1
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Yu S, Meng G, Tang W, Ma W, Wang R, Zhu X, Sun X, Feng H. cypress: an R/Bioconductor package for cell-type-specific differential expression analysis power assessment. Bioinformatics 2024; 40:btae511. [PMID: 39153205 PMCID: PMC11357793 DOI: 10.1093/bioinformatics/btae511] [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: 02/26/2024] [Revised: 07/24/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024] Open
Abstract
SUMMARY Recent methodology advances in computational signal deconvolution have enabled bulk transcriptome data analysis at a finer cell-type level. Through deconvolution, identifying cell-type-specific differentially expressed (csDE) genes is drawing increasing attention in clinical applications. However, researchers still face a number of difficulties in adopting csDE genes detection methods in practice, especially in their experimental design. Here we present cypress, the first experimental design and statistical power analysis tool in csDE genes identification. This tool can reliably model purified cell-type-specific (CTS) profiles, cell-type compositions, biological and technical variations, offering a high-fidelity simulator for bulk RNA-seq convolution and deconvolution. cypress conducts simulation and evaluates the impact of multiple influencing factors, by various statistical metrics, to help researchers optimize experimental design and conduct power analysis. AVAILABILITY AND IMPLEMENTATION cypress is an open-source R/Bioconductor package at https://bioconductor.org/packages/cypress/.
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Affiliation(s)
- Shilin Yu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, United States
| | - Guanqun Meng
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Wen Tang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Wenjing Ma
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Rui Wang
- Department of Surgery, Case Western Reserve University, Cleveland, OH 44106, United States
- Division of Surgical Oncology, Department of Surgery, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, United States
| | - Xiongwei Zhu
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Xiaobo Sun
- School of Statistics and Mathematics, Zhongnan University of Economics and Law, Wuhan, Hubei 430073, China
| | - Hao Feng
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, United States
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2
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Fadaie M, Khalafiyan A, Ghafouri E, Ranjbarnejad T, Moein S. A Systems Biology Approach to the Pathogenesis of Celiac Disease: Identification of Potential Protective and Promoting Mechanisms. Adv Biomed Res 2024; 13:42. [PMID: 39224401 PMCID: PMC11368239 DOI: 10.4103/abr.abr_229_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 01/01/2024] [Accepted: 01/20/2024] [Indexed: 09/04/2024] Open
Abstract
Background Celiac disease (CeD) is an autoimmune enteropathy triggered by dietary gluten. Almost 90% of CeD patients have HLA-DQ2 or -DQ8 haplotypes. As a high proportion of first-degree relatives (FDRs) of CeD patients have the same haplotype, it is assumed that they are at a higher risk of disease development than the general population. Nevertheless, the prevalence of CeD among FDRs is considerably low (7.5%). Materials and Methods In order to figure out this discrepancy, a microarray dataset of intestinal mucosal biopsies of CeD patients, FDRs, and control groups was reanalyzed, and a protein-protein interaction network was constructed. Results Principal component analysis showed that CeD and FDR groups are far away in terms of gene expression. Comparing differentially expressed genes of both networks demonstrated inverse expression of some genes mainly related to cell cycle mechanisms. Moreover, analysis of the modular structures of up- and downregulated gene networks determined activation of protein degradation mechanisms and inhibition of ribosome-related protein synthesis in celiac patients with an upside-down pattern in FDRs. Conclusions The top-down systems biology approach determined some regulatory pathways with inverse function in CeD and FDR groups. These genes and molecular mechanisms could be a matter of investigation as potential druggable targets or prognostic markers in CeD.
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Affiliation(s)
- Mahmood Fadaie
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Anis Khalafiyan
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Ghafouri
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Tayebeh Ranjbarnejad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shiva Moein
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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3
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Moerkens R, Mooiweer J, Ramírez-Sánchez AD, Oelen R, Franke L, Wijmenga C, Barrett RJ, Jonkers IH, Withoff S. An iPSC-derived small intestine-on-chip with self-organizing epithelial, mesenchymal, and neural cells. Cell Rep 2024; 43:114247. [PMID: 38907996 DOI: 10.1016/j.celrep.2024.114247] [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: 02/23/2024] [Revised: 04/10/2024] [Accepted: 05/02/2024] [Indexed: 06/24/2024] Open
Abstract
Human induced pluripotent stem cell (hiPSC)-derived intestinal organoids are valuable tools for researching developmental biology and personalized therapies, but their closed topology and relative immature state limit applications. Here, we use organ-on-chip technology to develop a hiPSC-derived intestinal barrier with apical and basolateral access in a more physiological in vitro microenvironment. To replicate growth factor gradients along the crypt-villus axis, we locally expose the cells to expansion and differentiation media. In these conditions, intestinal epithelial cells self-organize into villus-like folds with physiological barrier integrity, and myofibroblasts and neurons emerge and form a subepithelial tissue in the bottom channel. The growth factor gradients efficiently balance dividing and mature cell types and induce an intestinal epithelial composition, including absorptive and secretory lineages, resembling the composition of the human small intestine. This well-characterized hiPSC-derived intestine-on-chip system can facilitate personalized studies on physiological processes and therapy development in the human small intestine.
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Affiliation(s)
- Renée Moerkens
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Joram Mooiweer
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Aarón D Ramírez-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Roy Oelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Robert J Barrett
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; F. Widjaja Foundation Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Iris H Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands.
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4
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Robert ME, Ciacci C, Lebwohl B. Opportunities for Improving Biopsy and Non-Biopsy-Based Diagnosis of Celiac Disease. Gastroenterology 2024; 167:79-89. [PMID: 38302007 DOI: 10.1053/j.gastro.2024.01.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/03/2024]
Abstract
The accumulating data regarding a non-biopsy diagnosis of celiac disease has led to its adoption in certain scenarios, although debate on whether and when to use non-biopsy criteria in clinical practice is ongoing. Despite the growing popularity and evidence basis for a biopsy-free approach to diagnosis in the context of highly elevated serologies, there will continue to be a role for a biopsy in some groups. This review summarizes the current evidence supporting a non-biopsy approach and arguments supporting continued reliance on biopsy, and focuses on opportunities to improve both approaches.
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Affiliation(s)
- Marie E Robert
- Department of Pathology, Medicine (Digestive Diseases) and Human and Translational Immunology, Yale University School of Medicine, New Haven, Connecticut
| | - Carolina Ciacci
- Department of Medicine, Surgery, Dentistry, Scuola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy.
| | - Benjamin Lebwohl
- Department of Medicine, Columbia University Irving Medical Center, New York, New York; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
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5
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Ruiz-Arenas C, Marín-Goñi I, Wang L, Ochoa I, Pérez-Jurado L, Hernaez M. NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders. Nucleic Acids Res 2024; 52:e44. [PMID: 38597610 PMCID: PMC11109970 DOI: 10.1093/nar/gkae197] [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: 09/20/2023] [Revised: 01/23/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024] Open
Abstract
Grouping gene expression into gene set activity scores (GSAS) provides better biological insights than studying individual genes. However, existing gene set projection methods cannot return representative, robust, and interpretable GSAS. We developed NetActivity, a machine learning framework that generates GSAS based on a sparsely-connected autoencoder, where each neuron in the inner layer represents a gene set. We proposed a three-tier training that yielded representative, robust, and interpretable GSAS. NetActivity model was trained with 1518 GO biological processes terms and KEGG pathways and all GTEx samples. NetActivity generates GSAS robust to the initialization parameters and representative of the original transcriptome, and assigned higher importance to more biologically relevant genes. Moreover, NetActivity returns GSAS with a more consistent definition and higher interpretability than GSVA and hipathia, state-of-the-art gene set projection methods. Finally, NetActivity enables combining bulk RNA-seq and microarray datasets in a meta-analysis of prostate cancer progression, highlighting gene sets related to cell division, key for disease progression. When applied to metastatic prostate cancer, gene sets associated with cancer progression were also altered due to drug resistance, while a classical enrichment analysis identified gene sets irrelevant to the phenotype. NetActivity is publicly available in Bioconductor and GitHub.
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Affiliation(s)
- Carlos Ruiz-Arenas
- Computational Biology Program, CIMA University of Navarra, idiSNA, Pamplona 31008, Spain
- Department MELIS, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Irene Marín-Goñi
- Computational Biology Program, CIMA University of Navarra, idiSNA, Pamplona 31008, Spain
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Idoia Ochoa
- Department of Electrical and Electronics Engineering, Tecnun, University of Navarra, Donostia, Spain
- Institute for Data Science and Artificial Inteligence (DATAI), University of Navarra, Pamplona 31008, Spain
| | - Luis A Pérez-Jurado
- Department MELIS, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- Genetics Service, Hospital del Mar & Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Mikel Hernaez
- Computational Biology Program, CIMA University of Navarra, idiSNA, Pamplona 31008, Spain
- Institute for Data Science and Artificial Inteligence (DATAI), University of Navarra, Pamplona 31008, Spain
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Oftedal BE, Sjøgren T, Wolff ASB. Interferon autoantibodies as signals of a sick thymus. Front Immunol 2024; 15:1327784. [PMID: 38455040 PMCID: PMC10917889 DOI: 10.3389/fimmu.2024.1327784] [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: 10/25/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024] Open
Abstract
Type I interferons (IFN-I) are key immune messenger molecules that play an important role in viral defense. They act as a bridge between microbe sensing, immune function magnitude, and adaptive immunity to fight infections, and they must therefore be tightly regulated. It has become increasingly evident that thymic irregularities and mutations in immune genes affecting thymic tolerance can lead to the production of IFN-I autoantibodies (autoAbs). Whether these biomarkers affect the immune system or tissue integrity of the host is still controversial, but new data show that IFN-I autoAbs may increase susceptibility to severe disease caused by certain viruses, including SARS-CoV-2, herpes zoster, and varicella pneumonia. In this article, we will elaborate on disorders that have been identified with IFN-I autoAbs, discuss models of how tolerance to IFN-Is is lost, and explain the consequences for the host.
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Affiliation(s)
- Bergithe E. Oftedal
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Thea Sjøgren
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Anette S. B. Wolff
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
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Banerjee P, Sood A, Midha V, Narang V, Grover J, Senapati S. A duodenal mucosa transcriptome study identified reduced expression of a novel gene CDH18 in celiac disease. Dig Liver Dis 2024; 56:258-264. [PMID: 37813809 DOI: 10.1016/j.dld.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND Celiac disease (CD) a complex immune disease that affects duodenal mucosa. Identification of tissue specific biomarkers is expected to improve the existing biopsy based CD diagnosis. AIMS To investigate the differentially expressed genes (DEGs) in duodenal mucosa tissue to identify clinically relevant gene expression pattern in CD. METHODS Whole RNA extracted from the duodenal biopsies of three CD patients and four non-CD controls were sequenced. Significant DEGs were identified. Prioritized DEGs were validated using qRT-PCR in an independent group (CD=23; Control=26). Enriched pathways were analyzed, protein-protein interaction networks were evaluated. RESULTS 923 DEGs comprising of 135 up-regulated, and 788 down-regulated genes, with p-value≤0.05; log2FC>2 or <-2 were identified. A novel down-regulated gene CDH18 (p = 0.03; log2FC=-0.74) was identified. Previously known CXCL9 was replicated. CDH18, a trans-membrane protein was found to interact with other CDH proteins, α/β catenins, and other membrane transporters such as SLC and ABCB. Pathways and protein networks contributing in channel activity (p = 2.15E-12), membrane transporters (p = 2.15E-12), and cellular adhesion (p = 8.05E-6) were identified. CONCLUSIONS CDH18, a novel DEG identified in the present study is a pivotal gene involved in maintaining epithelial membrane organization and integrity. The functional significance of lower expression of CDH18 in pathogenesis of CD warranted to be investigated. CDH18 expression could be tested for its effectiveness in diagnostic, prognostic and therapeutic purposes.
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Affiliation(s)
- Pratibha Banerjee
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151401, Punjab, India
| | - Ajit Sood
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, 141001, Punjab, India
| | - Vandana Midha
- Department of Medicine, Dayanand Medical College and Hospital, Ludhiana, 141001, Punjab, India
| | - Vikram Narang
- Department of Pathology, Dayanand Medical College and Hospital, Ludhiana, 141001, Punjab, India
| | - Jasmine Grover
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, 141001, Punjab, India
| | - Sabyasachi Senapati
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151401, Punjab, India.
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8
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Chen S, Liu X, Wang Z, Zheng D, Wang Y, Yan Y, Peng X, Ye Q, Chen Y. Transcriptome profile and immune infiltrated landscape revealed a novel role of γδT cells in mediating pyroptosis in celiac disease. J Transl Med 2023; 21:497. [PMID: 37488584 PMCID: PMC10364383 DOI: 10.1186/s12967-023-04359-1] [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: 10/12/2022] [Accepted: 07/16/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Celiac disease (CeD) is a primary malabsorption syndrome with no specific therapy, which greatly affects the quality of life. Since the pathogenesis of CeD remains riddled, based on multiple transcriptome profiles, this study aimed to establish an immune interaction network and elucidated new mechanisms involved in the pathogenesis of CeD, providing potentially new evidence for the diagnosis and treatment of CeD. METHODS Three microarray and three RNA sequencing datasets of human duodenal tissue with or without CeD were included in Gene Expression Omnibus and respectively merged into derivation and validation cohorts. Differential expression gene and functional enrichment analysis were developed, then pyroptosis enrichment score (PES) model was established to quantify pyroptosis levels. Immune infiltration and co-expression network were constructed based on Xcell database. Protein-protein interaction and weighted gene co-expression network analysis were determined to identify pyroptosis relative hub genes, whose predictive efficiency were tested using a least absolute shrinkage and selection operator (LASSO) regression model. CeD animal and in vitro cell line models were established to verify the occurrence of pyroptosis and molecules expression employing immunofluorescence, western blotting, cell counting kit-8 assay and enzyme-linked immunosorbent assay. Analysis of single-cell RNAseq (scRNAseq) was performed using "Seurat" R package. RESULTS Differentially expressed genes (DEGs) (137) were identified in derivation cohort whose function was mainly enriched in interferon response and suppression of metabolism. Since an enrichment of pyroptosis pathway in CeD was unexpectedly discovered, a PES model with high efficiency was constructed and verified with two external databases, which confirmed that pyroptosis was significantly upregulated in CeD epithelia. γδT cells exhibited high expression of IFN-γ were the most relevant cells associated with pyroptosis and occupied a greater weight in the LASSO predictive model of CeD. An accumulation of GSDMD expressed in epithelia was identified using scRNAseq, while animal model and in vitro experiments confirmed that epithelium cells were induced to become "pre-pyroptotic" status via IFN-γ/IRF1/GSDMD axis. Furthermore, gluten intake triggered pyroptosis via caspase-1/GSDMD/IL-1β pathway. CONCLUSION Our study demonstrated that pyroptosis was involved in the pathogenesis of CeD, and elucidated the novel role of γδT cells in mediating epithelial cell pyroptosis.
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Affiliation(s)
- Shuze Chen
- Department of Gastroenterology, Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xiuying Liu
- Department of Gastroenterology, Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zhi Wang
- Integrative Clinical Microecology Center, Shenzhen Key Laboratory of Gastrointestinal Microbiota and Disease, Shenzhen Clinical Research Center for Digestive Disease, Shenzhen Technology Research Center of Gut Microbiota Transplantation, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Dekai Zheng
- Department of Gastroenterology, Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Ying Wang
- Integrative Clinical Microecology Center, Shenzhen Key Laboratory of Gastrointestinal Microbiota and Disease, Shenzhen Clinical Research Center for Digestive Disease, Shenzhen Technology Research Center of Gut Microbiota Transplantation, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Yiling Yan
- Department of Gastroenterology, Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xiaojie Peng
- Integrative Clinical Microecology Center, Shenzhen Key Laboratory of Gastrointestinal Microbiota and Disease, Shenzhen Clinical Research Center for Digestive Disease, Shenzhen Technology Research Center of Gut Microbiota Transplantation, Shenzhen Hospital, Southern Medical University, Shenzhen, China
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qiujuan Ye
- Department of Gastroenterology, Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Ye Chen
- Department of Gastroenterology, Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- Integrative Clinical Microecology Center, Shenzhen Key Laboratory of Gastrointestinal Microbiota and Disease, Shenzhen Clinical Research Center for Digestive Disease, Shenzhen Technology Research Center of Gut Microbiota Transplantation, Shenzhen Hospital, Southern Medical University, Shenzhen, China.
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9
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Braun T, Sosnovski KE, Amir A, BenShoshan M, VanDussen KL, Karns R, Levhar N, Abbas-Egbariya H, Hadar R, Efroni G, Castel D, Avivi C, Rosen MJ, Grifiths AM, Walters TD, Mack DR, Boyle BM, Ali SA, Moore SR, Schirmer M, Xavier RJ, Kugathasan S, Jegga AG, Weiss B, Mayer C, Barshack I, Ben-Horin S, Ulitsky I, Beucher A, Ferrer J, Hyams JS, Denson LA, Haberman Y. Mucosal transcriptomics highlight lncRNAs implicated in ulcerative colitis, Crohn's disease, and celiac disease. JCI Insight 2023; 8:e170181. [PMID: 37261910 PMCID: PMC10443795 DOI: 10.1172/jci.insight.170181] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/31/2023] [Indexed: 06/03/2023] Open
Abstract
Ulcerative colitis (UC), Crohn's disease (CD), and celiac disease are prevalent intestinal inflammatory disorders with nonsatisfactory therapeutic interventions. Analyzing patient data-driven cohorts can highlight disease pathways and new targets for interventions. Long noncoding RNAs (lncRNAs) are attractive candidates, since they are readily targetable by RNA therapeutics, show relative cell-specific expression, and play key cellular functions. Uniformly analyzing gut mucosal transcriptomics from 696 subjects, we have highlighted lncRNA expression along the gastrointestinal (GI) tract, demonstrating that, in control samples, lncRNAs have a more location-specific expression in comparison with protein-coding genes. We defined dysregulation of lncRNAs in treatment-naive UC, CD, and celiac diseases using independent test and validation cohorts. Using the Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT) inception UC cohort, we defined and prioritized lncRNA linked with UC severity and prospective outcomes, and we highlighted lncRNAs linked with gut microbes previously implicated in mucosal homeostasis. HNF1A-AS1 lncRNA was reduced in all 3 conditions and was further reduced in more severe UC form. Similarly, the reduction of HNF1A-AS1 ortholog in mice gut epithelia showed higher sensitivity to dextran sodium sulfate-induced colitis, which was coupled with alteration in the gut microbial community. These analyses highlight prioritized dysregulated lncRNAs that can guide future preclinical studies for testing them as potential targets.
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Affiliation(s)
- Tzipi Braun
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Katya E. Sosnovski
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amnon Amir
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Marina BenShoshan
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kelli L. VanDussen
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Rebekah Karns
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Nina Levhar
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Haya Abbas-Egbariya
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rotem Hadar
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Gilat Efroni
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - David Castel
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Camila Avivi
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Michael J. Rosen
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Center for Pediatric IBD and Celiac Disease, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | | | | | - David R. Mack
- Children’s Hospital of East Ontario, Ottawa, Ontario, Canada
| | | | - Syed Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sean R. Moore
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA
| | | | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Anil G. Jegga
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Department of Computer Science, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Engineering, Cincinnati, Ohio, USA
| | - Batya Weiss
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chen Mayer
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Iris Barshack
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shomron Ben-Horin
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Igor Ulitsky
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Anthony Beucher
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Jorge Ferrer
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, the Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Spain
| | - Jeffrey S. Hyams
- Connecticut Children’s Medical Center, Hartford, Connecticut, USA
| | - Lee A. Denson
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Yael Haberman
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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10
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Shoda T, Rochman M, Collins MH, Caldwell JM, Mack LE, Osswald GA, Mukkada VA, Putnam PE, Rothenberg ME. Molecular analysis of duodenal eosinophilia. J Allergy Clin Immunol 2023; 151:1027-1039. [PMID: 36592704 PMCID: PMC10102870 DOI: 10.1016/j.jaci.2022.12.814] [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] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/18/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Eosinophilic duodenitis (EoD), characterized by nonspecific gastrointestinal symptoms and increased numbers of duodenal eosinophils, may be in the eosinophilic gastrointestinal disease spectrum. However, diagnostic thresholds and pathogenic processes of duodenal tissue eosinophilia are inadequately characterized. OBJECTIVE We aimed to define an EoD transcriptome and pathologic pathways. METHODS RNA sequencing and histologic features of human duodenal biopsy samples were analyzed as a function of duodenal eosinophils levels. For analyses, we defined EoD as more than 52 peak eosinophils/hpf (n = 8), duodenal eosinophilia as 30 to 52 eosinophils/hpf (n = 11), and normal controls as fewer than 30 eosinophils/hpf (n = 8). Associations between gene expression and histologic features were analyzed with Spearman correlation. RESULTS We identified 382 differentially expressed genes (EoD transcriptome) between EoD and normal controls (>2-fold change [adjusted P < .05]). The EoD transcriptome distinguished EoD from controls (duodenal eosinophilia and normal controls). The duodenal eosinophil count was correlated with a distinct EoD transcriptome when 50 to 60 peak eosinophils/hpf were present. The EoD transcriptome was enriched in genes involved in IL-4/IL-13 signaling, mast cells, and myeloid progenitor cells. Among duodenal histologic features, lamina propria eosinophil sheets was the most associated with transcriptomic changes (r = 0.66; P < .01). EoD gene signatures were shared with eosinophilic esophagitis and eosinophilic gastritis but not with eosinophilic colitis or celiac disease. CONCLUSION We have identified an EoD transcriptomic signature that emerges at 50 to 60 peak eosinophils/hpf and established EoD as part of a spectrum of upper eosinophilic gastrointestinal disorder associated with type 2 immunity and distinct from eosinophilic colitis and celiac disease. These findings provide a basis for improving diagnosis and treatment.
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Affiliation(s)
- Tetsuo Shoda
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Mark Rochman
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Margaret H Collins
- Division of Pathology and Laboratory Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Julie M Caldwell
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Lydia E Mack
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Garrett A Osswald
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Vincent A Mukkada
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Philip E Putnam
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio.
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11
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AbdullGaffar B, Farhan R. "Brunner gland inflammation in Crohn's disease and Celiac disease: Overlapping inflammatory patterns suggest a possible link". Ann Diagn Pathol 2023; 64:152133. [PMID: 37019032 DOI: 10.1016/j.anndiagpath.2023.152133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/07/2023]
Abstract
Similar to celiac disease, inflammatory bowel disease frequently manifests in the duodenum. Histopathologic studies focused on mucosal alterations with little attention to submucosal Brunner glands. Recently, several studies have demonstrated overlapping features between Crohn's disease and celiac disease suggesting a putative link. However, histopathologic studies evaluating this possible link are limited, and those that are focused on Brunner glands are lacking. The present study aims to explore whether Crohn's disease and celiac disease display shared or overlapping inflammatory changes in Brunner glands. We performed a retrospective review study over 17-years retrieving duodenal biopsy specimens containing Brunner gland lobules in patients with Crohn's disease, celiac disease, and ulcerative colitis. We found 10 out of 126 duodenal biopsies (8 %) in patients with Crohn's disease and 6 out of 134 (4.5 %) duodenal biopsies in patients with celiac disease sharing inflammatory patterns in duodenal Brunner gland lobules. Both diseases showed interstitial intralobular and interlobular mixed chronic inflammation with variable fibrosis. Focally enhanced active inflammation of Brunner gland lobules was more characteristic of Crohn's disease. Intralobular epithelioid granulomas and multinucleated giant cells were specific to Crohn's disease. Ulcerative colitis patients did not show similar features. The interstitial focally enhanced chronic inflammatory pattern was significantly (p < 0.05) associated with both diseases, while the other inflammatory patterns were not (p > 0.05). This overlapping inflammatory pattern in Brunner glands in patients with Crohn's disease and celiac disease is supportive of the previously reported link between the two diseases. Pathologists should pay more attention to Brunner glands when evaluating duodenal biopsies. Further studies are warranted to validate these observations and their relevance in the pathogenesis of autoinflammatory gastrointestinal diseases.
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Affiliation(s)
| | - Rabiah Farhan
- Histology unit, Dubai hospital, United Arab Emirates
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12
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Dotsenko V, Sioofy-Khojine AB, Hyöty H, Viiri K. Human intestinal organoid models for celiac disease research. Methods Cell Biol 2023; 179:173-193. [PMID: 37625874 DOI: 10.1016/bs.mcb.2023.01.008] [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] [Indexed: 03/19/2023]
Abstract
Celiac disease pathogenesis, in addition to immune cell component, encompasses pathogenic events also in the duodenal epithelium. In celiac disease patients, exposure to dietary gluten induces drastic changes in epithelial differentiation and elicit cellular response to inflammatory cytokines. The autoantigen in celiac disease, transglutaminase 2 (TG2) enzyme, has been also suggested to play its pathogenic gliadin deamidation event in the intestinal epithelium. Therefore in vitro epithelial cell-line models have been exploited in the past to study these pathogenic mechanisms, but they are hampered by their simplistic nature lacking proper cell-type composition and intestinal environ. Moreover, these cell models harbor many cancer-related mutations in tumor suppressor genes making them unsuitable for studying cell differentiation. Intestinal organoids provide a near-native epithelial cell model to study pathogenic agents and mechanisms related to celiac disease. Here we describe protocols to initiate and maintain celiac patient-derived organoid cultures and how to grow them in alternative ways allowing their exploitation in different kind of experiments.
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Affiliation(s)
- Valeriia Dotsenko
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere University Hospital, Tampere, Finland
| | | | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Fimlab Laboratories, Tampere, Finland
| | - Keijo Viiri
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere University Hospital, Tampere, Finland.
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13
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Meng G, Tang W, Huang E, Li Z, Feng H. A comprehensive assessment of cell type-specific differential expression methods in bulk data. Brief Bioinform 2023; 24:bbac516. [PMID: 36472568 PMCID: PMC9851321 DOI: 10.1093/bib/bbac516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/08/2022] [Accepted: 10/29/2022] [Indexed: 12/12/2022] Open
Abstract
Accounting for cell type compositions has been very successful at analyzing high-throughput data from heterogeneous tissues. Differential gene expression analysis at cell type level is becoming increasingly popular, yielding biomarker discovery in a finer granularity within a particular cell type. Although several computational methods have been developed to identify cell type-specific differentially expressed genes (csDEG) from RNA-seq data, a systematic evaluation is yet to be performed. Here, we thoroughly benchmark six recently published methods: CellDMC, CARseq, TOAST, LRCDE, CeDAR and TCA, together with two classical methods, csSAM and DESeq2, for a comprehensive comparison. We aim to systematically evaluate the performance of popular csDEG detection methods and provide guidance to researchers. In simulation studies, we benchmark available methods under various scenarios of baseline expression levels, sample sizes, cell type compositions, expression level alterations, technical noises and biological dispersions. Real data analyses of three large datasets on inflammatory bowel disease, lung cancer and autism provide evaluation in both the gene level and the pathway level. We find that csDEG calling is strongly affected by effect size, baseline expression level and cell type compositions. Results imply that csDEG discovery is a challenging task itself, with room to improvements on handling low signal-to-noise ratio and low expression genes.
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Affiliation(s)
- Guanqun Meng
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA
| | - Wen Tang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA
| | - Emina Huang
- Department of Surgery, The University of Texas Southwestern Medical Center, Dallas, 75390, Texas, USA
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, 77030, Texas, USA
| | - Hao Feng
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA
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14
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Zheng Z, Zhan S, Zhou Y, Huang G, Chen P, Li B. Pediatric Crohn's disease diagnosis aid via genomic analysis and machine learning. Front Pediatr 2023; 11:991247. [PMID: 37033178 PMCID: PMC10076664 DOI: 10.3389/fped.2023.991247] [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: 07/11/2022] [Accepted: 03/10/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Determination of pediatric Crohn's disease (CD) remains a major diagnostic challenge. However, the rapidly emerging field of artificial intelligence has demonstrated promise in developing diagnostic models for intractable diseases. Methods We propose an artificial neural network model of 8 gene markers identified by 4 classification algorithms based on Gene Expression Omnibus database for diagnostic of pediatric CD. Results The model achieved over 85% accuracy and area under ROC curve value in both training set and testing set for diagnosing pediatric CD. Additionally, immune infiltration analysis was performed to address why these markers can be integrated to develop a diagnostic model. Conclusion This study supports further clinical facilitation of precise disease diagnosis by integrating genomics and machine learning algorithms in open-access database.
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Affiliation(s)
- Zhiwei Zheng
- Department of Pediatrics, Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Zhongshan, China
- Correspondence: Zhiwei Zheng
| | - Sha Zhan
- School of Chinese Medicine, Jinan University, Guangzhou, China
| | - Yongmao Zhou
- Department of Pediatrics, Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Zhongshan, China
| | - Ganghua Huang
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Pan Chen
- Department of Pediatrics, Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Zhongshan, China
| | - Baofei Li
- Department of Pediatrics, Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Zhongshan, China
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15
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Liu D, Chen YY, Li QQ, Xu M, Liao JT, Wang B. Integrative bioinformatics analysis to identify the effects of circadian rhythm on Crohn’s disease. Front Mol Biosci 2022; 9:961481. [PMID: 36172047 PMCID: PMC9511471 DOI: 10.3389/fmolb.2022.961481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Crohn’s disease (CD) is a multifactorial inflammatory bowel disease characterized by complex aberrant autoimmune disorders. Currently, the involvement of the circadian rhythm in the pathogenesis of CD is unknown.Methods: Bulk and single-cell RNA-seq data and associated clinical data from patients with CD were downloaded from the Gene Expression Omnibus (GEO). Single-sample gene set enrichment analysis was performed to calculate the enrichment score (ES) of circadian rhythm-related genes. Differential expression analysis was used to identify differentially expressed genes. Functional enrichment analysis was used to explore potential disease mechanisms. CIBERSORT was used to estimate immune cell abundance. Single-cell RNA-seq data were analyzed using the R package “Seurat.”Results: The ES of circadian rhythm-related genes was lower in the CD tissue than in the normal tissue. Ubiquitin-specific protease 2 (USP2), a circadian rhythm-related gene, was identified as a potential modulator of CD pathogenesis. USP2 expression was reduced in CD and was associated with disease severity. Moreover, the analysis of bulk RNA-seq and single-cell RNA-seq data showed that monocyte and neutrophil abundance was elevated in CD and was negatively correlated with USP2 expression. It should be noted that USP2 expression in acinar cells was negatively correlated with monocyte and neutrophil abundance. Functional enrichment analysis revealed several canonical pathways to be enriched in CD, including the interleukin-17 signaling pathway, tumor necrosis factor signaling pathway, cytokine–cytokine receptor interaction, toll-like receptor signaling pathway, and nod-like receptor signaling pathway.Conclusion: Aberrant expression of circadian rhythm-related genes is correlated with CD pathogenesis. USP2 might be related to crosstalk among the different cell types in CD. These findings provide insights into future chronotherapy for CD.
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Affiliation(s)
- Dan Liu
- Department of Gastroenterology Medicine, Hunan Provincial People’s Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Yin-Yun Chen
- Department of Gastroenterology Medicine, Hunan Provincial People’s Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Qing-qing Li
- Department of Gastroenterology Medicine, Hunan Provincial People’s Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Ming Xu
- Department of Gastroenterology Medicine, Hunan Provincial People’s Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Jiang-Tao Liao
- Department of Gastroenterology Medicine, Hunan Provincial People’s Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Ben Wang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratary of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Ben Wang,
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16
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Ohara TE, Colonna M, Stappenbeck TS. Adaptive differentiation promotes intestinal villus recovery. Dev Cell 2022; 57:166-179.e6. [PMID: 35016013 PMCID: PMC9092613 DOI: 10.1016/j.devcel.2021.12.012] [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] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/28/2021] [Accepted: 12/10/2021] [Indexed: 01/26/2023]
Abstract
Loss of differentiated cells to tissue damage is a hallmark of many diseases. In slow-turnover tissues, long-lived differentiated cells can re-enter the cell cycle or transdifferentiate to another cell type to promote repair. Here, we show that in a high-turnover tissue, severe damage to the differentiated compartment induces progenitors to transiently acquire a unique transcriptional and morphological postmitotic state. We highlight this in an acute villus injury model in the mouse intestine, where we identified a population of progenitor-derived cells that covered injured villi. These atrophy-induced villus epithelial cells (aVECs) were enriched for fetal markers but were differentiated and lineage committed. We further established a role for aVECs in maintaining barrier integrity through the activation of yes-associated protein (YAP). Notably, loss of YAP activity led to impaired villus regeneration. Thus, we define a key repair mechanism involving the activation of a fetal-like program during injury-induced differentiation, a process we term "adaptive differentiation."
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Affiliation(s)
- Takahiro E Ohara
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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17
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Tan IL, Coutinho de Almeida R, Modderman R, Stachurska A, Dekens J, Barisani D, Meijer CR, Roca M, Martinez-Ojinaga E, Shamir R, Auricchio R, Korponay-Szabó IR, Castillejo G, Szajewska H, Koletzko S, Zhernakova A, Kumar V, Li Y, Visschedijk MC, Weersma RK, Troncone R, Mearin ML, Wijmenga C, Jonkers I, Withoff S. Circulating miRNAs as Potential Biomarkers for Celiac Disease Development. Front Immunol 2021; 12:734763. [PMID: 34950132 PMCID: PMC8688806 DOI: 10.3389/fimmu.2021.734763] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/05/2021] [Indexed: 12/11/2022] Open
Abstract
Background & Aims Celiac disease (CeD), an immune-mediated disease with enteropathy triggered by gluten, affects ~1% of the general European population. Currently, there are no biomarkers to predict CeD development. MicroRNAs (miRNAs) are short RNAs involved in post-transcriptional gene regulation, and certain disease- and stage-specific miRNA profiles have been found previously. We aimed to investigate whether circulating miRNAs can predict the development of CeD. Methods Using next-generation miRNA-sequencing, we determined miRNAs in >200 serum samples from 53 participants of the PreventCD study, of whom 33 developed CeD during follow-up. Following study inclusion at 3 months of age, samples were drawn at predefined ages, diagnosis (first anti-transglutaminase antibody (TGA) positivity or diagnostic biopsy) and after the start of a gluten-free diet (GFD). This allowed identification of circulating miRNAs that are deregulated before TGA positivity. For validation of the biomarkers for CeD and GFD response, two additional cohorts were included in subsequent meta-analyses. Additionally, miRNAs were measured in duodenal biopsies in a case-control cohort. Results 53 circulating miRNAs were increased (27) or decreased (26) in CeD versus controls. We assessed specific trends in these individual miRNAs in the PreventCD cohort by grouping the pre-diagnostic samples of the CeD patients (all had negative TGA) by how close to seroconversion (first sample positive TGA) the samples were taken. 8/53 miRNAs differed significantly between controls and samples taken <1 year before TGA positivity: miR-21-3p, miR-374a-5p, 144-3p, miR-500a-3p, miR-486-3p let-7d-3p, let-7e-5p and miR-3605-3p. 6/26 downregulated miRNAs reconstituted upon GFD, including miR-150-5p/-3p, whereas no upregulated miRNAs were downregulated upon GFD. 15/53 biomarker candidates also differed between CeD biopsies and controls, with a concordant direction, indicating that these circulating miRNAs might originate from the intestine. Conclusions We identified 53 circulating miRNAs that are potential early biomarkers for CeD, of which several can be detected more than a year before TGA positivity and some start to normalize upon GFD.
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Affiliation(s)
- Ineke L Tan
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Rodrigo Coutinho de Almeida
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, Netherlands
| | - Rutger Modderman
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Anna Stachurska
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Jackie Dekens
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands.,Center of Development and Innovation, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Donatella Barisani
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Caroline R Meijer
- Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - María Roca
- Celiac Disease and Digestive Immunopathology Unit, Instituto de Investigación Sanitaria La Fe, La Fe University Hospital, Valencia, Spain
| | - Eva Martinez-Ojinaga
- Celiac Disease and Digestive Immunopathology Unit, Instituto de Investigación Sanitaria La Fe, La Fe University Hospital, Madrid, Spain
| | - Raanan Shamir
- Institute of Pediatric Gastroenterology, Nutrition, and Liver Diseases, Schneider Children's Medical Center, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Renata Auricchio
- Department of Medical Translational Sciences and European Laboratory for the Investigation of Food Induced Diseases, University Federico II, Naples, Italy
| | - Ilma R Korponay-Szabó
- Coeliac Disease Center, Heim Pál National Paediatric Institute, Budapest, Hungary and Dept. of Paediatrics, Faculty of Medicine and Clinical Center, University of Debrecen, Debrecen, Hungary
| | - Gemma Castillejo
- Unitat de gastroenterologia pediàtrica, Hospital Universitari Sant Joan de Reus, Universitat Rovira i virgili, Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
| | - Hania Szajewska
- Department of Paediatrics, The Medical University of Warsaw, Warsaw, Poland
| | - Sibylle Koletzko
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München (LMU) Klinikum Munich, Munich, Germany.,Department of Pediatric Gastroenterology and Nutrition, School of Medicine Collegium Medicum University of Warmia and Mazury, Olsztyn, Poland
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands.,Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | - Yang Li
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands.,Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM) & TWINCORE, Joint Ventures Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Riccardo Troncone
- Department of Medical Translational Sciences and European Laboratory for the Investigation of Food Induced Diseases, University Federico II, Naples, Italy
| | - M Luisa Mearin
- Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Iris Jonkers
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
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18
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Friedrich M, Pohin M, Jackson MA, Korsunsky I, Bullers SJ, Rue-Albrecht K, Christoforidou Z, Sathananthan D, Thomas T, Ravindran R, Tandon R, Peres RS, Sharpe H, Wei K, Watts GFM, Mann EH, Geremia A, Attar M, McCuaig S, Thomas L, Collantes E, Uhlig HH, Sansom SN, Easton A, Raychaudhuri S, Travis SP, Powrie FM. IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies. Nat Med 2021; 27:1970-1981. [PMID: 34675383 PMCID: PMC8604730 DOI: 10.1038/s41591-021-01520-5] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023]
Abstract
Current inflammatory bowel disease (IBD) therapies are ineffective in a high proportion of patients. Combining bulk and single-cell transcriptomics, quantitative histopathology and in situ localization across three cohorts of patients with IBD (total n = 376), we identify coexpressed gene modules within the heterogeneous tissular inflammatory response in IBD that map to distinct histopathological and cellular features (pathotypes). One of these pathotypes is defined by high neutrophil infiltration, activation of fibroblasts and vascular remodeling at sites of deep ulceration. Activated fibroblasts in the ulcer bed display neutrophil-chemoattractant properties that are IL-1R, but not TNF, dependent. Pathotype-associated neutrophil and fibroblast signatures are increased in nonresponders to several therapies across four independent cohorts (total n = 343). The identification of distinct, localized, tissular pathotypes will aid precision targeting of current therapeutics and provides a biological rationale for IL-1 signaling blockade in ulcerating disease.
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Affiliation(s)
- Matthias Friedrich
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Mathilde Pohin
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Matthew A Jackson
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Ilya Korsunsky
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Samuel J Bullers
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Kevin Rue-Albrecht
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Zoe Christoforidou
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Dharshan Sathananthan
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Tom Thomas
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Rahul Ravindran
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Ruchi Tandon
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Raphael Sanches Peres
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Hannah Sharpe
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kevin Wei
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gerald F M Watts
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth H Mann
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Alessandra Geremia
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Moustafa Attar
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sarah McCuaig
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Lloyd Thomas
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Elena Collantes
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Department of Paediatrics, John Radcliffe Hospital, Oxford, UK
| | - Stephen N Sansom
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Alistair Easton
- Old Road Campus Research Building, Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Simon P Travis
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Fiona M Powrie
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
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19
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A Combined mRNA- and miRNA-Sequencing Approach Reveals miRNAs as Potential Regulators of the Small Intestinal Transcriptome in Celiac Disease. Int J Mol Sci 2021; 22:ijms222111382. [PMID: 34768815 PMCID: PMC8583991 DOI: 10.3390/ijms222111382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/14/2021] [Accepted: 10/17/2021] [Indexed: 12/14/2022] Open
Abstract
Celiac disease (CeD) is triggered by gluten and results in inflammation and villous atrophy of the small intestine. We aimed to explore the role of miRNA-mediated deregulation of the transcriptome in CeD. Duodenal biopsies of CeD patients (n = 33) and control subjects (n = 10) were available for miRNA-sequencing, with RNA-sequencing also available for controls (n = 5) and CeD (n = 6). Differential expression analysis was performed to select CeD-associated miRNAs and genes. MiRNA‒target transcript pairs selected from public databases that also displayed a strong negative expression correlation in the current dataset (R < -0.7) were used to construct a CeD miRNA‒target transcript interaction network. The network includes 2030 miRNA‒target transcript interactions, including 423 experimentally validated pairs. Pathway analysis found that interactions are involved in immune-related pathways (e.g., interferon signaling) and metabolic pathways (e.g., lipid metabolism). The network includes 13 genes previously prioritized to be causally deregulated by CeD-associated genomic variants, including STAT1. CeD-associated miRNAs might play a role in promoting inflammation and decreasing lipid metabolism in the small intestine, thereby contributing unbalanced cell turnover in the intestinal crypt. Some CeD-associated miRNAs deregulate genes that are also affected by genomic CeD-risk variants, adding an additional layer of complexity to the deregulated transcriptome in CeD.
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20
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Stamnaes J. Insights from tissue "omics" analysis on intestinal remodeling in celiac disease. Proteomics 2021; 21:e2100057. [PMID: 34633755 DOI: 10.1002/pmic.202100057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 12/20/2022]
Abstract
Celiac disease (CeD) is a prevalent intestinal disorder that only develops in genetically susceptible individuals when they mount a harmful CD4+ T-cell response towards gluten peptides. Intake of gluten leads to inflammation and remodeling of the small intestine with symptoms such as nausea and diarrhea. The only current treatment is a lifelong gluten free diet. The immunological basis for CeD is well characterized but the mechanisms that drive intestinal remodeling are still poorly understood. Transcriptome or proteome analysis of intestinal biopsies gives a global snapshot of all processes that occur in the tissue, including alterations in the epithelial cell layer. This paper will introduce concepts of intestinal remodeling, recapitulate the current understanding of CeD pathogenesis and discuss findings from relevant tissue "omics" studies. On the basis of this review, I give perspectives on what tissue "omics" studies can tell us about disease pathogenesis with a particular focus on the gluten induced intestinal remodeling.
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Affiliation(s)
- Jorunn Stamnaes
- Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
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21
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Gandini A, Gededzha MP, De Maayer T, Barrow P, Mayne E. Diagnosing coeliac disease: A literature review. Hum Immunol 2021; 82:930-936. [PMID: 34462157 DOI: 10.1016/j.humimm.2021.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/14/2021] [Accepted: 07/30/2021] [Indexed: 12/14/2022]
Abstract
Coeliac disease (CD) is an autoimmune gastroenteropathy triggered by gliadin and gliadin-tissue transglutaminase (tTG) complexes. CD is one of the few autoimmune diseases with an accurate, non-invasive serological test. Anti-endomysial, anti-tTG and anti-deaminated gliadin peptides (DGP) antibodies are currently used for serological tests with tTG ELISAs being the superior test. Duodenal biopsy, although invasive, is the gold standard for CD diagnosis. HLA genotyping and flow cytometry can also be used as supplementary tests. The incidence of CD is rising globally although the reasons for this remain unclear. In addition, the true incidence of coeliac disease in African populations remains unknown although recent work suggests that South African populations express the alleles associated with this disease. This review examines the pathogenesis and diagnosis of coeliac disease and considers novel and innovative biomarkers in its diagnosis specifically in an African population.
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Affiliation(s)
- Anastasia Gandini
- University of Witwatersrand, South Africa; National Health Laboratory Service, South Africa; Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Maemu P Gededzha
- University of Witwatersrand, South Africa; National Health Laboratory Service, South Africa; Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tim De Maayer
- University of Witwatersrand, South Africa; Rahima Moosa Mother and Child Hospital, South Africa
| | - Peter Barrow
- University of Witwatersrand, South Africa; Wits University Donald Gordon Medical Centre, South Africa
| | - Elizabeth Mayne
- University of Witwatersrand, South Africa; National Health Laboratory Service, South Africa; Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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22
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Taavela J, Viiri K, Välimäki A, Sarin J, Salonoja K, Mäki M, Isola J. Apolipoprotein A4 Defines the Villus-Crypt Border in Duodenal Specimens for Celiac Disease Morphometry. Front Immunol 2021; 12:713854. [PMID: 34394117 PMCID: PMC8358775 DOI: 10.3389/fimmu.2021.713854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/19/2021] [Indexed: 12/18/2022] Open
Abstract
Histological evaluation of the small intestinal mucosa is the cornerstone of celiac disease diagnostics and an important outcome in scientific studies. Gluten-dependent injury can be evaluated either with quantitative morphometry or grouped classifications. A drawback of mucosal readings is the subjective assessment of the border where the crypt epithelium changes to the differentiated villus epithelium. We studied potential immunohistochemical markers for the detection of the villus-crypt border: apolipoprotein A4 (APOA4), Ki-67, glucose transporter 2, keratin 20, cytochrome P450 3A4 and intestinal fatty-acid binding protein. Among these, villus-specific APOA4 was chosen as the best candidate for further studies. Hematoxylin-eosin (H&E)- and APOA4 stained duodenal biopsy specimens from 74 adult patients were evaluated by five observers to determine the villus-to-crypt ratio (VH : CrD). APOA4 delineated the villus to crypt epithelium transition clearly, and the correlation coefficient of VH : CrD values between APOA4 and H&E was excellent (r=0.962). The VH : CrD values were lower in APOA4 staining (p<0.001) and a conversion factor of 0.2 in VH : CrD measurements was observed to make the two methods comparable to each other. In the intraobserver analysis, the doubled standard deviations, representing the error ranges, were 0.528 for H&E and 0.388 for APOA4 staining, and the ICCs were 0.980 and 0.971, respectively. In the interobserver analysis, the average error ranges were 1.017 for H&E and 0.847 for APOA4 staining, and the ICCs were better for APOA4 than for H&E staining in all analyses. In conclusion, the reliability and reproducibility of morphometrical VH : CrD readings are improved with the use of APOA4 staining.
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Affiliation(s)
- Juha Taavela
- Central Finland Central Hospital, Jyväskylä, Finland.,Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Keijo Viiri
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anna Välimäki
- Fimlab Laboratories Inc, Tampere, Finland.,Jilab Inc, Tampere, Finland
| | | | | | - Markku Mäki
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Tampere University Hospital, Tampere, Finland
| | - Jorma Isola
- Jilab Inc, Tampere, Finland.,Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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23
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Lerner A, Sobolevskaia P, Churilov L, Shoenfeld Y. Alpha-enolase involvement in intestinal and extraintestinal manifestations of celiac disease. J Transl Autoimmun 2021; 4:100109. [PMID: 34189450 PMCID: PMC8219987 DOI: 10.1016/j.jtauto.2021.100109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 01/13/2023] Open
Abstract
Celiac disease is a life-long intestinal autoimmune disease, characterized by the gluten intolerance and chronic enteric inflammation. Traditionally presented by intestinal manifestations, however, a shift toward extra intestinal presentation is taking place. One of the affected organs is the nervous systems presented by neuropsychiatric manifestations, hence the mechanism and pathways are not clear. The presence of neuronal and alpha-enolases and their corresponding antibodies were noticed in the mucosa and serum of celiac disease patients, as well as in other various autoimmune diseases with psycho-neurological manifestations. The aims of the present review are to screen the literature on different isoforms of enolase, mainly alpha enolase, and their specific antibodies and to suggest their potential pathophysiological mechanisms relaying the enolases to intestinal or extraintestinal celiac disease manifestations. The shared aspects between the enolases and celiac disease and the cross-talks between alpha-enolase and tissue transglutaminase suggest new potential pathophysiological mechanisms that might drive celiac disease evolvement.
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Affiliation(s)
- Aaron Lerner
- Chaim Sheba Medical Center, The Zabludowicz Research Center for Autoimmune Diseases, Tel Hashomer, Israel
| | | | | | - Yehuda Shoenfeld
- Chaim Sheba Medical Center, The Zabludowicz Research Center for Autoimmune Diseases, Tel Hashomer, Israel.,Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Visiting Professor), Moscow, Russia.,Ariel University, Ariel, Israel
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24
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Wolf J, Willscher E, Loeffler-Wirth H, Schmidt M, Flemming G, Zurek M, Uhlig HH, Händel N, Binder H. Deciphering the Transcriptomic Heterogeneity of Duodenal Coeliac Disease Biopsies. Int J Mol Sci 2021; 22:ijms22052551. [PMID: 33806322 PMCID: PMC7961974 DOI: 10.3390/ijms22052551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Coeliac disease (CD) is a clinically heterogeneous autoimmune disease with variable presentation and progression triggered by gluten intake. Molecular or genetic factors contribute to disease heterogeneity, but the reasons for different outcomes are poorly understood. Transcriptome studies of tissue biopsies from CD patients are scarce. Here, we present a high-resolution analysis of the transcriptomes extracted from duodenal biopsies of 24 children and adolescents with active CD and 21 individuals without CD but with intestinal afflictions as controls. The transcriptomes of CD patients divide into three groups-a mixed group presenting the control cases, and CD-low and CD-high groups referring to lower and higher levels of CD severity. Persistence of symptoms was weakly associated with subgroup, but the highest marsh stages were present in subgroup CD-high, together with the highest cell cycle rates as an indicator of virtually complete villous atrophy. Considerable variation in inflammation-level between subgroups was further deciphered into immune cell types using cell type de-convolution. Self-organizing maps portrayal was applied to provide high-resolution landscapes of the CD-transcriptome. We find asymmetric patterns of miRNA and long non-coding RNA and discuss the effect of epigenetic regulation. Expression of genes involved in interferon gamma signaling represent suitable markers to distinguish CD from non-CD cases. Multiple pathways overlay in CD biopsies in different ways, giving rise to heterogeneous transcriptional patterns, which potentially provide information about etiology and the course of the disease.
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Affiliation(s)
- Johannes Wolf
- Department of Laboratory Medicine at Hospital “St. Georg” Leipzig, 04129 Leipzig, Germany;
- Immuno Deficiency Centre Leipzig (IDCL) at Hospital St. Georg Leipzig, Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiency Diseases, 04129 Leipzig, Germany
| | - Edith Willscher
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
| | - Henry Loeffler-Wirth
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
| | - Maria Schmidt
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
| | - Gunter Flemming
- Paediatric Gastroenterology Unit, University Hospital for Children and Adolescents, 04103 Leipzig, Germany;
| | - Marlen Zurek
- Children’s Hospital of the Clinical Centre “Sankt Georg”, 04129 Leipzig, Germany; (M.Z.); (N.H.)
| | - Holm H. Uhlig
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research Centre, Experimental Medicine, Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Oxford OX4 2PG, UK;
| | - Norman Händel
- Children’s Hospital of the Clinical Centre “Sankt Georg”, 04129 Leipzig, Germany; (M.Z.); (N.H.)
| | - Hans Binder
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
- Correspondence:
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25
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Ramírez-Sánchez AD, Tan IL, Gonera-de Jong B, Visschedijk MC, Jonkers I, Withoff S. Molecular Biomarkers for Celiac Disease: Past, Present and Future. Int J Mol Sci 2020; 21:E8528. [PMID: 33198309 PMCID: PMC7697360 DOI: 10.3390/ijms21228528] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/10/2020] [Indexed: 12/19/2022] Open
Abstract
Celiac disease (CeD) is a complex immune-mediated disorder that is triggered by dietary gluten in genetically predisposed individuals. CeD is characterized by inflammation and villous atrophy of the small intestine, which can lead to gastrointestinal complaints, malnutrition, and malignancies. Currently, diagnosis of CeD relies on serology (antibodies against transglutaminase and endomysium) and small-intestinal biopsies. Since small-intestinal biopsies require invasive upper-endoscopy, and serology cannot predict CeD in an early stage or be used for monitoring disease after initiation of a gluten-free diet, the search for non-invasive biomarkers is ongoing. Here, we summarize current and up-and-coming non-invasive biomarkers that may be able to predict, diagnose, and monitor the progression of CeD. We further discuss how current and emerging techniques, such as (single-cell) transcriptomics and genomics, can be used to uncover the pathophysiology of CeD and identify non-invasive biomarkers.
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Affiliation(s)
- Aarón D. Ramírez-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands; (A.D.R.-S.); (I.L.T.); (I.J.)
| | - Ineke L. Tan
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands; (A.D.R.-S.); (I.L.T.); (I.J.)
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands;
| | - B.C. Gonera-de Jong
- Department of Pediatrics, Wilhelmina Hospital Assen, 9401 RK Assen, The Netherlands;
| | - Marijn C. Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands;
| | - Iris Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands; (A.D.R.-S.); (I.L.T.); (I.J.)
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands; (A.D.R.-S.); (I.L.T.); (I.J.)
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26
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Couper R. Future of paediatric gastroenterology. J Paediatr Child Health 2020; 56:1674-1676. [PMID: 33197984 DOI: 10.1111/jpc.15023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 05/30/2020] [Indexed: 12/16/2022]
Abstract
This article explores what an 'ideal' paediatric gastroenterology department in the future should look like and what it could potentially provide if given carte blanche by health funds.
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Affiliation(s)
- Richard Couper
- Department of Gastroenterology, Women's and Children's Hospital, Adelaide, South Australia, Australia.,University Department of Paediatrics, University of Adelaide, Adelaide, South Australia, Australia
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27
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Haberman Y. Tissue-based Gene Expression as Potential Biomarkers for IBD Course. Inflamm Bowel Dis 2020; 26:1485-1489. [PMID: 32812640 PMCID: PMC7500516 DOI: 10.1093/ibd/izaa217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Indexed: 01/07/2023]
Abstract
Inflammatory bowel diseases (IBDs) are highly heterogeneous in disease phenotype, behavior, and response to therapy. Diagnostic and therapeutic decisions in IBD are based primarily on clinical and endoscopic severity and histopathologic analysis of intestinal biopsies. With this approach, however, only a minority of patients experience durable remission. This may be due to substantial heterogeneity in disease pathogenicity that is not accounted for by current classification systems. Patients can present with similar clinical and endoscopic severity and receive similar therapy but show divergent response ranging from mucosal/transmural healing to nonresponse. Using mucosal biopsy samples that are already obtained as part of the clinical practice to support the diagnosis and state-of-the-art high throughput sequencing approaches can detect the widest range in host gene expression in the actual lining of the affected gut. These analyses can better dissect disease heterogeneity and guide potential treatment response. Here we review studies that use gut tissue-based gene expression profiles to predict disease outcome in IBD.
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Affiliation(s)
- Yael Haberman
- Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, OH, USA,Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Israel,Address correspondence to: Yael Haberman, MD, PhD, Division of Pediatric Gastroenterology, Hepatology, & Nutrition, Cincinnati Children’s Hospital Medical Center, MLC 2010, 3333 Burnet Avenue, Cincinnati, OH 45229, USA. E-mail:
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28
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Dotsenko V, Oittinen M, Taavela J, Popp A, Peräaho M, Staff S, Sarin J, Leon F, Isola J, Mäki M, Viiri K. Genome-Wide Transcriptomic Analysis of Intestinal Mucosa in Celiac Disease Patients on a Gluten-Free Diet and Postgluten Challenge. Cell Mol Gastroenterol Hepatol 2020; 11:13-32. [PMID: 32745639 PMCID: PMC7593586 DOI: 10.1016/j.jcmgh.2020.07.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/24/2020] [Accepted: 07/24/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Gluten challenge studies are instrumental in understanding the pathophysiology of celiac disease. Our aims in this study were to reveal early gluten-induced transcriptomic changes in duodenal biopsies and to find tools for clinics. METHODS Duodenal biopsies were collected from 15 celiac disease patients on a strict long-term gluten-free diet (GFD) prior to and post a gluten challenge (PGC) and from 6 healthy control individuals (DC). Biopsy RNA was subjected to genome-wide 3' RNA-Seq. Sequencing data was used to determine the differences between the three groups and was compared to sequencing data from the public repositories. The biopsies underwent morphometric analyses. RESULTS In DC vs. GFD group comparisons, 167 differentially expressed genes were identified with 117 genes downregulated and 50 genes upregulated. In PGC vs. GFD group comparisons, 417 differentially expressed genes were identified with 195 genes downregulated and 222 genes upregulated. Celiac disease patients on a GFD were not "healthy". In particular, genes encoding proteins for transporting small molecules were expressed less. In addition to the activation of immune response genes, a gluten challenge induced hyperactive intestinal wnt-signaling and consequent immature crypt gene expression resulting in less differentiated epithelium. Biopsy gene expression in response to a gluten challenge correlated with the extent of the histological damage. Regression models using only four gene transcripts described 97.2% of the mucosal morphology and 98.0% of the inflammatory changes observed. CONCLUSIONS Our gluten challenge trial design provided an opportunity to study the transition from health to disease. The results show that even on a strict GFD, despite being deemed healthy, patients reveal patterns of ongoing disease. Here, a transcriptomic regression model estimating the extent of gluten-induced duodenal mucosal injury is presented.
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Affiliation(s)
- Valeriia Dotsenko
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University Hospital, Tampere University Tampere, Finland
| | - Mikko Oittinen
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University Hospital, Tampere University Tampere, Finland
| | - Juha Taavela
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University Hospital, Tampere University Tampere, Finland,Department of Internal Medicine, Central Finland Central Hospital, Jyväskylä, Finland
| | - Alina Popp
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University Hospital, Tampere University Tampere, Finland,Pediatric Department, Carol Davila University of Medicine and Pharmacy, Alessandrescu-Rusescu National Institute for Mother and Child Health, Bucharest, Romania
| | - Markku Peräaho
- Department of Internal Medicine, Central Finland Central Hospital, Jyväskylä, Finland
| | - Synnöve Staff
- Department of Obstetrics and Gynecology and Tays Cancer Centre, Faculty of Medicine and Health Technology, Tampere University Hospital, Tampere University, Tampere, Finland
| | - Jani Sarin
- Laboratory of Cancer Biology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland,Jilab Inc, Tampere, Finland
| | | | - Jorma Isola
- Laboratory of Cancer Biology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland,Jilab Inc, Tampere, Finland
| | - Markku Mäki
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University Hospital, Tampere University Tampere, Finland
| | - Keijo Viiri
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University Hospital, Tampere University Tampere, Finland,Correspondence Address correspondence to: Keijo Viiri, PhD, Faculty of Medicine and Health Technology, Tampere University and Tampere University Hospital, Arvo Ylpön katu 34, Tampere, FIN-33520, Finland; fax: +35833641369.
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