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Xin S, Liu X, He C, Gao H, Wang B, Hua R, Gao L, Shang H, Sun F, Xu J. Inflammation accelerating intestinal fibrosis: from mechanism to clinic. Eur J Med Res 2024; 29:335. [PMID: 38890719 PMCID: PMC11184829 DOI: 10.1186/s40001-024-01932-2] [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: 02/21/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024] Open
Abstract
Intestinal fibrosis is a prevalent complication of IBD that that can frequently be triggered by prolonged inflammation. Fibrosis in the gut can cause a number of issues, which continue as an ongoing challenge to healthcare systems worldwide. The primary causes of intestinal fibrosis are soluble molecules, G protein-coupled receptors, epithelial-to-mesenchymal or endothelial-to-mesenchymal transition, and the gut microbiota. Fresh perspectives coming from in vivo and in vitro experimental models demonstrate that fibrogenic pathways might be different, at least to some extent, independent of the ones that influence inflammation. Understanding the distinctive procedures of intestinal fibrogenesis should provide a realistic foundation for targeting and blocking specific fibrogenic pathways, estimating the risk of fibrotic consequences, detecting early fibrotic alterations, and eventually allowing therapy development. Here, we first summarize the inflammatory and non-inflammatory components of fibrosis, and then we elaborate on the underlying mechanism associated with multiple cytokines in fibrosis, providing the framework for future clinical practice. Following that, we discuss the relationship between modernization and disease, as well as the shortcomings of current studies. We outline fibrosis diagnosis and therapy, as well as our recommendations for the future treatment of intestinal fibrosis. We anticipate that the global review will provides a wealth of fresh knowledge and suggestions for future fibrosis clinical practice.
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Affiliation(s)
- Shuzi Xin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Xiaohui Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Chengwei He
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Han Gao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
- Department of Clinical Laboratory, Aerospace Clinical Medical College, Aerospace Central Hospital, Beijing, 100039, China
| | - Boya Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Rongxuan Hua
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Lei Gao
- Department of Intelligent Medical Engineering, School of Biomedical Engineering, Capital Medical University, Beijing, 100069, China
| | - Hongwei Shang
- Experimental Center for Morphological Research Platform, Capital Medical University, Beijing, 100069, China
| | - Fangling Sun
- Department of Laboratory Animal Research, Xuan Wu Hospital, Capital Medical University, Beijing, 100053, China.
| | - Jingdong Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
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Zou Z, Li R, Huang X, Chen M, Tan J, Wu M. Identification and validation of immune-related methylated genes as diagnostic and prognostic biomarkers of nasopharyngeal carcinoma. Head Neck 2024; 46:192-211. [PMID: 37929674 DOI: 10.1002/hed.27569] [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: 02/16/2023] [Revised: 09/26/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is a common malignancy occurring in the head and neck. Identification of immune-related methylated biomarkers might be helpful for NPC detection and prognostic evaluation. METHODS A co-methylation network based on WGCNA was constructed to identify modules associated with NPC and immune cells. In combination with differentially expressed genes (DEGs) and immune-related genes from ImmPort database, the candidate immune-related methylated genes (IRMGs) were obtained. RESULTS Our combined analysis identified 12 IRMGs. Among them, both the methylation and mRNA expression of CCL28, CSK, and PRKCB were correlated with the infiltration of B cells. CD1D, CR2, and GDF10 were favorable markers. Demethylation experiments validated that downregulation of GDF10, PRKCB, SLC40A1, and TGFBR3 in NPC resulted from promoter hypermethylation. Additionally, a diagnostic model was developed and exhibited high discriminative accuracy. CONCLUSIONS These results provided a group of immune-related methylated biomarkers that may help with the diagnosis and prognosis of NPC.
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Affiliation(s)
- Zhenning Zou
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Rujia Li
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Xueshan Huang
- The First Clinical Medical College, Guangdong Medical University, Zhanjiang, China
| | - Mei Chen
- The First Clinical Medical College, Guangdong Medical University, Zhanjiang, China
| | - Jingyi Tan
- School of Pharmacy, Guangdong Medical University, Zhanjiang, China
| | - Minhua Wu
- School of Basic Medicine, Guangdong Medical University, Zhanjiang, China
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de Langen P, Hammal F, Guéret E, Mouren JC, Spinelli L, Ballester B. Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues. CELL GENOMICS 2023; 3:100411. [PMID: 37868033 PMCID: PMC10589727 DOI: 10.1016/j.xgen.2023.100411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/29/2023] [Accepted: 09/04/2023] [Indexed: 10/24/2023]
Abstract
Intergenic transcription in normal and cancerous tissues is pervasive but incompletely understood. To investigate this, we constructed an atlas of over 180,000 consensus RNA polymerase II (RNAPII)-bound intergenic regions from 900 RNAPII chromatin immunoprecipitation sequencing (ChIP-seq) experiments in normal and cancer samples. Through unsupervised analysis, we identified 51 RNAPII consensus clusters, many of which mapped to specific biotypes and revealed tissue-specific regulatory signatures. We developed a meta-clustering methodology to integrate our RNAPII atlas with active transcription across 28,797 RNA sequencing (RNA-seq) samples from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Encyclopedia of DNA Elements (ENCODE). This analysis revealed strong tissue- and disease-specific interconnections between RNAPII occupancy and transcriptional activity. We demonstrate that intergenic transcription at RNAPII-bound regions is a novel per-cancer and pan-cancer biomarker. This biomarker displays genomic and clinically relevant characteristics, distinguishing cancer subtypes and linking to overall survival. Our results demonstrate the effectiveness of coherent data integration to uncover intergenic transcriptional activity in normal and cancer tissues.
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Affiliation(s)
| | | | - Elise Guéret
- Aix Marseille Univ, INSERM, TAGC, Marseille, France
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Kawabe N, Matsuoka K, Komeda K, Muraki N, Takaba M, Togami Y, Ito Y, Yamada M, Sunaga N, Girard L, Minna JD, Cai L, Xie Y, Tanaka I, Morise M, Sato M. Silencing of GRHL2 induces epithelial‑to‑mesenchymal transition in lung cancer cell lines with different effects on proliferation and clonogenic growth. Oncol Lett 2023; 26:391. [PMID: 37600329 PMCID: PMC10433723 DOI: 10.3892/ol.2023.13977] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/04/2023] [Indexed: 08/22/2023] Open
Abstract
Grainyhead-like 2 (GRHL2) is a transcription factor that suppresses epithelial-to-mesenchymal transition (EMT). It has been previously shown that GRHL2 can confer both oncogenic and tumor-suppressive roles in human cancers, including breast, pancreatic and colorectal cancers. However, its role in lung cancer remains elusive. In the present study, a meta-analysis of multiple gene expression datasets with clinical data revealed that GRHL2 expression was increased in lung cancer compared with that in the normal tissues. Copy number analysis of GRHL2, performed using datasets of whole exome sequencing involving 151 lung cancer cell lines, revealed frequent amplifications, suggesting that the increased GRHL2 expression may have resulted from gene amplification. A survival meta-analysis of GRHL2 using The Cancer Genome Atlas (TCGA) dataset showed no association of GRHL2 expression with overall survival. GRHL2 expression was found to be associated with EMT status in lung cancer in TCGA dataset and lung cancer cell lines. GRHL2 knockdown induced partial EMT in the hTERT/Cdk4-immortalized normal lung epithelial cell line HBEC4KT without affecting proliferation measured by CCK-8 assays. In addition, GRHL2 silencing caused three lung cancer cell lines, H1975, H2009 and H441, to undergo partial EMT. However, the proliferative effects differed significantly. GRHL2 silencing promoted proliferation but not colony formation in H1975 cells whilst suppressing colony formation without affecting proliferation in H2009 cells, but it did not affect proliferation in H441 cells. These results suggest cell type-dependent effects of GRHL2 knockdown. Downstream, GRHL2 silencing enhanced the phosphorylation of AKT and ERK, assessed by western blotting with phospho-specific antibodies, in HBEC4KT, H1975 and H2009 cell lines but not in the H441 cell line. By contrast, transient GRHL2 overexpression did not affect A549 cell proliferation, which lack detectable endogenous expression of the GRHL2 protein. However, GRHL2 overexpression did suppress E-cadherin expression in A549 cells. These results suggested that GRHL2 does not only function as a tumor suppressor of EMT but can also behave as an oncogene depending on the lung cancer cell-type context.
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Affiliation(s)
- Nozomi Kawabe
- Division of Host Defense Sciences, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi 461-8673, Japan
| | - Kohei Matsuoka
- Division of Host Defense Sciences, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi 461-8673, Japan
| | - Kazuki Komeda
- Division of Host Defense Sciences, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi 461-8673, Japan
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Nao Muraki
- Division of Host Defense Sciences, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi 461-8673, Japan
| | - Miho Takaba
- Division of Host Defense Sciences, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi 461-8673, Japan
| | - Yasuha Togami
- Division of Host Defense Sciences, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi 461-8673, Japan
| | - Yumeno Ito
- Division of Host Defense Sciences, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi 461-8673, Japan
| | - Mizuki Yamada
- Division of Host Defense Sciences, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi 461-8673, Japan
| | - Noriaki Sunaga
- Department of Respiratory Medicine, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75230-8593, USA
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75230-8593, USA
| | - Ling Cai
- Quantitative Biomedical Research Center, Peter O'Donnell School of Public Health, UT Southwestern Medical Center, Dallas, TX 75230-8593, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, Peter O'Donnell School of Public Health, UT Southwestern Medical Center, Dallas, TX 75230-8593, USA
| | - Ichidai Tanaka
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Masahiro Morise
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Mitsuo Sato
- Division of Host Defense Sciences, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi 461-8673, Japan
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Comprehensive Analysis of GDF10 Methylation Site-Associated Genes as Prognostic Markers for Endometrial Cancer. JOURNAL OF ONCOLOGY 2022; 2022:7117083. [PMID: 36262352 PMCID: PMC9576415 DOI: 10.1155/2022/7117083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022]
Abstract
Growth differentiation factor-10 (GDF10) with its methylation trait has recently been found to play a crucial regulatory and communication role in cancers. This investigation aims to identify GDF10 methylation site-associated genes that are closely associated with endometrial cancer (EC) patients' survival based on normal and UCEC samples from the UCSC Xena database. Our study revealed for the first time that EC exhibited significantly higher levels of GDF10 promoter methylation in comparison with normal tissues. Multiple differentiated methylation sites, which have prognostic value due to their apparent survival differences, were found in the GDF10 promoter region. We performed weighted gene coexpression network analysis (WGCNA) on EC tissues and paraneoplastic tissues while using these differentially methylated sites as phenotypes for selecting the most correlated key modules and their internal genes. To obtain a gene set, the key module genes and differentially expressed genes (DEGs) of EC were intersected. The least absolute shrinkage and selection operator (LASSO) regression along with multivariate Cox regression were performed from the gene set and we screened out the key genes B4GALNT3, DNAJC22, and GREB1. Finally, a prognostic model was validated for effectiveness based on these genes. Additionally, Kaplan-Meier analysis and time-dependent receiver operating characteristics (ROC) were applied to assess and verify the model, and they showed good prognosis prediction. Moreover, the differences in risk scores were statistically significant with age, tumor stage, and grade. They may be related to the immune infiltration of tumors as well. In conclusion, based on the methylation-related genes associated with GDF10, we developed a prognosis model for EC patients. It might provide a fresh view for further research and treatment of EC.
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