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Uehara E, Abe K, Tanase-Nakao K, Muroya K, Hattori A, Matsubara K, Fukami M, Narumi S. Molecular and Clinical Features of Congenital Hypothyroidism due to Multiple DUOX2 Variants. Thyroid 2024. [PMID: 38757580 DOI: 10.1089/thy.2024.0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Background: DUOX2 is one of the major causative genes of congenital hypothyroidism (CH). Still, the mutation spectrum and clinical outcomes of biallelic DUOX2 variants are not fully understood. This study aimed to elucidate the molecular features and long-term clinical manifestations of CH caused by multiple pathogenic DUOX2 variants. Methods: A total of 255 patients with CH were screened for rare variants of 11 known causative genes. DUOX2 variants were classified according to their protein structure and residual activity. In vitro assays were performed for several variants of unknown function. Clinical analyses were conducted for patients with multiple pathogenic variants of DUOX2 but not of other genes. Results: We identified 24 pathogenic variants of DUOX2, together with two benign variants and seven variants of uncertain significance, in 63 patients. The pathogenic variants included three missense substitutions and one frameshift variant that have not been linked to CH. Twenty-one patients carried multiple pathogenic DUOX2 variants without any other pathogenic gene variants. Three of the 21 patients harbored homozygous variants. Family analysis, long-read amplicon sequencing, and haplotype phasing confirmed compound heterozygosity of the DUOX2 variants in 14 patients, whereas the allelic positions of the variants in the remaining four patients could not be determined. Of the 21 patients, 19 were treated with levothyroxine; their ages at drug withdrawal ranged from 9 months to 21.4 years. Three patients required retreatment after drug-free intervals of 6 months, 8 months, and 10 years. There were no differences in the clinical severity among patients with DUOX2 amorphic/amorphic, amorphic/hypomorphic, and hypomorphic/hypomorphic variants. Conclusions: These results broaden the mutation spectrum of DUOX2. Furthermore, our data imply that patients with multiple pathogenic DUOX2 variants typically exhibit transient CH without significant genotype-phenotype correlations. Most importantly, this study demonstrated for the first time that these patients are at risk of developing recurrent hypothyroidism after a long drug-free interval.
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Affiliation(s)
- Erika Uehara
- National Research Institute for Child Health and Development, Molecular Endocrinology, Tokyo, Tokyo, Japan
- Tohoku University School of Medicine, Advanced Pediatric Medicine, Sendai, Miyagi, Japan;
| | - Kiyomi Abe
- Keio University School of Medicine, Pediatrics, Tokyo, Japan
- Tokyo Saiseikai Central Hospital, Pediatrics, Tokyo, Japan;
| | - Kanako Tanase-Nakao
- National Research Institute for Child Health and Development, Molecular Endocrinology, Tokyo, Japan;
| | - Koji Muroya
- Kanagawa Children's Medical Center, Endocrinology and Metabolism, Yokohama, Kanagawa, Japan;
| | - Atsushi Hattori
- National Research Institute for Child Health and Development, Molecular Endocrinology, Tokyo, Tokyo, Japan
- National Research Institute for Child Health and Development, Division of Diversity Research, Tokyo, Japan;
| | - Keiko Matsubara
- National Research Institute for Child Health and Development, Molecular Endocrinology, Tokyo, Tokyo, Japan
- National Research Institute for Child Health and Development, Division of Diversity Research, Tokyo, Tokyo, Japan;
| | - Maki Fukami
- National Research Institute for Child Health and Development, Molecular Endocrinology, Tokyo, Tokyo, Japan
- National Research Institute for Child Health and Development, Division of Diversity Research, Tokyo, Tokyo, Japan;
| | - Satoshi Narumi
- Keio University School of Medicine, Pediatrics, Tokyo, Japan
- National Research Institute for Child Health and Development, Molecular Endocrinology, Tokyo, Tokyo, Japan;
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2
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Li P, Wang L, Tang Z, Wang Y, Liu Z, Ge W, Huang Y. Ustekinumab in pediatric patients with Crohn's disease: safety, and efficacy results from a multicenter retrospective study in China. Front Pediatr 2024; 12:1371322. [PMID: 38665375 PMCID: PMC11043477 DOI: 10.3389/fped.2024.1371322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Background Ustekinumab (UST) is approved as an effective therapy for Crohn's disease (CD) in adults. Off-label use is increasing in the pediatric population, more data on safety and efficacy in pediatric patients with CD is urgently needed. Aims This study aimed to evaluate the clinical efficacy and safety of UST in children and adolescents with Crohn's disease. Methods This multicenter retrospective study carried out at three tertiary care centers, and identified children who received their first dose of UST at 18 years old or younger and followed up for a minimum of 24 weeks. Data on demographics, disease behavior, location and activity, treatment history were collected. The primary outcomes were clinical remission at weeks 24-32 and weeks 48-56 of UST therapy. Secondary outcomes were clinical response at the same time points, endoscopic remission, changes in C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), albumin and fecal calprotectin, improvement in growth parameters, and rate of adverse events. Results Sixteen patients were included, and 11/13 (84.6%) continued to receive UST after 1 year. Our data demonstrate that the clinical remission rates were 41.7% at weeks 24∼32 with the Weighted pediatric CD activity index (wPCDAI) was lower than baseline (43.8, IQR: 31.3-51.9 vs.15, IQR: 5.6-25, p < 0.001) and 75% at weeks 48-56 with wPCDAI was lower than baseline (42.5, IQR: 23.8-50 vs. 7.5, IQR: 0-13.8, p = 0.004). Five of eleven children achieved endoscopic remission. No serious adverse events were recorded during the study period. Conclusions UST is efficacious and safe in pediatric patients with CD. Pediatric patients could benefit from UST as either a primary or secondary biologic therapy for the induction, or maintenance of remission of CD.
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Affiliation(s)
- Ping Li
- Department of Gastroenterology, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Lin Wang
- Department of Gastroenterology, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Zifei Tang
- Department of Gastroenterology, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Yuhuan Wang
- Department of Gastroenterology, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Zhanju Liu
- Department of Gastroenterology, The Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
| | - Wensong Ge
- Department of Gastroenterology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Huang
- Department of Gastroenterology, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
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3
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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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4
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Stemmer E, Zahavi T, Kellerman M, Sinberger LA, Shrem G, Salmon‐Divon M. Exploring potential biomarkers and therapeutic targets in inflammatory bowel disease: insights from a mega-analysis approach. Front Immunol 2024; 15:1353402. [PMID: 38510241 PMCID: PMC10951083 DOI: 10.3389/fimmu.2024.1353402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Background Understanding the molecular pathogenesis of inflammatory bowel disease (IBD) has led to the discovery of new therapeutic targets that are more specific and effective. Our aim was to explore the molecular pathways and genes involved in IBD pathogenesis and to identify new therapeutic targets and novel biomarkers that can aid in the diagnosis of the disease. Methods To obtain the largest possible number of samples and analyze them comprehensively, we used a mega-analysis approach. This involved reprocessing raw data from multiple studies and analyzing them using bioinformatic and machine learning techniques. Results We analyzed a total of 697 intestinal biopsies of Ulcerative Colitis (n = 386), Crohn's disease (n = 183) and non-IBD controls (n = 128). A machine learning analysis detected 34 genes whose collective expression effectively distinguishes inflamed biopsies of IBD patients from non-IBD control samples. Most of these genes were upregulated in IBD. Notably, among these genes, three novel lncRNAs have emerged as potential contributors to IBD development: ENSG00000285744, ENSG00000287626, and MIR4435-2HG. Furthermore, by examining the expression of 29 genes, among the 34, in blood samples from IBD patients, we detected a significant upregulation of 12 genes (p-value < 0.01), underscoring their potential utility as non-invasive diagnostic biomarkers. Finally, by utilizing the CMap library, we discovered potential compounds that should be explored in future studies for their therapeutic efficacy in IBD treatment. Conclusion Our findings contribute to the understanding of IBD pathogenesis, suggest novel biomarkers for IBD diagnosis and offer new prospects for therapeutic intervention.
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Affiliation(s)
- Edia Stemmer
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Tamar Zahavi
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Maoz Kellerman
- Department of Molecular Biology, Ariel University, Ariel, Israel
- Kaleidoo, Bar Lev High Tech Park, Misgav, Israel
| | | | - Guy Shrem
- Obstetrics, Gynecology and Infertility (OB&GYN) Department Maccabi Healthcare Services, Tel Aviv, Israel
| | - Mali Salmon‐Divon
- Department of Molecular Biology, Ariel University, Ariel, Israel
- Adelson School of Medicine, Ariel University, Ariel, Israel
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5
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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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6
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Ward J, Zhang S, Sikora A, Michalski R, Yin Y, D'Alessio A, McLoughlin RM, Jaquet V, Fieschi F, Knaus UG. VEO-IBD NOX1 variant highlights a structural region essential for NOX/DUOX catalytic activity. Redox Biol 2023; 67:102905. [PMID: 37820403 PMCID: PMC10571032 DOI: 10.1016/j.redox.2023.102905] [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: 07/11/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic intestinal disorders that result from an inappropriate inflammatory response to the microbiota in genetically susceptible individuals, often triggered by environmental stressors. Part of this response is the persistent inflammation and tissue injury associated with deficiency or excess of reactive oxygen species (ROS). The NADPH oxidase NOX1 is highly expressed in the intestinal epithelium, and inactivating NOX1 missense mutations are considered a risk factor for developing very early onset IBD. Albeit NOX1 has been linked to wound healing and host defence, many questions remain about its role in intestinal homeostasis and acute inflammatory conditions. Here, we used in vivo imaging in combination with inhibitor studies and germ-free conditions to conclusively identify NOX1 as essential superoxide generator for microbiota-dependent peroxynitrite production in homeostasis and during early endotoxemia. NOX1 loss-of-function variants cannot support peroxynitrite production, suggesting that the gut barrier is persistently weakened in these patients. One of the loss-of-function NOX1 variants, NOX1 p. Asn122His, features replacement of an asparagine residue located in a highly conserved HxxxHxxN motif. Modelling the NOX1-p22phox complex revealed near the distal heme an internal pocket restricted by His119 and Asn122 that is part of the oxygen reduction site. Functional studies in several human NADPH oxidases show that substitution of asparagine with amino acids with larger side chains is not tolerated, while smaller side chains can support catalytic activity. Thus, we identified a previously unrecognized structural feature required for the electron transfer mechanism in human NADPH oxidases.
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Affiliation(s)
- Josie Ward
- School of Medicine, Conway Institute, University College Dublin, Dublin, Ireland
| | - Suisheng Zhang
- School of Medicine, Conway Institute, University College Dublin, Dublin, Ireland
| | - Adam Sikora
- Faculty of Chemistry, Institute of Applied Radiation Chemistry, Lodz University of Technology, Lodz, Poland
| | - Radoslaw Michalski
- Faculty of Chemistry, Institute of Applied Radiation Chemistry, Lodz University of Technology, Lodz, Poland
| | - Yuting Yin
- School of Medicine, Conway Institute, University College Dublin, Dublin, Ireland
| | - Aurora D'Alessio
- School of Medicine, Conway Institute, University College Dublin, Dublin, Ireland
| | - Rachel M McLoughlin
- Host-Pathogen Interactions Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Vincent Jaquet
- Department of Pathology and Immunology and READS Unit, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, UMR5075, Institut de Biologie Structurale, Grenoble, France; Institut Universitaire de France (IUF), Paris, France.
| | - Ulla G Knaus
- School of Medicine, Conway Institute, University College Dublin, Dublin, Ireland.
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7
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Abstract
Inflammatory bowel disease (IBD) represents a spectrum of disease, which is characterized by chronic gastrointestinal inflammation. Monogenic mutations driving IBD pathogenesis are more highly represented in early-onset compared to adult-onset disease. The pathogenic genes which dysregulate host immune responses in monogenic IBD affect both the innate (ie, intestinal barrier, phagocytes) and adaptive immune systems (ie, T cells, B cells). Advanced genomic and targeted functional testing can improve clinical decision making and present increased opportunities for precision medicine approaches in this important patient population.
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Affiliation(s)
- Atiye Olcay Bilgic Dagci
- Division of Pediatric Rheumatology, University of Michigan, C.S Mott Children's Hospital, 1500 East Medical Center Drive Medical Professional Building Floor 2, Ann Arbor, MI 48109-5718, USA.
| | - Kelly Colleen Cushing
- Division of Gastroenterology, U-M Inflammatory Bowel Disease Program, University of Michigan, 3912 Taubman Center, 1500 East Medical Center Drive, SPC 5362, Ann Arbor, MI 48109-5362, USA
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8
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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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9
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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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