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Kumar N, Prakash PG, Wentland C, Kurian SM, Jethva G, Brinkmann V, Mollenkopf HJ, Krammer T, Toussaint C, Saliba AE, Biebl M, Jürgensen C, Wiedenmann B, Meyer TF, Gurumurthy RK, Chumduri C. Decoding spatiotemporal transcriptional dynamics and epithelial fibroblast crosstalk during gastroesophageal junction development through single cell analysis. Nat Commun 2024; 15:3064. [PMID: 38594232 PMCID: PMC11004180 DOI: 10.1038/s41467-024-47173-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 03/22/2024] [Indexed: 04/11/2024] Open
Abstract
The gastroesophageal squamocolumnar junction (GE-SCJ) is a critical tissue interface between the esophagus and stomach, with significant relevance in the pathophysiology of gastrointestinal diseases. Despite this, the molecular mechanisms underlying GE-SCJ development remain unclear. Using single-cell transcriptomics, organoids, and spatial analysis, we examine the cellular heterogeneity and spatiotemporal dynamics of GE-SCJ development from embryonic to adult mice. We identify distinct transcriptional states and signaling pathways in the epithelial and mesenchymal compartments of the esophagus and stomach during development. Fibroblast-epithelial interactions are mediated by various signaling pathways, including WNT, BMP, TGF-β, FGF, EGF, and PDGF. Our results suggest that fibroblasts predominantly send FGF and TGF-β signals to the epithelia, while epithelial cells mainly send PDGF and EGF signals to fibroblasts. We observe differences in the ligands and receptors involved in cell-cell communication between the esophagus and stomach. Our findings provide insights into the molecular mechanisms underlying GE-SCJ development and fibroblast-epithelial crosstalk involved, paving the way to elucidate mechanisms during adaptive metaplasia development and carcinogenesis.
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Affiliation(s)
- Naveen Kumar
- Laboratory of Infections, Carcinogenesis and Regeneration, Medical Biotechnology Section, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
- Department of Microbiology, University of Würzburg, Würzburg, Germany
| | | | | | | | - Gaurav Jethva
- Department of Microbiology, University of Würzburg, Würzburg, Germany
| | - Volker Brinkmann
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Hans-Joachim Mollenkopf
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Tobias Krammer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Christophe Toussaint
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Institute of Molecular Infection Biology (IMIB), Würzburg, Germany
| | - Matthias Biebl
- Surgical Clinic Campus Charité Mitte, Charité University Medicine, Berlin, Germany
| | - Christian Jürgensen
- Department of Hepatology and Gastroenterology, Charité University Medicine, Berlin, Germany
| | - Bertram Wiedenmann
- Department of Hepatology and Gastroenterology, Charité University Medicine, Berlin, Germany
| | - Thomas F Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Rajendra Kumar Gurumurthy
- Department of Microbiology, University of Würzburg, Würzburg, Germany
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Cindrilla Chumduri
- Laboratory of Infections, Carcinogenesis and Regeneration, Medical Biotechnology Section, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark.
- Department of Microbiology, University of Würzburg, Würzburg, Germany.
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany.
- Department of Hepatology and Gastroenterology, Charité University Medicine, Berlin, Germany.
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Wei C, Zhang H, Fu M, Ye J, Yao B. Novel compound heterozygous variants in the CSPP1 gene causes Joubert syndrome: case report and literature review of the CSPP1 gene's pathogenic mechanism. Front Pediatr 2024; 12:1305754. [PMID: 38586154 PMCID: PMC10995352 DOI: 10.3389/fped.2024.1305754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 03/04/2024] [Indexed: 04/09/2024] Open
Abstract
Joubert syndrome (JS) is a rare autosomal recessive neurodevelopmental condition characterized by congenital mid-hindbrain abnormalities and a variety of clinical manifestations. This article describes a case of Joubert syndrome type 21 with microcephaly, seizures, developmental delay and language regression, caused by a CSPP1 gene variant and examines the contributing variables. This paper advances the understanding of JS by summarizing the literature and offering detection patterns for practitioners with clinical suspicions of JS.
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Affiliation(s)
| | | | | | - Jingping Ye
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Baozhen Yao
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
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Wu Z, Wang X, Liang H, Liu F, Li Y, Zhang H, Wang C, Wang Q. Identification of Signature Genes of Dilated Cardiomyopathy Using Integrated Bioinformatics Analysis. Int J Mol Sci 2023; 24:ijms24087339. [PMID: 37108502 PMCID: PMC10139023 DOI: 10.3390/ijms24087339] [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: 03/26/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Dilated cardiomyopathy (DCM) is characterized by left ventricular or biventricular enlargement with systolic dysfunction. To date, the underlying molecular mechanisms of dilated cardiomyopathy pathogenesis have not been fully elucidated, although some insights have been presented. In this study, we combined public database resources and a doxorubicin-induced DCM mouse model to explore the significant genes of DCM in full depth. We first retrieved six DCM-related microarray datasets from the GEO database using several keywords. Then we used the "LIMMA" (linear model for microarray data) R package to filter each microarray for differentially expressed genes (DEGs). Robust rank aggregation (RRA), an extremely robust rank aggregation method based on sequential statistics, was then used to integrate the results of the six microarray datasets to filter out the reliable differential genes. To further improve the reliability of our results, we established a doxorubicin-induced DCM model in C57BL/6N mice, using the "DESeq2" software package to identify DEGs in the sequencing data. We cross-validated the results of RRA analysis with those of animal experiments by taking intersections and identified three key differential genes (including BEX1, RGCC and VSIG4) associated with DCM as well as many important biological processes (extracellular matrix organisation, extracellular structural organisation, sulphur compound binding, and extracellular matrix structural components) and a signalling pathway (HIF-1 signalling pathway). In addition, we confirmed the significant effect of these three genes in DCM using binary logistic regression analysis. These findings will help us to better understand the pathogenesis of DCM and may be key targets for future clinical management.
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Affiliation(s)
- Zhimin Wu
- Department of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Xu Wang
- Department of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Hao Liang
- Department of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Fangfang Liu
- Department of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Yingxuan Li
- Department of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Huaxing Zhang
- Core Facilities and Centers, Hebei Medical University, Shijiazhuang 050017, China
| | - Chunying Wang
- Department of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Qiao Wang
- Department of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
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Biomolecular condensation involving the cytoskeleton. Brain Res Bull 2023; 194:105-117. [PMID: 36690162 DOI: 10.1016/j.brainresbull.2023.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/07/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
Biomolecular condensation of proteins contributes to the organization of the cytoplasm and nucleoplasm. A number of condensation processes appear to be directly involved in regulating the structure, function and dynamics of the cytoskeleton. Liquid-liquid phase separation of cytoskeleton proteins, together with polymerization modulators, promotes cytoskeletal fiber nucleation and branching. Furthermore, the attachment of protein condensates to the cytoskeleton can contribute to cytoskeleton stability and organization, regulate transport, create patterns of functional reaction containers, and connect the cytoskeleton with membranes. Surface-bound condensates can exert and buffer mechanical forces that give stability and flexibility to the cytoskeleton, thus, may play a large role in cell biology. In this review, we introduce the concept and role of cellular biomolecular condensation, explain its special function on cytoskeletal fiber surfaces, and point out potential definition and experimental caveats. We review the current literature on protein condensation processes related to the actin, tubulin, and intermediate filament cytoskeleton, and discuss some of them in the context of neurobiology. In summary, we provide an overview about biomolecular condensation in relation to cytoskeleton structure and function, which offers a base for the exploration and interpretation of cytoskeletal condensates in neurobiology.
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Senju Y, Hibino E. Moesin-ezrin-radixin-like protein merlin: Its conserved and distinct functions from those of ERM proteins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184076. [PMID: 36302494 DOI: 10.1016/j.bbamem.2022.184076] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Yosuke Senju
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan.
| | - Emi Hibino
- Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi, Japan
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