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Shumway AJ, Shanahan MT, Hollville E, Chen K, Beasley C, Villanueva JW, Albert S, Lian G, Cure MR, Schaner M, Zhu LC, Bantumilli S, Deshmukh M, Furey TS, Sheikh SZ, Sethupathy P. Aberrant miR-29 is a predictive feature of severe phenotypes in pediatric Crohn's disease. JCI Insight 2024; 9:e168800. [PMID: 38385744 DOI: 10.1172/jci.insight.168800] [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: 01/12/2023] [Accepted: 01/10/2024] [Indexed: 02/23/2024] Open
Abstract
Crohn's disease (CD) is a chronic inflammatory gut disorder. Molecular mechanisms underlying the clinical heterogeneity of CD remain poorly understood. MicroRNAs (miRNAs) are important regulators of gut physiology, and several have been implicated in the pathogenesis of adult CD. However, there is a dearth of large-scale miRNA studies for pediatric CD. We hypothesized that specific miRNAs uniquely mark pediatric CD. We performed small RNA-Seq of patient-matched colon and ileum biopsies from treatment-naive pediatric patients with CD (n = 169) and a control cohort (n = 108). Comprehensive miRNA analysis revealed 58 miRNAs altered in pediatric CD. Notably, multinomial logistic regression analysis revealed that index levels of ileal miR-29 are strongly predictive of severe inflammation and stricturing. Transcriptomic analyses of transgenic mice overexpressing miR-29 show a significant reduction of the tight junction protein gene Pmp22 and classic Paneth cell markers. The dramatic loss of Paneth cells was confirmed by histologic assays. Moreover, we found that pediatric patients with CD with elevated miR-29 exhibit significantly lower Paneth cell counts, increased inflammation scores, and reduced levels of PMP22. These findings strongly indicate that miR-29 upregulation is a distinguishing feature of pediatric CD, highly predictive of severe phenotypes, and associated with inflammation and Paneth cell loss.
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Affiliation(s)
| | - Michael T Shanahan
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | | | - Kevin Chen
- Center for Gastrointestinal Biology and Disease
- Department of Genetics
| | | | | | - Sara Albert
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - Grace Lian
- Center for Gastrointestinal Biology and Disease
| | | | | | - Lee-Ching Zhu
- Department of Pathology and Laboratory Medicine, and
| | | | | | - Terrence S Furey
- Center for Gastrointestinal Biology and Disease
- Department of Genetics
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shehzad Z Sheikh
- Center for Gastrointestinal Biology and Disease
- Department of Genetics
| | - Praveen Sethupathy
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA
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2
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Hung YH, Capeling M, Villanueva JW, Kanke M, Shanahan MT, Huang S, Cubitt R, Rinaldi VD, Schimenti JC, Spence JR, Sethupathy P. Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model. BMC Genomics 2023; 24:641. [PMID: 37884859 PMCID: PMC10601309 DOI: 10.1186/s12864-023-09743-1] [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] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are important post-transcriptional gene regulators controlling cellular lineage specification and differentiation during embryonic development, including the gastrointestinal system. However, miRNA-mediated regulatory mechanisms involved in early embryonic development of human small intestine (SI) remains underexplored. To explore candidate roles for miRNAs in prenatal SI lineage specification in humans, we used a multi-omic analysis strategy in a directed differentiation model that programs human pluripotent stem cells toward the SI lineage. RESULTS We leveraged small RNA-seq to define the changing miRNA landscape, and integrated chromatin run-on sequencing (ChRO-seq) and RNA-seq to define genes subject to significant post-transcriptional regulation across the different stages of differentiation. Small RNA-seq profiling revealed temporal dynamics of miRNA signatures across different developmental events of the model, including definitive endoderm formation, SI lineage specification and SI regional patterning. Our multi-omic, integrative analyses showed further that the elevation of miR-182 and reduction of miR-375 are key events during SI lineage specification. We demonstrated that loss of miR-182 leads to an increase in the foregut master marker SOX2. We also used single-cell analyses in murine adult intestinal crypts to support a life-long role for miR-375 in the regulation of Zfp36l2. Finally, we uncovered opposing roles of SMAD4 and WNT signaling in regulating miR-375 expression during SI lineage specification. Beyond the mechanisms highlighted in this study, we also present a web-based application for exploration of post-transcriptional regulation and miRNA-mediated control in the context of early human SI development. CONCLUSION The present study uncovers a novel facet of miRNAs in regulating prenatal SI development. We leveraged multi-omic, systems biology approaches to discover candidate miRNA regulators associated with early SI developmental events in a human organoid model. In this study, we highlighted miRNA-mediated post-transcriptional regulation relevant to the event of SI lineage specification. The candidate miRNA regulators that we identified for the other stages of SI development also warrant detailed characterization in the future.
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Affiliation(s)
- Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Meghan Capeling
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan W Villanueva
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Michael T Shanahan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rebecca Cubitt
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Vera D Rinaldi
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - John C Schimenti
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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Villanueva JW, Kwong L, Han T, Martinez SA, Shanahan MT, Kanke M, Dow LE, Danko CG, Sethupathy P. Comprehensive microRNA analysis across genome-edited colorectal cancer organoid models reveals miR-24 as a candidate regulator of cell survival. BMC Genomics 2022; 23:792. [DOI: 10.1186/s12864-022-09018-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
AbstractSomatic mutations drive colorectal cancer (CRC) by disrupting gene regulatory mechanisms. Distinct combinations of mutations can result in unique changes to regulatory mechanisms leading to variability in the efficacy of therapeutics. MicroRNAs are important regulators of gene expression, and their activity can be altered by oncogenic mutations. However, it is unknown how distinct combinations of CRC-risk mutations differentially affect microRNAs. Here, using genetically-modified mouse intestinal organoid (enteroid) models, we identify 12 different modules of microRNA expression patterns across different combinations of mutations common in CRC. We also show that miR-24-3p is aberrantly upregulated in genetically-modified mouse enteroids irrespective of mutational context. Furthermore, we identify an enrichment of miR-24-3p predicted targets in downregulated gene lists from various mutational contexts compared to WT. In follow-up experiments, we demonstrate that miR-24-3p promotes CRC cell survival in multiple cell contexts. Our novel characterization of genotype-specific patterns of miRNA expression offer insight into the mechanisms that drive inter-tumor heterogeneity and highlight candidate microRNA therapeutic targets for the advancement of precision medicine for CRC.
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Villanueva JW, Kwong L, Han T, Martinez SA, Pan FC, Shanahan MT, Kanke M, Chen S, Dow LE, Danko CG, Sethupathy P. Abstract 1474: Genome edited colorectal cancer organoid models reveal distinct microRNA activity patterns across different mutation profiles. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Colorectal cancer (CRC) is the third most common cancer and second leading cause of cancer-related deaths worldwide. DNA mutations drive colon tumor formation by disrupting gene regulatory mechanisms that facilitate cell survival and growth. Distinct combinations of mutations can result in unique changes to these gene regulatory mechanisms leading to variability in responses to available therapeutics. MicroRNAs (miRNAs) are important regulators of gene expression in CRC and it is known that their expression can be altered by oncogenic mutations. However, it is unknown how distinct combinations of CRC-risk mutations differentially affect the regulation and expression of miRNAs. We hypothesize that some miRNAs will exhibit strong genotype-dependent changes in CRC whereas others will be altered irrespective of genotype. Utilizing sequencing data from The Cancer Genome Atlas (TCGA) and cutting-edge intestinal organoid (enteroid) models with different combinations of oncogenic mutations that commonly occur in CRC, we identified several distinct patterns of genotype-dependent miRNA expression. We also found a suite of miRNAs that are up-regulated in a mutation-independent manner. Among these, we demonstrated that miR-24-3p is a candidate master regulator of genes that are down-regulated in all mutational-contexts. RT-qPCR for miR-24-3p in genetically modified human colonoids with different combinations of oncogenic mutations further supports that miR-24-3p is elevated across various mutational contexts. Functional studies in the HCT116 cell line revealed that miR-24-3p controls the number of metabolically active, viable cells by regulating apoptosis but not proliferation. Moreover, follow-up ex vivo studies in mouse enteroids confirmed that miR-24 controls intestinal cell survival. To identify candidate gene targets that mediate the function of miR-24-3p, I performed an RNA-sequencing (RNA-seq) analysis and identified HMOX1 and PRSS8 as top candidate miR-24-3p targets. These findings suggest that miR-24-3p is a genotype-independent regulator of tumor cell apoptosis in CRC and merits further investigation. Overall, our findings provide a novel perspective on approaches for precision medicine in CRC.
Citation Format: Jonathan W. Villanueva, Lawrence Kwong, Teng Han, Salvador Alonso Martinez, Fong Cheng Pan, Michael T. Shanahan, Matt Kanke, Shuibing Chen, Lukas E. Dow, Charles G. Danko, Praveen Sethupathy. Genome edited colorectal cancer organoid models reveal distinct microRNA activity patterns across different mutation profiles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1474.
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Affiliation(s)
| | | | - Teng Han
- 2Weill Cornell Medicine, New York City, NY
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Kanke M, Kennedy Ng MM, Connelly S, Singh M, Schaner M, Shanahan MT, Wolber EA, Beasley C, Lian G, Jain A, Long MD, Barnes EL, Herfarth HH, Isaacs KL, Hansen JJ, Kapadia M, Guillem JG, Feschotte C, Furey TS, Sheikh SZ, Sethupathy P. Single-Cell Analysis Reveals Unexpected Cellular Changes and Transposon Expression Signatures in the Colonic Epithelium of Treatment-Naïve Adult Crohn's Disease Patients. Cell Mol Gastroenterol Hepatol 2022; 13:1717-1740. [PMID: 35158099 PMCID: PMC9046244 DOI: 10.1016/j.jcmgh.2022.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The intestinal barrier comprises a monolayer of specialized intestinal epithelial cells (IECs) that are critical in maintaining mucosal homeostasis. Dysfunction within various IEC fractions can alter intestinal permeability in a genetically susceptible host, resulting in a chronic and debilitating condition known as Crohn's disease (CD). Defining the molecular changes in each IEC type in CD will contribute to an improved understanding of the pathogenic processes and the identification of cell type-specific therapeutic targets. We performed, at single-cell resolution, a direct comparison of the colonic epithelial cellular and molecular landscape between treatment-naïve adult CD and non-inflammatory bowel disease control patients. METHODS Colonic epithelial-enriched, single-cell sequencing from treatment-naïve adult CD and non-inflammatory bowel disease patients was investigated to identify disease-induced differences in IEC types. RESULTS Our analysis showed that in CD patients there is a significant skew in the colonic epithelial cellular distribution away from canonical LGR5+ stem cells, located at the crypt bottom, and toward one specific subtype of mature colonocytes, located at the crypt top. Further analysis showed unique changes to gene expression programs in every major cell type, including a previously undescribed suppression in CD of most enteroendocrine driver genes as well as L-cell markers including GCG. We also dissect an incompletely understood SPIB+ cell cluster, revealing at least 4 subclusters that likely represent different stages of a maturational trajectory. One of these SPIB+ subclusters expresses crypt-top colonocyte markers and is up-regulated significantly in CD, whereas another subcluster strongly expresses and stains positive for lysozyme (albeit no other canonical Paneth cell marker), which surprisingly is greatly reduced in expression in CD. In addition, we also discovered transposable element markers of colonic epithelial cell types as well as transposable element families that are altered significantly in CD in a cell type-specific manner. Finally, through integration with data from genome-wide association studies, we show that genes implicated in CD risk show heretofore unknown cell type-specific patterns of aberrant expression in CD, providing unprecedented insight into the potential biological functions of these genes. CONCLUSIONS Single-cell analysis shows a number of unexpected cellular and molecular features, including transposable element expression signatures, in the colonic epithelium of treatment-naïve adult CD.
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Affiliation(s)
- Matt Kanke
- Biomedical Sciences, Cornell University, Ithaca, New York
| | - Meaghan M Kennedy Ng
- Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sean Connelly
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Manvendra Singh
- Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Matthew Schaner
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Elizabeth A Wolber
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Caroline Beasley
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Grace Lian
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Animesh Jain
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Millie D Long
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Edward L Barnes
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Hans H Herfarth
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kim L Isaacs
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jonathon J Hansen
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Muneera Kapadia
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jose Gaston Guillem
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Cedric Feschotte
- Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Terrence S Furey
- Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
| | - Shehzad Z Sheikh
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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6
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Shanahan MT, Kanke M, Oyesola OO, Hung YH, Koch-Laskowski K, Singh AP, Peck BCE, Biraud M, Sheahan B, Cortes JE, Gong H, Sahoo DK, Cubitt R, Kurpios NA, Mochel JP, Allenspach K, McElroy SJ, Ding S, von Moltke J, Dekaney CM, Tait-Wojno ED, Sethupathy P. Multiomic analysis defines the first microRNA atlas across all small intestinal epithelial lineages and reveals novel markers of almost all major cell types. Am J Physiol Gastrointest Liver Physiol 2021; 321:G668-G681. [PMID: 34643097 PMCID: PMC8887887 DOI: 10.1152/ajpgi.00222.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/07/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 01/31/2023]
Abstract
MicroRNA-mediated regulation is critical for the proper development and function of the small intestinal (SI) epithelium. However, it is not known which microRNAs are expressed in each of the cell types of the SI epithelium. To bridge this important knowledge gap, we performed comprehensive microRNA profiling in all major cell types of the mouse SI epithelium. We used flow cytometry and fluorescence-activated cell sorting with multiple reporter mouse models to isolate intestinal stem cells, enterocytes, goblet cells, Paneth cells, enteroendocrine cells, tuft cells, and secretory progenitors. We then subjected these cell populations to small RNA-sequencing. The resulting atlas revealed highly enriched microRNA markers for almost every major cell type (https://sethupathy-lab.shinyapps.io/SI_miRNA/). Several of these lineage-enriched microRNAs (LEMs) were observed to be embedded in annotated host genes. We used chromatin-run-on sequencing to determine which of these LEMs are likely cotranscribed with their host genes. We then performed single-cell RNA-sequencing to define the cell type specificity of the host genes and embedded LEMs. We observed that the two most enriched microRNAs in secretory progenitors are miR-1224 and miR-672, the latter of which we found is deleted in hominin species. Finally, using several in vivo models, we established that miR-152 is a Paneth cell-specific microRNA.NEW & NOTEWORTHY In this study, first, microRNA atlas (and searchable web server) across all major small intestinal epithelial cell types is presented. We have demonstrated microRNAs that uniquely mark several lineages, including enteroendocrine and tuft. Identification of a key marker of mouse secretory progenitor cells, miR-672, which we show is deleted in humans. We have used several in vivo models to establish miR-152 as a specific marker of Paneth cells, which are highly understudied in terms of microRNAs.
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Affiliation(s)
- Michael T Shanahan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Oyebola O Oyesola
- Department of Immunology, University of Washington, Seattle, Washington
| | - Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Kieran Koch-Laskowski
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Ajeet P Singh
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Bailey C E Peck
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Mandy Biraud
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Breanna Sheahan
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Josca E Cortes
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Huiyu Gong
- Department of Pediatrics, University of Iowa, Iowa City, Iowa
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa
| | - Dipak K Sahoo
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Rebecca Cubitt
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Natasza A Kurpios
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Jonathan P Mochel
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Karin Allenspach
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Steven J McElroy
- Department of Pediatrics, University of Iowa, Iowa City, Iowa
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa
| | - Shengli Ding
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, North Carolina
| | - Jakob von Moltke
- Department of Immunology, University of Washington, Seattle, Washington
| | - Christopher M Dekaney
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Elia D Tait-Wojno
- Department of Immunology, University of Washington, Seattle, Washington
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
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7
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Oyesola OO, Shanahan MT, Kanke M, Mooney BM, Webb LM, Smita S, Matheson MK, Campioli P, Pham D, Früh SP, McGinty JW, Churchill MJ, Cahoon JL, Sundaravaradan P, Flitter BA, Mouli K, Nadjsombati MS, Kamynina E, Peng SA, Cubitt RL, Gronert K, Lord JD, Rauch I, von Moltke J, Sethupathy P, Tait Wojno ED. PGD2 and CRTH2 counteract Type 2 cytokine-elicited intestinal epithelial responses during helminth infection. J Exp Med 2021; 218:e20202178. [PMID: 34283207 PMCID: PMC8294949 DOI: 10.1084/jem.20202178] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 04/28/2021] [Accepted: 06/21/2021] [Indexed: 01/22/2023] Open
Abstract
Type 2 inflammation is associated with epithelial cell responses, including goblet cell hyperplasia, that promote worm expulsion during intestinal helminth infection. How these epithelial responses are regulated remains incompletely understood. Here, we show that mice deficient in the prostaglandin D2 (PGD2) receptor CRTH2 and mice with CRTH2 deficiency only in nonhematopoietic cells exhibited enhanced worm clearance and intestinal goblet cell hyperplasia following infection with the helminth Nippostrongylus brasiliensis. Small intestinal stem, goblet, and tuft cells expressed CRTH2. CRTH2-deficient small intestinal organoids showed enhanced budding and terminal differentiation to the goblet cell lineage. During helminth infection or in organoids, PGD2 and CRTH2 down-regulated intestinal epithelial Il13ra1 expression and reversed Type 2 cytokine-mediated suppression of epithelial cell proliferation and promotion of goblet cell accumulation. These data show that the PGD2-CRTH2 pathway negatively regulates the Type 2 cytokine-driven epithelial program, revealing a mechanism that can temper the highly inflammatory effects of the anti-helminth response.
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Affiliation(s)
- Oyebola O. Oyesola
- Department of Immunology, University of Washington, Seattle, WA
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Michael T. Shanahan
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Matt Kanke
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| | | | - Lauren M. Webb
- Department of Immunology, University of Washington, Seattle, WA
| | - Shuchi Smita
- Department of Immunology, University of Washington, Seattle, WA
| | | | - Pamela Campioli
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Duc Pham
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Simon P. Früh
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - John W. McGinty
- Department of Immunology, University of Washington, Seattle, WA
| | - Madeline J. Churchill
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR
| | | | | | - Becca A. Flitter
- Vision Science Program, School of Optometry, University of California, Berkeley, Berkeley, CA
| | - Karthik Mouli
- Vision Science Program, School of Optometry, University of California, Berkeley, Berkeley, CA
| | | | - Elena Kamynina
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Seth A. Peng
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Rebecca L. Cubitt
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Karsten Gronert
- Vision Science Program, School of Optometry, University of California, Berkeley, Berkeley, CA
| | - James D. Lord
- Benaroya Research Institute at Virginia Mason Medical Center, Division of Gastroenterology, Seattle, WA
| | - Isabella Rauch
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR
| | | | - Praveen Sethupathy
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
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8
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Toyonaga T, Steinbach EC, Keith BP, Barrow JB, Schaner MR, Wolber EA, Beasley C, Huling J, Wang Y, Allbritton NL, Chaumont N, Sadiq TS, Koruda MJ, Jain A, Long MD, Barnes EL, Herfarth HH, Isaacs KL, Hansen JJ, Shanahan MT, Rahbar R, Furey TS, Sethupathy P, Sheikh SZ. Decreased Colonic Activin Receptor-Like Kinase 1 Disrupts Epithelial Barrier Integrity in Patients With Crohn's Disease. Cell Mol Gastroenterol Hepatol 2020; 10:779-796. [PMID: 32561494 PMCID: PMC7502566 DOI: 10.1016/j.jcmgh.2020.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Intestinal epithelial cell (IEC) barrier dysfunction is critical to the development of Crohn's disease (CD). However, the mechanism is understudied. We recently reported increased microRNA-31-5p (miR-31-5p) expression in colonic IECs of CD patients, but downstream targets and functional consequences are unknown. METHODS microRNA-31-5p target genes were identified by integrative analysis of RNA- and small RNA-sequencing data from colonic mucosa and confirmed by quantitative polymerase chain reaction in colonic IECs. Functional characterization of activin receptor-like kinase 1 (ACVRL1 or ALK1) in IECs was performed ex vivo using 2-dimensional cultured human primary colonic IECs. The impact of altered colonic ALK1 signaling in CD for the risk of surgery and endoscopic relapse was evaluated by a multivariate regression analysis and a Kaplan-Meier estimator. RESULTS ALK1 was identified as a target of miR-31-5p in colonic IECs of CD patients and confirmed using a 3'-untranslated region reporter assay. Activation of ALK1 restricted the proliferation of colonic IECs in a 5-ethynyl-2-deoxyuridine proliferation assay and down-regulated the expression of stemness-related genes. Activated ALK1 signaling increased colonic IEC differentiation toward colonocytes. Down-regulated ALK1 signaling was associated with increased stemness and decreased colonocyte-specific marker expression in colonic IECs of CD patients compared with healthy controls. Activation of ALK1 enhanced epithelial barrier integrity in a transepithelial electrical resistance permeability assay. Lower colonic ALK1 expression was identified as an independent risk factor for surgery and was associated with a higher risk of endoscopic relapse in CD patients. CONCLUSIONS Decreased colonic ALK1 disrupted colonic IEC barrier integrity and was associated with poor clinical outcomes in CD patients.
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Affiliation(s)
- Takahiko Toyonaga
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Erin C. Steinbach
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina,Division of Rheumatology, Allergy and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Benjamin P. Keith
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina,Department of Genetics, Department of Biology, Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jasmine B. Barrow
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Matthew R. Schaner
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Elisabeth A. Wolber
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Caroline Beasley
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jennifer Huling
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yuli Wang
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Nancy L. Allbritton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Nicole Chaumont
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Timothy S. Sadiq
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mark J. Koruda
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Animesh Jain
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Millie D. Long
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Edward L. Barnes
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Hans H. Herfarth
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kim L. Isaacs
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jonathan J. Hansen
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael T. Shanahan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Reza Rahbar
- Department of Surgery, Rex Healthcare of Wakefield, North Carolina
| | - Terrence S. Furey
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina,Department of Genetics, Department of Biology, Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Shehzad Z. Sheikh
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina,Correspondence Address correspondence to: Shehzad Z. Sheikh, MD, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, North Carolina 27599. fax: (919) 843-2585.
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9
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Singh AP, Hung YH, Shanahan MT, Kanke M, Bonfini A, Dame MK, Biraud M, Peck BC, Oyesola OO, Freund JM, Cubitt RL, Curry EG, Gonzalez LM, Bewick GA, Tait-Wojno ED, Kurpios NA, Ding S, Spence JR, Dekaney CM, Buchon N, Sethupathy P. Enteroendocrine Progenitor Cell-Enriched miR-7 Regulates Intestinal Epithelial Proliferation in an Xiap-Dependent Manner. Cell Mol Gastroenterol Hepatol 2019; 9:447-464. [PMID: 31756561 PMCID: PMC7021555 DOI: 10.1016/j.jcmgh.2019.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/29/2019] [Accepted: 11/07/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS The enteroendocrine cell (EEC) lineage is important for intestinal homeostasis. It was recently shown that EEC progenitors contribute to intestinal epithelial growth and renewal, but the underlying mechanisms remain poorly understood. MicroRNAs are under-explored along the entire EEC lineage trajectory, and comparatively little is known about their contributions to intestinal homeostasis. METHODS We leverage unbiased sequencing and eight different mouse models and sorting methods to identify microRNAs enriched along the EEC lineage trajectory. We further characterize the functional role of EEC progenitor-enriched miRNA, miR-7, by in vivo dietary study as well as ex vivo enteroid in mice. RESULTS First, we demonstrate that miR-7 is highly enriched across the entire EEC lineage trajectory and is the most enriched miRNA in EEC progenitors relative to Lgr5+ intestinal stem cells. Next, we show in vivo that in EEC progenitors miR-7 is dramatically suppressed under dietary conditions that favor crypt division and suppress EEC abundance. We then demonstrate by functional assays in mouse enteroids that miR-7 exerts robust control of growth, as determined by budding (proxy for crypt division), EdU and PH3 staining, and likely regulates EEC abundance also. Finally, we show by single-cell RNA sequencing analysis that miR-7 regulates Xiap in progenitor/stem cells and we demonstrate in enteroids that the effects of miR-7 on mouse enteroid growth depend in part on Xiap and Egfr signaling. CONCLUSIONS This study demonstrates for the first time that EEC progenitor cell-enriched miR-7 is altered by dietary perturbations and that it regulates growth in enteroids via intact Xiap and Egfr signaling.
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Affiliation(s)
- Ajeet P. Singh
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Michael T. Shanahan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Alessandro Bonfini
- Cornell Institute of Host-Microbe Interactions and Disease. Department of Entomology, Cornell University, New York
| | - Michael K. Dame
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Mandy Biraud
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina
| | - Bailey C.E. Peck
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Oyebola O. Oyesola
- Baker Institute of Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York
| | - John M. Freund
- Department of Clinical Sciences, North Carolina State University, Raleigh, North Carolina
| | - Rebecca L. Cubitt
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Ennessa G. Curry
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Liara M. Gonzalez
- Department of Clinical Sciences, North Carolina State University, Raleigh, North Carolina
| | - Gavin A. Bewick
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Elia D. Tait-Wojno
- Baker Institute of Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York
| | - Natasza A. Kurpios
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Shengli Ding
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Christopher M. Dekaney
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina
| | - Nicolas Buchon
- Cornell Institute of Host-Microbe Interactions and Disease. Department of Entomology, Cornell University, New York
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York,Correspondence Address correspondence to: Praveen Sethupathy, PhD, Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, 618 Tower Road T7 006D, Veterinary Research Tower, Ithaca, New York 14850. fax: (607) 253–4447.
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10
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Schoenborn AA, von Furstenberg RJ, Valsaraj S, Hussain FS, Stein M, Shanahan MT, Henning SJ, Gulati AS. The enteric microbiota regulates jejunal Paneth cell number and function without impacting intestinal stem cells. Gut Microbes 2018; 10:45-58. [PMID: 29883265 PMCID: PMC6363071 DOI: 10.1080/19490976.2018.1474321] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 06/27/2017] [Revised: 04/06/2018] [Accepted: 05/01/2018] [Indexed: 02/03/2023] Open
Abstract
Paneth cells (PCs) are epithelial cells found in the small intestine, next to intestinal stem cells (ISCs) at the base of the crypts. PCs secrete antimicrobial peptides (AMPs) that regulate the commensal gut microbiota. In contrast, little is known regarding how the enteric microbiota reciprocally influences PC function. In this study, we sought to characterize the impact of the enteric microbiota on PC biology in the mouse small intestine. This was done by first enumerating jejunal PCs in germ-free (GF) versus conventionally raised (CR) mice. We next evaluated the possible functional consequences of altered PC biology in these experimental groups by assessing epithelial proliferation, ISC numbers, and the production of AMPs. We found that PC numbers were significantly increased in CR versus GF mice; however, there were no differences in ISC numbers or cycling activity between groups. Of the AMPs assessed, only Reg3γ transcript expression was significantly increased in CR mice. Intriguingly, this increase was abrogated in cultured CR versus GF enteroids, and could not be re-induced with various bacterial ligands. Our findings demonstrate the enteric microbiota regulates PC function by increasing PC numbers and inducing Reg3γ expression, though the latter effect may not involve direct interactions between bacteria and the intestinal epithelium. In contrast, the enteric microbiota does not appear to regulate jejunal ISC census and proliferation. These are critical findings for investigators using GF mice and the enteroid system to study PC and ISC biology.
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Affiliation(s)
- Alexi A Schoenborn
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- b Department of Pediatrics, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Richard J von Furstenberg
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- c Department of Medicine, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Smrithi Valsaraj
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- b Department of Pediatrics, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Farah S Hussain
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- c Department of Medicine, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Molly Stein
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- b Department of Pediatrics, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Michael T Shanahan
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- c Department of Medicine, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Susan J Henning
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- c Department of Medicine, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- d Department of Cellular and Molecular Physiology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Ajay S Gulati
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- b Department of Pediatrics, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- e Department of Pathology and Laboratory Medicine , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
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11
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Wellman AS, Metukuri MR, Kazgan N, Xu X, Xu Q, Ren NSX, Czopik A, Shanahan MT, Kang A, Chen W, Azcarate-Peril MA, Gulati AS, Fargo DC, Guarente L, Li X. Intestinal Epithelial Sirtuin 1 Regulates Intestinal Inflammation During Aging in Mice by Altering the Intestinal Microbiota. Gastroenterology 2017; 153:772-786. [PMID: 28552621 PMCID: PMC5581719 DOI: 10.1053/j.gastro.2017.05.022] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [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: 09/07/2016] [Revised: 05/05/2017] [Accepted: 05/19/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Intestinal epithelial homeostasis is maintained by complex interactions among epithelial cells, commensal gut microorganisms, and immune cells. Disruption of this homeostasis is associated with disorders such as inflammatory bowel disease (IBD), but the mechanisms of this process are not clear. We investigated how Sirtuin 1 (SIRT1), a conserved mammalian NAD+-dependent protein deacetylase, senses environmental stress to alter intestinal integrity. METHODS We performed studies of mice with disruption of Sirt1 specifically in the intestinal epithelium (SIRT1 iKO, villin-Cre+, Sirt1flox/flox mice) and control mice (villin-Cre-, Sirt1flox/flox) on a C57BL/6 background. Acute colitis was induced in some mice by addition of 2.5% dextran sodium sulfate to drinking water for 5-9 consecutive days. Some mice were given antibiotics via their drinking water for 4 weeks to deplete their microbiota. Some mice were fed with a cholestyramine-containing diet for 7 days to sequester their bile acids. Feces were collected and proportions of microbiota were analyzed by 16S rRNA amplicon sequencing and quantitative PCR. Intestines were collected from mice and gene expression profiles were compared by microarray and quantitative PCR analyses. We compared levels of specific mRNAs between colon tissues from age-matched patients with ulcerative colitis (n=10) vs without IBD (n=8, controls). RESULTS Mice with intestinal deletion of SIRT1 (SIRT1 iKO) had abnormal activation of Paneth cells starting at the age of 5-8 months, with increased activation of NF-κB, stress pathways, and spontaneous inflammation at 22-24 months of age, compared with control mice. SIRT1 iKO mice also had altered fecal microbiota starting at 4-6 months of age compared with control mice, in part because of altered bile acid metabolism. Moreover, SIRT1 iKO mice with defective gut microbiota developed more severe colitis than control mice. Intestinal tissues from patients with ulcerative colitis expressed significantly lower levels of SIRT1 mRNA than controls. Intestinal tissues from SIRT1 iKO mice given antibiotics, however, did not have signs of inflammation at 22-24 months of age, and did not develop more severe colitis than control mice at 4-6 months. CONCLUSIONS In analyses of intestinal tissues, colitis induction, and gut microbiota in mice with intestinal epithelial disruption of SIRT1, we found this protein to prevent intestinal inflammation by regulating the gut microbiota. SIRT1 might therefore be an important mediator of host-microbiome interactions. Agents designed to activate SIRT1 might be developed as treatments for IBDs.
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Affiliation(s)
- Alicia S Wellman
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Mallikarjuna R Metukuri
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Nevzat Kazgan
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Xiaojiang Xu
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Qing Xu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Natalie S X Ren
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Agnieszka Czopik
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Michael T Shanahan
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ashley Kang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; NIEHS Scholars Connect Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Willa Chen
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology and Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ajay S Gulati
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - David C Fargo
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Leonard Guarente
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina.
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12
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Peck BCE, Shanahan MT, Singh AP, Sethupathy P. Gut Microbial Influences on the Mammalian Intestinal Stem Cell Niche. Stem Cells Int 2017; 2017:5604727. [PMID: 28904533 PMCID: PMC5585682 DOI: 10.1155/2017/5604727] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/02/2017] [Indexed: 02/07/2023] Open
Abstract
The mammalian intestinal epithelial stem cell (IESC) niche is comprised of diverse epithelial, immune, and stromal cells, which together respond to environmental changes within the lumen and exert coordinated regulation of IESC behavior. There is growing appreciation for the role of the gut microbiota in modulating intestinal proliferation and differentiation, as well as other aspects of intestinal physiology. In this review, we evaluate the diverse roles of known niche cells in responding to gut microbiota and supporting IESCs. Furthermore, we discuss the potential mechanisms by which microbiota may exert their influence on niche cells and possibly on IESCs directly. Finally, we present an overview of the benefits and limitations of available tools to study niche-microbe interactions and provide our recommendations regarding their use and standardization. The study of host-microbe interactions in the gut is a rapidly growing field, and the IESC niche is at the forefront of host-microbe activity to control nutrient absorption, endocrine signaling, energy homeostasis, immune response, and systemic health.
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Affiliation(s)
- Bailey C E Peck
- Department of Surgery, School of Medicine, University of Michigan, Ann Arbor, MI 48105, USA
| | - Michael T Shanahan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ajeet P Singh
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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13
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Shanahan MT, Carroll IM, Grossniklaus E, White A, von Furstenberg RJ, Barner R, Fodor AA, Henning SJ, Sartor RB, Gulati AS. Mouse Paneth cell antimicrobial function is independent of Nod2. Gut 2014; 63:903-10. [PMID: 23512834 PMCID: PMC3844066 DOI: 10.1136/gutjnl-2012-304190] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Although polymorphisms of the NOD2 gene predispose to the development of ileal Crohn's disease, the precise mechanisms of this increased susceptibility remain unclear. Previous work has shown that transcript expression of the Paneth cell (PC) antimicrobial peptides (AMPs) α-defensin 4 and α-defensin-related sequence 10 are selectively decreased in Nod2(-/-) mice. However, the specific mouse background used in this previous study is unclear. In light of recent evidence suggesting that mouse strain strongly influences PC antimicrobial activity, we sought to characterise PC AMP function in commercially available Nod2(-/-) mice on a C57BL/6 (B6) background. Specifically, we hypothesised that Nod2(-/-) B6 mice would display reduced AMP expression and activity. DESIGN Wild-type (WT) and Nod2(-/-) B6 ileal AMP expression was assessed via real-time PCR, acid urea polyacrylamide gel electrophoresis and mass spectrometry. PCs were enumerated using flow cytometry. Functionally, α-defensin bactericidal activity was evaluated using a gel-overlay antimicrobial assay. Faecal microbial composition was determined using 454-sequencing of the bacterial 16S gene in cohoused WT and Nod2(-/-) littermates. RESULTS WT and Nod2(-/-) B6 mice displayed similar PC AMP expression patterns, equivalent α-defensin profiles, and identical antimicrobial activity against commensal and pathogenic bacterial strains. Furthermore, minimal differences in gut microbial composition were detected between the two cohoused, littermate mouse groups. CONCLUSIONS Our data reveal that Nod2 does not directly regulate PC antimicrobial activity in B6 mice. Moreover, we demonstrate that previously reported Nod2-dependent influences on gut microbial composition may be overcome by environmental factors, such as cohousing with WT littermates.
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Affiliation(s)
- Michael T Shanahan
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ian M Carroll
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Emily Grossniklaus
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Andrew White
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Richard J von Furstenberg
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Roshonda Barner
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Anthony A Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Susan J Henning
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - R Balfour Sartor
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ajay S Gulati
- Department of Pediatrics, Division of Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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14
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Abstract
Paneth cells are long-lived secretory cells that reside in the base of the crypts of Lieberkühn of the small intestine. They produce an arsenal of molecules that are involved in numerous biological processes, ranging from the control of gut microbial populations to supporting the intestinal stem cell niche. Because of these important functions, Paneth cell abnormalities are becoming implicated in a variety of disease processes. As such, it is necessary to establish parameters that will allow for the comprehensive study of Paneth cells in health and disease. In this addendum, we highlight critical design aspects involved in the study of Paneth cells and their downstream effects on the intestinal microbiota. The importance of this approach is demonstrated by our recent findings that Nod2 does not regulate mouse Paneth cell antimicrobial function, in contrast to previous reports. This work defines key issues to consider when studying Paneth cells in mouse systems.
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Affiliation(s)
- Michael T Shanahan
- Department of Medicine; Division of Gastroenterology and Hepatology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Ian M Carroll
- Department of Medicine; Division of Gastroenterology and Hepatology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Ajay S Gulati
- Department of Pediatrics; Division of Gastroenterology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Correspondence to: Ajay S Gulati,
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15
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Packey CD, Shanahan MT, Manick S, Bower MA, Ellermann M, Tonkonogy SL, Carroll IM, Sartor RB. Molecular detection of bacterial contamination in gnotobiotic rodent units. Gut Microbes 2013; 4:361-70. [PMID: 23887190 PMCID: PMC3839980 DOI: 10.4161/gmic.25824] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [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] [Indexed: 02/03/2023] Open
Abstract
Gnotobiotic rodents provide an important technique to study the functional roles of commensal bacteria in host physiology and pathophysiology. To ensure sterility, these animals must be screened frequently for contamination. The traditional screening approaches of culturing and Gram staining feces have inherent limitations, as many bacteria are uncultivable and fecal Gram stains are difficult to interpret. Thus, we developed and validated molecular methods to definitively detect and identify contamination in germ-free (GF) and selectively colonized animals. Fresh fecal pellets were collected from rodents housed in GF isolators, spontaneously contaminated ex-GF isolators, selectively colonized isolators and specific pathogen-free (SPF) conditions. DNA isolated from mouse and rat fecal samples was amplified by polymerase chain reaction (PCR) and subjected to quantitative PCR (qPCR) using universal primers that amplify the 16S rRNA gene from all bacterial groups. PCR products were sequenced to identify contaminating bacterial species. Random amplification of polymorphic DNA (RAPD) PCR profiles verified bacterial inoculation of selectively colonized animals. These PCR techniques more accurately detected and identified GF isolator contamination than current standard approaches. These molecular techniques can be utilized to more definitively screen GF and selectively colonized animals for bacterial contamination when Gram stain and/or culture results are un-interpretable or inconsistent.
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Affiliation(s)
- Christopher D Packey
- Department of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Department of Microbiology and Immunology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Center for Gastrointestinal Biology and Diseases; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Michael T Shanahan
- Department of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Center for Gastrointestinal Biology and Diseases; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Sayeed Manick
- Department of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Maureen A Bower
- The National Gnotobiotic Rodent Resource Center; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Melissa Ellermann
- Department of Microbiology and Immunology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Susan L Tonkonogy
- Center for Gastrointestinal Biology and Diseases; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,College of Veterinary Medicine, North Carolina State University; Raleigh, NC USA
| | - Ian M Carroll
- Department of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Center for Gastrointestinal Biology and Diseases; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - R Balfour Sartor
- Department of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Department of Microbiology and Immunology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Center for Gastrointestinal Biology and Diseases; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,The National Gnotobiotic Rodent Resource Center; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Correspondence to: R Balfour Sartor,
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16
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Gulati AS, Shanahan MT, Arthur JC, Grossniklaus E, von Furstenberg RJ, Kreuk L, Henning SJ, Jobin C, Sartor RB. Mouse background strain profoundly influences Paneth cell function and intestinal microbial composition. PLoS One 2012; 7:e32403. [PMID: 22384242 PMCID: PMC3288091 DOI: 10.1371/journal.pone.0032403] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 01/30/2012] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Increasing evidence supports the central role of Paneth cells in maintaining intestinal host-microbial homeostasis. However, the direct impact of host genotype on Paneth cell function remains unclear. Here, we characterize key differences in Paneth cell function and intestinal microbial composition in two widely utilized, genetically distinct mouse strains (C57BL/6 and 129/SvEv). In doing so, we demonstrate critical influences of host genotype on Paneth cell activity and the enteric microbiota. METHODOLOGY AND PRINCIPAL FINDINGS Paneth cell numbers were determined by flow cytometry. Antimicrobial peptide (AMP) expression was evaluated using quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR), acid urea-polyacrylamide gel electrophoresis, and mass spectrometry. Effects of mouse background on microbial composition were assessed by reciprocal colonization of germ-free mice from both background strains, followed by compositional analysis of resultant gut bacterial communities using terminal restriction fragment length polymorphism analysis and 16 S qPCR. Our results revealed that 129/SvEv mice possessed fewer Paneth cells and a divergent AMP profile relative to C57BL/6 counterparts. Novel 129/SvEv á-defensin peptides were identified, including Defa2/18v, Defa11, Defa16, and Defa18. Host genotype profoundly affected the global profile of the intestinal microbiota, while both source and host factors were found to influence specific bacterial groups. Interestingly, ileal α-defensins from 129/SvEv mice displayed attenuated antimicrobial activity against pro-inflammatory E. coli strains, a bacterial species found to be expanded in these animals. CONCLUSIONS AND SIGNIFICANCE This work establishes the important impact of host genotype on Paneth cell function and the composition of the intestinal microbiota. It further identifies specific AMP and microbial alterations in two commonly used inbred mouse strains that have varying susceptibilities to a variety of disorders, ranging from obesity to intestinal inflammation. This will be critical for future studies utilizing these murine backgrounds to study the effects of Paneth cells and the intestinal microbiota on host health and disease.
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Affiliation(s)
- Ajay S Gulati
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, North Carolina, United States of America.
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Shanahan MT, Tanabe H, Ouellette AJ. Strain-specific polymorphisms in Paneth cell α-defensins of C57BL/6 mice and evidence of vestigial myeloid α-defensin pseudogenes. Infect Immun 2011; 79:459-73. [PMID: 21041494 PMCID: PMC3019906 DOI: 10.1128/iai.00996-10] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 10/12/2010] [Accepted: 10/17/2010] [Indexed: 12/18/2022] Open
Abstract
Paneth cells at the base of small intestinal crypts secrete microbicidal α-defensins, termed cryptdins (Crps) in mice, as mediators of innate immunity. Proteomic studies show that five abundant Paneth cell α-defensins in C57BL/6 mice are strain specific in that they have not been identified in other inbred strains of mice. Two C57BL/6-specific peptides are coded for by the Defcr20 and -21 genes evident in the NIH C57BL/6 genome but absent from the Celera mixed-strain assembly, which excludes C57BL/6 data and differs from the NIH build with respect to the organization of the α-defensin gene locus. Conversely, C57BL/6 mice lack the Crp1, -2, -4, and -6 peptides and their corresponding Defcr1, -2, -4, and -6 genes, which are common to several mouse strains, including those of the Celera assembly. In C57BL/6 mice, α-defensin gene diversification appears to have occurred by tandem duplication of a multigene cassette that was not found in the mixed-strain assembly. Both mouse genome assemblies contain conserved α-defensin pseudogenes that are closely related to functional myeloid α-defensin genes in the rat, suggesting that the neutrophil α-defensin defect in mice resulted from progressive gene loss. Given the role of α-defensins in shaping the composition of the enteric microflora, such polymorphisms may influence outcomes in mouse models of disease or infection.
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Affiliation(s)
- Michael T. Shanahan
- Department of Pathology and Laboratory Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Hiroki Tanabe
- Department of Pathology and Laboratory Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - André J. Ouellette
- Department of Pathology and Laboratory Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
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Ouellette AJ, Tanabe H, Shanahan MT. Paneth Cell α‐Defensin Polymorphisms in C57Bl/6 Mice and Identification of Vestigial Myeloid α‐Defensin Genes in the Mouse Genome. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.518.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Hiroki Tanabe
- Health Policy BureauMinistry of Health, Labour and WelfareTokyo100‐8916Japan
| | - Michael T. Shanahan
- Medicine, Div of Gastroenterology & HepatologyUniversity of North Carolina School of MedicineChapel HillNC
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Shanahan MT, Vidrich A, Shirafuji Y, Dubois CL, Henschen-Edman A, Hagen SJ, Cohn SM, Ouellette AJ. Elevated expression of Paneth cell CRS4C in ileitis-prone SAMP1/YitFc mice: regional distribution, subcellular localization, and mechanism of action. J Biol Chem 2010; 285:7493-504. [PMID: 20056603 DOI: 10.1074/jbc.m109.083220] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Paneth cells at the base of small intestinal crypts of Lieberkühn secrete host defense peptides and proteins, including alpha-defensins, as mediators of innate immunity. Mouse Paneth cells also express alpha-defensin-related Defcr-rs genes that code for cysteine-rich sequence 4C (CRS4C) peptides that have a unique CPX triplet repeat motif. In ileitis-prone SAMP1/YitFc mice, Paneth cell levels of CRS4C mRNAs and peptides are induced more than a 1000-fold relative to non-prone strains as early as 4 weeks of age, with the mRNA and peptide levels highest in distal ileum and below detection in duodenum. CRS4C-1 peptides are found exclusively in Paneth cells where they occur only in dense core granules and thus are secreted to function in the intestinal lumen. CRS4C bactericidal peptide activity is membrane-disruptive in that it permeabilizes Escherichia coli and induces rapid microbial cell K(+) efflux, but in a manner different from mouse alpha-defensin cryptdin-4. In in vitro studies, inactive pro-CRS4C-1 is converted to bactericidal CRS4C-1 peptide by matrix metalloproteinase-7 (MMP-7) proteolysis of the precursor proregion at the same residue positions that MMP-7 activates mouse pro-alpha-defensins. The absence of processed CRS4C in protein extracts of MMP-7-null mouse ileum demonstrates the in vivo requirement for intracellular MMP-7 in pro-CRS4C processing.
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Affiliation(s)
- Michael T Shanahan
- Department of Microbiology and Molecular Genetics, School of Medicine, College of Health Sciences, University of California, Irvine, California 92697-4800, USA
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Hadjicharalambous C, Sheynis T, Jelinek R, Shanahan MT, Ouellette AJ, Gizeli E. Mechanisms of alpha-defensin bactericidal action: comparative membrane disruption by Cryptdin-4 and its disulfide-null analogue. Biochemistry 2009; 47:12626-34. [PMID: 18973303 DOI: 10.1021/bi800335e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mammalian alpha-defensins all have a conserved triple-stranded beta-sheet structure that is constrained by an invariant tridisulfide array, and the peptides exert bactericidal effects by permeabilizing the target cell envelope. Curiously, the disordered, disulfide-null variant of mouse alpha-defensin cryptdin-4 (Crp4), termed (6C/A)-Crp4, has bactericidal activity equal to or greater than that of the native peptide, providing a rationale for comparing the mechanisms by which the peptides interact with and disrupt phospholipid vesicles of defined composition. For both live Escherichia coli ML35 cells and model membranes, disordered (6C/A)-Crp4 induced leakage in a manner similar to that of Crp4 but had less overall membrane permeabilizing activity. Crp4 induction of the leakage of the fluorophore from electronegative liposomes was strongly dependent on vesicle lipid charge and composition, and the incorporation of cardiolipin into liposomes of low electronegative charge to mimic bacterial membrane composition conferred sensitivity to Crp4- and (6C/A)-Crp4-mediated vesicle lysis. Membrane perturbation studies using biomimetic lipid/polydiacetylene vesicles showed that Crp4 inserts more pronouncedly into membranes containing a high fraction of electronegative lipids or cardiolipin than (6C/A)-Crp4 does, correlating directly with measurements of induced leakage. Fluorescence resonance energy transfer experiments provided evidence that Crp4 translocates across highly charged or cardiolipin-containing membranes, in a process coupled with membrane permeabilization, but (6C/A)-Crp4 did not translocate across lipid bilayers and consistently displayed membrane surface association. Thus, despite the greater in vitro bactericidal activity of (6C/A)-Crp4, native, beta-sheet-containing Crp4 induces membrane permeabilization more effectively than disulfide-null Crp4 by translocating and forming transient membrane defects. (6C/A)-Crp4, on the other hand, appears to induce greater membrane disintegration.
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Affiliation(s)
- Chrystalleni Hadjicharalambous
- Institute of Molecular Biology and Biotechnology, FORTH, and Department of Biology, University of Crete, Heraklion, Crete, Greece
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Abstract
RNA editing is a process by which genomically encoded cytidines are converted to uridines in plant mitochondrial transcripts. This conversion usually changes the amino acid specified by a codon and converts an "aberrant" residue to the evolutionarily conserved amino acid. The selection of the edited cytidine is highly specific. The cis-acting sequences for editing site recognition have been examined in ribosomal protein S12 (rps12) transcripts and in transcripts for a second copy of an internal portion of the ribosomal protein S12 (rps12b). rps12b was created by recombination at 7 and 9 nucleotide sequences that included editing sites I and IV of rps12, thus affording an opportunity to study the editing of chimeric transcripts with rearrangement very near C to U editing sites. Rearrangements downstream of editing site IV did not affect the editing of that sequence, while rearrangement upstream of editing site I ablated editing at that cytidine residue. Secondary structure predictions indicated that RNA structure did not correlate with the editing of these substrates. These results taken together with other studies in the literature suggest that RNA editing site recognition is primarily dependent on the 5' flanking RNA sequence.
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Affiliation(s)
- R M Mulligan
- Department of Developmental and Cell Biology, University of California, Irvine 92697-2300, USA.
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