201
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Wheeler AM, Eberhard CD, Mosher EP, Yuan Y, Wilkins HN, Seneviratne HK, Orsburn BC, Bumpus NN. Achieving a Deeper Understanding of Drug Metabolism and Responses Using Single-Cell Technologies. Drug Metab Dispos 2023; 51:350-359. [PMID: 36627162 PMCID: PMC10029823 DOI: 10.1124/dmd.122.001043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 01/12/2023] Open
Abstract
Recent advancements in single-cell technologies have enabled detection of RNA, proteins, metabolites, and xenobiotics in individual cells, and the application of these technologies has the potential to transform pharmacological research. Single-cell data has already resulted in the development of human and model species cell atlases, identifying different cell types within a tissue, further facilitating the characterization of tumor heterogeneity, and providing insight into treatment resistance. Research discussed in this review demonstrates that distinct cell populations express drug metabolizing enzymes to different extents, indicating there may be variability in drug metabolism not only between organs, but within tissue types. Additionally, we put forth the concept that single-cell analyses can be used to expose underlying variability in cellular response to drugs, providing a unique examination of drug efficacy, toxicity, and metabolism. We will outline several of these techniques: single-cell RNA-sequencing and mass cytometry to characterize and distinguish different cell types, single-cell proteomics to quantify drug metabolizing enzymes and characterize cellular responses to drug, capillary electrophoresis-ultrasensitive laser-induced fluorescence detection and single-probe single-cell mass spectrometry for detection of drugs, and others. Emerging single-cell technologies such as these can comprehensively characterize heterogeneity in both cell-type-specific drug metabolism and response to treatment, enhancing progress toward personalized and precision medicine. SIGNIFICANCE STATEMENT: Recent technological advances have enabled the analysis of gene expression and protein levels in single cells. These types of analyses are important to investigating mechanisms that cannot be elucidated on a bulk level, primarily due to the variability of cell populations within biological systems. Here, we summarize cell-type-specific drug metabolism and how pharmacologists can utilize single-cell approaches to obtain a comprehensive understanding of drug metabolism and cellular heterogeneity in response to drugs.
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Affiliation(s)
- Abigail M Wheeler
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Colten D Eberhard
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Eric P Mosher
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Yuting Yuan
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Hannah N Wilkins
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Herana Kamal Seneviratne
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Benjamin C Orsburn
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Namandjé N Bumpus
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
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202
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Yan ZJ, Chen L, Wang HY. To be or not to be: The double-edged sword roles of liver progenitor cells. Biochim Biophys Acta Rev Cancer 2023; 1878:188870. [PMID: 36842766 DOI: 10.1016/j.bbcan.2023.188870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/11/2023] [Accepted: 01/28/2023] [Indexed: 02/28/2023]
Abstract
Given the liver's remarkable and unique regenerative capacity, researchers have long focused on liver progenitor cells (LPCs) and liver cancer stem cells (LCSCs). LPCs can differentiate into both hepatocytes and cholangiocytes. However, the mechanism underlying cell conversion and its distinct contribution to liver homeostasis and tumorigenesis remain unclear. In this review, we discuss the complicated conversions involving LPCs and LCSCs. As the critical intermediate state in malignant transformation, LPCs play double-edged sword roles. LPCs are not only involved in hepatic wound-healing responses by supplementing liver cells and bile duct cells in the damaged liver but may transform into LCSCs under dysregulation of key signaling pathways, resulting in refractory malignant liver tumors. Because LPC lineages are temporally and spatially dynamic, we discuss crucial LPC subgroups and summarize regulatory factors correlating with the trajectories of LPCs and LCSCs in the liver tumor microenvironment. This review elaborates on the double-edged sword roles of LPCs to help understand the liver's regenerative potential and tumor heterogeneity. Understanding the sources and transformations of LPCs is essential in determining how to exploit their regenerative capacity in the future.
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Affiliation(s)
- Zi-Jun Yan
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/National Center for Liver Cancer, Shanghai 200438, PR China; Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, PR China; Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, PR China
| | - Lei Chen
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/National Center for Liver Cancer, Shanghai 200438, PR China; Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, PR China; Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, PR China.
| | - Hong-Yang Wang
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/National Center for Liver Cancer, Shanghai 200438, PR China; Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, PR China; Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, PR China.
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203
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Cao L, Wu D, Qin L, Tan D, Fan Q, Jia X, Yang M, Zhou T, Feng C, Lu Y, He Y. Single-Cell RNA Transcriptome Profiling of Liver Cells of Short-Term Alcoholic Liver Injury in Mice. Int J Mol Sci 2023; 24:ijms24054344. [PMID: 36901774 PMCID: PMC10002329 DOI: 10.3390/ijms24054344] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/23/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Alcoholic liver disease (ALD) is currently considered a global healthcare problem with limited pharmacological treatment options. There are abundant cell types in the liver, such as hepatocytes, endothelial cells, Kupffer cells and so on, but little is known about which kind of liver cells play the most important role in the process of ALD. To obtain a cellular resolution of alcoholic liver injury pathogenesis, 51,619 liver single-cell transcriptomes (scRNA-seq) with different alcohol consumption durations were investigated, 12 liver cell types were identified, and the cellular and molecular mechanisms of the alcoholic liver injury were revealed. We found that more aberrantly differential expressed genes (DEGs) were present in hepatocytes, endothelial cells, and Kupffer cells than in other cell types in alcoholic treatment mice. Alcohol promoted the pathological processes of liver injury; the specific mechanisms involved: lipid metabolism, oxidative stress, hypoxia, complementation and anticoagulation, and hepatocyte energy metabolism on hepatocytes; NO production, immune regulation, epithelial and cell migration on endothelial cells; antigen presentation and energy metabolism on Kupffer cells, based on the GO analysis. In addition, our results showed that some transcription factors (TFs) are activated in alcohol-treated mice. In conclusion, our study improves the understanding of liver cell heterogeneity in alcohol-fed mice at the single-cell level. It has potential value for understanding key molecular mechanisms and improving current prevention and treatment strategies for short-term alcoholic liver injury.
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Affiliation(s)
- Ligang Cao
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi 563000, China
| | - Di Wu
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi 563000, China
- Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Lin Qin
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi 563000, China
- Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Daopeng Tan
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi 563000, China
- Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Qingjie Fan
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi 563000, China
- Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Xiaohuan Jia
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi 563000, China
| | - Mengting Yang
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi 563000, China
| | - Tingting Zhou
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi 563000, China
| | - Chengcheng Feng
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi 563000, China
| | - Yanliu Lu
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi 563000, China
- Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Yuqi He
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi 563000, China
- Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
- Correspondence:
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204
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Carpentier N, Urbani L, Dubruel P, Van Vlierberghe S. The native liver as inspiration to create superior in vitro hepatic models. Biomater Sci 2023; 11:1091-1115. [PMID: 36594602 DOI: 10.1039/d2bm01646j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Drug induced liver injury (DILI) is one of the major reasons of drug withdrawal during the different phases of drug development. The later in the drug development a drug is discovered to be toxic, the higher the economical as well as the ethical impact will be. In vitro models for early detection of drug liver toxicity are under constant development, however to date a superior model of the liver is still lacking. Ideally, a highly reliable model should be established to maintain the different hepatic cell functionalities to the greatest extent possible, during a period of time long enough to allow for tracking of the toxicity of compounds. In the case of DILI, toxicity can appear even after months of exposure. To reach this goal, an in vitro model should be developed that mimics the in vivo liver environment, function and response to external stimuli. The different approaches for the development of liver models currently used in the field of tissue engineering will be described in this review. Combining different technologies, leading to optimal materials, cells and 3D-constructs will ultimately lead to an ideal superior model that fully recapitulates the liver.
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Affiliation(s)
- Nathan Carpentier
- Polymer Chemistry & Biomaterials Group, Centre of Macromolecular Chemistry, Ghent University, Ghent, Belgium.
| | - Luca Urbani
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London SE5 9NT, UK.,Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Peter Dubruel
- Polymer Chemistry & Biomaterials Group, Centre of Macromolecular Chemistry, Ghent University, Ghent, Belgium.
| | - Sandra Van Vlierberghe
- Polymer Chemistry & Biomaterials Group, Centre of Macromolecular Chemistry, Ghent University, Ghent, Belgium.
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205
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Huppert SS, Schwartz RE. Multiple Facets of Cellular Homeostasis and Regeneration of the Mammalian Liver. Annu Rev Physiol 2023; 85:469-493. [PMID: 36270290 PMCID: PMC9918695 DOI: 10.1146/annurev-physiol-032822-094134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Liver regeneration occurs in response to diverse injuries and is capable of functionally reestablishing the lost parenchyma. This phenomenon has been known since antiquity, encapsulated in the Greek myth where Prometheus was to be punished by Zeus for sharing the gift of fire with humanity by having an eagle eat his liver daily, only to have the liver regrow back, thus ensuring eternal suffering and punishment. Today, this process is actively leveraged clinically during living donor liver transplantation whereby up to a two-thirds hepatectomy (resection or removal of part of the liver) on a donor is used for transplant to a recipient. The donor liver rapidly regenerates to recover the lost parenchymal mass to form a functional tissue. This astonishing regenerative process and unique capacity of the liver are examined in further detail in this review.
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Affiliation(s)
- Stacey S Huppert
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA;
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA;
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
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206
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Ziegler AE, Fittje P, Müller LM, Ahrenstorf AE, Hagemann K, Hagen SH, Hess LU, Niehrs A, Poch T, Ravichandran G, Löbl SM, Padoan B, Brias S, Hennesen J, Richard M, Richert L, Peine S, Oldhafer KJ, Fischer L, Schramm C, Martrus G, Bunders MJ, Altfeld M, Lunemann S. The co-inhibitory receptor TIGIT regulates NK cell function and is upregulated in human intrahepatic CD56 bright NK cells. Front Immunol 2023; 14:1117320. [PMID: 36845105 PMCID: PMC9948018 DOI: 10.3389/fimmu.2023.1117320] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/17/2023] [Indexed: 02/11/2023] Open
Abstract
The crosstalk between NK cells and their surrounding environment is enabled through activating and inhibitory receptors, which tightly control NK cell activity. The co-inhibitory receptor TIGIT decreases NK cell cytotoxicity and is involved in NK cell exhaustion, but has also been associated with liver regeneration, highlighting that the contribution of human intrahepatic CD56bright NK cells in regulating tissue homeostasis remains incompletely understood. A targeted single-cell mRNA analysis revealed distinct transcriptional differences between matched human peripheral blood and intrahepatic CD56bright NK cells. Multiparameter flow cytometry identified a cluster of intrahepatic NK cells with overlapping high expression of CD56, CD69, CXCR6, TIGIT and CD96. Intrahepatic CD56bright NK cells also expressed significantly higher protein surface levels of TIGIT, and significantly lower levels of DNAM-1 compared to matched peripheral blood CD56bright NK cells. TIGIT+ CD56bright NK cells showed diminished degranulation and TNF-α production following stimulation. Co-incubation of peripheral blood CD56bright NK cells with human hepatoma cells or primary human hepatocyte organoids resulted in migration of NK cells into hepatocyte organoids and upregulation of TIGIT and downregulation of DNAM-1 expression, in line with the phenotype of intrahepatic CD56bright NK cells. Intrahepatic CD56bright NK cells represent a transcriptionally, phenotypically, and functionally distinct population of NK cells that expresses higher levels of TIGIT and lower levels of DNAM-1 than matched peripheral blood CD56bright NK cells. Increased expression of inhibitory receptors by NK cells within the liver environment can contribute to tissue homeostasis and reduction of liver inflammation.
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Affiliation(s)
- Annerose E. Ziegler
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Pia Fittje
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Luisa M. Müller
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Annika E. Ahrenstorf
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Kerri Hagemann
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Sven H. Hagen
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Leonard U. Hess
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Annika Niehrs
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Tobias Poch
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gevitha Ravichandran
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sebastian M. Löbl
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Benedetta Padoan
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Sébastien Brias
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jana Hennesen
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Myrtille Richard
- University of Bordeaux, Institut National de la Santé et de la Recherche Médicale, Bordeaux Population Health Research Center, UMR1219 and Inria, Team Statistics in systems biology and translationnal medicine (SISTM), Bordeaux, France
| | - Laura Richert
- University of Bordeaux, Institut National de la Santé et de la Recherche Médicale, Bordeaux Population Health Research Center, UMR1219 and Inria, Team Statistics in systems biology and translationnal medicine (SISTM), Bordeaux, France
| | - Sven Peine
- Institute for Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Karl J. Oldhafer
- Department of General and Abdominal Surgery, Asklepios Hospital Barmbek, Semmelweis University of Medicine, Hamburg, Germany
| | - Lutz Fischer
- Department of Visceral Transplant Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Schramm
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Martin Zeitz Centre for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Glòria Martrus
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Madeleine J. Bunders
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marcus Altfeld
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Sebastian Lunemann
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
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207
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Muench MO, Fomin ME, Gutierrez AG, López-Terrada D, Gilfanova R, Nosworthy C, Beyer AI, Ostolaza G, Kats D, Matlock KL, Cairo S, Keller C. CD203c is expressed by human fetal hepatoblasts and distinguishes subsets of hepatoblastoma. Front Oncol 2023; 13:927852. [PMID: 36845728 PMCID: PMC9947649 DOI: 10.3389/fonc.2023.927852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Background & Aims Hepatocytic cells found during prenatal development have unique features compared to their adult counterparts, and are believed to be the precursors of pediatric hepatoblastoma. The cell-surface phenotype of hepatoblasts and hepatoblastoma cell lines was evaluated to discover new markers of these cells and gain insight into the development of hepatocytic cells and the phenotypes and origins of hepatoblastoma. Methods Human midgestation livers and four pediatric hepatoblastoma cell lines were screened using flow cytometry. Expression of over 300 antigens was evaluated on hepatoblasts defined by their expression of CD326 (EpCAM) and CD14. Also analyzed were hematopoietic cells, expressing CD45, and liver sinusoidal-endothelial cells (LSECs), expressing CD14 but lacking CD45 expression. Select antigens were further examined by fluorescence immunomicroscopy of fetal liver sections. Antigen expression was also confirmed on cultured cells by both methods. Gene expression analysis by liver cells, 6 hepatoblastoma cell lines, and hepatoblastoma cells was performed. Immunohistochemistry was used to evaluate CD203c, CD326, and cytokeratin-19 expression on three hepatoblastoma tumors. Results Antibody screening identified many cell surface markers commonly or divergently expressed by hematopoietic cells, LSECs, and hepatoblasts. Thirteen novel markers expressed on fetal hepatoblasts were identified including ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (ENPP-3/CD203c), which was found to be expressed by hepatoblasts with widespread expression in the parenchyma of the fetal liver. In culture CD203c+CD326++ cells resembled hepatocytic cells with coexpression of albumin and cytokeratin-19 confirming a hepatoblast phenotype. CD203c expression declined rapidly in culture whereas the loss of CD326 was not as pronounced. CD203c and CD326 were co-expressed on a subset of hepatoblastoma cell lines and hepatoblastomas with an embryonal pattern. Conclusions CD203c is expressed on hepatoblasts and may play a role in purinergic signaling in the developing liver. Hepatoblastoma cell lines were found to consist of two broad phenotypes consisting of a cholangiocyte-like phenotype that expressed CD203c and CD326 and a hepatocyte-like phenotype with diminished expression of these markers. CD203c was expressed by some hepatoblastoma tumors and may represent a marker of a less differentiated embryonal component.
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Affiliation(s)
- Marcus O. Muench
- Vitalant Research Institute, San Francisco, CA, United States,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, United States,*Correspondence: Marcus O. Muench,
| | - Marina E. Fomin
- Vitalant Research Institute, San Francisco, CA, United States
| | | | - Dolores López-Terrada
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States,Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX, United States
| | | | | | - Ashley I. Beyer
- Vitalant Research Institute, San Francisco, CA, United States
| | | | - Dina Kats
- Pediatric Cancer Biology, Children’s Cancer Therapy Development Institute, Beaverton, OR, United States
| | | | - Stefano Cairo
- Research and Development Unit, XenTech, Evry, France
| | - Charles Keller
- Pediatric Cancer Biology, Children’s Cancer Therapy Development Institute, Beaverton, OR, United States
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208
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Chen J, Ng YK, Lin L, Zhang X, Li S. On triangle inequalities of correlation-based distances for gene expression profiles. BMC Bioinformatics 2023; 24:40. [PMID: 36755234 PMCID: PMC9906874 DOI: 10.1186/s12859-023-05161-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 01/25/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Distance functions are fundamental for evaluating the differences between gene expression profiles. Such a function would output a low value if the profiles are strongly correlated-either negatively or positively-and vice versa. One popular distance function is the absolute correlation distance, [Formula: see text], where [Formula: see text] is similarity measure, such as Pearson or Spearman correlation. However, the absolute correlation distance fails to fulfill the triangle inequality, which would have guaranteed better performance at vector quantization, allowed fast data localization, as well as accelerated data clustering. RESULTS In this work, we propose [Formula: see text] as an alternative. We prove that [Formula: see text] satisfies the triangle inequality when [Formula: see text] represents Pearson correlation, Spearman correlation, or Cosine similarity. We show [Formula: see text] to be better than [Formula: see text], another variant of [Formula: see text] that satisfies the triangle inequality, both analytically as well as experimentally. We empirically compared [Formula: see text] with [Formula: see text] in gene clustering and sample clustering experiment by real-world biological data. The two distances performed similarly in both gene clustering and sample clustering in hierarchical clustering and PAM (partitioning around medoids) clustering. However, [Formula: see text] demonstrated more robust clustering. According to the bootstrap experiment, [Formula: see text] generated more robust sample pair partition more frequently (P-value [Formula: see text]). The statistics on the time a class "dissolved" also support the advantage of [Formula: see text] in robustness. CONCLUSION [Formula: see text], as a variant of absolute correlation distance, satisfies the triangle inequality and is capable for more robust clustering.
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Affiliation(s)
- Jiaxing Chen
- grid.35030.350000 0004 1792 6846Department of Computer Science, City University of Hong Kong, Hong Kong, China ,grid.469245.80000 0004 1756 4881Department of Computer Science, Beijing Normal University - Hong Kong Baptist University United International College, Zhuhai, People’s Republic of China
| | - Yen Kaow Ng
- grid.35030.350000 0004 1792 6846Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Lu Lin
- grid.35030.350000 0004 1792 6846Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China.
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209
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Alvarez M, Benhammou JN, Rao S, Mishra L, Pisegna JR, Pajukanta P. Isolation of Nuclei from Human Snap-frozen Liver Tissue for Single-nucleus RNA Sequencing. Bio Protoc 2023; 13:e4601. [PMID: 36874905 PMCID: PMC9976782 DOI: 10.21769/bioprotoc.4601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/03/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023] Open
Abstract
Single-nucleus RNA sequencing (snRNA-seq) provides a powerful tool for studying cell type composition in heterogenous tissues. The liver is a vital organ composed of a diverse set of cell types; thus, single-cell technologies could greatly facilitate the deconvolution of liver tissue composition and various downstream omics analyses at the cell-type level. Applying single-cell technologies to fresh liver biopsies can, however, be very challenging, and snRNA-seq of snap-frozen liver biopsies requires some optimization given the high nucleic acid content of the solid liver tissue. Therefore, an optimized protocol for snRNA-seq specifically targeted for the use of frozen liver samples is needed to improve our understanding of human liver gene expression at the cell-type resolution. We present a protocol for performing nuclei isolation from snap-frozen liver tissues, as well as guidance on the application of snRNA-seq. We also provide guidance on optimizing the protocol to different tissue and sample types.
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Affiliation(s)
- Marcus Alvarez
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Jihane N. Benhammou
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Department of Medicine, VA Greater Los Angeles Healthcare System, CA, USA
| | - Shuyun Rao
- Center for Translational Medicine, Department of Surgery, George Washington University, Washington DC, USA
| | - Lopa Mishra
- Center for Translational Medicine, Department of Surgery, George Washington University, Washington DC, USA
- Institute for Bioelectronic Medicine, Feinstein Institutes for Medical Research; Divisions of Gastroenterology and Hepatology, Department of Medicine, Northwell Health, Manhasset, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Joseph R. Pisegna
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Department of Medicine, VA Greater Los Angeles Healthcare System, CA, USA
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
- Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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210
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He J, Deng C, Krall L, Shan Z. ScRNA-seq and ST-seq in liver research. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:11. [PMID: 36732412 PMCID: PMC9895469 DOI: 10.1186/s13619-022-00152-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
Abstract
Spatial transcriptomics, which combine gene expression data with spatial information, has quickly expanded in recent years. With application of this method in liver research, our knowledge about liver development, regeneration, and diseases have been greatly improved. While this field is moving forward, a variety of problems still need to be addressed, including sensitivity, limited capacity to obtain exact single-cell information, data processing methods, as well as others. Methods like single-cell RNA sequencing (scRNA-seq) are usually used together with spatial transcriptome sequencing (ST-seq) to clarify cell-specific gene expression. In this review, we explore how advances of scRNA-seq and ST-seq, especially ST-seq, will pave the way to new opportunities to investigate fundamental questions in liver research. Finally, we will discuss the strengths, limitations, and future perspectives of ST-seq in liver research.
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Affiliation(s)
- Jia He
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Chengxiang Deng
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Leonard Krall
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Zhao Shan
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650091, China.
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211
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Rezvani M, Vallier L, Guillot A. Modeling Nonalcoholic Fatty Liver Disease in the Dish Using Human-Specific Platforms: Strategies and Limitations. Cell Mol Gastroenterol Hepatol 2023; 15:1135-1145. [PMID: 36740045 PMCID: PMC10031472 DOI: 10.1016/j.jcmgh.2023.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/07/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a chronic liver disease affecting multiple cell types of the human liver. The high prevalence of NAFLD and the lack of approved therapies increase the demand for reliable models for the preclinical discovery of drug targets. In the last decade, multiple proof-of-principle studies have demonstrated human-specific NAFLD modeling in the dish. These systems have included technologies based on human induced pluripotent stem cell derivatives, liver tissue section cultures, intrahepatic cholangiocyte organoids, and liver-on-a-chip. These platforms differ in functional maturity, multicellularity, scalability, and spatial organization. Identifying an appropriate model for a specific NAFLD-related research question is challenging. Therefore, we review different platforms for their strengths and limitations in modeling NAFLD. To define the fidelity of the current human in vitro NAFLD models in depth, we define disease hallmarks within the NAFLD spectrum that range from steatosis to severe fibroinflammatory tissue injury. We discuss how the most common methods are efficacious in modeling genetic contributions and aspects of the early NAFLD-related tissue response. We also highlight the shortcoming of current models to recapitulate the complexity of inter-organ crosstalk and the chronic process of liver fibrosis-to-cirrhosis that usually takes decades in patients. Importantly, we provide methodological overviews and discuss implementation hurdles (eg, reproducibility or costs) to help choose the most appropriate NAFLD model for the individual research focus: hepatocyte injury, ductular reaction, cellular crosstalk, or other applications. In sum, we highlight current strategies and deficiencies to model NAFLD in the dish and propose a framework for the next generation of human-specific investigations.
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Affiliation(s)
- Milad Rezvani
- Charité Universitätsmedizin Berlin, Department of Pediatric Gastroenterology, Nephrology and Metabolic Medicine, Berlin, Germany; Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Berlin Institute of Health, Center for Regenerative Therapies (BCRT), Berlin, Germany; Berlin Institute of Health, Clinician-Scientist Program, Berlin, Germany
| | - Ludovic Vallier
- Berlin Institute of Health, Center for Regenerative Therapies (BCRT), Berlin, Germany; Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Adrien Guillot
- Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, Department of Hepatology & Gastroenterology, Berlin, Germany.
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212
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Chen S, Wang B, Zhou J, Wu X, Meng T, Liu H, Wang T, Zhao X, Wu S, Kong Y, Ou X, Jia J, Wee A, You H, Sun Y. A new glutamine synthetase index to evaluate hepatic lobular restoration in advanced fibrosis during anti-HBV therapy. J Med Virol 2023; 95:e28555. [PMID: 36738235 DOI: 10.1002/jmv.28555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Hepatic lobular architecture distortion is a deleterious turning point and a crucial histological feature of advanced liver fibrosis in chronic liver diseases. Regression of fibrosis has been documented in chronic hepatitis B (CHB) patients. However, whether lobular architecture could be restored following fibrosis regression after antiviral therapy is still unclear. Glutamine synthetase (GS) is generally expressed by perivenular hepatocytes around hepatic veins (HV). In this study, we defined abnormal lobular architecture (GSPT ) as GS expressing in the vicinity of portal tracts (PT), which denotes parenchymal extinction and lobular collapse. We defined normal lobular architecture (GSHV ) as GS positivity area not approximating PTs. Therefore, we propose a new GS-index, defined as the percentage of GSHV /(GSHV + GSPT ), to evaluate the extent of architectural disruption and restoration. We evaluated 43 CHB patients with advanced fibrosis (Ishak stage ≥4). Posttreatment liver biopsy was performed after 78 weeks of anti-HBV therapy. The median GS-index improved from 7% (interquartile range [IQR]: 0%-23%) at baseline to 36% (IQR: 20%-57%) at Week 78 (p < 0.001). Totals of 22 patients (51%) had significant GS-index improvement from 0% (IQR: 0%-13%) to 55% (IQR: 44%-81%), while the other half had almost no change between 17% (IQR: 0%-33%) to 20% (IQR: 12%-31%). When GS-index78w ≥ 50% was used to define hepatic lobular restoration, 37% of patients (16/43) achieved lobular restoration, with much improvement in alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels (median value of ∆/Baseline in ALT: restored vs. nonrestored was 79.1% vs. 48.8%, p = 0.018; median value of ∆/Baseline in AST: restored vs. nonrestored was 69.1% vs. 32.5%, p = 0.005). More importantly, lobular restoration correlated with fibrosis regression (median value of ∆/Baseline in Ishak stage: restored vs. nonrestored was 25.0% vs. 0%, p = 0.008). Therefore, in the era of antiviral therapy for CHB, restoration of hepatic lobular architecture is achievable in patients with advanced fibrosis. GS-index provides additional insight into fibrosis regression that goes beyond collagen degradation.
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Affiliation(s)
- Shuyan Chen
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Bingqiong Wang
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Jialing Zhou
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Xiaoning Wu
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Tongtong Meng
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Hui Liu
- Department of Pathology, Beijing You-an Hospital, Capital Medical University, Beijing, China
| | - Tailing Wang
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Xinyan Zhao
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Shanshan Wu
- Clinical Epidemiology and EBM Unit, Beijing Friendship Hospital, Capital Medical University, Beijing Clinical Research Institute, Beijing, China
| | - Yuanyuan Kong
- Clinical Epidemiology and EBM Unit, Beijing Friendship Hospital, Capital Medical University, Beijing Clinical Research Institute, Beijing, China
| | - Xiaojuan Ou
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Jidong Jia
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Aileen Wee
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Hong You
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Yameng Sun
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
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213
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Little A, Medford A, O'Brien A, Childs J, Pan S, Machado J, Chakraborty S, Glaser S. Recent Advances in Intrahepatic Biliary Epithelial Heterogeneity. Semin Liver Dis 2023; 43:1-12. [PMID: 36522162 DOI: 10.1055/s-0042-1758833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Biliary epithelium (i.e., cholangiocytes) is a heterogeneous population of epithelial cells in the liver, which line small and large bile ducts and have individual responses and functions dependent on size and location in the biliary tract. We discuss the recent findings showing that the intrahepatic biliary tree is heterogeneous regarding (1) morphology and function, (2) hormone expression and signaling (3), response to injury, and (4) roles in liver regeneration. This review overviews the significant characteristics and differences of the small and large cholangiocytes. Briefly, it outlines the in vitro and in vivo models used in the heterogeneity evaluation. In conclusion, future studies addressing biliary heterogeneity's role in the pathogenesis of liver diseases characterized by ductular reaction may reveal novel therapeutic approaches.
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Affiliation(s)
- Ashleigh Little
- Department of Medical Physiology, Texas A&M University School of Medicine, Bryan, Texas
| | - Abigail Medford
- Department of Medical Physiology, Texas A&M University School of Medicine, Bryan, Texas
| | - April O'Brien
- Department of Medical Physiology, Texas A&M University School of Medicine, Bryan, Texas
| | - Jonathan Childs
- Department of Medical Physiology, Texas A&M University School of Medicine, Bryan, Texas
| | - Sharon Pan
- Department of Medical Physiology, Texas A&M University School of Medicine, Bryan, Texas
| | - Jolaine Machado
- Department of Medical Physiology, Texas A&M University School of Medicine, Bryan, Texas
| | - Sanjukta Chakraborty
- Department of Medical Physiology, Texas A&M University School of Medicine, Bryan, Texas
| | - Shannon Glaser
- Department of Medical Physiology, Texas A&M University School of Medicine, Bryan, Texas
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214
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HtrA2 Independently Predicts Poor Prognosis and Correlates with Immune Cell Infiltration in Hepatocellular Carcinoma. JOURNAL OF ONCOLOGY 2023; 2023:4067418. [PMID: 36704205 PMCID: PMC9873461 DOI: 10.1155/2023/4067418] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/28/2022] [Accepted: 01/07/2023] [Indexed: 01/19/2023]
Abstract
High-temperature requirement protein A2 (HtrA2), a mitochondrial protein, is related to apoptosis regulation. However, the role of HtrA2 in hepatocellular carcinoma (HCC) remains unclear. In the present study, we explored the prognostic value and expression pattern of HtrA2 in HCC and confirmed its independent value for predicting outcomes via Cox analyses. LinkedOmics and GEPIA2 were used to construct the coexpression and functional networks of HtrA2. Additionally, the data obtained from TCGA was analyzed to investigate the relationship between the infiltration of immune cells and HtrA2 mRNA expression. Finally, the expression pattern of HtrA2 in HCC was confirmed by wet-lab experiments. The results showed high HtrA2 expression (P < 0.001) presented in tumor tissues in TCGA-HCC. Moreover, high HtrA2 expression was confirmed to be associated with poor HCC patient survival (P < 0.05). HtrA2 has also been recognized as an essential risk factor for overall survival (P=0.01, HR = 1.654, 95% CI 1.128-2.425), disease-specific survival (P=0.004, HR = 2.204, 95% CI 1.294-3.753), and progression-free interval (P=0.007, HR = 1.637, 95% CI 1.145-2.341) of HCC. HCC patients with low HtrA2 methylation had worse overall survival than patients with high methylation (P=0.0019). Functional network analysis suggests that HtrA2 regulates mitochondrial homeostasis through pathways involving multiple microRNAs and transcription factors in HCC. In addition, HtrA2 expression correlated with infiltrating levels of multiple immune cell populations. At last, increased expression of HtrA2 in HCC was confirmed using wet-lab experiments. Our study provides evidence that the upregulation of HtrA2 in HCC is an independent predictor of prognosis. Our results provide the foundation for further study on the roles of HtrA2 in HCC tumorigenesis.
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215
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Oderberg IM, Goessling W. Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish. JCI Insight 2023; 8:163929. [PMID: 36625346 PMCID: PMC9870093 DOI: 10.1172/jci.insight.163929] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/22/2022] [Indexed: 01/11/2023] Open
Abstract
The liver is a highly regenerative organ, yet the presence of a dedicated stem cell population remains controversial. Here, we interrogate a severe hepatocyte injury model in adult zebrafish to define that regeneration involves a stem cell population. After near-total hepatocyte ablation, single-cell transcriptomic and high-resolution imaging analyses throughout the entire regenerative timeline reveal that biliary epithelial cells undergo transcriptional and morphological changes to become hepatocytes. As a population, biliary epithelial cells give rise to both hepatocytes and biliary epithelial cells. Biliary epithelial cells proliferate and dedifferentiate to express hepatoblast transcription factors prior to hepatocyte differentiation. This process is characterized by increased MAPK, PI3K, and mTOR signaling, and chemical inhibition of these pathways impairs biliary epithelial cell proliferation and fate conversion. We conclude that, upon severe hepatocyte ablation in the adult liver, biliary epithelial cells act as facultative liver stem cells in an EGFR-PI3K-mTOR-dependent manner.
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Affiliation(s)
- Isaac M. Oderberg
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Wolfram Goessling
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts USA.,Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Harvard-MIT Division of Health Sciences and Technology, Boston, Massachusetts, USA.,Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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216
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Woestemeier A, Scognamiglio P, Zhao Y, Wagner J, Muscate F, Casar C, Siracusa F, Cortesi F, Agalioti T, Müller S, Sagebiel A, Konczalla L, Wahib R, Karstens KF, Giannou AD, Duprée A, Wolter S, Wong MN, Mühlig AK, Bielecka AA, Bansal V, Zhang T, Mann O, Puelles VG, Huber TB, Lohse AW, Izbicki JR, Palm NW, Bonn S, Huber S, Gagliani N. Multicytokine-producing CD4+ T cells characterize the livers of patients with NASH. JCI Insight 2023; 8:153831. [PMID: 36625344 PMCID: PMC9870087 DOI: 10.1172/jci.insight.153831] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/17/2022] [Indexed: 01/11/2023] Open
Abstract
A role of CD4+ T cells during the progression from nonalcoholic fatty liver disease (NAFLD) to nonalcoholic steatohepatitis (NASH) has been suggested, but which polarization state of these cells characterizes this progression and the development of fibrosis remain unclear. In addition, a gut-liver axis has been suggested to play a role in NASH, but the role of CD4+ T cells in this axis has just begun to be investigated. Combining single-cell RNA sequencing and multiple-parameter flow cytometry, we provide the first cell atlas to our knowledge focused on liver-infiltrating CD4+ T cells in patients with NAFLD and NASH, showing that NASH is characterized by a population of multicytokine-producing CD4+ T cells. Among these cells, only those with a Th17 polarization state were enriched in patients with advanced fibrosis. In parallel, we observed that Bacteroides appeared to be enriched in the intestine of NASH patients and to correlate with the frequency of multicytokine-producing CD4+ T cells. In short, we deliver a CD4+ T cell atlas of NAFLD and NASH, providing the rationale to target CD4+ T cells with a Th17 polarization state to block fibrosis development. Finally, our data offer an early indication to test whether multicytokine-producing CD4+ T cells are part of the gut-liver axis characterizing NASH.
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Affiliation(s)
| | | | - Yu Zhao
- Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology (ZMNH)
| | - Jonas Wagner
- Department for General, Visceral and Thoracic Surgery
| | | | - Christian Casar
- Department for General, Visceral and Thoracic Surgery
- Bioinformatics Core, and
| | | | | | | | - Simone Müller
- Department for General, Visceral and Thoracic Surgery
| | | | | | - Ramez Wahib
- Department for General, Visceral and Thoracic Surgery
| | | | | | - Anna Duprée
- Department for General, Visceral and Thoracic Surgery
| | - Stefan Wolter
- Department for General, Visceral and Thoracic Surgery
| | - Milagros N. Wong
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Anne K. Mühlig
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- University’s Children Hospital, UKE Hamburg, Hamburg, Germany
| | - Agata A. Bielecka
- Department of Immunobiology, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Vikas Bansal
- Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology (ZMNH)
| | - Tianran Zhang
- Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology (ZMNH)
| | - Oliver Mann
- Department for General, Visceral and Thoracic Surgery
| | - Victor G. Puelles
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Tobias B. Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - Noah W. Palm
- Department of Immunobiology, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Stefan Bonn
- Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology (ZMNH)
| | | | - Nicola Gagliani
- Department for General, Visceral and Thoracic Surgery
- I Department of Medicine
- Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
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217
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Zhang C, Li J, Cheng Y, Meng F, Song JW, Fan X, Fan H, Li J, Fu YL, Zhou MJ, Hu W, Wang SY, Fu YJ, Zhang JY, Xu RN, Shi M, Hu X, Zhang Z, Ren X, Wang FS. Single-cell RNA sequencing reveals intrahepatic and peripheral immune characteristics related to disease phases in HBV-infected patients. Gut 2023; 72:153-167. [PMID: 35361683 PMCID: PMC9763233 DOI: 10.1136/gutjnl-2021-325915] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/16/2022] [Indexed: 02/04/2023]
Abstract
OBJECTIVE A comprehensive immune landscape for HBV infection is pivotal to achieve HBV cure. DESIGN We performed single-cell RNA sequencing of 2 43 000 cells from 46 paired liver and blood samples of 23 individuals, including six immune tolerant, 5 immune active (IA), 3 acute recovery (AR), 3 chronic resolved and 6 HBV-free healthy controls (HCs). Flow cytometry and histological assays were applied in a second HBV cohort for validation. RESULTS Both IA and AR were characterised by high levels of intrahepatic exhausted CD8+ T (Tex) cells. In IA, Tex cells were mainly derived from liver-resident GZMK+ effector memory T cells and self-expansion. By contrast, peripheral CX3CR1+ effector T cells and GZMK+ effector memory T cells were the main source of Tex cells in AR. In IA but not AR, significant cell-cell interactions were observed between Tex cells and regulatory CD4+ T cells, as well as between Tex and FCGR3A+ macrophages. Such interactions were potentially mediated through human leukocyte antigen class I molecules together with their receptors CANX and LILRBs, respectively, contributing to the dysfunction of antiviral immune responses. By contrast, CX3CR1+GNLY+ central memory CD8+ T cells were concurrently expanded in both liver and blood of AR, providing a potential surrogate marker for viral resolution. In clinic, intrahepatic Tex cells were positively correlated with serum alanine aminotransferase levels and histological grading scores. CONCLUSION Our study dissects the coordinated immune responses for different HBV infection phases and provides a rich resource for fully understanding immunopathogenesis and developing effective therapeutic strategies.
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Affiliation(s)
- Chao Zhang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jiesheng Li
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China,Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yongqian Cheng
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Fanping Meng
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jin-Wen Song
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xing Fan
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Hongtao Fan
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Jing Li
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yu-Long Fu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ming-Ju Zhou
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Wei Hu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Si-Yu Wang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yuan-Jie Fu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ji-Yuan Zhang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ruo-Nan Xu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ming Shi
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xueda Hu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China .,Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Xianwen Ren
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China .,Changping Laboratory, Beijing, China
| | - Fu-Sheng Wang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
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218
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Guo WX, Yang SY, Guo L, Feng JK, Xue J, Shi J, Lau WY, Yu D, Cheng SQ. A new and rare type of hepatocellular carcinoma: Survival and gene analysis of portal vein tumour thrombus-type hepatocellular carcinoma. Pathol Res Pract 2023; 241:154260. [PMID: 36509007 DOI: 10.1016/j.prp.2022.154260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/07/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Portal vein tumour thrombus (PVTT) in patients with hepatocellular carcinoma (HCC) is known as a major complication associated with poor survival. We clinically defined a new and rare type of HCC, PVTT-type HCC (PVTT-HCC), in a small group of HCC patients with HCC presenting only as PVTT without a demonstrable parenchyma tumour. The clinicopathological and biological features of PVTT-HCC are not clear. METHODS The data for patients who had PVTT-HCC with histologically confirmed HCC from January 2004 to December 2012 at the Eastern Hepatobiliary Surgery Hospital were retrospectively analysed. The survival outcomes of patients with PVTT-HCC were compared with those of HCC patients with PVTT (HCC-PVTT). Propensity score matching (PSM) analysis was performed to match patients at a ratio of 1:3. Then, we performed RNA-Seq analysis of liver samples from PVTT-HCC and HCC-PVTT patients to identify and compare differentially expressed genes and biological pathways between the two groups. RESULTS We observed and collected 10 rare cases of PVTT-HCC and performed a prospective cohort study to compare overall survival (OS) between PVTT-HCC and HCC-PVTT. PVTT invaded the main portal vein in 10 PVTT-HCC patients. Univariate and multivariate analyses demonstrated that ChildPugh (A/B), different treatments (LR/non-LR), and different groups were independent risk factors for OS. The median OS was 10.3 months (95 % CI = 6.7-13.8) in the HCC-PVTT group and 7.5 months (95 % CI = 2.8-12.1) in the PVTT-HCC group (P = 0.042). From RNA-Seq, 1630 differentially expressed genes were obtained, of which 731 were upregulated and 899 downregulated in PVTT-HCC compared with HCC-PVTT. CONCLUSIONS The survival outcomes of patients with PVTT-HCC were worse than those of patients with HCC-PVTT. RNA-Seq demonstrated differential gene expression between PVTT-HCC and HCC-PVTT, indicating that the former may have distinguishing biological characteristics and be a new and rare type of HCC.
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Affiliation(s)
- Wei-Xing Guo
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Shi-Ye Yang
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Lei Guo
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Jin-Kai Feng
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Jie Xue
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Jie Shi
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Wan Yee Lau
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Dong Yu
- Center for Translational Medicine, Second Military Medical University, Shanghai, China.
| | - Shu-Qun Cheng
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China.
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Secretin alleviates biliary and liver injury during late-stage primary biliary cholangitis via restoration of secretory processes. J Hepatol 2023; 78:99-113. [PMID: 35987275 DOI: 10.1016/j.jhep.2022.07.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 07/22/2022] [Accepted: 07/29/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND & AIMS Primary biliary cholangitis (PBC) is characterised by ductopenia, ductular reaction, impairment of anion exchanger 2 (AE2) and the 'bicarbonate umbrella'. Ductulo-canalicular junction (DCJ) derangement is hypothesised to promote PBC progression. The secretin (Sct)/secretin receptor (SR) axis regulates cystic fibrosis transmembrane receptor (CFTR) and AE2, thus promoting choleresis. We evaluated the role of Sct/SR signalling on biliary secretory processes and subsequent injury in a late-stage PBC mouse model and human samples. METHODS At 32 weeks of age, female and male wild-type and dominant-negative transforming growth factor beta receptor II (late-stage PBC model) mice were treated with Sct for 1 or 8 weeks. Bulk RNA-sequencing was performed in isolated cholangiocytes from mouse models. RESULTS Biliary Sct/SR/CFTR/AE2 expression and bile bicarbonate levels were reduced in late-stage PBC mouse models and human samples. Sct treatment decreased bile duct loss, ductular reaction, inflammation, and fibrosis in late-stage PBC models. Sct reduced hepatic bile acid levels, modified bile acid composition, and restored the DCJ and 'bicarbonate umbrella'. RNA-sequencing identified that Sct promoted mature epithelial marker expression, specifically anterior grade protein 2 (Agr2). Late-stage PBC models and human samples exhibited reduced biliary mucin 1 levels, which were enhanced by Sct treatment. CONCLUSION Loss of Sct/SR signalling in late-stage PBC results in a faulty 'bicarbonate umbrella' and reduced Agr2-mediated mucin production. Sct restores cholangiocyte secretory processes and DCJ formation through enhanced mature cholangiocyte phenotypes and bile duct growth. Sct treatment may be beneficial for individuals with late-stage PBC. IMPACT AND IMPLICATIONS Secretin (Sct) regulates biliary proliferation and bicarbonate secretion in cholangiocytes via its receptor, SR, and in mouse models and human samples of late-stage primary biliary cholangitis (PBC), the Sct/SR axis is blunted along with loss of the protective 'bicarbonate umbrella'. We found that both short- and long-term Sct treatment ameliorated ductular reaction, immune cell influx, and liver fibrosis in late-stage PBC mouse models. Importantly, Sct treatment promoted bicarbonate and mucin secretion and hepatic bile acid efflux, thus reducing cholestatic and toxic bile acid-associated injury in late-stage PBC mouse models. Our work perpetuates the hypothesis that PBC pathogenesis hinges on secretory defects, and restoration of secretory processes that promote the 'bicarbonate umbrella' may be important for amelioration of PBC-associated damage.
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Du X, Lai S, Zhao W, Xu X, Xu W, Zeng T, Tian Y, Lu L. Single-cell RNA sequencing revealed the liver heterogeneity between egg-laying duck and ceased-laying duck. BMC Genomics 2022; 23:857. [PMID: 36577943 PMCID: PMC9798604 DOI: 10.1186/s12864-022-09089-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND In the late phase of production, ducks untimely cease laying, leading to a lower feed conversion. Liver plays a vital role in the synthesis and transport of yolk materials during egg formation in birds. However, the molecular mechanism of liver in ceased-laying duck is far from clear, higher resolution and deeper analysis is needed. Sing-cell RNA-sequencing of 10 × Genomics platform can help to map the liver single cell gene expression atlas of Shaoxing duck and provide new insights into the liver between egg-laying and ceased-laying ducks. RESULTS About 20,000 single cells were profiled and 22 clusters were identified. All the clusters were identified as 6 cell types. The dominant cell type is hepatocyte, accounted for about 60% of all the cells. Of note, the heterogeneity of cells between egg-laying duck and ceased-laying duck mainly occurred in hepatocytes. Cells of cluster 3 and 12 were the unique hepatocyte states of egg-laying ducks, while cells of cluster 0 and 15 were the unique hepatocyte states of ceased-laying ducks. The expression mode of yolk precursor transporters, lipid metabolizing enzymes and fibrinogens were different in hepatocytes between egg-laying duck and ceased-laying duck. APOV1, VTG2, VTG1, APOB, RBP, VTDB and SCD might be activated in egg-laying ducks, while APOA1, APOA4, APOC3, FGB and FGG might be activated in ceased-laying ducks. CONCLUSIONS Our study further proofs that APOV1 and APOB play key roles in egg production, rather than APOA1 and APOA4. It is also the first to detect a correlation between the higher expression of APOC3, FGB, FGG and ceased-laying in duck.
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Affiliation(s)
- Xue Du
- grid.410744.20000 0000 9883 3553State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang China ,grid.443483.c0000 0000 9152 7385College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, China
| | - Shujing Lai
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wanqiu Zhao
- grid.410744.20000 0000 9883 3553Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310022 Zhejiang China
| | - Xiaoqin Xu
- grid.411527.40000 0004 0610 111XInstitute of Ecology, China West Normal University, Nanchong, 637002 Sichuan China
| | - Wenwu Xu
- grid.410744.20000 0000 9883 3553State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang China
| | - Tao Zeng
- grid.410744.20000 0000 9883 3553State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang China
| | - Yong Tian
- grid.410744.20000 0000 9883 3553State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang China
| | - Lizhi Lu
- grid.410744.20000 0000 9883 3553State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang China
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Subramanian A, Alperovich M, Yang Y, Li B. Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomics. Genome Biol 2022; 23:267. [PMID: 36575523 PMCID: PMC9793662 DOI: 10.1186/s13059-022-02820-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/23/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Quality control (QC) of cells, a critical first step in single-cell RNA sequencing data analysis, has largely relied on arbitrarily fixed data-agnostic thresholds applied to QC metrics such as gene complexity and fraction of reads mapping to mitochondrial genes. The few existing data-driven approaches perform QC at the level of samples or studies without accounting for biological variation. RESULTS We first demonstrate that QC metrics vary with both tissue and cell types across technologies, study conditions, and species. We then propose data-driven QC (ddqc), an unsupervised adaptive QC framework to perform flexible and data-driven QC at the level of cell types while retaining critical biological insights and improved power for downstream analysis. ddqc applies an adaptive threshold based on the median absolute deviation on four QC metrics (gene and UMI complexity, fraction of reads mapping to mitochondrial and ribosomal genes). ddqc retains over a third more cells when compared to conventional data-agnostic QC filters. Finally, we show that ddqc recovers biologically meaningful trends in gradation of gene complexity among cell types that can help answer questions of biological interest such as which cell types express the least and most number of transcripts overall, and ribosomal transcripts specifically. CONCLUSIONS ddqc retains cell types such as metabolically active parenchymal cells and specialized cells such as neutrophils which are often lost by conventional QC. Taken together, our work proposes a revised paradigm to quality filtering best practices-iterative QC, providing a data-driven QC framework compatible with observed biological diversity.
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Affiliation(s)
- Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Brigham and Womens's Hospital, Harvard Medical School, Boston, USA.
| | - Mikhail Alperovich
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT PRIMES, Massachusetts Institute of Technology, Cambridge, MA, USA
- Lexington High School, Lexington, MA, USA
- Present Address: Wake Technical Community College, Raleigh, USA
| | - Yiming Yang
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Present Address: Department of Cellular and Tissue Genomics, Genentech Inc., South San Francisco, CA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Present Address: Department of Cellular and Tissue Genomics, Genentech Inc., South San Francisco, CA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
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222
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Roehlen N, Saviano A, El Saghire H, Crouchet E, Nehme Z, Del Zompo F, Jühling F, Oudot MA, Durand SC, Duong FHT, Cherradi S, Gonzalez Motos V, Almeida N, Ponsolles C, Heydmann L, Ostyn T, Lallement A, Pessaux P, Felli E, Cavalli A, Sgrignani J, Thumann C, Koutsopoulos O, Fuchs BC, Hoshida Y, Hofmann M, Vyberg M, Viuff BM, Galsgaard ED, Elson G, Toso A, Meyer M, Iacone R, Schweighoffer T, Teixeira G, Moll S, De Vito C, Roskams T, Davidson I, Heide D, Heikenwälder M, Zeisel MB, Lupberger J, Mailly L, Schuster C, Baumert TF. A monoclonal antibody targeting nonjunctional claudin-1 inhibits fibrosis in patient-derived models by modulating cell plasticity. Sci Transl Med 2022; 14:eabj4221. [PMID: 36542691 DOI: 10.1126/scitranslmed.abj4221] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tissue fibrosis is a key driver of end-stage organ failure and cancer, overall accounting for up to 45% of deaths in developed countries. There is a large unmet medical need for antifibrotic therapies. Claudin-1 (CLDN1) is a member of the tight junction protein family. Although the role of CLDN1 incorporated in tight junctions is well established, the function of nonjunctional CLDN1 (njCLDN1) is largely unknown. Using highly specific monoclonal antibodies targeting a conformation-dependent epitope of exposed njCLDN1, we show in patient-derived liver three-dimensional fibrosis and human liver chimeric mouse models that CLDN1 is a mediator and target for liver fibrosis. Targeting CLDN1 reverted inflammation-induced hepatocyte profibrogenic signaling and cell fate and suppressed the myofibroblast differentiation of hepatic stellate cells. Safety studies of a fully humanized antibody in nonhuman primates did not reveal any serious adverse events even at high steady-state concentrations. Our results provide preclinical proof of concept for CLDN1-specific monoclonal antibodies for the treatment of advanced liver fibrosis and cancer prevention. Antifibrotic effects in lung and kidney fibrosis models further indicate a role of CLDN1 as a therapeutic target for tissue fibrosis across organs. In conclusion, our data pave the way for further therapeutic exploration of CLDN1-targeting therapies for fibrotic diseases in patients.
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Affiliation(s)
- Natascha Roehlen
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Antonio Saviano
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France.,Institut Hospitalo-Universitaire (IHU), Pôle Hépato-digestif, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Houssein El Saghire
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Emilie Crouchet
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Zeina Nehme
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Fabio Del Zompo
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Frank Jühling
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Marine A Oudot
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Sarah C Durand
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - François H T Duong
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Sara Cherradi
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Victor Gonzalez Motos
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Nuno Almeida
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Clara Ponsolles
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Laura Heydmann
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Tessa Ostyn
- Department of Imaging and Pathology, University of Leuven, 3000 Leuven, Belgium
| | - Antonin Lallement
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France.,Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 67400 Illkirch, France
| | - Patrick Pessaux
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France.,Institut Hospitalo-Universitaire (IHU), Pôle Hépato-digestif, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Emanuele Felli
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France.,Institut Hospitalo-Universitaire (IHU), Pôle Hépato-digestif, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Christine Thumann
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Olga Koutsopoulos
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Bryan C Fuchs
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yujin Hoshida
- Liver Tumor Translational Research Program, Harold C. Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maike Hofmann
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Mogens Vyberg
- Center of RNA Medicine, Department of Clinical Medicine, Aalborg University Copenhagen, 2450 København, Denmark.,Department of Pathology, Copenhagen University Hospital Hvidovre, 2650 Hvidovre, Denmark
| | | | | | - Greg Elson
- Alentis Therapeutics, 4123 Allschwil, Switzerland
| | - Alberto Toso
- Alentis Therapeutics, 4123 Allschwil, Switzerland
| | - Markus Meyer
- Alentis Therapeutics, 4123 Allschwil, Switzerland
| | | | | | | | - Solange Moll
- Department of Pathology, University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Claudio De Vito
- Department of Pathology, University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Tania Roskams
- Department of Imaging and Pathology, University of Leuven, 3000 Leuven, Belgium
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 67400 Illkirch, France
| | - Danijela Heide
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Mirjam B Zeisel
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Joachim Lupberger
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Laurent Mailly
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Catherine Schuster
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France
| | - Thomas F Baumert
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR-S1110, 67000 Strasbourg, France.,Institut Hospitalo-Universitaire (IHU), Pôle Hépato-digestif, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France.,Institut Universitaire de France, 75006 Paris, France
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Gou H, Liu S, Liu L, Luo M, Qin S, He K, Yang X. Obeticholic acid and 5β-cholanic acid 3 exhibit anti-tumor effects on liver cancer through CXCL16/CXCR6 pathway. Front Immunol 2022; 13:1095915. [PMID: 36605219 PMCID: PMC9807878 DOI: 10.3389/fimmu.2022.1095915] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common type of liver malignancy with a high incidence and mortality rate. Previous in vitro and in vivo studies have confirmed that liver sinusoidal endothelial cells (LSEC) secrete CXCL16, which acts as a messenger to increase the hepatic accumulation of CXCR6+ natural killer T (NKT) cells and exert potent antitumor effects. However, evidence for this process in humans is lacking and its clinical significance is still unclear. In this study, by dissecting the human HCC single-cell RNA-seq data, we verified this process through cellphoneDB. NKT cells in patients with high expression of CXCL16 exhibited a higher activation state and produced more interferon-γ (IFN-γ) compared with those with low expression. We next investigated the signaling pathways between activated (CD69 high) and unactivated NKT cells (CD69 low) using NKT cell-developmental trajectories and functional enrichment analyses. In vivo experiments, we found that farnesoid X receptor agonist (obeticholic acid) combined with the takeda G protein coupled receptor 5 antagonist (5β-cholanic acid 3) exhibited significant tumor suppressive effects in the orthotopic liver tumor model and this result may be related to the CXCL16/CXCR6 axis. In conclusion, our study provides the basis and potential strategies for HCC immunotherapy based on NKT cells.
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Affiliation(s)
- Haoxian Gou
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China,Academician Workstation of Sichuan Province, Luzhou, China
| | - Shenglu Liu
- Academician Workstation of Sichuan Province, Luzhou, China
| | - Linxin Liu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Ming Luo
- Academician Workstation of Sichuan Province, Luzhou, China
| | - Shu Qin
- Academician Workstation of Sichuan Province, Luzhou, China
| | - Kai He
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China,Academician Workstation of Sichuan Province, Luzhou, China,*Correspondence: Xiaoli Yang, ; Kai He,
| | - Xiaoli Yang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China,Academician Workstation of Sichuan Province, Luzhou, China,*Correspondence: Xiaoli Yang, ; Kai He,
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Chen Y, Zhang H, Sun X. Improving the performance of single-cell RNA-seq data mining based on relative expression orderings. Brief Bioinform 2022; 24:6931720. [PMID: 36528803 PMCID: PMC9851298 DOI: 10.1093/bib/bbac556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/10/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
The advent of single-cell RNA-sequencing (scRNA-seq) provides an unprecedented opportunity to explore gene expression profiles at the single-cell level. However, gene expression values vary over time and under different conditions even within the same cell. There is an urgent need for more stable and reliable feature variables at the single-cell level to depict cell heterogeneity. Thus, we construct a new feature matrix called the delta rank matrix (DRM) from scRNA-seq data by integrating an a priori gene interaction network, which transforms the unreliable gene expression value into a stable gene interaction/edge value on a single-cell basis. This is the first time that a gene-level feature has been transformed into an interaction/edge-level for scRNA-seq data analysis based on relative expression orderings. Experiments on various scRNA-seq datasets have demonstrated that DRM performs better than the original gene expression matrix in cell clustering, cell identification and pseudo-trajectory reconstruction. More importantly, the DRM really achieves the fusion of gene expressions and gene interactions and provides a method of measuring gene interactions at the single-cell level. Thus, the DRM can be used to find changes in gene interactions among different cell types, which may open up a new way to analyze scRNA-seq data from an interaction perspective. In addition, DRM provides a new method to construct a cell-specific network for each single cell instead of a group of cells as in traditional network construction methods. DRM's exceptional performance is due to its extraction of rich gene-association information on biological systems and stable characterization of cells.
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Affiliation(s)
- Yuanyuan Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China,College of Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Zhang
- College of Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Sun
- Corresponding author: Xiao Sun, State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China. Tel: +8613951989906; E-mail:
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Tsomidis I, Notas G, Xidakis C, Voumvouraki A, Samonakis DN, Koulentaki M, Kouroumalis E. Enzymes of Fibrosis in Chronic Liver Disease. Biomedicines 2022; 10:biomedicines10123179. [PMID: 36551935 PMCID: PMC9776355 DOI: 10.3390/biomedicines10123179] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction: Liver fibrosis has been extensively studied at the cellular and molecular level, but very few data exist on the final enzymatic stages of collagen synthesis (prolyl hydroxylase, PH) and degradation (matrix metalloproteinases, MMPs), particularly in primary biliary cholangitis (PBC). Aim: We studied enzyme activities in liver tissue from patients with chronic liver diseases and compared them to normal livers. Patients: Eighteen patients with PBC of early and late stages (Ludwig’s classification) and seven on treatment with ursodeoxycholate (UDCA) were studied and compared to 34 patients with alcoholic liver disease (ALD), 25 patients with chronic viral liver disease and five normal biopsies. Sera were available from a total of 140 patients. Methods: The tritiated water released from the tritiated proline was measured in PH assessment. 14C intact and heat-denatured collagen substrates were used to measure collagenase and gelatinases, respectively. 3H Elastin was the substrate for elastase. In serum, ELISAs were used for MMP-1, TIMP-1, and TIMP-2 measurements while MMP-2 and MMP-9 were estimated by zymography. Results: PH was significantly increased in early and late PBC. Collagenase was reduced only in the late stages (p < 0.01), where the ratio PH/collagenase was increased. UDCA treatment restored values to almost normal. Gelatinases were reduced in late stages (p < 0.05). In contrast to PBC and ALD fibrosis, collagen synthesis is not increased in viral fibrosis. The balance shifted towards collagen deposition due to reduced degradation. Interestingly, gelatinolytic activity is not impaired in ALD. Elastase was similar to controls in all diseases studied. TIMP-1 was reduced in early PBC and viral and alcoholic hepatitis and cirrhosis (p < 0.001). Conclusions: (1) There is evidence that collagen synthesis increases in the early stages of PBC, but the collagenolytic mechanism may compensate for the increased synthesis. (2) In viral disease, fibrosis may be due to decreased degradation rather than increased synthesis. (3) The final biochemical stages of liver fibrosis may be quantitatively different according to underlying etiology.
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Affiliation(s)
- Ioannis Tsomidis
- First Department of Internal Medicine, AHEPA University Hospital, 54621 Thessaloniki, Chalkidiki, Greece
- Laboratory of Gastroenterology and Hepatology, School of Medicine, University of Crete, 71500 Heraklion, Crete, Greece
| | - George Notas
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71500 Heraklion, Crete, Greece
| | - Costas Xidakis
- Laboratory of Gastroenterology and Hepatology, School of Medicine, University of Crete, 71500 Heraklion, Crete, Greece
| | - Argyro Voumvouraki
- First Department of Internal Medicine, AHEPA University Hospital, 54621 Thessaloniki, Chalkidiki, Greece
| | - Dimitrios N Samonakis
- Department of Gastroenterology, PAGNI University Hospital, School of Medicine, University of Crete, 71500 Heraklion, Crete, Greece
| | - Mairi Koulentaki
- Department of Gastroenterology, PAGNI University Hospital, School of Medicine, University of Crete, 71500 Heraklion, Crete, Greece
| | - Elias Kouroumalis
- Laboratory of Gastroenterology and Hepatology, School of Medicine, University of Crete, 71500 Heraklion, Crete, Greece
- Department of Gastroenterology, PAGNI University Hospital, School of Medicine, University of Crete, 71500 Heraklion, Crete, Greece
- Correspondence:
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226
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Oh JM, An M, Son DS, Choi J, Cho YB, Yoo CE, Park WY. Comparison of cell type distribution between single-cell and single-nucleus RNA sequencing: enrichment of adherent cell types in single-nucleus RNA sequencing. Exp Mol Med 2022; 54:2128-2134. [PMID: 36460793 PMCID: PMC9794763 DOI: 10.1038/s12276-022-00892-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 08/23/2022] [Accepted: 09/20/2022] [Indexed: 12/03/2022] Open
Abstract
Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) is an effective technique for estimating the cellular composition and transcriptional profiles of individual cells from fresh tissue. Single-nucleus RNA sequencing (snRNA-seq) is necessary to perform this type of analysis in frozen or difficult-to-dissociate tissues, which cannot be subjected to scRNA-seq. This difference in the state of tissues leads to variation in cell-type distributions among each platform. To identify the characteristics of these methods and their differences, scRNA-seq and snRNA-seq were performed in parallel for colon and liver tissues. The two platforms revealed similar diversity but different proportions of cell types in matched tissues. The proportions of epithelial cells in the colon and hepatocytes in the liver were relatively high in snRNA-seq and that of immune cells was relatively high in scRNA-seq. This difference could be explained by variations in the expression scores of adhesion genes due to the disruption of the cytoplasmic contents during scRNA-seq. The enrichment of epithelial cells in the colon resulted in a discrepancy in the differentiation of epithelial cells. This enrichment was also well matched with the images of hematoxylin and eosin staining and the estimated distribution of cell types in bulk RNA sequencing. These results showed that snRNA-seq could be used to analyze tissues that cannot be subjected to scRNA-seq and provides more information in specific cell type analysis.
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Affiliation(s)
- Jin-Mi Oh
- grid.414964.a0000 0001 0640 5613Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Minae An
- grid.414964.a0000 0001 0640 5613Innovative Institute for Precision Medicine, Samsung Medical Center, Seoul, Korea
| | - Dae-Soon Son
- grid.256753.00000 0004 0470 5964School of Big Data Science, Data Science Convergence Research Center, Hallym University, Chuncheon, 24252 Korea
| | - Jinhyuk Choi
- grid.222754.40000 0001 0840 2678Department of Legal Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Yong Beom Cho
- grid.414964.a0000 0001 0640 5613Department of Surgery, Sungkyunkwan University, Samsung Medical Center, Seoul, Korea ,grid.264381.a0000 0001 2181 989XDepartment of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea
| | - Chang Eun Yoo
- grid.414964.a0000 0001 0640 5613Basic Research Support Center, Samsung Research Institute for Future Medicine/Samsung Medical Center, Seoul, Korea
| | - Woong-Yang Park
- grid.414964.a0000 0001 0640 5613Samsung Genome Institute, Samsung Medical Center, Seoul, Korea ,grid.264381.a0000 0001 2181 989XDepartment of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea ,Geninus Inc, Seoul, Korea ,grid.264381.a0000 0001 2181 989XDepartment of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
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227
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Jiang YJ, Gao JF, Lin LH, Li H, Meng QG, Qu YF, Ji X. Single-cell transcriptomes from turtle livers reveal sensitivity of hepatic immune cells to bacteria-infection. FISH & SHELLFISH IMMUNOLOGY 2022; 131:847-854. [PMID: 36273515 DOI: 10.1016/j.fsi.2022.10.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
The liver is important in the synthesis, metabolism and storage of nutrients, detoxification and immune response of the body, and the liver immune response against exogenous pathogens from the intestinal tract plays a key role in the immune activities. However, the cellular composition of the liver immune atlas remains sparsely studied in reptiles. We used single-cell RNA sequencing to identify the cellular profile of the liver of the Chinese soft-shelled turtle (Pelodiscus sinensis). We obtained the transcriptional landscape based on 9938 cells from the fractionation of fresh hepatic tissues from two individuals, uninfected and infected with bacteria (Aeromonas hydrophila). We identified seven hepatic immune cell subsets, including plasma, erythroid, T/NK, B, endothelial, dendritic and Kupffer cells. Bacteria-infection altered the number of liver immune cells, as revealed by the fact that the infected turtle had more plasma, endothelial and Kupffer cells and fewer T/NK, dendritic and erythroid cells than did the uninfected turtle. Our study is the first to provide a comprehensive view of the hepatic immune landscape of P. sinensis at the single-cell resolution that outlines the characteristics of immune cells in the turtle liver and provides a liver transcriptome baseline for turtle immunology.
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Affiliation(s)
- Yi-Jin Jiang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Jian-Fang Gao
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Qing-Guo Meng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
| | - Xiang Ji
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, Zhejiang, China.
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228
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Abstract
Metabolic diseases, including obesity, diabetes mellitus and cardiovascular disease, are a major threat to health in the modern world, but efforts to understand the underlying mechanisms and develop rational treatments are limited by the lack of appropriate human model systems. Notably, advances in stem cell and organoid technology allow the generation of cellular models that replicate the histological, molecular and physiological properties of human organs. Combined with marked improvements in gene editing tools, human stem cells and organoids provide unprecedented systems for studying mechanisms of metabolic diseases. Here, we review progress made over the past decade in the generation and use of stem cell-derived metabolic cell types and organoids in metabolic disease research, especially obesity and liver diseases. In particular, we discuss the limitations of animal models and the advantages of stem cells and organoids, including their application to metabolic diseases. We also discuss mechanisms of drug action, understanding the efficacy and toxicity of existing therapies, screening for new treatments and pursuing personalized therapies. We highlight the potential of combining stem cell-derived organoids with gene editing and functional genomics to revolutionize the approach to finding treatments for metabolic diseases.
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Affiliation(s)
- Wenxiang Hu
- Department of Basic Research, Guangzhou Laboratory, Guangdong, China.
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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229
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Rodrigues FS, Ciccarelli FD, Malanchi I. Reflected stemness as a potential driver of the tumour microenvironment. Trends Cell Biol 2022; 32:979-987. [PMID: 35589467 DOI: 10.1016/j.tcb.2022.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 01/21/2023]
Abstract
A fundamental requirement for cancer initiation is the activation of developmental programmes by mutant cells. Oncogenic signals often confer an undifferentiated, stem cell-like phenotype that supports the long-term proliferative potential of cancer cells. Although cancer is a genetically driven disease, mutations in cancer-driver genes alone are insufficient for tumour formation, and the proliferation of cells harbouring oncogenic mutations depends on their microenvironment. In this Opinion article we discuss how the reprogrammed status of cancer cells not only represents the essence of their tumorigenicity but triggers 'reflected stemness' in their surrounding normal counterparts. We propose that this reciprocal interaction underpins the establishment of the tumour microenvironment (TME).
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Affiliation(s)
- Felipe S Rodrigues
- Tumour-Host Interaction Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Ilaria Malanchi
- Tumour-Host Interaction Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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230
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Luo P, Chen J, Zhang Q, Xia F, Wang C, Bai Y, Tang H, Liu D, Gu L, Du Q, Xiao W, Yang C, Wang J. Dissection of cellular and molecular mechanisms of aristolochic acid-induced hepatotoxicity via single-cell transcriptomics. PRECISION CLINICAL MEDICINE 2022; 5:pbac023. [PMID: 36349141 PMCID: PMC9635452 DOI: 10.1093/pcmedi/pbac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 09/15/2022] [Indexed: 11/18/2022] Open
Abstract
Background Aristolochic acids (AAs), a class of carcinogenic and mutagenic natural products from Aristolochia and Asarum plants, are well-known to be responsible for inducing nephrotoxicity and urothelial carcinoma. Recently, accumulating evidence suggests that exposure to AAs could also induce hepatotoxicity and even hepatocellular carcinoma, though the mechanisms are poorly defined. Methods Here, we aimed to dissect the underlying cellular and molecular mechanisms of aristolochic acid I (AAI)-induced hepatotoxicity by using advanced single-cell RNA sequencing (scRNA-seq) and proteomics techniques. We established the first single-cell atlas of mouse livers in response to AAI. Results In hepatocytes, our results indicated that AAI activated NF-κB and STAT3 signaling pathways, which may contribute to the inflammatory response and apoptosis. In liver sinusoidal endothelial cells (LSECs), AAI activated multiple oxidative stress and inflammatory associated signaling pathways and induced apoptosis. Importantly, AAI induced infiltration of cytotoxic T cells and activation of proinflammatory macrophage and neutrophil cells in the liver to produce inflammatory cytokines to aggravate inflammation. Conclusions Collectively, our study provides novel knowledge of AAs-induced molecular characteristics of hepatotoxicity at a single-cell level and suggests future treatment options for AAs associated hepatotoxicity.
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Affiliation(s)
- Piao Luo
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing 100700, China
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jiayun Chen
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qian Zhang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing 100700, China
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Fei Xia
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Chen Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yunmeng Bai
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Huan Tang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Dandan Liu
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Liwei Gu
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qingfeng Du
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Wei Xiao
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Department of Nephrology, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
| | - Chuanbin Yang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Jigang Wang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing 100700, China
- Center for Reproductive Medicine, Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan 523125, China
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231
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Xue R, Zhang Q, Cao Q, Kong R, Xiang X, Liu H, Feng M, Wang F, Cheng J, Li Z, Zhan Q, Deng M, Zhu J, Zhang Z, Zhang N. Liver tumour immune microenvironment subtypes and neutrophil heterogeneity. Nature 2022; 612:141-147. [PMID: 36352227 DOI: 10.1038/s41586-022-05400-x] [Citation(s) in RCA: 231] [Impact Index Per Article: 115.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/30/2022] [Indexed: 11/10/2022]
Abstract
The heterogeneity of the tumour immune microenvironment (TIME), organized by various immune and stromal cells, is a major contributing factor of tumour metastasis, relapse and drug resistance1-3, but how different TIME subtypes are connected to the clinical relevance in liver cancer remains unclear. Here we performed single-cell RNA-sequencing (scRNA-seq) analysis of 189 samples collected from 124 patients and 8 mice with liver cancer. With more than 1 million cells analysed, we stratified patients into five TIME subtypes, including immune activation, immune suppression mediated by myeloid or stromal cells, immune exclusion and immune residence phenotypes. Different TIME subtypes were spatially organized and associated with chemokine networks and genomic features. Notably, tumour-associated neutrophil (TAN) populations enriched in the myeloid-cell-enriched subtype were associated with an unfavourable prognosis. Through in vitro induction of TANs and ex vivo analyses of patient TANs, we showed that CCL4+ TANs can recruit macrophages and that PD-L1+ TANs can suppress T cell cytotoxicity. Furthermore, scRNA-seq analysis of mouse neutrophil subsets revealed that they are largely conserved with those of humans. In vivo neutrophil depletion in mouse models attenuated tumour progression, confirming the pro-tumour phenotypes of TANs. With this detailed cellular heterogeneity landscape of liver cancer, our study illustrates diverse TIME subtypes, highlights immunosuppressive functions of TANs and sheds light on potential immunotherapies targeting TANs.
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Affiliation(s)
- Ruidong Xue
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Qiming Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China
| | - Qi Cao
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Ruirui Kong
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Xiao Xiang
- Beijing Key Surgical Basic Research Laboratory of Liver Cirrhosis and Liver Cancer, Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China
| | - Hengkang Liu
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Mei Feng
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Fangyanni Wang
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Jinghui Cheng
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Zhao Li
- Beijing Key Surgical Basic Research Laboratory of Liver Cirrhosis and Liver Cancer, Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China
| | - Qimin Zhan
- International Cancer Institute, Peking University Health Science Center, Beijing, China
| | - Mi Deng
- International Cancer Institute, Peking University Health Science Center, Beijing, China
| | - Jiye Zhu
- Beijing Key Surgical Basic Research Laboratory of Liver Cirrhosis and Liver Cancer, Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China.
| | - Zemin Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China. .,Changping Laboratory, Beijing, China.
| | - Ning Zhang
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China. .,International Cancer Institute, Peking University Health Science Center, Beijing, China. .,Yunnan Baiyao Group, Kunming, China.
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232
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Björkström NK. Immunobiology of the biliary tract system. J Hepatol 2022; 77:1657-1669. [PMID: 36116989 PMCID: PMC7615184 DOI: 10.1016/j.jhep.2022.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/09/2022] [Accepted: 08/17/2022] [Indexed: 12/04/2022]
Abstract
The biliary tract is a complex tubular organ system spanning from the liver to the duodenum. It is the site of numerous acute and chronic disorders, many of unknown origin, that are often associated with cancer development and for which there are limited treatment options. Cholangiocytes with proinflammatory capacities line the lumen and specialised types of immune cells reside in close proximity. Recent technological breakthroughs now permit spatiotemporal assessments of immune cells within distinct niches and have increased our understanding of immune cell tissue residency. In this review, a comprehensive overview of emerging knowledge on the immunobiology of the biliary tract system is provided, with a particular emphasis on the role of distinct immune cells in biliary disorders.
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Affiliation(s)
- Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden.
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233
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Xu X, Zhang Q, Li M, Lin S, Liang S, Cai L, Zhu H, Su R, Yang C. Microfluidic single‐cell multiomics analysis. VIEW 2022. [DOI: 10.1002/viw.20220034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
- Xing Xu
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Qiannan Zhang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Mingyin Li
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Shiyan Lin
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Shanshan Liang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Linfeng Cai
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Huanghuang Zhu
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Rui Su
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Chaoyong Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
- Institute of Molecular Medicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
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234
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Chen Y, Tang L. The crosstalk between parenchymal cells and macrophages: A keeper of tissue homeostasis. Front Immunol 2022; 13:1050188. [PMID: 36505488 PMCID: PMC9732730 DOI: 10.3389/fimmu.2022.1050188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022] Open
Abstract
Non-parenchymal cells (NPCs) and parenchymal cells (PCs) collectively perform tissue-specific functions. PCs play significant roles and continuously adjust the intrinsic functions and metabolism of organs. Tissue-resident macrophages (TRMs) are crucial members of native NPCs in tissues and are essential for immune defense, tissue repair and development, and homeostasis maintenance. As a plastic-phenotypic and prevalent cluster of NPCs, TRMs dynamically assist PCs in functioning by producing cytokines, inflammatory and anti-inflammatory signals, growth factors, and proteolytic enzymes. Furthermore, the PCs of tissues modulate the functional activity and polarization of TRMs. Dysregulation of the PC-TRM crosstalk axis profoundly impacts many essential physiological functions, including synaptogenesis, gastrointestinal motility and secretion, cardiac pulsation, gas exchange, blood filtration, and metabolic homeostasis. This review focuses on the PC-TRM crosstalk in mammalian vital tissues, along with their interactions with tissue homeostasis maintenance and disorders. Thus, this review highlights the fundamental biological significance of the regulatory network of PC-TRM in tissue homeostasis.
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235
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Overbey EG, Das S, Cope H, Madrigal P, Andrusivova Z, Frapard S, Klotz R, Bezdan D, Gupta A, Scott RT, Park J, Chirko D, Galazka JM, Costes SV, Mason CE, Herranz R, Szewczyk NJ, Borg J, Giacomello S. Challenges and considerations for single-cell and spatially resolved transcriptomics sample collection during spaceflight. CELL REPORTS METHODS 2022; 2:100325. [PMID: 36452864 PMCID: PMC9701605 DOI: 10.1016/j.crmeth.2022.100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have experienced rapid development in recent years. The findings of spaceflight-based scRNA-seq and SRT investigations are likely to improve our understanding of life in space and our comprehension of gene expression in various cell systems and tissue dynamics. However, compared to their Earth-based counterparts, gene expression experiments conducted in spaceflight have not experienced the same pace of development. Out of the hundreds of spaceflight gene expression datasets available, only a few used scRNA-seq and SRT. In this perspective piece, we explore the growing importance of scRNA-seq and SRT in space biology and discuss the challenges and considerations relevant to robust experimental design to enable growth of these methods in the field.
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Affiliation(s)
- Eliah G. Overbey
- Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, New York, NY, USA
| | - Saswati Das
- Department of Biochemistry, Atal Bihari Vajpayee Institute of Medical Sciences & Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Henry Cope
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
| | - Pedro Madrigal
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Zaneta Andrusivova
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Solène Frapard
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rebecca Klotz
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, German
- yuri GmbH, Meckenbeuren, Germany
| | | | - Ryan T. Scott
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | | | - Jonathan M. Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Sylvain V. Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Christopher E. Mason
- Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | - Raul Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid 28040, Spain
| | - Nathaniel J. Szewczyk
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Joseph Borg
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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236
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Hess S, Kendall TJ, Pena M, Yamane K, Soong D, Adams L, Truman R, Rambukkana A. In vivo partial reprogramming by bacteria promotes adult liver organ growth without fibrosis and tumorigenesis. Cell Rep Med 2022; 3:100820. [PMID: 36384103 PMCID: PMC9729881 DOI: 10.1016/j.xcrm.2022.100820] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 05/04/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022]
Abstract
Ideal therapies for regenerative medicine or healthy aging require healthy organ growth and rejuvenation, but no organ-level approach is currently available. Using Mycobacterium leprae (ML) with natural partial cellular reprogramming capacity and its animal host nine-banded armadillos, we present an evolutionarily refined model of adult liver growth and regeneration. In infected armadillos, ML reprogram the entire liver and significantly increase total liver/body weight ratio by increasing healthy liver lobules, including hepatocyte proliferation and proportionate expansion of vasculature, and biliary systems. ML-infected livers are microarchitecturally and functionally normal without damage, fibrosis, or tumorigenesis. Bacteria-induced reprogramming reactivates liver progenitor/developmental/fetal genes and upregulates growth-, metabolism-, and anti-aging-associated markers with minimal change in senescence and tumorigenic genes, suggesting bacterial hijacking of homeostatic, regeneration pathways to promote de novo organogenesis. This may facilitate the unraveling of endogenous pathways that effectively and safely re-engage liver organ growth, with broad therapeutic implications including organ regeneration and rejuvenation.
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Affiliation(s)
- Samuel Hess
- Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK; Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh, UK
| | - Timothy J Kendall
- Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK; Centre for Inflammation Research, The University of Edinburgh, Edinburgh, UK; Edinburgh Pathology, The University of Edinburgh, Edinburgh, UK
| | - Maria Pena
- US Department of Health and Human Services, Health Resources and Services Administration, Healthcare Systems Bureau, National Hansen's Disease Program, Baton Rouge, LA, USA
| | - Keitaro Yamane
- Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK; Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh, UK
| | - Daniel Soong
- Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK; Medical Research Council Centre for Reproductive Health, The University of Edinburgh, Edinburgh, UK
| | - Linda Adams
- US Department of Health and Human Services, Health Resources and Services Administration, Healthcare Systems Bureau, National Hansen's Disease Program, Baton Rouge, LA, USA
| | - Richard Truman
- US Department of Health and Human Services, Health Resources and Services Administration, Healthcare Systems Bureau, National Hansen's Disease Program, Baton Rouge, LA, USA; Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Anura Rambukkana
- Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK; Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh, UK; Edinburgh Infectious Diseases, The University of Edinburgh, Edinburgh, UK; Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK.
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237
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Brougham-Cook A, Kimmel HRC, Monckton CP, Owen D, Khetani SR, Underhill GH. Engineered matrix microenvironments reveal the heterogeneity of liver sinusoidal endothelial cell phenotypic responses. APL Bioeng 2022; 6:046102. [PMID: 36345318 PMCID: PMC9637025 DOI: 10.1063/5.0097602] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022] Open
Abstract
Fibrosis is one of the hallmarks of chronic liver disease and is associated with aberrant wound healing. Changes in the composition of the liver microenvironment during fibrosis result in a complex crosstalk of extracellular cues that promote altered behaviors in the cell types that comprise the liver sinusoid, particularly liver sinusoidal endothelial cells (LSECs). Recently, it has been observed that LSECs may sustain injury before other fibrogenesis-associated cells of the sinusoid, implicating LSECs as key actors in the fibrotic cascade. A high-throughput cellular microarray platform was used to deconstruct the collective influences of defined combinations of extracellular matrix (ECM) proteins, substrate stiffness, and soluble factors on primary human LSEC phenotype in vitro. We observed remarkable heterogeneity in LSEC phenotype as a function of stiffness, ECM, and soluble factor context. LYVE-1 and CD-31 expressions were highest on 1 kPa substrates, and the VE-cadherin junction localization was highest on 25 kPa substrates. Also, LSECs formed distinct spatial patterns of LYVE-1 expression, with LYVE-1+ cells observed in the center of multicellular domains, and pattern size regulated by microenvironmental context. ECM composition also influenced a substantial dynamic range of expression levels for all markers, and the collagen type IV was observed to promote elevated expressions of LYVE-1, VE-cadherin, and CD-31. These studies highlight key microenvironmental regulators of LSEC phenotype and reveal unique spatial patterning of the sinusoidal marker LYVE-1. Furthermore, these data provide insight into understanding more precisely how LSECs respond to fibrotic microenvironments, which will aid drug development and identification of targets to treat liver fibrosis.
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Affiliation(s)
- Aidan Brougham-Cook
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Hannah R. C. Kimmel
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Chase P. Monckton
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Daniel Owen
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Salman R. Khetani
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Gregory H. Underhill
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA,Author to whom correspondence should be addressed:. Tel.: 217–244-2169
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238
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Calcagno DM, Taghdiri N, Ninh VK, Mesfin JM, Toomu A, Sehgal R, Lee J, Liang Y, Duran JM, Adler E, Christman KL, Zhang K, Sheikh F, Fu Z, King KR. Single-cell and spatial transcriptomics of the infarcted heart define the dynamic onset of the border zone in response to mechanical destabilization. NATURE CARDIOVASCULAR RESEARCH 2022; 1:1039-1055. [PMID: 39086770 PMCID: PMC11290420 DOI: 10.1038/s44161-022-00160-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/03/2022] [Indexed: 08/02/2024]
Abstract
The border zone (BZ) of the infarcted heart is a geographically complex and biologically enigmatic interface separating poorly perfused infarct zones (IZs) from remote zones (RZs). The cellular and molecular mechanisms of myocardial BZs are not well understood because microdissection inevitably combines them with uncontrolled amounts of RZs and IZs. Here, we use single-cell/nucleus RNA sequencing, spatial transcriptomics and multiplexed RNA fluorescence in situ hybridization to redefine the BZ based on cardiomyocyte transcriptomes. BZ1 (Nppa + Xirp2 -) forms a hundreds-of-micrometer-thick layer of morphologically intact cells adjacent to RZs that are detectable within an hour of injury. Meanwhile, BZ2 (Nppa + Xirp2 +) forms a near-single-cell-thick layer of morphologically distorted cardiomyocytes at the IZ edge that colocalize with matricellular protein-expressing myofibroblasts and express predominantly mechanotransduction genes. Surprisingly, mechanical injury alone is sufficient to induce BZ genes. We propose a 'loss of neighbor' hypothesis to explain how ischemic cell death mechanically destabilizes the BZ to induce its transcriptional response.
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Affiliation(s)
- D. M. Calcagno
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- These authors contributed equally: D.M. Calcagno, N. Taghdiri
| | - N. Taghdiri
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- These authors contributed equally: D.M. Calcagno, N. Taghdiri
| | - V. K. Ninh
- Division of Cardiology and Cardiovascular Institute, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - J. M. Mesfin
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - A. Toomu
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - R. Sehgal
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - J. Lee
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Y. Liang
- Division of Cardiology and Cardiovascular Institute, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - J. M. Duran
- Division of Cardiology and Cardiovascular Institute, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - E. Adler
- Division of Cardiology and Cardiovascular Institute, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - K. L. Christman
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - K. Zhang
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - F. Sheikh
- Division of Cardiology and Cardiovascular Institute, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Z. Fu
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - K. R. King
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Division of Cardiology and Cardiovascular Institute, Department of Medicine, University of California San Diego, La Jolla, CA, USA
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239
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Peng J, Li F, Wang J, Wang C, Jiang Y, Liu B, He J, Yuan K, Pan C, Lin M, Zhou B, Chen L, Gao D, Zhao Y. Identification of a rare Gli1 + progenitor cell population contributing to liver regeneration during chronic injury. Cell Discov 2022; 8:118. [PMID: 36316325 PMCID: PMC9622734 DOI: 10.1038/s41421-022-00474-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022] Open
Abstract
In adults, hepatocytes are mainly replenished from the existing progenitor pools of hepatocytes and cholangiocytes during chronic liver injury. However, it is unclear whether other cell types in addition to classical hepatocytes and cholangiocytes contribute to hepatocyte regeneration after chronic liver injuries. Here, we identified a new biphenotypic cell population that contributes to hepatocyte regeneration during chronic liver injuries. We found that a cell population expressed Gli1 and EpCAM (EpCAM+Gli1+), which was further characterized with both epithelial and mesenchymal identities by single-cell RNA sequencing. Genetic lineage tracing using dual recombinases revealed that Gli1+ nonhepatocyte cell population could generate hepatocytes after chronic liver injury. EpCAM+Gli1+ cells exhibited a greater capacity for organoid formation with functional hepatocytes in vitro and liver regeneration upon transplantation in vivo. Collectively, these findings demonstrate that EpCAM+Gli1+ cells can serve as a new source of liver progenitor cells and contribute to liver repair and regeneration.
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Affiliation(s)
- Jiayin Peng
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Fei Li
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Jia Wang
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Chaoxiong Wang
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Yiao Jiang
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Biao Liu
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Juan He
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Kai Yuan
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Chenyu Pan
- grid.24516.340000000123704535Department of General Surgery, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Moubin Lin
- grid.24516.340000000123704535Department of General Surgery, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bin Zhou
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Luonan Chen
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Dong Gao
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China ,grid.9227.e0000000119573309Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Yun Zhao
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China ,grid.440637.20000 0004 4657 8879School of Life Science and Technology, ShanghaiTech University, Shanghai, China ,grid.410726.60000 0004 1797 8419Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang China
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240
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Liao J, Qian J, Fang Y, Chen Z, Zhuang X, Zhang N, Shao X, Hu Y, Yang P, Cheng J, Hu Y, Yu L, Yang H, Zhang J, Lu X, Shao L, Wu D, Gao Y, Chen H, Fan X. De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution. Nat Commun 2022; 13:6498. [PMID: 36310179 PMCID: PMC9618574 DOI: 10.1038/s41467-022-34271-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 10/19/2022] [Indexed: 12/25/2022] Open
Abstract
Uncovering the tissue molecular architecture at single-cell resolution could help better understand organisms' biological and pathological processes. However, bulk RNA-seq can only measure gene expression in cell mixtures, without revealing the transcriptional heterogeneity and spatial patterns of single cells. Herein, we introduce Bulk2Space ( https://github.com/ZJUFanLab/bulk2space ), a deep learning framework-based spatial deconvolution algorithm that can simultaneously disclose the spatial and cellular heterogeneity of bulk RNA-seq data using existing single-cell and spatial transcriptomics references. The use of bulk transcriptomics to validate Bulk2Space unveils, in particular, the spatial variance of immune cells in different tumor regions, the molecular and spatial heterogeneity of tissues during inflammation-induced tumorigenesis, and spatial patterns of novel genes in different cell types. Moreover, Bulk2Space is utilized to perform spatial deconvolution analysis on bulk transcriptome data from two different mouse brain regions derived from our in-house developed sequencing approach termed Spatial-seq. We have not only reconstructed the hierarchical structure of the mouse isocortex but also further annotated cell types that were not identified by original methods in the mouse hypothalamus.
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Affiliation(s)
- Jie Liao
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Jingyang Qian
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Yin Fang
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China
- Hangzhou Innovation Center, Zhejiang University, 310058, Hangzhou, China
| | - Zhuo Chen
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China
- Hangzhou Innovation Center, Zhejiang University, 310058, Hangzhou, China
| | - Xiang Zhuang
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China
- Hangzhou Innovation Center, Zhejiang University, 310058, Hangzhou, China
| | - Ningyu Zhang
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China
- Hangzhou Innovation Center, Zhejiang University, 310058, Hangzhou, China
| | - Xin Shao
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Yining Hu
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Penghui Yang
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Junyun Cheng
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
- Innovation Center in Zhejiang University, State Key Laboratory of Component-Based Chinese Medicine, 310058, Hangzhou, China
| | - Yang Hu
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
- Innovation Center in Zhejiang University, State Key Laboratory of Component-Based Chinese Medicine, 310058, Hangzhou, China
| | - Lingqi Yu
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Haihong Yang
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China
- Hangzhou Innovation Center, Zhejiang University, 310058, Hangzhou, China
| | - Jinlu Zhang
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China
| | - Xiaoyan Lu
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
- Innovation Center in Zhejiang University, State Key Laboratory of Component-Based Chinese Medicine, 310058, Hangzhou, China
| | - Li Shao
- Institute of Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, 310015, Hangzhou, China
| | - Dan Wu
- College of Biomedical Engineering and Instrument Science, Zhejiang University, 310013, Hangzhou, China
| | - Yue Gao
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, 100850, Beijing, China.
| | - Huajun Chen
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China.
- Hangzhou Innovation Center, Zhejiang University, 310058, Hangzhou, China.
| | - Xiaohui Fan
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China.
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China.
- Innovation Center in Zhejiang University, State Key Laboratory of Component-Based Chinese Medicine, 310058, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, China.
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241
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Pita-Juarez Y, Karagkouni D, Kalavros N, Melms JC, Niezen S, Delorey TM, Essene AL, Brook OR, Pant D, Skelton-Badlani D, Naderi P, Huang P, Pan L, Hether T, Andrews TS, Ziegler CGK, Reeves J, Myloserdnyy A, Chen R, Nam A, Phelan S, Liang Y, Amin AD, Biermann J, Hibshoosh H, Veregge M, Kramer Z, Jacobs C, Yalcin Y, Phillips D, Slyper M, Subramanian A, Ashenberg O, Bloom-Ackermann Z, Tran VM, Gomez J, Sturm A, Zhang S, Fleming SJ, Warren S, Beechem J, Hung D, Babadi M, Padera RF, MacParland SA, Bader GD, Imad N, Solomon IH, Miller E, Riedel S, Porter CBM, Villani AC, Tsai LTY, Hide W, Szabo G, Hecht J, Rozenblatt-Rosen O, Shalek AK, Izar B, Regev A, Popov Y, Jiang ZG, Vlachos IS. A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.27.514070. [PMID: 36324805 PMCID: PMC9628199 DOI: 10.1101/2022.10.27.514070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.
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Affiliation(s)
- Yered Pita-Juarez
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dimitra Karagkouni
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nikolaos Kalavros
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, HMS Initiative for RNA Medicine / Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Sebastian Niezen
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Toni M Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam L Essene
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Olga R Brook
- Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Deepti Pant
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Disha Skelton-Badlani
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Pourya Naderi
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Pinzhu Huang
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Liuliu Pan
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Tallulah S Andrews
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada
| | - Carly G K Ziegler
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Andriy Myloserdnyy
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Rachel Chen
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Andy Nam
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Yan Liang
- NanoString Technologies, Inc., Seattle, WA, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Molly Veregge
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Zachary Kramer
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Christopher Jacobs
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Yusuf Yalcin
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Devan Phillips
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Michal Slyper
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | | | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zohar Bloom-Ackermann
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Victoria M Tran
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James Gomez
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander Sturm
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shuting Zhang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen J Fleming
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Deborah Hung
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Mehrtash Babadi
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert F Padera
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sonya A MacParland
- 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
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, Toronto, ON, Canada
| | - Nasser Imad
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Isaac H Solomon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Eric Miller
- NanoString Technologies, Inc., Seattle, WA, USA
| | - Stefan Riedel
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Linus T-Y Tsai
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Winston Hide
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Gyongyi Szabo
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Jonathan Hecht
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Alex K Shalek
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Yury Popov
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Z Gordon Jiang
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Ioannis S Vlachos
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, HMS Initiative for RNA Medicine / Beth Israel Deaconess Medical Center, Boston, MA, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA
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242
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Pita-Juarez Y, Karagkouni D, Kalavros N, Melms JC, Niezen S, Delorey TM, Essene AL, Brook OR, Pant D, Skelton-Badlani D, Naderi P, Huang P, Pan L, Hether T, Andrews TS, Ziegler CGK, Reeves J, Myloserdnyy A, Chen R, Nam A, Phelan S, Liang Y, Amin AD, Biermann J, Hibshoosh H, Veregge M, Kramer Z, Jacobs C, Yalcin Y, Phillips D, Slyper M, Subramanian A, Ashenberg O, Bloom-Ackermann Z, Tran VM, Gomez J, Sturm A, Zhang S, Fleming SJ, Warren S, Beechem J, Hung D, Babadi M, Padera RF, MacParland SA, Bader GD, Imad N, Solomon IH, Miller E, Riedel S, Porter CBM, Villani AC, Tsai LTY, Hide W, Szabo G, Hecht J, Rozenblatt-Rosen O, Shalek AK, Izar B, Regev A, Popov Y, Jiang ZG, Vlachos IS. A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 36324805 DOI: 10.1101/2022.08.06.503037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.
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243
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Tripura C, Gunda S, Vishwakarma SK, Thatipalli AR, Jose J, Jerald MK, Khan AA, Pande G. Long-term and non-invasive in vivo tracking of DiD dye-labeled human hepatic progenitors in chronic liver disease models. World J Hepatol 2022; 14:1884-1898. [PMID: 36340748 PMCID: PMC9627437 DOI: 10.4254/wjh.v14.i10.1884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/02/2022] [Accepted: 10/04/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Chronic liver diseases (CLD) are the major public health burden due to the continuous increasing rate of global morbidity and mortality. The inherent limitations of organ transplantation have led to the development of stem cell-based therapy as a supportive and promising therapeutic option. However, identifying the fate of transplanted cells in vivo represents a crucial obstacle.
AIM To evaluate the potential applicability of DiD dye as a cell labeling agent for long-term, and non-invasive in vivo tracking of transplanted cells in the liver.
METHODS Magnetically sorted, epithelial cell adhesion molecule positive (1 × 106 cells/mL) fetal hepatic progenitor cells were labeled with DiD dye and transplanted into the livers of CLD-severe combined immunodeficiency (SCID) mice. Near-infrared (NIR) imaging was performed for in vivo tracking of the DiD-labeled transplanted cells along with colocalization of hepatic markers for up to 80 d. The existence of human cells within mouse livers was identified using Alu polymerase chain reaction and sequencing.
RESULTS NIR fluorescence imaging of CLD-SCID mice showed a positive fluorescence signal of DiD at days 7, 15, 30, 45, 60, and 80 post-transplantation. Furthermore, positive staining of cytokeratin, c-Met, and albumin colocalizing with DiD fluorescence clearly demonstrated that the fluorescent signal of hepatic markers emerged from the DiD-labeled transplanted cells. Recovery of liver function was also observed with serum levels of glutamic-oxaloacetic transaminase, glutamate-pyruvate transaminase, and bilirubin. The detection of human-specific Alu sequence from the transplanted mouse livers provided evidence for the survival of transplanted cells at day 80.
CONCLUSION DiD-labeling is promising for long-term and non-invasive in vivo cell tracking, and understanding the regenerative mechanisms incurred by the transplanted cells.
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Affiliation(s)
- Chaturvedula Tripura
- Cell and Stem Cell Biology, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Srinivas Gunda
- Cell and Stem Cell Biology, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Sandeep Kumar Vishwakarma
- Central Laboratory for Stem Cell Research and Translational Medicine, Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences, Hyderabad 500058, Telangana, India
| | - Avinash Raj Thatipalli
- Cell and Stem Cell Biology, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Jedy Jose
- Cell and Stem Cell Biology, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Mahesh Kumar Jerald
- Cell and Stem Cell Biology, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Aleem Ahmed Khan
- Central Laboratory for Stem Cell Research and Translational Medicine, Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences, Hyderabad 500058, Telangana, India
| | - Gopal Pande
- Cell and Stem Cell Biology, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
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244
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When the Guest Meets the Host: Assessing the Immune Reconstitution of the Liver Graft One Cell at a Time. Transplantation 2022; 107:822-823. [PMID: 36289557 DOI: 10.1097/tp.0000000000004366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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245
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Lee J, Kim CM, Cha JH, Park JY, Yu YS, Wang HJ, Sung PS, Jung ES, Bae SH. Multiplexed Digital Spatial Protein Profiling Reveals Distinct Phenotypes of Mononuclear Phagocytes in Livers with Advanced Fibrosis. Cells 2022; 11:3387. [PMID: 36359782 PMCID: PMC9654480 DOI: 10.3390/cells11213387] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 07/29/2023] Open
Abstract
Background and Aims: Intrahepatic mononuclear phagocytes (MPs) are critical for the initiation and progression of liver fibrosis. In this study, using multiplexed digital spatial protein profiling, we aimed to derive a unique protein signature predicting advanced liver fibrosis. Methods: Snap-frozen liver tissues from various chronic liver diseases were subjected to spatially defined protein-based multiplexed profiling (Nanostring GeoMXTM). A single-cell RNA sequencing analysis was performed using Gene Expression Omnibus (GEO) datasets from normal and cirrhotic livers. Results: Sixty-four portal regions of interest (ROIs) were selected for the spatial profiling. Using the results from the CD68+ area, a highly sensitive and specific immune-related protein signature (CD68, HLA-DR, OX40L, phospho-c-RAF, STING, and TIM3) was developed to predict advanced (F3 and F4) fibrosis. A combined analysis of single-cell RNA sequencing data from GEO datasets (GSE136103) and spatially-defined, protein-based multiplexed profiling revealed that most proteins upregulated in F0-F2 livers in portal CD68+ cells were specifically marked in tissue monocytes, whereas proteins upregulated in F3 and F4 livers were marked in scar-associated macrophages (SAMacs) and tissue monocytes. Internal validation using mRNA expression data with the same cohort tissues demonstrated that mRNA levels for TREM2, CD9, and CD68 are significantly higher in livers with advanced fibrosis. Conclusions: In patients with advanced liver fibrosis, portal MPs comprise of heterogeneous populations composed of SAMacs, Kupffer cells, and tissue monocytes. This is the first study that used spatially defined protein-based multiplexed profiling, and we have demonstrated the critical difference in the phenotypes of portal MPs between livers with early- or late-stage fibrosis.
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Affiliation(s)
- Jaejun Lee
- Department of Internal Medicine, Armed Forces Goyang Hospital, Goyang 10267, Korea
- The Catholic University Liver Research Center, Department of Biomedical Science, The Graduates School of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | | | - Jung Hoon Cha
- The Catholic University Liver Research Center, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | | | - Yun Suk Yu
- CbsBioscience, Inc., Daejeon 34036, Korea
| | - Hee Jung Wang
- Department of Surgery, Inje University Haeundae Paik Hospital, Busan 48108, Korea
| | - Pil Soo Sung
- The Catholic University Liver Research Center, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Eun Sun Jung
- Department of Hospital pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Si Hyun Bae
- The Catholic University Liver Research Center, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, College of Medicine, Eunpyeong St. Mary’s Hospital, The Catholic University of Korea, Seoul 03383, Korea
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246
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Huang JH, Wang J, Chai XQ, Li ZC, Jiang YH, Li J, Liu X, Fan J, Cai JB, Liu F. The Intratumoral Bacterial Metataxonomic Signature of Hepatocellular Carcinoma. Microbiol Spectr 2022; 10:e0098322. [PMID: 36173308 PMCID: PMC9602924 DOI: 10.1128/spectrum.00983-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/11/2022] [Indexed: 12/30/2022] Open
Abstract
Microbiota is implicated in hepatocellular carcinoma (HCC). The spectrum of intratumoral microbiota associated with HCC progression remains elusive. Fluorescence in situ hybridization revealed that microbial DNAs were distributed in the cytosol of liver hepatocytes and erythrocytes. Viable anaerobic or aerobic bacteria were recovered in HCC tissues by fresh tissue culture. We performed a comprehensive DNA sequencing of bacterial 16S rRNA genes in 156 samples from 28 normal liver, 64 peritumoral, and 64 HCC tissues, and the DNA sequencing yielded 4.2 million high-quality reads. Both alpha and beta diversity in peritumor and HCC microbiota were increased compared to normal controls. The most predominant phyla in HCC were Patescibacteria, Proteobacteria, Bacteroidota, Firmicutes, and Actinobacteriota. phyla of Proteobacteria, Firmicutes, and Actinobacteriota, and classes of Bacilli and Actinobacteria, were consistently enriched in peritumor and HCC tissues, while Gammaproteobacteria was especially abundant in HCC tissues compared to normal controls. Streptococcaceae and Lactococcus were the marker taxa of HCC cirrhosis. The Staphylococcus branch and Caulobacter branch were selectively enriched in HBV-negative HCCs. The abundance of Proteobacteria, Gammaproteobacteria, Firmicutes, Actinobacteriota, and Saccharimonadia were associated with the clinicopathological features of HCC patients. The inferred functions of different taxa were changed between the microbiota of normal liver and peritumor/HCC. Random forest machine learning achieved great discriminative performance in HCC prediction (area under the curve [AUC] = 1.00 in the training cohort, AUC = 0.950 for top five class signature, and AUC = 0.943 for the top 50 operational taxonomy units [OTUs] in the validation cohort). Our analysis highlights the complexity and diversity of the liver and HCC microbiota and established a specific intratumoral microbial signature for the potential prediction of HCC. IMPORTANCE Gut microbiome is an important regulator of hepatic inflammation, detoxification, and immunity, and contributes to the carcinogenesis of liver cancer. Intratumoral bacteria are supposed to be closer to the tumor cells, forming a microenvironment that may be relevant to the pathological process of hepatocellular carcinoma (HCC). However, the presence of viable intratumoral bacteria remains unclear. It is worth exploring whether the metataxonomic characteristics of intratumoral bacteria can be used as a potential marker for HCC prediction. Here, we present the first evidence of the existence of viable intratumoral bacteria in HCC using the tissue culture method. We revealed that microbial DNAs were distributed in the cytosol of liver hepatocytes and erythrocytes. We analyzed the diversity, structure, and abundance of normal liver and HCC microbiota. We built a machine learning model for HCC prediction using intratumoral bacterial features. We show that specific taxa represent potential targets for both therapeutic and diagnostic interventions.
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Affiliation(s)
- Jian-Hang Huang
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
| | - Jie Wang
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
- Department of Liver Surgery and Transplantation of Zhongshan Hospital, Liver Cancer Institute of Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Xiao-Qiang Chai
- Department of Liver Surgery and Transplantation of Zhongshan Hospital, Liver Cancer Institute of Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Zhong-Chen Li
- Department of Liver Surgery and Transplantation of Zhongshan Hospital, Liver Cancer Institute of Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Ying-Hua Jiang
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
| | - Jun Li
- Department of General Surgery, Shanghai TongRen Hospital, Shanghai, China
| | - Xing Liu
- Department of Central Laboratory Medicine, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation of Zhongshan Hospital, Liver Cancer Institute of Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Jia-Bin Cai
- Department of Liver Surgery and Transplantation of Zhongshan Hospital, Liver Cancer Institute of Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Feng Liu
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
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247
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Spatial transcriptome profiling of normal human liver. Sci Data 2022; 9:633. [PMID: 36261431 PMCID: PMC9581974 DOI: 10.1038/s41597-022-01676-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
The comprehensive study of the spatial-cellular anatomy of the human liver is critical to addressing the cellular origins of liver disease. Here we conducted spatial transcriptomics on normal human liver tissue sections, providing detailed information of liver zonation at the transcriptional level. We present 6581 high-quality spots from normal livers of two human donors. In this dataset, cells were mainly hepatocytes, and we classified them into four sub-groups. Collectively, these data provide a reliable reference for studies on spatial heterogeneity of liver lobules. Measurement(s) | mRNA Expression | Technology Type(s) | spatial transcriptomics | Sample Characteristic - Organism | Homo sapiens |
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248
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Lang T, Pelaseyed T. Discovery of a MUC3B gene reconstructs the membrane mucin gene cluster on human chromosome 7. PLoS One 2022; 17:e0275671. [PMID: 36256656 PMCID: PMC9578598 DOI: 10.1371/journal.pone.0275671] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 09/21/2022] [Indexed: 11/12/2022] Open
Abstract
Human tissue surfaces are coated with mucins, a family of macromolecular sugar-laden proteins serving diverse functions from lubrication to the formation of selective biochemical barriers against harmful microorganisms and molecules. Membrane mucins are a distinct group of mucins that are attached to epithelial cell surfaces where they create a dense glycocalyx facing the extracellular environment. All mucin proteins carry long stretches of tandemly repeated sequences that undergo extensive O-linked glycosylation to form linear mucin domains. However, the repetitive nature of mucin domains makes them prone to recombination and renders their genetic sequences particularly difficult to read with standard sequencing technologies. As a result, human mucin genes suffer from significant sequence gaps that have hampered the investigation of gene function in health and disease. Here we leveraged a recent human genome assembly to characterize a previously unmapped MUC3B gene located at the q22 locus on chromosome 7, within a cluster of four structurally related membrane mucin genes that we name the MUC3 cluster. We found that MUC3B shares high sequence identity with the known MUC3A gene and that the two genes are governed by evolutionarily conserved regulatory elements. Furthermore, we show that MUC3A, MUC3B, MUC12, and MUC17 in the human MUC3 cluster are expressed in intestinal epithelial cells (IECs). Our results complete existing genetic gaps in the MUC3 cluster which is a conserved genetic unit in vertebrates. We anticipate our results to be the starting point for the detection of disease-associated polymorphisms in the human MUC3 cluster. Moreover, our study provides the basis for the exploration of intestinal mucin gene function in widely used experimental models such as human intestinal organoids and genetic mouse models.
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Affiliation(s)
- Tiange Lang
- Big Data Decision Institution, Jinan University, Tianhe, Guangzhou, China
| | - Thaher Pelaseyed
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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249
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Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space. Nat Commun 2022; 13:6118. [PMID: 36253379 PMCID: PMC9574176 DOI: 10.1038/s41467-022-33758-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Computational tools for integrative analyses of diverse single-cell experiments are facing formidable new challenges including dramatic increases in data scale, sample heterogeneity, and the need to informatively cross-reference new data with foundational datasets. Here, we present SCALEX, a deep-learning method that integrates single-cell data by projecting cells into a batch-invariant, common cell-embedding space in a truly online manner (i.e., without retraining the model). SCALEX substantially outperforms online iNMF and other state-of-the-art non-online integration methods on benchmark single-cell datasets of diverse modalities, (e.g., single-cell RNA sequencing, scRNA-seq, single-cell assay for transposase-accessible chromatin use sequencing, scATAC-seq), especially for datasets with partial overlaps, accurately aligning similar cell populations while retaining true biological differences. We showcase SCALEX's advantages by constructing continuously expandable single-cell atlases for human, mouse, and COVID-19 patients, each assembled from diverse data sources and growing with every new data. The online data integration capacity and superior performance makes SCALEX particularly appropriate for large-scale single-cell applications to build upon previous scientific insights.
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250
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A comprehensive transcriptomic comparison of hepatocyte model systems improves selection of models for experimental use. Commun Biol 2022; 5:1094. [PMID: 36241695 PMCID: PMC9568534 DOI: 10.1038/s42003-022-04046-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2022] Open
Abstract
The myriad of available hepatocyte in vitro models provides researchers the possibility to select hepatocyte-like cells (HLCs) for specific research goals. However, direct comparison of hepatocyte models is currently challenging. We systematically searched the literature and compared different HLCs, but reported functions were limited to a small subset of hepatic functions. To enable a more comprehensive comparison, we developed an algorithm to compare transcriptomic data across studies that tested HLCs derived from hepatocytes, biliary cells, fibroblasts, and pluripotent stem cells, alongside primary human hepatocytes (PHHs). This revealed that no HLC covered the complete hepatic transcriptome, highlighting the importance of HLC selection. HLCs derived from hepatocytes had the highest transcriptional resemblance to PHHs regardless of the protocol, whereas the quality of fibroblasts and PSC derived HLCs varied depending on the protocol used. Finally, we developed and validated a web application (HLCompR) enabling comparison for specific pathways and addition of new HLCs. In conclusion, our comprehensive transcriptomic comparison of HLCs allows selection of HLCs for specific research questions and can guide improvements in culturing conditions.
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