1
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Cui X, Dong X, Hu M, Zhou W, Shi W. Large field of view and spatial region of interest transcriptomics in fixed tissue. Commun Biol 2024; 7:1020. [PMID: 39164496 PMCID: PMC11335973 DOI: 10.1038/s42003-024-06694-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 08/07/2024] [Indexed: 08/22/2024] Open
Abstract
Expression profiling in spatially defined regions is crucial for systematically understanding tissue complexity. Here, we report a method of photo-irradiation for in-situ barcoding hybridization and ligation sequencing, named PBHL-seq, which allows targeted expression profiling from the photo-irradiated region of interest in intact fresh frozen and formalin fixation and paraffin embedding (FFPE) tissue samples. PBHL-seq uses photo-caged oligodeoxynucleotides for in situ reverse transcription followed by spatially targeted barcoding of cDNAs to create spatially indexed transcriptomes of photo-illuminated regions. We recover thousands of differentially enriched transcripts from different regions by applying PBHL-seq to OCT-embedded tissue (E14.5 mouse embryo and mouse brain) and FFPE mouse embryo (E15.5). We also apply PBHL-seq to the subcellular microstructures (cytoplasm and nucleus, respectively) and detect thousands of differential expression genes. Thus, PBHL-seq provides an accessible workflow for expression profiles from the region of interest in frozen and FFPE tissue at subcellular resolution with areas expandable to centimeter scale, while preserving the sample intact for downstream analysis to promote the development of transcriptomics.
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Affiliation(s)
- Xiaonan Cui
- Single Cell Systems Biology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Xue Dong
- Single Cell Systems Biology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Mengzhu Hu
- Single Cell Systems Biology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Wenjian Zhou
- Single Cell Systems Biology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Weiyang Shi
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
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2
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Zhang X, Ma J, Li H, Zhai Y, He F, Wang X, Li Y. OrganogenesisDB: A Comprehensive Database Exploring the Cell-Type Identities and Gene Expression Dynamics during Organogenesis. SMALL METHODS 2024:e2301758. [PMID: 38967205 DOI: 10.1002/smtd.202301758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 06/02/2024] [Indexed: 07/06/2024]
Abstract
Organogenesis, the phase of embryonic development that starts at the end of gastrulation and continues until birth is the critical process for understanding cellular differentiation and maturation during organ development. The rapid development of single-cell transcriptomics technology has led to many novel discoveries in understanding organogenesis while also accumulating a large quantity of data. To fill this gap, OrganogenesisDB (http://organogenesisdb.com/), which is a comprehensive database dedicated to exploring cell-type identification and gene expression dynamics during organogenesis, is developed. OrganogenesisDB contains single-cell RNA sequencing data for more than 1.4 million cells from 49 published datasets spanning various developmental stages. Additionally, 3324 cell markers are manually curated for 1120 cell types across 9 human organs and 4 mouse organs. OrganogenesisDB leverages various analysis tools to assist users in annotating and understanding cell types at different developmental stages and helps in mining and presenting genes that exhibit specific patterns and play key regulatory roles during cell maturation and differentiation. This work provides a critical resource and useful tool for deciphering cell lineage determination and uncovering the mechanisms underlying organogenesis.
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Affiliation(s)
- Xinshuai Zhang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
- Research Unit of Proteomics-Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing, 102206, China
| | - Jiacheng Ma
- Tsinghua-Peking Center for Life Sciences, School of Lifescience, Tsinghua University, Beijing, 100084, China
| | - Hongchao Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
- College of Life Science, Hebei University, Baoding, Hebei, 071002, China
| | - Yuanjun Zhai
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Fuchu He
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
- Research Unit of Proteomics-Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing, 102206, China
| | - Xiaowen Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
- Research Unit of Proteomics-Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing, 102206, China
| | - Yang Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
- Research Unit of Proteomics-Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing, 102206, China
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3
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Saiki N, Nio Y, Yoneyama Y, Kawamura S, Iwasawa K, Kawakami E, Araki K, Fukumura J, Sakairi T, Kono T, Ohmura R, Koido M, Funata M, Thompson WL, Cruz-Encarnacion P, Chen YW, Takebe T. Self-Organization of Sinusoidal Vessels in Pluripotent Stem Cell-derived Human Liver Bud Organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601804. [PMID: 39005378 PMCID: PMC11245015 DOI: 10.1101/2024.07.02.601804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The induction of tissue-specific vessels in in vitro living tissue systems remains challenging. Here, we directly differentiated human pluripotent stem cells into CD32b+ putative liver sinusoidal progenitors (iLSEP) by dictating developmental pathways. By devising an inverted multilayered air-liquid interface (IMALI) culture, hepatic endoderm, septum mesenchyme, arterial and sinusoidal quadruple progenitors self-organized to generate and sustain hepatocyte-like cells neighbored by divergent endothelial subsets composed of CD32blowCD31high, LYVE1+STAB1+CD32bhighCD31lowTHBD-vWF-, and LYVE1-THBD+vWF+ cells. Wnt2 mediated sinusoidal-to-hepatic intercellular crosstalk potentiates hepatocyte differentiation and branched endothelial network formation. Intravital imaging revealed iLSEP developed fully patent human vessels with functional sinusoid-like features. Organoid-derived hepatocyte- and sinusoid-derived coagulation factors enabled correction of in vitro clotting time with Factor V, VIII, IX, and XI deficient patients' plasma and rescued the severe bleeding phenotype in hemophilia A mice upon transplantation. Advanced organoid vascularization technology allows for interrogating key insights governing organ-specific vessel development, paving the way for coagulation disorder therapeutics.
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Affiliation(s)
- Norikazu Saiki
- Institute of Research, Tokyo Medical and Dental University (TMDU), Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
- Organoid Medicine project, T-CiRA joint program, Fujisawa, Kanagawa 251-8555, Japan
| | - Yasunori Nio
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd, Fujisawa, Kanagawa 251-8555, Japan
- Organoid Medicine project, T-CiRA joint program, Fujisawa, Kanagawa 251-8555, Japan
| | - Yosuke Yoneyama
- Institute of Research, Tokyo Medical and Dental University (TMDU), Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Shuntaro Kawamura
- Institute of Research, Tokyo Medical and Dental University (TMDU), Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kentaro Iwasawa
- Division of Gastroenterology, Hepatology and Nutrition & Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | - Eri Kawakami
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd, Fujisawa, Kanagawa 251-8555, Japan
- Organoid Medicine project, T-CiRA joint program, Fujisawa, Kanagawa 251-8555, Japan
| | - Kohei Araki
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd, Fujisawa, Kanagawa 251-8555, Japan
- Organoid Medicine project, T-CiRA joint program, Fujisawa, Kanagawa 251-8555, Japan
| | - Junko Fukumura
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd, Fujisawa, Kanagawa 251-8555, Japan
- Organoid Medicine project, T-CiRA joint program, Fujisawa, Kanagawa 251-8555, Japan
| | - Tsuyoshi Sakairi
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd, Fujisawa, Kanagawa 251-8555, Japan
- Organoid Medicine project, T-CiRA joint program, Fujisawa, Kanagawa 251-8555, Japan
| | - Tamaki Kono
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd, Fujisawa, Kanagawa 251-8555, Japan
- Organoid Medicine project, T-CiRA joint program, Fujisawa, Kanagawa 251-8555, Japan
| | - Rio Ohmura
- Institute of Research, Tokyo Medical and Dental University (TMDU), Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
- Organoid Medicine project, T-CiRA joint program, Fujisawa, Kanagawa 251-8555, Japan
| | - Masaru Koido
- Organoid Medicine project, T-CiRA joint program, Fujisawa, Kanagawa 251-8555, Japan
| | - Masaaki Funata
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd, Fujisawa, Kanagawa 251-8555, Japan
- Organoid Medicine project, T-CiRA joint program, Fujisawa, Kanagawa 251-8555, Japan
| | - Wendy L. Thompson
- Division of Gastroenterology, Hepatology and Nutrition & Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | | | - Ya-Wen Chen
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Regenerative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Airway Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Center for Epithelial and Airway Biology and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Takanori Takebe
- Institute of Research, Tokyo Medical and Dental University (TMDU), Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
- Organoid Medicine project, T-CiRA joint program, Fujisawa, Kanagawa 251-8555, Japan
- Division of Gastroenterology, Hepatology and Nutrition & Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
- The Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
- Communication Design Center, Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa, Japan
- Department of Genome Biology, Graduate School of Medicine, and Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka 565-0871, Japan
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4
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Yoshimoto K, Maki K, Adachi T, Kamei KI. Cyclic Stretching Enhances Angiocrine Signals at Liver Bud Stage from Human Pluripotent Stem Cells in Two-Dimensional Culture. Tissue Eng Part A 2024; 30:426-439. [PMID: 38062736 DOI: 10.1089/ten.tea.2023.0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024] Open
Abstract
Angiocrine signals during the development and growth of organs, including the liver, intestine, lung, and bone, are essential components of intercellular communication. The signals elicited during the liver bud stage are critical for vascularization and enhanced during the intercellular communication between the cells negative for kinase insert domain receptor (KDR) (KDR- cells) and the cells positive for KDR (KDR+ cells), which constitute the liver bud. However, the use of a human pluripotent stem cell (hPSC)-derived system has not facilitated the generation of a perfusable vascularized liver organoid that allows elucidation of liver development and has great potential for liver transplantation. This is largely owing to the lack of fundamental understanding to induce angiocrine signals in KDR- and KDR+ cells during the liver bud stage. We hypothesized that mechanical stimuli of cyclic stretching/pushing by the fetal heart adjacent to the liver bud could be the main contributor to promoting angiocrine signals in KDR- and KDR+ cells during the liver bud stage. In this study, we show that an organ-on-a-chip platform allows the emulation of an in vivo-like mechanical environment for the liver bud stage in vitro and investigate the role of cyclic mechanical stretching (cMS) to angiocrine signals in KDR- and KDR+ cells derived from hPSCs. RNA sequencing revealed that the expression of genes associated with epithelial-to-mesenchymal transition, including angiocrine signals, such as hepatocyte growth factor (HGF) and matrix metallopeptidase 9 (MMP9), were increased by cMS in cocultured KDR- and KDR+ cells. The expression and secretions of HGF and MMP9 were increased by 1.98- and 1.69-fold and 3.23- and 3.72-fold with cMS in the cocultured KDR- and KDR+ cells but were not increased by cMS in the monocultured KDR- and KDR+ cells, respectively. Finally, cMS during the liver bud stage did not lead to the dedifferentiation of hepatocytes, as the cells with cMS showed hepatic maker expression (CYP3A4, CYP3A7, ALB, and AAT) and 1.71-fold higher CYP3A activity than the cells without cMS, during 12 day-hepatocyte maturation after halting cMS. Our findings provide new insights into the mechanical factors during the liver bud stage and directions for future improvements in the engineered liver tissue.
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Affiliation(s)
- Koki Yoshimoto
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Kyoto, Japan
- Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Biosystems Science, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Koichiro Maki
- Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Biosystems Science, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Taiji Adachi
- Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Biosystems Science, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Ken-Ichiro Kamei
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Kyoto, Japan
- Wuya College of Innovation, Shenyang Pharmaceutical University, Liaoning, China
- Department of Pharmaceutics, Shenyang Pharmaceutical University, Liaoning, China
- Programs of Biology and Bioengineering, Divisions of Science and Engineering, New York University Abu Dhabi, Abu Dhabi, UAE
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, Brooklyn, New York, USA
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5
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Du K, Jun JH, Dutta RK, Diehl AM. Plasticity, heterogeneity, and multifunctionality of hepatic stellate cells in liver pathophysiology. Hepatol Commun 2024; 8:e0411. [PMID: 38619452 PMCID: PMC11019831 DOI: 10.1097/hc9.0000000000000411] [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] [Received: 12/29/2023] [Accepted: 01/26/2024] [Indexed: 04/16/2024] Open
Abstract
HSCs, the resident pericytes of the liver, have consistently been at the forefront of liver research due to their crucial roles in various hepatic pathological processes. Prior literature often depicted HSCs in a binary framework, categorizing them as either quiescent or activated. However, recent advances in HSC research, particularly the advent of single-cell RNA-sequencing, have revolutionized our understanding of these cells. This sophisticated technique offers an unparalleled, high-resolution insight into HSC populations, uncovering a spectrum of diversity and functional heterogeneity across various physiological states of the liver, ranging from liver development to the liver aging process. The single-cell RNA-sequencing revelations have also highlighted the intrinsic plasticity of HSCs and underscored their complex roles in a myriad of pathophysiological processes, including liver injury, repair, and carcinogenesis. This review aims to integrate and clarify these recent discoveries, focusing on how the inherent plasticity of HSCs is central to their dynamic roles both in maintaining liver homeostasis and orchestrating responses to liver injury. Future research will clarify whether findings from rodent models can be translated to human livers and guide how these insights are harnessed to develop targeted therapeutic interventions.
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Yang C, Xie W, Fu H, Zhi M, Zhang H, Guo Y, Wang J. Single-cell RNA sequencing reveals the heterogeneity of hepatic non-parenchymal cell responses to chronic PFO5DoDA exposure in male mice. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 347:123721. [PMID: 38462192 DOI: 10.1016/j.envpol.2024.123721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
Perfluoroalkyl ether carboxylic acids (PFECA) have emerged as novel alternatives to legacy per- and polyfluoroalkyl substances (PFAS). Existing research has revealed hepatoxicity induced by various PFAS, including PFECA. However, these studies have primarily focused on overall changes in whole liver tissue, particularly in hepatocytes, with the impact of PFAS on diverse liver non-parenchymal cells (NPCs) still inadequately understood. In the present study, we examined the heterogeneous responses of hepatic NPCs following exposure to perfluoro-3,5,7,9,11-pentaoxadodecanoic acid (PFO5DoDA), a type of PFECA, by administering PFO5DoDA (5 μg/L)-contaminated water to male mice for one year. Single-cell RNA sequencing (scRNA-seq) of 15 008 cells from the liver identified 10 distinct NPC populations. Notably, although relative liver weight remained largely unchanged following exposure to 5 μg/L PFO5DoDA, there was an observed increase in proliferating cells, indicating that proliferating NPCs may contribute to the hepatomegaly frequently noted in PFAS-exposed livers. There was also a considerable alteration in the composition of hepatic NPCs. Specifically, the total number of B cells decreased substantially, while many other cells, such as monocytes and macrophages, increased after PFO5DoDA exposure. In addition, interactions among the hepatic NPC populations changed variously after PFO5DoDA exposure. The findings emphasize the heterogeneity in the responses of hepatic NPCs to PFO5DoDA exposure. Taken together, the changes in immune cell populations and their intercellular interactions suggest that PFO5DoDA disrupts immune homeostasis in the liver. These findings offer new insights into the cellular mechanisms of PFAS-induced liver damage.
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Affiliation(s)
- Chunyu Yang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Yantai University, Yantai, 264005, China
| | - Wei Xie
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Yantai University, Yantai, 264005, China
| | - Huayu Fu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Yantai University, Yantai, 264005, China
| | - Mengxue Zhi
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Yantai University, Yantai, 264005, China
| | - Hongxia Zhang
- Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong Guo
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianshe Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Yantai University, Yantai, 264005, China.
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7
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Roehrig A, Hirsch TZ, Pire A, Morcrette G, Gupta B, Marcaillou C, Imbeaud S, Chardot C, Gonzales E, Jacquemin E, Sekiguchi M, Takita J, Nagae G, Hiyama E, Guérin F, Fabre M, Aerts I, Taque S, Laithier V, Branchereau S, Guettier C, Brugières L, Fresneau B, Zucman-Rossi J, Letouzé E. Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma. Nat Commun 2024; 15:3031. [PMID: 38589411 PMCID: PMC11001886 DOI: 10.1038/s41467-024-47280-x] [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: 04/06/2023] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Hepatoblastomas (HB) display heterogeneous cellular phenotypes that influence the clinical outcome, but the underlying mechanisms are poorly understood. Here, we use a single-cell multiomic strategy to unravel the molecular determinants of this plasticity. We identify a continuum of HB cell states between hepatocytic (scH), liver progenitor (scLP) and mesenchymal (scM) differentiation poles, with an intermediate scH/LP population bordering scLP and scH areas in spatial transcriptomics. Chromatin accessibility landscapes reveal the gene regulatory networks of each differentiation pole, and the sequence of transcription factor activations underlying cell state transitions. Single-cell mapping of somatic alterations reveals the clonal architecture of each tumor, showing that each genetic subclone displays its own range of cellular plasticity across differentiation states. The most scLP subclones, overexpressing stem cell and DNA repair genes, proliferate faster after neo-adjuvant chemotherapy. These results highlight how the interplay of clonal evolution and epigenetic plasticity shapes the potential of HB subclones to respond to chemotherapy.
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Affiliation(s)
- Amélie Roehrig
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, INSERM, Paris, France
| | - Theo Z Hirsch
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, INSERM, Paris, France
| | - Aurore Pire
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, INSERM, Paris, France
| | - Guillaume Morcrette
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, INSERM, Paris, France
- Department of Pathology, Robert Debré and Necker-Enfants Malades Hospitals, APHP, Paris, France
| | - Barkha Gupta
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, INSERM, Paris, France
| | | | - Sandrine Imbeaud
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, INSERM, Paris, France
| | | | - Emmanuel Gonzales
- Pediatric Hepatology and Liver Transplantation Unit, National Reference Centre for Rare Pediatric Liver Diseases, FILFOIE, ERN RARE LIVER, APHP, Bicêtre University Hospital, University of Paris-Saclay, Le Kremlin Bicêtre, and INSERM UMR_S 1193, Hepatinov, University of Paris-Saclay, Orsay, France
| | - Emmanuel Jacquemin
- Pediatric Hepatology and Liver Transplantation Unit, National Reference Centre for Rare Pediatric Liver Diseases, FILFOIE, ERN RARE LIVER, APHP, Bicêtre University Hospital, University of Paris-Saclay, Le Kremlin Bicêtre, and INSERM UMR_S 1193, Hepatinov, University of Paris-Saclay, Orsay, France
| | - Masahiro Sekiguchi
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Genta Nagae
- Genome Science Laboratory, Research Center for Advanced Science and Technology (RCAST), the University of Tokyo, Tokyo, Japan
| | - Eiso Hiyama
- Department of Pediatric Surgery, Hiroshima University Hospital, Hiroshima, Japan
- Department of Biomedical Science, Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan
| | - Florent Guérin
- Department of Pediatric Surgery, Bicêtre Hospital, APHP, Paris-Saclay University, Orsay, France
| | - Monique Fabre
- Department of Pathology, Hôpital Universitaire Necker-Enfants malades, AP-HP, Paris, France
| | - Isabelle Aerts
- Oncology Center SIREDO, Institut Curie, PSL Research University, Paris, France
| | - Sophie Taque
- Département de Pédiatrie, CHU Fontenoy, Rennes, France
| | - Véronique Laithier
- Department of Children Oncology, Centre Hospitalier Universitaire Besançon, Besançon, France
| | - Sophie Branchereau
- Department of Pediatric Surgery, Bicêtre Hospital, APHP, Paris-Saclay University, Orsay, France
| | - Catherine Guettier
- Department of Pathology Hôpital Bicêtre-AP-HP, INSERM U1193, Paris-Saclay University, Orsay, France
| | - Laurence Brugières
- Gustave Roussy, Université Paris-Saclay, Department of Children and Adolescents Oncology, Villejuif, France
| | - Brice Fresneau
- Gustave Roussy, Université Paris-Saclay, Department of Children and Adolescents Oncology, Villejuif, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, INSERM, Paris, France.
- Hôpital Européen Georges Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France.
| | - Eric Letouzé
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, INSERM, Paris, France.
- CRCI2NA, Nantes Université, INSERM, CNRS, Nantes, France.
- University Hospital Hôtel-Dieu, Nantes, France.
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8
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Chen N, Liu S, Qin D, Guan D, Chen Y, Hou C, Zheng S, Wang L, Chen X, Chen W, Zhang L. Fate tracking reveals differences between Reelin + hepatic stellate cells (HSCs) and Desmin + HSCs in activation, migration and proliferation. Cell Prolif 2023; 56:e13500. [PMID: 37246473 PMCID: PMC10693182 DOI: 10.1111/cpr.13500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/20/2023] [Accepted: 05/02/2023] [Indexed: 05/30/2023] Open
Abstract
The activation of hepatic stellate cells (HSCs) is the main cause of liver fibrogenesis in response to different etiologies of chronic liver injuries. HSCs are heterogeneous, but the lack of specific markers to distinguish different HSC subset hinders the development of targeted therapy for liver fibrosis. In this study, we aim to reveal new HSC subsets by cell fate tracking. We constructed a novel ReelinCreERT2 transgenic mouse model to track the fate of cells expressing Reelin and their progeny (Reelin+ cells). And we investigated the property of Reelin+ cells, such as differentiation and proliferation, in hepatotoxic (carbon tetrachloride; CCl4 ) or cholestatic (bile duct ligation; BDL) liver injury models by immunohistochemistry. Our study revealed that Reelin+ cells were a new HSC subset. In terms of activation, migration, and proliferation, Reelin+ HSCs displayed different properties from Desmin+ HSCs (total HSCs) in cholestatic liver injury model but shared similar properties to total HSCs in hepatotoxic liver injury model. Besides, we did not find evidence that Reelin+ HSCs transdifferentiated into hepatocytes or cholangiocytes through mesenchymal-epithelial transition (MET). In this study, our genetic cell fate tracking data reveal that ReelinCreERT2-labelled cells are a new HSC subset, which provides new insights into targeted therapy for liver fibrosis.
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Affiliation(s)
- Ning Chen
- College of Veterinary Medicine/Bio‐medical Center/Huazhong Agricultural UniversityWuhanChina
| | - Shenghui Liu
- College of Veterinary Medicine/Bio‐medical Center/Huazhong Agricultural UniversityWuhanChina
| | - Dan Qin
- College of Veterinary Medicine/Bio‐medical Center/Huazhong Agricultural UniversityWuhanChina
| | - Dian Guan
- College of Veterinary Medicine/Bio‐medical Center/Huazhong Agricultural UniversityWuhanChina
| | - Yaqing Chen
- College of Veterinary Medicine/Bio‐medical Center/Huazhong Agricultural UniversityWuhanChina
| | - Chenjiao Hou
- College of Veterinary Medicine/Bio‐medical Center/Huazhong Agricultural UniversityWuhanChina
| | - Songyun Zheng
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Liqiang Wang
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney DiseasesNational Clinical Research Center for Kidney DiseasesBeijingChina
| | - Xiangmei Chen
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney DiseasesNational Clinical Research Center for Kidney DiseasesBeijingChina
| | - Wei Chen
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food ScienceZhejiang UniversityHangzhouChina
| | - Lisheng Zhang
- College of Veterinary Medicine/Bio‐medical Center/Huazhong Agricultural UniversityWuhanChina
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9
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Sun J, Qu H, Ali W, Chen Y, Wang T, Ma Y, Yuan Y, Gu J, Bian J, Liu Z, Zou H. Co-exposure to cadmium and microplastics promotes liver fibrosis through the hemichannels -ATP-P2X7 pathway. CHEMOSPHERE 2023; 344:140372. [PMID: 37802476 DOI: 10.1016/j.chemosphere.2023.140372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Microplastics (MPs) and cadmium (Cd) are important environmental pollutants, that damage the liver. However, the effect and mechanism of combined Cd and MPs exposure on liver fibrosis are still largely unknown. In this study investigated, Cd + MPs exposure increased superoxide anion production and promoted extracellular ATP release compared with exposure to Cd or MPs individually. Cd + MPs increased inflammatory cell infiltration, activated the P2X7-NLRP3 signaling pathway, and promoted inflammatory factor release. Cd + MPs aggravated Cd- or MPs-induced liver fibrosis and induced liver inflammation. In AML12/HSC-T6 cell in vitro poisoning model, exposure of AML12 cells to Cd + MPs increased the opening of connexin hemichannels and promoted extracellular ATP release. Treatment of HSC-T6 cells with the supernatant of AML12 cells exposed to Cd + MPs significantly promoted HSC-T6 cell activation. Treatment of HSC-T6 cells with different concentrations of ATP produced similar results. TAT-Gap19TFA, an inhibitor of connexin hemichannels, significantly inhibited the ATP release and activation of Cd + MPs-treated HSC-T6 cells. Finally, the expression of the ATP receptor P2X7 was silenced in HSC-T6 cells, which significantly inhibited their activation. In conclusion, exposure to Cd + MPs promoted liver fibrosis through the ATP-P2X7 pathway and synergistically affected liver inflammation and fibrosis.
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Affiliation(s)
- Jian Sun
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Huayi Qu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Waseem Ali
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yan Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Tao Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yonggang Ma
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yan Yuan
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Jianhong Gu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Jianchun Bian
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Zongping Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
| | - Hui Zou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
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10
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Pouyabahar D, Chung SW, Pezzutti OI, Perciani CT, Wang X, Ma XZ, Jiang C, Camat D, Chung T, Sekhon M, Manuel J, Chen XC, McGilvray ID, MacParland SA, Bader GD. A rat liver cell atlas reveals intrahepatic myeloid heterogeneity. iScience 2023; 26:108213. [PMID: 38026201 PMCID: PMC10651689 DOI: 10.1016/j.isci.2023.108213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 08/20/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
The large size and vascular accessibility of the laboratory rat (Rattus norvegicus) make it an ideal hepatic animal model for diseases that require surgical manipulation. Often, the disease susceptibility and outcomes of inflammatory pathologies vary significantly between strains. This study uses single-cell transcriptomics to better understand the complex cellular network of the rat liver, as well as to unravel the cellular and molecular sources of inter-strain hepatic variation. We generated single-cell and single-nucleus transcriptomic maps of the livers of healthy Dark Agouti and Lewis rat strains and developed a factor analysis-based bioinformatics analysis pipeline to study data covariates, such as strain and batch. Using this approach, we discovered transcriptomic variation within the hepatocyte and myeloid populations that underlie distinct cell states between rat strains. This finding will help provide a reference for future investigations on strain-dependent outcomes of surgical experiment models.
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Affiliation(s)
- Delaram Pouyabahar
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Sai W. Chung
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Olivia I. Pezzutti
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Catia T. Perciani
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xinle Wang
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xue-Zhong Ma
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Chao Jiang
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Damra Camat
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Trevor Chung
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Manmeet Sekhon
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Justin Manuel
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xu-Chun Chen
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Ian D. McGilvray
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Sonya A. MacParland
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, 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, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
- Princess Margaret Research Institute, University Health Network, Toronto, ON, Canada
- The Multiscale Human Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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11
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Rao L, Cai L, Huang L. Single-cell dynamics of liver development in postnatal pigs. Sci Bull (Beijing) 2023; 68:2583-2597. [PMID: 37783617 DOI: 10.1016/j.scib.2023.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/21/2023] [Accepted: 09/14/2023] [Indexed: 10/04/2023]
Abstract
The postnatal development of the liver, an essential organ for metabolism and immunity, remains poorly characterized at the single-cell resolution. Here, we generated single-nucleus and single-cell transcriptomes of 84,824 pig liver cells at four postnatal time points: day 30, 42, 150, and 730. We uncovered 23 cell types, including three rare cell types: plasmacytoid dendritic cells, CAVIN3+IGF2+ endothelial cells, and EBF1+ fibroblasts. The latter two were verified by multiplex immunohistochemistry. Trajectory and gene regulatory analyses revealed 33 genes that encode transcription factors associated with hepatocyte development and function, including NFIL3 involved in regulating hepatic metabolism. We characterized the spatiotemporal heterogeneity of liver endothelial cells, identified and validated leucine zipper protein 2 (LUZP2) as a novel adult liver sinusoidal endothelial cell-specific transcription factor. Lymphoid cells (NK and T cells) governed the immune system of the pig liver since day 30. Furthermore, we identified a cluster of tissue-resident NK cells, which displayed virus defense functions, maintained proliferative features at day 730, and manifested a higher conservative transcription factor expression pattern in humans than in mouse liver. Our study presents the most comprehensive postnatal liver development single-cell atlas and demonstrates the metabolic and immune changes across the four age stages.
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Affiliation(s)
- Lin Rao
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Liping Cai
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lusheng Huang
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China.
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12
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Cogliati B, Yashaswini CN, Wang S, Sia D, Friedman SL. Friend or foe? The elusive role of hepatic stellate cells in liver cancer. Nat Rev Gastroenterol Hepatol 2023; 20:647-661. [PMID: 37550577 PMCID: PMC10671228 DOI: 10.1038/s41575-023-00821-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/06/2023] [Indexed: 08/09/2023]
Abstract
Liver fibrosis is a substantial risk factor for the development and progression of liver cancer, which includes hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA). Studies utilizing cell fate mapping and single-cell transcriptomics techniques have identified quiescent perisinusoidal hepatic stellate cells (HSCs) as the primary source of activated collagen-producing HSCs and liver cancer-associated fibroblasts (CAFs) in HCC and liver metastasis, complemented in iCCA by contributions from portal fibroblasts. At the same time, integrative computational analysis of single-cell, single-nucleus and spatial RNA sequencing data have revealed marked heterogeneity among HSCs and CAFs, with distinct subpopulations displaying unique gene expression signatures and functions. Some of these subpopulations have divergent roles in promoting or inhibiting liver fibrogenesis and carcinogenesis. In this Review, we discuss the dual roles of HSC subpopulations in liver fibrogenesis and their contribution to liver cancer promotion, progression and metastasis. We review the transcriptomic and functional similarities between HSC and CAF subpopulations, highlighting the pathways that either promote or prevent fibrosis and cancer, and the immunological landscape from which these pathways emerge. Insights from ongoing studies will yield novel strategies for developing biomarkers, assessing prognosis and generating new therapies for both HCC and iCCA prevention and treatment.
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Affiliation(s)
- Bruno Cogliati
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, SP, Brazil
| | | | - Shuang Wang
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniela Sia
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott L Friedman
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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13
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Lotto J, Cullum R, Drissler S, Arostegui M, Garside VC, Fuglerud BM, Clement-Ranney M, Thakur A, Underhill TM, Hoodless PA. Cell diversity and plasticity during atrioventricular heart valve EMTs. Nat Commun 2023; 14:5567. [PMID: 37689753 PMCID: PMC10492828 DOI: 10.1038/s41467-023-41279-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/29/2023] [Indexed: 09/11/2023] Open
Abstract
Epithelial-to-mesenchymal transitions (EMTs) of both endocardium and epicardium guide atrioventricular heart valve formation, but the cellular complexity and small scale of this tissue have restricted analyses. To circumvent these issues, we analyzed over 50,000 murine single-cell transcriptomes from embryonic day (E)7.75 hearts to E12.5 atrioventricular canals. We delineate mesenchymal and endocardial bifurcation during endocardial EMT, identify a distinct, transdifferentiating epicardial population during epicardial EMT, and reveal the activation of epithelial-mesenchymal plasticity during both processes. In Sox9-deficient valves, we observe increased epithelial-mesenchymal plasticity, indicating a role for SOX9 in promoting endothelial and mesenchymal cell fate decisions. Lastly, we deconvolve cell interactions guiding the initiation and progression of cardiac valve EMTs. Overall, these data reveal mechanisms of emergence of mesenchyme from endocardium or epicardium at single-cell resolution and will serve as an atlas of EMT initiation and progression with broad implications in regenerative medicine and cancer biology.
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Affiliation(s)
- Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | | | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | - Martin Arostegui
- Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Victoria C Garside
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Bettina M Fuglerud
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | | | - Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - T Michael Underhill
- Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada.
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
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14
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Lotto J, Stephan TL, Hoodless PA. Fetal liver development and implications for liver disease pathogenesis. Nat Rev Gastroenterol Hepatol 2023; 20:561-581. [PMID: 37208503 DOI: 10.1038/s41575-023-00775-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/21/2023]
Abstract
The metabolic, digestive and homeostatic roles of the liver are dependent on proper crosstalk and organization of hepatic cell lineages. These hepatic cell lineages are derived from their respective progenitors early in organogenesis in a spatiotemporally controlled manner, contributing to the liver's specialized and diverse microarchitecture. Advances in genomics, lineage tracing and microscopy have led to seminal discoveries in the past decade that have elucidated liver cell lineage hierarchies. In particular, single-cell genomics has enabled researchers to explore diversity within the liver, especially early in development when the application of bulk genomics was previously constrained due to the organ's small scale, resulting in low cell numbers. These discoveries have substantially advanced our understanding of cell differentiation trajectories, cell fate decisions, cell lineage plasticity and the signalling microenvironment underlying the formation of the liver. In addition, they have provided insights into the pathogenesis of liver disease and cancer, in which developmental processes participate in disease emergence and regeneration. Future work will focus on the translation of this knowledge to optimize in vitro models of liver development and fine-tune regenerative medicine strategies to treat liver disease. In this Review, we discuss the emergence of hepatic parenchymal and non-parenchymal cells, advances that have been made in in vitro modelling of liver development and draw parallels between developmental and pathological processes.
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Affiliation(s)
- Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada.
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada.
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15
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Rahmawati FN, Iba T, Naito H, Shimizu S, Konishi H, Jia W, Takakura N. Single-cell sequencing reveals the existence of fetal vascular endothelial stem cell-like cells in mouse liver. Stem Cell Res Ther 2023; 14:227. [PMID: 37649114 PMCID: PMC10468894 DOI: 10.1186/s13287-023-03460-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND A resident vascular endothelial stem cell (VESC) population expressing CD157 and CD200 has been identified recently in the adult mouse. However, the origin of this population and how it develops has not been characterized, nor has it been determined whether VESC-like cells are present during the perinatal period. Here, we investigated the presence of perinatal VESC-like cells and their relationship with the adult VESC-like cell population. METHODS We applied single-cell RNA sequencing of endothelial cells (ECs) from embryonic day (E) 14, E18, postnatal day (P) 7, P14, and week (W) 8 liver and investigated transcriptomic changes during liver EC development. We performed flow cytometry, immunofluorescence, colony formation assays, and transplantation assays to validate the presence of and to assess the function of CD157+ and CD200+ ECs in the perinatal period. RESULTS We identified CD200- expressing VESC-like cells in the perinatal period. These cells formed colonies in vitro and had high proliferative ability. The RNA velocity tool and transplantation assay results indicated that the projected fate of this population was toward adult VESC-like cells expressing CD157 and CD200 1 week after birth. CONCLUSION Our study provides a comprehensive atlas of liver EC development and documents VESC-like cell lineage commitment at single-cell resolution.
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Affiliation(s)
- Fitriana N Rahmawati
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Tomohiro Iba
- Department of Physiology, School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Hisamichi Naito
- Department of Physiology, School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Shota Shimizu
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Hirotaka Konishi
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Weizhen Jia
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Nobuyuki Takakura
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan.
- Immunology Frontier Research Center, Osaka University, Suita, Japan.
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan.
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16
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Trinh LT, Osipovich AB, Liu B, Shrestha S, Cartailler JP, Wright CVE, Magnuson MA. Single-Cell RNA Sequencing of Sox17-Expressing Lineages Reveals Distinct Gene Regulatory Networks and Dynamic Developmental Trajectories. Stem Cells 2023; 41:643-657. [PMID: 37085274 PMCID: PMC10465087 DOI: 10.1093/stmcls/sxad030] [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: 01/24/2023] [Accepted: 04/04/2023] [Indexed: 04/23/2023]
Abstract
During early embryogenesis, the transcription factor SOX17 contributes to hepato-pancreato-biliary system formation and vascular-hematopoietic emergence. To better understand Sox17 function in the developing endoderm and endothelium, we developed a dual-color temporal lineage-tracing strategy in mice combined with single-cell RNA sequencing to analyze 6934 cells from Sox17-expressing lineages at embryonic days 9.0-9.5. Our analyses showed 19 distinct cellular clusters combined from all 3 germ layers. Differential gene expression, trajectory and RNA-velocity analyses of endothelial cells revealed a heterogenous population of uncommitted and specialized endothelial subtypes, including 2 hemogenic populations that arise from different origins. Similarly, analyses of posterior foregut endoderm revealed subsets of hepatic, pancreatic, and biliary progenitors with overlapping developmental potency. Calculated gene-regulatory networks predict gene regulons that are dominated by cell type-specific transcription factors unique to each lineage. Vastly different Sox17 regulons found in endoderm versus endothelial cells support the differential interactions of SOX17 with other regulatory factors thereby enabling lineage-specific regulatory actions.
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Affiliation(s)
- Linh T Trinh
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Anna B Osipovich
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
| | - Bryan Liu
- College of Arts and Sciences, Vanderbilt University, Nashville, TN, USA
| | - Shristi Shrestha
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
| | | | - Christopher V E Wright
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Mark A Magnuson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN, USA
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17
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Wang S, Chen S, Sun J, Han P, Xu B, Li X, Zhong Y, Xu Z, Zhang P, Mi P, Zhang C, Li L, Zhang H, Xia Y, Li S, Heikenwalder M, Yuan D. m 6A modification-tuned sphingolipid metabolism regulates postnatal liver development in male mice. Nat Metab 2023; 5:842-860. [PMID: 37188818 DOI: 10.1038/s42255-023-00808-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Different organs undergo distinct transcriptional, epigenetic and physiological alterations that guarantee their functional maturation after birth. However, the roles of epitranscriptomic machineries in these processes have remained elusive. Here we demonstrate that expression of RNA methyltransferase enzymes Mettl3 and Mettl14 gradually declines during postnatal liver development in male mice. Liver-specific Mettl3 deficiency causes hepatocyte hypertrophy, liver injury and growth retardation. Transcriptomic and N6-methyl-adenosine (m6A) profiling identify the neutral sphingomyelinase, Smpd3, as a target of Mettl3. Decreased decay of Smpd3 transcripts due to Mettl3 deficiency results in sphingolipid metabolism rewiring, characterized by toxic ceramide accumulation and leading to mitochondrial damage and elevated endoplasmic reticulum stress. Pharmacological Smpd3 inhibition, Smpd3 knockdown or Sgms1 overexpression that counteracts Smpd3 can ameliorate the abnormality of Mettl3-deficent liver. Our findings demonstrate that Mettl3-N6-methyl-adenosine fine-tunes sphingolipid metabolism, highlighting the pivotal role of an epitranscriptomic machinery in coordination of organ growth and the timing of functional maturation during postnatal liver development.
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Affiliation(s)
- Shiguan Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shanze Chen
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Jianfeng Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Pan Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bowen Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xinying Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Youquan Zhong
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Hubei Jiangxia Laboratory, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Zaichao Xu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Hubei Jiangxia Laboratory, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Peng Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ping Mi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lixiang Li
- Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan, China
- Shandong Provincial Clinical Research Center for Digestive Disease, Jinan, China
| | - Haiyan Zhang
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, China
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Hubei Jiangxia Laboratory, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China.
| | - Shiyang Li
- Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan, China.
- Advanced Medical Research Institute, Shandong University, Jinan, China.
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany.
- The M3 Research Institute, Eberhard Karls University Tübingen, Tübingen, Germany.
| | - Detian Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Shandong Provincial Clinical Research Center for Digestive Disease, Jinan, China.
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18
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Parab S, Setten E, Astanina E, Bussolino F, Doronzo G. The tissue-specific transcriptional landscape underlines the involvement of endothelial cells in health and disease. Pharmacol Ther 2023; 246:108418. [PMID: 37088448 DOI: 10.1016/j.pharmthera.2023.108418] [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: 11/05/2022] [Revised: 03/23/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
Endothelial cells (ECs) that line vascular and lymphatic vessels are being increasingly recognized as important to organ function in health and disease. ECs participate not only in the trafficking of gases, metabolites, and cells between the bloodstream and tissues but also in the angiocrine-based induction of heterogeneous parenchymal cells, which are unique to their specific tissue functions. The molecular mechanisms regulating EC heterogeneity between and within different tissues are modeled during embryogenesis and become fully established in adults. Any changes in adult tissue homeostasis induced by aging, stress conditions, and various noxae may reshape EC heterogeneity and induce specific transcriptional features that condition a functional phenotype. Heterogeneity is sustained via specific genetic programs organized through the combinatory effects of a discrete number of transcription factors (TFs) that, at the single tissue-level, constitute dynamic networks that are post-transcriptionally and epigenetically regulated. This review is focused on outlining the TF-based networks involved in EC specialization and physiological and pathological stressors thought to modify their architecture.
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Affiliation(s)
- Sushant Parab
- Department of Oncology, University of Torino, IT, Italy; Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy
| | - Elisa Setten
- Department of Oncology, University of Torino, IT, Italy; Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy
| | - Elena Astanina
- Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy
| | - Federico Bussolino
- Department of Oncology, University of Torino, IT, Italy; Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy.
| | - Gabriella Doronzo
- Department of Oncology, University of Torino, IT, Italy; Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy
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19
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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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20
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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] [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
- grid.440773.30000 0000 9342 2456State 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
- grid.440773.30000 0000 9342 2456State 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
- grid.440773.30000 0000 9342 2456State 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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21
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Kaur S, Kidambi S, Ortega-Ribera M, Thuy LTT, Nieto N, Cogger VC, Xie WF, Tacke F, Gracia-Sancho J. In Vitro Models for the Study of Liver Biology and Diseases: Advances and Limitations. Cell Mol Gastroenterol Hepatol 2022; 15:559-571. [PMID: 36442812 PMCID: PMC9868680 DOI: 10.1016/j.jcmgh.2022.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
In vitro models of liver (patho)physiology, new technologies, and experimental approaches are progressing rapidly. Based on cell lines, induced pluripotent stem cells or primary cells derived from mouse or human liver as well as whole tissue (slices), such in vitro single- and multicellular models, including complex microfluidic organ-on-a-chip systems, provide tools to functionally understand mechanisms of liver health and disease. The International Society of Hepatic Sinusoidal Research (ISHSR) commissioned this working group to review the currently available in vitro liver models and describe the advantages and disadvantages of each in the context of evaluating their use for the study of liver functionality, disease modeling, therapeutic discovery, and clinical applicability.
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Affiliation(s)
- Savneet Kaur
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Srivatsan Kidambi
- Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, Nebraska
| | - Martí Ortega-Ribera
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Le Thi Thanh Thuy
- Department of Hepatology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Natalia Nieto
- Department of Pathology, University of Illinois at Chicago, Chicago, Illinois
| | - Victoria C Cogger
- Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Wei-Fen Xie
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jordi Gracia-Sancho
- Liver Vascular Biology, IDIBAPS Biomedical Research Institute, CIBEREHD, Barcelona, Spain; Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland; Department for BioMedical Research, Visceral Surgery and Medicine, University of Bern, Switzerland.
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22
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Human multilineage pro-epicardium/foregut organoids support the development of an epicardium/myocardium organoid. Nat Commun 2022; 13:6981. [PMID: 36379937 PMCID: PMC9666429 DOI: 10.1038/s41467-022-34730-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 11/03/2022] [Indexed: 11/16/2022] Open
Abstract
The epicardium, the outer epithelial layer that covers the myocardium, derives from a transient organ known as pro-epicardium, crucial during heart organogenesis. The pro-epicardium develops from lateral plate mesoderm progenitors, next to septum transversum mesenchyme, a structure deeply involved in liver embryogenesis. Here we describe a self-organized human multilineage organoid that recreates the co-emergence of pro-epicardium, septum transversum mesenchyme and liver bud. Additionally, we study the impact of WNT, BMP and retinoic acid signaling modulation on multilineage organoid specification. By co-culturing these organoids with cardiomyocyte aggregates, we generated a self-organized heart organoid comprising an epicardium-like layer that fully surrounds a myocardium-like tissue. These heart organoids recapitulate the impact of epicardial cells on promoting cardiomyocyte proliferation and structural and functional maturation. Therefore, the human heart organoids described herein, open the path to advancing knowledge on how myocardium-epicardium interaction progresses during heart organogenesis in healthy or diseased settings.
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23
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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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24
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Decoding Single-cell Landscape and Intercellular Crosstalk in the Transplanted Liver. Transplantation 2022; 107:890-902. [PMID: 36413145 DOI: 10.1097/tp.0000000000004365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND Liver transplantation (LT) is the most effective treatment for various end-stage liver diseases. However, the cellular complexity and intercellular crosstalk of the transplanted liver have constrained analyses of graft reconstruction after LT. METHODS We established an immune-tolerated orthotopic LT mouse model to understand the physiological process of graft recovery and intercellular crosstalk. We employed single-cell RNA sequencing and cytometry by time-of-flight to comprehensively reveal the cellular landscape. RESULTS We identified an acute and stable phase during perioperative graft recovery. Using single-cell technology, we made detailed annotations of the cellular landscape of the transplanted liver and determined dynamic modifications of these cells during LT. We found that 96% of graft-derived immune cells were replaced by recipient-derived cells from the preoperative to the stable phase. However, CD206 + MerTK + macrophages and CD49a + CD49b - natural killer cells were composed of both graft and recipient sources even in the stable phase. Intriguingly, the transcriptional profiles of these populations exhibited tissue-resident characteristics, suggesting that recipient-derived macrophages and natural killer cells have the potential to differentiate into 'tissue-resident cells' after LT. Furthermore, we described the transcriptional characteristics of these populations and implicated their role in regulating the metabolic and immune remodeling of the transplanted liver. CONCLUSIONS In summary, this study delineated a cell atlas (type-proportion-source-time) of the transplanted liver and shed light on the physiological process of graft reconstruction and graft-recipient crosstalk.
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25
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Wesley BT, Ross ADB, Muraro D, Miao Z, Saxton S, Tomaz RA, Morell CM, Ridley K, Zacharis ED, Petrus-Reurer S, Kraiczy J, Mahbubani KT, Brown S, Garcia-Bernardo J, Alsinet C, Gaffney D, Horsfall D, Tysoe OC, Botting RA, Stephenson E, Popescu DM, MacParland S, Bader G, McGilvray ID, Ortmann D, Sampaziotis F, Saeb-Parsy K, Haniffa M, Stevens KR, Zilbauer M, Teichmann SA, Vallier L. Single-cell atlas of human liver development reveals pathways directing hepatic cell fates. Nat Cell Biol 2022; 24:1487-1498. [PMID: 36109670 DOI: 10.1038/s41556-022-00989-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/29/2022] [Indexed: 12/14/2022]
Abstract
The liver has been studied extensively due to the broad number of diseases affecting its vital functions. However, therapeutic advances have been hampered by the lack of knowledge concerning human hepatic development. Here, we addressed this limitation by describing the developmental trajectories of different cell types that make up the human liver at single-cell resolution. These transcriptomic analyses revealed that sequential cell-to-cell interactions direct functional maturation of hepatocytes, with non-parenchymal cells playing essential roles during organogenesis. We utilized this information to derive bipotential hepatoblast organoids and then exploited this model system to validate the importance of signalling pathways in hepatocyte and cholangiocyte specification. Further insights into hepatic maturation also enabled the identification of stage-specific transcription factors to improve the functionality of hepatocyte-like cells generated from human pluripotent stem cells. Thus, our study establishes a platform to investigate the basic mechanisms directing human liver development and to produce cell types for clinical applications.
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Affiliation(s)
- Brandon T Wesley
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Alexander D B Ross
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Daniele Muraro
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Zhichao Miao
- Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Sarah Saxton
- Departments of Bioengineering and Pathology, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Rute A Tomaz
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Carola M Morell
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Katherine Ridley
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Ekaterini D Zacharis
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Sandra Petrus-Reurer
- Department of Surgery, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Judith Kraiczy
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | | | - Stephanie Brown
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | | | | | | | - Dave Horsfall
- Digital Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Olivia C Tysoe
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Gary Bader
- University of Toronto, Toronto, Ontario, Canada
| | - Ian D McGilvray
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, Ontario, Canada
| | - Daniel Ortmann
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Fotios Sampaziotis
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Hinxton, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Kelly R Stevens
- Departments of Bioengineering and Pathology, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Matthias Zilbauer
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Hinxton, UK
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Surgery, University of Cambridge, Cambridge, UK.
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26
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Lee IS, Takebe T. Narrative engineering of the liver. Curr Opin Genet Dev 2022; 75:101925. [PMID: 35700688 PMCID: PMC10118678 DOI: 10.1016/j.gde.2022.101925] [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: 03/13/2022] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 11/30/2022]
Abstract
Liver organoids are primary or pluripotent stem cell-derived three-dimensional structures that recapitulate regenerative or ontogenetic processes in vitro towards biomedical applications including disease modelling and diagnostics, drug safety and efficacy prediction, and therapeutic use. The cellular composition and structural organization of liver organoids may vary depending on the goal at hand, and the key challenge in general is to direct their development in a rational and controlled fashion for gaining targeted maturity, reproducibility, and scalability. Such endeavor begins with a detailed understanding of the biological processes in space and time behind hepatogenesis, followed by precise translation of these narrative processes through a bioengineering approach. Here, we discuss advancements in liver organoid technology through the lens of 'narrative engineering' in an attempt to synergize evolving understanding around molecular and cellular landscape governing hepatogenesis with engineering-inspired approaches for organoidgenesis.
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Affiliation(s)
- Inkyu S Lee
- Division of Gastroenterology, Hepatology & Nutrition, Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Takanori Takebe
- Division of Gastroenterology, Hepatology & Nutrition, Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; Communication Design Center, Advanced Medical Research Center, Yokohama City University Graduate School of Medicine, Japan.
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27
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Deng M, Wang Y, Yan Y. Mining cell–cell signaling in single-cell transcriptomics atlases. Curr Opin Cell Biol 2022; 76:102101. [DOI: 10.1016/j.ceb.2022.102101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 03/16/2022] [Accepted: 04/24/2022] [Indexed: 12/22/2022]
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28
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Gómez-Salinero JM, Izzo F, Lin Y, Houghton S, Itkin T, Geng F, Bram Y, Adelson RP, Lu TM, Inghirami G, Xiang JZ, Lis R, Redmond D, Schreiner R, Rabbany SY, Landau DA, Schwartz RE, Rafii S. Specification of fetal liver endothelial progenitors to functional zonated adult sinusoids requires c-Maf induction. Cell Stem Cell 2022; 29:593-609.e7. [PMID: 35364013 PMCID: PMC9290393 DOI: 10.1016/j.stem.2022.03.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/29/2021] [Accepted: 03/08/2022] [Indexed: 12/13/2022]
Abstract
The liver vascular network is patterned by sinusoidal and hepatocyte co-zonation. How intra-liver vessels acquire their hierarchical specialized functions is unknown. We study heterogeneity of hepatic vascular cells during mouse development through functional and single-cell RNA-sequencing. The acquisition of sinusoidal endothelial cell identity is initiated during early development and completed postnatally, originating from a pool of undifferentiated vascular progenitors at E12. The peri-natal induction of the transcription factor c-Maf is a critical switch for the sinusoidal identity determination. Endothelium-restricted deletion of c-Maf disrupts liver sinusoidal development, aberrantly expands postnatal liver hematopoiesis, promotes excessive postnatal sinusoidal proliferation, and aggravates liver pro-fibrotic sensitivity to chemical insult. Enforced c-Maf overexpression in generic human endothelial cells switches on a liver sinusoidal transcriptional program that maintains hepatocyte function. c-Maf represents an inducible intra-organotypic and niche-responsive molecular determinant of hepatic sinusoidal cell identity and lays the foundation for the strategies for vasculature-driven liver repair.
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Affiliation(s)
- Jesus Maria Gómez-Salinero
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Franco Izzo
- Division of Hematology and Medical Oncology, Department of Medicine, and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Yang Lin
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sean Houghton
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tomer Itkin
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Fuqiang Geng
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert P Adelson
- Bioengineering Program, Fred DeMatteis School of Engineering and Applied Science, Hofstra University, Hempstead, NY, USA
| | - Tyler M Lu
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Raphael Lis
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - David Redmond
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ryan Schreiner
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sina Y Rabbany
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Bioengineering Program, Fred DeMatteis School of Engineering and Applied Science, Hofstra University, Hempstead, NY, USA
| | - Dan A Landau
- Division of Hematology and Medical Oncology, Department of Medicine, and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Shahin Rafii
- Division of Regenerative Medicine, Hartman Institute for Therapeutic Organ Regeneration, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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Abstract
In this issue of Cell Stem Cell, Gómez-Salinero et al. (2022) identify c-Maf as a driver for murine liver sinusoidal endothelial cell (LSEC) fate and function during liver development, homeostasis, and repair. Similarly, c-Maf defines human LSECs, and its overexpression specializes generic HUVECs into functional induced-LSECs, potentiating regenerative therapeutics.
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Affiliation(s)
- Anna R Smith
- Section of Gastroenterology, Center for Regenerative Medicine (CReM), Department of Medicine, Boston University and Boston Medical Center, Boston, MA, USA
| | - Valerie Gouon-Evans
- Section of Gastroenterology, Center for Regenerative Medicine (CReM), Department of Medicine, Boston University and Boston Medical Center, Boston, MA, USA.
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30
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Xu J, Hao S, Shi Q, Deng Q, Jiang Y, Guo P, Yuan Y, Shi X, Shangguan S, Zheng H, Lai G, Huang Y, Wang Y, Song Y, Liu Y, Wu L, Wang Z, Cheng J, Wei X, Cheng M, Lai Y, Volpe G, Esteban MA, Hou Y, Liu C, Liu L. Transcriptomic Profile of the Mouse Postnatal Liver Development by Single-Nucleus RNA Sequencing. Front Cell Dev Biol 2022; 10:833392. [PMID: 35465320 PMCID: PMC9019599 DOI: 10.3389/fcell.2022.833392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jiangshan Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Shijie Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Quan Shi
- BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Qiuting Deng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Yujia Jiang
- BGI-Shenzhen, Shenzhen, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Pengcheng Guo
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yue Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Xuyang Shi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Shuncheng Shangguan
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Huiwen Zheng
- BGI-Shenzhen, Shenzhen, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Guangyao Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | | | | | | | | | - Liang Wu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | | | - Jiehui Cheng
- Guangdong Hospital of Traditional Chinese Medicine, Zhuhai, China
| | | | - Mengnan Cheng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Yiwei Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Giacomo Volpe
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori‘Giovanni Paolo II’, Bari, Italy
| | - Miguel A. Esteban
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | | | | | - Longqi Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
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31
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Holczbauer Á, Wangensteen KJ, Shin S. Cellular origins of regenerating liver and hepatocellular carcinoma. JHEP Rep 2022; 4:100416. [PMID: 35243280 PMCID: PMC8873941 DOI: 10.1016/j.jhepr.2021.100416] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 02/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the predominant primary cancer arising from the liver and is one of the major causes of cancer-related mortality worldwide. The cellular origin of HCC has been a topic of great interest due to conflicting findings regarding whether it originates in hepatocytes, biliary cells, or facultative stem cells. These cell types all undergo changes during liver injury, and there is controversy about their contribution to regenerative responses in the liver. Most HCCs emerge in the setting of chronic liver injury from viral hepatitis, fatty liver disease, alcohol, and environmental exposures. The injuries are marked by liver parenchymal changes such as hepatocyte regenerative nodules, biliary duct cellular changes, expansion of myofibroblasts that cause fibrosis and cirrhosis, and inflammatory cell infiltration, all of which may contribute to carcinogenesis. Addressing the cellular origin of HCC is the key to identifying the earliest events that trigger it. Herein, we review data on the cells of origin in regenerating liver and HCC and the implications of these findings for prevention and treatment. We also review the origins of childhood liver cancer and other rare cancers of the liver.
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32
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Wang J, Huang D, Yu H, Cheng Y, Ren H, Zhao Y. Developing tissue engineering strategies for liver regeneration. ENGINEERED REGENERATION 2022. [DOI: 10.1016/j.engreg.2022.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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33
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Liang Y, Kaneko K, Xin B, Lee J, Sun X, Zhang K, Feng GS. Temporal analyses of postnatal liver development and maturation by single-cell transcriptomics. Dev Cell 2022; 57:398-414.e5. [PMID: 35134346 PMCID: PMC8842999 DOI: 10.1016/j.devcel.2022.01.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 11/10/2021] [Accepted: 01/05/2022] [Indexed: 02/09/2023]
Abstract
The postnatal development and maturation of the liver, the major metabolic organ, are inadequately understood. We have analyzed 52,834 single-cell transcriptomes and identified 31 cell types or states in mouse livers at postnatal days 1, 3, 7, 21, and 56. We observe unexpectedly high levels of hepatocyte heterogeneity in the developing liver and the progressive construction of the zonated metabolic functions from pericentral to periportal hepatocytes, which is orchestrated with the development of sinusoid endothelial, stellate, and Kupffer cells. Trajectory and gene regulatory analyses capture 36 transcription factors, including a circadian regulator, Bhlhe40, in programming liver development. Remarkably, we identified a special group of macrophages enriched at day 7 with a hybrid phenotype of macrophages and endothelial cells, which may regulate sinusoidal construction and Treg-cell function. This study provides a comprehensive atlas that covers all hepatic cell types and is instrumental for further dissection of liver development, metabolism, and disease.
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Affiliation(s)
- Yan Liang
- Department of Pathology, Division of Biological Sciences, and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kota Kaneko
- Department of Pathology, Division of Biological Sciences, and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bing Xin
- Department of Pathology, Division of Biological Sciences, and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jin Lee
- Department of Pathology, Division of Biological Sciences, and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xin Sun
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gen-Sheng Feng
- Department of Pathology, Division of Biological Sciences, and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
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34
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Gifre-Renom L, Daems M, Luttun A, Jones EAV. Organ-Specific Endothelial Cell Differentiation and Impact of Microenvironmental Cues on Endothelial Heterogeneity. Int J Mol Sci 2022; 23:ijms23031477. [PMID: 35163400 PMCID: PMC8836165 DOI: 10.3390/ijms23031477] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Endothelial cells throughout the body are heterogeneous, and this is tightly linked to the specific functions of organs and tissues. Heterogeneity is already determined from development onwards and ranges from arterial/venous specification to microvascular fate determination in organ-specific differentiation. Acknowledging the different phenotypes of endothelial cells and the implications of this diversity is key for the development of more specialized tissue engineering and vascular repair approaches. However, although novel technologies in transcriptomics and proteomics are facilitating the unraveling of vascular bed-specific endothelial cell signatures, still much research is based on the use of insufficiently specialized endothelial cells. Endothelial cells are not only heterogeneous, but their specialized phenotypes are also dynamic and adapt to changes in their microenvironment. During the last decades, strong collaborations between molecular biology, mechanobiology, and computational disciplines have led to a better understanding of how endothelial cells are modulated by their mechanical and biochemical contexts. Yet, because of the use of insufficiently specialized endothelial cells, there is still a huge lack of knowledge in how tissue-specific biomechanical factors determine organ-specific phenotypes. With this review, we want to put the focus on how organ-specific endothelial cell signatures are determined from development onwards and conditioned by their microenvironments during adulthood. We discuss the latest research performed on endothelial cells, pointing out the important implications of mimicking tissue-specific biomechanical cues in culture.
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Affiliation(s)
- Laia Gifre-Renom
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, Katholieke Universiteit Leuven (KU Leuven), BE-3000 Leuven, Belgium; (L.G.-R.); (M.D.); (A.L.)
| | - Margo Daems
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, Katholieke Universiteit Leuven (KU Leuven), BE-3000 Leuven, Belgium; (L.G.-R.); (M.D.); (A.L.)
| | - Aernout Luttun
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, Katholieke Universiteit Leuven (KU Leuven), BE-3000 Leuven, Belgium; (L.G.-R.); (M.D.); (A.L.)
| | - Elizabeth A. V. Jones
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, Katholieke Universiteit Leuven (KU Leuven), BE-3000 Leuven, Belgium; (L.G.-R.); (M.D.); (A.L.)
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, 6229 ER Maastricht, The Netherlands
- Correspondence:
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35
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He L, Lu A, Qin L, Zhang Q, Ling H, Tan D, He Y. Application of single-cell RNA sequencing technology in liver diseases: a narrative review. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1598. [PMID: 34790804 PMCID: PMC8576673 DOI: 10.21037/atm-21-4824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/14/2021] [Indexed: 11/26/2022]
Abstract
Objective This review aimed to summarize the application of single-cell transcriptome sequencing technology in liver diseases. Background The increasing application of single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) in life science and biomedical research has greatly improved our understanding of cellular heterogeneity in immunology, oncology, and developmental biology. scRNA-seq has proven to be a powerful tool for identifying and classifying cell subsets, characterizing rare or small cell subsets and tracking cell differentiation along the dynamic cell stages. Globally, liver disease has high rates of morbidity and mortality, and its exact pathological mechanism remains unclear, current treatment options are limited to clearance of the underlying cause or liver transplantation, which cannot overwhelm and cure liver diseases. scRNA-seq provides many novel insights for healthy and diseased livers. Methods In this review, we searched for related articles in the PubMed database and summarized the advances of scRNA-seq in revealing the molecular mechanisms of liver development, regeneration, and disease. We also discussed the challenges and future application potential of scRNA-seq, which is expected to enhance the ability to explore the field of liver research and accelerate the clinical application of liver precision medicine. Conclusions With the continuous improvement of scRNA-seq technology, scRNA-seq is expected to unlock new avenues for liver biology exploration, liver disease diagnosis, and personalized treatment, which will pave the way for breakthrough innovation in personalized medicine.
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Affiliation(s)
- Lian He
- The Key Laboratory of Basic Pharmacology of Minstry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Anjing Lu
- The Key Laboratory of Basic Pharmacology of Minstry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi, China.,Shanghai Nature-Standard Technology Service Co., Ltd., Shanghai, China
| | - Lin Qin
- The Key Laboratory of Basic Pharmacology of Minstry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Qianru Zhang
- The Key Laboratory of Basic Pharmacology of Minstry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Hua Ling
- School of Pharmacy, Georgia Campus-Philadelphia College of Osteopathic Medicine, Suwanee, GA, USA
| | - Daopeng Tan
- The Key Laboratory of Basic Pharmacology of Minstry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Yuqi He
- The Key Laboratory of Basic Pharmacology of Minstry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi, China
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36
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Tobisawa Y, Fujita N, Yamamoto H, Ohyama C, Irie F, Yamaguchi Y. The cell surface hyaluronidase TMEM2 is essential for systemic hyaluronan catabolism and turnover. J Biol Chem 2021; 297:101281. [PMID: 34624311 PMCID: PMC8561002 DOI: 10.1016/j.jbc.2021.101281] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 11/26/2022] Open
Abstract
As a major component of the extracellular matrix, hyaluronan (HA) plays an important role in defining the biochemical and biophysical properties of tissues. In light of the extremely rapid turnover of HA and the impact of this turnover on HA biology, elucidating the molecular mechanisms underlying HA catabolism is key to understanding the in vivo functions of this unique polysaccharide. Here, we show that TMEM2, a recently identified cell surface hyaluronidase, plays an essential role in systemic HA turnover. Employing induced global Tmem2 knockout mice (Tmem2iKO), we determined the effects of Tmem2 ablation not only on the accumulation of HA in bodily fluids and organs, but also on the process of HA degradation in vivo. Within 3 weeks of tamoxifen-induced Tmem2 ablation, Tmem2iKO mice exhibit pronounced accumulation of HA in circulating blood and various organs, reaching levels as high as 40-fold above levels observed in control mice. Experiments using lymphatic and vascular injection of fluorescent HA tracers demonstrate that ongoing HA degradation in the lymphatic system and the liver is significantly impaired in Tmem2iKO mice. We also show that Tmem2 is strongly expressed in endothelial cells in the subcapsular sinus of lymph nodes and in the liver sinusoid, two primary sites implicated in systemic HA turnover. Our results establish TMEM2 as a physiologically relevant hyaluronidase with an essential role in systemic HA catabolism in vivo, acting primarily on the surface of endothelial cells in the lymph nodes and liver.
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Affiliation(s)
- Yuki Tobisawa
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Naoki Fujita
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Hayato Yamamoto
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA; Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Chikara Ohyama
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Fumitoshi Irie
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Yu Yamaguchi
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
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37
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Yang W, He H, Wang T, Su N, Zhang F, Jiang K, Zhu J, Zhang C, Niu K, Wang L, Yuan X, Liu N, Li L, Wei W, Hu J. Single-Cell Transcriptomic Analysis Reveals a Hepatic Stellate Cell-Activation Roadmap and Myofibroblast Origin During Liver Fibrosis in Mice. Hepatology 2021; 74:2774-2790. [PMID: 34089528 PMCID: PMC8597108 DOI: 10.1002/hep.31987] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/14/2021] [Accepted: 05/26/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIMS HSCs and portal fibroblasts (PFs) are the major sources of collagen-producing myofibroblasts during liver fibrosis, depending on different etiologies. However, the mechanisms by which their dynamic gene expression directs the transition from the quiescent to the activated state-as well as their contributions to fibrotic myofibroblasts-remain unclear. Here, we analyze the activation of HSCs and PFs in CCL4 -induced and bile duct ligation-induced fibrosis mouse models, using single-cell RNA sequencing and lineage tracing. APPROACH AND RESULTS We demonstrate that HSCs, rather than PFs, undergo dramatic transcriptomic changes, with the sequential activation of inflammatory, migrative, and extracellular matrix-producing programs. The data also reveal that HSCs are the exclusive source of myofibroblasts in CCL4 -treated liver, while PFs are the major source of myofibroblasts in early cholestatic liver fibrosis. Single-cell and lineage-tracing analysis also uncovers differential gene-expression features between HSCs and PFs; for example, nitric oxide receptor soluble guanylate cyclase is exclusively expressed in HSCs, but not in PFs. The soluble guanylate cyclase stimulator Riociguat potently reduced liver fibrosis in CCL4 -treated livers but showed no therapeutic efficacy in bile duct ligation livers. CONCLUSIONS This study provides a transcriptional roadmap for the activation of HSCs during liver fibrosis and yields comprehensive evidence that the differential transcriptomic features of HSCs and PFs, along with their relative contributions to liver fibrosis of different etiologies, should be considered in developing effective antifibrotic therapeutic strategies.
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Affiliation(s)
- Wu Yang
- Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
| | - Hao He
- Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
| | - Tongtong Wang
- Laboratory of Translational Nutritional BiologyDepartment Health Sciences and TechnologySwiss Federal Institute of Technology ZurichZurichSwitzerland
| | - Nan Su
- Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
| | - Feng Zhang
- Department of Histoembryology, Genetics and Developmental BiologyShanghai Key Laboratory of Reproductive MedicineShanghai JiaoTong University School of MedicineShanghaiChina
| | - Kai Jiang
- Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina
| | - Jing Zhu
- Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
| | - Chonghe Zhang
- Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
| | - Kongyan Niu
- Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina
| | - Luyue Wang
- University of Chinese Academy of SciencesBeijingChina,CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghaiChina
| | - Xiaodong Yuan
- Division of Life Sciences and MedicineDepartment of Organ Transplantation CenterTransplant & Immunology Laboratorythe First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiChina
| | - Nan Liu
- Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
| | - Lingjie Li
- Department of Histoembryology, Genetics and Developmental BiologyShanghai Key Laboratory of Reproductive MedicineShanghai JiaoTong University School of MedicineShanghaiChina
| | - Wu Wei
- University of Chinese Academy of SciencesBeijingChina,CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghaiChina
| | - Junhao Hu
- Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
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38
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Ma C, Zhang L, He T, Cao H, Ren X, Ma C, Yang J, Huang R, Pan G. Single cell Raman spectroscopy to identify different stages of proliferating human hepatocytes for cell therapy. Stem Cell Res Ther 2021; 12:555. [PMID: 34717753 PMCID: PMC8556950 DOI: 10.1186/s13287-021-02619-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/23/2021] [Indexed: 12/11/2022] Open
Abstract
Background Cell therapy provides hope for treatment of advanced liver failure. Proliferating human hepatocytes (ProliHHs) were derived from primary human hepatocytes (PHH) and as potential alternative for cell therapy in liver diseases. Due to the continuous decline of mature hepatic genes and increase of progenitor like genes during ProliHHs expanding, it is challenge to monitor the critical changes of the whole process. Raman microspectroscopy is a noninvasive, label free analytical technique with high sensitivity capacity. In this study, we evaluated the potential and feasibility to identify ProliHHs from PHH with Raman spectroscopy. Methods Raman spectra were collected at least 600 single spectrum for PHH and ProliHHs at different stages (Passage 1 to Passage 4). Linear discriminant analysis and a two-layer machine learning model were used to analyze the Raman spectroscopy data. Significant differences in Raman bands were validated by the associated conventional kits. Results Linear discriminant analysis successfully classified ProliHHs at different stages and PHH. A two-layer machine learning model was established and the overall accuracy was at 84.6%. Significant differences in Raman bands have been found within different ProliHHs cell groups, especially changes at 1003 cm−1, 1206 cm−1 and 1440 cm−1. These changes were linked with reactive oxygen species, hydroxyproline and triglyceride levels in ProliHHs, and the hypothesis were consistent with the corresponding assay results. Conclusions In brief, Raman spectroscopy was successfully employed to identify different stages of ProliHHs during dedifferentiation process. The approach can simultaneously trace multiple changes of cellular components from somatic cells to progenitor cells. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02619-9.
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Affiliation(s)
- Chen Ma
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ludi Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Science, Beijing, China
| | - Ting He
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Huiying Cao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiongzhao Ren
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Chenhui Ma
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiale Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruimin Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Guoyu Pan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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39
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Ogoke O, Guiggey D, Mon T, Shamul C, Ross S, Rao S, Parashurama N. Spatiotemporal imaging and analysis of mouse and human liver bud morphogenesis. Dev Dyn 2021; 251:662-686. [PMID: 34665487 DOI: 10.1002/dvdy.429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 09/07/2021] [Accepted: 09/28/2021] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The process of liver organogenesis has served as a paradigm for organ formation. However, there remains a lack of understanding regarding early mouse and human liver bud morphogenesis and early liver volumetric growth. Elucidating dynamic changes in liver volumes is critical for understanding organ development, implementing toxicological studies, and for modeling hPSC-derived liver organoid growth. New visualization, analysis, and experimental techniques are desperately needed. RESULTS Here, we combine observational data with digital resources, new 3D imaging approaches, retrospective analysis of liver volume data, mathematical modeling, and experiments with hPSC-derived liver organoids. Mouse and human liver organogenesis, characterized by exponential growth, demonstrate distinct spatial features and growth curves over time, which we mathematically modeled using Gompertz models. Visualization of liver-epithelial and septum transversum mesenchyme (STM) interactions suggests extended interactions, which together with new spatial features may be responsible for extensive exponential growth. These STM interactions are modeled with a novel in vitro human pluripotent stem cell (hPSC)-derived hepatic organoid system that exhibits cell migration. CONCLUSIONS Our methods enhance our understanding of liver organogenesis, with new 3D visualization, analysis, mathematical modeling, and in vitro models with hPSCs. Our approach highlights mouse and human differences and provides potential hypothesis for further investigation in vitro and in vivo.
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Affiliation(s)
- Ogechi Ogoke
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Daniel Guiggey
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Tala Mon
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Claire Shamul
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Shatoni Ross
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Saroja Rao
- Department of Biological Sciences, College of Arts and Sciences, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Natesh Parashurama
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA.,Clinical and Translation Research Center (CTRC), University at Buffalo (State University of New York), Buffalo, New York, USA.,Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA.,Center for Cell, Gene, and Tissue Engineering (CGTE), University at Buffalo (State University of New York), Buffalo, New York, USA
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40
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Wang ZY, Keogh A, Waldt A, Cuttat R, Neri M, Zhu S, Schuierer S, Ruchti A, Crochemore C, Knehr J, Bastien J, Ksiazek I, Sánchez-Taltavull D, Ge H, Wu J, Roma G, Helliwell SB, Stroka D, Nigsch F. Single-cell and bulk transcriptomics of the liver reveals potential targets of NASH with fibrosis. Sci Rep 2021; 11:19396. [PMID: 34588551 PMCID: PMC8481490 DOI: 10.1038/s41598-021-98806-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/15/2021] [Indexed: 12/11/2022] Open
Abstract
Fibrosis is characterized by the excessive production of collagen and other extracellular matrix (ECM) components and represents a leading cause of morbidity and mortality worldwide. Previous studies of nonalcoholic steatohepatitis (NASH) with fibrosis were largely restricted to bulk transcriptome profiles. Thus, our understanding of this disease is limited by an incomplete characterization of liver cell types in general and hepatic stellate cells (HSCs) in particular, given that activated HSCs are the major hepatic fibrogenic cell population. To help fill this gap, we profiled 17,810 non-parenchymal cells derived from six healthy human livers. In conjunction with public single-cell data of fibrotic/cirrhotic human livers, these profiles enable the identification of potential intercellular signaling axes (e.g., ITGAV-LAMC1, TNFRSF11B-VWF and NOTCH2-DLL4) and master regulators (e.g., RUNX1 and CREB3L1) responsible for the activation of HSCs during fibrogenesis. Bulk RNA-seq data of NASH patient livers and rodent models for liver fibrosis of diverse etiologies allowed us to evaluate the translatability of candidate therapeutic targets for NASH-related fibrosis. We identified 61 liver fibrosis-associated genes (e.g., AEBP1, PRRX1 and LARP6) that may serve as a repertoire of translatable drug target candidates. Consistent with the above regulon results, gene regulatory network analysis allowed the identification of CREB3L1 as a master regulator of many of the 61 genes. Together, this study highlights potential cell-cell interactions and master regulators that underlie HSC activation and reveals genes that may represent prospective hallmark signatures for liver fibrosis.
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Affiliation(s)
- Zhong-Yi Wang
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland.
| | - Adrian Keogh
- Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Annick Waldt
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Rachel Cuttat
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Marilisa Neri
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Shanshan Zhu
- China Novartis Institutes for BioMedical Research, Shanghai, 201203, China
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Alexandra Ruchti
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | | | - Judith Knehr
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Julie Bastien
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Iwona Ksiazek
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Daniel Sánchez-Taltavull
- Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Hui Ge
- China Novartis Institutes for BioMedical Research, Shanghai, 201203, China
| | - Jing Wu
- China Novartis Institutes for BioMedical Research, Shanghai, 201203, China
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Stephen B Helliwell
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
- Rejuveron Life Sciences AG, 8952, Schlieren, Switzerland
| | - Deborah Stroka
- Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Florian Nigsch
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland.
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41
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Quantitative lineage analysis identifies a hepato-pancreato-biliary progenitor niche. Nature 2021; 597:87-91. [PMID: 34433966 DOI: 10.1038/s41586-021-03844-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/21/2021] [Indexed: 02/07/2023]
Abstract
Studies based on single cells have revealed vast cellular heterogeneity in stem cell and progenitor compartments, suggesting continuous differentiation trajectories with intermixing of cells at various states of lineage commitment and notable degrees of plasticity during organogenesis1-5. The hepato-pancreato-biliary organ system relies on a small endoderm progenitor compartment that gives rise to a variety of different adult tissues, including the liver, pancreas, gall bladder and extra-hepatic bile ducts6,7. Experimental manipulation of various developmental signals in the mouse embryo has underscored important cellular plasticity in this embryonic territory6. This is reflected in the existence of human genetic syndromes as well as congenital malformations featuring multi-organ phenotypes in liver, pancreas and gall bladder6. Nevertheless, the precise lineage hierarchy and succession of events leading to the segregation of an endoderm progenitor compartment into hepatic, biliary and pancreatic structures have not yet been established. Here we combine computational modelling approaches with genetic lineage tracing to accurately reconstruct the hepato-pancreato-biliary lineage tree. We show that a multipotent progenitor subpopulation persists in the pancreato-biliary organ rudiment, contributing cells not only to the pancreas and gall bladder but also to the liver. Moreover, using single-cell RNA sequencing and functional experiments we define a specialized niche that supports this subpopulation in a multipotent state for an extended time during development. Together these findings indicate sustained plasticity underlying hepato-pancreato-biliary development that might also explain the rapid expansion of the liver while attenuating pancreato-biliary growth.
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42
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Campbell SA, Stephan TL, Lotto J, Cullum R, Drissler S, Hoodless PA. Signalling pathways and transcriptional regulators orchestrating liver development and cancer. Development 2021; 148:272023. [PMID: 34478514 DOI: 10.1242/dev.199814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Liver development is controlled by key signals and transcription factors that drive cell proliferation, migration, differentiation and functional maturation. In the adult liver, cell maturity can be perturbed by genetic and environmental factors that disrupt hepatic identity and function. Developmental signals and fetal genetic programmes are often dysregulated or reactivated, leading to dedifferentiation and disease. Here, we highlight signalling pathways and transcriptional regulators that drive liver cell development and primary liver cancers. We also discuss emerging models derived from pluripotent stem cells, 3D organoids and bioengineering for improved studies of signalling pathways in liver cancer and regenerative medicine.
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Affiliation(s)
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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43
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Kordes C, Bock HH, Reichert D, May P, Häussinger D. Hepatic stellate cells: current state and open questions. Biol Chem 2021; 402:1021-1032. [PMID: 34008380 DOI: 10.1515/hsz-2021-0180] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/03/2021] [Indexed: 01/14/2023]
Abstract
This review article summarizes 20 years of our research on hepatic stellate cells within the framework of two collaborative research centers CRC575 and CRC974 at the Heinrich Heine University. Over this period, stellate cells were identified for the first time as mesenchymal stem cells of the liver, and important functions of these cells in the context of liver regeneration were discovered. Furthermore, it was determined that the space of Disse - bounded by the sinusoidal endothelium and hepatocytes - functions as a stem cell niche for stellate cells. Essential elements of this niche that control the maintenance of hepatic stellate cells have been identified alongside their impairment with age. This article aims to highlight previous studies on stellate cells and critically examine and identify open questions and future research directions.
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Affiliation(s)
- Claus Kordes
- Clinic of Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University, Moorenstraße 5, D-40225 Düsseldorf, Germany
| | - Hans H Bock
- Clinic of Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University, Moorenstraße 5, D-40225 Düsseldorf, Germany
| | - Doreen Reichert
- Clinic of Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University, Moorenstraße 5, D-40225 Düsseldorf, Germany
| | - Petra May
- Clinic of Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University, Moorenstraße 5, D-40225 Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic of Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University, Moorenstraße 5, D-40225 Düsseldorf, Germany
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44
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Angiodiversity and organotypic functions of sinusoidal endothelial cells. Angiogenesis 2021; 24:289-310. [PMID: 33745018 PMCID: PMC7982081 DOI: 10.1007/s10456-021-09780-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/04/2021] [Indexed: 02/08/2023]
Abstract
‘Angiodiversity’ refers to the structural and functional heterogeneity of endothelial cells (EC) along the segments of the vascular tree and especially within the microvascular beds of different organs. Organotypically differentiated EC ranging from continuous, barrier-forming endothelium to discontinuous, fenestrated endothelium perform organ-specific functions such as the maintenance of the tightly sealed blood–brain barrier or the clearance of macromolecular waste products from the peripheral blood by liver EC-expressed scavenger receptors. The microvascular bed of the liver, composed of discontinuous, fenestrated liver sinusoidal endothelial cells (LSEC), is a prime example of organ-specific angiodiversity. Anatomy and development of LSEC have been extensively studied by electron microscopy as well as linage-tracing experiments. Recent advances in cell isolation and bulk transcriptomics or single-cell RNA sequencing techniques allowed the identification of distinct LSEC molecular programs and have led to the identification of LSEC subpopulations. LSEC execute homeostatic functions such as fine tuning the vascular tone, clearing noxious substances from the circulation, and modulating immunoregulatory mechanisms. In recent years, the identification and functional analysis of LSEC-derived angiocrine signals, which control liver homeostasis and disease pathogenesis in an instructive manner, marks a major change of paradigm in the understanding of liver function in health and disease. This review summarizes recent advances in the understanding of liver vascular angiodiversity and the functional consequences resulting thereof.
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