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Wang H, Liu J, Zhu P, Shi L, Liu Y, Yang X, Yang X. Single-nucleus transcriptome reveals cell dynamic response of liver during the late chick embryonic development. Poult Sci 2024; 103:103979. [PMID: 38941785 PMCID: PMC11261130 DOI: 10.1016/j.psj.2024.103979] [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: 03/18/2024] [Revised: 05/29/2024] [Accepted: 06/10/2024] [Indexed: 06/30/2024] Open
Abstract
The late embryonic development of the liver, a major metabolic organ, remains poorly characterized at single cell resolution. Here, we used single-nucleus RNA-sequencing (snRNA-seq) to characterize the chicken liver cells at 2 embryonic development time points (E14 and D1). We uncovered 8 cell types including hepatocytes, endothelial cells, hepatic stellate cells, erythrocytes, cholangiocytes, kupffer cells, mesothelial cells, and lymphocytes. And we discovered significant differences in the abundance of different cell types between E14 and D1. Moreover, we characterized the heterogeneity of hepatocytes, endothelial cells, and mesenchymal cells based on the gene regulatory networks of each clusters. Trajectory analyses revealed 128 genes associated with hepatocyte development and function, including apolipoprotein genes involved hepatic lipid metabolism and NADH dehydrogenase subunits involved hepatic oxidative phosphorylation. Furthermore, we identified the differentially expressed genes (DEGs) between E14 and D1 at the cellular levels, which contribute to changes in liver development and function. These DEGs were significantly enriched in PPAR signaling pathways and lipid metabolism related pathways. Our results presented the single-cell mapping of chick embryonic liver at late stages of development and demonstrated the metabolic changes across the 2 age stages at the cellular level, which can help to further study the molecular development mechanism of embryonic liver.
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Affiliation(s)
- Huimei Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Jiongyan Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Pinhui Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Lin Shi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yanli Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Xin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
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Fan Y, Bian X, Meng X, Li L, Fu L, Zhang Y, Wang L, Zhang Y, Gao D, Guo X, Lammi MJ, Peng G, Sun S. Unveiling inflammatory and prehypertrophic cell populations as key contributors to knee cartilage degeneration in osteoarthritis using multi-omics data integration. Ann Rheum Dis 2024; 83:926-944. [PMID: 38325908 PMCID: PMC11187367 DOI: 10.1136/ard-2023-224420] [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: 05/11/2023] [Accepted: 01/23/2024] [Indexed: 02/09/2024]
Abstract
OBJECTIVES Single-cell and spatial transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome landscape and osteoarthritis (OA)-critical cell populations. METHODS Single-cell RNA sequencing and spatially resolved transcriptomic technology have been applied to characterise the cellular heterogeneity of human knee articular cartilage which were collected from 8 OA donors, and 3 non-OA control donors, and a total of 19 samples. The novel chondrocyte population and marker genes of interest were validated by immunohistochemistry staining, quantitative real-time PCR, etc. The OA-critical cell populations were validated through integrative analyses of publicly available bulk RNA sequencing data and large-scale genome-wide association studies. RESULTS We identified 33 cell population-specific marker genes that define 11 chondrocyte populations, including 9 known populations and 2 new populations, that is, pre-inflammatory chondrocyte population (preInfC) and inflammatory chondrocyte population (InfC). The novel findings that make this an important addition to the literature include: (1) the novel InfC activates the mediator MIF-CD74; (2) the prehypertrophic chondrocyte (preHTC) and hypertrophic chondrocyte (HTC) are potentially OA-critical cell populations; (3) most OA-associated differentially expressed genes reside in the articular surface and superficial zone; (4) the prefibrocartilage chondrocyte (preFC) population is a major contributor to the stratification of patients with OA, resulting in both an inflammatory-related subtype and a non-inflammatory-related subtype. CONCLUSIONS Our results highlight InfC, preHTC, preFC and HTC as potential cell populations to target for therapy. Also, we conclude that profiling of those cell populations in patients might be used to stratify patient populations for defining cohorts for clinical trials and precision medicine.
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Affiliation(s)
- Yue Fan
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
- Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, Shaanxi Province; Key Laboratory of Trace Elements and Endemic Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education; Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xuzhao Bian
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Xiaogao Meng
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Lei Li
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Laiyi Fu
- School of Automation Science and Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yanan Zhang
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Long Wang
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
- Center for Evidence-Based Medicine and Clinical Research, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yan Zhang
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
- Department of Orthopaedics, Honghui Hospital, Xi'an, Shaanxi, China
| | - Dalong Gao
- Department of Orthopaedics, The Central Hospital of Xianyang, Xianyang, China
| | - Xiong Guo
- Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, Shaanxi Province; Key Laboratory of Trace Elements and Endemic Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Mikko Juhani Lammi
- Department of Integrative Medical Biology, University of Umeå, Umeå, Sweden
| | - Guangdun Peng
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shiquan Sun
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
- Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, Shaanxi Province; Key Laboratory of Trace Elements and Endemic Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education; Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, Shaanxi, China
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3
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Nagy N, Hádinger N, Tóth O, Rácz GA, Pintér T, Gál Z, Urbán M, Gócza E, Hiripi L, Acsády L, Vértessy BG. Characterization of dUTPase expression in mouse postnatal development and adult neurogenesis. Sci Rep 2024; 14:13139. [PMID: 38849394 PMCID: PMC11161619 DOI: 10.1038/s41598-024-63405-0] [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: 09/25/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
The enzyme dUTPase has an essential role in maintaining genomic integrity. In mouse, nuclear and mitochondrial isoforms of the enzyme have been described. Here we present the isoform-specific mRNA expression levels in different murine organs during development using RT-qPCR. In this study, we analyzed organs of 14.5-day embryos and of postnatal 2-, 4-, 10-week- and 13-month-old mice. We demonstrate organ-, sex- and developmental stage-specific differences in the mRNA expression levels of both isoforms. We found high mRNA expression level of the nuclear isoform in the embryo brain, and the expression level remained relatively high in the adult brain as well. This was surprising, since dUTPase is known to play an important role in proliferating cells, and mass production of neural cells is completed by adulthood. Thus, we investigated the pattern of the dUTPase protein expression specifically in the adult brain with immunostaining and found that dUTPase is present in the germinative zones, the subventricular and the subgranular zones, where neurogenesis occurs and in the rostral migratory stream where neuroblasts migrate to the olfactory bulb. These novel findings suggest that dUTPase may have a role in cell differentiation and indicate that accurate dTTP biosynthesis can be vital, especially in neurogenesis.
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Affiliation(s)
- Nikolett Nagy
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary.
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar tudósok körútja 2, 1117, Budapest, Hungary.
| | - Nóra Hádinger
- Laboratory of Thalamus Research, Institute of Experimental Medicine, HUN-REN, Szigony utca 43, 1083, Budapest, Hungary
| | - Otília Tóth
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar tudósok körútja 2, 1117, Budapest, Hungary
- Department of Applied Biotechnology and Food Sciences, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111, Budapest, Hungary
| | - Gergely Attila Rácz
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar tudósok körútja 2, 1117, Budapest, Hungary
- Department of Applied Biotechnology and Food Sciences, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111, Budapest, Hungary
| | - Tímea Pintér
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert utca 4, 2100, Gödöllő, Hungary
| | - Zoltán Gál
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert utca 4, 2100, Gödöllő, Hungary
| | - Martin Urbán
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert utca 4, 2100, Gödöllő, Hungary
| | - Elen Gócza
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert utca 4, 2100, Gödöllő, Hungary
| | - László Hiripi
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert utca 4, 2100, Gödöllő, Hungary
- Laboratory Animal Science Coordination Center, Semmelweis University, Nagyvárad tér 4, 1089, Budapest, Hungary
| | - László Acsády
- Laboratory of Thalamus Research, Institute of Experimental Medicine, HUN-REN, Szigony utca 43, 1083, Budapest, Hungary
| | - Beáta G Vértessy
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar tudósok körútja 2, 1117, Budapest, Hungary.
- Department of Applied Biotechnology and Food Sciences, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111, Budapest, Hungary.
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Fan Y, Li L, Sun S. Powerful and accurate detection of temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data with TDEseq. Genome Biol 2024; 25:96. [PMID: 38622747 PMCID: PMC11020788 DOI: 10.1186/s13059-024-03237-3] [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: 09/22/2023] [Accepted: 04/03/2024] [Indexed: 04/17/2024] Open
Abstract
We present a non-parametric statistical method called TDEseq that takes full advantage of smoothing splines basis functions to account for the dependence of multiple time points in scRNA-seq studies, and uses hierarchical structure linear additive mixed models to model the correlated cells within an individual. As a result, TDEseq demonstrates powerful performance in identifying four potential temporal expression patterns within a specific cell type. Extensive simulation studies and the analysis of four published scRNA-seq datasets show that TDEseq can produce well-calibrated p-values and up to 20% power gain over the existing methods for detecting temporal gene expression patterns.
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Affiliation(s)
- Yue Fan
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
- Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region; NHC Key Laboratory of Environment and Endemic Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Lei Li
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
- Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region; NHC Key Laboratory of Environment and Endemic Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Shiquan Sun
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China.
- Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region; NHC Key Laboratory of Environment and Endemic Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China.
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, 710061, People's Republic of China.
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, Shaanxi, 710061, People's Republic of China.
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5
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Gupta K, Xu JP, Diamond T, de Jong IEM, Glass A, Llewellyn J, Theise ND, Waisbourd-Zinman O, Winkler JD, Behrens EM, Mesaros C, Wells RG. Low-dose biliatresone treatment of pregnant mice causes subclinical biliary disease in their offspring: Evidence for a spectrum of neonatal injury. PLoS One 2024; 19:e0301824. [PMID: 38578745 PMCID: PMC10997102 DOI: 10.1371/journal.pone.0301824] [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: 12/05/2023] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
Biliary atresia is a neonatal disease characterized by damage, inflammation, and fibrosis of the liver and bile ducts and by abnormal bile metabolism. It likely results from a prenatal environmental exposure that spares the mother and affects the fetus. Our aim was to develop a model of fetal injury by exposing pregnant mice to low-dose biliatresone, a plant toxin implicated in biliary atresia in livestock, and then to determine whether there was a hepatobiliary phenotype in their pups. Pregnant mice were treated orally with 15 mg/kg/d biliatresone for 2 days. Histology of the liver and bile ducts, serum bile acids, and liver immune cells of pups from treated mothers were analyzed at P5 and P21. Pups had no evidence of histological liver or bile duct injury or fibrosis at either timepoint. In addition, growth was normal. However, serum levels of glycocholic acid were elevated at P5, suggesting altered bile metabolism, and the serum bile acid profile became increasingly abnormal through P21, with enhanced glycine conjugation of bile acids. There was also immune cell activation observed in the liver at P21. These results suggest that prenatal exposure to low doses of an environmental toxin can cause subclinical disease including liver inflammation and aberrant bile metabolism even in the absence of histological changes. This finding suggests a wide potential spectrum of disease after fetal biliary injury.
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Affiliation(s)
- Kapish Gupta
- Department of Medicine, Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for Engineering MechanoBiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jimmy P. Xu
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tamir Diamond
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Iris E. M. de Jong
- Department of Medicine, Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for Engineering MechanoBiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andrew Glass
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jessica Llewellyn
- Department of Medicine, Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for Engineering MechanoBiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Neil D. Theise
- Department of Pathology, School of Medicine, New York University, New York, New York, United States of America
| | - Orith Waisbourd-Zinman
- Institute for Gastroenterology, Nutrition and Liver Diseases, Schneider Children’s Medical Center of Israel, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Jeffrey D. Winkler
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Edward M. Behrens
- Division of Rheumatology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Clementina Mesaros
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Rebecca G. Wells
- Department of Medicine, Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for Engineering MechanoBiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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6
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Zuo B, Yang F, Huang L, Han J, Li T, Ma Z, Cao L, Li Y, Bai X, Jiang M, He Y, Xia L. Endothelial Slc35a1 Deficiency Causes Loss of LSEC Identity and Exacerbates Neonatal Lipid Deposition in the Liver in Mice. Cell Mol Gastroenterol Hepatol 2024; 17:1039-1061. [PMID: 38467191 PMCID: PMC11061248 DOI: 10.1016/j.jcmgh.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND & AIMS The functional maturation of the liver largely occurs after birth. In the early stages of life, the liver of a newborn encounters enormous high-fat metabolic stress caused by the consumption of breast milk. It is unclear how the maturing liver adapts to high lipid metabolism. Liver sinusoidal endothelial cells (LSECs) play a fundamental role in establishing liver vasculature and are decorated with many glycoproteins on their surface. The Slc35a1 gene encodes a cytidine-5'-monophosphate (CMP)-sialic acid transporter responsible for transporting CMP-sialic acids between the cytoplasm and the Golgi apparatus for protein sialylation. This study aimed to determine whether endothelial sialylation plays a role in hepatic vasculogenesis and functional maturation. METHODS Endothelial-specific Slc35a1 knockout mice were generated. Liver tissues were collected for histologic analysis, lipidomic profiling, RNA sequencing, confocal immunofluorescence, and immunoblot analyses. RESULTS Endothelial Slc35a1-deficient mice exhibited excessive neonatal hepatic lipid deposition, severe liver damage, and high mortality. Endothelial deletion of Slc35a1 led to sinusoidal capillarization and disrupted hepatic zonation. Mechanistically, vascular endothelial growth factor receptor 2 (VEGFR2) in LSECs was desialylated and VEGFR2 signaling was enhanced in Slc35a1-deficient mice. Inhibition of VEGFR2 signaling by SU5416 alleviated lipid deposition and restored hepatic vasculature in Slc35a1-deficient mice. CONCLUSIONS Our findings suggest that sialylation of LSECs is critical for maintaining hepatic vascular development and lipid homeostasis. Targeting VEGFR2 signaling may be a new strategy to prevent liver disorders associated with abnormal vasculature and lipid deposition.
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Affiliation(s)
- Bin Zuo
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Key Laboratory of Thrombosis and Hemostasis of National Health Commission, The First Affiliated Hospital of Soochow University, Suzhou, China; Engineering Center of Hematological Disease of Ministry of Education, Cyrus Tang Hematology Center, Soochow University, Suzhou, China
| | - Fei Yang
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Key Laboratory of Thrombosis and Hemostasis of National Health Commission, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Lulu Huang
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Key Laboratory of Thrombosis and Hemostasis of National Health Commission, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jingjing Han
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Key Laboratory of Thrombosis and Hemostasis of National Health Commission, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Tianyi Li
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Key Laboratory of Thrombosis and Hemostasis of National Health Commission, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhenni Ma
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Key Laboratory of Thrombosis and Hemostasis of National Health Commission, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Lijuan Cao
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Key Laboratory of Thrombosis and Hemostasis of National Health Commission, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yun Li
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Key Laboratory of Thrombosis and Hemostasis of National Health Commission, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xia Bai
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Key Laboratory of Thrombosis and Hemostasis of National Health Commission, The First Affiliated Hospital of Soochow University, Suzhou, China; Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China; State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Miao Jiang
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Key Laboratory of Thrombosis and Hemostasis of National Health Commission, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yang He
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Key Laboratory of Thrombosis and Hemostasis of National Health Commission, The First Affiliated Hospital of Soochow University, Suzhou, China; Engineering Center of Hematological Disease of Ministry of Education, Cyrus Tang Hematology Center, Soochow University, Suzhou, China; Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
| | - Lijun Xia
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Key Laboratory of Thrombosis and Hemostasis of National Health Commission, The First Affiliated Hospital of Soochow University, Suzhou, China; Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China; Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma.
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7
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Huang Y, Liu X, Wang HY, Chen JY, Zhang X, Li Y, Lu Y, Dong Z, Liu K, Wang Z, Wang Q, Fan G, Zou J, Liu S, Shao C. Single-cell transcriptome landscape of zebrafish liver reveals hepatocytes and immune cell interactions in understanding nonalcoholic fatty liver disease. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109428. [PMID: 38325594 DOI: 10.1016/j.fsi.2024.109428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/27/2024] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is becoming the most common chronic liver disease in the world. Immunity is the major contributing factor in NAFLD; however, the interaction of immune cells and hepatocytes in disease progression has not been fully elucidated. As a popular species for studying NAFLD, zebrafish, whose liver is a complex immune system mediated by immune cells and non-immune cells in maintaining immune tolerance and homeostasis. Understanding the cellular composition and immune environment of zebrafish liver is of great significance for its application in NAFLD. Here, we established a liver atlas that consists of 10 cell types using single-cell RNA sequencing (scRNA-seq). By examining the heterogeneity of hepatocytes and analyzing the expression of NAFLD-associated genes in the specific cluster, we provide a potential target cell model to study NAFLD. Additionally, our analysis identified two subtypes of distinct resident macrophages with inflammatory and non-inflammatory functions and characterized the successive stepwise development of T cell subclusters in the liver. Importantly, we uncovered the possible regulation of macrophages and T cells on target cells of fatty liver by analyzing the cellular interaction between hepatocytes and immune cells. Our data provide valuable information for an in-depth study of immune cells targeting hepatocytes to regulate the immune balance in NAFLD.
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Affiliation(s)
- Yingyi Huang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266072, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266072, Qingdao, Shandong, China
| | - Xiang Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266072, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266072, Qingdao, Shandong, China
| | - Hong-Yan Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266072, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266072, Qingdao, Shandong, China
| | - Jian-Yang Chen
- BGI Research, 266555, Qingdao, Shandong, China; Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, Shandong, China
| | - Xianghui Zhang
- BGI Research, 266555, Qingdao, Shandong, China; Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, Shandong, China
| | - Yubang Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266072, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266072, Qingdao, Shandong, China
| | - Yifang Lu
- BGI Research, 266555, Qingdao, Shandong, China; Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, Shandong, China
| | - Zhongdian Dong
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, 524088, Zhanjiang, Guangdong, China
| | - Kaiqiang Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266072, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266072, Qingdao, Shandong, China
| | - Zhongduo Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, 524088, Zhanjiang, Guangdong, China
| | - Qian Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266072, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266072, Qingdao, Shandong, China
| | - Guangyi Fan
- BGI Research, 266555, Qingdao, Shandong, China; Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, Shandong, China; BGI Research, 518083, Shenzhen, China
| | - Jun Zou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, 201306, Shanghai, China
| | - Shanshan Liu
- MGI Tech, 518083, Shenzhen, China; BGI Research, 518083, Shenzhen, China.
| | - Changwei Shao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266072, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266072, Qingdao, Shandong, China.
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8
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Li L, He Y, Liu K, Liu L, Shan S, Liu H, Ren J, Sun S, Wang M, Jia J, Wang P. GITRL impairs hepatocyte repopulation by liver progenitor cells to aggravate inflammation and fibrosis by GITR +CD8 + T lymphocytes in CDE Mice. Cell Death Dis 2024; 15:114. [PMID: 38321001 PMCID: PMC10847460 DOI: 10.1038/s41419-024-06506-y] [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: 01/04/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/08/2024]
Abstract
As an alternative pathway for liver regeneration, liver progenitor cells and their derived ductular reaction cells increase during the progression of many chronic liver diseases. However, the mechanism underlying their hepatocyte repopulation after liver injury remains unknown. Here, we conducted progenitor cell lineage tracing in mice and found that fewer than 2% of hepatocytes were derived from liver progenitor cells after 9 weeks of injury with a choline-deficient diet supplemented with ethionine (CDE), and this percentage increased approximately three-fold after 3 weeks of recovery. We also found that the proportion of liver progenitor cells double positive for the ligand of glucocorticoid-induced tumour necrosis factor receptor (GITRL, also called Tnfsf18) and SRY-related HMG box transcription 9 (Sox9) among nonparenchymal cells increased time-dependently upon CDE injury and reduced after recovery. When GITRL was conditionally knocked out from hepatic progenitor cells, its expression in nonparenchymal cells was downregulated by approximately fifty percent, and hepatocyte repopulation increased by approximately three folds. Simultaneously, conditional knockout of GITRL reduced the proportion of liver-infiltrating CD8+ T lymphocytes and glucocorticoid-induced tumour necrosis factor receptor (GITR)-positive CD8+ T lymphocytes. Mechanistically, GITRL stimulated cell proliferation but suppressed the differentiation of liver progenitor organoids into hepatocytes, and CD8+ T cells further reduced their hepatocyte differentiation by downregulating the Wnt/β-catenin pathway. Therefore, GITRL expressed by liver progenitor cells impairs hepatocyte differentiation, thus hindering progenitor cell-mediated liver regeneration.
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Affiliation(s)
- Li Li
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
- National Clinical Research Center for Digestive Disease, Beijing, 100069, China
- Beijing Key Laboratory on Translational Medicine on Cirrhosis, Beijing, 100050, China
| | - Yu He
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
- National Clinical Research Center for Digestive Disease, Beijing, 100069, China
- Beijing Key Laboratory on Translational Medicine on Cirrhosis, Beijing, 100050, China
| | - Kai Liu
- Beijing Clinical Research Institute, Beijing, 100050, China
| | - Lin Liu
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
- National Clinical Research Center for Digestive Disease, Beijing, 100069, China
- Beijing Key Laboratory on Translational Medicine on Cirrhosis, Beijing, 100050, China
| | - Shan Shan
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
- National Clinical Research Center for Digestive Disease, Beijing, 100069, China
- Beijing Key Laboratory on Translational Medicine on Cirrhosis, Beijing, 100050, China
| | - Helin Liu
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
- National Clinical Research Center for Digestive Disease, Beijing, 100069, China
- Beijing Key Laboratory on Translational Medicine on Cirrhosis, Beijing, 100050, China
| | - Jiangbo Ren
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
- National Clinical Research Center for Digestive Disease, Beijing, 100069, China
- Beijing Key Laboratory on Translational Medicine on Cirrhosis, Beijing, 100050, China
| | - Shujie Sun
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
- National Clinical Research Center for Digestive Disease, Beijing, 100069, China
- Beijing Key Laboratory on Translational Medicine on Cirrhosis, Beijing, 100050, China
| | - Min Wang
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
- National Clinical Research Center for Digestive Disease, Beijing, 100069, China
- Beijing Key Laboratory on Translational Medicine on Cirrhosis, Beijing, 100050, China
| | - Jidong Jia
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
- National Clinical Research Center for Digestive Disease, Beijing, 100069, China.
- Beijing Key Laboratory on Translational Medicine on Cirrhosis, Beijing, 100050, China.
| | - Ping Wang
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
- National Clinical Research Center for Digestive Disease, Beijing, 100069, China.
- Beijing Key Laboratory on Translational Medicine on Cirrhosis, Beijing, 100050, China.
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9
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Chiang IKN, Humphrey D, Mills RJ, Kaltzis P, Pachauri S, Graus M, Saha D, Wu Z, Young P, Sim CB, Davidson T, Hernandez‐Garcia A, Shaw CA, Renwick A, Scott DA, Porrello ER, Wong ES, Hudson JE, Red‐Horse K, del Monte‐Nieto G, Francois M. Sox7-positive endothelial progenitors establish coronary arteries and govern ventricular compaction. EMBO Rep 2023; 24:e55043. [PMID: 37551717 PMCID: PMC10561369 DOI: 10.15252/embr.202255043] [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: 03/14/2022] [Revised: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 08/09/2023] Open
Abstract
The cardiac endothelium influences ventricular chamber development by coordinating trabeculation and compaction. However, the endothelial-specific molecular mechanisms mediating this coordination are not fully understood. Here, we identify the Sox7 transcription factor as a critical cue instructing cardiac endothelium identity during ventricular chamber development. Endothelial-specific loss of Sox7 function in mice results in cardiac ventricular defects similar to non-compaction cardiomyopathy, with a change in the proportions of trabecular and compact cardiomyocytes in the mutant hearts. This phenotype is paralleled by abnormal coronary artery formation. Loss of Sox7 function disrupts the transcriptional regulation of the Notch pathway and connexins 37 and 40, which govern coronary arterial specification. Upon Sox7 endothelial-specific deletion, single-nuclei transcriptomics analysis identifies the depletion of a subset of Sox9/Gpc3-positive endocardial progenitor cells and an increase in erythro-myeloid cell lineages. Fate mapping analysis reveals that a subset of Sox7-null endothelial cells transdifferentiate into hematopoietic but not cardiomyocyte lineages. Our findings determine that Sox7 maintains cardiac endothelial cell identity, which is crucial to the cellular cross-talk that drives ventricular compaction and coronary artery development.
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Affiliation(s)
- Ivy KN Chiang
- Centenary Institute, Royal Prince Alfred HospitalThe University of SydneySydneyNSWAustralia
| | - David Humphrey
- The Victor Chang Cardiac Research InstituteDarlinghurstNSWAustralia
| | - Richard J Mills
- QIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
| | - Peter Kaltzis
- The Australian Regenerative Medicine InstituteMonash UniversityClaytonVICAustralia
| | - Shikha Pachauri
- Centenary Institute, Royal Prince Alfred HospitalThe University of SydneySydneyNSWAustralia
| | - Matthew Graus
- Centenary Institute, Royal Prince Alfred HospitalThe University of SydneySydneyNSWAustralia
| | - Diptarka Saha
- The Australian Regenerative Medicine InstituteMonash UniversityClaytonVICAustralia
| | - Zhijian Wu
- The Australian Regenerative Medicine InstituteMonash UniversityClaytonVICAustralia
| | - Paul Young
- The Victor Chang Cardiac Research InstituteDarlinghurstNSWAustralia
| | - Choon Boon Sim
- The Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVICAustralia
| | - Tara Davidson
- Centenary Institute, Royal Prince Alfred HospitalThe University of SydneySydneyNSWAustralia
| | | | - Chad A Shaw
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Alexander Renwick
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Daryl A Scott
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Enzo R Porrello
- The Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVICAustralia
- Melbourne Centre for Cardiovascular Genomics and Regenerative MedicineThe Royal Children's HospitalMelbourneVICAustralia
- Department of Anatomy and Physiology, School of Biomedical SciencesThe University of MelbourneMelbourneVICAustralia
| | - Emily S Wong
- The Victor Chang Cardiac Research InstituteDarlinghurstNSWAustralia
| | - James E Hudson
- QIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
| | | | | | - Mathias Francois
- Centenary Institute, Royal Prince Alfred HospitalThe University of SydneySydneyNSWAustralia
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10
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Pan Q, Li B, Lin D, Miao YR, Luo T, Yue T, Luo Q, Guo AY, Zhang Z. scLiverDB: a Database of Human and Mouse Liver Transcriptome Landscapes at Single-Cell Resolution. SMALL METHODS 2023; 7:e2201421. [PMID: 37259264 DOI: 10.1002/smtd.202201421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 04/17/2023] [Indexed: 06/02/2023]
Abstract
The liver is critical for the digestive and immune systems. Although the physiology and pathology of liver have been well studied and many scRNA-seq data are generated, a database and landscape for characterizing cell types and gene expression in different liver diseases or developmental stages at single-cell resolution are lacking. Hence, scLiverDB is developed, a specialized database for human and mouse liver transcriptomes to unravel the landscape of liver cell types, cell heterogeneity and gene expression at single-cell resolution across various liver diseases/cell types/developmental stages. To date, 62 datasets including 9,050 samples and 1,741,734 cells is curated. A uniform workflow is used, which included quality control, dimensional reduction, clustering, and cell-type annotation to analyze datasets on the same platform; integrated manual and automatic methods for accurate cell-type identification and provided a user-friendly web interface with multiscale functions. There are two case studies to show the usefulness of scLiverDB, which identified the LTB (lymphotoxin Beta) gene as a potential biomarker of lymphoid cells differentiation and showed the expression changes of Foxa3 (forkhead box A3) in liver chronic progressive diseases. This work provides a crucial resource to resolve molecular and cellular information in normal, diseased, and developing human and mouse livers.
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Affiliation(s)
- Qi Pan
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Borui Li
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Dong Lin
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Ya-Ru Miao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Tao Luo
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Tao Yue
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qingming Luo
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China
| | - An-Yuan Guo
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhihong Zhang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China
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11
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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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12
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Fang J, Singh S, Cheng C, Natarajan S, Sheppard H, Abu-Zaid A, Durbin AD, Lee HW, Wu Q, Steele J, Connelly JP, Jin H, Chen W, Fan Y, Pruett-Miller SM, Rehg JE, Koo SC, Santiago T, Emmons J, Cairo S, Wang R, Glazer ES, Murphy AJ, Chen T, Davidoff AM, Armengol C, Easton J, Chen X, Yang J. Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma. Nat Commun 2023; 14:4003. [PMID: 37414763 PMCID: PMC10326052 DOI: 10.1038/s41467-023-39717-6] [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: 03/21/2022] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
A lack of relevant genetic models and cell lines hampers our understanding of hepatoblastoma pathogenesis and the development of new therapies for this neoplasm. Here, we report an improved MYC-driven hepatoblastoma-like murine model that recapitulates the pathological features of embryonal type of hepatoblastoma, with transcriptomics resembling the high-risk gene signatures of the human disease. Single-cell RNA-sequencing and spatial transcriptomics identify distinct subpopulations of hepatoblastoma cells. After deriving cell lines from the mouse model, we map cancer dependency genes using CRISPR-Cas9 screening and identify druggable targets shared with human hepatoblastoma (e.g., CDK7, CDK9, PRMT1, PRMT5). Our screen also reveals oncogenes and tumor suppressor genes in hepatoblastoma that engage multiple, druggable cancer signaling pathways. Chemotherapy is critical for human hepatoblastoma treatment. A genetic mapping of doxorubicin response by CRISPR-Cas9 screening identifies modifiers whose loss-of-function synergizes with (e.g., PRKDC) or antagonizes (e.g., apoptosis genes) the effect of chemotherapy. The combination of PRKDC inhibition and doxorubicin-based chemotherapy greatly enhances therapeutic efficacy. These studies provide a set of resources including disease models suitable for identifying and validating potential therapeutic targets in human high-risk hepatoblastoma.
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Affiliation(s)
- Jie Fang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shivendra Singh
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Changde Cheng
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sivaraman Natarajan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather Sheppard
- Comparative Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ahmed Abu-Zaid
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adam D Durbin
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ha Won Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qiong Wu
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jacob Steele
- Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon P Connelly
- Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jerold E Rehg
- Comparative Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Selene C Koo
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Teresa Santiago
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Joseph Emmons
- VPC Diagnostic Laboratory, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stefano Cairo
- Champions Oncology, 1330 Piccard dr, Rockville, MD, USA
| | - Ruoning Wang
- Center for Childhood Cancer and Blood Disease, Hematology/Oncology & BMT, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
| | - Evan S Glazer
- Department of Surgery, College of Medicine, The University of Tennessee Health Science Center, 910 Madison Ave., Suite 325, Memphis, TN, USA
| | - Andrew J Murphy
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Surgery, College of Medicine, The University of Tennessee Health Science Center, 910 Madison Ave., Suite 325, Memphis, TN, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Surgery, College of Medicine, The University of Tennessee Health Science Center, 910 Madison Ave., Suite 325, Memphis, TN, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Carolina Armengol
- Childhood Liver Oncology Group, Germans Trias i Pujol Research Institute (IGTP), Translational Program in Cancer Research (CARE), Badalona, Spain
- CIBER, Hepatic and Digestive Diseases, Barcelona, Spain
- CIBERehd, Madrid, Spain
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA.
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Pathology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA.
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13
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Hou YT, Wu CC, Wang WT, Yang WT, Liao YH, Chen CY. Monitoring Cultured Rat Hepatocytes Using RNA-Seq In Vitro. Int J Mol Sci 2023; 24:ijms24087534. [PMID: 37108701 PMCID: PMC10139060 DOI: 10.3390/ijms24087534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Compared to other techniques, RNA sequencing (RNA-Seq) has the advantage of having details of the expression abundance of all transcripts in a single run. In this study, we used RNA-Seq to monitor the maturity and dynamic characteristics of in vitro hepatocyte cultures. Hepatocytes, including mature hepatocytes and small hepatocytes, were analyzed in vitro using RNA-Seq and quantitative polymerase chain reaction (qPCR). The results demonstrated that the gene expression profiles measured by RNA-Seq showed a similar trend to the expression profiles measured by qPCR, and can be used to infer the success of in vitro hepatocyte cultures. The results of the differential analysis, which compared mature hepatocytes against small hepatocytes, revealed 836 downregulated and 137 upregulated genes. In addition, the success of the hepatocyte cultures could be explained by the gene list screened from the adopted gene enrichment test. In summary, we demonstrated that RNA-Seq could become an effective method for monitoring the whole transcriptome of hepatocyte cultures and provide a more comprehensive list of factors related to the differentiation of small hepatocytes into mature hepatocytes. This monitoring system not only shows high potential in medical applications but may also be a novel method for the clinical diagnosis of liver-related diseases.
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Affiliation(s)
- Yung-Te Hou
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Chia-Chun Wu
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Wen-Ting Wang
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Wen-Tse Yang
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Ying-Hsiu Liao
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Chien-Yu Chen
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 106, Taiwan
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14
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Ceccacci E, Villa E, Santoro F, Minucci S, Ruhrberg C, Fantin A. A Refined Single Cell Landscape of Haematopoiesis in the Mouse Foetal Liver. J Dev Biol 2023; 11:15. [PMID: 37092477 PMCID: PMC10123705 DOI: 10.3390/jdb11020015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/13/2023] [Accepted: 03/18/2023] [Indexed: 04/25/2023] Open
Abstract
During prenatal life, the foetal liver is colonised by several waves of haematopoietic progenitors to act as the main haematopoietic organ. Single cell (sc) RNA-seq has been used to identify foetal liver cell types via their transcriptomic signature and to compare gene expression patterns as haematopoietic development proceeds. To obtain a refined single cell landscape of haematopoiesis in the foetal liver, we have generated a scRNA-seq dataset from a whole mouse E12.5 liver that includes a larger number of cells than prior datasets at this stage and was obtained without cell type preselection to include all liver cell populations. We combined mining of this dataset with that of previously published datasets at other developmental stages to follow transcriptional dynamics as well as the cell cycle state of developing haematopoietic lineages. Our findings corroborate several prior reports on the timing of liver colonisation by haematopoietic progenitors and the emergence of differentiated lineages and provide further molecular characterisation of each cell population. Extending these findings, we demonstrate the existence of a foetal intermediate haemoglobin profile in the mouse, similar to that previously identified in humans, and a previously unidentified population of primitive erythroid cells in the foetal liver.
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Affiliation(s)
- Elena Ceccacci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Emanuela Villa
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Department of Biosciences, University of Milan, Via G. Celoria 26, 20133 Milan, Italy
| | - Fabio Santoro
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy
| | - Christiana Ruhrberg
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Alessandro Fantin
- Department of Biosciences, University of Milan, Via G. Celoria 26, 20133 Milan, Italy
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15
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Blériot C, Dalmas É, Ginhoux F, Venteclef N. Inflammatory and immune etiology of type 2 diabetes. Trends Immunol 2023; 44:101-109. [PMID: 36604203 DOI: 10.1016/j.it.2022.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 01/04/2023]
Abstract
Type 2 diabetes (T2D) represents a global threat affecting millions of patients worldwide. However, its causes remain incompletely dissected and we lack the tools to predict which individuals will develop T2D. Although there is a clear proven clinical association of T2D with metabolic disorders such as obesity and nonalcoholic fatty liver disease (NAFLD), the existence of a significant number of nondiabetic obese subjects suggests yet-uncovered features of such relationships. Here, we propose that a significant proportion of individuals may harbor an immune profile that renders them susceptible to developing T2D. We note the heterogeneity of circulating monocytes and tissue macrophages in organs that are key to metabolic disorders such as liver, white adipose tissue (WAT), and endocrine pancreas, as well as their contribution to T2D genesis.
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Affiliation(s)
- Camille Blériot
- Institut Necker-Enfants Malades (INEM), Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Paris, France; Gustave Roussy Cancer Campus, Villejuif, France.
| | - Élise Dalmas
- Institut Necker-Enfants Malades (INEM), Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Paris, France.
| | - Florent Ginhoux
- Gustave Roussy Cancer Campus, Villejuif, France; Singapore Immunology Network (SIgN), Agency for Science, Technology, and Research (A∗STAR), Singapore 138648, Singapore; Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore; Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nicolas Venteclef
- Institut Necker-Enfants Malades (INEM), Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Paris, France
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16
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Kambhampati S, Murphy S, Uosaki H, Kwon C. Cross-Organ Transcriptomic Comparison Reveals Universal Factors During Maturation. J Comput Biol 2022; 29:1031-1044. [PMID: 35802489 PMCID: PMC9499449 DOI: 10.1089/cmb.2021.0349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Various cell types can be derived from stem cells. However, these cells are immature and do not match their adult counterparts in functional capabilities, limiting their use in disease modeling and cell therapies. Thus, it is crucial to understand the mechanisms of maturation in vivo. However, it is unknown if there are genes and pathways conserved across organs during maturation. To address this, we performed a time-series analysis of the transcriptome of the mouse heart, brain, liver, and kidney and analyzed their trajectories over time. In addition, gene regulatory networks were reconstructed to determine overlapping expression patterns. Based on these, we identified commonly upregulated and downregulated pathways across all four organs. Key upstream regulators were also predicted based on the temporal expression of downstream genes. These findings suggest the presence of universal regulators during organ maturation, which may help us develop a general strategy to mature stem cell-derived cells in vitro.
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Affiliation(s)
- Sandeep Kambhampati
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sean Murphy
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hideki Uosaki
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Chulan Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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17
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Hoekzema RS, Marsh L, Sumray O, Carroll TM, Lu X, Byrne HM, Harrington HA. Multiscale Methods for Signal Selection in Single-Cell Data. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1116. [PMID: 36010781 PMCID: PMC9407339 DOI: 10.3390/e24081116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Analysis of single-cell transcriptomics often relies on clustering cells and then performing differential gene expression (DGE) to identify genes that vary between these clusters. These discrete analyses successfully determine cell types and markers; however, continuous variation within and between cell types may not be detected. We propose three topologically motivated mathematical methods for unsupervised feature selection that consider discrete and continuous transcriptional patterns on an equal footing across multiple scales simultaneously. Eigenscores (eigi) rank signals or genes based on their correspondence to low-frequency intrinsic patterning in the data using the spectral decomposition of the Laplacian graph. The multiscale Laplacian score (MLS) is an unsupervised method for locating relevant scales in data and selecting the genes that are coherently expressed at these respective scales. The persistent Rayleigh quotient (PRQ) takes data equipped with a filtration, allowing the separation of genes with different roles in a bifurcation process (e.g., pseudo-time). We demonstrate the utility of these techniques by applying them to published single-cell transcriptomics data sets. The methods validate previously identified genes and detect additional biologically meaningful genes with coherent expression patterns. By studying the interaction between gene signals and the geometry of the underlying space, the three methods give multidimensional rankings of the genes and visualisation of relationships between them.
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Affiliation(s)
- Renee S. Hoekzema
- Mathematical Institute, University of Oxford, Oxford OX1 2JD, UK
- Department of Mathematics, Free University of Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Lewis Marsh
- Mathematical Institute, University of Oxford, Oxford OX1 2JD, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX1 2JD, UK
| | - Otto Sumray
- Mathematical Institute, University of Oxford, Oxford OX1 2JD, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX1 2JD, UK
| | - Thomas M. Carroll
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX1 2JD, UK
| | - Xin Lu
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX1 2JD, UK
| | - Helen M. Byrne
- Mathematical Institute, University of Oxford, Oxford OX1 2JD, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX1 2JD, UK
| | - Heather A. Harrington
- Mathematical Institute, University of Oxford, Oxford OX1 2JD, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX1 2JD, UK
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18
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Iannacone M, Blériot C, Andreata F, Ficht X, Laura C, Garcia-Manteiga JM, Uderhardt S, Ginhoux F. Response to contamination of isolated mouse Kupffer cells with liver sinusoidal endothelial cells. Immunity 2022; 55:1141-1142. [PMID: 35830819 DOI: 10.1016/j.immuni.2022.06.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matteo Iannacone
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy.
| | - Camille Blériot
- Inserm U1015, Institut Gustave Roussy, Villejuif 94800, France
| | - Francesco Andreata
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy
| | - Xenia Ficht
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy
| | - Chiara Laura
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy
| | - Jose M Garcia-Manteiga
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy
| | - Stefan Uderhardt
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen 91054, Germany, Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen 91054, Germany
| | - Florent Ginhoux
- Inserm U1015, Institut Gustave Roussy, Villejuif 94800, France; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore; Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 169856, Singapore; Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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19
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Arzalluz-Luque A, Salguero P, Tarazona S, Conesa A. acorde unravels functionally interpretable networks of isoform co-usage from single cell data. Nat Commun 2022; 13:1828. [PMID: 35383181 PMCID: PMC8983708 DOI: 10.1038/s41467-022-29497-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 03/16/2022] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing (AS) is a highly-regulated post-transcriptional mechanism known to modulate isoform expression within genes and contribute to cell-type identity. However, the extent to which alternative isoforms establish co-expression networks that may be relevant in cellular function has not been explored yet. Here, we present acorde, a pipeline that successfully leverages bulk long reads and single-cell data to confidently detect alternative isoform co-expression relationships. To achieve this, we develop and validate percentile correlations, an innovative approach that overcomes data sparsity and yields accurate co-expression estimates from single-cell data. Next, acorde uses correlations to cluster co-expressed isoforms into a network, unraveling cell type-specific alternative isoform usage patterns. By selecting same-gene isoforms between these clusters, we subsequently detect and characterize genes with co-differential isoform usage (coDIU) across cell types. Finally, we predict functional elements from long read-defined isoforms and provide insight into biological processes, motifs, and domains potentially controlled by the coordination of post-transcriptional regulation. The code for acorde is available at https://github.com/ConesaLab/acorde .
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Affiliation(s)
- Angeles Arzalluz-Luque
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain.,Institute for Integrative Systems Biology (CSIC-UV), Spanish National Research Council, Paterna, Valencia, Spain
| | - Pedro Salguero
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain
| | - Sonia Tarazona
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain.
| | - Ana Conesa
- Institute for Integrative Systems Biology (CSIC-UV), Spanish National Research Council, Paterna, Valencia, Spain. .,Microbiology and Cell Sciences Department, Institute for Food and Agricultural Research, University of Florida, Gainesville, FL, USA.
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20
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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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21
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Abstract
Yes-associated protein 1 (YAP1) is a transcriptional coactivator that activates transcriptional enhanced associate domain transcription factors upon inactivation of the Hippo signaling pathway, to regulate biological processes like proliferation, survival, and differentiation. YAP1 is most prominently expressed in biliary epithelial cells (BECs) in normal adult livers and during development. In the current review, we will discuss the multiple roles of YAP1 in the development and morphogenesis of bile ducts inside and outside the liver, as well as in orchestrating the cholangiocyte repair response to biliary injury. We will review how biliary repair can occur through the process of hepatocyte-to-BEC transdifferentiation and how YAP1 is pertinent to this process. We will also discuss the liver's capacity for metabolic reprogramming as an adaptive mechanism in extreme cholestasis, such as when intrahepatic bile ducts are absent due to YAP1 loss from hepatic progenitors. Finally, we will discuss the roles of YAP1 in the context of pediatric pathologies afflicting bile ducts, such as Alagille syndrome and biliary atresia. In conclusion, we will comprehensively discuss the spatiotemporal roles of YAP1 in biliary development and repair after biliary injury while describing key interactions with other well-known developmental pathways.
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Affiliation(s)
- Laura Molina
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine
| | - Kari Nejak-Bowen
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine,Pittsburgh Liver Research Center, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Satdarshan P. Monga
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine,Pittsburgh Liver Research Center, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania,Division of Gastroenterology, Hepatology, and Nutrition, University of Pittsburgh and UPMC, Pittsburgh, Pennsylvania
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22
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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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23
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Zhang W, Conway SJ, Liu Y, Snider P, Chen H, Gao H, Liu Y, Isidan K, Lopez KJ, Campana G, Li P, Ekser B, Francis H, Shou W, Kubal C. Heterogeneity of Hepatic Stellate Cells in Fibrogenesis of the Liver: Insights from Single-Cell Transcriptomic Analysis in Liver Injury. Cells 2021; 10:cells10082129. [PMID: 34440898 PMCID: PMC8391930 DOI: 10.3390/cells10082129] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/06/2021] [Accepted: 08/16/2021] [Indexed: 12/11/2022] Open
Abstract
Background & Aims: Liver fibrosis is a pathological healing process resulting from hepatic stellate cell (HSC) activation and the generation of myofibroblasts from activated HSCs. The precise underlying mechanisms of liver fibrogenesis are still largely vague due to lack of understanding the functional heterogeneity of activated HSCs during liver injury. Approach and Results: In this study, to define the mechanism of HSC activation, we performed the transcriptomic analysis at single-cell resolution (scRNA-seq) on HSCs in mice treated with carbon tetrachloride (CCl4). By employing LRAT-Cre:Rosa26mT/mG mice, we were able to isolate an activated GFP-positive HSC lineage derived cell population by fluorescence-activated cell sorter (FACS). A total of 8 HSC subpopulations were identified based on an unsupervised analysis. Each HSC cluster displayed a unique transcriptomic profile, despite all clusters expressing common mouse HSC marker genes. We demonstrated that one of the HSC subpopulations expressed high levels of mitosis regulatory genes, velocity, and monocle analysis indicated that these HSCs are at transitioning and proliferating phases at the beginning of HSCs activation and will eventually give rise to several other HSC subtypes. We also demonstrated cell clusters representing HSC-derived mature myofibroblast populations that express myofibroblasts hallmark genes with unique contractile properties. Most importantly, we found a novel HSC cluster that is likely to be critical in liver regeneration, immune reaction, and vascular remodeling, in which the unique profiles of genes such as Rgs5, Angptl6, and Meg3 are highly expressed. Lastly, we demonstrated that the heterogeneity of HSCs in the injured mouse livers is closely similar to that of cirrhotic human livers. Conclusions: Collectively, our scRNA-seq data provided insight into the landscape of activated HSC populations and the dynamic transitional pathway from HSC to myofibroblasts in response to liver injury.
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Affiliation(s)
- Wenjun Zhang
- Division of Transplant Surgery, Indiana University, Indianapolis, IN 46202, USA
| | - Simon J Conway
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ying Liu
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Paige Snider
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hanying Chen
- Genome Editing Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hongyu Gao
- The Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- The Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kadir Isidan
- Division of Transplant Surgery, Indiana University, Indianapolis, IN 46202, USA
| | - Kevin J Lopez
- Division of Transplant Surgery, Indiana University, Indianapolis, IN 46202, USA
| | - Gonzalo Campana
- Division of Transplant Surgery, Indiana University, Indianapolis, IN 46202, USA
| | - Ping Li
- Division of Transplant Surgery, Indiana University, Indianapolis, IN 46202, USA
| | - Burcin Ekser
- Division of Transplant Surgery, Indiana University, Indianapolis, IN 46202, USA
| | - Heather Francis
- Division of Gastroenterology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Weinian Shou
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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24
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Leo L, Colonna Romano N. Emerging Single-Cell Technological Approaches to Investigate Chromatin Dynamics and Centromere Regulation in Human Health and Disease. Int J Mol Sci 2021; 22:ijms22168809. [PMID: 34445507 PMCID: PMC8395756 DOI: 10.3390/ijms22168809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic regulators play a crucial role in establishing and maintaining gene expression states. To date, the main efforts to study cellular heterogeneity have focused on elucidating the variable nature of the chromatin landscape. Specific chromatin organisation is fundamental for normal organogenesis and developmental homeostasis and can be affected by different environmental factors. The latter can lead to detrimental alterations in gene transcription, as well as pathological conditions such as cancer. Epigenetic marks regulate the transcriptional output of cells. Centromeres are chromosome structures that are epigenetically regulated and are crucial for accurate segregation. The advent of single-cell epigenetic profiling has provided finer analytical resolution, exposing the intrinsic peculiarities of different cells within an apparently homogenous population. In this review, we discuss recent advances in methodologies applied to epigenetics, such as CUT&RUN and CUT&TAG. Then, we compare standard and emerging single-cell techniques and their relevance for investigating human diseases. Finally, we describe emerging methodologies that investigate centromeric chromatin specification and neocentromere formation.
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25
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Nuclear Organization during Hepatogenesis in Zebrafish Requires Uhrf1. Genes (Basel) 2021; 12:genes12071081. [PMID: 34356097 PMCID: PMC8304062 DOI: 10.3390/genes12071081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 01/07/2023] Open
Abstract
Acquisition of cellular fate during development is initiated and maintained by well-coordinated patterns of gene expression that are dictated by the epigenetic landscape and genome organization in the nucleus. While the epigenetic marks that mediate developmental gene expression patterns during organogenesis have been well studied, less is known about how epigenetic marks influence nuclear organization during development. This study examines the relationship between nuclear structure, chromatin accessibility, DNA methylation, and gene expression during hepatic outgrowth in zebrafish larvae. We investigate the relationship between these features using mutants that lack DNA methylation. Hepatocyte nuclear morphology was established coincident with hepatocyte differentiation at 80 h post-fertilization (hpf), and nuclear shape and size continued to change until the conclusion of outgrowth and morphogenesis at 120 hpf. Integrating ATAC-Seq analysis with DNA methylation profiling of zebrafish livers at 120 hpf showed that closed and highly methylated chromatin occupies most transposable elements and that open chromatin correlated with gene expression. DNA hypomethylation, due to mutation of genes encoding ubiquitin-like, containing PHD and RING Finger Domains 1 (uhrf1) and DNA methyltransferase (dnmt1), did not block hepatocyte differentiation, but had dramatic effects on nuclear organization. Hepatocytes in uhrf1 mutants have large, deformed nuclei with multiple nucleoli, downregulation of nucleolar genes, and a complete lack of the nuclear lamina. Loss of lamin B2 staining was phenocopied by dnmt1 mutation. Together, these data show that hepatocyte nuclear morphogenesis coincides with organ morphogenesis and outgrowth, and that DNA methylation directs chromatin organization, and, in turn, hepatocyte nuclear shape and size during liver development.
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26
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Richter ML, Deligiannis IK, Yin K, Danese A, Lleshi E, Coupland P, Vallejos CA, Matchett KP, Henderson NC, Colome-Tatche M, Martinez-Jimenez CP. Single-nucleus RNA-seq2 reveals functional crosstalk between liver zonation and ploidy. Nat Commun 2021; 12:4264. [PMID: 34253736 PMCID: PMC8275628 DOI: 10.1038/s41467-021-24543-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 06/24/2021] [Indexed: 12/19/2022] Open
Abstract
Single-cell RNA-seq reveals the role of pathogenic cell populations in development and progression of chronic diseases. In order to expand our knowledge on cellular heterogeneity, we have developed a single-nucleus RNA-seq2 method tailored for the comprehensive analysis of the nuclear transcriptome from frozen tissues, allowing the dissection of all cell types present in the liver, regardless of cell size or cellular fragility. We use this approach to characterize the transcriptional profile of individual hepatocytes with different levels of ploidy, and have discovered that ploidy states are associated with different metabolic potential, and gene expression in tetraploid mononucleated hepatocytes is conditioned by their position within the hepatic lobule. Our work reveals a remarkable crosstalk between gene dosage and spatial distribution of hepatocytes.
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Affiliation(s)
- M L Richter
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, Neuherberg, Germany
| | - I K Deligiannis
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, Neuherberg, Germany
| | - K Yin
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, Neuherberg, Germany
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, United Kingdom
| | - A Danese
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - E Lleshi
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, United Kingdom
| | - P Coupland
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, United Kingdom
| | - C A Vallejos
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - K P Matchett
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Little France Crescent, Edinburgh, United Kingdom
| | - N C Henderson
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Little France Crescent, Edinburgh, United Kingdom
| | - M Colome-Tatche
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Munich, Germany.
| | - C P Martinez-Jimenez
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, Neuherberg, Germany.
- TUM School of Medicine, Technical University of Munich, Munich, Germany.
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27
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Molina LM, Zhu J, Li Q, Pradhan-Sundd T, Krutsenko Y, Sayed K, Jenkins N, Vats R, Bhushan B, Ko S, Hu S, Poddar M, Singh S, Tao J, Sundd P, Singhi A, Watkins S, Ma X, Benos PV, Feranchak A, Michalopoulos G, Nejak-Bowen K, Watson A, Bell A, Monga SP. Compensatory hepatic adaptation accompanies permanent absence of intrahepatic biliary network due to YAP1 loss in liver progenitors. Cell Rep 2021; 36:109310. [PMID: 34233187 PMCID: PMC8280534 DOI: 10.1016/j.celrep.2021.109310] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 04/14/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022] Open
Abstract
Yes-associated protein 1 (YAP1) regulates cell plasticity during liver injury, regeneration, and cancer, but its role in liver development is unknown. We detect YAP1 activity in biliary cells and in cells at the hepatobiliary bifurcation in single-cell RNA sequencing analysis of developing livers. Deletion of Yap1 in hepatoblasts does not impair Notch-driven SOX9+ ductal plate formation but does prevent the formation of the abutting second layer of SOX9+ ductal cells, blocking the formation of a patent intrahepatic biliary tree. Intriguingly, these mice survive for 8 months with severe cholestatic injury and without hepatocyte-to-biliary transdifferentiation. Ductular reaction in the perihilar region suggests extrahepatic biliary proliferation, likely seeking the missing intrahepatic biliary network. Long-term survival of these mice occurs through hepatocyte adaptation via reduced metabolic and synthetic function, including altered bile acid metabolism and transport. Overall, we show YAP1 as a key regulator of bile duct development while highlighting a profound adaptive capability of hepatocytes.
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Affiliation(s)
- Laura M Molina
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Junjie Zhu
- Department of Pharmaceutical Sciences and Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Qin Li
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA
| | - Tirthadipa Pradhan-Sundd
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Yekaterina Krutsenko
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Khaled Sayed
- Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Ave, Pittsburgh, PA 15213, USA; Biomedical Engineering and Systems, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Nathaniel Jenkins
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ravi Vats
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA; Department of Bioengineering, School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bharat Bhushan
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Sungjin Ko
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Shikai Hu
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Minakshi Poddar
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sucha Singh
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Junyan Tao
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Prithu Sundd
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA
| | - Aatur Singhi
- Division of Anatomic Pathology, Department of Pathology, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA
| | - Simon Watkins
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Xiaochao Ma
- Department of Pharmaceutical Sciences and Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Ave, Pittsburgh, PA 15213, USA
| | - Andrew Feranchak
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - George Michalopoulos
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Kari Nejak-Bowen
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Alan Watson
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Aaron Bell
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Satdarshan P Monga
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA; Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA.
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28
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Hood R, Chen YH, Goldsmith JR. TNFAIP8 Regulates Intestinal Epithelial Cell Differentiation and May Alter Terminal Differentiation of Secretory Progenitors. Cells 2021; 10:871. [PMID: 33921306 PMCID: PMC8070212 DOI: 10.3390/cells10040871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 11/17/2022] Open
Abstract
The intestine is a highly proliferative dynamic environment that relies on constant self-renewal of the intestinal epithelium to maintain homeostasis. Tumor necrosis factor-alpha-induced protein 8 (TNFAIP8 or TIPE0) is a regulator of PI3K-mediated signaling. By binding to PIP2 and PIP3, TIPE family members locally activate PI3K activity while globally inhibiting PI3K activity through sequestration of membranous PIP2. Single-cell RNA sequencing survey of Tipe0-/- small intestine was used to investigate the role of TIPE0 in intestinal differentiation. Tipe0-/- intestinal cells were shown to shift towards an undifferentiated state, with the notable exception of goblet cells. Additionally, three possible novel regulators of terminal cell fate decisions in the secretory lineage were identified: Nupr1, Kdm4a, and Gatad1. We propose that these novel regulators drive changes involved in goblet cell (Nupr1) or tuft cell (Kdm4a and Gatad1) fate commitment and that TIPE0 may play a role in orchestrating terminal differentiation.
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Affiliation(s)
- Ryan Hood
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, 422 Curie Blvd, Philadelphia, PA 19104, USA
| | - Youhai H Chen
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, 422 Curie Blvd, Philadelphia, PA 19104, USA
| | - Jason R Goldsmith
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, 422 Curie Blvd, Philadelphia, PA 19104, USA
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29
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Sun C, Wang H, Ma Q, Chen C, Yue J, Li B, Zhang X. Time-course single-cell RNA sequencing reveals transcriptional dynamics and heterogeneity of limbal stem cells derived from human pluripotent stem cells. Cell Biosci 2021; 11:24. [PMID: 33485387 PMCID: PMC7824938 DOI: 10.1186/s13578-021-00541-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/15/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Human pluripotent stem cell-derived limbal stem cells (hPSC-derived LSCs) provide a promising cell source for corneal transplants and ocular surface reconstruction. Although recent efforts in the identification of LSC markers have increased our understanding of the biology of LSCs, much more remains to be characterized in the developmental origin, cell fate determination, and identity of human LSCs. The lack of knowledge hindered the establishment of efficient differentiation protocols for generating hPSC-derived LSCs and held back their clinical application. RESULTS Here, we performed a time-course single-cell RNA-seq to investigate transcriptional heterogeneity and expression changes of LSCs derived from human embryonic stem cells (hESCs). Based on current protocol, expression heterogeneity of reported LSC markers were identified in subpopulations of differentiated cells. EMT has been shown to occur during differentiation process, which could possibly result in generation of untargeted cells. Pseudotime trajectory analysis revealed transcriptional changes and signatures of commitment of hESCs-derived LSCs and their progeny-the transit amplifying cells. CONCLUSION Single-cell RNA-seq revealed time-course expression changes and significant transcriptional heterogeneity during hESC-derived LSC differentiation in vitro. Our results demonstrated candidate developmental trajectory and several new candidate markers for LSCs, which could facilitate elucidating the identity and developmental origin of human LSCs in vivo.
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Affiliation(s)
- Changbin Sun
- BGI-Shenzhen, Shenzhen, 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China
| | - Hailun Wang
- Department of Radiation Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Qiwang Ma
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China
| | - Chao Chen
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China
| | - Jianhui Yue
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China.,Section of Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bo Li
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China.
| | - Xi Zhang
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China.
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30
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Liu L, Borlak J. Advances in Liver Cancer Stem Cell Isolation and their Characterization. Stem Cell Rev Rep 2021; 17:1215-1238. [PMID: 33432485 DOI: 10.1007/s12015-020-10114-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2020] [Indexed: 12/24/2022]
Abstract
Over the last decade research on cancer stem cells (CSC) significantly contributed to a better understanding of tumor biology. Given their similarity to normal stem cells, i.e. self-renewal and pluripotency the need arises to develop robust protocols for the isolation and characterization of CSCs. As with other malignancies, hepatic tumors are composed of a heterogeneous population of cells including liver cancer stem cells (LCSC). Yet, a precise understanding of why stem cells become cancerous is still lacking. There is unmet need to develop robust protocols for the successful isolation of LCSCs from human tissue resection material as to assist in the development of molecular targeted therapies. Here we review the research progress made in the isolation and characterization of LCSCs by considering a wide range of cell surface markers and sorting methods, as applied to side populations, microsphere cultures and the gradient centrifugation method. We emphasize the different fluorescence activated cell sorting methods and the possibility to enrich LCSCs by immunomagnetic beads. We review the specificity of functional assays by considering ABCG transporter and ALDH1 enzyme activities and evaluate the in vivo tumorigenicity of LCSCs in highly sensitive bioassays. Finally, we evaluate different LCSC markers in association with viral and non-viral liver disease and explore the potential of novel drug delivery systems targeting CD133, EpCAM, CD13 and CD90 for the development of molecular targeted therapies. Graphical Abstract.
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Affiliation(s)
- Lu Liu
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Jürgen Borlak
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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31
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Oliveira AG, Fiorotto R. Novel approaches to liver disease diagnosis and modeling. Transl Gastroenterol Hepatol 2021; 6:19. [PMID: 33824923 PMCID: PMC7829068 DOI: 10.21037/tgh-20-109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/08/2020] [Indexed: 12/12/2022] Open
Abstract
Lack of a prompt and accurate diagnosis remains on top of the list of challenges faced by patients with rare liver diseases. Although rare liver diseases affect a significant percentage of the population as a group, when taken singularly they represent unique diseases and the approaches used for diagnosis of common liver diseases are insufficient. However, the development of new methods for the acquisition of molecular and clinical data (i.e., genomic, proteomics, metabolomics) and computational tools for their analysis and integration, together with advances in modeling diseases using stem cell-based technology [i.e., induced pluripotent stem cells (iPSCs) and tissue organoids] represent a promising and powerful tool to improve the clinical management of these patients. This is the goal of precision medicine, a novel approach of modern medicine that aims at delivering a specific treatment based on disease-specific biological insights and individual profile. This review will discuss the application and advances of these technologies and how they represent a new opportunity in hepatology.
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Affiliation(s)
- André G. Oliveira
- Department of Physiology and Biophysics, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Romina Fiorotto
- Department of Internal Medicine, Section of Digestive Diseases, Yale University School of Medicine, New Haven, USA
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32
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Chen T, Oh S, Gregory S, Shen X, Diehl AM. Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration. JCI Insight 2020. [DOI: 10.1172/jci.insight.141024 33208554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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33
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Chen T, Oh S, Gregory S, Shen X, Diehl AM. Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration. JCI Insight 2020; 5:141024. [PMID: 33208554 PMCID: PMC7710279 DOI: 10.1172/jci.insight.141024] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/08/2020] [Indexed: 01/07/2023] Open
Abstract
Adult liver has enormous regenerative capacity; it can regenerate after losing two-thirds of its mass while sustaining essential metabolic functions. How the liver balances dual demands for increased proliferative activity with maintenance of organ function is unknown but essential to prevent liver failure. Using partial hepatectomy (PHx) in mice to model liver regeneration, we integrated single-cell RNA- and ATAC-Seq to map state transitions in approximately 13,000 hepatocytes at single-cell resolution as livers regenerated, and validated key findings with IHC, to uncover how the organ regenerates hepatocytes while simultaneously fulfilling its vital tissue-specific functions. After PHx, hepatocytes rapidly and transiently diversified into multiple distinct populations with distinct functional bifurcation: some retained the chromatin landscapes and transcriptomes of hepatocytes in undamaged adult livers, whereas others transitioned to acquire chromatin landscapes and transcriptomes of fetal hepatocytes. Injury-related signaling pathways known to be critical for regeneration were activated in transitioning hepatocytes, and the most fetal-like hepatocytes exhibited chromatin landscapes that were enriched with transcription factors regulated by those pathways.
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Affiliation(s)
- Tianyi Chen
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Simon Gregory
- Department of Neurology, Duke University, Durham, North Carolina, USA
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, North Carolina, USA
| | - Anna Mae Diehl
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine and
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34
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Mu T, Xu L, Zhong Y, Liu X, Zhao Z, Huang C, Lan X, Lufei C, Zhou Y, Su Y, Xu L, Jiang M, Zhou H, Lin X, Wu L, Peng S, Liu S, Brix S, Dean M, Dunn NR, Zaret KS, Fu XY, Hou Y. Embryonic liver developmental trajectory revealed by single-cell RNA sequencing in the Foxa2 eGFP mouse. Commun Biol 2020; 3:642. [PMID: 33144666 PMCID: PMC7642341 DOI: 10.1038/s42003-020-01364-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 10/08/2020] [Indexed: 02/05/2023] Open
Abstract
The liver and gallbladder are among the most important internal organs derived from the endoderm, yet the development of the liver and gallbladder in the early embryonic stages is not fully understood. Using a transgenic Foxa2eGFP reporter mouse line, we performed single-cell full-length mRNA sequencing on endodermal and hepatic cells isolated from ten embryonic stages, ranging from E7.5 to E15.5. We identified the embryonic liver developmental trajectory from gut endoderm to hepatoblasts and characterized the transcriptome of the hepatic lineage. More importantly, we identified liver primordium as the nascent hepatic progenitors with both gut and liver features and documented dynamic gene expression during the epithelial-hepatic transition (EHT) at the stage of liver specification during E9.5–11.5. We found six groups of genes switched on or off in the EHT process, including diverse transcripitional regulators that had not been previously known to be expressed during EHT. Moreover, we identified and revealed transcriptional profiling of gallbladder primordium at E9.5. The present data provides a high-resolution resource and critical insights for understanding the liver and gallbladder development. The authors report a single cell-resolution gene expression atlas for the developing mouse liver and gallbladder using a transgenic Foxa2eGFP mouse line. By tracing the development of cells from gut endoderm to hepatoblasts they identify key transcriptional changes during liver specification.
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Affiliation(s)
- Tianhao Mu
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, 119615, Singapore.,Laboratory of Human Diseases and Immunotherapies, West China Hospital, Sichuan University, 610041, Chengdu, China.,Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, China.,GenEros Biopharma, 310018, Hangzhou, China
| | - Liqin Xu
- BGI-Shenzhen, 518033, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, 518120, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Soltofts Plads, 2800, Kongens Lyngby, Denmark
| | - Yu Zhong
- BGI-Shenzhen, 518033, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, 518120, Shenzhen, China.,School of Biology and Biological Engineering, South China University of Technology, 510006, Guangzhou, China
| | - Xinyu Liu
- GenEros Biopharma, 310018, Hangzhou, China.,Cancer Science Institute of Singapore, YLL School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Zhikun Zhao
- BGI-Shenzhen, 518033, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, 518120, Shenzhen, China
| | - Chaoben Huang
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xiaofeng Lan
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Chengchen Lufei
- GenEros Biopharma, 310018, Hangzhou, China.,Cancer Science Institute of Singapore, YLL School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Yi Zhou
- GenEros Biopharma, 310018, Hangzhou, China.,Cancer Science Institute of Singapore, YLL School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Yixun Su
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, 119615, Singapore.,Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Luang Xu
- Cancer Science Institute of Singapore, YLL School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Miaomiao Jiang
- BGI-Shenzhen, 518033, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, 518120, Shenzhen, China
| | - Hongpo Zhou
- BGI-Shenzhen, 518033, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, 518120, Shenzhen, China
| | - Xinxin Lin
- BGI-Shenzhen, 518033, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, 518120, Shenzhen, China
| | - Liang Wu
- BGI-Shenzhen, 518033, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, 518120, Shenzhen, China
| | - Siqi Peng
- BGI-Shenzhen, 518033, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, 518120, Shenzhen, China
| | - Shiping Liu
- BGI-Shenzhen, 518033, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, 518120, Shenzhen, China
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Soltofts Plads, 2800, Kongens Lyngby, Denmark
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Gaithersburg, MD, USA
| | - Norris R Dunn
- Endodermal Development and Differentiation Laboratory, Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, University of Pennsylvania, Perelman School of Medicine, Smilow Center for Translation Research, Philadelphia, PA, 19104, USA
| | - Xin-Yuan Fu
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, 119615, Singapore. .,Laboratory of Human Diseases and Immunotherapies, West China Hospital, Sichuan University, 610041, Chengdu, China. .,Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, China. .,GenEros Biopharma, 310018, Hangzhou, China. .,Cancer Science Institute of Singapore, YLL School of Medicine, National University of Singapore, Singapore, 117599, Singapore. .,State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China.
| | - Yong Hou
- BGI-Shenzhen, 518033, Shenzhen, China. .,China National GeneBank, BGI-Shenzhen, 518120, Shenzhen, China.
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35
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Buschur KL, Chikina M, Benos PV. Causal network perturbations for instance-specific analysis of single cell and disease samples. Bioinformatics 2020; 36:2515-2521. [PMID: 31873725 PMCID: PMC7178399 DOI: 10.1093/bioinformatics/btz949] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/22/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
MOTIVATION Complex diseases involve perturbation in multiple pathways and a major challenge in clinical genomics is characterizing pathway perturbations in individual samples. This can lead to patient-specific identification of the underlying mechanism of disease thereby improving diagnosis and personalizing treatment. Existing methods rely on external databases to quantify pathway activity scores. This ignores the data dependencies and that pathways are incomplete or condition-specific. RESULTS ssNPA is a new approach for subtyping samples based on deregulation of their gene networks. ssNPA learns a causal graph directly from control data. Sample-specific network neighborhood deregulation is quantified via the error incurred in predicting the expression of each gene from its Markov blanket. We evaluate the performance of ssNPA on liver development single-cell RNA-seq data, where the correct cell timing is recovered; and two TCGA datasets, where ssNPA patient clusters have significant survival differences. In all analyses ssNPA consistently outperforms alternative methods, highlighting the advantage of network-based approaches. AVAILABILITY AND IMPLEMENTATION http://www.benoslab.pitt.edu/Software/ssnpa/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kristina L Buschur
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.,Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA 15260, USA
| | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
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36
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Nault R, Fader KA, Bhattacharya S, Zacharewski TR. Single-Nuclei RNA Sequencing Assessment of the Hepatic Effects of 2,3,7,8-Tetrachlorodibenzo-p-dioxin. Cell Mol Gastroenterol Hepatol 2020; 11:147-159. [PMID: 32791302 PMCID: PMC7674514 DOI: 10.1016/j.jcmgh.2020.07.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIMS Characterization of cell specific transcriptional responses to hepatotoxicants is lost in the averages of bulk RNA-sequencing (RNA-seq). Single-cell/nuclei RNA-seq technologies enable the transcriptomes of individual cell (sub)types to be assessed within the context of in vivo models. METHODS Single-nuclei RNA-sequencing (snSeq) of frozen liver samples from male C57BL/6 mice gavaged with sesame oil vehicle or 30 μg/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) every 4 days for 28 days was used to demonstrate the application of snSeq for the evaluation of xenobiotics. RESULTS A total of 19,907 genes were detected across 16,015 nuclei from control and TCDD-treated livers. Eleven cell (sub)types reflected the expected cell diversity of the liver including distinct pericentral, midzonal, and periportal hepatocyte subpopulations. TCDD altered relative proportions of cell types and elicited cell-specific gene expression profiles. For example, macrophages increased from 0.5% to 24.7%, while neutrophils were only present in treated samples, consistent with histological evaluation. The number of differentially expressed genes (DEGs) in each cell type ranged from 122 (cholangiocytes) to 7625 (midcentral hepatocytes), and loosely correlated with the basal expression level of Ahr, the canonical mediator of TCDD and related compounds. In addition to the expected functions within each cell (sub)types, RAS signaling and related pathways were specifically enriched in nonparenchymal cells while metabolic process enrichment occurred primarily in hepatocytes. snSeq also identified the expansion of a Kupffer cell subtype highly expressing Gpnmb, as reported in a dietary NASH model. CONCLUSIONS We show that snSeq of frozen liver samples can be used to assess cell-specific transcriptional changes and population shifts in models of hepatotoxicity when examining freshly isolated cells is not feasible.
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Affiliation(s)
- Rance Nault
- Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Kelly A Fader
- Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Sudin Bhattacharya
- Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan; Department of Biomedical Engineering, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan; Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Tim R Zacharewski
- Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan.
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37
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Ghazanfar S, Lin Y, Su X, Lin DM, Patrick E, Han ZG, Marioni JC, Yang JYH. Investigating higher-order interactions in single-cell data with scHOT. Nat Methods 2020; 17:799-806. [PMID: 32661426 PMCID: PMC7610653 DOI: 10.1038/s41592-020-0885-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
Single-cell genomics has transformed our ability to examine cell fate choice. Examining cells along a computationally ordered 'pseudotime' offers the potential to unpick subtle changes in variability and covariation among key genes. We describe an approach, scHOT-single-cell higher-order testing-which provides a flexible and statistically robust framework for identifying changes in higher-order interactions among genes. scHOT can be applied for cells along a continuous trajectory or across space and accommodates various higher-order measurements including variability or correlation. We demonstrate the use of scHOT by studying coordinated changes in higher-order interactions during embryonic development of the mouse liver. Additionally, scHOT identifies subtle changes in gene-gene correlations across space using spatially resolved transcriptomics data from the mouse olfactory bulb. scHOT meaningfully adds to first-order differential expression testing and provides a framework for interrogating higher-order interactions using single-cell data.
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Affiliation(s)
- Shila Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Yingxin Lin
- School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Xianbin Su
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - David Ming Lin
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Ellis Patrick
- School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
| | - Jean Yee Hwa Yang
- School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales, Australia.
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.
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38
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Wang X, Yang L, Wang YC, Xu ZR, Feng Y, Zhang J, Wang Y, Xu CR. Comparative analysis of cell lineage differentiation during hepatogenesis in humans and mice at the single-cell transcriptome level. Cell Res 2020; 30:1109-1126. [PMID: 32690901 PMCID: PMC7784864 DOI: 10.1038/s41422-020-0378-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
During embryogenesis, the liver is the site of hepatogenesis and hematopoiesis and contains many cell lineages derived from the endoderm and mesoderm. However, the characteristics and developmental programs of many of these cell lineages remain unclear, especially in humans. Here, we performed single-cell RNA sequencing of whole human and mouse fetal livers throughout development. We identified four cell lineage families of endoderm-derived, erythroid, non-erythroid hematopoietic, and mesoderm-derived non-hematopoietic cells, and defined the developmental pathways of the major cell lineage families. In both humans and mice, we identified novel markers of hepatic lineages and an ID3+ subpopulation of hepatoblasts as well as verified that hepatoblast differentiation follows the “default-directed” model. Additionally, we found that human but not mouse fetal hepatocytes display heterogeneity associated with expression of metabolism-related genes. We described the developmental process of erythroid progenitor cells during human and mouse hematopoiesis. Moreover, despite the general conservation of cell differentiation programs between species, we observed different cell lineage compositions during hematopoiesis in the human and mouse fetal livers. Taken together, these results reveal the dynamic cell landscape of fetal liver development and illustrate the similarities and differences in liver development between species, providing an extensive resource for inducing various liver cell lineages in vitro.
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Affiliation(s)
- Xin Wang
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Department of Human Anatomy, Histology, and Embryology, and School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, 100871, China
| | - Li Yang
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Department of Human Anatomy, Histology, and Embryology, and School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, 100871, China
| | - Yan-Chun Wang
- Haidian Maternal & Child Health Hospital, Beijing, 100080, China
| | - Zi-Ran Xu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Department of Human Anatomy, Histology, and Embryology, and School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, 100871, China
| | - Ye Feng
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Department of Human Anatomy, Histology, and Embryology, and School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, 100871, China
| | - Jing Zhang
- Haidian Maternal & Child Health Hospital, Beijing, 100080, China
| | - Yi Wang
- Haidian Maternal & Child Health Hospital, Beijing, 100080, China
| | - Cheng-Ran Xu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Department of Human Anatomy, Histology, and Embryology, and School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, 100871, China.
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39
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Yang L, Lewis K. Erythroid Lineage Cells in the Liver: Novel Immune Regulators and Beyond. J Clin Transl Hepatol 2020; 8:177-183. [PMID: 32832398 PMCID: PMC7438359 DOI: 10.14218/jcth.2019.00031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/19/2019] [Accepted: 02/25/2020] [Indexed: 12/04/2022] Open
Abstract
The lineage of the erythroid cell has been revisited in recent years. Instead of being classified as simply inert oxygen carriers, emerging evidence has shown that they are a tightly regulated in immune potent population with potential developmental plasticity for lineage crossing. Erythroid cells have been reported to exert immune regulatory function through secreted cytokines, or cell-cell contact, depending on the conditions of the microenvironment and disease models. In this review, we explain the natural history of erythroid cells in the liver through a developmental lens, as it offers perspectives into newly recognized roles of this lineage in liver biology. Here, we review the known immune roles of erythroid cells and discuss the mechanisms in the context of disease models and stages. Then, we explore the capability of erythroid lineage as a cell source for regenerative medicine. We propose that the versatile lineage of erythroid cells provides an underappreciated and potentially promising area for basic and translational research in the field of liver disease.
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Affiliation(s)
- Li Yang
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Correspondence to: Li Yang, Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue; Cincinnati, OH 45229-3030, USA. Tel: +1-513-636-3008, E-mail:
| | - Kyle Lewis
- Division of Gastroenterology, Hepatology & Nutrition Developmental Biology Center for Stem Cell and Organoid Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
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40
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Kamies R, Martinez-Jimenez CP. Advances of single-cell genomics and epigenomics in human disease: where are we now? Mamm Genome 2020; 31:170-180. [PMID: 32270277 PMCID: PMC7368869 DOI: 10.1007/s00335-020-09834-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/28/2020] [Indexed: 02/07/2023]
Abstract
Cellular heterogeneity is revolutionizing the way to study, monitor and dissect complex diseases. This has been possible with the technological and computational advances associated to single-cell genomics and epigenomics. Deeper understanding of cell-to-cell variation and its impact on tissue function will open new avenues for early disease detection, accurate diagnosis and personalized treatments, all together leading to the next generation of health care. This review focuses on the recent discoveries that single-cell genomics and epigenomics have facilitated in the context of human health. It highlights the potential of single-cell omics to further advance the development of personalized treatments and precision medicine in cancer, diabetes and chronic age-related diseases. The promise of single-cell technologies to generate new insights about the differences in function between individual cells is just emerging, and it is paving the way for identifying biomarkers and novel therapeutic targets to tackle age, complex diseases and understand the effect of life style interventions and environmental factors.
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Affiliation(s)
- Rizqah Kamies
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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41
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Zhu D, Rostami MR, Zuo WL, Leopold PL, Crystal RG. Single-Cell Transcriptome Analysis of Mouse Liver Cell-Specific Tropism and Transcriptional Dysregulation Following Intravenous Administration of AAVrh.10 Vectors. Hum Gene Ther 2020; 31:590-604. [PMID: 32143547 PMCID: PMC7232697 DOI: 10.1089/hum.2019.366] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/16/2020] [Indexed: 01/20/2023] Open
Abstract
Capitalizing on liver tropism of adeno-associated viral (AAV) vectors, intravenous vector administration is commonly used to genetically modify hepatocytes, a strategy currently in clinical trials for a number of liver-based hereditary disorders. Although hepatocytes are known to exhibit extensive phenotypic heterogeneity influenced by liver zonation and dietary cycle, there is little data available for the tropism capacity, as well as the potential transcriptional dysregulation, of AAV vectors for specific liver cell types. To assess these issues, we employed single-cell RNA sequencing of the mouse liver after intravenous administration of the liver tropic AAVrh.10 vector to characterize cell-specific AAV-mediated transgene expression and transcriptome dysregulation. Wild-type 8-week-old male C57Bl/6 mice under normal feed cycle were randomly divided into three groups and intravenously administered phosphate-buffered saline (PBS), AAVrh.10Null (no transgene), or AAVrh.10mCherry (marker gene). Overall, a total of 46,500 liver cells were sequenced. The single-cell transcriptomic profiles were grouped into three separate clusters of hepatocytes (Ttr-enriched "Hep1," Tat-enriched "Hep2," and Alb-enriched "Hep3") and multiple other cell types. The hepatocyte diversity was driven by glucose and lipid homeostasis signaling. Assessment of the transgene expression demonstrated that AAVrh.10 is primarily Hep1-tropic, with a 10-gene signature positively correlated with AAVrh.10-mediated transgene expression. The transgene expression was less in Hep2 and Hep3 cells with a high receptor tyrosine kinase phenotype. Importantly, AAVrh.10 vector interactions with the liver markedly altered the transcriptional patterns of all cell types, with modified genes enriched in pathways of complement and coagulation cascade, cytochrome P450, peroxisome, antigen processing and presentation, and endoplasmic reticulum protein processing. These observations provide insights into the liver cell-specific consequences of AAV-mediated liver gene transfer, far beyond the well-known organ-specific expression of the vector-delivered transgene.
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Affiliation(s)
- Detu Zhu
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Mahboubeh R. Rostami
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Wu-lin Zuo
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Philip L. Leopold
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA
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42
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Su X, Long Q, Bo J, Shi Y, Zhao LN, Lin Y, Luo Q, Ghazanfar S, Zhang C, Liu Q, Wang L, He K, He J, Cui X, Yang JYH, Han ZG, Yang G, Sha JJ. Mutational and transcriptomic landscapes of a rare human prostate basal cell carcinoma. Prostate 2020; 80:508-517. [PMID: 32119131 DOI: 10.1002/pros.23965] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/11/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND As a rare subtype of prostate carcinoma, basal cell carcinoma (BCC) has not been studied extensively and thus lacks systematic molecular characterization. METHODS Here, we applied single-cell genomic amplification and RNA-Seq to a specimen of human prostate BCC (CK34βE12+ /P63+ /PAP- /PSA- ). The mutational landscape was obtained via whole exome sequencing of the amplification mixture of 49 single cells, and the transcriptomes of 69 single cells were also obtained. RESULTS The five putative driver genes mutated in BCC are CASC5, NUTM1, PTPRC, KMT2C, and TBX3, and the top three nucleotide substitutions are C>T, T>C, and C>A, similar to common prostate cancer. The distribution of the variant allele frequency values indicated that these single cells are from the same tumor clone. The 69 single cells were clustered into tumor, stromal, and immune cells based on their global transcriptomic profiles. The tumor cells specifically express basal cell markers like KRT5, KRT14, and KRT23 and epithelial markers EPCAM, CDH1, and CD24. The transcription factor covariance network analysis showed that the BCC tumor cells have distinct regulatory networks. By comparison with current prostate cancer datasets, we found that some of the bulk samples exhibit basal cell signatures. Interestingly, at single-cell resolution the gene expression patterns of prostate BCC tumor cells show uniqueness compared with that of common prostate cancer-derived circulating tumor cells. CONCLUSIONS This study, for the first time, discloses the comprehensive mutational and transcriptomic landscapes of prostate BCC, which lays a foundation for the understanding of its tumorigenesis mechanism and provides new insights into prostate cancers in general.
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Affiliation(s)
- Xianbin Su
- Department of Urology and Key Laboratory of Systems Biomedicine (Ministry of Education), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qi Long
- Key Laboratory for Regenerative Medicine (Ministry of Education), School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Juanjie Bo
- Department of Urology and Key Laboratory of Systems Biomedicine (Ministry of Education), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Li-Nan Zhao
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yingxin Lin
- Department of Statistics, Charles Perkins Center and School of Mathematics and Statistics, The University of Sydney, Sydney, Australia
| | - Qing Luo
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shila Ghazanfar
- Department of Statistics, Charles Perkins Center and School of Mathematics and Statistics, The University of Sydney, Sydney, Australia
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Chao Zhang
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Qiang Liu
- Department of Pathology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kunyan He
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian He
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaofang Cui
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jean Y H Yang
- Department of Statistics, Charles Perkins Center and School of Mathematics and Statistics, The University of Sydney, Sydney, Australia
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guoliang Yang
- Department of Urology and Key Laboratory of Systems Biomedicine (Ministry of Education), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian-Jun Sha
- Department of Urology and Key Laboratory of Systems Biomedicine (Ministry of Education), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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43
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Gong T, Zhang C, Ni X, Li X, Li J, Liu M, Zhan D, Xia X, Song L, Zhou Q, Ding C, Qin J, Wang Y. A time-resolved multi-omic atlas of the developing mouse liver. Genome Res 2020; 30:263-275. [PMID: 32051188 PMCID: PMC7050524 DOI: 10.1101/gr.253328.119] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 01/17/2020] [Indexed: 12/13/2022]
Abstract
Liver organogenesis and development are composed of a series of complex, well-orchestrated events. Identifying key factors and pathways governing liver development will help elucidate the physiological and pathological processes including those of cancer. We conducted multidimensional omics measurements including protein, mRNA, and transcription factor (TF) DNA-binding activity for mouse liver tissues collected from embryonic day 12.5 (E12.5) to postnatal week 8 (W8), encompassing major developmental stages. These data sets reveal dynamic changes of core liver functions and canonical signaling pathways governing development at both mRNA and protein levels. The TF DNA-binding activity data set highlights the importance of TF activity in early embryonic development. A comparison between mouse liver development and human hepatocellular carcinoma (HCC) proteomic profiles reveal that more aggressive tumors are characterized with the activation of early embryonic development pathways, whereas less aggressive ones maintain liver function-related pathways that are elevated in the mature liver. This work offers a panoramic view of mouse liver development and provides a rich resource to explore in-depth functional characterization.
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Affiliation(s)
- Tongqing Gong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Chunchao Zhang
- Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xiaotian Ni
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Institute of Lifeomics, Beijing 102206, China.,Department of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xianju Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Jin'e Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Dongdong Zhan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Institute of Lifeomics, Beijing 102206, China.,Department of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xia Xia
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Quan Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Institute of Lifeomics, Beijing 102206, China.,State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Institute of Lifeomics, Beijing 102206, China.,Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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44
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Cebola I. Liver gene regulatory networks: Contributing factors to nonalcoholic fatty liver disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1480. [PMID: 32020788 DOI: 10.1002/wsbm.1480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 12/17/2022]
Abstract
Metabolic diseases such as nonalcoholic fatty liver disease (NAFLD) result from complex interactions between intrinsic and extrinsic factors, including genetics and exposure to obesogenic environments. These risk factors converge in aberrant gene expression patterns in the liver, which are underlined by altered cis-regulatory networks. In homeostasis and in disease states, liver cis-regulatory networks are established by coordinated action of liver-enriched transcription factors (TFs), which define enhancer landscapes, activating broad gene programs with spatiotemporal resolution. Recent advances in DNA sequencing have dramatically expanded our ability to map active transcripts, enhancers and TF cistromes, and to define the 3D chromatin topology that contains these elements. Deployment of these technologies has allowed investigation of the molecular processes that regulate liver development and metabolic homeostasis. Moreover, genomic studies of NAFLD patients and NAFLD models have demonstrated that the liver undergoes pervasive regulatory rewiring in NAFLD, which is reflected by aberrant gene expression profiles. We have therefore achieved an unprecedented level of detail in the understanding of liver cis-regulatory networks, particularly in physiological conditions. Future studies should aim to map active regulatory elements with added levels of resolution, addressing how the chromatin landscapes of different cell lineages contribute to and are altered in NAFLD and NAFLD-associated metabolic states. Such efforts would provide additional clues into the molecular factors that trigger this disease. This article is categorized under: Biological Mechanisms > Metabolism Biological Mechanisms > Regulatory Biology Laboratory Methods and Technologies > Genetic/Genomic Methods.
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Affiliation(s)
- Inês Cebola
- Department of Metabolism, Digestion and Reproduction, Section of Genetics and Genomics, Imperial College London, London, UK
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45
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Kim T, Lo K, Geddes TA, Kim HJ, Yang JYH, Yang P. scReClassify: post hoc cell type classification of single-cell rNA-seq data. BMC Genomics 2019; 20:913. [PMID: 31874628 PMCID: PMC6929456 DOI: 10.1186/s12864-019-6305-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background Single-cell RNA-sequencing (scRNA-seq) is a fast emerging technology allowing global transcriptome profiling on the single cell level. Cell type identification from scRNA-seq data is a critical task in a variety of research such as developmental biology, cell reprogramming, and cancers. Typically, cell type identification relies on human inspection using a combination of prior biological knowledge (e.g. marker genes and morphology) and computational techniques (e.g. PCA and clustering). Due to the incompleteness of our current knowledge and the subjectivity involved in this process, a small amount of cells may be subject to mislabelling. Results Here, we propose a semi-supervised learning framework, named scReClassify, for ‘post hoc’ cell type identification from scRNA-seq datasets. Starting from an initial cell type annotation with potentially mislabelled cells, scReClassify first performs dimension reduction using PCA and next applies a semi-supervised learning method to learn and subsequently reclassify cells that are likely mislabelled initially to the most probable cell types. By using both simulated and real-world experimental datasets that profiled various tissues and biological systems, we demonstrate that scReClassify is able to accurately identify and reclassify misclassified cells to their correct cell types. Conclusions scReClassify can be used for scRNA-seq data as a post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure. It is implemented as an R package and is freely available from https://github.com/SydneyBioX/scReClassify
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Affiliation(s)
- Taiyun Kim
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, 2006, NSW, Australia.,Charles Perkins Centre, The University of Sydney, 2006, NSW, Australia
| | - Kitty Lo
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, 2006, NSW, Australia.,Charles Perkins Centre, The University of Sydney, 2006, NSW, Australia
| | - Thomas A Geddes
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, 2006, NSW, Australia.,Charles Perkins Centre, The University of Sydney, 2006, NSW, Australia.,School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 2006, NSW, Australia
| | - Hani Jieun Kim
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, 2006, NSW, Australia.,Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, 2145, NSW, Australia.,Charles Perkins Centre, The University of Sydney, 2006, NSW, Australia
| | - Jean Yee Hwa Yang
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, 2006, NSW, Australia.,Charles Perkins Centre, The University of Sydney, 2006, NSW, Australia
| | - Pengyi Yang
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, 2006, NSW, Australia. .,Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, 2145, NSW, Australia. .,Charles Perkins Centre, The University of Sydney, 2006, NSW, Australia.
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46
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Zeng T, Dai H. Single-Cell RNA Sequencing-Based Computational Analysis to Describe Disease Heterogeneity. Front Genet 2019; 10:629. [PMID: 31354786 PMCID: PMC6640157 DOI: 10.3389/fgene.2019.00629] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/17/2019] [Indexed: 12/25/2022] Open
Abstract
The trillions of cells in the human body can be viewed as elementary but essential biological units that achieve different body states, but the low resolution of previous cell isolation and measurement approaches limits our understanding of the cell-specific molecular profiles. The recent establishment and rapid growth of single-cell sequencing technology has facilitated the identification of molecular profiles of heterogeneous cells, especially on the transcription level of single cells [single-cell RNA sequencing (scRNA-seq)]. As a novel method, the robustness of scRNA-seq under changing conditions will determine its practical potential in major research programs and clinical applications. In this review, we first briefly presented the scRNA-seq-related methods from the point of view of experiments and computation. Then, we compared several state-of-the-art scRNA-seq analysis frameworks mainly by analyzing their performance robustness on independent scRNA-seq datasets for the same complex disease. Finally, we elaborated on our hypothesis on consensus scRNA-seq analysis and summarized the potential indicative and predictive roles of individual cells in understanding disease heterogeneity by single-cell technologies.
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Affiliation(s)
- Tao Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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47
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Prior N, Hindley CJ, Rost F, Meléndez E, Lau WWY, Göttgens B, Rulands S, Simons BD, Huch M. Lgr5 + stem and progenitor cells reside at the apex of a heterogeneous embryonic hepatoblast pool. Development 2019; 146:dev.174557. [PMID: 31142540 PMCID: PMC6602348 DOI: 10.1242/dev.174557] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/15/2019] [Indexed: 12/12/2022]
Abstract
During mouse embryogenesis, progenitors within the liver known as hepatoblasts give rise to adult hepatocytes and cholangiocytes. Hepatoblasts, which are specified at E8.5-E9.0, have been regarded as a homogeneous progenitor population that initiate differentiation from E13.5. Recently, scRNA-seq analysis has identified sub-populations of transcriptionally distinct hepatoblasts at E11.5. Here, we show that hepatoblasts are not only transcriptionally but also functionally heterogeneous, and that a subpopulation of E9.5-E10.0 hepatoblasts exhibit a previously unidentified early commitment to cholangiocyte fate. Importantly, we also identify a subpopulation constituting 2% of E9.5-E10.0 hepatoblasts that express the adult stem cell marker Lgr5, and generate both hepatocyte and cholangiocyte progeny that persist for the lifespan of the mouse. Combining lineage tracing and scRNA-seq, we show that Lgr5 marks E9.5-E10.0 bipotent liver progenitors residing at the apex of a hepatoblast hierarchy. Furthermore, isolated Lgr5+ hepatoblasts can be clonally expanded in vitro into embryonic liver organoids, which can commit to either hepatocyte or cholangiocyte fates. Our study demonstrates functional heterogeneity within E9.5 hepatoblasts and identifies Lgr5 as a marker for a subpopulation of bipotent liver progenitors.
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Affiliation(s)
- Nicole Prior
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Christopher J Hindley
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,The Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thompson Avenue, Cambridge, CB3 0HE, UK
| | - Fabian Rost
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany
| | - Elena Meléndez
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Winnie W Y Lau
- Department of Haematology and Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Berthold Göttgens
- Department of Haematology and Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Steffen Rulands
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,The Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thompson Avenue, Cambridge, CB3 0HE, UK.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauer Strasse 108, 01307 Dresden, Germany
| | - Benjamin D Simons
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,The Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thompson Avenue, Cambridge, CB3 0HE, UK.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QR, UK
| | - Meritxell Huch
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK .,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QR, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
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48
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scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets. Proc Natl Acad Sci U S A 2019; 116:9775-9784. [PMID: 31028141 DOI: 10.1073/pnas.1820006116] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Concerted examination of multiple collections of single-cell RNA sequencing (RNA-seq) data promises further biological insights that cannot be uncovered with individual datasets. Here we present scMerge, an algorithm that integrates multiple single-cell RNA-seq datasets using factor analysis of stably expressed genes and pseudoreplicates across datasets. Using a large collection of public datasets, we benchmark scMerge against published methods and demonstrate that it consistently provides improved cell type separation by removing unwanted factors; scMerge can also enhance biological discovery through robust data integration, which we show through the inference of development trajectory in a liver dataset collection.
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49
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Su X, Shi Y, Li R, Lu ZN, Zou X, Wu JX, Han ZG. Application of qPCR assays based on haloacids transporter gene dehp2 for discrimination of Burkholderia and Paraburkholderia. BMC Microbiol 2019; 19:36. [PMID: 30744555 PMCID: PMC6371555 DOI: 10.1186/s12866-019-1411-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/31/2019] [Indexed: 12/05/2022] Open
Abstract
Background A major facilitator superfamily transporter Dehp2 was recently shown to be playing an important role in transport and biodegradation of haloacids in Paraburkholderia caribensis MBA4, and Dehp2 is phylogenetically conserved in Burkholderia sensu lato. Results We designed both Burkholderia sensu stricto-specific and Paraburkholderia-specific qPCR assays based on dehp2 and 16S rRNA, and validated the qPCR assays in 12 bacterial strains. The qPCR assays could detect single species of Burkholderia sensu stricto or Paraburkholderia with high sensitivity and discriminate them in mixtures with high specificity over a wide dynamic range of relative concentrations. At relatively lower cost compared with sequencing-based approach, the qPCR assays will facilitate discrimination of Burkholderia sensu stricto and Paraburkholderia in a large number of samples. Conclusions For the first time, we report the utilization of a haloacids transporter gene for discriminative purpose in Burkholderia sensu lato. This enables not only quick decision on proper handling of putative pathogenic samples in Burkholderia sensu stricto group but also future exploitation of relevant species in Paraburkholderia group for haloacids biodegradation purposes. Electronic supplementary material The online version of this article (10.1186/s12866-019-1411-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianbin Su
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ruihong Li
- Shanghai Quality Safety Centre of Agricultural Products, Shanghai, China
| | - Zhao-Ning Lu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiao-Xiang Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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50
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Lafzi A, Moutinho C, Picelli S, Heyn H. Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies. Nat Protoc 2018; 13:2742-2757. [DOI: 10.1038/s41596-018-0073-y] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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