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Dang H, Polineni D, Pace RG, Stonebraker JR, Corvol H, Cutting GR, Drumm ML, Strug LJ, O’Neal WK, Knowles MR. Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation. PLoS One 2020; 15:e0239189. [PMID: 33253230 PMCID: PMC7703903 DOI: 10.1371/journal.pone.0239189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/02/2020] [Indexed: 12/18/2022] Open
Abstract
Genome wide association studies (GWAS) have identified several genomic loci with candidate modifiers of cystic fibrosis (CF) lung disease, but only a small proportion of the expected genetic contribution is accounted for at these loci. We leveraged expression data from CF cohorts, and Genotype-Tissue Expression (GTEx) reference data sets from multiple human tissues to generate predictive models, which were used to impute transcriptional regulation from genetic variance in our GWAS population. The imputed gene expression was tested for association with CF lung disease severity. By comparing and combining results from alternative approaches, we identified 379 candidate modifier genes. We delved into 52 modifier candidates that showed consensus between approaches, and 28 of them were near known GWAS loci. A number of these genes are implicated in the pathophysiology of CF lung disease (e.g., immunity, infection, inflammation, HLA pathways, glycosylation, and mucociliary clearance) and the CFTR protein biology (e.g., cytoskeleton, microtubule, mitochondrial function, lipid metabolism, endoplasmic reticulum/Golgi, and ubiquitination). Gene set enrichment results are consistent with current knowledge of CF lung disease pathogenesis. HLA Class II genes on chr6, and CEP72, EXOC3, and TPPP near the GWAS peak on chr5 are most consistently associated with CF lung disease severity across the tissues tested. The results help to prioritize genes in the GWAS regions, predict direction of gene expression regulation, and identify new candidate modifiers throughout the genome for potential therapeutic development.
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Affiliation(s)
- Hong Dang
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
| | - Deepika Polineni
- University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Rhonda G. Pace
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
| | - Jaclyn R. Stonebraker
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
| | - Harriet Corvol
- Pediatric Pulmonary Department, Assistance Publique-Hôpitaux sde Paris (AP-HP), Hôpital Trousseau, Institut National de la Santé et la Recherche Médicale (INSERM) U938, Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC), Paris 6, Paris, France
| | - Garry R. Cutting
- McKusick-Nathans Institute of Genetic Medicine, Baltimore, Maryland, United States of America
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Mitchell L. Drumm
- Department of Pediatrics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Lisa J. Strug
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Wanda K. O’Neal
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
| | - Michael R. Knowles
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
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Ye J, Xu B, Fan B, Zhang J, Yuan F, Chen Y, Sun Z, Yan X, Song Y, Song S, Yang M, Yu JK. Discovery of Selenocysteine as a Potential Nanomedicine Promotes Cartilage Regeneration With Enhanced Immune Response by Text Mining and Biomedical Databases. Front Pharmacol 2020; 11:1138. [PMID: 32792959 PMCID: PMC7394085 DOI: 10.3389/fphar.2020.01138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/13/2020] [Indexed: 12/21/2022] Open
Abstract
Background Unlike bone tissue, little progress has been made regarding cartilage regeneration, and many challenges remain. Furthermore, the key roles of cartilage lesion caused by traumas, focal lesion, or articular overstress remain unclear. Traumatic injuries to the meniscus as well as its degeneration are important risk factors for long-term joint dysfunction, degenerative joint lesions, and knee osteoarthritis (OA) a chronic joint disease characterized by degeneration of articular cartilage and hyperosteogeny. Nearly 50% of the individuals with meniscus injuries develop OA over time. Due to the limited inherent self-repair capacity of cartilage lesion, the Biomaterial drug-nanomedicine is considered to be a promising alternative. Therefore, it is important to elucidate the gene potential regeneration mechanisms and discover novel precise medication, which are identified through this study to investigate their function and role in pathogenesis. Methods We downloaded the mRNA microarray statistics GSE117999, involving paired cartilage lesion tissue samples from 12 OA patients and 12 patients from a control group. First, we analyzed these statistics to recognize the differentially expressed genes (DEGs). We then exposed the gene ontology (GO) annotation and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses for these DEGs. Protein-protein interaction (PPI) networks were then constructed, from which we attained eight significant genes after a functional interaction analysis. Finally, we identified a potential nanomedicine attained from this assay set, using a wide range of inhibitor information archived in the Search Tool for the Retrieval of Interacting Genes (STRING) database. Results Sixty-six DEGs were identified with our standards for meaning (adjusted P-value < 0.01, |log2 - FC| ≥1.2). Furthermore, we identified eight hub genes and one potential nanomedicine - Selenocysteine based on these integrative data. Conclusion We identified eight hub genes that could work as prospective biomarkers for the diagnostic and biomaterial drug treatment of cartilage lesion, involving the novel genes CAMP, DEFA3, TOLLIP, HLA-DQA2, SLC38A6, SLC3A1, FAM20A, and ANO8. Meanwhile, these genes were mainly associated with immune response, immune mediator induction, and cell chemotaxis. Significant support is provided for obtaining a series of novel gene targets, and we identify potential mechanisms for cartilage regeneration and final nanomedicine immunotherapy in regenerative medicine.
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Affiliation(s)
- Jing Ye
- Knee Surgery Department of the Institution of Sports Medicine, Peking University Third Hospital, Beijing Key Laboratory of Sports Injuries, Beijing, China
| | - Bingbing Xu
- Knee Surgery Department of the Institution of Sports Medicine, Peking University Third Hospital, Beijing Key Laboratory of Sports Injuries, Beijing, China
| | - Baoshi Fan
- School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Jiying Zhang
- Knee Surgery Department of the Institution of Sports Medicine, Peking University Third Hospital, Beijing Key Laboratory of Sports Injuries, Beijing, China
| | - Fuzhen Yuan
- Knee Surgery Department of the Institution of Sports Medicine, Peking University Third Hospital, Beijing Key Laboratory of Sports Injuries, Beijing, China
| | - Yourong Chen
- Knee Surgery Department of the Institution of Sports Medicine, Peking University Third Hospital, Beijing Key Laboratory of Sports Injuries, Beijing, China
| | - Zewen Sun
- Knee Surgery Department of the Institution of Sports Medicine, Peking University Third Hospital, Beijing Key Laboratory of Sports Injuries, Beijing, China
| | - Xin Yan
- Knee Surgery Department of the Institution of Sports Medicine, Peking University Third Hospital, Beijing Key Laboratory of Sports Injuries, Beijing, China
| | - Yifan Song
- Knee Surgery Department of the Institution of Sports Medicine, Peking University Third Hospital, Beijing Key Laboratory of Sports Injuries, Beijing, China
| | - Shitang Song
- Knee Surgery Department of the Institution of Sports Medicine, Peking University Third Hospital, Beijing Key Laboratory of Sports Injuries, Beijing, China
| | - Meng Yang
- School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Jia-Kuo Yu
- Knee Surgery Department of the Institution of Sports Medicine, Peking University Third Hospital, Beijing Key Laboratory of Sports Injuries, Beijing, China
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Husain Z, Kelly MA, Eisenbarth GS, Pugliese A, Awdeh ZL, Larsen CE, Alper CA. The MHC type 1 diabetes susceptibility gene is centromeric to HLA-DQB1. J Autoimmun 2007; 30:266-72. [PMID: 18065200 DOI: 10.1016/j.jaut.2007.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Revised: 10/19/2007] [Accepted: 10/19/2007] [Indexed: 10/22/2022]
Abstract
HLA-DQB1 is widely considered to be the major histocompatibility complex (MHC) susceptibility gene for type 1 diabetes (T1D). However, since inheritance of the gene in T1D is recessive, the presence of the protective HLA-DQB1 0602 allele with normal nucleotide sequence in some patients raises the question of whether HLA-DQB1 is not the susceptibility locus itself but merely a good marker. HLA-DQB1 0602 is part of a conserved extended haplotype (CEH) [HLA-B7, SC31, DR2] (B7, DR2) with fixed DNA over more than 1Mb of genomic DNA that normally carries a protective allele at the true susceptibility locus. We postulated that, in patients with HLA-DQB1 0602, the protective allele at the susceptibility locus has been replaced by a susceptibility allele through an ancient crossover at meiosis centromeric to HLA-DQB1. We analyzed single nucleotide polymorphisms (SNPs) distinguishing the HLA-DQA2 (the first expressed gene centromeric to HLA-DQB1) allele on the normal HLA-B7, DR2 CEH from those on susceptibility CEHs in T1D patients and controls with HLA-DQB1 0602. All but 1 of 20 healthy control HLA-DQB1 0602 haplotypes had identical (consensus) first intron HLA-DQA2 5-SNP haplotypes. Fifteen of 19 patients with HLA-DQB1 0602 were homozygous for 1 or more HLA-DQA2 SNPs differing from consensus HLA-DQA2 SNPs, providing evidence of crossover involving the HLA-DQA2 locus. The remaining 4 patients were heterozygous at all positions and therefore uninformative. The loss of dominant protection usually associated with HLA-DQB1 0602 haplotypes is consistent with a locus centromeric to HLA-DQB1 being a major determinant of MHC-associated susceptibility, and perhaps the true T1D susceptibility locus.
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Affiliation(s)
- Zaheed Husain
- Immune Disease Institute, 800 Huntington Avenue, Boston, MA 02115, USA
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