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Elshazli RM, Elsaid AM, Shawky DM, Barakat LAA. Genetic polymorphisms of ACE I/D, IL-1β G > A and IL-4 VNTR among Egyptian subjects with rheumatoid arthritis. Arch Physiol Biochem 2022; 128:576-585. [PMID: 31830807 DOI: 10.1080/13813455.2019.1703005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Various reports examined the contribution of ACE I/D, IL-1β G > A and IL-4 VNTR with the susceptibility to RA but with conflicting findings. The goal of this study is to assess the impact of these three variants with the susceptibility, clinical and biochemical markers in addition to different composite indices of RA. SUBJECTS AND METHODS This case-control survey enclosed 120 RA Egyptian patients who were emulated with 150 healthy controls from the same territory. Their genomic DNA was genotyped utilising the PCR approach. RESULTS RA patients with ACE allele (D) and IL-4 VNTR allele (2 R) were expressively higher emulated with healthy controls (p < .05). Nevertheless, RA patients with IL-1β (A allele) failed to achieve an apparent significant emulated with healthy controls (p > .05). CONCLUSIONS This work specifies a noteworthy association for ACE I/D and IL-4 VNTR but not IL-1β G > A polymorphisms with RA susceptibility among Egyptian subjects.
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Affiliation(s)
- Rami M Elshazli
- Department of Biochemistry, Faculty of Physical Therapy, Horus University - Egypt, New Damietta, Egypt
| | - Afaf M Elsaid
- Genetic Unit, Children Hospital, Mansoura University, Mansoura, Egypt
| | - Doaa M Shawky
- Department of Chemistry, Faculty of Science, Port Said University, Port Said, Egypt
| | - Lamiaa A A Barakat
- Department of Chemistry, Faculty of Science, Port Said University, Port Said, Egypt
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2
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Milchram L, Fischer A, Huber J, Soldo R, Sieghart D, Vierlinger K, Blüml S, Steiner G, Weinhäusel A. Functional Analysis of Autoantibody Signatures in Rheumatoid Arthritis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27041452. [PMID: 35209238 PMCID: PMC8876797 DOI: 10.3390/molecules27041452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/11/2022] [Accepted: 02/18/2022] [Indexed: 11/21/2022]
Abstract
For the identification of antigenic protein biomarkers for rheumatoid arthritis (RA), we conducted IgG profiling on high density protein microarrays. Plasma IgG of 96 human samples (healthy controls, osteoarthritis, seropositive and seronegative RA, n = 24 each) and time-series plasma of a pristane-induced arthritis (PIA) rat model (n = 24 total) were probed on AIT’s 16k protein microarray. To investigate the analogy of underlying disease pathways, differential reactivity analysis was conducted. A total of n = 602 differentially reactive antigens (DIRAGs) at a significance cutoff of p < 0.05 were identified between seropositive and seronegative RA for the human samples. Correlation with the clinical disease activity index revealed an inverse correlation of antibodies against self-proteins found in pathways relevant for antigen presentation and immune regulation. The PIA model showed n = 1291 significant DIRAGs within acute disease. Significant DIRAGs for (I) seropositive, (II) seronegative and (III) PIA were subjected to the Reactome pathway browser which also revealed pathways relevant for antigen presentation and immune regulation; of these, seven overlapping pathways had high significance. We therefore conclude that the PIA model reflects the biological similarities of the disease pathogenesis. Our data show that protein array analysis can elucidate biological differences and pathways relevant in disease as well be a useful additional layer of omics information.
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Affiliation(s)
- Lisa Milchram
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Anita Fischer
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
| | - Jasmin Huber
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Regina Soldo
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Daniela Sieghart
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
| | - Klemens Vierlinger
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Stephan Blüml
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
| | - Günter Steiner
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria
| | - Andreas Weinhäusel
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
- Correspondence:
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3
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Liu J, Chen N. A 9 mRNAs-based diagnostic signature for rheumatoid arthritis by integrating bioinformatic analysis and machine-learning. J Orthop Surg Res 2021; 16:44. [PMID: 33430905 PMCID: PMC7802293 DOI: 10.1186/s13018-020-02180-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/25/2020] [Indexed: 01/22/2023] Open
Abstract
Background Rheumatoid arthritis (RA) is an autoimmune rheumatic disease that carries a substantial burden for both patients and society. Early diagnosis of RA is essential to prevent disease progression and select an optimal therapeutic strategy. However, RA diagnosis is challenging, partly due to a lack of reliable biomarkers. Here, we aimed to explore the diagnostic signature and establish a predictive model of RA. Methods The mRNA expression profiling data of GSE17755, containing blood samples of 112 RA patients and 53 healthy control patients, were obtained from the Gene Expression Omnibus (GEO) database, followed by differential expression, GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis. A PPI network was constructed to select candidate hub genes, then logistic regression and random forest models were established based on the identified genes. Results Significantly, we identified 52 differentially expressed genes (DEGs), including 16 upregulated genes and 36 downregulated genes in RA samples compared with control samples. GO and KEGG analysis showed that several immune-related cellular processes were particularly enriched. We identified nine hub genes in the PPI network, including CFL1, COTL1, ACTG1, PFN1, LCP1, LCK, HLA-E, FYN, and HLA-DRA. The logistic regression and random forest models based on the nine identified genes reliably distinguished the RA samples from the healthy samples with substantially high AUC. Conclusion The diagnostic logistic regression and random forest models based on nine hub genes reliably predicted the occurrence of RA. Our findings could provide new insights into RA diagnostics. Supplementary Information The online version contains supplementary material available at 10.1186/s13018-020-02180-w.
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Affiliation(s)
- Jianyong Liu
- The First Department of Joint Surgery, Weifang People's Hospital Shandong Province (The First Affiliated Hospital of Weifang University), Weifang, 261041, Shandong, China
| | - Ningjie Chen
- The Department of Joint Surgery, Zibo Central Hospital, Shandong University, No 54 Gongqingtuan West Road, Zibo, 255036, Shandong, China.
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4
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Yu K, Davidson CE, Burshtyn DN. LILRB1 Intron 1 Has a Polymorphic Regulatory Region That Enhances Transcription in NK Cells and Recruits YY1. THE JOURNAL OF IMMUNOLOGY 2020; 204:3030-3041. [PMID: 32321755 DOI: 10.4049/jimmunol.2000164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/31/2020] [Indexed: 12/11/2022]
Abstract
LILRB1 is a highly polymorphic receptor expressed by subsets of innate and adaptive immune cells associated with viral and autoimmune diseases and targeted by pathogens for immune evasion. LILRB1 expression on human NK cells is variegated, and the frequency of LILRB1+ cells differs among people. However, little is known about the processes and factors mediating LILRB1 transcription in NK cells. LILRB1 gene expression in lymphoid and myeloid cells arises from two distinct promoters that are separated by the first exon and intron. In this study, we identified a polymorphic 3-kb region within LILRB1 intron 1 that is epigenetically marked as an active enhancer in human lymphoid cells and not monocytes. This region possesses multiple YY1 sites, and complexes of the promoter/enhancer combination were isolated using anti-YY1 in chromatin immunoprecipitation-loop. CRISPR-mediated deletion of the 3-kb region lowers LILRB1 expression in human NKL cells. Together, these results indicate the enhancer in intron 1 binds YY1 and suggest YY1 provides a scaffold function enabling enhancer function in regulating LILRB1 gene transcription in human NK cells.
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Affiliation(s)
- Kang Yu
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Chelsea E Davidson
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Deborah N Burshtyn
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2S2, Canada; .,Alberta Transplant Institute, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; and.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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5
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Siegel RJ, Bridges SL, Ahmed S. HLA-C: An Accomplice in Rheumatic Diseases. ACR Open Rheumatol 2019; 1:571-579. [PMID: 31777841 PMCID: PMC6858028 DOI: 10.1002/acr2.11065] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/08/2019] [Indexed: 01/14/2023] Open
Abstract
Human leukocyte antigen c (HLA-C) is a polymorphic membrane protein encoded by the HLA-C gene in the class I major histocompatibility complex. HLA-C plays an essential role in protection against cancer and viruses but has also been implicated in allograft rejection, preeclampsia, and autoimmune disease. This review summarizes reports and proposed mechanisms for the accessory role of HLA-C in rheumatic diseases. Historically, contributions of HLA-C to rheumatic diseases were eclipsed by the stronger association with HLA-DRB1 alleles containing the "shared epitope" with rheumatoid arthritis. Larger genetic association studies and more powerful analytical approaches have revealed independent associations of HLA-C with rheumatic disease-associated phenotypes, including development of anticitrullinated peptide antibodies. HLA-C functions by presenting antigens to T cells and by binding activatory and inhibitory receptors on natural killer (NK) cells, but the exact mechanisms by which the HLA-C locus contributes to autoimmunity are largely undefined. Studies have suggested that HLA-C and NK cell receptor polymorphisms may predict responsiveness to pharmacotherapy. Understanding the mechanisms of the role of HLA-C in rheumatic disease could uncover therapeutic targets or guide precision pharmacologic treatments.
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Affiliation(s)
- Ruby J. Siegel
- Department of Pharmaceutical SciencesWashington State University College of Pharmacy and Pharmaceutical SciencesSpokaneWashington
| | - S. Louis Bridges
- Division of Clinical Immunology and RheumatologyUniversity of Alabama at BirminghamBirminghamAlabama
| | - Salahuddin Ahmed
- Department of Pharmaceutical SciencesWashington State University College of Pharmacy and Pharmaceutical SciencesSpokaneWashington
- Division of RheumatologyUniversity of Washington School of MedicineSeattleWashington
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Bradford AM, Koirala R, Park CK, Lyons BA. Characterization of the full-length human Grb7 protein and a phosphorylation representative mutant. J Mol Recognit 2019; 32:e2803. [PMID: 31353673 DOI: 10.1002/jmr.2803] [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: 11/10/2022]
Abstract
It is well known the dimerization state of receptor tyrosine kinases (RTKs), in conjunction with binding partners such as the growth factor receptor bound protein 7 (Grb7) protein, plays an important role in cell signaling regulation. Previously, we proposed, downstream of RTKs, that the phosphorylation state of Grb7SH2 domain tyrosine residues could control Grb7 dimerization, and dimerization may be an important regulatory step in Grb7 binding to RTKs. In this manner, additional dimerization-dependent regulation could occur downstream of the membrane-bound kinase in RTK-mediated signaling pathways. Extrapolation to the full-length (FL) Grb7 protein, and the ability to test this hypothesis further, has been hampered by the availability of large quantities of pure and stable FL protein. Here, we report the biophysical characterization of the FL Grb7 protein and also a mutant representing a tyrosine-phosphorylated Grb7 protein form. Through size exclusion chromatography and analytical ultracentrifugation, we show the phosphorylated-tyrosine-mimic Y492E-FL-Grb7 protein (Y492E-FL-Grb7) is essentially monomeric at expected physiological concentrations. It has been shown previously the wild-type FL Grb7(WT-FLGrb7) protein is dimeric with a dissociation constant (Kd) of approximately 11μM. Our studies here measure a FL protein dimerization Kd of WT-FL-Grb7 within one order of magnitude at approximately 1μM. The approximate size and shape of the WT-FL-Grb7 in comparison the tyrosine-phosphorylation mimic Y492E-FL-Grb7 protein was determined by dynamic light scattering methods. In vitro phosphorylation of the Grb7SH2 domain indicates only one of the available tyrosine residues is phosphorylated, suggesting the same phosphorylation pattern could be relevant in the FL protein. The biophysical characterization studies in total are interpreted with a view towards understanding the functionally active Grb7 protein conformation.
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Affiliation(s)
| | - Rajan Koirala
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, USA
| | - Chad K Park
- Analytical Biophysics Core, Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Barbara A Lyons
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, USA
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7
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Martin CL, Jima D, Sharp GC, McCullough LE, Park SS, Gowdy KM, Skaar D, Cowley M, Maguire RL, Fuemmeler B, Collier D, Relton CL, Murphy SK, Hoyo C. Maternal pre-pregnancy obesity, offspring cord blood DNA methylation, and offspring cardiometabolic health in early childhood: an epigenome-wide association study. Epigenetics 2019; 14:325-340. [PMID: 30773972 PMCID: PMC6557549 DOI: 10.1080/15592294.2019.1581594] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/03/2023] Open
Abstract
Pre-pregnancy obesity is an established risk factor for adverse sex-specific cardiometabolic health in offspring. Epigenetic alterations, such as in DNA methylation (DNAm), are a hypothesized link; however, sex-specific epigenomic targets remain unclear. Leveraging data from the Newborn Epigenetics Study (NEST) cohort, linear regression models were used to identify CpG sites in cord blood leukocytes associated with pre-pregnancy obesity in 187 mother-female and 173 mother-male offsprings. DNAm in cord blood was measured using the Illumina HumanMethylation450k BeadChip. Replication analysis was conducted among the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Associations between pre-pregnancy obesity-associated CpG sites and offspring BMI z-score (BMIz) and blood pressure (BP) percentiles at 4-5-years of age were also examined. Maternal pre-pregnacy obesity was associated with 876 CpGs in female and 293 CpGs in male offspring (false discovery rate <5%). Among female offspring, 57 CpG sites, including the top 18, mapped to the TAPBP gene (range of effect estimates: -0.83% decrease to 4.02% increase in methylation). CpG methylation differences in the TAPBP gene were also observed among males (range of effect estimates: -0.30% decrease to 2.59% increase in methylation). While technically validated, none of the TAPBP CpG sites were replicated in ALSPAC. In NEST, methylation differences at CpG sites of the TAPBP gene were associated with BMI z-score (cg23922433 and cg17621507) and systolic BP percentile (cg06230948) in female and systolic (cg06230948) and diastolic (cg03780271) BP percentile in male offspring. Together, these findings suggest sex-specific effects, which, if causal, may explain observed sex-specific effects of maternal obesity.
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Affiliation(s)
- Chantel L Martin
- a Department of Epidemiology , Gillings School of Global Public Health, University of North Carolina , Chapel Hill , NC , USA
| | - Dereje Jima
- b Center of Human Health and the Environment , North Carolina State University , Raleigh , USA
- c Bioinformatics Research Center , North Carolina State University , Raleigh , NC , USA
| | - Gemma C Sharp
- d Medical Research Integrative Epidemiology Unit , Bristol Medical School, Population Health Sciences, University of Bristol , Bristol , UK
| | - Lauren E McCullough
- e Department of Epidemiology , Rollins School of Public Health, Emory University , Atlanta , GA , USA
| | - Sarah S Park
- f Department of Biological Sciences , North Carolina State University , Raleigh , NC , USA
| | - Kymberly M Gowdy
- g Department of Pharmacology and Toxicology , Brody School of Medicine, East Carolina University , Greenville , NC , USA
| | - David Skaar
- f Department of Biological Sciences , North Carolina State University , Raleigh , NC , USA
| | - Michael Cowley
- f Department of Biological Sciences , North Carolina State University , Raleigh , NC , USA
| | - Rachel L Maguire
- f Department of Biological Sciences , North Carolina State University , Raleigh , NC , USA
| | - Bernard Fuemmeler
- h Department of Health Behavior and Policy , Virginia Commonwealth University , Richmond , VA , USA
| | - David Collier
- i Department of Pediatrics , Brody School of Medicine, East Carolina University , Greenville , NC , USA
| | - Caroline L Relton
- d Medical Research Integrative Epidemiology Unit , Bristol Medical School, Population Health Sciences, University of Bristol , Bristol , UK
| | - Susan K Murphy
- j Division of Reproductive Sciences, Department of Obstetrics and Gynecology , Duke University School of Medicine , Durham , NC , USA
| | - Cathrine Hoyo
- b Center of Human Health and the Environment , North Carolina State University , Raleigh , USA
- f Department of Biological Sciences , North Carolina State University , Raleigh , NC , USA
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8
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Dagle JM, Ryckman KK, Spracklen CN, Momany AM, Cotten CM, Levy J, Page GP, Bell EF, Carlo WA, Shankaran S, Goldberg RN, Ehrenkranz RA, Tyson JE, Stoll BJ, Murray JC. Genetic variants associated with patent ductus arteriosus in extremely preterm infants. J Perinatol 2019; 39:401-408. [PMID: 30518802 PMCID: PMC6391165 DOI: 10.1038/s41372-018-0285-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/07/2018] [Accepted: 11/16/2018] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Patent ductus arteriosus (PDA) is a commonly observed condition in preterm infants. Prior studies have suggested a role for genetics in determining spontaneous ductal closure. Using samples from a large neonatal cohort we tested the hypothesis that common genetic variations are associated with PDA in extremely preterm infants. STUDY DESIGN Preterm infants (n = 1013) enrolled at NICHD Neonatal Research Network sites were phenotyped for PDA. DNA was genotyped for 1634 single nucleotide polymorphisms (SNPs) from candidate genes. Analyses were adjusted for ancestral eigenvalues and significant epidemiologic variables. RESULTS SNPs in several genes were associated with the clinical diagnosis of PDA and with surgical ligation in extremely preterm neonates diagnosed with PDA (p < 0.01). None of the associations were significant after correction for multiple comparisons. CONCLUSION We identified several common genetic variants associated with PDA. These findings may inform further studies on genetic risk factors for PDA in preterm infants.
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Affiliation(s)
- John M Dagle
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA.
| | - Kelli K Ryckman
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | | | - Allison M Momany
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | | | - Joshua Levy
- Social, Statistical and Environmental Sciences Unit, RTI International, Research Triangle Park, Durham, NC, USA
| | - Grier P Page
- Social, Statistical and Environmental Sciences Unit, RTI International, Atlanta, GA, USA
| | - Edward F Bell
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Waldemar A Carlo
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Seetha Shankaran
- Department of Pediatrics, Wayne State University, Detroit, MI, USA
| | | | - Richard A Ehrenkranz
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Jon E Tyson
- Department of Pediatrics, University of Texas Medical School at Houston, Houston, TX, USA
| | - Barbara J Stoll
- Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
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Zhang X, Bu Y, Zhu B, Zhao Q, Lv Z, Li B, Liu J. Global transcriptome analysis to identify critical genes involved in the pathology of osteoarthritis. Bone Joint Res 2018; 7:298-307. [PMID: 29922448 PMCID: PMC5987685 DOI: 10.1302/2046-3758.74.bjr-2017-0245.r1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Objectives The aim of this study was to identify key pathological genes in osteoarthritis (OA). Methods We searched and downloaded mRNA expression data from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs) of joint synovial tissues from OA and normal individuals. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analyses were used to assess the function of identified DEGs. The protein-protein interaction (PPI) network and transcriptional factors (TFs) regulatory network were used to further explore the function of identified DEGs. The quantitative real-time polymerase chain reaction (qRT-PCR) was applied to validate the result of bioinformatics analysis. Electronic validation was performed to verify the expression of selected DEGs. The diagnosis value of identified DEGs was accessed by receiver operating characteristic (ROC) analysis. Results A total of 1085 DEGs were identified. KEGG pathway analysis displayed that Wnt was a significantly enriched signalling pathway. Some hub genes with high interactions such as USP46, CPVL, FKBP5, FOSL2, GADD45B, PTGS1, and ZNF423 were identified in the PPI and TFs network. The results of qRT-PCR showed that GADD45B, ADAMTS1, and TFAM were down-regulated in joint synovial tissues of OA, which was consistent with the bioinformatics analysis. The expression levels of USP46, CPVL, FOSL2, and PTGS1 in electronic validation were compatible with the bio-informatics result. CPVL and TFAM had a potential diagnostic value for OA based on the ROC analysis. Conclusion The deregulated genes including USP46, CPVL, FKBP5, FOSL2, GADD45B, PTGS1, ZNF423, ADAMTS1, and TFAM might be involved in the pathology of OA. Cite this article: X. Zhang, Y. Bu, B. Zhu, Q. Zhao, Z. Lv, B. Li, J. Liu. Global transcriptome analysis to identify critical genes involved in the pathology of osteoarthritis. Bone Joint Res 2018;7:298–307. DOI: 10.1302/2046-3758.74.BJR-2017-0245.R1.
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Affiliation(s)
- X Zhang
- Department of Joint Surgery, Tianjin Hospital, Tianjin, China
| | - Y Bu
- Department of Joint Surgery, Tianjin Hospital, Tianjin, China
| | - B Zhu
- Department of Sports Medicine and Arthroscopic Surgery, Tianjin Hospital, Tianjin, China
| | - Q Zhao
- College of Clinical Medicine, Tianjin Medical University, Tianjin, China
| | - Z Lv
- College of Clinical Medicine, Tianjin Medical University, Tianjin, China
| | - B Li
- Department of Joint Surgery, Tianjin Hospital, Tianjin, China
| | - J Liu
- Department of Joint Surgery, Tianjin Hospital, Tianjin, China
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10
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Godamudunage MP, Foster A, Warren D, Lyons BA. Grb7 protein RA domain oligomerization. J Mol Recognit 2017; 30. [PMID: 28295715 DOI: 10.1002/jmr.2620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/26/2017] [Accepted: 01/28/2017] [Indexed: 11/05/2022]
Abstract
The growth factor receptor bound protein 7 (Grb7) is an adaptor protein that is often coamplified with the erythroblastosis oncogene B 2 receptor in 20% to 30% of breast cancer patients. Grb7 overexpression has been linked to increased cell migration and cancer metastasis. The ras associating and pleckstrin homology domain region of Grb7 has been reported to interact with various other downstream signaling proteins such as four and half Lin11, Isl-1, Mec-3 (LIM) domains isoform 2 and filamin α. These interactions are believed to play a role in regulating Grb7-mediated cell migration function. The full-length Grb7 protein has been shown to dimerize, and the oligomeric state of the Grb7SH2 domain has been extensively studied; however, the oligomerization state of the ras associating and pleckstrin homology domains, and the importance of this oligomerization in Grb7 function, is yet to be fully known. In this study, we characterize the oligomeric state of the Grb7RA domain using size exclusion chromatography, nuclear magnetic resonance, nuclear relaxation studies, glutaraldehyde cross linking, and dynamic light scattering. We report the Grb7RA domain can exist in transient multimeric forms and, based upon modeling results, postulate the potential role of Grb7RA domain oligomerization in Grb7 function.
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Affiliation(s)
- Malika P Godamudunage
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.,Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, 88003, USA
| | | | | | - Barbara A Lyons
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, 88003, USA
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11
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Damen MSMA, Agca R, Holewijn S, de Graaf J, Dos Santos JC, van Riel PL, Fransen J, Coenen MJH, Nurmohamed MT, Netea MG, Dinarello CA, Joosten LAB, Heinhuis B, Popa CD. IL-32 promoter SNP rs4786370 predisposes to modified lipoprotein profiles in patients with rheumatoid arthritis. Sci Rep 2017; 7:41629. [PMID: 28134327 PMCID: PMC5278556 DOI: 10.1038/srep41629] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/22/2016] [Indexed: 01/22/2023] Open
Abstract
Patients with rheumatoid arthritis (RA) are at higher risk of developing cardiovascular diseases (CVD). Interleukin (IL)-32 has previously been shown to be involved in the pathogenesis of RA and might be linked to the development of atherosclerosis. However, the exact mechanism linking IL-32 to CVD still needs to be elucidated. The influence of a functional genetic variant of IL-32 on lipid profiles and CVD risk was therefore studied in whole blood from individuals from the NBS cohort and RA patients from 2 independent cohorts. Lipid profiles were matched to the specific IL-32 genotypes. Allelic distribution was similar in all three groups. Interestingly, significantly higher levels of high density lipoprotein cholesterol (HDLc) were observed in individuals from the NBS cohort and RA patients from the Nijmegen cohort homozygous for the C allele (p = 0.0141 and p = 0.0314 respectively). In contrast, the CC-genotype was associated with elevated low density lipoprotein cholesterol (LDLc) and total cholesterol (TC) in individuals at higher risk for CVD (plaque positive) (p = 0.0396; p = 0.0363 respectively). Our study shows a functional effect of a promoter single-nucleotide polymorphism (SNP) in IL32 on lipid profiles in RA patients and individuals, suggesting a possible protective role of this SNP against CVD.
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Affiliation(s)
- Michelle S M A Damen
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rabia Agca
- Amsterdam Rheumatology immunology Center, Department of Rheumatology, location CU University Medical Center and Reade, Amsterdam, The Netherlands
| | | | - Jacqueline de Graaf
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Jéssica C Dos Santos
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.,Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Brazil
| | - Piet L van Riel
- Department of Rheumatology, Bernhoven Ziekenhuis, Uden, The Netherlands
| | - Jaap Fransen
- Department of Rheumatology, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands
| | - Marieke J H Coenen
- Radboud Institute for Health Sciences, Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Mike T Nurmohamed
- Amsterdam Rheumatology immunology Center, Department of Rheumatology, location CU University Medical Center and Reade, Amsterdam, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Charles A Dinarello
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.,School of Medicine, Division of infectious diseases, University of Colorado Denver, Aurora, Colorado 80045, United States of America
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Bas Heinhuis
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Calin D Popa
- Department of Rheumatology, Bernhoven Ziekenhuis, Uden, The Netherlands.,Department of Rheumatology, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands
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