1
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Kohda A, Kamakura S, Hayase J, Sumimoto H. The NADPH oxidases DUOX1 and DUOX2 are sorted to the apical plasma membrane in epithelial cells via their respective maturation factors DUOXA1 and DUOXA2. Genes Cells 2024. [PMID: 39126279 DOI: 10.1111/gtc.13153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]
Abstract
The membrane-integrated NADPH oxidases DUOX1 and DUOX2 are recruited to the apical plasma membrane in epithelial cells to release hydrogen peroxide, thereby playing crucial roles in various functions such as thyroid hormone synthesis and host defense. However, it has remained unknown about the molecular mechanism for apical sorting of DUOX1 and DUOX2. Here we show that DUOX1 and DUOX2 are correctly sorted to the apical membrane via the membrane-spanning DUOX maturation proteins DUOXA1 and DUOXA2, respectively, when co-expressed in MDCK epithelial cells. Impairment of N-glycosylation of DUOXA1 results in mistargeting of DUOX1 to the basolateral membrane. Similar to DUOX1 complexed with the glycosylation-defective DUOXA1, the naturally non-glycosylated oxidase NOX5, which forms a homo-oligomer, is targeted basolaterally. On the other hand, a mutant DUOXA2 deficient in N-glycosylation is less stable than the wild-type protein but still capable of recruiting DUOX2 to the apical membrane, whereas DUOX2 is missorted to the basolateral membrane when paired with DUOXA1. These findings indicate that DUOXA2 is crucial but its N-glycosylation is dispensable for DUOX2 apical recruitment; instead, its C-terminal region seems to be involved. Thus, apical sorting of DUOX1 and DUOX2 is likely regulated in a distinct manner by their respective partners DUOXA1 and DUOXA2.
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Affiliation(s)
- Akira Kohda
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Sachiko Kamakura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Junya Hayase
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Hideki Sumimoto
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
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2
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Baz-Redón N, Antolín M, Clemente M, Campos A, Mogas E, Fernández-Cancio M, Zafon E, García-Arumí E, Soler L, González-Llorens N, Aguilar-Riera C, Camats-Tarruella N, Yeste D. Patients with Thyroid Dyshormonogenesis and DUOX2 Variants: Molecular and Clinical Description and Genotype-Phenotype Correlation. Int J Mol Sci 2024; 25:8473. [PMID: 39126042 PMCID: PMC11313534 DOI: 10.3390/ijms25158473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 07/28/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Thyroid dyshormonogenesis (THD) is a heterogeneous group of genetic diseases caused by the total or partial defect in the synthesis or secretion of thyroid hormones. Genetic variants in DUOX2 can cause partial to total iodination organification defects and clinical heterogeneity, from transient to permanent congenital hypothyroidism. The aim of this study was to undertake a molecular characterization and genotype-phenotype correlation in patients with THD and candidate variants in DUOX2. A total of 31 (19.38%) patients from the Catalan Neonatal Screening Program presented with variants in DUOX2 that could explain their phenotype. Fifteen (48.39%) patients were compound heterozygous, 10 (32.26%) heterozygous, and 4 (12.90%) homozygous. In addition, 8 (26.67%) of these patients presented variants in other genes. A total of 35 variants were described, 10 (28.57%) of these variants have not been previously reported in literature. The most frequent variant in our cohort was c.2895_2898del/p.(Phe966SerfsTer29), classified as pathogenic according to reported functional studies. The final diagnosis of this cohort was permanent THD in 21 patients and transient THD in 10, according to reevaluation and/or need for treatment with levothyroxine. A clear genotype-phenotype correlation could not be identified; therefore, functional studies are necessary to confirm the pathogenicity of the variants.
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Affiliation(s)
- Noelia Baz-Redón
- Growth and Development Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (M.C.); (A.C.); (E.M.); (M.F.-C.); (N.C.-T.); (D.Y.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - María Antolín
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (M.A.); (E.Z.)
- Medicine Genetics Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
| | - María Clemente
- Growth and Development Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (M.C.); (A.C.); (E.M.); (M.F.-C.); (N.C.-T.); (D.Y.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Pediatric Endocrinology Section, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (L.S.); (N.G.-L.); (C.A.-R.)
- Pediatrics, Obstetrics and Gynecology and Preventive Medicine Department, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ariadna Campos
- Growth and Development Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (M.C.); (A.C.); (E.M.); (M.F.-C.); (N.C.-T.); (D.Y.)
- Pediatric Endocrinology Section, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (L.S.); (N.G.-L.); (C.A.-R.)
- Pediatrics, Obstetrics and Gynecology and Preventive Medicine Department, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Eduard Mogas
- Growth and Development Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (M.C.); (A.C.); (E.M.); (M.F.-C.); (N.C.-T.); (D.Y.)
- Pediatric Endocrinology Section, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (L.S.); (N.G.-L.); (C.A.-R.)
- Pediatrics, Obstetrics and Gynecology and Preventive Medicine Department, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Mónica Fernández-Cancio
- Growth and Development Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (M.C.); (A.C.); (E.M.); (M.F.-C.); (N.C.-T.); (D.Y.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Elisenda Zafon
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (M.A.); (E.Z.)
- Medicine Genetics Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
| | - Elena García-Arumí
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (M.A.); (E.Z.)
- Medicine Genetics Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
| | - Laura Soler
- Pediatric Endocrinology Section, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (L.S.); (N.G.-L.); (C.A.-R.)
| | - Núria González-Llorens
- Pediatric Endocrinology Section, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (L.S.); (N.G.-L.); (C.A.-R.)
| | - Cristina Aguilar-Riera
- Pediatric Endocrinology Section, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (L.S.); (N.G.-L.); (C.A.-R.)
| | - Núria Camats-Tarruella
- Growth and Development Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (M.C.); (A.C.); (E.M.); (M.F.-C.); (N.C.-T.); (D.Y.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Diego Yeste
- Growth and Development Group, Vall d’Hebron Research Institute (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (M.C.); (A.C.); (E.M.); (M.F.-C.); (N.C.-T.); (D.Y.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Pediatric Endocrinology Section, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (L.S.); (N.G.-L.); (C.A.-R.)
- Pediatrics, Obstetrics and Gynecology and Preventive Medicine Department, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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3
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Ou H, Ye X, Huang H, Cheng H. Constructing a screening model to obtain the functional herbs for the treatment of active ulcerative colitis based on herb-compound-target network and immuno-infiltration analysis. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:4693-4711. [PMID: 38117365 PMCID: PMC11166790 DOI: 10.1007/s00210-023-02900-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023]
Abstract
The therapeutic effect of most traditional Chinese medicines (TCM) on ulcerative colitis is unclear, The objective of this study was to develop a core herbal screening model aimed at facilitating the transition from active ulcerative colitis (UC) to inactive. We obtained the gene expression dataset GSE75214 for UC from the GEO database and analysed the differentially expressed genes (DEGs) between active and inactive groups. Gene modules associated with the active group were screened using WGCNA, and immune-related genes (IRGs) were obtained from the ImmPort database. The TCMSP database was utilized to acquire the herb-molecule-target network and identify the herb-related targets (HRT). We performed intersection operations on HRTs, DEGs, IRGs, and module genes to identify candidate genes and conducted enrichment analyses. Subsequently, three machine learning algorithms (SVM-REF analysis, Random Forest analysis, and LASSO regression analysis) were employed to refine the hubgene from the candidate genes. Based on the hub genes identified in this study, we conducted compound and herb matching and further screened herbs related to abdominal pain and blood in stool using the Symmap database.Besides, the stability between molecules and targets were assessed using molecular docking and molecular dynamic simulation methods. An intersection operation was performed on HRT, DEGs, IRGs, and module genes, leading to the identification of 23 candidate genes. Utilizing three algorithms (RandomForest, SVM-REF, and LASSO) for analyzing the candidate genes and identifying the intersection, we identified five core targets (CXCL2, DUOX2, LYZ, MMP9, and AGT) and 243 associated herbs. Hedysarum Multijugum Maxim. (Huangqi), Sophorae Flavescentis Radix (Kushen), Cotyledon Fimbriata Turcz. (Wasong), and Granati Pericarpium (Shiliupi) were found to be capable of relieving abdominal pain and hematochezia during active UC. Molecular docking demonstrated that the compounds of the four aforementioned herbs showed positive docking activity with their core targets. The results of molecular dynamic simulations indicated that well-docked active molecules had a more stable structure when bound to their target complexes. The study has shed light on the potential of TCMs in treating active UC from an immunomodulatory perspective, consequently, 5 core targets and 4 key herbs has been identified. These findings can provide a theoretical basis for subsequent management and treatment of active UC with TCM, as well as offer original ideas for further research and development of innovative drugs for alleviating UC.
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Affiliation(s)
- Haiya Ou
- Shenzhen Bao'an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Xiaopeng Ye
- Shenzhen Bao'an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Hongshu Huang
- Shenzhen Bao'an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Honghui Cheng
- Shenzhen Bao'an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China.
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4
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Jain S, Safo SE. DeepIDA-GRU: a deep learning pipeline for integrative discriminant analysis of cross-sectional and longitudinal multiview data with applications to inflammatory bowel disease classification. Brief Bioinform 2024; 25:bbae339. [PMID: 39007595 DOI: 10.1093/bib/bbae339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/29/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Biomedical research now commonly integrates diverse data types or views from the same individuals to better understand the pathobiology of complex diseases, but the challenge lies in meaningfully integrating these diverse views. Existing methods often require the same type of data from all views (cross-sectional data only or longitudinal data only) or do not consider any class outcome in the integration method, which presents limitations. To overcome these limitations, we have developed a pipeline that harnesses the power of statistical and deep learning methods to integrate cross-sectional and longitudinal data from multiple sources. In addition, it identifies key variables that contribute to the association between views and the separation between classes, providing deeper biological insights. This pipeline includes variable selection/ranking using linear and nonlinear methods, feature extraction using functional principal component analysis and Euler characteristics, and joint integration and classification using dense feed-forward networks for cross-sectional data and recurrent neural networks for longitudinal data. We applied this pipeline to cross-sectional and longitudinal multiomics data (metagenomics, transcriptomics and metabolomics) from an inflammatory bowel disease (IBD) study and identified microbial pathways, metabolites and genes that discriminate by IBD status, providing information on the etiology of IBD. We conducted simulations to compare the two feature extraction methods.
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Affiliation(s)
- Sarthak Jain
- Department of Electrical Engineering, University of Minnesota, Minneapolis, MN 55455, United States
| | - Sandra E Safo
- Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, MN 55455, United States
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5
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Grasberger H, Dumitrescu AM, Liao XH, Swanson EG, Weiss RE, Srichomkwun P, Pappa T, Chen J, Yoshimura T, Hoffmann P, França MM, Tagett R, Onigata K, Costagliola S, Ranchalis J, Vollger MR, Stergachis AB, Chong JX, Bamshad MJ, Smits G, Vassart G, Refetoff S. STR mutations on chromosome 15q cause thyrotropin resistance by activating a primate-specific enhancer of MIR7-2/MIR1179. Nat Genet 2024; 56:877-888. [PMID: 38714869 DOI: 10.1038/s41588-024-01717-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 03/14/2024] [Indexed: 05/22/2024]
Abstract
Thyrotropin (TSH) is the master regulator of thyroid gland growth and function. Resistance to TSH (RTSH) describes conditions with reduced sensitivity to TSH. Dominantly inherited RTSH has been linked to a locus on chromosome 15q, but its genetic basis has remained elusive. Here we show that non-coding mutations in a (TTTG)4 short tandem repeat (STR) underlie dominantly inherited RTSH in all 82 affected participants from 12 unrelated families. The STR is contained in a primate-specific Alu retrotransposon with thyroid-specific cis-regulatory chromatin features. Fiber-seq and RNA-seq studies revealed that the mutant STR activates a thyroid-specific enhancer cluster, leading to haplotype-specific upregulation of the bicistronic MIR7-2/MIR1179 locus 35 kb downstream and overexpression of its microRNA products in the participants' thyrocytes. An imbalance in signaling pathways targeted by these micro-RNAs provides a working model for this cause of RTSH. This finding broadens our current knowledge of genetic defects altering pituitary-thyroid feedback regulation.
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Affiliation(s)
- Helmut Grasberger
- Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra M Dumitrescu
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Committee on Molecular Metabolism and Nutrition, The University of Chicago, Chicago, IL, USA
| | - Xiao-Hui Liao
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Elliott G Swanson
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Roy E Weiss
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Theodora Pappa
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Junfeng Chen
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Takashi Yoshimura
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Phillip Hoffmann
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Rebecca Tagett
- Michigan Medicine BRCF Bioinformatics Core, University of Michigan, Ann Arbor, MI, USA
| | | | - Sabine Costagliola
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Jane Ranchalis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mitchell R Vollger
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman-Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Jessica X Chong
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Brotman-Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Michael J Bamshad
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman-Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Guillaume Smits
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
- Center of Human Genetics, Hôpital Erasme, Hôpital Universitaire de Bruxelles, and Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Gilbert Vassart
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Samuel Refetoff
- Department of Medicine, The University of Chicago, Chicago, IL, USA.
- Committee on Genetics, The University of Chicago, Chicago, IL, USA.
- Department of Pediatrics, The University of Chicago, Chicago, IL, USA.
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6
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Schwarz M, Gazdarica M, Froňková E, Svatoň M, Bronský J, Havlovicová M, Křepelová A, Macek M. Functional studies associate novel DUOX2 gene variants detected in heterozygosity to Crohn's disease. Mol Biol Rep 2024; 51:399. [PMID: 38456993 DOI: 10.1007/s11033-024-09317-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/05/2024] [Indexed: 03/09/2024]
Abstract
PURPOSE Crohn's disease is a chronic gastrointestinal inflammatory disease with possible extraintestinal symptoms. There are predisposing genetic factors and even monogenic variants of the disorder. One of the possible genetic factors are variants of the DUOX2 gene. The protein product of the DUOX2 gene is a dual oxidase enzyme producing H2O2 in the bowel. Reduced H2O2 levels impact mucosal homeostasis and contribute to the development of inflammatory bowel disease. Thus far, only 19 patients with IBD with the DUOX2 variants have been described. METHODS Here we present a case report of an adolescent female diagnosed at eleven years of age with IBD that was subsequently reclassified as Crohn's disease. She was treated with immunosuppressants and biological therapy but experienced additional complications. Her peripheral blood lymphocyte DNA was studied using massive parallel sequencing. Detected variants were functionally studied. RESULTS Whole exome sequencing found two novel DUOX2 gene variants: a de novo variant c.3646C>T; p.R1216W and a maternally inherited variant c.3391G>A; p.A1131T which were initially classified as variants of unknown significance. However, follow-up functional studies demonstrated that both DUOX2 variants led to impaired H2O2 generation, which led to their reclassification to the likely pathogenic class according to the ACMG.net. Therefore, we conclude that these variants are causative for the disease. CONCLUSIONS Identifying novel variants in patients with Crohn's disease and their families is important for precision medicine approaches and understanding of the pathogenesis of likely "monogenic" rare forms of inflammatory bowel disease.
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Affiliation(s)
- Martin Schwarz
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic.
- PRENET - Laboratoře Lékařské Genetiky s.r.o., Pardubice, Czech Republic.
| | - Matej Gazdarica
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Eva Froňková
- Department of Pediatric Hematology and Oncology, 2nd Medical Faculty, Childhood Leukaemia Investigation Prague, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Michael Svatoň
- Department of Pediatric Hematology and Oncology, 2nd Medical Faculty, Childhood Leukaemia Investigation Prague, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Jiří Bronský
- Department of Pediatrics, 2nd Medical Faculty, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Markéta Havlovicová
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Anna Křepelová
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Milan Macek
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
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7
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Zhu B, Bai Y, Yeo YY, Lu X, Rovira-Clavé X, Chen H, Yeung J, Gerber GK, Angelo M, Shalek AK, Nolan GP, Jiang S. A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583400. [PMID: 38496402 PMCID: PMC10942342 DOI: 10.1101/2024.03.04.583400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The intricate and dynamic interactions between the host immune system and its microbiome constituents undergo dynamic shifts in response to perturbations to the intestinal tissue environment. Our ability to study these events on the systems level is significantly limited by in situ approaches capable of generating simultaneous insights from both host and microbial communities. Here, we introduce Microbiome Cartography (MicroCart), a framework for simultaneous in situ probing of host features and its microbiome across multiple spatial modalities. We demonstrate MicroCart by comprehensively investigating the alterations in both gut host and microbiome components in a murine model of colitis by coupling MicroCart with spatial proteomics, transcriptomics, and glycomics platforms. Our findings reveal a global but systematic transformation in tissue immune responses, encompassing tissue-level remodeling in response to host immune and epithelial cell state perturbations, and bacterial population shifts, localized inflammatory responses, and metabolic process alterations during colitis. MicroCart enables a deep investigation of the intricate interplay between the host tissue and its microbiome with spatial multiomics.
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Affiliation(s)
- Bokai Zhu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Yunhao Bai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Yao Yu Yeo
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xiaowei Lu
- Mass Spectrometry Core Facility, Stanford University, Stanford, CA, United States
| | - Xavier Rovira-Clavé
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Han Chen
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
- Biological and Medical Informatics program, UCSF, San Francisco, CA, United States
| | - Jason Yeung
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Georg K Gerber
- Division of Computational Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Health Sciences and Technology, Harvard University and MIT, Cambridge, MA, USA
| | - Mike Angelo
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Alex K Shalek
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Sizun Jiang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
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8
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Hu R, Xiao J, Fan L. The Role of the Trace Element Selenium in Inflammatory Bowel Disease. Biol Trace Elem Res 2024:10.1007/s12011-024-04074-y. [PMID: 38363489 DOI: 10.1007/s12011-024-04074-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024]
Abstract
One set of chronic gastrointestinal disorders called inflammatory bowel disease (IBD) is defined by persistent, non-specific inflammation. Abdominal pain, hematochezia, diarrhea, and other symptoms are among its clinical signs. Currently, managing and treating IBD remains a significant challenge. Patients with IBD frequently have deficits in trace elements. Selenium (Se) is one of the necessary trace elements for normal organismal function. It has several regulatory effects, including anti-oxidation, anti-inflammatory, and defensive properties, via inducing the synthesis of selenoproteins. Patients with IBD have been shown to have lower Se levels in epidemiologic research studies. Several experimental models of IBD suggest that Se or selenoproteins play a key role in microinflammation. We discuss the relationship between Se and IBD in this review, with an emphasis on a summary of potential mechanisms of action and applications of Se in IBD.
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Affiliation(s)
- Ruifang Hu
- College of Clinical Medicine, Jining Medical University, Jining, 272013, Shandong Province, China
| | - Jinliang Xiao
- College of Clinical Medicine, Jining Medical University, Jining, 272013, Shandong Province, China
| | - Lijuan Fan
- Department of Gastroenterology, Jining No. 1 People's Hospital, Jining, 272000, Shandong Province, China.
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9
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Jurickova I, Dreskin BW, Angerman E, Bonkowski E, Tominaga K, Iwasawa K, Braun T, Takebe T, Helmrath MA, Haberman Y, Wells JM, Denson LA. Eicosatetraynoic Acid Regulates Pro-Fibrotic Pathways in an Induced Pluripotent Stem Cell Derived Macrophage:Human Intestinal Organoid Model of Crohn's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.577959. [PMID: 38352573 PMCID: PMC10862816 DOI: 10.1101/2024.01.30.577959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Background and Aims We previously identified small molecules predicted to reverse an ileal gene signature for future Crohn's Disease (CD) strictures. Here we used a new human intestinal organoid (HIO) model system containing macrophages to test a lead candidate, eicosatetraynoic acid (ETYA). Methods Induced pluripotent stem cell lines (iPSC) were derived from CD patients and differentiated into macrophages and HIOs. Macrophages and macrophage:HIO co-cultures were exposed to lipopolysaccharide (LPS) with and without ETYA pre-treatment. Cytospin and flow cytometry characterized macrophage morphology and activation markers, and RNA sequencing defined the global pattern of macrophage gene expression. TaqMan Low Density Array, Luminex multiplex assay, immunohistologic staining, and sirius red polarized light microscopy were performed to measure macrophage cytokine production and HIO pro-fibrotic gene expression and collagen content. Results iPSC-derived macrophages exhibited morphology similar to primary macrophages and expressed inflammatory macrophage cell surface markers including CD64 and CD68. LPS-stimulated macrophages expressed a global pattern of gene expression enriched in CD ileal inflammatory macrophages and matrisome secreted products, and produced cytokines and chemokines including CCL2, IL1B, and OSM implicated in refractory disease. ETYA suppressed CD64 abundance and pro-fibrotic gene expression pathways in LPS stimulated macrophages. Co-culture of LPS-primed macrophages with HIO led to up-regulation of fibroblast activation genes including ACTA2 and COL1A1 , and an increase in HIO collagen content. ETYA pre-treatment prevented pro-fibrotic effects of LPS-primed macrophages. Conclusions ETYA inhibits pro-fibrotic effects of LPS-primed macrophages upon co-cultured HIO. This model may be used in future untargeted screens for small molecules to treat refractory CD.
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10
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Wu J, Singleton SS, Bhuiyan U, Krammer L, Mazumder R. Multi-omics approaches to studying gastrointestinal microbiome in the context of precision medicine and machine learning. Front Mol Biosci 2024; 10:1337373. [PMID: 38313584 PMCID: PMC10834744 DOI: 10.3389/fmolb.2023.1337373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/27/2023] [Indexed: 02/06/2024] Open
Abstract
The human gastrointestinal (gut) microbiome plays a critical role in maintaining host health and has been increasingly recognized as an important factor in precision medicine. High-throughput sequencing technologies have revolutionized -omics data generation, facilitating the characterization of the human gut microbiome with exceptional resolution. The analysis of various -omics data, including metatranscriptomics, metagenomics, glycomics, and metabolomics, holds potential for personalized therapies by revealing information about functional genes, microbial composition, glycans, and metabolites. This multi-omics approach has not only provided insights into the role of the gut microbiome in various diseases but has also facilitated the identification of microbial biomarkers for diagnosis, prognosis, and treatment. Machine learning algorithms have emerged as powerful tools for extracting meaningful insights from complex datasets, and more recently have been applied to metagenomics data via efficiently identifying microbial signatures, predicting disease states, and determining potential therapeutic targets. Despite these rapid advancements, several challenges remain, such as key knowledge gaps, algorithm selection, and bioinformatics software parametrization. In this mini-review, our primary focus is metagenomics, while recognizing that other -omics can enhance our understanding of the functional diversity of organisms and how they interact with the host. We aim to explore the current intersection of multi-omics, precision medicine, and machine learning in advancing our understanding of the gut microbiome. A multidisciplinary approach holds promise for improving patient outcomes in the era of precision medicine, as we unravel the intricate interactions between the microbiome and human health.
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Affiliation(s)
- Jingyue Wu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Stephanie S. Singleton
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Urnisha Bhuiyan
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Lori Krammer
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
- Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
- The McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC, United States
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11
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Chandrasekaran P, Han Y, Zerbe CS, Heller T, DeRavin SS, Kreuzberg SA, Marciano BE, Siu Y, Jones DR, Abraham RS, Stephens MC, Tsou AM, Snapper S, Conlan S, Subramanian P, Quinones M, Grou C, Calderon V, Deming C, Leiding JW, Arnold DE, Logan BR, Griffith LM, Petrovic A, Mousallem TI, Kapoor N, Heimall JR, Barnum JL, Kapadia M, Wright N, Rayes A, Chandra S, Broglie LA, Chellapandian D, Deal CL, Grunebaum E, Lim SS, Mallhi K, Marsh RA, Murguia-Favela L, Parikh S, Touzot F, Cowan MJ, Dvorak CC, Haddad E, Kohn DB, Notarangelo LD, Pai SY, Puck JM, Pulsipher MA, Torgerson TR, Kang EM, Malech HL, Segre JA, Bryant CE, Holland SM, Falcone EL. Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease. J Allergy Clin Immunol 2023; 152:1619-1633.e11. [PMID: 37659505 PMCID: PMC11279821 DOI: 10.1016/j.jaci.2023.07.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 07/18/2023] [Accepted: 07/27/2023] [Indexed: 09/04/2023]
Abstract
BACKGROUND Chronic granulomatous disease (CGD) is caused by defects in any 1 of the 6 subunits forming the nicotinamide adenine dinucleotide phosphate oxidase complex 2 (NOX2), leading to severely reduced or absent phagocyte-derived reactive oxygen species production. Almost 50% of patients with CGD have inflammatory bowel disease (CGD-IBD). While conventional IBD therapies can treat CGD-IBD, their benefits must be weighed against the risk of infection. Understanding the impact of NOX2 defects on the intestinal microbiota may lead to the identification of novel CGD-IBD treatments. OBJECTIVE We sought to identify microbiome and metabolome signatures that can distinguish individuals with CGD and CGD-IBD. METHODS We conducted a cross-sectional observational study of 79 patients with CGD, 8 pathogenic variant carriers, and 19 healthy controls followed at the National Institutes of Health Clinical Center. We profiled the intestinal microbiome (amplicon sequencing) and stool metabolome, and validated our findings in a second cohort of 36 patients with CGD recruited through the Primary Immune Deficiency Treatment Consortium. RESULTS We identified distinct intestinal microbiome and metabolome profiles in patients with CGD compared to healthy individuals. We observed enrichment for Erysipelatoclostridium spp, Sellimonas spp, and Lachnoclostridium spp in CGD stool samples. Despite differences in bacterial alpha and beta diversity between the 2 cohorts, several taxa correlated significantly between both cohorts. We further demonstrated that patients with CGD-IBD have a distinct microbiome and metabolome profile compared to patients without CGD-IBD. CONCLUSION Intestinal microbiome and metabolome signatures distinguished patients with CGD and CGD-IBD, and identified potential biomarkers and therapeutic targets.
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Affiliation(s)
| | - Yu Han
- Division of Molecular Genetics and Pathology, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Md; Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Christa S Zerbe
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Theo Heller
- Translational Hepatology Section, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Md
| | - Suk See DeRavin
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Samantha A Kreuzberg
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Beatriz E Marciano
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Yik Siu
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY
| | - Drew R Jones
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY
| | - Roshini S Abraham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn; Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | | | - Amy M Tsou
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, Mass; Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medical College, New York, NY
| | - Scott Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Sean Conlan
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, Md
| | - Poorani Subramanian
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Md
| | - Mariam Quinones
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Md
| | - Caroline Grou
- Bioinformatics Core, Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | - Virginie Calderon
- Bioinformatics Core, Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | - Clayton Deming
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, Md
| | - Jennifer W Leiding
- Division of Allergy and Immunology, Department of Pediatrics, Johns Hopkins University, Baltimore, Md
| | - Danielle E Arnold
- Immune Deficiency-Cellular Therapy Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Md
| | - Brent R Logan
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, Wis
| | - Linda M Griffith
- Division of Allergy, Immunology, and Transplantation, NIAID, NIH, Bethesda, Md
| | - Aleksandra Petrovic
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital and Research Center, Seattle, Wash
| | - Talal I Mousallem
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Neena Kapoor
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Children's Hospital Los Angeles, Los Angeles, Calif
| | - Jennifer R Heimall
- Division of Allergy and Immunology, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Jessie L Barnum
- Division of Blood and Marrow Transplantation and Cellular Therapies, University of Pittsburgh Medical Center (UPMC) and Children's Hospital of Pittsburgh, Pittsburgh, Pa
| | - Malika Kapadia
- Department of Pediatrics, Harvard University Medical School, Boston, Mass
| | - Nicola Wright
- Section of Hematology/Immunology, Alberta Children's Hospital, University of Calgary, Calgary, Alberta, Canada
| | - Ahmad Rayes
- Intermountain Primary Children's Hospital, University of Utah, Salt Lake City, Utah
| | - Sharat Chandra
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Larisa A Broglie
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wis
| | - Deepak Chellapandian
- Center for Cell and Gene Therapy for Non-Malignant Conditions, Johns Hopkins All Children's Hospital, St Petersburg, Fla
| | - Christin L Deal
- Division of Allergy and Immunology, UPMC, Children's Hospital of Pittsburgh, Pittsburgh, Pa
| | - Eyal Grunebaum
- Division of Immunology and Allergy, Department of Pediatrics, Hospital for Sick Children, Toronto, Ontario, Canada; Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Si Lim
- Department of Pediatrics, John A. Burns School of Medicine, University of Hawai'i at Mānoa, Honolulu, Hawaii; University of Hawai'i Cancer Center, University of Hawai'i at Mānoa, Honolulu, Hawaii
| | | | - Rebecca A Marsh
- Cincinnati Children's Hospital Medical Center, and University of Cincinnati, Cincinnati, Ohio
| | - Luis Murguia-Favela
- Section of Hematology/Immunology, Alberta Children's Hospital, University of Calgary, Calgary, Alberta, Canada
| | - Suhag Parikh
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Ga
| | - Fabien Touzot
- Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Quebec, Canada; Department of Microbiology, Infectious Diseases, and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Morton J Cowan
- University of California San Francisco Benioff Children's Hospital, San Francisco, Calif
| | - Christopher C Dvorak
- University of California San Francisco Benioff Children's Hospital, San Francisco, Calif
| | - Elie Haddad
- Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Quebec, Canada; Department of Microbiology, Infectious Diseases, and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Donald B Kohn
- Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, Calif
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Sung-Yun Pai
- Immune Deficiency-Cellular Therapy Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Md
| | - Jennifer M Puck
- University of California San Francisco Benioff Children's Hospital, San Francisco, Calif
| | - Michael A Pulsipher
- Division of Pediatric Hematology and Oncology, Intermountain Primary Children's Hospital, Huntsman Cancer Institute at the University of Utah Spencer Fox Eccles School of Medicine, Salt Lake City, Utah
| | | | - Elizabeth M Kang
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Harry L Malech
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Julia A Segre
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, Md
| | - Clare E Bryant
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Emilia Liana Falcone
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md; Department of Microbiology, Infectious Diseases, and Immunology, Université de Montréal, Montreal, Quebec, Canada; Center for Immunity, Inflammation and Infectious Diseases, IRCM, Montreal, Quebec, Canada; Department of Medicine, Université de Montréal, Montreal, Quebec, Canada.
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12
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Castrillón-Betancur JC, López-Agudelo VA, Sommer N, Cleeves S, Bernardes JP, Weber-Stiehl S, Rosenstiel P, Sommer F. Epithelial Dual Oxidase 2 Shapes the Mucosal Microbiome and Contributes to Inflammatory Susceptibility. Antioxidants (Basel) 2023; 12:1889. [PMID: 37891968 PMCID: PMC10603924 DOI: 10.3390/antiox12101889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/03/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Reactive oxygen species (ROS) are highly reactive molecules formed from diatomic oxygen. They act as cellular signals, exert antibiotic activity towards invading microorganisms, but can also damage host cells. Dual oxidase 2 (DUOX2) is the main ROS-producing enzyme in the intestine, regulated by cues of the commensal microbiota and functions in pathogen defense. DUOX2 plays multiple roles in different organs and cell types, complicating the functional analysis using systemic deletion models. Here, we interrogate the precise role of epithelial DUOX2 for intestinal homeostasis and host-microbiome interactions. Conditional Duox2∆IEC mice lacking DUOX2, specifically in intestinal epithelial cells, were generated, and their intestinal mucosal immune phenotype and microbiome were analyzed. Inflammatory susceptibility was evaluated by challenging Duox2∆IEC mice in the dextran sodium sulfate (DSS) colitis model. DUOX2-microbiome interactions in humans were investigated by paired analyses of mucosal DUOX2 expression and fecal microbiome data in patients with intestinal inflammation. Under unchallenged conditions, we did not observe any obvious phenotype of Duox2∆IEC mice, although intestinal epithelial ROS production was drastically decreased, and the mucosal microbiome composition was altered. When challenged with DSS, Duox2∆IEC mice were protected from colitis, possibly by inhibiting ROS-mediated damage and fostering epithelial regenerative responses. Finally, in patients with intestinal inflammation, DUOX2 expression was increased in inflamed tissue, and high DUOX2 levels were linked to a dysbiotic microbiome. Our findings demonstrate that bidirectional DUOX2-microbiome interactions contribute to mucosal homeostasis, and their dysregulation may drive disease development, thus highlighting this axis as a therapeutic target to treat intestinal inflammation.
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Affiliation(s)
| | - Víctor Alonso López-Agudelo
- Institute of Clinical Molecular Biology, University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Nina Sommer
- Institute of Clinical Molecular Biology, University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Sven Cleeves
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs-Straße 1, 30625 Hannover, Germany
| | - Joana Pimenta Bernardes
- Institute of Clinical Molecular Biology, University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Saskia Weber-Stiehl
- Institute of Clinical Molecular Biology, University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Felix Sommer
- Institute of Clinical Molecular Biology, University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
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13
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Li J, Simmons AJ, Chiron S, Ramirez-Solano MA, Tasneem N, Kaur H, Xu Y, Revetta F, Vega PN, Bao S, Cui C, Tyree RN, Raber LW, Conner AN, Beaulieu DB, Dalal RL, Horst SN, Pabla BS, Huo Y, Landman BA, Roland JT, Scoville EA, Schwartz DA, Washington MK, Shyr Y, Wilson KT, Coburn LA, Lau KS, Liu Q. A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.560293. [PMID: 37873404 PMCID: PMC10592875 DOI: 10.1101/2023.09.30.560293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Crohn's disease (CD) is a complex chronic inflammatory disorder that may affect any part of gastrointestinal tract with extra-intestinal manifestations and associated immune dysregulation. To characterize heterogeneity in CD, we profiled single-cell transcriptomics of 170 samples from 65 CD patients and 18 non-inflammatory bowel disease (IBD) controls in both the terminal ileum (TI) and ascending colon (AC). Analysis of 202,359 cells identified a novel epithelial cell type in both TI and AC, featuring high expression of LCN2, NOS2, and DUOX2, and thus is named LND. LND cells, confirmed by high-resolution in-situ RNA imaging, were rarely found in non-IBD controls, but expanded significantly in active CD. Compared to other epithelial cells, genes defining LND cells were enriched in antimicrobial response and immunoregulation. Moreover, multiplexed protein imaging demonstrated that LND cell abundance was associated with immune infiltration. Cross-talk between LND and immune cells was explored by ligand-receptor interactions and further evidenced by their spatial colocalization. LND cells showed significant enrichment of expression specificity of IBD/CD susceptibility genes, revealing its role in immunopathogenesis of CD. Investigating lineage relationships of epithelial cells detected two LND cell subpopulations with different origins and developmental potential, early and late LND. The ratio of the late to early LND cells was related to anti-TNF response. These findings emphasize the pathogenic role of the specialized LND cell type in both Crohn's ileitis and Crohn's colitis and identify novel biomarkers associated with disease activity and treatment response.
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Affiliation(s)
- Jia Li
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Alan J. Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sophie Chiron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marisol A. Ramirez-Solano
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Naila Tasneem
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Harsimran Kaur
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yanwen Xu
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Frank Revetta
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paige N. Vega
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shunxing Bao
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Can Cui
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Regina N. Tyree
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Larry W. Raber
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anna N. Conner
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dawn B. Beaulieu
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robin L. Dalal
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara N. Horst
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Baldeep S. Pabla
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuankai Huo
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Bennett A. Landman
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Joseph T. Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville TN, USA
| | - Elizabeth A. Scoville
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - David A. Schwartz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Lori A. Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Ken S. Lau
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
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14
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Astarita G, Kelly RS, Lasky-Su J. Metabolomics and lipidomics strategies in modern drug discovery and development. Drug Discov Today 2023; 28:103751. [PMID: 37640150 PMCID: PMC10543515 DOI: 10.1016/j.drudis.2023.103751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Metabolomics and lipidomics have an increasingly pivotal role in drug discovery and development. In the context of drug discovery, monitoring changes in the levels or composition of metabolites and lipids relative to genetic variations yields functional insights, bolstering human genetics and (meta)genomic methodologies. This approach also sheds light on potential novel targets for therapeutic intervention. In the context of drug development, metabolite and lipid biomarkers contribute to enhanced success rates, promising a transformative impact on precision medicine. In this review, we deviate from analytical chemist-focused perspectives, offering an overview tailored to drug discovery. We provide introductory insight into state-of-the-art mass spectrometry (MS)-based metabolomics and lipidomics techniques utilized in drug discovery and development, drawing from the collective expertise of our research teams. We comprehensively outline the application of metabolomics and lipidomics in advancing drug discovery and development, spanning fundamental research, target identification, mechanisms of action, and the exploration of biomarkers.
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Affiliation(s)
- Giuseppe Astarita
- Georgetown University, Washington, DC, USA; Arkuda Therapeutics, Watertown, MA, USA.
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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15
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Rajeh A, Cornman HL, Gupta A, Szeto MD, Kambala A, Oladipo O, Parthasarathy V, Deng J, Wheelan S, Pritchard T, Kwatra MM, Semenov YR, Gusev A, Yegnasubramanian S, Kwatra SG. Somatic mutations reveal hyperactive Notch signaling and racial disparities in prurigo nodularis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.25.23295810. [PMID: 37808834 PMCID: PMC10557842 DOI: 10.1101/2023.09.25.23295810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Prurigo nodularis (PN) is a chronic inflammatory skin disease that disproportionately affects African Americans and is characterized by pruritic skin nodules of unknown etiology. Little is known about genetic alterations in PN pathogenesis, especially relating to somatic events which are often implicated in inflammatory conditions. We thus performed whole-exome sequencing on 54 lesional and nonlesional skin biopsies from 17 PN patients and 10 atopic dermatitis (AD) patients for comparison. Somatic mutational analysis revealed that PN lesional skin harbors pervasive somatic mutations in fibrotic, neurotropic, and cancer-associated genes. Nonsynonymous mutations were most frequent in NOTCH1 and the Notch signaling pathway, a regulator of cellular proliferation and tissue fibrosis, and NOTCH1 mutations were absent in AD. Somatic copy-number analysis, combined with expression data, showed that recurrently deleted and downregulated genes in PN lesional skin are associated with axonal guidance and extension. Follow-up immunofluorescence validation demonstrated increased NOTCH1 expression in PN lesional skin fibroblasts and increased Notch signaling in PN lesional dermis. Finally, multi-center data revealed a significantly increased risk of NOTCH1-associated diseases in PN patients. In characterizing the somatic landscape of PN, we uncover novel insights into its pathophysiology and identify a role for dysregulated Notch signaling in PN.
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Affiliation(s)
- Ahmad Rajeh
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hannah L Cornman
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anuj Gupta
- The Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Mindy D Szeto
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anusha Kambala
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olusola Oladipo
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Varsha Parthasarathy
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Junwen Deng
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah Wheelan
- Present affiliation: National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA
| | - Thomas Pritchard
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Madan M Kwatra
- Department of Anesthesiology, Duke University School of Medicine, Durham, NC, USA
| | - Yevgeniy R Semenov
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alexander Gusev
- Division of Genetics, Brigham & Women's Hospital, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Srinivasan Yegnasubramanian
- The Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shawn G Kwatra
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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16
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Parlato M, Cerf-Bensussan N. Another Breach in the Wall: Impaired Epithelial DUOX2 Activity Fuels Metabolic Syndrome. Cell Mol Gastroenterol Hepatol 2023; 16:648-649. [PMID: 37517801 PMCID: PMC10511920 DOI: 10.1016/j.jcmgh.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023]
Affiliation(s)
- Marianna Parlato
- Université Paris-Cité, Institut Imagine, Laboratory of Intestinal Immunity, INSERM U1163, Paris, France.
| | - Nadine Cerf-Bensussan
- Université Paris-Cité, Institut Imagine, Laboratory of Intestinal Immunity, INSERM U1163, Paris, France
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17
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Bao W, Wang L, Liu X, Li M. Predicting diagnostic biomarkers associated with immune infiltration in Crohn's disease based on machine learning and bioinformatics. Eur J Med Res 2023; 28:255. [PMID: 37496049 PMCID: PMC10369716 DOI: 10.1186/s40001-023-01200-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/26/2023] [Indexed: 07/28/2023] Open
Abstract
OBJECTIVE The objective of this study is to investigate potential biomarkers of Crohn's disease (CD) and the pathological importance of infiltration of associated immune cells in disease development using machine learning. METHODS Three publicly accessible CD gene expression profiles were obtained from the GEO database. Inflammatory tissue samples were selected and differentiated between colonic and ileal tissues. To determine the differentially expressed genes (DEGs) between CD and healthy controls, the larger sample size was merged as a training unit. The function of DEGs was comprehended through disease enrichment (DO) and gene set enrichment analysis (GSEA) on DEGs. Promising biomarkers were identified using the support vector machine-recursive feature elimination and lasso regression models. To further clarify the efficacy of potential biomarkers as diagnostic genes, the area under the ROC curve was observed in the validation group. Additionally, using the CIBERSORT approach, immune cell fractions from CD patients were examined and linked with potential biomarkers. RESULTS Thirty-four DEGs were identified in colon tissue, of which 26 were up-regulated and 8 were down-regulated. In ileal tissues, 50 up-regulated and 50 down-regulated DEGs were observed. Disease enrichment of colon and ileal DEGs primarily focused on immunity, inflammatory bowel disease, and related pathways. CXCL1, S100A8, REG3A, and DEFA6 in colon tissue and LCN2 and NAT8 in ileum tissue demonstrated excellent diagnostic value and could be employed as CD gene biomarkers using machine learning methods in conjunction with external dataset validation. In comparison to controls, antigen processing and presentation, chemokine signaling pathway, cytokine-cytokine receptor interactions, and natural killer cell-mediated cytotoxicity were activated in colonic tissues. Cytokine-cytokine receptor interactions, NOD-like receptor signaling pathways, and toll-like receptor signaling pathways were activated in ileal tissues. NAT8 was found to be associated with CD8 T cells, while CXCL1, S100A8, REG3A, LCN2, and DEFA6 were associated with neutrophils, indicating that immune cell infiltration in CD is closely connected. CONCLUSION CXCL1, S100A8, REG3A, and DEFA6 in colonic tissue and LCN2 and NAT8 in ileal tissue can be employed as CD biomarkers. Additionally, immune cell infiltration is crucial for CD development.
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Affiliation(s)
- Wenhui Bao
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Spleen and Gastroenterology, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, No.354 Beima Road, Hongqiao District, Tianjin, China
| | - Lin Wang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Nephrology Department, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoxiao Liu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Department of Comprehensive Rehabilitation, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Ming Li
- Spleen and Gastroenterology, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, No.354 Beima Road, Hongqiao District, Tianjin, China.
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18
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Luo JQ, Ren H, Chen MY, Zhao Q, Yang N, Liu Q, Gao YC, Zhou HH, Huang WH, Zhang W. Hydrochlorothiazide-induced glucose metabolism disorder is mediated by the gut microbiota via LPS-TLR4-related macrophage polarization. iScience 2023; 26:107130. [PMID: 37456847 PMCID: PMC10338205 DOI: 10.1016/j.isci.2023.107130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/09/2023] [Accepted: 06/10/2023] [Indexed: 07/18/2023] Open
Abstract
Hydrochlorothiazide (HCTZ) is reported to impair glucose tolerance and may induce new onset of diabetes, but the pharmacomicrobiomics of the adverse effect for HCTZ remains unknown. Mice-fed HCTZ exhibited insulin resistance and impaired glucose tolerance. By using FMT and antibiotic cocktail models, we found that HCTZ-induced metabolic disorder was mediated by commensal microbiota. HCTZ consumption disturbed the structure of the intestinal microbiota, causing abnormal elevation of Gram-negative Enterobacteriaceae and lipopolysaccharide (LPS) then leading to intestinal barrier dysfunction. Additionally, HCTZ activated TLR4 signaling and induced macrophage polarization and inflammation in the liver. Furthermore, HCTZ-induced macrophage polarization and metabolic disorder were abrogated by blocking TLR4 signaling. HCTZ consumption caused a significant increase in Gram-negative Enterobacteriaceae, which elevated the levels of LPS, thereby activating LPS/TLR4 pathway, promoting inflammation and macrophage polarization, and resulting in metabolic disorders. These findings revealed that the gut microbiome is the key medium underlying HCTZ-induced metabolic disorder.
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Affiliation(s)
- Jian-Quan Luo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, Hunan, P.R. China
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Changsha, China
| | - Huan Ren
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, Hunan, P.R. China
- Department of Pharmacy, Hunan Provincial People’s Hospital, the First Affiliated Hospital of Hunan Normal University, No.61 Western Jiefang Road, Changsha, Hunan, China
| | - Man-Yun Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, Hunan, P.R. China
| | - Qing Zhao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, Hunan, P.R. China
| | - Nian Yang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, Hunan, P.R. China
| | - Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, Hunan, P.R. China
| | - Yong-Chao Gao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, Hunan, P.R. China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, Hunan, P.R. China
| | - Wei-Hua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, Hunan, P.R. China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, Hunan, P.R. China
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19
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Hazime H, Ducasa GM, Santander AM, Brito N, González EE, Ban Y, Kaunitz J, Akiba Y, Fernández I, Burgueño JF, Abreu MT. Intestinal Epithelial Inactivity of Dual Oxidase 2 Results in Microbiome-Mediated Metabolic Syndrome. Cell Mol Gastroenterol Hepatol 2023; 16:557-572. [PMID: 37369278 PMCID: PMC10468370 DOI: 10.1016/j.jcmgh.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND & AIMS Metabolic syndrome (MetS) is characterized by obesity, glucose intolerance, and hepatic steatosis. Alterations in the gut microbiome play important roles in the development of MetS. However, the mechanisms by which this occurs are poorly understood. Dual oxidase 2 (DUOX2) is an antimicrobial reduced nicotinamide adenine dinucleotide phosphate oxidase expressed in the gut epithelium. Here, we posit that epithelial DUOX2 activity provides a mechanistic link between the gut microbiome and the development of MetS. METHODS Mice carrying an intestinal epithelial-specific deletion of dual oxidase maturation factor 1/2 (DA IEC-KO), and wild-type littermates were fed a standard diet and killed at 24 weeks. Metabolic alterations were determined by glucose tolerance, lipid tests, and body and organ weight measurements. DUOX2 activity was determined by Amplex Red. Intestinal permeability was determined by fluorescein isothiocyanate-dextran, microbial translocation assessments, and portal vein lipopolysaccharide measurements. Metagenomic analysis of the stool microbiome was performed. The role of the microbiome was assessed in antibiotic-treated mice. RESULTS DA IEC-KO males showed increased body and organ weights accompanied by glucose intolerance and increased plasma lipid and liver enzyme levels, and increased adiposity in the liver and adipose tissue. Expression of F4/80, CD68, uncoupling protein 1, carbohydrate response element binding protein, leptin, and adiponectin was altered in the liver and adipose tissue of DA IEC-KO males. DA IEC-KO males produced less epithelial H2O2, had altered relative abundance of Akkermansiaceae and Lachnospiraceae in stool, and showed increased portal vein lipopolysaccharides and intestinal permeability. Females were protected from barrier defects and MetS, despite producing less H2O2. Antibiotic depletion abrogated all MetS phenotypes observed. CONCLUSIONS Intestinal epithelial inactivity of DUOX2 promotes MetS in a microbiome-dependent manner.
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Affiliation(s)
- Hajar Hazime
- Division of Gastroenterology, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida; Department of Microbiology and Immunology, University of Miami-Miller School of Medicine, Miami, Florida
| | - G Michelle Ducasa
- Division of Gastroenterology, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida
| | - Ana M Santander
- Division of Gastroenterology, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida
| | - Nivis Brito
- Division of Gastroenterology, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida
| | - Eddy E González
- Division of Gastroenterology, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida
| | - Yuguang Ban
- Biostatistics and Bioinformatics Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami-Miller School of Medicine, Miami, Florida
| | - Jonathan Kaunitz
- Medical Service and Research Services, VA Greater Los Angeles Healthcare System, Los Angeles, California; Medical Service, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Yasutada Akiba
- Medical Service and Research Services, VA Greater Los Angeles Healthcare System, Los Angeles, California; Medical Service, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Irina Fernández
- Division of Gastroenterology, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida
| | - Juan F Burgueño
- Division of Gastroenterology, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida
| | - Maria T Abreu
- Division of Gastroenterology, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida; Department of Microbiology and Immunology, University of Miami-Miller School of Medicine, Miami, Florida.
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20
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Hsu NY, Nayar S, Gettler K, Talware S, Giri M, Alter I, Argmann C, Sabic K, Thin TH, Ko HBM, Werner R, Tastad C, Stappenbeck T, Azabdaftari A, Uhlig HH, Chuang LS, Cho JH. NOX1 is essential for TNFα-induced intestinal epithelial ROS secretion and inhibits M cell signatures. Gut 2023; 72:654-662. [PMID: 36191961 PMCID: PMC9998338 DOI: 10.1136/gutjnl-2021-326305] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 08/20/2022] [Indexed: 12/08/2022]
Abstract
OBJECTIVE Loss-of-function mutations in genes generating reactive oxygen species (ROS), such as NOX1, are associated with IBD. Mechanisms whereby loss of ROS drive IBD are incompletely defined. DESIGN ROS measurements and single-cell transcriptomics were performed on colonoids stratified by NOX1 genotype and TNFα stimulation. Clustering of epithelial cells from human UC (inflamed and uninflamed) scRNASeq was performed. Validation of M cell induction was performed by immunohistochemistry using UEA1 (ulex europaeus agglutin-1 lectin) and in vivo with DSS injury. RESULTS TNFα induces ROS production more in NOX1-WT versus NOX1-deficient murine colonoids under a range of Wnt-mediated and Notch-mediated conditions. scRNASeq from inflamed and uninflamed human colitis versus TNFα stimulated, in vitro colonoids defines substantially shared, induced transcription factors; NOX1-deficient colonoids express substantially lower levels of STAT3 (signal transducer and activator of transcription 3), CEBPD (CCAAT enhancer-binding protein delta), DNMT1 (DNA methyltransferase) and HIF1A (hypoxia-inducible factor) baseline. Subclustering unexpectedly showed marked TNFα-mediated induction of M cells (sentinel cells overlying lymphoid aggregates) in NOX1-deficient colonoids. M cell induction by UEA1 staining is rescued with H2O2 and paraquat, defining extra- and intracellular ROS roles in maintenance of LGR5+ stem cells. DSS injury demonstrated GP2 (glycoprotein-2), basal lymphoplasmacytosis and UEA1 induction in NOX1-deficiency. Principal components analyses of M cell genes and decreased DNMT1 RNA velocity correlate with UC inflammation. CONCLUSIONS NOX1 deficiency plus TNFα stimulation contribute to colitis through dysregulation of the stem cell niche and altered cell differentiation, enhancing basal lymphoplasmacytosis. Our findings prioritise ROS modulation for future therapies.
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Affiliation(s)
- Nai-Yun Hsu
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shikha Nayar
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kyle Gettler
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sayali Talware
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai Department of Medicine, New York, New York, USA
- The Icahn Genomic Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mamta Giri
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Isaac Alter
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ksenija Sabic
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tin Htwe Thin
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Huai-Bin Mabel Ko
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Robert Werner
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christopher Tastad
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thaddeus Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, Ohio, USA
| | - Aline Azabdaftari
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Ling-Shiang Chuang
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Judy H Cho
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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21
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Zhu LH, Dong J, Li WL, Kou ZY, Yang J. Genotype-Phenotype Correlations in Autosomal Dominant and Recessive APC Mutation-Negative Colorectal Adenomatous Polyposis. Dig Dis Sci 2023:10.1007/s10620-023-07890-9. [PMID: 36862359 DOI: 10.1007/s10620-023-07890-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/17/2023] [Indexed: 03/03/2023]
Abstract
The most prevalent type of intestinal polyposis, colorectal adenomatous polyposis (CAP), is regarded as a precancerous lesion of colorectal cancer with obvious genetic characteristics. Early screening and intervention can significantly improve patients' survival and prognosis. The adenomatous polyposis coli (APC) mutation is believed to be the primary cause of CAP. There is, however, a subset of CAP with undetectable pathogenic mutations in APC, known as APC (-)/CAP. The genetic predisposition to APC (-)/CAP has largely been associated with germline mutations in some susceptible genes, including the human mutY homologue (MUTYH) gene and the Nth-like DNA glycosylase 1 (NTHL1) gene, and DNA mismatch repair (MMR) can cause autosomal recessive APC (-)/CAP. Furthermore, autosomal dominant APC (-)/CAP could occur as a result of DNA polymerase epsilon (POLE)/DNA polymerase delta 1 (POLD1), axis inhibition protein 2 (AXIN2), and dual oxidase 2 (DUOX2) mutations. The clinical phenotypes of these pathogenic mutations vary greatly depending on their genetic characteristics. Therefore, in this study, we present a comprehensive review of the association between autosomal recessive and dominant APC (-)/CAP genotypes and clinical phenotypes and conclude that APC (-)/CAP is a disease caused by multiple genes with different phenotypes and interaction exists in the pathogenic genes.
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Affiliation(s)
- Li-Hua Zhu
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, No. 295 Xichang Rd, Kunming, 650032, China
| | - Jian Dong
- Department of Internal Medicine-Oncology, Third Affiliated Hospital, Kunming Medical University, Kunming, 650118, China
| | - Wen-Liang Li
- Colorectal Cancer Clinical Research Center, Third Affiliated Hospital, Kunming Medical University, Kunming, 650118, China
| | - Zhi-Yong Kou
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, No. 295 Xichang Rd, Kunming, 650032, China
| | - Jun Yang
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, No. 295 Xichang Rd, Kunming, 650032, China.
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22
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Big Data in Gastroenterology Research. Int J Mol Sci 2023; 24:ijms24032458. [PMID: 36768780 PMCID: PMC9916510 DOI: 10.3390/ijms24032458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
Studying individual data types in isolation provides only limited and incomplete answers to complex biological questions and particularly falls short in revealing sufficient mechanistic and kinetic details. In contrast, multi-omics approaches to studying health and disease permit the generation and integration of multiple data types on a much larger scale, offering a comprehensive picture of biological and disease processes. Gastroenterology and hepatobiliary research are particularly well-suited to such analyses, given the unique position of the luminal gastrointestinal (GI) tract at the nexus between the gut (mucosa and luminal contents), brain, immune and endocrine systems, and GI microbiome. The generation of 'big data' from multi-omic, multi-site studies can enhance investigations into the connections between these organ systems and organisms and more broadly and accurately appraise the effects of dietary, pharmacological, and other therapeutic interventions. In this review, we describe a variety of useful omics approaches and how they can be integrated to provide a holistic depiction of the human and microbial genetic and proteomic changes underlying physiological and pathophysiological phenomena. We highlight the potential pitfalls and alternatives to help avoid the common errors in study design, execution, and analysis. We focus on the application, integration, and analysis of big data in gastroenterology and hepatobiliary research.
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23
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Windfelder AG, Müller FHH, Mc Larney B, Hentschel M, Böhringer AC, von Bredow CR, Leinberger FH, Kampschulte M, Maier L, von Bredow YM, Flocke V, Merzendorfer H, Krombach GA, Vilcinskas A, Grimm J, Trenczek TE, Flögel U. High-throughput screening of caterpillars as a platform to study host-microbe interactions and enteric immunity. Nat Commun 2022; 13:7216. [PMID: 36433960 PMCID: PMC9700799 DOI: 10.1038/s41467-022-34865-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022] Open
Abstract
Mammalian models of human disease are expensive and subject to ethical restrictions. Here, we present an independent platform for high-throughput screening, using larvae of the tobacco hornworm Manduca sexta, combining diagnostic imaging modalities for a comprehensive characterization of aberrant phenotypes. For validation, we use bacterial/chemical-induced gut inflammation to generate a colitis-like phenotype and identify significant alterations in morphology, tissue properties, and intermediary metabolism, which aggravate with disease progression and can be rescued by antimicrobial treatment. In independent experiments, activation of the highly conserved NADPH oxidase DUOX, a key mediator of gut inflammation, leads to similar, dose-dependent alterations, which can be attenuated by pharmacological interventions. Furthermore, the developed platform could differentiate pathogens from mutualistic gastrointestinal bacteria broadening the scope of applications also to microbiomics and host-pathogen interactions. Overall, larvae-based screening can complement mammals in preclinical studies to explore innate immunity and host-pathogen interactions, thus representing a substantial contribution to improve mammalian welfare.
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Affiliation(s)
- Anton G Windfelder
- Institute of Zoology and Developmental Biology; Cellular Recognition and Defense Processes, Justus Liebig University Giessen, Giessen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
- Laboratory of Experimental Radiology, Justus Liebig University Giessen, Giessen, Germany
| | - Frank H H Müller
- Radiology and Nuclear Medicine Ludwigshafen, Ludwigshafen, Germany
| | - Benedict Mc Larney
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Imaging and Therapy Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Anna Christina Böhringer
- Department of Chemistry and Biology, School of Science and Technology, University of Siegen, Siegen, Germany
| | | | - Florian H Leinberger
- Institute of Zoology and Developmental Biology; Cellular Recognition and Defense Processes, Justus Liebig University Giessen, Giessen, Germany
| | - Marian Kampschulte
- Laboratory of Experimental Radiology, Justus Liebig University Giessen, Giessen, Germany
| | - Lorenz Maier
- Department of Nuclear Medicine, Inselspital Bern, Bern, Switzerland
| | - Yvette M von Bredow
- Institute of Zoology and Developmental Biology; Cellular Recognition and Defense Processes, Justus Liebig University Giessen, Giessen, Germany
| | - Vera Flocke
- Experimental Cardiovascular Imaging, Molecular Cardiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Hans Merzendorfer
- Department of Chemistry and Biology, School of Science and Technology, University of Siegen, Siegen, Germany
| | - Gabriele A Krombach
- Department of Diagnostic and Interventional Radiology, University-Hospital Giessen, Giessen, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
- Institute for Insect Biotechnology, Department of Applied Entomology, Justus Liebig University Giessen, Giessen, Germany
| | - Jan Grimm
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Imaging and Therapy Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Department, Weill Cornell Medical College, New York, NY, USA
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiology, Weill Cornell Medical Center, New York, NY, USA
| | - Tina E Trenczek
- Institute of Zoology and Developmental Biology; Cellular Recognition and Defense Processes, Justus Liebig University Giessen, Giessen, Germany.
| | - Ulrich Flögel
- Experimental Cardiovascular Imaging, Molecular Cardiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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24
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Hsu AP, Korzeniowska A, Aguilar CC, Gu J, Karlins E, Oler AJ, Chen G, Reynoso GV, Davis J, Chaput A, Peng T, Sun L, Lack JB, Bays DJ, Stewart ER, Waldman SE, Powell DA, Donovan FM, Desai JV, Pouladi N, Long Priel DA, Yamanaka D, Rosenzweig SD, Niemela JE, Stoddard J, Freeman AF, Zerbe CS, Kuhns DB, Lussier YA, Olivier KN, Boucher RC, Hickman HD, Frelinger J, Fierer J, Shubitz LF, Leto TL, Thompson GR, Galgiani JN, Lionakis MS, Holland SM. Immunogenetics associated with severe coccidioidomycosis. JCI Insight 2022; 7:e159491. [PMID: 36166305 PMCID: PMC9746810 DOI: 10.1172/jci.insight.159491] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/21/2022] [Indexed: 12/15/2022] Open
Abstract
Disseminated coccidioidomycosis (DCM) is caused by Coccidioides, pathogenic fungi endemic to the southwestern United States and Mexico. Illness occurs in approximately 30% of those infected, less than 1% of whom develop disseminated disease. To address why some individuals allow dissemination, we enrolled patients with DCM and performed whole-exome sequencing. In an exploratory set of 67 patients with DCM, 2 had haploinsufficient STAT3 mutations, and defects in β-glucan sensing and response were seen in 34 of 67 cases. Damaging CLEC7A and PLCG2 variants were associated with impaired production of β-glucan-stimulated TNF-α from PBMCs compared with healthy controls. Using ancestry-matched controls, damaging CLEC7A and PLCG2 variants were overrepresented in DCM, including CLEC7A Y238* and PLCG2 R268W. A validation cohort of 111 patients with DCM confirmed the PLCG2 R268W, CLEC7A I223S, and CLEC7A Y238* variants. Stimulation with a DECTIN-1 agonist induced DUOX1/DUOXA1-derived hydrogen peroxide [H2O2] in transfected cells. Heterozygous DUOX1 or DUOXA1 variants that impaired H2O2 production were overrepresented in discovery and validation cohorts. Patients with DCM have impaired β-glucan sensing or response affecting TNF-α and H2O2 production. Impaired Coccidioides recognition and decreased cellular response are associated with disseminated coccidioidomycosis.
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Affiliation(s)
- Amy P. Hsu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Agnieszka Korzeniowska
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Cynthia C. Aguilar
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Jingwen Gu
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Eric Karlins
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Gang Chen
- Marsico Lung Institute and Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Glennys V. Reynoso
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Joie Davis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Alexandria Chaput
- Valley Fever Center for Excellence, University of Arizona College of Medicine–Tucson, Tucson, Arizona, USA
| | - Tao Peng
- Valley Fever Center for Excellence, University of Arizona College of Medicine–Tucson, Tucson, Arizona, USA
| | - Ling Sun
- Marsico Lung Institute and Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Respiratory and Critical Care Medicine, Laboratory of Pulmonary Immunology and Inflammation, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Justin B. Lack
- NIAID Collaborative Bioinformatics Resource, NIAID, NIH, Bethesda, Maryland, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Derek J. Bays
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Sacramento, California, USA
| | - Ethan R. Stewart
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Sacramento, California, USA
| | - Sarah E. Waldman
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Sacramento, California, USA
| | - Daniel A. Powell
- Valley Fever Center for Excellence, University of Arizona College of Medicine–Tucson, Tucson, Arizona, USA
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Fariba M. Donovan
- Valley Fever Center for Excellence, University of Arizona College of Medicine–Tucson, Tucson, Arizona, USA
- Department of Medicine, University of Arizona College of Medicine–Tucson, Tucson, Arizona, USA
| | - Jigar V. Desai
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Nima Pouladi
- Center for Biomedical Informatics and Biostatistics and
- The Center for Applied Genetics and Genomic Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Debra A. Long Priel
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Daisuke Yamanaka
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
- Laboratory for Immunopharmacology of Microbial Products, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | | | - Julie E. Niemela
- Immunology Service, Department of Laboratory Medicine, Clinical Center and
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, Clinical Center and
| | - Alexandra F. Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Christa S. Zerbe
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Douglas B. Kuhns
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Yves A. Lussier
- Center for Biomedical Informatics and Biostatistics and
- The Center for Applied Genetics and Genomic Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Kenneth N. Olivier
- Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Richard C. Boucher
- Marsico Lung Institute and Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Heather D. Hickman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Jeffrey Frelinger
- Valley Fever Center for Excellence, University of Arizona College of Medicine–Tucson, Tucson, Arizona, USA
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Joshua Fierer
- VA HealthCare San Diego, San Diego, California, USA
- Division of Infectious Diseases, Departments of Pathology and Medicine, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Lisa F. Shubitz
- Valley Fever Center for Excellence, University of Arizona College of Medicine–Tucson, Tucson, Arizona, USA
| | - Thomas L. Leto
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - George R. Thompson
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Sacramento, California, USA
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, USA
| | - John N. Galgiani
- Valley Fever Center for Excellence, University of Arizona College of Medicine–Tucson, Tucson, Arizona, USA
- Department of Medicine, University of Arizona College of Medicine–Tucson, Tucson, Arizona, USA
| | - Michail S. Lionakis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Steven M. Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
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25
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Jurickova I, Bonkowski E, Angerman E, Novak E, Huron A, Akers, G, Iwasawa K, Braun T, Hadar R, Hooker M, Han S, Cutler DJ, Okou DT, Kugathasan S, Jegga A, Wells J, Takebe T, Mollen KP, Haberman Y, Denson LA. Eicosatetraynoic Acid and Butyrate Regulate Human Intestinal Organoid Mitochondrial and Extracellular Matrix Pathways Implicated in Crohn's Disease Strictures. Inflamm Bowel Dis 2022; 28:988-1003. [PMID: 35259271 PMCID: PMC9247849 DOI: 10.1093/ibd/izac037] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Indexed: 12/19/2022]
Abstract
BACKGROUND Perturbagen analysis of Crohn's disease (CD) ileal gene expression data identified small molecules including eicosatetraynoic acid (ETYA), which may exert an antifibrotic effect. We developed a patient-specific human intestinal organoid (HIO) model system to test small molecule regulation of mitochondrial and wound-healing functions implicated in stricturing behavior. METHODS HIOs were made from CD induced pluripotent stem cells with and without a loss-of-function haplotype in the DUOX2 gene implicated in ileal homeostasis and characterized under basal conditions and following exposure to butyrate and ETYA using RNA sequencing, flow cytometry, and immunofluorescent and polarized light microscopy. Mitochondrial activity was measured using high-resolution respirometry and tissue stiffness using atomic force microscopy. RESULTS HIOs expressed core mitochondrial and extracellular matrix (ECM) genes and enriched biologic functions implicated in CD ileal strictures; ECM gene expression was suppressed by both butyrate and ETYA, with butyrate also suppressing genes regulating epithelial proliferation. Consistent with this, butyrate, but not ETYA, exerted a profound effect on HIO epithelial mitochondrial function, reactive oxygen species production, and cellular abundance. Butyrate and ETYA suppressed HIO expression of alpha smooth muscle actin expressed by myofibroblasts, type I collagen, and collagen protein abundance. HIOs exhibited tissue stiffness comparable to normal human ileum; this was reduced by chronic ETYA exposure in HIOs carrying the DUOX2 loss-of-function haplotype. CONCLUSIONS ETYA regulates ECM genes implicated in strictures and suppresses collagen content and tissue stiffness in an HIO model. HIOs provide a platform to test personalized therapeutics, including small molecules prioritized by perturbagen analysis.
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Affiliation(s)
- Ingrid Jurickova
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Erin Bonkowski
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Elizabeth Angerman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Elizabeth Novak
- Division of General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Alex Huron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Grayce Akers,
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kentaro Iwasawa
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Tzipi Braun
- Department of Pediatrics, Sheba Medical Center, Tel-Aviv University, Tel-HaShomer, Israel
| | - Rotem Hadar
- Department of Pediatrics, Sheba Medical Center, Tel-Aviv University, Tel-HaShomer, Israel
| | - Maria Hooker
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Sarah Han
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David T Okou
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Subra Kugathasan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Anil Jegga
- Division of Biomedical Informatics, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - James Wells
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Takanori Takebe
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Institute of Research, Tokyo Medical and Dental University, Japan
| | - Kevin P Mollen
- Division of General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yael Haberman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, Sheba Medical Center, Tel-Aviv University, Tel-HaShomer, Israel
| | - Lee A Denson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
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26
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Novel biallelic mutations in the DUOX2 gene underlying very early-onset inflammatory bowel disease: A case report. Clin Immunol 2022; 238:109015. [DOI: 10.1016/j.clim.2022.109015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/09/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022]
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27
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Derakhshani A, Javadrashid D, Hemmat N, Dufour A, Solimando AG, Abdoli Shadbad M, Duijf PHG, Brunetti O, Silvestris N, Baradaran B. Identification of Common and Distinct Pathways in Inflammatory Bowel Disease and Colorectal Cancer: A Hypothesis Based on Weighted Gene Co-Expression Network Analysis. Front Genet 2022; 13:848646. [PMID: 35432477 PMCID: PMC9008839 DOI: 10.3389/fgene.2022.848646] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/14/2022] [Indexed: 12/12/2022] Open
Abstract
Patients with inflammatory bowel disease (IBD), including ulcerative colitis and Crohn’s disease, are at higher risk to develop colorectal cancer (CRC). However, the underlying mechanisms of this predisposition remain elusive. We performed in-depth comparative computational analyses to gain new insights, including weighted gene co-expression network analysis (WGCNA) and gene ontology and pathway enrichment analyses, using gene expression datasets from IBD and CRC patients. When individually comparing IBD and CRC to normal control samples, we identified clusters of highly correlated genes, differentially expressed genes, and module-trait associations specific for each disease. When comparing IBD to CRC, we identified common hub genes and commonly enriched pathways. Most notably, IBD and CRC share significantly increased expression of five genes (MMP10, LCN2, REG1A, REG3A, and DUOX2), enriched inflammatory and neutrophil activation pathways and, most notably, highly significant enrichment of IL-4 and IL-13 signaling. Thus, our work expands our knowledge about the intricate relationship between IBD and CRC development and provides new rationales for developing novel therapeutic strategies.
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Affiliation(s)
- Afshin Derakhshani
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Darya Javadrashid
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nima Hemmat
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Antoine Dufour
- Departments of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- McCaig Insitute, Hotchkiss Brain Institute and Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Antonio Giovanni Solimando
- Department of Biomedical Sciences and Human Oncology, School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | | | - Pascal H. G. Duijf
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Data Science, Queensland University of Technology, Brisbane, QLD, Australia
- Translational Research Institute, University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Oronzo Brunetti
- Medical Oncology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Nicola Silvestris
- Medical Oncology Unit, Department of Human Pathology “G. Barresi” , University of Messina, Messina, Italy
- *Correspondence: Nicola Silvestris, ; Behzad Baradaran,
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- *Correspondence: Nicola Silvestris, ; Behzad Baradaran,
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28
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Wang B, Zeng H, Zuo X, Yang X, Wang X, He D, Yuan J. TLR4-Dependent DUOX2 Activation Triggered Oxidative Stress and Promoted HMGB1 Release in Dry Eye. Front Med (Lausanne) 2022; 8:781616. [PMID: 35096875 PMCID: PMC8793023 DOI: 10.3389/fmed.2021.781616] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/09/2021] [Indexed: 12/30/2022] Open
Abstract
Dry eye disease (DED) is one of the most common ocular surface diseases worldwide. DED has been characterized by excessive accumulation of reactive oxygen species (ROS), following significant corneal epithelial cell death and ocular surface inflammation. However, the key regulatory factor remains unclear. In this study, we tended to explore whether DUOX2 contributed to DED development and the underlying mechanism. Human corneal epithelial (HCE) cells were treated with hyperosmolarity, C57BL/6 mice were injected of subcutaneous scopolamine to imitate DED. Expression of mRNA was investigated by RNA sequencing (RNA-seq) and quantitative real-time PCR (qPCR). Protein changes and distribution of DUOX2, high mobility group box 1 (HMGB1), Toll-like receptor 4 (TLR4), and 4-hydroxynonenal (4-HNE) were evaluated by western blot assays and immunofluorescence. Cell death was assessed by Cell Counting Kit-8 (CCK8), lactate dehydrogenase (LDH) release, and propidium iodide (PI) staining. Cellular ROS levels and mitochondrial membrane potential (MMP) were analyzed by flow cytometry. RNA-seq and western blot assay indicated a significant increase of DUOX2 dependent of TLR4 activation in DED both in vitro and in vivo. Immunofluorescence revealed significant translocation of HMGB1 within corneal epithelial cells under hyperosmolar stress. Interestingly, after ablated DUOX2 expression by siRNA, we found a remarkable decrease of ROS level and recovered MMP in HCE cells. Moreover, knockdown of DUOX2 greatly inhibited HMGB1 release, protected cell viability and abolished inflammatory activation. Taken together, our data here suggest that upregulation of DUOX2 plays a crucial role in ROS production, thereafter, induce HMGB1 release and cell death, which triggers ocular surface inflammation in DED.
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Affiliation(s)
- Bowen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China
| | - Hao Zeng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China
| | - Xin Zuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China
| | - Xue Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China
| | - Xiaoran Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China
| | - Dalian He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China
| | - Jin Yuan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China
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29
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Implication of Intestinal Barrier Dysfunction in Gut Dysbiosis and Diseases. Biomedicines 2022; 10:biomedicines10020289. [PMID: 35203499 PMCID: PMC8869546 DOI: 10.3390/biomedicines10020289] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
The intestinal mucosal barrier, also referred to as intestinal barrier, is widely recognized as a critical player in gut homeostasis maintenance as it ensures the complex crosstalk between gut microbes (both commensals and pathogens) and the host immune system. Highly specialized epithelial cells constantly cope with several protective and harmful agents to maintain the multiple physiological functions of the barrier as well as its integrity. However, both genetic defects and environmental factors can break such equilibrium, thus promoting gut dysbiosis, dysregulated immune-inflammatory responses, and even the development of chronic pathological conditions. Here, we review and discuss the molecular and cellular pathways underlying intestinal barrier structural and functional homeostasis, focusing on potential alterations that may undermine this fine balance.
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30
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Rees WD, Telkar N, Lin DTS, Wong MQ, Poloni C, Fathi A, Kobor M, Zachos NC, Steiner TS. An in vitro chronic damage model impairs inflammatory and regenerative responses in human colonoid monolayers. Cell Rep 2022; 38:110283. [PMID: 35045294 DOI: 10.1016/j.celrep.2021.110283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/20/2021] [Accepted: 12/28/2021] [Indexed: 12/18/2022] Open
Abstract
Acute damage to the intestinal epithelium can be repaired via de-differentiation of mature intestinal epithelial cells (IECs) to a stem-like state, but there is a lack of knowledge on how intestinal stem cells function after chronic injury, such as in inflammatory bowel disease (IBD). We developed a chronic-injury model in human colonoid monolayers by repeated rounds of air-liquid interface and submerged culture. We use this model to understand how chronic intestinal damage affects the ability of IECs to (1) respond to microbial stimulation, using the Toll-like receptor 5 (TLR5) agonist FliC and (2) regenerate and protect the epithelium from further damage. Repeated rounds of damage impair the ability of IECs to regrow and respond to TLR stimulation. We also identify mRNA expression and DNA methylation changes in genes associated with IBD and colon cancer. This methodology results in a human model of recurrent IEC injury like that which occurs in IBD.
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Affiliation(s)
- William D Rees
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada; Division of Hematology, Department of Medicine, Stanford University, Palo Alto, CA, USA
| | - Nikita Telkar
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada; BC Cancer Agency, University of British Columbia, Vancouver, BC, Canada
| | - David T S Lin
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - May Q Wong
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - Chad Poloni
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - Ayda Fathi
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - Michael Kobor
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - Nicholas C Zachos
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Theodore S Steiner
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada.
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Viladomiu M, Longman RS. Decoding the matrix: multiomics reveals host-microbe biomarker for inflammatory bowel disease. J Clin Invest 2021; 131:148902. [PMID: 33938448 DOI: 10.1172/jci148902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the intestine associated with genetic susceptibility and alterations in the intestinal microbiome. Multiomics data developed and analyzed over the last several decades have yielded an unprecedented amount of genetic and microbial data. But how do we pinpoint mechanistic insight into the host-microbe relationship that will ultimately enable better care for patients with IBD? In this issue of the JCI, Grasberger et al. undertook a major decoding effort to decipher this multiomic data matrix. The authors analyzed anonymized data from more than 2800 individuals to discover a link between heterozygous carriers of deleterious DUOX2 variants and high levels of plasma IL-17C. These findings provide an example of how harnessing big data can drive mechanistic discovery to define disease biomarkers that have the potential to improve clinical care in IBD.
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