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Vanheer L, Fantuzzi F, To SK, Schiavo A, Van Haele M, Ostyn T, Haesen T, Yi X, Janiszewski A, Chappell J, Rihoux A, Sawatani T, Roskams T, Pattou F, Kerr-Conte J, Cnop M, Pasque V. Inferring regulators of cell identity in the human adult pancreas. NAR Genom Bioinform 2023; 5:lqad068. [PMID: 37435358 PMCID: PMC10331937 DOI: 10.1093/nargab/lqad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/17/2023] [Accepted: 06/28/2023] [Indexed: 07/13/2023] Open
Abstract
Cellular identity during development is under the control of transcription factors that form gene regulatory networks. However, the transcription factors and gene regulatory networks underlying cellular identity in the human adult pancreas remain largely unexplored. Here, we integrate multiple single-cell RNA-sequencing datasets of the human adult pancreas, totaling 7393 cells, and comprehensively reconstruct gene regulatory networks. We show that a network of 142 transcription factors forms distinct regulatory modules that characterize pancreatic cell types. We present evidence that our approach identifies regulators of cell identity and cell states in the human adult pancreas. We predict that HEYL, BHLHE41 and JUND are active in acinar, beta and alpha cells, respectively, and show that these proteins are present in the human adult pancreas as well as in human induced pluripotent stem cell (hiPSC)-derived islet cells. Using single-cell transcriptomics, we found that JUND represses beta cell genes in hiPSC-alpha cells. BHLHE41 depletion induced apoptosis in primary pancreatic islets. The comprehensive gene regulatory network atlas can be explored interactively online. We anticipate our analysis to be the starting point for a more sophisticated dissection of how transcription factors regulate cell identity and cell states in the human adult pancreas.
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Affiliation(s)
- Lotte Vanheer
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Federica Fantuzzi
- ULB Center for Diabetes Research; Université Libre de Bruxelles; Route de Lennik 808, B-1070 Brussels, Belgium
| | - San Kit To
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Andrea Schiavo
- ULB Center for Diabetes Research; Université Libre de Bruxelles; Route de Lennik 808, B-1070 Brussels, Belgium
| | - Matthias Van Haele
- Department of Imaging and Pathology; Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven; Herestraat 49, B-3000 Leuven, Belgium
| | - Tessa Ostyn
- Department of Imaging and Pathology; Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven; Herestraat 49, B-3000 Leuven, Belgium
| | - Tine Haesen
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Xiaoyan Yi
- ULB Center for Diabetes Research; Université Libre de Bruxelles; Route de Lennik 808, B-1070 Brussels, Belgium
| | - Adrian Janiszewski
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Joel Chappell
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Adrien Rihoux
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Toshiaki Sawatani
- ULB Center for Diabetes Research; Université Libre de Bruxelles; Route de Lennik 808, B-1070 Brussels, Belgium
| | - Tania Roskams
- Department of Imaging and Pathology; Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven; Herestraat 49, B-3000 Leuven, Belgium
| | - Francois Pattou
- University of Lille, Inserm, CHU Lille, Institute Pasteur Lille, U1190-EGID, F-59000 Lille, France
- European Genomic Institute for Diabetes, F-59000 Lille, France
- University of Lille, F-59000 Lille, France
| | - Julie Kerr-Conte
- University of Lille, Inserm, CHU Lille, Institute Pasteur Lille, U1190-EGID, F-59000 Lille, France
- European Genomic Institute for Diabetes, F-59000 Lille, France
- University of Lille, F-59000 Lille, France
| | - Miriam Cnop
- ULB Center for Diabetes Research; Université Libre de Bruxelles; Route de Lennik 808, B-1070 Brussels, Belgium
- Division of Endocrinology; Erasmus Hospital, Université Libre de Bruxelles; Route de Lennik 808, B-1070 Brussels, Belgium
| | - Vincent Pasque
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
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Dynamics of hepatocyte-cholangiocyte cell-fate decisions during liver development and regeneration. iScience 2022; 25:104955. [PMID: 36060070 PMCID: PMC9437857 DOI: 10.1016/j.isci.2022.104955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/17/2022] [Accepted: 08/12/2022] [Indexed: 11/25/2022] Open
Abstract
The immense regenerative potential of the liver is attributed to the ability of its two key cell types – hepatocytes and cholangiocytes – to trans-differentiate to one another either directly or through intermediate progenitor states. However, the dynamic features of decision-making between these cell-fates during liver development and regeneration remains elusive. Here, we identify a core gene regulatory network comprising c/EBPα, TGFBR2, and SOX9 which is multistable in nature, enabling three distinct cell states – hepatocytes, cholangiocytes, and liver progenitor cells (hepatoblasts/oval cells) – and stochastic switching among them. Predicted expression signature for these three states are validated through multiple bulk and single-cell transcriptomic datasets collected across developmental stages and injury-induced liver repair. This network can also explain the experimentally observed spatial organization of phenotypes in liver parenchyma and predict strategies for efficient cellular reprogramming. Our analysis elucidates how the emergent dynamics of underlying regulatory networks drive diverse cell-fate decisions in liver development and regeneration. Identified minimal regulatory network to model liver development and regeneration Changes in phenotypic landscapes by in-silico perturbations of regulatory networks Ability to explain physiological spatial patterning of liver cell types Decoded strategies for efficient reprogramming among liver cell phenotypes
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Complement C1q mediates the expansion of periportal hepatic progenitor cells in senescence-associated inflammatory liver. Proc Natl Acad Sci U S A 2020; 117:6717-6725. [PMID: 32139604 DOI: 10.1073/pnas.1918028117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Most hepatocellular carcinomas (HCCs) develop in patients with chronic hepatitis, which creates a microenvironment for the growth of hepatic progenitor cells (HPCs) at the periportal area and subsequent development of HCCs. We investigated the signal from the inflammatory liver for this pathogenic process in the hepatic conditional β-catenin knockout mouse model. Senescent β-catenin-depleted hepatocytes in aged mice create an inflammatory microenvironment that stimulates periportal HPC expansion but arrests differentiation, which predisposes mice to the development of liver tumors. The release of complement C1q from macrophages in the inflammatory niche was identified as the unorthodox signal that activated the β-catenin pathway in periportal HPCs and was responsible for their expansion and de-differentiation. C1q inhibitors blocked the β-catenin pathway in both the expanding HPCs and the liver tumors but spared its orthodox pathway in pericentral normal hepatocytes. This mechanism has been validated in human liver specimens from patients with chronic hepatitis. Taken together, these results demonstrate that C1q- mediated activation of β-catenin pathway in periportal HPCs is a previously unrecognized mechanism for replenishing hepatocytes in the inflammatory liver and, if unchecked, for promoting hepatocarcinogenesis. C1q may become a new target for blocking carcinogenesis in patients with chronic hepatitis.
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Lo Re O, Mazza T, Giallongo S, Sanna P, Rappa F, Vinh Luong T, Li Volti G, Drovakova A, Roskams T, Van Haele M, Tsochatzis E, Vinciguerra M. Loss of histone macroH2A1 in hepatocellular carcinoma cells promotes paracrine-mediated chemoresistance and CD4 +CD25 +FoxP3 + regulatory T cells activation. Am J Cancer Res 2020; 10:910-924. [PMID: 31903159 PMCID: PMC6929991 DOI: 10.7150/thno.35045] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 10/06/2019] [Indexed: 12/11/2022] Open
Abstract
Rationale: Loss of histone macroH2A1 induces appearance of cancer stem cells (CSCs)-like cells in hepatocellular carcinoma (HCC). How CSCs interact with the tumor microenvironment and the adaptive immune system is unclear. Methods: We screened aggressive human HCC for macroH2A1 and CD44 CSC marker expression. We also knocked down (KD) macroH2A1 in HCC cells, and performed integrated transcriptomic and secretomic analyses. Results: Human HCC showed low macroH2A1 and high CD44 expression compared to control tissues. MacroH2A1 KD CSC-like cells transferred paracrinally their chemoresistant properties to parental HCC cells. MacroH2A1 KD conditioned media transcriptionally reprogrammed parental HCC cells activated regulatory CD4+/CD25+/FoxP3+ T cells (Tregs). Conclusions: Loss of macroH2A1 in HCC cells drives cancer stem-cell propagation and evasion from immune surveillance.
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Meta-Analysis of Human and Mouse Biliary Epithelial Cell Gene Profiles. Cells 2019; 8:cells8101117. [PMID: 31547151 PMCID: PMC6829476 DOI: 10.3390/cells8101117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/03/2019] [Accepted: 09/18/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Chronic liver diseases are frequently accompanied with activation of biliary epithelial cells (BECs) that can differentiate into hepatocytes and cholangiocytes, providing an endogenous back-up system. Functional studies on BECs often rely on isolations of an BEC cell population from healthy and/or injured livers. However, a consensus on the characterization of these cells has not yet been reached. The aim of this study was to compare the publicly available transcriptome profiles of human and mouse BECs and to establish gene signatures that can identify quiescent and activated human and mouse BECs. METHODS We used publicly available transcriptome data sets of human and mouse BECs, compared their profiles and analyzed co-expressed genes and pathways. By merging both human and mouse BEC-enriched genes, we obtained a quiescent and activation gene signature and tested them on BEC-like cells and different liver diseases using gene set enrichment analysis. In addition, we identified several genes from both gene signatures to identify BECs in a scRNA sequencing data set. RESULTS Comparison of mouse BEC transcriptome data sets showed that the isolation method and array platform strongly influences their general profile, still most populations are highly enriched in most genes currently associated with BECs. Pathway analysis on human and mouse BECs revealed the KRAS signaling as a new potential pathway in BEC activation. We established a quiescent and activated BEC gene signature that can be used to identify BEC-like cells and detect BEC enrichment in alcoholic hepatitis, non-alcoholic steatohepatitis (NASH) and peribiliary sclerotic livers. Finally, we identified a gene set that can distinguish BECs from other liver cells in mouse and human scRNAseq data. CONCLUSIONS Through a meta-analysis of human and mouse BEC gene profiles we identified new potential pathways in BEC activation and created unique gene signatures for quiescent and activated BECs. These signatures and pathways will help in the further characterization of this progenitor cell type in mouse and human liver development and disease.
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Liu S, Zhou Z, Jia Y, Xue J, Liu Z, Cheng K, Cheng S, Liu S. Identification of portal vein tumor thrombus with an independent clonal origin in hepatocellular carcinoma via multi-omics data analysis. Cancer Biol Med 2019; 16:147-170. [PMID: 31119055 PMCID: PMC6528462 DOI: 10.20892/j.issn.2095-3941.2018.0184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Objective Multiple mechanisms underlying the development of portal vein tumor thrombus (PVTT) in hepatocellular carcinoma (HCC) have been reported recently. However, the origins of PVTT remain unknown. Increasing multi-omics data on PVTTs in HCCs have made it possible to investigate whether PVTTs originate from the corresponding primary tumors (Ts). Methods The clonal relationship between PVTTs and their corresponding primary Ts was investigated using datasets deposited in public databases. One DNA copy number variations dataset and three gene expression datasets were downloaded for the analyses. Clonality analysis was performed to investigate the clonal relationship between PVTTs and Ts from an individual patient. Differential gene expression analysis was applied to investigate the gene expression profiles of PVTTs and Ts. Results One out of 19 PVTTs had no clonal relationship with its corresponding T, whereas the others did. The PVTTs with independent clonal origin showed different gene expression and enrichment in biological processes from the primary Ts. Based on the unique gene expression profiles, a gene signature including 24 genes was used to identify pairs of PVTTs and primary Ts without any clonal relationship. Validation in three datasets showed that these types of pairs of PVTTs and Ts can be identified by the 24-gene signature. Conclusions Our findings show a direct evidence for PVTT origin and consolidate the heterogeneity of PVTTs observed in clinic. The results suggest that PVTT investigation at a molecular level is clinically necessary for diagnosis and treatment.
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Affiliation(s)
- Shupeng Liu
- Clinical Research Center, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Zaixin Zhou
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Yin Jia
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Jie Xue
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200433, China
| | - Zhiyong Liu
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Kai Cheng
- Clinical Research Center, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Shuqun Cheng
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200433, China
| | - Shanrong Liu
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
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