1
|
Mukherjee A, Abraham S, Singh A, Balaji S, Mukunthan KS. From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies. Mol Biotechnol 2024:10.1007/s12033-024-01133-6. [PMID: 38565775 DOI: 10.1007/s12033-024-01133-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
In the dynamic landscape of targeted therapeutics, drug discovery has pivoted towards understanding underlying disease mechanisms, placing a strong emphasis on molecular perturbations and target identification. This paradigm shift, crucial for drug discovery, is underpinned by big data, a transformative force in the current era. Omics data, characterized by its heterogeneity and enormity, has ushered biological and biomedical research into the big data domain. Acknowledging the significance of integrating diverse omics data strata, known as multi-omics studies, researchers delve into the intricate interrelationships among various omics layers. This review navigates the expansive omics landscape, showcasing tailored assays for each molecular layer through genomes to metabolomes. The sheer volume of data generated necessitates sophisticated informatics techniques, with machine-learning (ML) algorithms emerging as robust tools. These datasets not only refine disease classification but also enhance diagnostics and foster the development of targeted therapeutic strategies. Through the integration of high-throughput data, the review focuses on targeting and modeling multiple disease-regulated networks, validating interactions with multiple targets, and enhancing therapeutic potential using network pharmacology approaches. Ultimately, this exploration aims to illuminate the transformative impact of multi-omics in the big data era, shaping the future of biological research.
Collapse
Affiliation(s)
- Arnab Mukherjee
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Suzanna Abraham
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Akshita Singh
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - K S Mukunthan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India.
| |
Collapse
|
2
|
Zhang H, Kalla R, Chen J, Zhao J, Zhou X, Adams A, Noble A, Ventham NT, Wellens J, Ho GT, Dunlop MG, Nowak JK, Ding Y, Liu Z, Satsangi J, Theodoratou E, Li X. Altered DNA methylation within DNMT3A, AHRR, LTA/TNF loci mediates the effect of smoking on inflammatory bowel disease. Nat Commun 2024; 15:595. [PMID: 38238335 PMCID: PMC10796384 DOI: 10.1038/s41467-024-44841-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
This work aims to investigate how smoking exerts effect on the development of inflammatory bowel disease (IBD). A prospective cohort study and a Mendelian randomization study are first conducted to evaluate the association between smoking behaviors, smoking-related DNA methylation and the risks of Crohn's disease (CD) and ulcerative colitis (UC). We then perform both genome-wide methylation analysis and co-localization analysis to validate the observed associations. Compared to never smoking, current and previous smoking habits are associated with increased CD (P = 7.09 × 10-10) and UC (P < 2 × 10-16) risk, respectively. DNA methylation alteration at cg17742416 [DNMT3A] is linked to both CD (P = 7.30 × 10-8) and UC (P = 1.04 × 10-4) risk, while cg03599224 [LTA/TNF] is associated with CD risk (P = 1.91 × 10-6), and cg14647125 [AHRR] and cg23916896 [AHRR] are linked to UC risk (P = 0.001 and 0.002, respectively). Our study identifies biological mechanisms and pathways involved in the effects of smoking on the pathogenesis of IBD.
Collapse
Affiliation(s)
- Han Zhang
- Department of Big Data in Health Science School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Rahul Kalla
- Edinburgh IBD Science Unit, Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Jie Chen
- Department of Big Data in Health Science School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianhui Zhao
- Department of Big Data in Health Science School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xuan Zhou
- Department of Big Data in Health Science School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Alex Adams
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Alexandra Noble
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Nicholas T Ventham
- Academic Coloproctology, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Judith Wellens
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Department of Chronic Diseases and Metabolism, Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Gwo-Tzer Ho
- Edinburgh IBD Science Unit, Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Dunlop
- Cancer Research UK Scotland Centre and Medical Research Council Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Jan Krzysztof Nowak
- Department of Paediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Yuan Ding
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhanju Liu
- Center for IBD Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| | - Evropi Theodoratou
- Cancer Research UK Scotland Centre and Medical Research Council Human Genetics Unit, University of Edinburgh, Edinburgh, UK.
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK.
| | - Xue Li
- Department of Big Data in Health Science School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
3
|
Zeng Z, Jiang M, Li X, Yuan J, Zhang H. Precision medicine in inflammatory bowel disease. Precis Clin Med 2023; 6:pbad033. [PMID: 38638127 PMCID: PMC11025389 DOI: 10.1093/pcmedi/pbad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/13/2023] [Indexed: 04/20/2024] Open
Abstract
Inflammatory bowel disease (IBD) is an incurable disease characterized by remission-relapse cycles throughout its course. Both Crohn's disease (CD) and ulcerative colitis (UC), the two main forms of IBD, exhibit tendency to develop complications and substantial heterogeneity in terms of frequency and severity of relapse, thus posing great challenges to the clinical management for IBD. Current treatment strategies are effective in different ways in induction and maintenance therapies for IBD. Recent advances in studies of genetics, pharmacogenetics, proteomics and microbiome provide a strong driving force for identifying molecular markers of prognosis and treatment response, which should help clinicians manage IBD patients more effectively, and then, improve clinical outcomes and reduce treatment costs of patients. In this review, we summarize and discuss precision medicine in IBD, focusing on predictive markers of disease course and treatment response, and monitoring indices during therapeutic drug monitoring.
Collapse
Affiliation(s)
- Zhen Zeng
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mingshan Jiang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xi Li
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
- General Practice Ward/International Medical Center Ward, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jing Yuan
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hu Zhang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| |
Collapse
|
4
|
Chew DCH, Khoo XH, Lee TS, Chin KY, Raja Ali RA, Muhammad Nawawi KN, Wan Ibrahim NR, Hilmi I. A Systematic Review on the Increasing Incidence of Inflammatory Bowel Disease in Southeast Asia: Looking Beyond the Urbanization Phenomenon. Inflamm Bowel Dis 2023:izad189. [PMID: 37935628 DOI: 10.1093/ibd/izad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Indexed: 11/09/2023]
Abstract
The incidence of inflammatory bowel disease (IBD) has been increasing in Southeast Asia (SEA) in tandem with its economic growth and urbanization over the past 2 decades. Specific characteristics of IBD in SEA are similar to East Asia and the West, such as the declining ratio of ulcerative colitis to Crohn's disease. However, exceptionally low familial aggregation is seen. Smoking is also not a common risk factor in patients with Crohn's disease. The incidence of perianal disease is higher in SEA than in Australia and is comparable to the West. In a multiracial population, such as Singapore and Malaysia, Indians have the highest incidence and prevalence rates, which are likely to be due to important putative mutations. For instance, a higher frequency of the NOD2 predisposing mutation SNP5 and IBD risk allele IGR2198a and IGR2092a were found in Indians. Although differences in the genetic constitution play an important role in the epidemiology and prognosis of IBD in SEA, the emergence of this disease offers a unique opportunity to identify potential exposomes that contribute to its pathogenesis.
Collapse
Affiliation(s)
- Deborah Chia Hsin Chew
- Gastroenterology and hepatology Unit, Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Xin-Hui Khoo
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Tiong See Lee
- Department of Gastroenterology and Hepatology, Selayang Hospital, Kuala Lumpur, Malaysia
| | - Kok-Yong Chin
- Department of Pharmacology, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Raja Affendi Raja Ali
- Gastroenterology and hepatology Unit, Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Khairul Najmi Muhammad Nawawi
- Gastroenterology and hepatology Unit, Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | | | - Ida Hilmi
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
5
|
Fiocchi C. Omics and Multi-Omics in IBD: No Integration, No Breakthroughs. Int J Mol Sci 2023; 24:14912. [PMID: 37834360 PMCID: PMC10573814 DOI: 10.3390/ijms241914912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
The recent advent of sophisticated technologies like sequencing and mass spectroscopy platforms combined with artificial intelligence-powered analytic tools has initiated a new era of "big data" research in various complex diseases of still-undetermined cause and mechanisms. The investigation of these diseases was, until recently, limited to traditional in vitro and in vivo biological experimentation, but a clear switch to in silico methodologies is now under way. This review tries to provide a comprehensive assessment of state-of-the-art knowledge on omes, omics and multi-omics in inflammatory bowel disease (IBD). The notion and importance of omes, omics and multi-omics in both health and complex diseases like IBD is introduced, followed by a discussion of the various omics believed to be relevant to IBD pathogenesis, and how multi-omics "big data" can generate new insights translatable into useful clinical tools in IBD such as biomarker identification, prediction of remission and relapse, response to therapy, and precision medicine. The pitfalls and limitations of current IBD multi-omics studies are critically analyzed, revealing that, regardless of the types of omes being analyzed, the majority of current reports are still based on simple associations of descriptive retrospective data from cross-sectional patient cohorts rather than more powerful longitudinally collected prospective datasets. Given this limitation, some suggestions are provided on how IBD multi-omics data may be optimized for greater clinical and therapeutic benefit. The review concludes by forecasting the upcoming incorporation of multi-omics analyses in the routine management of IBD.
Collapse
Affiliation(s)
- Claudio Fiocchi
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland, OH 44195, USA;
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| |
Collapse
|
6
|
Kamal S, Parkash N, Beattie W, Christensen B, Segal JP. Are We Ready to Reclassify Crohn's Disease Using Molecular Classification? J Clin Med 2023; 12:5786. [PMID: 37762727 PMCID: PMC10532006 DOI: 10.3390/jcm12185786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/21/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
Crohn's disease (CD) is a type of inflammatory bowel disease. The number of IBD cases worldwide was estimated to be 4.9 million in 2019. CD exhibits heterogeneity in clinical presentation, anatomical involvement, disease behaviour, clinical course and response to treatment. The classical description of CD involves transmural inflammation with skip lesions anywhere along the entire gastrointestinal tract. The complexity and heterogeneity of Crohn's disease is not currently reflected in the conventional classification system. Though the knowledge of Crohn's pathophysiology remains far from understood, the established complex interplay of the omics-genomics, transcriptomics, proteomics, epigenomics, metagenomics, metabolomics, lipidomics and immunophenomics-provides numerous targets for potential molecular markers of disease. Advancing technology has enabled identification of small molecules within these omics, which can be extrapolated to differentiate types of Crohn's disease. The multi-omic future of Crohn's disease is promising, with potential for advancements in understanding of its pathogenesis and implementation of personalised medicine.
Collapse
Affiliation(s)
- Shahed Kamal
- Department of Gastroenterology, Northern Hospital, Epping, Melbourne VIC 3076, Australia
| | - Nikita Parkash
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - William Beattie
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - Britt Christensen
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
| | - Jonathan P. Segal
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
| |
Collapse
|
7
|
Scalia F, Carini F, David S, Giammanco M, Mazzola M, Rappa F, Bressan NI, Maida G, Tomasello G. Inflammatory Bowel Diseases: An Updated Overview on the Heat Shock Protein Involvement. Int J Mol Sci 2023; 24:12129. [PMID: 37569505 PMCID: PMC10419025 DOI: 10.3390/ijms241512129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) represent chronic idiopathic disorders, including Crohn's disease (CD) and ulcerative colitis (UC), in which one of the trigger factors is represented by aberrant immune interactions between the intestinal epithelium and the intestinal microbiota. The involvement of heat shock proteins (HSPs) as etiological and pathogenetic factors is becoming of increasing interest. HSPs were found to be differentially expressed in the intestinal tissues and sera of patients with CD and UC. It has been shown that HSPs can play a dual role in the disease, depending on the stage of progression. They can support the inflammatory and fibrosis process, but they can also act as protective factors during disease progression or before the onset of one of the worst complications of IBD, colorectal cancer. Furthermore, HSPs are able to mediate the interaction between the intestinal microbiota and intestinal epithelial cells. In this work, we discuss the involvement of HSPs in IBD considering their genetic, epigenetic, immune and molecular roles, referring to the most recent works present in the literature. With our review, we want to shed light on the importance of further exploring the role of HSPs, or even better, the role of the molecular chaperone system (CS), in IBD: various molecules of the CS including HSPs may have diagnostic, prognostic and therapeutic potential, promoting the creation of new drugs that could overcome the side-effects of the therapies currently used.
Collapse
Affiliation(s)
- Federica Scalia
- Biomedicine, Neurosciences and Advanced Diagnostics BIND, School of Medicine, University of Palermo, 90133 Palermo, Italy; (F.C.); (M.M.); (F.R.); (G.M.); (G.T.)
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Francesco Carini
- Biomedicine, Neurosciences and Advanced Diagnostics BIND, School of Medicine, University of Palermo, 90133 Palermo, Italy; (F.C.); (M.M.); (F.R.); (G.M.); (G.T.)
- Hospital University School of Medicine, P. Giaccone, 90127 Palermo, Italy
| | - Sabrina David
- Department Surgical, Oncological and Oral Sciences, School of Medicine, University of Palermo, 90133 Palermo, Italy; (S.D.); (M.G.)
| | - Marco Giammanco
- Department Surgical, Oncological and Oral Sciences, School of Medicine, University of Palermo, 90133 Palermo, Italy; (S.D.); (M.G.)
| | - Margherita Mazzola
- Biomedicine, Neurosciences and Advanced Diagnostics BIND, School of Medicine, University of Palermo, 90133 Palermo, Italy; (F.C.); (M.M.); (F.R.); (G.M.); (G.T.)
| | - Francesca Rappa
- Biomedicine, Neurosciences and Advanced Diagnostics BIND, School of Medicine, University of Palermo, 90133 Palermo, Italy; (F.C.); (M.M.); (F.R.); (G.M.); (G.T.)
- Institute of Translational Pharmacology (IFT), Section of Palermo, Italy National Research Council of Italy (CNR), 90146 Palermo, Italy
| | | | - Giorgio Maida
- Biomedicine, Neurosciences and Advanced Diagnostics BIND, School of Medicine, University of Palermo, 90133 Palermo, Italy; (F.C.); (M.M.); (F.R.); (G.M.); (G.T.)
| | - Giovanni Tomasello
- Biomedicine, Neurosciences and Advanced Diagnostics BIND, School of Medicine, University of Palermo, 90133 Palermo, Italy; (F.C.); (M.M.); (F.R.); (G.M.); (G.T.)
| |
Collapse
|
8
|
Nowak JK, Kalla R, Satsangi J. Current and emerging biomarkers for ulcerative colitis. Expert Rev Mol Diagn 2023; 23:1107-1119. [PMID: 37933807 DOI: 10.1080/14737159.2023.2279611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]
Abstract
INTRODUCTION Ulcerative colitis (UC) is a chronic illness requiring lifelong management that could be enhanced by personalizing care using biomarkers. AREAS COVERED The main biomarker discovery modalities are reviewed, highlighting recent results across the spectrum of applications, including diagnostics (serum anti-αvβ6 antibodies achieving an area under the curve [AUC] = 0.99; serum oncostatin M AUC = 0.94), disease activity assessment (fecal calprotectin and serum trefoil factor 3: AUC > 0.90), prognostication of the need for treatment escalation (whole blood transcriptomic panels and CLEC5A/CDH2 ratio: AUC > 0.90), prediction of treatment response, and early identification of patients with subclinical disease. The use of established biomarkers is discussed, along with new evidence regarding autoantibodies, proteins, proteomic panels, transcriptomic signatures, deoxyribonucleic acid methylation patterns, and UC-specific glycomic and metabolic disturbances. EXPERT OPINION Novel biomarkers will pave the way for optimized UC care. However, validation, simplification, and direct clinical translation of complex models may prove challenging. Currently, few candidates exist to assess key characteristics, such as UC susceptibility, histological disease activity, drug response, and long-term disease behavior. Further research will likely not only reveal new tools to tackle these issues but also contribute to understanding UC pathogenesis mechanisms.
Collapse
Affiliation(s)
- Jan K Nowak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Rahul Kalla
- Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, UK
| |
Collapse
|
9
|
Ventham NT, Kennedy NA, Kalla R, Adams AT, Noble A, Ennis H, Mowat C, Dunlop MG, Satsangi J. Genome-Wide Methylation Profiling in 229 Patients With Crohn's Disease Requiring Intestinal Resection: Epigenetic Analysis of the Trial of Prevention of Post-operative Crohn's Disease (TOPPIC). Cell Mol Gastroenterol Hepatol 2023; 16:431-450. [PMID: 37331566 PMCID: PMC10372903 DOI: 10.1016/j.jcmgh.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/20/2023]
Abstract
BACKGROUND & AIMS DNA methylation alterations may provide important insights into gene-environment interaction in cancer, aging, and complex diseases, such as inflammatory bowel disease (IBD). We aim first to determine whether the circulating DNA methylome in patients requiring surgery may predict Crohn's disease (CD) recurrence following intestinal resection; and second to compare the circulating methylome seen in patients with established CD with that we had reported in a series of inception cohorts. METHODS TOPPIC was a placebo-controlled, randomized controlled trial of 6-mercaptopurine at 29 UK centers in patients with CD undergoing ileocolic resection between 2008 and 2012. Genomic DNA was extracted from whole blood samples from 229 of the 240 patients taken before intestinal surgery and analyzed using 450KHumanMethylation and Infinium Omni Express Exome arrays (Illumina, San Diego, CA). Coprimary objectives were to determine whether methylation alterations may predict clinical disease recurrence; and to assess whether the epigenetic alterations previously reported in newly diagnosed IBD were present in the patients with CD recruited into the TOPPIC study. Differential methylation and variance analysis was performed comparing patients with and without clinical evidence of recurrence. Secondary analyses included investigation of methylation associations with smoking, genotype (MeQTLs), and chronologic age. Validation of our previously published case-control observation of the methylome was performed using historical control data (CD, n = 123; Control, n = 198). RESULTS CD recurrence in patients following surgery is associated with 5 differentially methylated positions (Holm P < .05), including probes mapping to WHSC1 (P = 4.1 × 10-9, Holm P = .002) and EFNA3 (P = 4.9 × 10-8, Holm P = .02). Five differentially variable positions are demonstrated in the group of patients with evidence of disease recurrence including a probe mapping to MAD1L1 (P = 6.4 × 10-5). DNA methylation clock analyses demonstrated significant age acceleration in CD compared with control subjects (GrimAge + 2 years; 95% confidence interval, 1.2-2.7 years), with some evidence for accelerated aging in patients with CD with disease recurrence following surgery (GrimAge +1.04 years; 95% confidence interval, -0.04 to 2.22). Significant methylation differences between CD cases and control subjects were seen by comparing this cohort in conjunction with previously published control data, including validation of our previously described differentially methylated positions (RPS6KA2 P = 1.2 × 10-19, SBNO2 = 1.2 × 10-11) and regions (TXK [false discovery rate, P = 3.6 × 10-14], WRAP73 [false discovery rate, P = 1.9 × 10-9], VMP1 [false discovery rate, P = 1.7 × 10-7], and ITGB2 [false discovery rate, P = 1.4 × 10-7]). CONCLUSIONS We demonstrate differential methylation and differentially variable methylation in patients developing clinical recurrence within 3 years of surgery. Moreover, we report replication of the CD-associated methylome, previously characterized only in adult and pediatric inception cohorts, in patients with medically refractory disease needing surgery.
Collapse
Affiliation(s)
- Nicholas T Ventham
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom.
| | - Nicholas A Kennedy
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Rahul Kalla
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Alex T Adams
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Alexandra Noble
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Holly Ennis
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Craig Mowat
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Malcolm G Dunlop
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Jack Satsangi
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| |
Collapse
|
10
|
Zhao Z, Zhang L, Ocansey DKW, Wang B, Mao F. The role of mesenchymal stem cell-derived exosome in epigenetic modifications in inflammatory diseases. Front Immunol 2023; 14:1166536. [PMID: 37261347 PMCID: PMC10227589 DOI: 10.3389/fimmu.2023.1166536] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/04/2023] [Indexed: 06/02/2023] Open
Abstract
Epigenetic modification is a complex process of reversible and heritable alterations in gene function, and the combination of epigenetic and metabolic alterations is recognized as an important causative factor in diseases such as inflammatory bowel disease (IBD), osteoarthritis (OA), systemic lupus erythematosus (SLE), and even tumors. Mesenchymal stem cell (MSC) and MSC-derived exosome (MSC-EXO) are widely studied in the treatment of inflammatory diseases, where they appear to be promising therapeutic agents, partly through the potent regulation of epigenetic modifications such as DNA methylation, acetylation, phosphorylation, and expression of regulatory non-coding RNAs, which affects the occurrence and development of inflammatory diseases. In this review, we summarize the current research on the role of MSC-EXO in inflammatory diseases through their modulation of epigenetic modifications and discuss its potential application in the treatment of inflammatory diseases.
Collapse
Affiliation(s)
- Zihan Zhao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Li Zhang
- Nanjing Lishui People’s Hospital, Zhongda Hospital Lishui Branch, Southeast University, Nanjing, China
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, China
- Directorate of University Health Services, University of Cape Coast, Cape Coast, Ghana
| | - Bo Wang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, China
| |
Collapse
|
11
|
Rodríguez-Lago I, Blackwell J, Mateos B, Marigorta UM, Barreiro-de Acosta M, Pollok R. Recent Advances and Potential Multi-Omics Approaches in the Early Phases of Inflammatory Bowel Disease. J Clin Med 2023; 12:jcm12103418. [PMID: 37240524 DOI: 10.3390/jcm12103418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/01/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Inflammatory bowel disease leads to debilitating gastrointestinal symptoms and reduced quality of life, resulting in a significant burden on healthcare utilization and costs. Despite substantial advancements in diagnosis and treatment, there may still be considerable delays in diagnosing some patients. To reduce disease progression before the full disease spectrum appears and improve prognostic outcomes, several strategies have concentrated on early intervention and prevention. Recent evidence shows that initial immune response changes and endoscopic lesions may exist for years before diagnosis, implying the existence of a preclinical phase of inflammatory bowel disease comparable to findings in other immune-mediated disorders. In this review, we highlight the most relevant findings regarding preclinical inflammatory bowel disease and the prospective role of novel omics techniques in this field.
Collapse
Affiliation(s)
- Iago Rodríguez-Lago
- Gastroenterology Department, Hospital Universitario de Galdakao, 48960 Galdakao, Spain
- Biocruces Bizkaia Health Research Institute, 48960 Galdakao, Spain
- Deusto University, 48007 Bilbao, Spain
| | | | - Beatriz Mateos
- Integrative Genomics Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Urko M Marigorta
- Integrative Genomics Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Sciences, 48009 Bilbao, Spain
| | - Manuel Barreiro-de Acosta
- Gastroenterology Department, Hospital Clínico Universitario de Santiago, 15706 Santiago de Compostela, Spain
| | - Richard Pollok
- Gastroenterology Department, St George's University of London, London SW17 0RE, UK
| |
Collapse
|
12
|
Ross ADB, Zilbauer M. Validation of IBD-associated Whole-blood DNA Methylation Changes-Where Do We Go From Here? J Crohns Colitis 2023; 17:151-152. [PMID: 36367402 DOI: 10.1093/ecco-jcc/jjac163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Alexander D B Ross
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- University Department of Paediatrics, University of Cambridge, Cambridge, UK
- University Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Matthias Zilbauer
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- University Department of Paediatrics, University of Cambridge, Cambridge, UK
| |
Collapse
|