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Shen HT, Hung CS, Davis C, Su CM, Liao LM, Shih HM, Lee KD, Ansar M, Lin RK. Hypermethylation of the Gene Body in SRCIN1 Is Involved in Breast Cancer Cell Proliferation and Is a Potential Blood-Based Biomarker for Early Detection and a Poor Prognosis. Biomolecules 2024; 14:571. [PMID: 38785978 PMCID: PMC11118508 DOI: 10.3390/biom14050571] [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: 04/10/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Breast cancer is a leading cause of cancer mortality in women worldwide. Using the Infinium MethylationEPIC BeadChip, we analyzed plasma sample methylation to identify the SRCIN1 gene in breast cancer patients. We assessed SRCIN1-related roles and pathways for their biomarker potential. To verify the methylation status, quantitative methylation-specific PCR (qMSP) was performed on genomic DNA and circulating cell-free DNA samples, and mRNA expression analysis was performed using RT‒qPCR. The results were validated in a Western population; for this analysis, the samples included plasma samples from breast cancer patients from the USA and from The Cancer Genome Atlas (TCGA) cohort. To study the SRCIN1 pathway, we conducted cell viability assays, gene manipulation and RNA sequencing. SRCIN1 hypermethylation was identified in 61.8% of breast cancer tissues from Taiwanese patients, exhibiting specificity to this malignancy. Furthermore, its presence correlated significantly with unfavorable 5-year overall survival outcomes. The levels of methylated SRCIN1 in the blood of patients from Taiwan and the USA correlated with the stage of breast cancer. The proportion of patients with high methylation levels increased from 0% in healthy individuals to 63.6% in Stage 0, 80% in Stage I and 82.6% in Stage II, with a sensitivity of 78.5%, an accuracy of 90.3% and a specificity of 100%. SRCIN1 hypermethylation was significantly correlated with increased SRCIN1 mRNA expression (p < 0.001). Knockdown of SRCIN1 decreased the viability of breast cancer cells. SRCIN1 silencing resulted in the downregulation of ESR1, BCL2 and various cyclin protein expressions. SRCIN1 hypermethylation in the blood may serve as a noninvasive biomarker, facilitating early detection and prognosis evaluation, and SRCIN1-targeted therapies could be used in combination regimens for breast cancer patients.
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Affiliation(s)
- Hsieh-Tsung Shen
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110301, Taiwan; (H.-T.S.); (H.-M.S.); (K.-D.L.)
- EG BioMed US Inc., Covina, CA 91722, USA;
| | - Chin-Sheng Hung
- EG BioMed US Inc., Covina, CA 91722, USA;
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan;
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235041, Taiwan;
- Division of Breast Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei 110301, Taiwan
| | - Clilia Davis
- International Master Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan;
| | - Chih-Ming Su
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan;
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235041, Taiwan;
| | - Li-Min Liao
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235041, Taiwan;
| | - Hsiu-Ming Shih
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110301, Taiwan; (H.-T.S.); (H.-M.S.); (K.-D.L.)
| | - Kuan-Der Lee
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110301, Taiwan; (H.-T.S.); (H.-M.S.); (K.-D.L.)
- Comprehensive Cancer Center, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Muhamad Ansar
- Ph.D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Ruo-Kai Lin
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110301, Taiwan; (H.-T.S.); (H.-M.S.); (K.-D.L.)
- EG BioMed US Inc., Covina, CA 91722, USA;
- Ph.D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, Taipei 110301, Taiwan
- Graduate Institute of Pharmacognosy, Ph.D. Program in Drug Discovery and Development Industry, Masters Program for Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei 110301, Taiwan
- Clinical Trial Center, Taipei Medical University Hospital, Taipei 110301, Taiwan
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Yan L, Gu C, Gao S, Wei B. Epigenetic regulation and therapeutic strategies in ulcerative colitis. Front Genet 2023; 14:1302886. [PMID: 38169708 PMCID: PMC10758477 DOI: 10.3389/fgene.2023.1302886] [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: 09/27/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Ulcerative colitis (UC) is an inflammatory bowel disease, and is characterized by the diffuse inflammation and ulceration in the colon and rectum mucosa, even extending to the caecum. Epigenetic modifications, including DNA methylations, histone modifications and non-coding RNAs, are implicated in the differentiation, maturation, and functional modulation of multiple immune and non-immune cell types, and are influenced and altered in various chronic inflammatory diseases, including UC. Here we review the relevant studies revealing the differential epigenetic features in UC, and summarize the current knowledge about the immunopathogenesis of UC through epigenetic regulation and inflammatory signaling networks, regarding DNA methylation, histone modification, miRNAs and lncRNAs. We also discuss the epigenetic-associated therapeutic strategies for the alleviation and treatment of UC, which will provide insights to intervene in the immunopathological process of UC in view of epigenetic regulation.
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Affiliation(s)
- Liwei Yan
- The First Clinical College, Shandong University of Traditional Chinese Medicine, Jinan, China
- Departments of Anorectal Surgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chao Gu
- Departments of Anorectal Surgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shanyu Gao
- Departments of Anorectal Surgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Benzheng Wei
- Center for Medical Artificial Intelligence, Shandong University of Traditional Chinese Medicine, Jinan, China
- Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Jinan, China
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Qin W, Jiang M, Lu S, Hu Y, Gan F, Fang W, Chen D, Bo Z. Effects of external environment on promoter methylation of PIK3R5 and related pathway regulation in steroid-induced femoral head necrosis. ENVIRONMENTAL RESEARCH 2023; 238:117116. [PMID: 37709244 DOI: 10.1016/j.envres.2023.117116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/03/2023] [Accepted: 09/09/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Steroid-induced Avascular Necrosis of the Femoral Head (SANFH) is a condition characterized by the necrosis of the femoral head caused by long-term or high-dose hormone usage. Studies have shown that the PI3K/AKT pathway plays a crucial regulatory role in the development of SANFH. The aim of this study is to determine how external environmental factors induce changes in endogenous hormone levels, how these changes lead to steroid-induced femoral head necrosis, and the interrelationship between the changes in PIK3R5 promoter methylation levels and the regulation of the associated signaling pathways. METHODS Femoral head samples underwent molecular sequencing analysis. Candidate genes were screened by differential gene analysis and functional enrichment analysis.Methylation level of candidate gene PIK3R5 was verified by methylation-specific PCR(MS-PCR). SANFH model was constructed in New Zealand white rabbits, and the model results were verified by magnetic resonance imaging (MRI) and haematoxylin-eosin (HE) staining.The expression of PIK3R5, PI3K and AKT in rabbit models and human specimens was verified by real-time fluorescence quantitative PCR(RT-qPCR) and Western Blot(WB), respectively. RESULTS Human femoral head sequencing results indicate distinct differences in the methylation level and mRNA expression of PIK3R5 in SANFH. MS-PCR results showed the methylation level of SANFH patients was significantly higher than that of the control group (P < 0.01). The RT-qPCR results showed that PIK3R5 and PI3K expression levels in the SANFH group were lower than those in the control group (P < 0.05), and the WB experiment results were consistent with the RT-qPCR results. The MRI and HE staining results showed that the rabbit model of SANFH was successfully constructed, and the results of RT-qPCR and WB were consistent with the results of human tissues. CONCLUSION During the occurrence and development of SANFH, PIK3R5 gene regulates the PI3K/AKT pathway through methylation modification, promotes the oxidative stress response of cells, and accelerates the disease process.
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Affiliation(s)
- Wentao Qin
- Department of Bone and Joint Surgery, Guangxi Medical University First Affiliated Hospital, Nanning, China
| | - Mingyang Jiang
- Department of Bone and Joint Surgery, Guangxi Medical University First Affiliated Hospital, Nanning, China
| | - Shenyi Lu
- Department of Rehabilitation, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yang Hu
- Department of Bone and Joint Surgery, Guangxi Medical University First Affiliated Hospital, Nanning, China; Department of Sports Medicine and Joint Surgery, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, China
| | - Fu Gan
- Department of Rehabilitation, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Weijun Fang
- Department of Emergency, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.
| | - Dongxu Chen
- Department of Sports Medicine and Joint Surgery, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, China.
| | - Zhandong Bo
- Department of Bone and Joint Surgery, Guangxi Medical University First Affiliated Hospital, Nanning, China.
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Beheshti-Maal A, Tamimi A, Iravani S, Memarnejadian A, Sorouri M, Aghdaei HA, Zali MR, Hossein Khannazer N, Vosough M. PSC associated inflammatory bowel disease: a distinct entity. Expert Rev Gastroenterol Hepatol 2022; 16:129-139. [PMID: 35078376 DOI: 10.1080/17474124.2022.2031979] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Primary sclerosing cholangitis (PSC) is a rare, chronic, and progressive cholestatic disease involving intra- and/or extrahepatic bile ducts. PSC in many patients results in end-stage liver diseases. Nearly 60% of the PSC patients suffer from concomitant inflammatory bowel diseases (IBDs). Classically, IBDs are divided into two principle types: Crohn's disease (CD) and ulcerative colitis (UC). However, with growing knowledge, PSC-associated IBD (PSC-IBD) seems to be a rather distinct entity with specific genetics, clinical, and microbiota characteristics. AREAS COVERED In this article, we aim to review the unique characteristics of PSC-IBD from clinical, genetic, and microbiota point of view. EXPERT OPINION PSC-IBD's unique characteristics contribute to the notion that it could be a distinct entity. Acknowledgment of PSC-IBD as a novel entity necessitates designing new clinical guidelines for diagnosis and developing novel therapies.
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Affiliation(s)
- Alireza Beheshti-Maal
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Acecr, Tehran, Iran
| | - Atena Tamimi
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Acecr, Tehran, Iran
| | - Shahrokh Iravani
- Gastroenterology and Hepatobiliary Research Center, Imam Reza Hospital, Tehran, Iran
| | | | - Majid Sorouri
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nikoo Hossein Khannazer
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Acecr, Tehran, Iran
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5
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Mackiewicz T, Sowa A, Fichna J. Biomarkers for Early Detection of Colitis-associated Colorectal Cancer - Current Concepts, Future Trends. Curr Drug Targets 2021; 22:137-145. [PMID: 32077822 DOI: 10.2174/1389450121666200220123844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/20/2019] [Accepted: 01/29/2020] [Indexed: 02/08/2023]
Abstract
Colitis-associated colorectal cancer (CAC) remains a critical complication of ulcerative colitis (UC) with a mortality of approximately 15%, which makes early CAC diagnosis crucial. The current standard of surveillance, with repetitive colonoscopies and histological testing of biopsied mucosa samples, is burdensome and expensive, and therefore less invasive methods and reliable biomarkers are needed. Significant progress has been made, thanks to continuous extensive research in this field, however, no clinically relevant biomarker has been established so far. This review of the current literature presents the genetic and molecular differences between CAC and sporadic colorectal cancer and covers progress made in the early detection of CAC carcinogenesis. It focuses on biomarkers under development, which can easily be tested in samples of body fluids or breath and, once made clinically available, will help to differentiate between progressors (UC patients who will develop dysplasia) from non-progressors and enable early intervention to decrease the risk of cancer development.
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Affiliation(s)
- Tomasz Mackiewicz
- Department Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | | | - Jakub Fichna
- Department Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
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Wang Y, Zhang M, Hu X, Qin W, Wu H, Wei M. Colon cancer-specific diagnostic and prognostic biomarkers based on genome-wide abnormal DNA methylation. Aging (Albany NY) 2020; 12:22626-22655. [PMID: 33202377 PMCID: PMC7746390 DOI: 10.18632/aging.103874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/25/2020] [Indexed: 12/11/2022]
Abstract
Abnormal DNA methylation is a major early contributor to colon cancer (COAD) development. We conducted a cohort-based systematic investigation of genome-wide DNA methylation using 299 COAD and 38 normal tissue samples from TCGA. Through conditional screening and machine learning with a training cohort, we identified one hypomethylated and nine hypermethylated differentially methylated CpG sites as potential diagnostic biomarkers, and used them to construct a COAD-specific diagnostic model. Unlike previous models, our model precisely distinguished COAD from nine other cancer types (e.g., breast cancer and liver cancer; error rate ≤ 0.05) and from normal tissues in the training cohort (AUC = 1). The diagnostic model was verified using a validation cohort from The Cancer Genome Atlas (AUC = 1) and five independent cohorts from the Gene Expression Omnibus (AUC ≥ 0.951). Using Cox regression analyses, we established a prognostic model based on six CpG sites in the training cohort, and verified the model in the validation cohort. The prognostic model sensitively predicted patients’ survival (p ≤ 0.00011, AUC ≥ 0.792) independently of important clinicopathological characteristics of COAD (e.g., gender and age). Thus, our DNA methylation analysis provided precise biomarkers and models for the early diagnosis and prognostic evaluation of COAD.
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Affiliation(s)
- Yilin Wang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, Liaoning Province, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, Liaoning Province, P. R. China
| | - Ming Zhang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, Liaoning Province, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, Liaoning Province, P. R. China
| | - Xiaoyun Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, Liaoning Province, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, Liaoning Province, P. R. China
| | - Wenyan Qin
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, Liaoning Province, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, Liaoning Province, P. R. China
| | - Huizhe Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, Liaoning Province, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, Liaoning Province, P. R. China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, Liaoning Province, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, Liaoning Province, P. R. China
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Quraishi MN, Acharjee A, Beggs AD, Horniblow R, Tselepis C, Gkoutos G, Ghosh S, Rossiter AE, Loman N, van Schaik W, Withers D, Walters JRF, Hirschfield GM, Iqbal TH. A Pilot Integrative Analysis of Colonic Gene Expression, Gut Microbiota, and Immune Infiltration in Primary Sclerosing Cholangitis-Inflammatory Bowel Disease: Association of Disease With Bile Acid Pathways. J Crohns Colitis 2020; 14:935-947. [PMID: 32016358 PMCID: PMC7392170 DOI: 10.1093/ecco-jcc/jjaa021] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Although a majority of patients with PSC have colitis [PSC-IBD; primary sclerosing cholangitis-inflammatory bowel disease], this is phenotypically different from ulcerative colitis [UC]. We sought to define further the pathophysiological differences between PSC-IBD and UC, by applying a comparative and integrative approach to colonic gene expression, gut microbiota and immune infiltration data. METHODS Colonic biopsies were collected from patients with PSC-IBD [n = 10], UC [n = 10], and healthy controls [HC; n = 10]. Shotgun RNA-sequencing for differentially expressed colonic mucosal genes [DEGs], 16S rRNA analysis for microbial profiling, and immunophenotyping were performed followed by multi-omic integration. RESULTS The colonic transcriptome differed significantly between groups [p = 0.01]. Colonic transcriptomes from HC were different from both UC [1343 DEGs] and PSC-IBD [4312 DEGs]. Of these genes, only 939 had shared differential gene expression in both UC and PSC-IBD compared with HC. Imputed pathways were predominantly associated with upregulation of immune response and microbial defense in both disease cohorts compared with HC. There were 1692 DEGs between PSC-IBD and UC. Bile acid signalling pathways were upregulated in PSC-IBD compared with UC [p = 0.02]. Microbiota profiles were different between the three groups [p = 0.01]; with inferred function in PSC-IBD also being consistent with dysregulation of bile acid metabolism. Th17 cells and IL17-producing CD4 cells were increased in both PSC-IBD and UC when compared with HC [p < 0.05]. Multi-omic integration revealed networks involved in bile acid homeostasis and cancer regulation in PSC-IBD. CONCLUSIONS Colonic transcriptomic and microbiota analysis in PSC-IBD point toward dysregulation of colonic bile acid homeostasis compared with UC. This highlights important mechanisms and suggests the possibility of novel approaches in treating PSC-IBD.
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Affiliation(s)
- Mohammed Nabil Quraishi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Department of Gastroenterology, Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, UK
- University of Birmingham Microbiome Treatment Centre, University of Birmingham, Birmingham, UK
- Centre for Liver and Gastroenterology Research, NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
| | - Animesh Acharjee
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Institute of Translational Medicine, University Hospitals Birmingham, Birmingham, UK
| | - Andrew D Beggs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Richard Horniblow
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Chris Tselepis
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Georgios Gkoutos
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Centre for Liver and Gastroenterology Research, NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
- Institute of Translational Medicine, University Hospitals Birmingham, Birmingham, UK
- MRC Health Data Research UK [HDR UK], Wellcome Trust, London, UK
- NIHR Experimental Cancer Medicine Centre, NIHR Surgical Reconstruction and Microbiology Research Centre, Birmingham, UK
| | - Subrata Ghosh
- Department of Gastroenterology, Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, UK
- Centre for Liver and Gastroenterology Research, NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
- Institute of Translational Medicine, University Hospitals Birmingham, Birmingham, UK
| | - A E Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Nicholas Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - David Withers
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | | | - Gideon M Hirschfield
- Centre for Liver and Gastroenterology Research, NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
- Toronto Centre for Liver Disease, University of Toronto, Toronto General Hospital, Toronto, ON, Canada
| | - Tariq H Iqbal
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Department of Gastroenterology, Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, UK
- University of Birmingham Microbiome Treatment Centre, University of Birmingham, Birmingham, UK
- Centre for Liver and Gastroenterology Research, NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
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Randazzo D, Khalique U, Belanto JJ, Kenea A, Talsness DM, Olthoff JT, Tran MD, Zaal KJ, Pak K, Pinal-Fernandez I, Mammen AL, Sackett D, Ervasti JM, Ralston E. Persistent upregulation of the β-tubulin tubb6, linked to muscle regeneration, is a source of microtubule disorganization in dystrophic muscle. Hum Mol Genet 2019; 28:1117-1135. [PMID: 30535187 DOI: 10.1093/hmg/ddy418] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/26/2018] [Accepted: 12/02/2018] [Indexed: 12/20/2022] Open
Abstract
In healthy adult skeletal muscle fibers microtubules form a three-dimensional grid-like network. In the mdx mouse, a model of Duchenne muscular dystrophy (DMD), microtubules are mostly disordered, without periodicity. These microtubule defects have been linked to the mdx mouse pathology. We now report that increased expression of the beta 6 class V β-tubulin (tubb6) contributes to the microtubule changes of mdx muscles. Wild-type muscle fibers overexpressing green fluorescent protein (GFP)-tubb6 (but not GFP-tubb5) have disorganized microtubules whereas mdx muscle fibers depleted of tubb6 (but not of tubb5) normalize their microtubules, suggesting that increasing tubb6 is toxic. However, tubb6 increases spontaneously during differentiation of mouse and human muscle cultures. Furthermore, endogenous tubb6 is not uniformly expressed in mdx muscles but is selectively increased in fiber clusters, which we identify as regenerating. Similarly, mdx-based rescued transgenic mice that retain a higher than expected tubb6 level show focal expression of tubb6 in subsets of fibers. Tubb6 is also upregulated in cardiotoxin-induced mouse muscle regeneration, in human myositis and DMD biopsies, and the tubb6 level correlates with that of embryonic myosin heavy chain, a regeneration marker. In conclusion, modulation of a β-tubulin isotype plays a role in muscle differentiation and regeneration. Increased tubb6 expression and microtubule reorganization are not pathological per se but reflect a return to an earlier developmental stage. However, chronic elevation of tubb6, as occurs in the mdx mouse, may contribute to the repeated cycles of regeneration and to the pathology of the disease.
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Affiliation(s)
- Davide Randazzo
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Umara Khalique
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Joseph J Belanto
- Department of Biochemistry, Molecular Biology, and Biophysics, and Program in Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Aster Kenea
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Dana M Talsness
- Department of Biochemistry, Molecular Biology, and Biophysics, and Program in Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - John T Olthoff
- Department of Biochemistry, Molecular Biology, and Biophysics, and Program in Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Michelle D Tran
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kristien J Zaal
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Katherine Pak
- Laboratory of Muscle Stem Cells and Gene Regulation, Muscle Disease Unit, NIAMS, NIH, Bethesda, MD, USA
| | - Iago Pinal-Fernandez
- Laboratory of Muscle Stem Cells and Gene Regulation, Muscle Disease Unit, NIAMS, NIH, Bethesda, MD, USA.,Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew L Mammen
- Laboratory of Muscle Stem Cells and Gene Regulation, Muscle Disease Unit, NIAMS, NIH, Bethesda, MD, USA.,Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dan Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, USA
| | - James M Ervasti
- Department of Biochemistry, Molecular Biology, and Biophysics, and Program in Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Evelyn Ralston
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
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Beggs AD, Mehta S, Deeks JJ, James JD, Caldwell GM, Dilworth MP, Stockton JD, Blakeway D, Pestinger V, Vince A, Taniere P, Iqbal T, Magill L, Matthews G, Morton DG. Validation of epigenetic markers to identify colitis associated cancer: Results of module 1 of the ENDCAP-C study. EBioMedicine 2019; 39:265-271. [PMID: 30473377 PMCID: PMC6355942 DOI: 10.1016/j.ebiom.2018.11.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/04/2018] [Accepted: 11/16/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Chronic inflammation caused by ulcerative colitis (UC) causes a pro-neoplastic drive in the inflamed colon, leading to a markedly greater risk of invasive malignancy compared to the general population. Despite surveillance protocols, 50% of cases proceed to cancer before neoplasia is detected. The Enhanced Neoplasia Detection and Cancer Prevention in Chronic Colitis (ENDCaP-C) trial is an observational multi-centre test accuracy study to ascertain the role of molecular markers in improving the detection of dysplasia. We aimed to validate previously identified biomarkers of neoplasia in a retrospective cohort and create predictive models for later validation in a prospective cohort. METHODS A retrospective analysis using bisulphite pyrosequencing of an 11 marker panel (SFRP1, SFRP2, SRP4, SRP5, WIF1, TUBB6, SOX7, APC1A, APC2, MINT1, RUNX3) in samples from 35 patients with cancer, 78 with dysplasia and 343 without neoplasia undergoing surveillance for UC associated neoplasia across 6 medical centres. Predictive models for UC associated cancer/dysplasia were created in the setting of neoplastic and non-neoplastic mucosa. FINDINGS For neoplastic mucosa a five marker panel (SFRP2, SFRP4, WIF1, APC1A, APC2) was accurate in detecting pre-cancerous and invasive neoplasia (AUC = 0.83; 95% CI: 0.79, 0.88), and dysplasia (AUC = 0.88; (0.84, 0.91). For non-neoplastic mucosa a four marker panel (APC1A, SFRP4, SFRP5, SOX7) had modest accuracy (AUC = 0.68; 95% CI: 0.62,0.73) in predicting associated bowel neoplasia through the methylation signature of distant non-neoplastic colonic mucosa. INTERPRETATION This multiplex methylation marker panel is accurate in the detection of ulcerative colitis associated dysplasia and neoplasia and is currently being validated in a prospective clinical trial. FUNDING The ENDCAP-C study was funded by the National Institute for Health Research Efficacy and Mechanism Evaluation (EME) Programme (11/100/29).
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Affiliation(s)
- Andrew D Beggs
- Institute of Cancer & Genomic Science, University of Birmingham, UK.
| | - Samir Mehta
- Birmingham Clinical Trials Unit, University of Birmingham, UK
| | - Jonathan J Deeks
- Birmingham Clinical Trials Unit, University of Birmingham, UK; National Institute for Health Research (NIHR), Birmingham Inflammation Biomedical Research Centre, UK
| | - Jonathan D James
- Institute of Cancer & Genomic Science, University of Birmingham, UK
| | | | - Mark P Dilworth
- Institute of Cancer & Genomic Science, University of Birmingham, UK
| | | | - Daniel Blakeway
- Institute of Cancer & Genomic Science, University of Birmingham, UK
| | | | - Alexandra Vince
- Birmingham Clinical Trials Unit, University of Birmingham, UK
| | | | - Tariq Iqbal
- Institute of Cancer & Genomic Science, University of Birmingham, UK
| | - Laura Magill
- Birmingham Clinical Trials Unit, University of Birmingham, UK
| | - Glenn Matthews
- Institute of Cancer & Genomic Science, University of Birmingham, UK
| | - Dion G Morton
- Institute of Cancer & Genomic Science, University of Birmingham, UK
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