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Wang Q, Zhang SX, Chang MJ, Qiao J, Wang CH, Li XF, Yu Q, He PF. Characteristics of the Gut Microbiome and Its Relationship With Peripheral CD4+ T Cell Subpopulations and Cytokines in Rheumatoid Arthritis. Front Microbiol 2022; 13:799602. [PMID: 35185845 PMCID: PMC8851473 DOI: 10.3389/fmicb.2022.799602] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/07/2022] [Indexed: 12/17/2022] Open
Abstract
This study investigated the association between intestinal microbiota abundance and diversity and cluster of differentiation (CD)4+ T cell subpopulations, cytokine levels, and disease activity in rheumatoid arthritis RA. A total of 108 rheumatoid arthritis (RA) patients and 99 healthy control (HC) subjects were recruited. PICRUSt2 was used for functional metagenomic predictions. Absolute counts of peripheral CD4+ T cell subpopulations and cytokine levels were detected by flow cytometry and with a cytokine bead array, respectively. Correlations were analyzed with the Spearman rank correlation test. The results showed that the diversity of intestinal microbiota was decreased in RA patients compared to HCs. At the phylum level, the abundance of Firmicutes, Fusobacteriota, and Bacteroidota was decreased while that of Actinobacteria and Proteobacteria was increased and at the genus level, the abundance of Faecalibacterium, Blautia, and Escherichia-Shigella was increased while that of Bacteroides and Coprococcus was decreased in RA patients compared to HC subjects. The linear discriminant analysis effect size indicated that Bifidobacterium was the most significant genus in RA. The most highly enriched Kyoto Encyclopedia of Genes and Genomes pathway in RA patients was amino acid metabolism. The relative abundance of Megamonas, Monoglobus, and Prevotella was positively correlated with CD4+ T cell counts and cytokine levels; and the relative numbers of regulatory T cells (Tregs) and T helper (Th17)/Treg ratio were negatively correlated with disease activity in RA. These results suggest that dysbiosis of certain bacterial lineages and alterations in gut microbiota metabolism lead to changes in the host immune profile that contribute to RA pathogenesis.
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Affiliation(s)
- Qi Wang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
| | - Sheng-Xiao Zhang
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
- Department of Rheumatology and Immunology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Min-Jing Chang
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- School of Management, Shanxi Medical University, Taiyuan, China
| | - Jun Qiao
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
- Department of Rheumatology and Immunology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Cai-Hong Wang
- Department of Rheumatology and Immunology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Xiao-Feng Li
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
- Department of Rheumatology and Immunology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Qi Yu
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- School of Management, Shanxi Medical University, Taiyuan, China
- *Correspondence: Qi Yu,
| | - Pei-Feng He
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- School of Management, Shanxi Medical University, Taiyuan, China
- Pei-Feng He,
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4
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Sánchez-Maldonado JM, Cáliz R, López-Nevot MÁ, Cabrera-Serrano AJ, Moñiz-Díez A, Canhão H, Ter Horst R, Quartuccio L, Sorensen SB, Glintborg B, Hetland ML, Filipescu I, Pérez-Pampin E, Conesa-Zamora P, Swierkot J, den Broeder AA, De Vita S, Petersen ERB, Li Y, Ferrer MA, Escudero A, Netea MG, Coenen MJH, Andersen V, Fonseca JE, Jurado M, Bogunia-Kubik K, Collantes E, Sainz J. Validation of GWAS-Identified Variants for Anti-TNF Drug Response in Rheumatoid Arthritis: A Meta-Analysis of Two Large Cohorts. Front Immunol 2021; 12:672255. [PMID: 34777329 PMCID: PMC8579100 DOI: 10.3389/fimmu.2021.672255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/11/2021] [Indexed: 12/29/2022] Open
Abstract
We aimed to validate the association of 28 GWAS-identified genetic variants for response to TNF inhibitors (TNFi) in a discovery cohort of 1361 rheumatoid arthritis (RA) patients monitored in routine care and ascertained through the REPAIR consortium and DANBIO registry. We genotyped selected markers and evaluated their association with response to TNFi after 6 months of treatment according to the change in disease activity score 28 (ΔDAS28). Next, we confirmed the most interesting results through meta-analysis of our data with those from the DREAM cohort that included 706 RA patients treated with TNFi. The meta-analysis of the discovery cohort and DREAM registry including 2067 RA patients revealed an overall association of the LINC02549rs7767069 SNP with a lower improvement in DAS28 that remained significant after correction for multiple testing (per-allele ORMeta=0.83, PMeta=0.000077; PHet=0.61). In addition, we found that each copy of the LRRC55rs717117G allele was significantly associated with lower improvement in DAS28 in rheumatoid factor (RF)-positive patients (per-allele ORMeta=0.67, P=0.00058; PHet=0.06) whereas an opposite but not significant effect was detected in RF-negative subjects (per-allele ORMeta=1.38, P=0.10; PHet=0.45; PInteraction=0.00028). Interestingly, although the identified associations did not survive multiple testing correction, the meta-analysis also showed overall and RF-specific associations for the MAFBrs6071980 and CNTN5rs1813443 SNPs with decreased changes in DAS28 (per-allele ORMeta_rs6071980 = 0.85, P=0.0059; PHet=0.63 and ORMeta_rs1813443_RF+=0.81, P=0.0059; PHet=0.69 and ORMeta_rs1813443_RF-=1.00, P=0.99; PHet=0.12; PInteraction=0.032). Mechanistically, we found that subjects carrying the LINC02549rs7767069T allele had significantly increased numbers of CD45RO+CD45RA+ T cells (P=0.000025) whereas carriers of the LINC02549rs7767069T/T genotype showed significantly increased levels of soluble scavengers CD5 and CD6 in serum (P=0.00037 and P=0.00041). In addition, carriers of the LRRC55rs717117G allele showed decreased production of IL6 after stimulation of PBMCs with B burgdorferi and E coli bacteria (P=0.00046 and P=0.00044), which suggested a reduced IL6-mediated anti-inflammatory effect of this marker to worsen the response to TNFi. In conclusion, this study confirmed the influence of the LINC02549 and LRRC55 loci to determine the response to TNFi in RA patients and suggested a weak effect of the MAFB and CNTN5 loci that need to be further investigated.
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Affiliation(s)
- Jose Manuel Sánchez-Maldonado
- Genomic Oncology Area, Centre for Genomics and Oncological Research (GENYO), Parque tecnológico de la Salud (PTS) Granada, Granada, Spain.,Hematology Department, Virgen de las Nieves University Hospital, Granada, Spain.,Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain
| | - Rafael Cáliz
- Genomic Oncology Area, Centre for Genomics and Oncological Research (GENYO), Parque tecnológico de la Salud (PTS) Granada, Granada, Spain.,Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain.,Department of Rheumatology, Virgen de las Nieves University Hospital, Granada, Spain
| | - Miguel Ángel López-Nevot
- Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain.,Immunology Department, Virgen de las Nieves University Hospital, Granada, Spain
| | - Antonio José Cabrera-Serrano
- Genomic Oncology Area, Centre for Genomics and Oncological Research (GENYO), Parque tecnológico de la Salud (PTS) Granada, Granada, Spain.,Hematology Department, Virgen de las Nieves University Hospital, Granada, Spain.,Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain
| | - Ana Moñiz-Díez
- Genomic Oncology Area, Centre for Genomics and Oncological Research (GENYO), Parque tecnológico de la Salud (PTS) Granada, Granada, Spain.,Hematology Department, Virgen de las Nieves University Hospital, Granada, Spain.,Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain
| | - Helena Canhão
- EpiDoC Unit, CEDOC, NOVA Medical School and National School of Public Health, Universidade Nova de Lisboa, Lisbon, Portugal.,Comprehensive Health Research Center (CHRC), NOVA Medical School, Lisbon, Portugal
| | - Rob Ter Horst
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Nijmegen Medical Center, Nijmegen, Netherlands
| | - Luca Quartuccio
- Department of Medical Area, Clinic of Rheumatology, University of Udine, Udine, Italy
| | - Signe B Sorensen
- Molecular Diagnostic and Clinical Research Unit, IRS-Center Sonderjylland, University Hospital of Southern Jutland, Aabenraa, Denmark.,Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Bente Glintborg
- The Danish Rheumatologic Biobank and Copenhagen Center for Arthritis Research (DANBIO) Registry, The Danish Rheumatologic Biobank and Copenhagen Center for Arthritis Research (COPECARE), Center for Rheumatology and Spine Diseases, Centre of Head and Orthopaedics, Rigshospitalet, Glostrup, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Merete L Hetland
- The Danish Rheumatologic Biobank and Copenhagen Center for Arthritis Research (DANBIO) Registry, The Danish Rheumatologic Biobank and Copenhagen Center for Arthritis Research (COPECARE), Center for Rheumatology and Spine Diseases, Centre of Head and Orthopaedics, Rigshospitalet, Glostrup, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ileana Filipescu
- Rheumatology Department, University of Medicine and Pharmacy "Iuliu Hatieganu", Cluj-Napoca, Romania
| | - Eva Pérez-Pampin
- Rheumatology Unit, University Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - Pablo Conesa-Zamora
- Clinical Analysis Department, Santa Lucía University Hospital, Cartagena, Spain
| | - Jerzy Swierkot
- Department of Rheumatology and Internal Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Alfons A den Broeder
- Radboud Institute for Health Sciences, Department of Rheumatology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Salvatore De Vita
- Department of Medical Area, Clinic of Rheumatology, University of Udine, Udine, Italy
| | - Eva Rabing Brix Petersen
- Department of Biochemistry and Immunology, University Hospital of Southern Jutland, Aabenraa, Denmark
| | - Yang Li
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Nijmegen Medical Center, Nijmegen, Netherlands.,Centre for Individualised Infection Medicine (CiiM) & Centre for Experimental and Clinical Infection Research (TWINCORE), Helmholtz-Centre for Infection Research (HZI) and The Hannover Medical School (MHH), Hannover, Germany
| | - Miguel A Ferrer
- Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain
| | - Alejandro Escudero
- Rheumatology Department, Reina Sofía Hospital/Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC)/University of Córdoba, Córdoba, Spain
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Nijmegen Medical Center, Nijmegen, Netherlands.,Department for Immunology & Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Marieke J H Coenen
- Radboud Institute for Health Sciences, Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Vibeke Andersen
- Department of Medical Area, Clinic of Rheumatology, University of Udine, Udine, Italy.,Molecular Diagnostic and Clinical Research Unit, IRS-Center Sonderjylland, University Hospital of Southern Jutland, Aabenraa, Denmark.,Institute of Regional Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - João E Fonseca
- Rheumatology and Metabolic Bone Diseases Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHLN), Lisbon, Portugal.,Rheumatology Research Unit, Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Lisbon Academic Medical Center, Lisbon, Portugal
| | - Manuel Jurado
- Genomic Oncology Area, Centre for Genomics and Oncological Research (GENYO), Parque tecnológico de la Salud (PTS) Granada, Granada, Spain.,Hematology Department, Virgen de las Nieves University Hospital, Granada, Spain.,Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain
| | - Katarzyna Bogunia-Kubik
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Eduardo Collantes
- Rheumatology Department, Reina Sofía Hospital/Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC)/University of Córdoba, Córdoba, Spain
| | - Juan Sainz
- Genomic Oncology Area, Centre for Genomics and Oncological Research (GENYO), Parque tecnológico de la Salud (PTS) Granada, Granada, Spain.,Hematology Department, Virgen de las Nieves University Hospital, Granada, Spain.,Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain.,Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
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