title: New genes associated with rheumatoid arthritis identified by gene expression profiling.
abstract: In this study, we aimed to find new genes associated with rheumatoid arthritis (RA) so that more comprehensive genes would be used for monitoring and/or diagnosing patients. Illumina digital gene expression profiling was applied in two sample types - peripheral blood mononuclear cells (PBMCs) and synovial cells to compare the gene expression pattern between 17 patients with RA and three control groups (six osteoarthritis patients, three ankylosing spondylitis patients and 17 healthy controls). Bioinformatics was performed on pathway analysis and protein-protein interaction networks. Four novel genes from PBMCs - DHRS3, TTC38, SAP30BP and LPIN2 - were found to be associated with RA and further confirmed through quantitative real-time polymerase chain reaction. Five new differentially expressed genes (EPYC, LIFR, GLDN, TADA3 and ZNRF3) found in synovial cells were not confirmed. Pathway analyses revealed 10 significantly enriched pathways, and a protein-protein interaction network analysis showed that four novel PBMC-derived genes were connected to previously reported genes by four intermediate genes. Therefore, we proposed that four newly identified PBMC-derived genes could be integrated with previously reported RA-associated genes to monitor and/or diagnose RA.
authors.affiliation: The Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: H
authors.identifier: http://orcid.org/0000-0002-6894-0571
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing, China.
authors.forename: J
authors.initials: J
authors.lastname: Guo
authors.affiliation: The Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: J
authors.initials: J
authors.lastname: Jiang
authors.affiliation: The Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: W
authors.initials: W
authors.lastname: Wu
authors.affiliation: Department of Rheumatology and Immunology, Qianfoshan Hospital, Jinan, China.
authors.forename: X
authors.initials: X
authors.lastname: Chang
authors.affiliation: Department of Rheumatology and Immunology, Shenzhen Second People's Hospital, Shenzhen, China.
authors.forename: H
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing, China.
authors.forename: Z
authors.initials: Z
authors.lastname: Li
authors.affiliation: The Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: J
authors.initials: J
authors.lastname: Zhao
mesh_terms: D000328:Adult; D000429:Alcohol Oxidoreductases / Q000235:genetics*; D001172:Arthritis, Rheumatoid / Q000235:genetics* / Q000503:physiopathology; D002352:Carrier Proteins / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation / Q000235:genetics; D020022:Genetic Predisposition to Disease; D064368:Healthy Volunteers; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000378:metabolism; D008297:Male; D008875:Middle Aged; D009687:Nuclear Proteins / Q000235:genetics*; D010003:Osteoarthritis / Q000235:genetics / Q000503:physiopathology; D060066:Protein Interaction Maps / Q000235:genetics; D015398:Signal Transduction; D013167:Spondylitis, Ankylosing / Q000235:genetics / Q000503:physiopathology; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D002352:Carrier Proteins; C502575:LPIN2 protein, human; D009687:Nuclear Proteins; C500210:SAP30BP protein, human; D014157:Transcription Factors; C000625319:tetratricopeptide repeat protein 38, human; D000429:Alcohol Oxidoreductases
keywords: PBMCs; RA-associated; case/control; differentially expressed genes (DEGs); gene expression; rheumatoid arthritis