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Ma Q, Meng M, Zhou X, Guo W, Feng K, Huang T, Cai YD. Identification of Key Genes in Fetal Gut Development at Single-Cell Level by Exploiting Machine Learning Techniques. Proteomics 2024:e202400104. [PMID: 39324223 DOI: 10.1002/pmic.202400104] [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: 03/24/2024] [Revised: 08/29/2024] [Accepted: 09/11/2024] [Indexed: 09/27/2024]
Abstract
The study of fetal gut development is critical due to its substantial influence on immediate neonatal and long-term adult health. Current research largely focuses on microbiome colonization, gut immunity, and barrier function, alongside the impact of external factors on these phenomena. Limited research has been dedicated to the categorization of developing fetal gut cells. Our study aimed to enhance our understanding of fetal gut development by employing advanced machine-learning techniques on single-cell sequencing data. This dataset consisted of 62,849 samples, each characterized by 33,694 distinct gene features. Four feature ranking algorithms were utilized to sort features according to their significance, resulting in four feature lists. Then, these lists were fed into an incremental feature selection method to extract essential genes, classification rules, and build efficient classifiers. Several important genes were recognized by multiple feature ranking algorithms, such as FGG, MDK, RBP1, RBP2, IGFBP7, and SPON2. These features were key in differentiating specific developing intestinal cells, including epithelial, immune, mesenchymal, and vasculature cells of the colon, duo jejunum, and ileum cells. The classification rules showed special gene expression patterns on some intestinal cell types and the efficient classifiers can be useful tools for identifying intestinal cells.
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Affiliation(s)
- QingLan Ma
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Mei Meng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - XianChao Zhou
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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Ouahed JD, Griffith A, Collen LV, Snapper SB. Breaking Down Barriers: Epithelial Contributors to Monogenic IBD Pathogenesis. Inflamm Bowel Dis 2024; 30:1189-1206. [PMID: 38280053 DOI: 10.1093/ibd/izad319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Indexed: 01/29/2024]
Abstract
Monogenic causes of inflammatory bowel diseases (IBD) are increasingly being discovered. To date, much attention has been placed in those resulting from inborn errors of immunity. Therapeutic efforts have been largely focused on offering personalized immune modulation or curative bone marrow transplant for patients with IBD and underlying immune disorders. To date, less emphasis has been placed on monogenic causes of IBD that pertain to impairment of the intestinal epithelial barrier. Here, we provide a comprehensive review of monogenic causes of IBD that result in impaired intestinal epithelial barrier that are categorized into 6 important functions: (1) epithelial cell organization, (2) epithelial cell intrinsic functions, (3) epithelial cell apoptosis and necroptosis, (4) complement activation, (5) epithelial cell signaling, and (6) control of RNA degradation products. We illustrate how impairment of any of these categories can result in IBD. This work reviews the current understanding of the genes involved in maintaining the intestinal barrier, the inheritance patterns that result in dysfunction, features of IBD resulting from these disorders, and pertinent translational work in this field.
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Affiliation(s)
- Jodie D Ouahed
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexandra Griffith
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lauren V Collen
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
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Müller JH, Plage H, Elezkurtaj S, Mandelkow T, Huang Z, Lurati MCJ, Raedler JB, Debatin NF, Vettorazzi E, Samtleben H, Hofbauer S, Furlano K, Neymeyer J, Goranova I, Ralla B, Weinberger S, Horst D, Roßner F, Schallenberg S, Marx AH, Fisch M, Rink M, Slojewski M, Kaczmarek K, Ecke T, Hallmann S, Koch S, Adamini N, Lennartz M, Minner S, Simon R, Sauter G, Zecha H, Schlomm T, Bady E. Loss of TROP2 and epithelial cell adhesion molecule expression is linked to grade progression in pTa but unrelated to disease outcome in pT2-4 urothelial bladder carcinomas. Front Oncol 2024; 13:1342367. [PMID: 38282671 PMCID: PMC10811247 DOI: 10.3389/fonc.2023.1342367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024] Open
Abstract
Introduction Trophoblast cell surface antigen 2 (TROP2; EpCAM2) is a transmembrane glycoprotein which is closely related to EpCAM (EpCAM; EpCAM1). Both proteins share partial overlapping functions in epithelial development and EpCAM expression but have not been comparatively analyzed together in bladder carcinomas. TROP2 constitutes the target for the antibody-drug conjugate Sacituzumab govitecan (SG; TrodelvyTM) which has been approved for treatment of metastatic urothelial carcinoma by the United States Food and Drug administration (FDA) irrespective of its TROP2 expression status. Methods To evaluate the potential clinical significance of subtle differences in TROP2 and EpCAM expression in urothelial bladder cancer, both proteins were analyzed by multiplex fluorescence immunohistochemistry in combination with a deep-learning based algorithm for automated cell detection on more than 2,700 urothelial bladder carcinomas in a tissue microarray (TMA) format. Results The staining pattern of TROP2 and EpCAM were highly similar. For both proteins, the staining intensity gradually decreased from pTa G2 low grade (TROP2: 68.8±36.1; EpCAM: 21.5±11.7) to pTa G2 high grade (64.6±38.0; 19.3±12.2) and pTa G3 (52.1±38.7; 16.0±13.0, p<0.001 each). In pT2-4 carcinomas, the average TROP2 and EpCAM staining intensity was intermediate (61.8±40.9; 18.3±12.3). For both proteins, this was significantly lower than in pTa G2 low grade (p<0.001 each) but also higher than in pTa G3 tumors (p=0.022 for TROP2, p=0.071 for EpCAM). Within pT2-4 carcinomas, the TROP2 and EpCAM staining level was unrelated to pT, grade, UICC-category, and overall or tumor-specific patient survival. The ratio TROP2/EpCAM was unrelated to malignant phenotype and patient prognosis. Conclusion Our data show that TROP2 and EpCAM expression is common and highly interrelated in urothelial neoplasms. Despite of a progressive loss of TROP2/EpCAM during tumor cell dedifferentiation in pTa tumors, the lack of associations with clinicopathological parameters in pT2-4 cancer argues against a major cancer driving role of both proteins for the progression of urothelial neoplasms.
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Affiliation(s)
- Jan H. Müller
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Henning Plage
- Department of Urology, Charité Berlin, Berlin, Germany
| | | | - Tim Mandelkow
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Zhihao Huang
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Magalie C. J. Lurati
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jonas B. Raedler
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- College of Arts and Sciences, Boston University, Fürth, Germany
| | - Nicolaus F. Debatin
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eik Vettorazzi
- Department of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - Kira Furlano
- Department of Urology, Charité Berlin, Berlin, Germany
| | - Jörg Neymeyer
- Department of Urology, Charité Berlin, Berlin, Germany
| | | | | | | | - David Horst
- Insitute of Pathology, Charité Berlin, Berlin, Germany
| | | | | | - Andreas H. Marx
- Department of Pathology, Academic Hospital Fuerth, Fuerth, Germany
| | - Margit Fisch
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Rink
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marcin Slojewski
- Department of Urology, University Hospital Stettin, Stettin, Poland
| | | | - Thorsten Ecke
- Department of Urology, Helios Hospital Bad Saarow, Bad Saarow, Germany
| | - Steffen Hallmann
- Department of Urology, Helios Hospital Bad Saarow, Bad Saarow, Germany
| | - Stefan Koch
- Department of Pathology, Helios Hospital Bad Saarow, Bad Saarow, Germany
| | - Nico Adamini
- Department of Urology, Albertinen Hospital, Hamburg, Germany
| | - Maximilian Lennartz
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Henrik Zecha
- Department of Urology, Albertinen Hospital, Hamburg, Germany
| | | | - Elena Bady
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Szabo R, Kawaguchi M, Kataoka H, Bugge TH. Early-onset tufting enteropathy in HAI-2-deficient mice is independent of matriptase-mediated cleavage of EpCAM. Development 2023; 150:dev201801. [PMID: 37539662 PMCID: PMC10482385 DOI: 10.1242/dev.201801] [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: 03/22/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023]
Abstract
Congenital tufting enteropathy (CTE) is a life-threatening intestinal disorder resulting from loss-of-function mutations in EPCAM and SPINT2. Mice deficient in Spint2, encoding the protease inhibitor HAI-2, develop CTE-like intestinal failure associated with a progressive loss of the EpCAM protein, which is caused by unchecked activity of the serine protease matriptase (ST14). Here, we show that loss of HAI-2 leads to increased proteolytic processing of EpCAM. Elimination of the reported matriptase cleavage site strongly suppressed proteolytic processing of EpCAM in vitro and in vivo. Unexpectedly, expression of cleavage-resistant EpCAM failed to prevent intestinal failure and postnatal lethality in Spint2-deficient mice. In addition, genetic inactivation of intestinal matriptase (St14) counteracted the effect of Spint2 deficiency in mice expressing cleavage-resistant EpCAM, indicating that matriptase does not drive intestinal dysfunction by excessive proteolysis of EpCAM. Interestingly, mice expressing cleavage-resistant EpCAM developed late-onset intestinal defects and exhibited a shortened lifespan even in the presence of HAI-2, suggesting that EpCAM cleavage is indispensable for EpCAM function. Our findings provide new insights into the role of EpCAM and the etiology of the enteropathies driven by Spint2 deficiency.
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Affiliation(s)
- Roman Szabo
- Proteases and Tissue Remodeling Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Makiko Kawaguchi
- Section of Oncopathology and Regenerative Biology, Department of Pathology, Faculty of Medicine, University of Miyazaki, Miyazaki 8891692, Japan
| | - Hiroaki Kataoka
- Section of Oncopathology and Regenerative Biology, Department of Pathology, Faculty of Medicine, University of Miyazaki, Miyazaki 8891692, Japan
| | - Thomas H. Bugge
- Proteases and Tissue Remodeling Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
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Higashi T, Saito AC, Fukazawa Y, Furuse M, Higashi AY, Ono M, Chiba H. EpCAM proteolysis and release of complexed claudin-7 repair and maintain the tight junction barrier. J Cell Biol 2022; 222:213688. [PMID: 36378161 PMCID: PMC9671161 DOI: 10.1083/jcb.202204079] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/09/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
TJs maintain the epithelial barrier by regulating paracellular permeability. Since TJs are under dynamically fluctuating intercellular tension, cells must continuously survey and repair any damage. However, the underlying mechanisms allowing cells to sense TJ damage and repair the barrier are not yet fully understood. Here, we showed that proteinases play an important role in the maintenance of the epithelial barrier. At TJ break sites, EpCAM-claudin-7 complexes on the basolateral membrane become accessible to apical membrane-anchored serine proteinases (MASPs) and the MASPs cleave EpCAM. Biochemical data and imaging analysis suggest that claudin-7 released from EpCAM contributes to the rapid repair of damaged TJs. Knockout (KO) of MASPs drastically reduced barrier function and live-imaging of TJ permeability showed that MASPs-KO cells exhibited increased size, duration, and frequency of leaks. Together, our results reveal a novel mechanism of TJ maintenance through the localized proteolysis of EpCAM at TJ leaks, and provide a better understanding of the dynamic regulation of epithelial permeability.
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Affiliation(s)
- Tomohito Higashi
- Department of Basic Pathology, Fukushima Medical University, Fukushima, Japan,Correspondence to Tomohito Higashi:
| | - Akira C. Saito
- Department of Basic Pathology, Fukushima Medical University, Fukushima, Japan
| | - Yugo Fukazawa
- Division of Brain Structure and Function, Faculty of Medical Science, Life Science Innovation Center, University of Fukui, Fukui, Japan
| | - Mikio Furuse
- Division of Cell Structure, National Institute for Physiological Sciences, Okazaki, Aichi, Japan,Department of Physiological Sciences, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Atsuko Y. Higashi
- Department of Basic Pathology, Fukushima Medical University, Fukushima, Japan
| | - Masahiro Ono
- Department of Basic Pathology, Fukushima Medical University, Fukushima, Japan
| | - Hideki Chiba
- Department of Basic Pathology, Fukushima Medical University, Fukushima, Japan
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