, but not with HBV DNA or viral proteins. CONCLUSION Our comprehensive multi-parametric analysis of human livers revealed distinct inflammatory profiles and pronounced differences in intrahepatic gene profiles across all chronic HBV phases in comparison to healthy liver. LAY SUMMARY Immunological studies on chronic HBV remain largely restricted to assessment of peripheral responses due to the limited access to the site of infection, the liver. In this study, we comprehensively analyzed livers from a well-defined cohort of patients with chronic HBV and uninfected controls with state-of-the-art techniques, and evaluated the differences in gene expression profiles and inflammation characteristics across distinct disease phases in patients with chronic HBV.
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Affiliation(s)
- Noe Rico Montanari
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | | | - Michael Doukas
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | | | - Li Li
- Gilead Sciences, Foster City, CA, USA
| | - Jose D Debes
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Medicine, Division of Gastroenterology & Division of Infectious Diseases, University of Minnesota, Minneapolis, MN, USA
| | | | - Andre Boonstra
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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Van Hees S, Cuypers B, Bourgeois S, Groothuismink ZMA, Meysman P, Van der Vlies P, de Knegt R, Vonghia L, Michielsen P, Francque S, Laukens K, Boonstra A, Vanwolleghem T. Sorted B cell transcriptomes point towards actively regulated B cell responses during ongoing chronic hepatitis B infections. Cell Immunol 2021; 362:104283. [PMID: 33548734 DOI: 10.1016/j.cellimm.2021.104283] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/08/2020] [Accepted: 01/04/2021] [Indexed: 12/17/2022]
Abstract
The natural course of chronic hepatitis B virus (HBV) infections follows distinct clinical disease phases, characterized by fluctuating levels of serum HBV DNA and ALT. The immune cells and their features that govern these clinical disease transitions remain unknown. In the current study, we performed RNA sequencing on purified B cells from blood (n = 42) and liver (n = 10) of healthy controls and chronic HBV patients. We found distinct gene expression profiles between healthy controls and chronic HBV patients, as evidenced by 190 differentially expressed genes (DEG), but also between the clinical phenotypes of a chronic HBV infection (17-110 DEG between each phase). Numerous immune pathways, including the B cell receptor pathway were upregulated in liver B cells when compared to peripheral B cells. Further investigation of the detected DEG suggested an activation of B cells during HBeAg seroconversion and an active regulation of B cell signalling in the liver.
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Affiliation(s)
- Stijn Van Hees
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium; Laboratory of Experimental Medicine and Paediatrics, Antwerp University, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Bart Cuypers
- Department of Biomedical Sciences, Institute of Tropical Medicine, Kronenburgstraat 43, 2000 Antwerp, Belgium; Department of Mathematics and Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerp, Belgium
| | - Stefan Bourgeois
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium; Department of Gastroenterology and Hepatology, ZNA Stuivenberg, Antwerp, Belgium
| | - Zwier M A Groothuismink
- Department of Gastroenterology and Hepatology, Erasmus Medical Center Rotterdam, the Netherlands
| | - Pieter Meysman
- Department of Mathematics and Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerp, Belgium
| | | | - Rob de Knegt
- Department of Gastroenterology and Hepatology, Erasmus Medical Center Rotterdam, the Netherlands
| | - Luisa Vonghia
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium; Laboratory of Experimental Medicine and Paediatrics, Antwerp University, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Peter Michielsen
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium; Laboratory of Experimental Medicine and Paediatrics, Antwerp University, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Sven Francque
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium; Laboratory of Experimental Medicine and Paediatrics, Antwerp University, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Kris Laukens
- Department of Mathematics and Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerp, Belgium
| | - Andre Boonstra
- Department of Gastroenterology and Hepatology, Erasmus Medical Center Rotterdam, the Netherlands
| | - Thomas Vanwolleghem
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium; Laboratory of Experimental Medicine and Paediatrics, Antwerp University, Universiteitsplein 1, 2610 Antwerp, Belgium; Department of Gastroenterology and Hepatology, Erasmus Medical Center Rotterdam, the Netherlands.
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Boeijen LL, van Oord GW, Hou J, van der Heide-Mulder M, Gaggar A, Li L, Fletcher SP, de Knegt RJ, Boonstra A. Gene expression profiling of human tissue-resident immune cells: Comparing blood and liver. J Leukoc Biol 2018; 105:603-608. [PMID: 30480838 PMCID: PMC6924273 DOI: 10.1002/jlb.6ab0718-278r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/06/2018] [Accepted: 11/01/2018] [Indexed: 12/17/2022] Open
Abstract
In this study, we describe a method to reliably characterize intrahepatic leukocyte populations using flow cytometry and next‐generation RNA sequencing on fresh human liver biopsies. Over the last decades, immune responses of viral hepatitis patients, and of other liver diseases, have been incompletely characterized. Most studies include peripheral blood samples only, foregoing the possibility to investigate the site of inflammation directly. Here, we show that with an optimized protocol that combines cell sorting and RNA sequencing, we can perform a side by side comparison of both intrahepatic and peripheral immune cells. Using core liver biopsies from chronic hepatitis B virus patients, we show that the expression levels of IFN‐stimulated genes and leukocyte‐specific genes are markedly different in the liver compartment as compared to the peripheral blood. These observations emphasize the need to sample the liver directly. The variation of gene expression profiles in these chronic hepatitis B patients was considerable, despite the uniform treatment with nucleotide analogs and absence of liver inflammation in these patients. Finally, we show that this method can provide a detailed characterization of previously undetected liver‐specific effects of novel candidate therapeutic compounds.
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Affiliation(s)
- Lauke L Boeijen
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Gertine W van Oord
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jun Hou
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marieke van der Heide-Mulder
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Anuj Gaggar
- Gilead Sciences, Foster City, California, USA
| | - Li Li
- Gilead Sciences, Foster City, California, USA
| | | | - Robert J de Knegt
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - André Boonstra
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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