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Xie Q, Zhang Z, Chen Z, Sun J, Li M, Wang Q, Pan Y. Integration of Selection Signatures and Protein Interactions Reveals NR6A1, PAPPA2, and PIK3C2B as the Promising Candidate Genes Underlying the Characteristics of Licha Black Pig. BIOLOGY 2023; 12:biology12040500. [PMID: 37106701 PMCID: PMC10135650 DOI: 10.3390/biology12040500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Licha black (LI) pig has the specific characteristics of larger body length and appropriate fat deposition among Chinese indigenous pigs. Body length is one of the external traits that affect production performance, and fat deposition influences meat quality. However, the genetic characteristics of LI pigs have not yet been systematically uncovered. Here, the genomic information from 891 individuals of LI pigs, commercial pigs, and other Chinese indigenous pigs was used to analyze the breed characteristics of the LI pig with runs of homozygosity, haplotype, and FST selection signatures. The results showed the growth traits-related genes (i.e., NR6A1 and PAPPA2) and the fatness traits-related gene (i.e., PIK3C2B) were the promising candidate genes that closely related to the characteristics of LI pigs. In addition, the protein–protein interaction network revealed the potential interactions between the promising candidate genes and the FASN gene. The RNA expression data from FarmGTEx indicated that the RNA expression levels of NR6A1, PAPPA2, PIK3C2B, and FASN were highly correlated in the ileum. This study provides valuable molecular insights into the mechanisms that affect pig body length and fat deposition, which can be used in the further breeding process to improve meat quality and commercial profitability.
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Feng R, Lu M, Yin C, Xu K, Liu L, Xu P. Identification of candidate genes and pathways associated with juvenile idiopathic arthritis by integrative transcriptome-wide association studies and mRNA expression profiles. Arthritis Res Ther 2023; 25:19. [PMID: 36755318 PMCID: PMC9906884 DOI: 10.1186/s13075-023-03003-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
AIM Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic disease of childhood, with genetic susceptibility and pathological processes such as autoimmunity and autoinflammation, but its pathogenesis is unclear. We conducted a transcriptome-wide association study (TWAS) using expression interpolation from a large-scale genome-wide association study (GWAS) dataset to identify genes, biological pathways, and environmental chemicals associated with JIA. METHODS We obtained published GWAS data on JIA for TWAS and used mRNA expression profiling to validate the genes identified by TWAS. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. A protein-protein interaction (PPI) network was generated, and central genes were obtained using Molecular Complex Detection (MCODE). Finally, chemical gene expression datasets were obtained from the Comparative Toxicogenomics database for chemical genome enrichment analysis. RESULTS TWAS identified 1481 genes associated with JIA, and 154 differentially expressed genes were identified based on mRNA expression profiles. After comparing the results of TWAS and mRNA expression profiles, we obtained eight overlapping genes. GO and KEGG enrichment analyses of the genes identified by TWAS yielded 163 pathways, and PPI network analysis as well as MCODE resolution identified a total of eight clusters. Through chemical gene set enrichment analysis, 287 environmental chemicals associated with JIA were identified. CONCLUSION By integrating TWAS and mRNA expression profiles, genes, biological pathways, and environmental chemicals associated with JIA were identified. Our findings provide new insights into the pathogenesis of JIA, including candidate genetic and environmental factors contributing to its onset and progression.
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Affiliation(s)
- Ruoyang Feng
- grid.452452.00000 0004 1757 9282Department of Joint Surgery, HongHui Hospital, Xian Jiaotong University, Xi’an, 710054 Shanxi China
| | - Mengnan Lu
- grid.452672.00000 0004 1757 5804Department of Pediatrics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China
| | - Chunyan Yin
- grid.452672.00000 0004 1757 5804Department of Pediatrics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi China
| | - Ke Xu
- grid.452452.00000 0004 1757 9282Department of Joint Surgery, HongHui Hospital, Xian Jiaotong University, Xi’an, 710054 Shanxi China
| | - Lin Liu
- grid.452452.00000 0004 1757 9282Department of Joint Surgery, HongHui Hospital, Xian Jiaotong University, Xi’an, 710054 Shanxi China
| | - Peng Xu
- Department of Joint Surgery, HongHui Hospital, Xian Jiaotong University, Xi'an, 710054, Shanxi, China.
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Drummer DJ, Lavin KM, Graham ZA, O'Bryan SM, McAdam JS, Lixandrão ME, Seay R, Aban I, Siegel HJ, Ghanem E, Singh JA, Bonfitto A, Antone J, Reiman R, Hutchins E, Van Keuren-Jensen K, Schutzler SE, Barnes CL, Ferrando AA, Bridges SL, Bamman MM. Muscle transcriptomic circuits linked to periarticular physiology in end-stage osteoarthritis. Physiol Genomics 2022; 54:501-513. [PMID: 36278270 PMCID: PMC9762959 DOI: 10.1152/physiolgenomics.00092.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/08/2022] [Accepted: 10/20/2022] [Indexed: 02/01/2023] Open
Abstract
The ability of individuals with end-stage osteoarthritis (OA) to functionally recover from total joint arthroplasty is highly inconsistent. The molecular mechanisms driving this heterogeneity have yet to be elucidated. Furthermore, OA disproportionately impacts females, suggesting a need for identifying female-specific therapeutic targets. We profiled the skeletal muscle transcriptome in females with end-stage OA (n = 20) undergoing total knee or hip arthroplasty using RNA-Seq. Single-gene differential expression (DE) analyses tested for DE genes between skeletal muscle overlaying the surgical (SX) joint and muscle from the contralateral (CTRL) leg. Network analyses were performed using Pathway-Level Information ExtractoR (PLIER) to summarize genes into latent variables (LVs), i.e., gene circuits, and link them to biological pathways. LV differences in SX versus CTRL muscle and across sources of muscle tissue (vastus medialis, vastus lateralis, or tensor fascia latae) were determined with ANOVA. Linear models tested for associations between LVs and muscle phenotype on the SX side (inflammation, function, and integrity). DE analysis revealed 360 DE genes (|Log2 fold-difference| ≥ 1, FDR ≤ 0.05) between the SX and CTRL limbs, many associated with inflammation and lipid metabolism. PLIER analyses revealed circuits associated with protein degradation and fibro-adipogenic cell gene expression. Muscle inflammation and function were linked to an LV associated with endothelial cell gene expression highlighting a potential regulatory role of endothelial cells within skeletal muscle. These findings may provide insight into potential therapeutic targets to improve OA rehabilitation before and/or following total joint replacement.
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Affiliation(s)
- Devin J Drummer
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kaleen M Lavin
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Florida Institute for Human and Machine Cognition, Pensacola, Florida
| | - Zachary A Graham
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Florida Institute for Human and Machine Cognition, Pensacola, Florida
- Birmingham VA Medical Center, Birmingham, Alabama
| | - Samia M O'Bryan
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jeremy S McAdam
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Florida Institute for Human and Machine Cognition, Pensacola, Florida
| | - Manoel E Lixandrão
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado
| | - Regina Seay
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Inmaculada Aban
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Herrick J Siegel
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Orthopaedic Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Elie Ghanem
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Orthopaedic Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jasvinder A Singh
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Birmingham VA Medical Center, Birmingham, Alabama
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Comprehensive Arthritis, Musculoskeletal, Bone, and Autoimmunity Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Anna Bonfitto
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Jerry Antone
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Rebecca Reiman
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Elizabeth Hutchins
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, Arizona
| | | | - Scott E Schutzler
- Department of Geriatrics and Center for Translational Research in Aging and Longevity, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - C Lowry Barnes
- Department of Orthopaedic Surgery, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Arny A Ferrando
- Department of Geriatrics and Center for Translational Research in Aging and Longevity, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - S Louis Bridges
- Department of Medicine, Hospital for Special Surgery, New York, New York
- Division of Rheumatology, Weill Cornell Medical Center, New York, New York
| | - Marcas M Bamman
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Florida Institute for Human and Machine Cognition, Pensacola, Florida
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Wang W, Ou Z, Peng J, Zhou Y, Wang N. A transcriptome-wide association study provides new insights into the etiology of osteoarthritis. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1116. [PMID: 36388797 PMCID: PMC9652510 DOI: 10.21037/atm-22-4471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/09/2022] [Indexed: 11/23/2022]
Abstract
Background Osteoarthritis (OA) is a common clinical disease caused by a variety of factors, including genetic variants. Although genome-wide association studies (GWAS) have been performed to elucidate the genetic basis of OA, some loci of risk located in noncoding regions of the genome have been neglected. Therefore, we integrated multiple data types to detect the genetic component of gene expression in OA patients through transcriptome-wide association studies (TWAS) and summary-data-based Mendelian randomization (SMR) analysis. Methods TWAS was performed by integrating the larger GWAS summary-data for OA (n=30,727 cases, n=297,191 controls) and 2 expression weight sets (muscle-skeletal tissue and whole blood). Colocalization analysis, conditional analysis, and fine-mapping analysis were also conducted. A broad description of the identified associations was obtained. In addition, a causal relationship between certain risk genes and OA was identified with SMR. Results New significant genome-wide associations were found, including on chromosome 1q36.12 (rs1555024, P=4.24E-07) near the ASAP3 and TCEA3 genes, on chromosome 17q24.2 (rs2521348, P=1.01E-06) near the ABCA9 gene, on chromosome 20q11.22 (rs224331, P=8.17E-09) near the UQCC1 and MYH7B genes, and on chromosome 21q21.3 (rs2832155, P=5.39E-08) near the RWDD2B gene. In addition, SMR results exhibited that upregulated UQCC1 and downregulated ASAP3 were associated with OA development and both had a significant causal relationship with OA. Conclusions We revealed some novel OA-associated genes and risk loci by integrating multiple data types and analysis methods, thus providing new clues for the study of genetic mechanisms of OA.
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Affiliation(s)
- Weiwei Wang
- Department of Osteoarthritis and Sports Medicine, Ruikang Hospital Affiliated to Guangxi University of Traditional Chinese Medicine, Nanning, China
| | - Zhixue Ou
- Department of Osteoarthritis and Sports Medicine, Guilin Hospital of Traditional Chinese Medicine, Guilin, China
| | - Jianlan Peng
- Department of Osteoarthritis and Sports Medicine, Ruikang Hospital Affiliated to Guangxi University of Traditional Chinese Medicine, Nanning, China
| | - Yi Zhou
- Department of Osteoarthritis and Sports Medicine, Ruikang Hospital Affiliated to Guangxi University of Traditional Chinese Medicine, Nanning, China
| | - Ning Wang
- Department of Massage, The First Affiliated Hospital of Guangxi University of Traditional Chinese Medicine, Nanning, China
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Lu M, Feng R, Liu Y, Qin Y, Deng H, Xiao Y, Yin C. Identifying celiac disease-related chemicals by transcriptome-wide association study and chemical-gene interaction analyses. Front Genet 2022; 13:990483. [PMID: 36118884 PMCID: PMC9478571 DOI: 10.3389/fgene.2022.990483] [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: 08/16/2022] [Indexed: 11/22/2022] Open
Abstract
Celiac disease (CeD) is one of the most common intestinal inflammatory diseases, and its incidence and prevalence have increased over time. CeD affects multiple organs and systems in the body, and environmental factors play a key role in its complex pathogenesis. Although gluten exposure is known to be the causative agent, many unknown environmental factors can trigger or exacerbate CeD. In this study, we investigated the influence of genetic and environmental factors on CeD. Data from a CeD genome-wide association study that included 12,041 CeD cases and 12,228 controls were used to conduct a transcriptome-wide association study (TWAS) using FUSION software. Gene expression reference data were obtained for the small intestine, whole blood, peripheral blood, and lymphocytes. We performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses using the significant genes identified by the TWAS and conducted a protein–protein interaction network analysis based on the STRING database to detect the function of TWAS-identified genes for CeD. We also performed a chemical-related gene set enrichment analysis (CGSEA) using the TWAS-identified genes to test the relationships between chemicals and CeD. The TWAS identified 8,692 genes, including 101 significant genes (padjusted < 0.05). The CGSEA identified 2,559 chemicals, including 178 chemicals that were significantly correlated with CeD. This study performed a TWAS (for genetic factors) and CGSEA (for environmental factors) and identified several CeD-associated genes and chemicals. The findings expand our understanding of the genetic and environmental factors related to immune-mediated diseases.
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Affiliation(s)
- Mengnan Lu
- Department of Pediatrics, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Ruoyang Feng
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiao Tong University, Xi’an, China
| | - Yuesheng Liu
- Department of Pediatrics, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Yujie Qin
- Department of Pediatrics, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Hongyang Deng
- Department of Pediatrics, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Yanfeng Xiao
- Department of Pediatrics, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
- *Correspondence: Yanfeng Xiao, ; Chunyan Yin,
| | - Chunyan Yin
- Department of Pediatrics, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
- *Correspondence: Yanfeng Xiao, ; Chunyan Yin,
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Ni J, Wang P, Yin KJ, Yang XK, Cen H, Sui C, Wu GC, Pan HF. Novel insight into the aetiology of rheumatoid arthritis gained by a cross-tissue transcriptome-wide association study. RMD Open 2022; 8:e002529. [PMID: 37582060 PMCID: PMC9462377 DOI: 10.1136/rmdopen-2022-002529] [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: 06/24/2022] [Accepted: 08/23/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Although genome-wide association studies (GWASs) have identified more than 100 loci associated with rheumatoid arthritis (RA) susceptibility, the causal genes and biological mechanisms remain largely unknown. METHODS A cross-tissue transcriptome-wide association study (TWAS) using the unified test for molecular signaturestool was performed to integrate GWAS summary statistics from 58 284 individuals (14 361 RA cases and 43 923 controls) with gene-expression matrix in the Genotype-Tissue Expression project. Subsequently, a single tissue by using FUSION software was conducted to validate the significant associations. We also compared the TWAS with different gene-based methodologies, including Summary Data Based Mendelian Randomization (SMR) and Multimarker Analysis of Genomic Annotation (MAGMA). Further in silico analyses (conditional and joint analysis, differential expression analysis and gene-set enrichment analysis) were used to deepen our understanding of genetic architecture and comorbidity aetiology of RA. RESULTS We identified a total of 47 significant candidate genes for RA in both cross-tissue and single-tissue test after multiple testing correction, of which 40 TWAS-identified genes were verified by SMR or MAGMA. Among them, 13 genes were situated outside of previously reported significant loci by RA GWAS. Both TWAS-based and MAGMA-based enrichment analyses illustrated the shared genetic determinants among autoimmune thyroid disease, asthma, type I diabetes mellitus and RA. CONCLUSION Our study unveils 13 new candidate genes whose predicted expression is associated with risk of RA, providing new insights into the underlying genetic architecture of RA.
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Affiliation(s)
- Jing Ni
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Peng Wang
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, China
| | - Kang-Jia Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Xiao-Ke Yang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Han Cen
- Department of Preventive Medicine, Ningbo University Medical School, Ningbo, Zhejiang, China
| | - Cong Sui
- Department of Orthopedics Trauma, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Guo-Cui Wu
- Department of Obstetrics and Gynecological Nursing, School of Nursing, Anhui Medical University, Hefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
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Feng R, Lu M, Yang Y, Luo P, Liu L, Xu K, Xu P. Genome- and transcriptome-wide association studies show that pulmonary embolism is associated with bone-forming proteins. Expert Rev Hematol 2022; 15:951-958. [PMID: 35848930 DOI: 10.1080/17474086.2022.2103534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Pulmonary embolism (PE) is a leading cause of death in stroke patients and a severe health burden worldwide. There is a pressing need to understand the mechanisms by which it occurs and to identify at-risk patients efficiently and accurately. OBJECTIVES The aim of this paper was to analyze the genetic correlation between PE and human plasma proteins through genome-wide association study (GWAS) with transcriptome-wide association study (TWAS), in combination with mRNA expression profiling at three levels: DNA, RNA, and protein. METHODS First, based on data from GWAS in European populations, we performed a linkage disequilibrium score regression (LDSC) analysis of plasma proteins and PE in 3,283 individuals and additionally analyzed the genetic association between PE and fracture. Then, we performed a TWAS on PE GWAS data using skeletal muscle and blood for gene expression references. Finally, we validated the genetic correlation between PE and human plasma proteins by co-matching the genes encoding the identified proteins and those identified using TWAS with the differentially expressed genes obtained from mRNA expression profiling of PE (Figure1). RESULTS We identified five plasma proteins associated with PE, including hydroxycarboxylic acid receptor 2, defensin 118, and bone morphogenetic protein (BMP) 7, as well as a relationship between PE and fracture. Comparison of genes encoding these proteins with genes obtained from TWAS and then with differentially expressed genes obtained from PE mRNA expression profiling revealed that PE was highly correlated with the BMP family of genes.
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Affiliation(s)
- Ruoyang Feng
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shanxi, 710054, China
| | - Mengnan Lu
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yanni Yang
- Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Pan Luo
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shanxi, 710054, China
| | - Lin Liu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shanxi, 710054, China
| | - Ke Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shanxi, 710054, China
| | - Peng Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shanxi, 710054, China
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Feng R, Lu M, Liu L, Xu K, Xu P. Transcriptome-Wide Association Studies and Integration Analysis of mRNA Expression Profiles Identify Candidate Genes and Pathways Associated With Ankylosing Spondylitis. Front Immunol 2022; 13:814303. [PMID: 35619696 PMCID: PMC9128383 DOI: 10.3389/fimmu.2022.814303] [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: 11/13/2021] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
This study aimed to identify susceptibility genes and pathways associated with ankylosing spondylitis (AS) by integrating whole transcriptome-wide association study (TWAS) analysis and mRNA expression profiling data. AS genome-wide association study (GWAS) summary data from the large GWAS database were used. This included data of 1265 AS patients and 452264 controls. A TWAS of AS was conducted using these data. The analysis software used was FUSION, and Epstein-Barr virus–transformed lymphocytes, transformed fibroblasts, peripheral blood, and whole blood were used as gene expression references. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed for the important genes identified via TWAS. Protein-protein interaction (PPI) network analysis based on the STRING database was also performed to detect genes shared by TWAS and mRNA expression profiles in AS. TWAS identified 920 genes (P <0.05) and analyzed mRNA expression profiles to obtain 1183 differential genes. Following comparison of the TWAS results and mRNA expression characteristics, we obtained 70 overlapping genes and performed GO and KEGG enrichment analyses of these genes to obtain 16 pathways. Via PPI network analysis, we obtained the protein interaction network and performed MCODE analysis to acquire the HUB genes. Similarly, we performed GO and KEGG analyses on the genes identified by TWAS, obtained 98 pathways after screening, and analyzed protein interactions via the PPI network. Through the integration of TWAS and mRNA expression analysis, genes related to AS and GO and KEGG terms were determined, providing new evidence and revealing the pathogenesis of AS. Our AS TWAS work identified novel genes associated with AS, as well as suggested potential tissues and pathways of action for these TWAS AS genes, providing a new direction for research into the pathogenesis of AS.
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Affiliation(s)
- Ruoyang Feng
- Department of Joint Surgery, HongHui Hospital, Xian Jiaotong University, Xi'an, China
| | - Mengnan Lu
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lin Liu
- Department of Joint Surgery, HongHui Hospital, Xian Jiaotong University, Xi'an, China
| | - Ke Xu
- Department of Joint Surgery, HongHui Hospital, Xian Jiaotong University, Xi'an, China
| | - Peng Xu
- Department of Joint Surgery, HongHui Hospital, Xian Jiaotong University, Xi'an, China
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Huan C, Gao J. Insight into the potential pathogenesis of human osteoarthritis via single-cell RNA sequencing data on osteoblasts. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:6344-6361. [PMID: 35603405 DOI: 10.3934/mbe.2022297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Osteoarthritis (OA) is the most common degenerative joint disease caused by osteoblastic lineage cells. However, a comprehensive molecular program for osteoblasts in human OA remains underdeveloped. The single-cell gene expression of osteoblasts and microRNA array data were from human. After processing the single-cell RNA sequencing (scRNA-seq) data, it was subjected to principal component analysis (PCA) and T-Stochastic neighbor embedding analysis (TSNE). Differential expression analysis was aimed to find marker genes. Gene-ontology (GO) enrichment, Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis and Gene set enrichment analysis (GSEA) were applied to characterize the molecular function of osteoblasts with marker genes. Protein-protein interaction (PPI) networks and core module were established for marker genes by using the STRING database and Cytoscape software. All nodes in the core module were considered to be hub genes. Subsequently, we predicted the potential miRNA of hub genes through the miRWalk, miRDB and TargetScan database and experimentally verified the miRNA by GSE105027. Finally, miRNA-mRNA regulatory network was constructed using the Cytoscape software. We characterized the single-cell expression profiling of 4387 osteoblasts from normal and OA sample. The proportion of osteoblasts subpopulations changed dramatically in the OA, with 70.42% of the pre-osteoblasts. 117 marker genes were included and the results of GO analysis show that up-regulated marker genes enriched in collagen-containing extracellular matrix were highly expressed in the pre-osteoblasts cluster. Both KEGG and GSEA analyses results indicated that IL-17 and NOD-like receptor signaling pathways were enriched in down-regulated marker genes. We visualize the weight of marker genes and constructed the core module in PPI network. In potential mRNA-miRNA regulatory network, hsa-miR-449a and hsa-miR-218-5p may be involved in the development of OA. Our study found that alterations in osteoblasts state and cellular molecular function in the subchondral bone region may be involved in the pathogenesis of osteoarthritis.
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Affiliation(s)
- Changxiang Huan
- Zhongshan Clinical Collage of Dalian University, Dalian 116000, China
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Cao J, Ding H, Shang J, Ma L, Wang Q, Feng S. Weighted gene co-expression network analysis reveals specific modules and hub genes related to immune infiltration of osteoarthritis. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1525. [PMID: 34790731 PMCID: PMC8576690 DOI: 10.21037/atm-21-4566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/19/2021] [Indexed: 12/26/2022]
Abstract
Background The incidence of osteoarthritis (OA), a chronic degenerative disease, is increasing every year. There is no effective clinical treatment for OA and the pathological mechanism remains unclear. Early diagnosis is an effective strategy to control the progress of OA. In this study, we aimed to identify potential early diagnostic biomarkers. Methods We downloaded the gene expression profile dataset, GSE51588 and GSE55235, from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) public database. The differentially expressed genes (DEGs) were screened out using the “limma” R package. Weighted gene co-expression network analysis (WGCNA) was utilized to build the co-expression network between the normal and OA samples. A Venn diagram was constructed to detect the hub genes. Potential molecular mechanisms and signaling pathways were enriched by gene set variation analysis (GSVA). Single sample gene set enrichment analysis (ssGSEA) was used to identify the immune infiltration of OA. Results We screened out three hub genes based on WGCNA and DEGs in this study. GSVA results showed that nuclear factor interleukin-3 (NFIL3) was related to tumor necrosis factor alpha (TNF-α) signaling via nuclear factor kappa-B (NF-κB), the reactive oxygen species pathway, and myelocytomatosis (MYC) targets v2. Highly-expressed ADM (adrenomedullin) pathways included TNF-α signaling via NF-κB, the reactive oxygen species pathway, and ultraviolet (UV) response up. OGN (osteoglycin)-enriched pathways included epithelial mesenchymal transition, coagulation, and peroxisome. Conclusions We identified three hub genes (NFIL3, ADM, and OGN) that were correlated to the development and progression of OA, which may provide new biomarkers for early diagnosis.
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Affiliation(s)
- Jiangang Cao
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Han Ding
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Jun Shang
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Lei Ma
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Qi Wang
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Shiqing Feng
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
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Li C, Zheng Z. Males and Females Have Distinct Molecular Events in the Articular Cartilage during Knee Osteoarthritis. Int J Mol Sci 2021; 22:ijms22157876. [PMID: 34360640 PMCID: PMC8346087 DOI: 10.3390/ijms22157876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/15/2021] [Accepted: 07/21/2021] [Indexed: 12/25/2022] Open
Abstract
Osteoarthritis (OA) is a major public health challenge that imposes a remarkable burden on the affected individuals and the healthcare system. Based on the clinical observation, males and females have different prevalence rates and severity levels of OA. Thus, sex-based differences may play essential roles in OA’s prognosis and treatment outcomes. To date, the comprehensive understanding of the relationship between sex and OA is still largely lacking. In the current study, we analyzed a published transcriptome dataset of knee articular cartilage (GSE114007) from 18 healthy (five females, 13 males) and 20 OA (11 females, nine males) donors to provide a slight insight into this important but complex issue. First, comparing female healthy cartilage samples with those of males revealed 36 differential expression genes (DEGs), indicating the fundamental sex-related differences at the molecular level. Meanwhile, 923 DEGs were distinguished between OA and healthy female cartilage, which can be enriched to 15 Reactome pathways. On the other hand, when comparing OA and healthy male cartilage, there are only 419 DEGs were identified, and only six pathways were enriched against the Reactome database. The different signaling response to OA in the male and female cartilage was further enforced by recognizing 50 genes with significantly different OA-responsive expression fold changes in males and females. Particularly, 14 Reactome pathways, such as “Extracellular matrix organization”, “Collagen biosynthesis and modifying enzymes”, “Dissolution of fibrin clot”, and “Platelet Aggregation (Plug formation)”, can be noted from these 50 sex-dependent OA-responsive genes. Overall, the current study explores the Sex as a Biological Variable (SABV) at the transcriptomic level in the knee articular cartilage in both healthy status and OA event, which could help predict the differential OA prognosis and treatment outcome of males and female patients.
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Affiliation(s)
- Chenshuang Li
- Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Zhong Zheng
- Division of Growth and Development, Section of Orthodontics, School of Dentistry, University of California, Los Angeles, CA 90095, USA
- Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Correspondence: ; Tel.: +1-(310)-206-5646
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