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Mukhopadhyay S, Saha S, Chakraborty S, Prasad P, Ghosh A, Aich P. Differential colitis susceptibility of Th1- and Th2-biased mice: A multi-omics approach. PLoS One 2022; 17:e0264400. [PMID: 35263357 PMCID: PMC8906622 DOI: 10.1371/journal.pone.0264400] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/09/2022] [Indexed: 01/08/2023] Open
Abstract
The health and economic burden of colitis is increasing globally. Understanding the role of host genetics and metagenomics is essential to establish the molecular basis of colitis pathogenesis. In the present study, we have used a common composite dose of DSS to compare the differential disease severity response in C57BL/6 (Th1 biased) and BALB/c (Th2 biased) mice with zero mortality rates. We employed multi-omics approaches and developed a newer vector analysis approach to understand the molecular basis of the disease pathogenesis. In the current report, comparative transcriptomics, metabonomics, and metagenomics analyses revealed that the Th1 background of C57BL/6 induced intense inflammatory responses throughout the treatment period. On the contrary, the Th2 background of BALB/c resisted severe inflammatory responses by modulating the host’s inflammatory, metabolic, and gut microbial profile. The multi-omics approach also helped us discover some unique metabolic and microbial markers associated with the disease severity. These biomarkers could be used in diagnostics.
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Affiliation(s)
- Sohini Mukhopadhyay
- School of Biological Sciences, National Institute of Science Education and Research (NISER), HBNI, Khurdha, Odisha, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, India
| | - Subha Saha
- Institute of Life Sciences, NALCO Square, Bhubaneswar, Odisha, India
| | - Subhayan Chakraborty
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, India
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, Khurdha, Odisha, India
| | - Punit Prasad
- Institute of Life Sciences, NALCO Square, Bhubaneswar, Odisha, India
| | - Arindam Ghosh
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, India
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, Khurdha, Odisha, India
| | - Palok Aich
- School of Biological Sciences, National Institute of Science Education and Research (NISER), HBNI, Khurdha, Odisha, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, India
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2
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Interplay between Cellular and Molecular Mechanisms Underlying Inflammatory Bowel Diseases Development-A Focus on Ulcerative Colitis. Cells 2020; 9:cells9071647. [PMID: 32659925 PMCID: PMC7408467 DOI: 10.3390/cells9071647] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are defined by the continuous inflammation of the gastrointestinal tract. During inflammation, the number of pathogens in the intestinal epithelium increases, leading to inflammasome assembly. Inflammasome activation is meant to protect the intestinal epithelial barrier from further damage by maintaining homeostasis. Although its purpose is to protect the cells, excessive nucleotide-binding oligomerization domain-like receptor and pyrin domain-containing protein 3 (NLRP3) inflammasome assembly is responsible for the synthesis of a high number of pro-inflammatory cytokines. The activation of two crucial pathways, autophagy process, and unfolded protein response, is initiated for restoring homeostasis. Aberrant expression of miRNAs and lncRNAs also interfere with the pathogenic mechanisms of IBD, as these non-coding transcripts play key roles in regulation of biological processes, such as inflammation and immunity. This review thoroughly describes the cellular and molecular mechanism that trigger and perpetuate inflammation in ulcerative colitis (UC) patients.
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Yang L, Bian Y, Li Z, Yan Y, Li J, Li W, Zeng L. Identification of potential biomarkers and pathways in ulcerative colitis with combined public mRNA and miRNA expression microarray data analysis. J Gastrointest Oncol 2019; 10:847-858. [PMID: 31602322 DOI: 10.21037/jgo.2019.06.06] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Ulcerative colitis (UC) is a chronic, relapsing and non-specific inflammatory disease, involving various genes and pathways in their pathogenesis. Increasing evidences have showed that microRNAs (miRNAs) act as key post-transcriptional regulators of gene expression in UC. This current study aimed to identify key miRNAs, potential target genes, and relevant pathways involved in UC to uncover their underlying molecular mechanisms by using bioinformatics analysis. Methods The mRNA and miRNA expression profiles were retrieved and downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and miRNAs (DEMIs) were obtained by using the R software package. Results A total of 79 DEGs and 47 DEMIs were obtained. And a panel of miRNAs and their target mRNAs were identified. It showed that miR-1231 may be a key regulator for DUOX2 and TFF1. CCL11 may be potentially targeted by miR-625. MMP1 may play vital roles in the development of UC by regulating the miR-1228/PPAR signaling pathway. In addition, we validated the most significantly up/down-expressed miRNAs (miR-92b, miR-625) and two of their corresponding target mRNAs (AQP8 and TAGAP, CCL11 and CHI3L1) in colon tissues of UC models preliminarily. The results were consistent with the microarray analysis. Conclusions These findings may provide new insights into representing key mechanisms associated with the development of UC.
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Affiliation(s)
- Lili Yang
- School of First Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Jingwen Library, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yaoyao Bian
- School of Nursing, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhengjun Li
- Management School, Lancaster University, Lancaster, LA1 4YW, UK
| | - Yan Yan
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Junyi Li
- School of First Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wenlin Li
- Jingwen Library, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Li Zeng
- School of First Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Jingwen Library, Nanjing University of Chinese Medicine, Nanjing 210023, China
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Haberman Y, Karns R, Dexheimer PJ, Schirmer M, Somekh J, Jurickova I, Braun T, Novak E, Bauman L, Collins MH, Mo A, Rosen MJ, Bonkowski E, Gotman N, Marquis A, Nistel M, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, Leleiko NS, Heyman MB, Grifiths AM, Patel AS, Noe JD, Aronow BJ, Kugathasan S, Walters TD, Gibson G, Thomas SD, Mollen K, Shen-Orr S, Huttenhower C, Xavier RJ, Hyams JS, Denson LA. Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response. Nat Commun 2019; 10:38. [PMID: 30604764 PMCID: PMC6318335 DOI: 10.1038/s41467-018-07841-3] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/28/2018] [Indexed: 02/07/2023] Open
Abstract
Molecular mechanisms driving disease course and response to therapy in ulcerative colitis (UC) are not well understood. Here, we use RNAseq to define pre-treatment rectal gene expression, and fecal microbiota profiles, in 206 pediatric UC patients receiving standardised therapy. We validate our key findings in adult and paediatric UC cohorts of 408 participants. We observe a marked suppression of mitochondrial genes and function across cohorts in active UC, and that increasing disease severity is notable for enrichment of adenoma/adenocarcinoma and innate immune genes. A subset of severity genes improves prediction of corticosteroid-induced remission in the discovery cohort; this gene signature is also associated with response to anti-TNFα and anti-α4β7 integrin in adults. The severity and therapeutic response gene signatures were in turn associated with shifts in microbes previously implicated in mucosal homeostasis. Our data provide insights into UC pathogenesis, and may prioritise future therapies for nonresponders to current approaches.
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Affiliation(s)
- Yael Haberman
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
- Sheba Medical Center, Tel Hashomer, affiliated with the Tel Aviv University, Tel Aviv, 5265601, Israel
| | - Rebekah Karns
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Phillip J Dexheimer
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Melanie Schirmer
- Broad Institute of MIT and Harvard University, Cambridge, 02142, MA, USA
| | - Judith Somekh
- Faculty of Medicine, Technion, Haifa, 3109601, Israel
- Department of Information Systems, University of Haifa, Haifa, 3498838, Israel
| | - Ingrid Jurickova
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Tzipi Braun
- Sheba Medical Center, Tel Hashomer, affiliated with the Tel Aviv University, Tel Aviv, 5265601, Israel
| | - Elizabeth Novak
- Children's Hospital of Pittsburgh, Pittsburgh, 15224, PA, USA
| | - Laura Bauman
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
- Department of Pediatrics, University of California at San Diego, La Jolla, 92162, CA, USA
| | - Margaret H Collins
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Angela Mo
- Georgia Institute of Technology, Atlanta, 30332, GA, USA
| | - Michael J Rosen
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Erin Bonkowski
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Nathan Gotman
- Collaborative Studies Coordinating Center, University of North Carolina, Chapel Hill, 27516, NC, USA
| | - Alison Marquis
- Collaborative Studies Coordinating Center, University of North Carolina, Chapel Hill, 27516, NC, USA
| | - Mason Nistel
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Paul A Rufo
- Harvard-Children's Hospital Boston, Boston, 02115, MA, USA
| | - Susan S Baker
- Women & Children's Hospital of Buffalo WCHOB, Buffalo, 14222, NY, USA
| | | | - James Markowitz
- Cohen Children's Medical Center of New York, 11040, New Hyde Park, NY, USA
| | | | - Joel R Rosh
- Goryeb Children's Hospital-Atlantic Health, Morristown, 07960, NJ, USA
| | | | - David R Mack
- Children's Hospital of East Ontario, Ottawa, Ontario, K1P 1J1, Canada
| | | | - Sapana Shah
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, 15224, PA, USA
| | | | - Melvin B Heyman
- University of California at San Francisco, San Francisco, 94143, CA, USA
| | | | | | - Joshua D Noe
- Medical College of Wisconsin, Milwaukee, 53226, WI, USA
| | - Bruce J Aronow
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | | | | | - Greg Gibson
- Georgia Institute of Technology, Atlanta, 30332, GA, USA
| | - Sonia Davis Thomas
- Collaborative Studies Coordinating Center, University of North Carolina, Chapel Hill, 27516, NC, USA
- RTI International, Research Triangle Park, 27709, NC, USA
| | - Kevin Mollen
- Children's Hospital of Pittsburgh, Pittsburgh, 15224, PA, USA
| | - Shai Shen-Orr
- Faculty of Medicine, Technion, Haifa, 3109601, Israel
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard University, Cambridge, 02142, MA, USA
- Harvard School of Public Health, Boston, 02115, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard University, Cambridge, 02142, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, 02114, MA, USA
| | - Jeffrey S Hyams
- Connecticut Children's Medical Center, Hartford, 06106, CT, USA
| | - Lee A Denson
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA.
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Chan SN, Low END, Raja Ali RA, Mokhtar NM. Delineating inflammatory bowel disease through transcriptomic studies: current review of progress and evidence. Intest Res 2018; 16:374-383. [PMID: 30090036 PMCID: PMC6077315 DOI: 10.5217/ir.2018.16.3.374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/23/2018] [Accepted: 01/29/2018] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel disease (IBD), which comprises of Crohn's disease and ulcerative colitis, is an idiopathic relapsing and remitting disease in which the interplay of different environment, microbial, immunological and genetic factors that attribute to the progression of the disease. Numerous studies have been conducted in multiple aspects including clinical, endoscopy and histopathology for the diagnostics and treatment of IBD. However, the molecular mechanism underlying the aetiology and pathogenesis of IBD is still poorly understood. This review tries to critically assess the scientific evidence at the transcriptomic level as it would help in the discovery of RNA molecules in tissues or serum between the healthy and diseased or different IBD subtypes. These molecular signatures could potentially serve as a reliable diagnostic or prognostic biomarker. Researchers have also embarked on the study of transcriptome to be utilized in targeted therapy. We focus on the evaluation and discussion related to the publications reporting the different approaches and techniques used in investigating the transcriptomic changes in IBD with the intention to offer new perspectives to the landscape of the disease.
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Affiliation(s)
- Seow-Neng Chan
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Eden Ngah Den Low
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Raja Affendi Raja Ali
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Norfilza Mohd Mokhtar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
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Sarvestani SK, Signs SA, Lefebvre V, Mack S, Ni Y, Morton A, Chan ER, Li X, Fox P, Ting A, Kalady MF, Cruise M, Ashburn J, Stiene J, Lai W, Liska D, Xiang S, Huang EH. Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids. Oncotarget 2018; 9:28717-28730. [PMID: 29983891 PMCID: PMC6033374 DOI: 10.18632/oncotarget.25617] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 05/24/2018] [Indexed: 02/07/2023] Open
Abstract
Ulcerative colitis (UC) is a prevalent form of inflammatory bowel disease (IBD) whose pathogenic mechanisms remain unclear. Elucidating these mechanisms is important to reduce UC symptoms and to prevent UC progression into colitis-associated colon cancer (CAC). Our goal was to develop and validate faithful, human-derived, UC models and analyze them at histologic, transcriptomic and epigenetic levels to allow mechanistic studies of UC and CAC pathogenesis. We generated patient-derived primary-organoid cultures from UC and non-IBD colonic epithelium. We phenotyped them histologically and used next-generation-sequencing approaches to profile whole transcriptomes and epigenomes of organoids and primary tissues. Tissue organization and expression of mucin 2 (MUC2) and lysozyme (LYZ) demonstrated histologic faithfulness of organoids to healthy and diseased colonic epithelium. Transcriptomic analyses showed increased expression of inflammatory pathways in UC patient-derived organoids and tissues. Profiling for active enhancers using the H3K27ac histone modification revealed UC-derived organoid enrichment for pathways indicative of gastrointestinal cancer, including S100 calcium-binding protein P (S100P), and revealed novel markers for GI cancer, including both LYZ and neuropeptide S receptor 1 (NPSR1). Immunolocalization showed increased levels of LYZ, S100P, and NPSR1 proteins in UC and CAC. In conclusion, primary colonic organoid cultures from UC and non-IBD patients can be established that faithfully represent diseased or normal colonic states. These models reveal precancerous molecular pathways that are already activated in UC. The findings demonstrate the suitability of primary organoids for dissecting UC and CAC pathogenic mechanisms and suggest new targets for therapeutic intervention.
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Affiliation(s)
- Samaneh K Sarvestani
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Steven A Signs
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Veronique Lefebvre
- Department of Cell and Molecular Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Stephen Mack
- Department of Pediatrics Baylor College of Medicine, Houston, Texas, USA
| | - Ying Ni
- Department of Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Andrew Morton
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ernest R Chan
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Xiaoxia Li
- Department of Immunology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Paul Fox
- Department of Cell and Molecular Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Angela Ting
- Department of Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Matthew F Kalady
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Colorectal Surgery, Cleveland Clinic, Cleveland, Ohio, USA
| | - Michael Cruise
- Department of Pathology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jean Ashburn
- Department of Surgery, Wake Forest School of Medicine, Salem, North Carolina, USA
| | - Jennifer Stiene
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Wei Lai
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - David Liska
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Colorectal Surgery, Cleveland Clinic, Cleveland, Ohio, USA
| | - Shao Xiang
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Emina H Huang
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Colorectal Surgery, Cleveland Clinic, Cleveland, Ohio, USA
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Abstract
BACKGROUND Cellular oxidative stress and genetic susceptibility have been implicated in the multifactorial etiology of ulcerative colitis (UC). The nuclear genome association with UC has been intensely investigated, but the role of the mitochondrial DNA (mtDNA) has received far less attention and may account for part of the missing heritability. This study is a comprehensive analysis of the mtDNA contribution to UC susceptibility. METHODS The association of mitochondrial single-nucleotide polymorphisms (mtSNPs) and haplogroups with UC was tested in 488 cases and 833 controls of European ancestry from the NIDDK IBD Genetics Consortium Ulcerative Colitis Genome-Wide Association Study available through dbGaP and from the Illumina Genotype Control Database (studies 64 and 65). RESULTS No evidence of population stratification could be detected using 218 ancestry informative markers for European Americans. Seven of the 58 tested mtSNPs were nominally associated with UC, and A10550G in MT-ND4L withstands the Bonferroni correction (P = 1.29E-06, odds ratio [ORG] [95% confidence interval (CI)] = 4.80 [2.54-9.05], 10550G allele: 8.1% of patients and 1.9% of controls). A10550G remains equally associated after conditional analyses on the 11 UC genome-wide association studies (GWAS) top SNPs (6.35E-07 < Pcond < 4.58E-06), which suggests that it constitutes an independent risk factor from nuclear-encoded susceptibility loci. We detected additive (but not multiplicative) epistatic interactions between A10550G and all 11 top GWAS hits. Subhaplogroup K1 (P = 0.021, OR [95% CI] = 1.71 [1.08-2.69]) increased the risk for UC, whereas the U5b lineage conferred protection (P = 0.016, OR [95% CI] = 0.34 [0.14-0.82]). CONCLUSIONS These results suggest that UC has a dual mitochondrial and nuclear genetic control that warrants further replication in independent data sets and reinforces its etiopathogenic complexity.
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