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Deng Y, Wang C, Yang R, Yang Q. The role of RETN in stomach adenocarcinoma (STAD): insights from pan-cancer analysis of RNA-seq data based on the TCGA database. Discov Oncol 2025; 16:921. [PMID: 40413699 DOI: 10.1007/s12672-025-02755-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2025] [Accepted: 05/19/2025] [Indexed: 05/27/2025] Open
Abstract
OBJECTIVE To analyze the expression and significance of resistin (RETN) in pan-cancer and determine the prospect of RETN as a biomarker for STAD, providing a new diagnostic and therapeutic target for STAD. METHODS Based on the RNA-seq data from the TCGA database, RETN was comprehensively analyzed from the perspective of pan-cancer. Firstly, the expression of RETN, correlation of immune infiltration, diagnostic efficacy and prognostic value in pan-cancer were investigated. Subsequently, the potential value of RETN as a biomarker for STAD was evaluated. Finally, the potential mechanisms of RETN in STAD were explored, including single-cell expression, PPI, functional enrichment analysis, single-gene correlation, gene co-expression analysis, and immune infiltration correlation. RESULTS RETN is upregulated in most tumors and is associated with a variety of immune cells. As a potential biomarker, RETN showed good diagnostic efficacy and prognostic value in a variety of tumors. The prediction model based on pathological stage, sex, age and RETN has a good prediction effect on the overall survival of STAD patients. Single-cell expression analysis showed that RETN was mainly expressed by DC cells and mononuclear/macrophage cells in STAD. Subsequently, RETN and related genes were analyzed from the perspective of PPI and functional enrichment, and the results showed that these genes/proteins were mainly involved in regulating hormone secretion and insulin response. Finally, RETN is also closely associated with immune cells in STAD. CONCLUSIONS RETN is a promising biomarker related to the diagnosis and prognosis of STAD, and is expected to become a new diagnostic and therapeutic target for STAD.
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Affiliation(s)
- Yaxing Deng
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Jiangyang District, Luzhou, Sichuan, China
| | - Chenglin Wang
- Department of Emergency Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Rui Yang
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Jiangyang District, Luzhou, Sichuan, China
| | - Qingqiang Yang
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Jiangyang District, Luzhou, Sichuan, China.
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2
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Syed F, Ballew O, Lee CC, Rana J, Krishnan P, Castela A, Weaver SA, Chalasani NS, Thomaidou SF, Demine S, Chang G, Coomans de Brachène A, Alvelos MI, Vazquez EM, Marselli L, Orr K, Felton JL, Liu J, Kaddis JS, Marchetti P, Zaldumbide A, Scheuner D, Eizirik DL, Evans-Molina C. Pharmacological inhibition of tyrosine protein-kinase 2 reduces islet inflammation and delays type 1 diabetes onset in mice. EBioMedicine 2025:105734. [PMID: 40335415 DOI: 10.1016/j.ebiom.2025.105734] [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: 09/17/2024] [Revised: 02/20/2025] [Accepted: 04/14/2025] [Indexed: 05/09/2025] Open
Abstract
BACKGROUND Tyrosine protein-kinase 2 (TYK2) mediates inflammatory signalling through multiple cytokines, including interferon-α (IFNα), interleukin (IL)-12, and IL-23. TYK2 missense mutations protect against type 1 diabetes (T1D), and inhibition of TYK2 shows promise in other autoimmune conditions. METHODS We evaluated the effects of specific TYK2 inhibitors (TYK2is) in pre-clinical models of T1D, including human β cells, cadaveric islets, iPSC-derived islets, and mouse models. FINDINGS In vitro studies showed that TYK2is prevented IFNα-induced β cell HLA class I up-regulation, endoplasmic reticulum stress, and chemokine production. In co-culture studies, pre-treatment of β cells with TYK2i prevented IFNα-induced antigenic peptide presentation and alloreactive and autoreactive T cell degranulation. In vivo administration of BMS-986202 in two mouse models of T1D (RIP-LCMV-GP and NOD mice) reduced systemic and tissue-localised inflammation, prevented β cell death, and delayed T1D onset. Transcriptional phenotyping of pancreatic islets, pancreatic lymph nodes, and spleen highlighted a role for TYK2 inhibition in modulating signalling pathways associated with inflammation, translational control, stress signalling, secretory function, immunity, and diabetes. Additionally, TYK2i treatment changed the composition of innate and adaptive immune cell populations in the blood and disease target tissues. INTERPRETATION These findings indicate that TYK2i has beneficial effects on both the immune and endocrine compartments in models of T1D, thus supporting a path forward for testing TYK2is in human T1D. FUNDING This work was supported by the National Institutes of Health (NIH), Veteran Affairs (VA), Breakthrough T1D, and gifts from the Sigma Beta Sorority, the Ball Brothers Foundation, and the George and Frances Ball Foundation.
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Affiliation(s)
- Farooq Syed
- Indiana University School of Medicine, Indianapolis, IN, USA; Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Diabetes-Immunology, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Olivia Ballew
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Chih-Chun Lee
- Indiana University School of Medicine, Indianapolis, IN, USA; Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jyoti Rana
- Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Preethi Krishnan
- Indiana University School of Medicine, Indianapolis, IN, USA; Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Angela Castela
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Staci A Weaver
- Indiana University School of Medicine, Indianapolis, IN, USA; Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Sofia F Thomaidou
- Department of Cell and Chemical Biology, Leiden University Medical Center, the Netherlands
| | - Stephane Demine
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Garrick Chang
- Department of Physics, Indiana University Indianapolis, Indianapolis, IN, USA
| | | | - Maria Ines Alvelos
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Eugenia Martin Vazquez
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Lorella Marselli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Kara Orr
- Indiana University School of Medicine, Indianapolis, IN, USA; Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jamie L Felton
- Indiana University School of Medicine, Indianapolis, IN, USA; Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jing Liu
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN, USA
| | - John S Kaddis
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Arnaud Zaldumbide
- Department of Cell and Chemical Biology, Leiden University Medical Center, the Netherlands
| | | | - Decio L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium.
| | - Carmella Evans-Molina
- Indiana University School of Medicine, Indianapolis, IN, USA; Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; Richard L. Roudebush VA Medical Center, Indianapolis, IN, USA.
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Ling L, Hu T, Zhou C, Chen S, Chou L, Chen Y, Hu Z, Huang K, Chen J, Wang Y, Wang J. Low Expression MCEMP1 Promotes Lung Adenocarcinoma Progression and its Clinical Value. Curr Cancer Drug Targets 2025; 25:281-293. [PMID: 38676531 DOI: 10.2174/0115680096292054240409070618] [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: 12/08/2023] [Revised: 03/09/2024] [Accepted: 03/13/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Lung cancer is a highly prevalent tumor with a lack of biological markers that reflect its progression. Mast cell surface membrane protein 1 (MCEMP1, also known as C19ORF59) has not been reported in lung adenocarcinoma (LUAD). OBJECTIVE We aimed to investigate the role of MCEMP1 in LUAD. METHODS MCEMP1 expression in LUAD was analyzed using The Cancer Genome Atlas (TCGA) data, and conducted univariate and multivariate Cox regression analyses to evaluate the prognostic significance of MCEMP1 expression in TCGA. Tumor Immune Estimation Resource (TIMER) was used for examining the correlation between MCEMP1 expression and immune cell infiltration in LUAD. Furthermore, proliferation, migration, invasion, and colony-forming ability were investigated using LUAD cell lines. RESULTS MCEMP1 expression in LUAD patient tissues and was correlated with lymph node metastasis, differentiation level, and tumor status. The Area under Curve (AUC) value of MCEMP1 for the Receiver Operating Characteristic (ROC) curve analysis was 0.984. The immune infiltration analysis revealed a correlation between MCEMP1 expression and the extent of macrophages and neutrophil infiltration in LUAD. Additionally, MCEMP1 has low expression in clinical samples, MCEMP1 overexpressed in LUAD cells substantially reduced cell growth, migration, and invasion of malignant cells. CONCLUSION Low expression MCEMP1 promotes LUAD progression, which provides new insights and a potential biological target for future LUAD therapies.
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Affiliation(s)
- Liqun Ling
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Tianqi Hu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Chenkang Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Shuhui Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Lunan Chou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Yuxin Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Zhaoting Hu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Kate Huang
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Jie Chen
- Department of ICU, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Yumin Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, 325015, China
| | - Junjun Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
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Syed F, Ballew O, Lee CC, Rana J, Krishnan P, Castela A, Weaver SA, Chalasani NS, Thomaidou SF, Demine S, Chang G, Coomans de Brachène A, Alvelos MI, Marselli L, Orr K, Felton JL, Liu J, Marchetti P, Zaldumbide A, Scheuner D, Eizirik DL, Evans-Molina C. Pharmacological inhibition of tyrosine protein-kinase 2 reduces islet inflammation and delays type 1 diabetes onset in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585925. [PMID: 38766166 PMCID: PMC11100605 DOI: 10.1101/2024.03.20.585925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Tyrosine protein-kinase 2 (TYK2), a member of the Janus kinase family, mediates inflammatory signaling through multiple cytokines, including interferon-α (IFNα), interleukin (IL)-12, and IL-23. Missense mutations in TYK2 are associated with protection against type 1 diabetes (T1D), and inhibition of TYK2 shows promise in the management of other autoimmune conditions. Here, we evaluated the effects of specific TYK2 inhibitors (TYK2is) in pre-clinical models of T1D. First, human β cells, cadaveric donor islets, and iPSC-derived islets were treated in vitro with IFNα in combination with a small molecule TYK2i (BMS-986165 or a related molecule BMS-986202). TYK2 inhibition prevented IFNα-induced β cell HLA class I up-regulation, endoplasmic reticulum stress, and chemokine production. In co-culture studies, pre-treatment of β cells with a TYK2i prevented IFNα-induced activation of T cells targeting an epitope of insulin. In vivo administration of BMS-986202 in two mouse models of T1D (RIP-LCMV-GP mice and NOD mice) reduced systemic and tissue-localized inflammation, prevented β cell death, and delayed T1D onset. Transcriptional phenotyping of pancreatic islets, pancreatic lymph nodes (PLN), and spleen during early disease pathogenesis highlighted a role for TYK2 inhibition in modulating signaling pathways associated with inflammation, translational control, stress signaling, secretory function, immunity, and diabetes. Additionally, TYK2i treatment changed the composition of innate and adaptive immune cell populations in the blood and disease target tissues, resulting in an immune phenotype with a diminished capacity for β cell destruction. Overall, these findings indicate that TYK2i has beneficial effects in both the immune and endocrine compartments in models of T1D, thus supporting a path forward for testing TYK2 inhibitors in human T1D.
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Affiliation(s)
- Farooq Syed
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Olivia Ballew
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Chih-Chun Lee
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jyoti Rana
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Preethi Krishnan
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Angela Castela
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Staci A. Weaver
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Sofia F. Thomaidou
- Department of Cell and Chemical Biology, Leiden University Medical Center, The Netherlands
| | - Stephane Demine
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Garrick Chang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | | | - Maria Ines Alvelos
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Lorella Marselli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Kara Orr
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jamie L. Felton
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jing Liu
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN, USA
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Arnaud Zaldumbide
- Department of Cell and Chemical Biology, Leiden University Medical Center, The Netherlands
| | | | - Decio L. Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Carmella Evans-Molina
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
- Richard L. Roudebush VA Medical Center, Indianapolis, IN, USA
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Perrot CY, Karampitsakos T, Unterman A, Adams T, Marlin K, Arsenault A, Zhao A, Kaminski N, Katlaps G, Patel K, Bandyopadhyay D, Herazo-Maya JD. Mast-cell expressed membrane protein-1 is expressed in classical monocytes and alveolar macrophages in idiopathic pulmonary fibrosis and regulates cell chemotaxis, adhesion, and migration in a TGFβ-dependent manner. Am J Physiol Cell Physiol 2024; 326:C964-C977. [PMID: 38189137 PMCID: PMC11193480 DOI: 10.1152/ajpcell.00563.2023] [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: 10/24/2023] [Revised: 12/31/2023] [Accepted: 12/31/2023] [Indexed: 01/09/2024]
Abstract
Mast-cell expressed membrane protein-1 (MCEMP1) is higher in patients with idiopathic pulmonary fibrosis (IPF) with an increased risk of death. Here we aimed to establish the mechanistic role of MCEMP1 in pulmonary fibrosis. We identified increased MCEMP1 expression in classical monocytes and alveolar macrophages in IPF compared with controls. MCEMP1 is upregulated by transforming growth factor beta (TGFβ) at the mRNA and protein levels in monocytic leukemia THP-1 cells. TGFβ-mediated MCEMP1 upregulation results from the cooperation of SMAD3 and SP1 via concomitant binding to SMAD3/SP1 cis-regulatory elements within the MCEMP1 promoter. We also found that MCEMP1 regulates TGFβ-mediated monocyte chemotaxis, adhesion, and migration. Our results suggest that MCEMP1 may regulate the migration and transition of monocytes to monocyte-derived alveolar macrophages during pulmonary fibrosis development and progression.NEW & NOTEWORTHY MCEMP1 is highly expressed in circulating classical monocytes and alveolar macrophages in IPF, is regulated by TGFβ, and participates in the chemotaxis, adhesion, and migration of circulating monocytes by modulating the effect of TGFβ in RHO activity.
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Affiliation(s)
- Carole Y Perrot
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Ubben Center for Pulmonary Fibrosis Research, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States
| | - Theodoros Karampitsakos
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Ubben Center for Pulmonary Fibrosis Research, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States
| | - Avraham Unterman
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, Connecticut, United States
- Pulmonary Fibrosis Center of Excellence, Tel Aviv Sourasky Medical Center, Sackler School of Medicine, Institute of Pulmonary Medicine, Tel Aviv University, Tel Aviv, Israel
- Genomic Research Laboratory for Lung Fibrosis, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Taylor Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, Connecticut, United States
| | - Krystin Marlin
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Ubben Center for Pulmonary Fibrosis Research, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States
| | - Alyssa Arsenault
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Ubben Center for Pulmonary Fibrosis Research, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States
| | - Amy Zhao
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, Connecticut, United States
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, Connecticut, United States
| | - Gundars Katlaps
- Division of Cardiothoracic Surgery, Department of Surgery, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States
- Center for Advanced Lung Disease and Lung Transplant Program, Tampa General Hospital, Tampa, Florida, United States
| | - Kapilkumar Patel
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Ubben Center for Pulmonary Fibrosis Research, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States
- Center for Advanced Lung Disease and Lung Transplant Program, Tampa General Hospital, Tampa, Florida, United States
| | - Debabrata Bandyopadhyay
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Ubben Center for Pulmonary Fibrosis Research, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States
- Center for Advanced Lung Disease and Lung Transplant Program, Tampa General Hospital, Tampa, Florida, United States
| | - Jose D Herazo-Maya
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Ubben Center for Pulmonary Fibrosis Research, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States
- Center for Advanced Lung Disease and Lung Transplant Program, Tampa General Hospital, Tampa, Florida, United States
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Perrot CY, Karampitsakos T, Unterman A, Adams T, Marlin K, Arsenault A, Zhao A, Kaminski N, Katlaps G, Patel K, Bandyopadhyay D, Herazo-Maya JD. Mast-Cell Expressed Membrane Protein-1 (MCEMP1) is expressed in classical monocytes and alveolar macrophages in Idiopathic Pulmonary Fibrosis and regulates cell chemotaxis, adhesion, and migration in a TGFβ dependent manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.07.561349. [PMID: 37873485 PMCID: PMC10592658 DOI: 10.1101/2023.10.07.561349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background Mast-Cell Expressed Membrane Protein-1 (MCEMP1) is higher in Idiopathic Pulmonary Fibrosis (IPF) patients with increased risk of death and poor outcomes. Here we seek to establish the mechanistic role of MCEMP1 in pulmonary fibrosis. Methods MCEMP1 expression was analyzed by single-cell RNA sequencing, immunofluorescence in Peripheral Blood Mononuclear Cells (PBMC) as well as in lung tissues from IPF patients and controls. Chromatin Immunoprecipitation (ChiP) and Proximity Ligation Assay (PLA) were used to study the transcriptional regulation of MCEMP1 . Transient RNA interference and lentivirus transduction were used to knockdown and knock-in MCEMP1 in THP-1 cells to study chemotaxis, adhesion, and migration. Bulk RNA sequencing was used to identify the mechanisms by which MCEMP1 participates in monocyte function. Active RHO pull-down assay was used to validate bulk RNA sequencing results. Results We identified increased MCEMP1 expression in classical monocytes and alveolar macrophages in IPF compared to controls. MCEMP1 was upregulated by TGFβ at the mRNA and protein levels in THP-1. TGFβ-mediated MCEMP1 upregulation results from the cooperation of SMAD3 and SP1 via concomitant binding to SMAD3/SP1 cis -regulatory elements within the MCEMP1 promoter. In terms of its function, we found that MCEMP1 regulates TGFβ-mediated monocyte chemotaxis, adhesion, and migration. 400 differentially expressed genes were found to increase after TGFβ stimulation of THP-1, further increased in MCEMP1 knock-in cells treated with TGFβ and decreased in MCEMP1 knockdown cells treated with TGFβ. GO annotation analysis of these genes showed enrichment for positive regulation of RHO GTPase activity and signal transduction. While TGFβ enhanced RHO GTPase activity in THP-1 cells, this effect was attenuated following MCEMP1 knockdown. Conclusion MCEMP1 is highly expressed in circulating classical monocytes and alveolar macrophages in IPF. MCEMP1 is regulated by TGFβ and participates in the chemotaxis, adhesion, and migration of circulating monocytes by modulating the effect of TGFβ in RHO activity. Our results suggest that MCEMP1 may regulate the migration and transition of monocytes to monocyte-derived alveolar macrophages during pulmonary fibrosis development and progression.
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Tong Q, Ling Y. A prognostic model based on regulatory T-cell-related genes in gastric cancer: Systematic construction and validation. Int J Exp Pathol 2023; 104:226-236. [PMID: 37350375 PMCID: PMC10500170 DOI: 10.1111/iep.12487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/22/2022] [Accepted: 06/01/2023] [Indexed: 06/24/2023] Open
Abstract
Human gastrointestinal tumours have been shown to contain massive numbers of tumour infiltrating regulatory T cells (Tregs), the presence of which are closely related to tumour immunity. This study was designed to develop new Treg-related prognostic biomarkers to monitor the prognosis of patients with gastric cancer (GC). Treg-related prognostic genes were screened from Treg-related differentially expressed genes in GC patients by using Cox regression analysis, based on which a prognostic model was constructed. Then, combined with RiskScore, survival curve, survival status assessment and ROC analysis, these genes were used to verify the accuracy of the model, whose independent prognostic ability was also evaluated. Six Treg-related prognostic genes (CHRDL1, APOC3, NPTX1, TREML4, MCEMP1, GH2) in GC were identified, and a 6-gene Treg-related prognostic model was constructed. Survival analysis revealed that patients had a higher survival rate in the low-risk group. Combining clinicopathological features, we performed univariate and multivariate regression analyses, with results establishing that the RiskScore was an independent prognostic factor. Predicted 1-, 3- and 5-year survival rates of GC patients had a good fit with the actual survival rates according to nomogram results. In addition patients in the low-risk group had higher tumour mutational burden (TMB) values. Gene Set Enrichment Analysis (GSEA) demonstrated that genes in the high-risk group were significantly enriched in pathways related to immune inflammation, tumour proliferation and migration. In general, we constructed a 6-gene Treg-associated GC prognostic model with good prediction accuracy, where RiskScore could act as an independent prognostic factor. This model is expected to provide a reference for clinicians to estimate the prognosis of GC patients.
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Affiliation(s)
- Qin Tong
- Department of Gastrointestinal SurgeryJinhua Guangfu HospitalJinhuaChina
| | - Yingjie Ling
- Department of Gastrointestinal SurgeryJinhua Guangfu HospitalJinhuaChina
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Ning J, Sun K, Fan X, Jia K, Meng L, Wang X, Li H, Ma R, Liu S, Li F, Wang X. Use of machine learning-based integration to develop an immune-related signature for improving prognosis in patients with gastric cancer. Sci Rep 2023; 13:7019. [PMID: 37120631 PMCID: PMC10148812 DOI: 10.1038/s41598-023-34291-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/27/2023] [Indexed: 05/01/2023] Open
Abstract
Gastric cancer is one of the most common malignancies. Although some patients benefit from immunotherapy, the majority of patients have unsatisfactory immunotherapy outcomes, and the clinical significance of immune-related genes in gastric cancer remains unknown. We used the single-sample gene set enrichment analysis (ssGSEA) method to evaluate the immune cell content of gastric cancer patients from TCGA and clustered patients based on immune cell scores. The Weighted Correlation Network Analysis (WGCNA) algorithm was used to identify immune subtype-related genes. The patients in TCGA were randomly divided into test 1 and test 2 in a 1:1 ratio, and a machine learning integration process was used to determine the best prognostic signatures in the total cohort. The signatures were then validated in the test 1 and the test 2 cohort. Based on a literature search, we selected 93 previously published prognostic signatures for gastric cancer and compared them with our prognostic signatures. At the single-cell level, the algorithms "Seurat," "SCEVAN", "scissor", and "Cellchat" were used to demonstrate the cell communication disturbance of high-risk cells. WGCNA and univariate Cox regression analysis identified 52 prognosis-related genes, which were subjected to 98 machine-learning integration processes. A prognostic signature consisting of 24 genes was identified using the StepCox[backward] and Enet[alpha = 0.7] machine learning algorithms. This signature demonstrated the best prognostic performance in the overall, test1 and test2 cohort, and outperformed 93 previously published prognostic signatures. Interaction perturbations in cellular communication of high-risk T cells were identified at the single-cell level, which may promote disease progression in patients with gastric cancer. We developed an immune-related prognostic signature with reliable validity and high accuracy for clinical use for predicting the prognosis of patients with gastric cancer.
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Affiliation(s)
- Jingyuan Ning
- Department of Immunology, Immunology Department of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Keran Sun
- Department of Immunology, Immunology Department of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Xiaoqing Fan
- Department of Immunology, Immunology Department of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Keqi Jia
- Department of Pathology, Shijiazhuang People's Hospital, Shijiazhuang, People's Republic of China
| | - Lingtong Meng
- Department of Immunology, Immunology Department of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Xiuli Wang
- Department of Laboratory, The Second Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Hui Li
- Department of Oncology, Shijiazhuang Fourth Hospital, Shijiazhuang, People's Republic of China
| | - Ruixiao Ma
- Department of Oncology, Shijiazhuang Fourth Hospital, Shijiazhuang, People's Republic of China
| | - Subin Liu
- Department of Oncology, Shijiazhuang Fourth Hospital, Shijiazhuang, People's Republic of China
| | - Feng Li
- Department of Oncology, Shijiazhuang Fourth Hospital, Shijiazhuang, People's Republic of China
| | - Xiaofeng Wang
- Department of Immunology, Immunology Department of Hebei Medical University, Shijiazhuang, People's Republic of China.
- Department of Oncology, Shijiazhuang Fourth Hospital, Shijiazhuang, People's Republic of China.
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9
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Chan KR, Koh CWT, Ng DHL, Qin S, Ooi JSG, Ong EZ, Zhang SLX, Sam H, Kalimuddin S, Low JGH, Ooi EE. Early peripheral blood MCEMP1 and HLA-DRA expression predicts COVID-19 prognosis. EBioMedicine 2023; 89:104472. [PMID: 36801619 PMCID: PMC9934388 DOI: 10.1016/j.ebiom.2023.104472] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Mass vaccination has dramatically reduced the incidence of severe COVID-19, with most cases now presenting as self-limiting upper respiratory tract infections. However, those with co-morbidities, the elderly and immunocompromised, as well as the unvaccinated, remain disproportionately vulnerable to severe COVID-19 and its sequelae. Furthermore, as the effectiveness of vaccination wanes with time, immune escape SARS-CoV-2 variants could emerge to cause severe COVID-19. Reliable prognostic biomarkers for severe disease could be used as early indicator of re-emergence of severe COVID-19 as well as for triaging of patients for antiviral therapy. METHODS We performed a systematic review and re-analysis of 7 publicly available datasets, analysing a total of 140 severe and 181 mild COVID-19 patients, to determine the most consistent differentially regulated genes in peripheral blood of severe COVID-19 patients. In addition, we included an independent cohort where blood transcriptomics of COVID-19 patients were prospectively and longitudinally monitored previously, to track the time in which these gene expression changes occur before nadir of respiratory function. Single cell RNA-sequencing of peripheral blood mononuclear cells from publicly available datasets was then used to determine the immune cell subsets involved. FINDINGS The most consistent differentially regulated genes in peripheral blood of severe COVID-19 patients were MCEMP1, HLA-DRA and ETS1 across the 7 transcriptomics datasets. Moreover, we found significantly heightened MCEMP1 and reduced HLA-DRA expression as early as four days before the nadir of respiratory function, and the differential expression of MCEMP1 and HLA-DRA occurred predominantly in CD14+ cells. The online platform which we developed is publicly available at https://kuanrongchan-covid19-severity-app-t7l38g.streamlitapp.com/, for users to query gene expression differences between severe and mild COVID-19 patients in these datasets. INTERPRETATION Elevated MCEMP1 and reduced HLA-DRA gene expression in CD14+ cells during the early phase of disease are prognostic of severe COVID-19. FUNDING K.R.C is funded by the National Medical Research Council (NMRC) of Singapore under the Open Fund Individual Research Grant (MOH-000610). E.E.O. is funded by the NMRC Senior Clinician-Scientist Award (MOH-000135-00). J.G.H.L. is funded by the NMRC under the Clinician-Scientist Award (NMRC/CSAINV/013/2016-01). S.K. is funded by the NMRC under the Transition Award. This study was sponsored in part by a generous gift from The Hour Glass.
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Affiliation(s)
- Kuan Rong Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.
| | - Clara W T Koh
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Dorothy H L Ng
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Shijie Qin
- Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Justin S G Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Eugenia Z Ong
- Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Summer L X Zhang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Huizhen Sam
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Shirin Kalimuddin
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Jenny G H Low
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore; Department of Infectious Diseases, Singapore General Hospital, Singapore; Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Eng Eong Ooi
- Department of Infectious Diseases, Singapore General Hospital, Singapore; Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore
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10
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Miao J, Yang Z, Guo W, Liu L, Song P, Ding C, Guan W. Integrative analysis of the proteome and transcriptome in gastric cancer identified LRP1B as a potential biomarker. Biomark Med 2022; 16:1101-1111. [PMID: 36606427 DOI: 10.2217/bmm-2022-0288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Background: The aim of this study was to discover unique membrane proteins associated with gastric cancer (GC) in proteomics analysis. Methods: Using a data-independent acquisition strategy, we compared the relative expression levels of membrane proteins in GC. Results: A total of 2774 differentially expressed membrane proteins were identified between GC and normal cell lines. Conjoint analysis of transcriptomes and proteomes provided 11 potential biomarkers (GPRC5A, PSAT1, NUDCD1, RCC2, IPO4, FAM91A1, KANK2, PRADC1, NME4, METTL7A and LRP1B) for further exploration. Downregulation of LRP1B in GC was validated by immunohistochemistry. Moreover, LRP1B demonstrated an area under the receiver operating characteristic curve of 0.917 in differentiating GC from normal tissues. Conclusion: LRP1B was identified as a meaningful indicator assisting in GC detection and labeling of tumor boundaries.
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Affiliation(s)
- Ji Miao
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Zhi Yang
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Wen Guo
- Department of Pathology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, China
| | - Lixiang Liu
- Department of General Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210008, China
| | - Peng Song
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Chao Ding
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Wenxian Guan
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
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