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Pang X, Song H, Li X, Xu F, Lei B, Wang F, Xu J, Qi L, Wang L, Tan G. Transcriptomic analyses of treatment-naïve pediatric ulcerative colitis patients and exploration of underlying disease pathogenesis. J Transl Med 2023; 21:30. [PMID: 36647141 PMCID: PMC9843999 DOI: 10.1186/s12967-023-03881-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/08/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Ulcerative colitis (UC) is a form of chronic inflammatory bowel disease of nonspecific origin. This study used an RNA-Sequencing (RNA-Seq) approach to evaluate the transcriptomic landscape of a well-stratified treatment-naïve pediatric UC patient population by comparing them with healthy control children. The data were analyzed to evaluate the mechanisms driving UC-related intestinal inflammation and fibrosis. METHODS Intestinal mucosal samples from five pediatric UC patients and five healthy controls were analyzed by RNA-Seq, and results were verified by qPCR. A CRISPR/Cas9 approach was used to knock out the expression of HLA-DRB5, and molecular biology techniques were used for additional mechanistic studies. RESULTS In these analyses, 2290 genes were found to be differentially expressed between the UC and control samples, of which 1258 and 1032 were upregulated and downregulated, respectively. Gene Ontology analysis showed that these genes were enriched in extracellular matrix (ECM)-related processes and that 7 of 8 differentially expressed genes of interest (PIK3CD, IL1β, IL1α, TIMP1, MMP1, MMP12, COL6A3, and HLADRB5) were upregulated and involved in ECM-receptor interaction and inflammatory bowel disease-related pathways. Increased HLA-DRB5 expression driven by intestinal bacteria was found to promote IL-1α secretion, leading to intestinal inflammation and fibrosis, suggesting a possible target for the treatment of UC. CONCLUSION These data suggest that intestinal inflammation is present in pediatric UC patients for extended periods before the onset of symptoms, and intestinal fibrosis begins even during the early stages of UC. Intestinal bacteria were also found to trigger intestinal inflammation and fibrosis, with HLA-DRB5 playing a central role in this process.
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Affiliation(s)
- Xiaoli Pang
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Hongxiao Song
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
| | - Xiaolu Li
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Fengchao Xu
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
| | - Bingxun Lei
- grid.430605.40000 0004 1758 4110Department of Anesthesia, The First Hospital of Jilin University, Changchun, China
| | - Fei Wang
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
| | - Jing Xu
- grid.430605.40000 0004 1758 4110Health Examination Center, The First Hospital of Jilin University, Changchun, China
| | - Lingli Qi
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Libo Wang
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Guangyun Tan
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
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2
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Tsamadou C, Engelhardt D, Platzbecker U, Sala E, Valerius T, Wagner-Drouet E, Wulf G, Kröger N, Murawski N, Einsele H, Schaefer-Eckart K, Freitag S, Casper J, Kaufmann M, Dürholt M, Hertenstein B, Klein S, Ringhoffer M, Frank S, Neuchel C, Schrezenmeier H, Mytilineos J, Fuerst D. HLA-DRB3/4/5 Matching Improves Outcome of Unrelated Hematopoietic Stem Cell Transplantation. Front Immunol 2022; 12:771449. [PMID: 34970261 PMCID: PMC8712639 DOI: 10.3389/fimmu.2021.771449] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/18/2021] [Indexed: 12/25/2022] Open
Abstract
The HLA-DRB3/4/5 loci are closely linked to the HLA-DRB1 gene. Mismatches in these loci occur with a frequency of about 8%–12% in otherwise 10/10 HLA-matched transplant pairs. There is preliminary evidence that these disparities may associate with increased acute graft-versus-host disease (GvHD) rates. The aim of this study was to analyze a large cohort of German patients and their donors for HLA-DRB3/4/5 compatibility and to correlate the HLA-DRB3/4/5 matching status with the outcome of unrelated hematopoietic stem cell transplantation (uHSCT). To this end, 3,410 patients and their respective donors were HLA-DRB3/4/5 and HLA-DPB1 typed by amplicon-based next-generation sequencing (NGS). All patients included received their first allogeneic transplant for malignant hematologic diseases between 2000 and 2014. Mismatches in the antigen recognition domain (ARD) of HLA-DRB3/4/5 genes were correlated with clinical outcome. HLA-DRB3/4/5 incompatibility was seen in 12.5% (n = 296) and 17.8% (n = 185) of the 10/10 and 9/10 HLA-matched cases, respectively. HLA-DRB3/4/5 mismatches in the ARD associated with a worse overall survival (OS), as shown in univariate (5-year OS: 46.1% vs. 39.8%, log-rank p = 0.038) and multivariate analyses [hazard ratio (HR) 1.25, 95% CI 1.02–1.54, p = 0.034] in the otherwise 10/10 HLA-matched subgroup. The worse outcome was mainly driven by a significantly higher non-relapse mortality (HR 1.35, 95% CI 1.05–1.73, p = 0.017). In the 9/10 HLA-matched cases, the effect was not statistically significant. Our study results suggest that mismatches within the ARD of HLA-DRB3/4/5 genes significantly impact the outcome of otherwise fully matched uHSCT and support their consideration upon donor selection in the future.
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Affiliation(s)
- Chrysanthi Tsamadou
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg - Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Daphne Engelhardt
- Institute of Transfusion Medicine, University of Ulm, Ulm, Germany.,Department of Otorhinolaryngology, Head and Neck Surgery, University of Ulm, Ulm, Germany
| | - Uwe Platzbecker
- Department of Hematology/Oncology, University of Leipzig, Leipzig, Germany
| | - Elisa Sala
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Thomas Valerius
- Section for Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian Albrechts University, Kiel, Germany
| | - Eva Wagner-Drouet
- Department of Medicine III, Johannes Gutenberg-University, Mainz, Germany
| | - Gerald Wulf
- Department of Hematology/Oncology, Georg-August-University, Göttingen, Germany
| | - Nicolaus Kröger
- Department of Stem Cell Transplantation, University Hospital Hamburg Eppendorf, Hamburg, Germany
| | - Niels Murawski
- Department of Internal Medicine I, Universitätsklinikum des Saarlandes, Homburg, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | | | - Sebastian Freitag
- Department of Medicine III, Hematology/Oncology/Palliative Care, Rostock University Medical Center, Rostock, Germany
| | - Jochen Casper
- Department of Oncology and Hematology, Klinikum Oldenburg, University Clinic, Oldenburg, Germany
| | - Martin Kaufmann
- 2nd Department of Internal Medicine, Oncology and Hematology, Robert Bosch Hospital, Stuttgart, Germany
| | - Mareike Dürholt
- Hematology/Oncology, Evangelic Clinic Essen-Werden, Essen-Werden, Germany
| | | | - Stefan Klein
- Universitätsmedizin Mannheim, Med. Klinik III, Mannheim, Germany
| | - Mark Ringhoffer
- Medizinische Klinik III, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | - Sandra Frank
- DRST -Deutsches Register für Stammzelltransplantationen, German Registry for Stem Cell Transplantation, Ulm, Germany
| | - Christine Neuchel
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg - Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Hubert Schrezenmeier
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg - Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Joannis Mytilineos
- DRST -Deutsches Register für Stammzelltransplantationen, German Registry for Stem Cell Transplantation, Ulm, Germany.,ZKRD-Zentrales Knochenmarkspender-Register für Deutschland, German National Bone Marrow Donor Registry, Ulm, Germany
| | - Daniel Fuerst
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg - Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
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3
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Su WM, Gu XJ, Hou YB, Zhang LY, Cao B, Ou RW, Wu Y, Chen XP, Song W, Zhao B, Shang HF, Chen YP. Association Analysis of WNT3, HLA-DRB5 and IL1R2 Polymorphisms in Chinese Patients With Parkinson's Disease and Multiple System Atrophy. Front Genet 2021; 12:765833. [PMID: 34868249 PMCID: PMC8636743 DOI: 10.3389/fgene.2021.765833] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/29/2021] [Indexed: 02/05/2023] Open
Abstract
Background: The association between inflammation and neurodegeneration has long been observed in parkinson's disease (PD) and multiple system atrophy (MSA). Previous genome-wide association studies (GWAS) and meta-analyses have identified several risk loci in inflammation-associated genes associated with PD. Objective: To investigate whether polymorphisms in some inflammation-associated genes could modulate the risk of developing PD and MSA in a Southwest Chinese population. Methods: A total of 2,706 Chinese subjects comprising 1340 PD, 483 MSA and 883 healthy controls were recruited in the study. Three polymorphisms (rs2074404 GG/GT/TT, rs17425622 CC/CT/TT, rs34043159 CC/CT/TT) in genes linked to inflammation in all the subjects were genotyped by using the Sequenom iPLEX Assay. Results: The allele G of WNT3 rs2074404 can increase risk on PD (OR: 1.048, 95% CI: 1.182-1.333, p = 0.006), exclusively in the LOPD subgroup (OR: 1.166, 95% CI:1.025-1.327, p = 0.019), but not in EOPD or MSA. And the recessive model analysis also demonstrated an increased PD risk in GG genotype of this locus (OR = 1.331, p = 0.007). However, no significant differences were observed in the genotype distributions and alleles of HLA-DRB5 rs17425622 and IL1R2 rs34043159 between the PD patients and controls, between the MSA patients and controls, or between subgroups of PD or MSA and controls. Conclusion: Our results suggested the allele G of WNT3 rs2074404 have an adverse effect on PD and particularly, on the LOPD subgroup among a Chinese population.
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Affiliation(s)
- Wei-Ming Su
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China.,Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China.,Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiao-Jing Gu
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China.,Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China.,Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yan-Bing Hou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China.,Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China.,Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ling-Yu Zhang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China.,Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China.,Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Bei Cao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China.,Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China.,Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ru-Wei Ou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China.,Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China.,Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Wu
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China.,Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China.,Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xue-Ping Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China.,Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China.,Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Song
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China.,Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China.,Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Bi Zhao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China.,Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China.,Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hui-Fang Shang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China.,Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China.,Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yong-Ping Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China.,Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China.,Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
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4
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Yang Z, Zhang Q, Yu H, Du H, Li L, He Y, Zhu S, Li C, Zhang S, Luo B, Gao Y. Genetic association study of a novel indel polymorphism in HSPA1B with the risk of sudden cardiac death in the Chinese populations. Forensic Sci Int 2020; 318:110637. [PMID: 33309992 DOI: 10.1016/j.forsciint.2020.110637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/16/2020] [Accepted: 11/29/2020] [Indexed: 12/12/2022]
Abstract
Sudden cardiac death (SCD) has become a global problem due to its high mortality in the general population. Identification of genetic factors predisposed to SCD is significant since it enables genetic testing that would contribute to molecular diagnosis and risk stratification of SCD. It has been reported that HSPA1B gene mutations might be related with SCD. In this study, based on candidate-gene-based approach and systematic screening strategy, a 5-base pair insertion/deletion (Indel) polymorphism (rs3036297) in the 3'UTR of HSPA1B gene was selected to perform a case-control study aiming to investigate its association with SCD susceptibility in Chinese populations. Logistic regression analysis showed that the insertion allele of rs3036297 was correlated with a comparatively lower risk for SCD [OR=0.58, 95%CI=0.43-0.77, P=1.28×10-4] compared with the deletion allele. Luciferase activity assay indicated that HSPA1B expression could be regulated by rs3036297 through interfering binding with miR-134-5p. Furthermore, analysis of database from Haploreg and GTEx revealed that the rs3036297 variant was involved in potential cis-regulatory element with the promoter of HLA-DRB5 through a long-range interaction and the deletion allele of rs3036297 increased HLA-DRB5 expression. In conclusion, the rs3036297 variant may regulate HSPA1B expression via a mechanism of miRNA binding and HLA-DRB5 expression via a long-range promoter interaction through which contributed to SCD susceptibility. Therefore, rs3036297 would be a potential marker for molecular diagnosis and genetic counseling of SCD.
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Affiliation(s)
- Zhenzhen Yang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China; Institute of Forensic Sciences, Henan University of Economics and Law, Zhengzhou, China
| | - Qing Zhang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Huan Yu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Hailin Du
- Nanjing Red Cross Blood Center, Nanjing, China
| | - Lijuan Li
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yan He
- Department of Epidemiology, Medical College of Soochow University, Suzhou, China
| | - Shaohua Zhu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Bin Luo
- Department of Forensic Pathology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Yuzhen Gao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China.
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Barsakis K, Babrzadeh F, Chi A, Mallempati K, Pickle W, Mindrinos M, Fernández-Viña MA. Complete nucleotide sequence characterization of DRB5 alleles reveals a homogeneous allele group that is distinct from other DRB genes. Hum Immunol 2019; 80:437-448. [PMID: 30954494 PMCID: PMC6622178 DOI: 10.1016/j.humimm.2019.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/23/2019] [Accepted: 04/01/2019] [Indexed: 01/28/2023]
Abstract
Next Generation Sequencing allows for testing and typing of entire genes of the HLA region. A better and comprehensive sequence assessment can be achieved by the inclusion of full gene sequences of all the common alleles at a given locus. The common alleles of DRB5 are under-characterized with the full exon-intron sequence of two alleles available. In the present study the DRB5 genes from 18 subjects alleles were cloned and sequenced; haplotype analysis showed that 17 of them had a single copy of DRB5 and one consanguineous subject was homozygous at all HLA loci. Methodological approaches including robust and efficient long-range PCR amplification, molecular cloning, nucleotide sequencing and de novo sequence assembly were combined to characterize DRB5 alleles. DRB5 sequences covering from 5'UTR to the end of intron 5 were obtained for DRB5*01:01, 01:02 and 02:02; partial coverage including a segment spanning exon 2 to exon 6 was obtained for DRB5*01:03, 01:08N and 02:03. Phylogenetic analysis of the generated sequences showed that the DRB5 alleles group together and have distinctive differences with other DRB loci. Novel intron variants of DRB5*01:01:01, 01:02 and 02:02 were identified. The newly characterized DRB5 intron variants of each DRB5 allele were found in subjects harboring distinct associations with alleles of DRB1, B and/or ethnicity. The new information provided by this study provides reference sequences for HLA typing methodologies. Extending sequence coverage may lead to identify the disease susceptibility factors of DRB5 containing haplotypes while the unexpected intron variations may shed light on understanding of the evolution of the DRB region.
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Affiliation(s)
- Konstantinos Barsakis
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Biology, University of Crete, Heraklion, Crete 71003, Greece
| | - Farbod Babrzadeh
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Anjo Chi
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Kalyan Mallempati
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - William Pickle
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Michael Mindrinos
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
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