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Original Research Full Report: Basic and Translational—Alimentary Tract| Volume 161, ISSUE 1, P255-270.e4, July 01, 2021

Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection Associates With Functional Alterations in Circulating microRNAs

  • Tanya M. Monaghan
    Correspondence
    Correspondence Address correspondence to: Tanya M. Monaghan, BSc, BM, PhD, MRCP, NIHR Nottingham Digestive Diseases Biomedical Research Centre, W/E 1381, E Floor, West Block, Queen’s Medical Centre Campus, Derby Road, Nottingham NG7 2UH, United Kingdom.
    Affiliations
    National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom

    Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
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  • Anna M. Seekatz
    Affiliations
    Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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  • Nicholas O. Markham
    Affiliations
    Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA

    Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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  • Tung On Yau
    Affiliations
    Department of Biosciences, John van Geest Cancer Research Centre, Centre for Health Aging and Understanding Disease, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
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  • Maria Hatziapostolou
    Affiliations
    Department of Biosciences, John van Geest Cancer Research Centre, Centre for Health Aging and Understanding Disease, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
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  • Tahseen Jilani
    Affiliations
    Advanced Data Analysis Centre, School of Computer Science, University of Nottingham, Nottingham, United Kingdom
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  • Niki Christodoulou
    Affiliations
    Department of Biosciences, John van Geest Cancer Research Centre, Centre for Health Aging and Understanding Disease, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
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  • Brandi Roach
    Affiliations
    Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
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  • Eleni Birli
    Affiliations
    Department of Biosciences, John van Geest Cancer Research Centre, Centre for Health Aging and Understanding Disease, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
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  • Odette Pomenya
    Affiliations
    Department of Biosciences, John van Geest Cancer Research Centre, Centre for Health Aging and Understanding Disease, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
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  • Thomas Louie
    Affiliations
    Department of Microbiology and infectious Diseases, University of Calgary, Calgary, Alberta, Canada
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  • D. Borden Lacy
    Affiliations
    Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA

    Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
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  • Peter Kim
    Affiliations
    Department of Mathematics and Statistics, University of Guelph, Ontario, Canada
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  • Christine Lee
    Affiliations
    Vancouver Island Health Authority, Victoria, British Columbia, Canada

    Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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  • Dina Kao
    Correspondence
    Dina Kao, MD, Division of Gastroenterology, Department of Medicine, University of Alberta, 8540 112th Street, Edmonton, Alberta T6G 2X8, Canada.
    Affiliations
    Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
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  • Christos Polytarchou
    Correspondence
    Christos Polytarchou, PhD, John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, G11 8NS, United Kingdom.
    Affiliations
    Department of Biosciences, John van Geest Cancer Research Centre, Centre for Health Aging and Understanding Disease, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
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      Background and aims

      The molecular mechanisms underlying successful fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infection (rCDI) remain poorly understood. The primary objective of this study was to characterize alterations in microRNAs (miRs) following FMT for rCDI.

      Methods

      Sera from 2 prospective multicenter randomized controlled trials were analyzed for miRNA levels with the use of the Nanostring nCounter platform and quantitative reverse-transcription (RT) polymerase chain reaction (PCR). In addition, rCDI-FMT and toxin-treated animals and ex vivo human colonoids were used to compare intestinal tissue and circulating miRs. miR inflammatory gene targets in colonic epithelial and peripheral blood mononuclear cells were evaluated by quantitative PCR (qPCR) and 3′UTR reporter assays. Colonic epithelial cells were used for mechanistic, cytoskeleton, cell growth, and apoptosis studies.

      Results

      miRNA profiling revealed up-regulation of 64 circulating miRs 4 and 12 weeks after FMT compared with screening, of which the top 6 were validated in the discovery cohort by means of RT-qPCR. In a murine model of relapsing-CDI, RT-qPCR analyses of sera and cecal RNA extracts demonstrated suppression of these miRs, an effect reversed by FMT. In mouse colon and human colonoids, C difficile toxin B (TcdB) mediated the suppressive effects of CDI on miRs. CDI dysregulated DROSHA, an effect reversed by FMT. Correlation analyses, qPCR ,and 3′UTR reporter assays revealed that miR-23a, miR-150, miR-26b, and miR-28 target directly the 3′UTRs of IL12B, IL18, FGF21, and TNFRSF9, respectively. miR-23a and miR-150 demonstrated cytoprotective effects against TcdB.

      Conclusions

      These results provide novel and provocative evidence that modulation of the gut microbiome via FMT induces alterations in circulating and intestinal tissue miRs. These findings contribute to a greater understanding of the molecular mechanisms underlying FMT and identify new potential targets for therapeutic intervention in rCDI.

      Graphical abstract

      Keywords

      Abbreviations used in this paper:

      AGO (argonaute), FGF (fibroblast growth factor), FMT (fecal microbiota transplantation), IL (interleukin), pri-miRNA (primary microRNA transcript), rCDI (recurrent Clostridioides difficile infection), Tcd (C difficile toxin), TNF (tumor necrosis factor), TNFRSF9 (TNF receptor superfamily member 9)
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