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Singh P, Guin D, Pattnaik B, Kukreti R. Mapping the genetic architecture of idiopathic pulmonary fibrosis: Meta-analysis and epidemiological evidence of case-control studies. Gene 2024; 895:147993. [PMID: 37977320 DOI: 10.1016/j.gene.2023.147993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/23/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a rare and devastating fibrotic lung disorder with unknown etiology. Although it is believed that genetic component is an important risk factor for IPF, a comprehensive understanding of its genetic landscape is lacking. Hence, we aimed to highlight the susceptibility genes and pathways implicated in IPF pathogenesis through a two-staged systematic literature search of genetic association studies on IPF, followed by meta-analysis and pathway enrichment analysis. METHODS This study was performed based on PRISMA guidelines (PROSPERO, registration number: CRD42022297970). The first search was performed (using PubMed and Web of Science) retrieving a total of 5642 articles, of which 52 were eligible for inclusion in the first stage. The second search was performed (using PubMed, Web of Science and Scopus) for ten polymorphisms, identified from the first search, with 2 or more studies. Finally, seven polymorphisms, [rs35705950/MUC5B, rs2736100/TERT, rs2609255/FAM13A, rs2076295/DSP, rs12610495/DPP9, rs111521887/TOLLIP and rs1800470/TGF-β1] qualified for meta-analyses. The epidemiological credibility was evaluated using Venice criteria. RESULTS From the systematic review, 222 polymorphisms in 118 genes showed a significant association with IPF susceptibility. Meta-analyses findings revealed significant association of rs35705950/T [OR = 3.92(3.26-4.57)], rs2609255/G [OR = 1.50(1.18-1.82)], rs2076295/G [OR = 1.19(0.82-1.756)], rs12610495/G [OR = 1.28(1.12-1.44)], rs2736100/C [OR = 0.68(0.54-0.82), rs111521887/G [OR = 1.34(1.06-1.61)] and suggestive evidence for rs1800470/T [OR = 1.08(0.82-1.34)] with IPF susceptibility. Four polymorphisms- rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk. Gene ontology and pathway enrichment analysis performed on IPF risk-associated genes identified a critical role of genes in mucin production, immune response and inflammation, host defence, cell-cell adhesion and telomere maintenance. CONCLUSIONS Our findings present the most prominent IPF-associated genetic risk variants involved in alveolar epithelial injuries (MUC5B, TERT, FAM13A, DSP, DPP9) and epithelial-mesenchymal transition (TOLLIP, TGF-β1), providing genetic and biological insights into IPF pathogenesis. However, further experimental research and human studies with larger sample sizes, diverse ethnic representation, and rigorous design are warranted.
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Affiliation(s)
- Pooja Singh
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, India; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Debleena Guin
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, New Delhi, India; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Bijay Pattnaik
- Centre of Excellence for Translational Research in Asthma and Lung Diseases, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India; Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Ritushree Kukreti
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, India; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India.
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Hu Y, Li Z, Ren Y, Dai H. Association of family sequence similarity gene 13A gene polymorphism and interstitial lung disease susceptibility: A systematic review and meta-analysis. Mol Genet Genomic Med 2023; 11:e2279. [PMID: 37786320 PMCID: PMC10655521 DOI: 10.1002/mgg3.2279] [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: 03/29/2023] [Revised: 07/31/2023] [Accepted: 08/17/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Among present reports, the T/G allelic variation at the rs2609255 locus of the family sequence similarity gene 13A (FAM13A) was considerable associated with susceptibility to interstitial lung diseases (ILDs). In this study, we summarized relevant studies and applied a meta-analysis to explore whether the polymorphism of rs2609255 site of the FAM13A gene can be utilized to predict susceptibility to idiopathic pulmonary fibrosis (IPF) patients or rheumatoid arthritis-associated interstitial lung disease (RA-ILD) or silicosis patients in different populations for the first time. METHODS We compared the frequency of G allele on rs2609255 site of FAM13A between the control subjects and IPF or RA-ILD or silicosis patients from different races by using meta-analysis. Nine studies were involved in this meta-analysis, including five IPF studies, two RA-ILD studies, and two silicosis studies, and containing 14 subgroups. We conducted separate meta-analyses for different races. RESULTS In all individuals, a substantial link between the G allele of the FAM13A rs2609255 polymorphism and IPF (OR: 1.47, 95% CI: 1.33-1.63, p < 0.00001) was indicated. After dividing by ethnicity, the G allele was illustrated to be considerable correlation with IPF in Asian (OR: 2.63, 95% CI: 1.81-3.81, p < 0.00001) and with RA-ILD individuals (OR: 3.27, 95% CI: 1.26-8.49, p = 0.01). Conversely, there was no correlation with the G allele and IPF in European individuals (OR: 1.27, 95% CI: 0.89-1.83, p = 0.13) or silicosis in Chinese individuals (OR: 1.20, 95% CI: 0.99-1.46, p = 0.07). CONCLUSION This is the first meta-analysis that provides evidence that the rs2609255 of FAM13A might increase susceptibility to RA-ILD, and IPF especially in Asian but not in European individuals, and not be correlated with silicosis in Chinese individuals, which indicated the differences in susceptibility to disease by race were noteworthy.
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Affiliation(s)
- Yinan Hu
- National Center for Respiratory MedicineBeijingP.R. China
- National Clinical Research Center for Respiratory DiseasesBeijingP.R. China
- Institute of Respiratory Medicine, Chinese Academy of Medical SciencesBeijingP.R. China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory MedicineChina‐Japan Friendship HospitalBeijingP.R. China
| | - Zhen Li
- China‐Japan Friendship HospitalBeijingP.R. China
- Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingP.R. China
| | - Yanhong Ren
- National Center for Respiratory MedicineBeijingP.R. China
- National Clinical Research Center for Respiratory DiseasesBeijingP.R. China
- Institute of Respiratory Medicine, Chinese Academy of Medical SciencesBeijingP.R. China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory MedicineChina‐Japan Friendship HospitalBeijingP.R. China
| | - Huaping Dai
- National Center for Respiratory MedicineBeijingP.R. China
- National Clinical Research Center for Respiratory DiseasesBeijingP.R. China
- Institute of Respiratory Medicine, Chinese Academy of Medical SciencesBeijingP.R. China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory MedicineChina‐Japan Friendship HospitalBeijingP.R. China
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Kishore A, Sikorova K, Kocourkova L, Petrkova J, Doubkova M, Jakubec P, Rębała K, Dubaniewicz A, Petrek M. Evaluation of genetic risk, its clinical manifestation and disease management based on 18 susceptibility gene markers among West-Slavonic patients with sarcoidosis. Gene 2023:147577. [PMID: 37336276 DOI: 10.1016/j.gene.2023.147577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
Sarcoidosis is a heterogenous, multisystemic inflammatory disease that primarily affects lungs. In this study, we multiplex genotyped 18 single-nucleotide polymorphisms (SNPs) to replicate the findings from previous genome-wide association studies (GWAS) and candidate gene studies, and extended analyses to different clinical manifestations (Lofgren syndrome and chest X-ray [CXR] stages) including treatment response among West-Slavonic subjects (564 sarcoidosis patients and 301 healthy controls). We confirm the replication (with Bonferroni correction) of ANXA11 rs1049550 as protective variant for sarcoidosis (odds ratio [OR]=0.71, p=1.33×10-3), non-LS (OR=0.66, p=2.71×10-4) and CXR stages 2-4 (OR=0.62, p=7.48×10-5) compared to controls in West-Slavonic population. We also validate the association of risk variants C6orf10 rs3129927 (OR=2.61, p=2.60×10-8), TNFA rs1800629 (OR=1.56, p=6.65×10-4), ATF6B rs3130288 (OR=2.75, p=1.06×10-9) and HLA-DQA1 rs2187668 (OR=1.74, p=8.83×10-4) with sarcoidosis compared to controls. For sub-phenotypes compared to controls, risk variants C6orf10 rs3129927 (OR=5.35, p=1.07×10-12), TNFA rs1800629 (OR=2.66, p=5.94×10-7), ATF6B rs3130288 (OR=5.24, p=5.21×10-13), LRRC16A rs9295661 (OR=2.97, p=4.29×10-4), HLA-DQA1 rs2187668 (OR=3.14, p=1.09×10-6) and HLA-DRA rs3135394 (OR=5.23, p=8.25×10-13) were associated with LS while C6orf10 rs3129927 (OR=1.96, p=4.27×10-4) and ATF6B rs3130288 (OR=2.15, p=3.36×10-5) were associated with non-LS. For CXR stages compared to controls, C6orf10 rs3129927 (OR=3.67, p=3.63×10-11), TNFA rs1800629 (OR=1.84, p=1.32×10-4), ATF6B rs3129927 (OR=3.63, p=1.82×10-11), HLA-DQA1 rs2187668 (OR=2.13, p=9.59×10-5) and HLA-DRA rs3135394 (OR=3.42, p=3.45×10-10) were risk variants for early CXR stages 0-1 while C6orf10 rs3129927 (OR=1.99, p=5.51×10-4), ATF6B rs3129927 (OR=2.23, p=3.52×10-5) and HLA-DRA rs3135394 (OR=1.85, p=2.00×10-3) were risk variants for advanced CXR stages 2-4. The present findings nominate gene variants as plausible prognostic markers for clinical phenotypes, treatment response and disease resolution/progression and may form the basis for establishing genotype-phenotype relationships in patients with sarcoidosis among West-Slavonic population.
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Affiliation(s)
- Amit Kishore
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic; AccuScript Consultancy, Ludhiana, Punjab, India
| | - Katerina Sikorova
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
| | - Lenka Kocourkova
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic; Laboratory of Cardiogenomics LEM, University Hospital Olomouc, Czech Republic
| | - Jana Petrkova
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic; Laboratory of Cardiogenomics LEM, University Hospital Olomouc, Czech Republic
| | - Martina Doubkova
- Department of Pulmonary Diseases and Tuberculosis, Masaryk University and University Hospital Brno, Czech Republic
| | - Petr Jakubec
- Department of Respiratory Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Czech Republic
| | - Krzysztof Rębała
- Department of Forensic Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Anna Dubaniewicz
- Department of Pulmonology, Medical University of Gdansk, Poland.
| | - Martin Petrek
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic.
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Neatu R, Enekwa I, Thompson DJ, Schwalbe EC, Fois G, Abdelaal G, Veuger S, Frick M, Braubach P, Moschos SA. The Idiopathic Pulmonary Fibrosis-Associated Single Nucleotide Polymorphism RS35705950 Is Transcribed in a MUC5B Promoter Associated Long Non-Coding RNA (AC061979.1). Noncoding RNA 2022; 8:ncrna8060083. [PMID: 36548182 PMCID: PMC9781688 DOI: 10.3390/ncrna8060083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
LncRNAs are involved in regulatory processes in the human genome, including gene expression. The rs35705950 SNP, previously associated with IPF, overlaps with the recently annotated lncRNA AC061979.1, a 1712 nucleotide transcript located within the MUC5B promoter at chromosome 11p15.5. To document the expression pattern of the transcript, we processed 3.9 TBases of publicly available RNA-SEQ data across 27 independent studies involving lung airway epithelial cells. Epithelial lung cells showed expression of this putative pancRNA. The findings were independently validated in cell lines and primary cells. The rs35705950 is found within a conserved region (from fish to primates) within the expressed sequence indicating functional importance. These results implicate the rs35705950-containing AC061979.1 pancRNA as a novel component of the MUC5B expression control minicircuitry.
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Affiliation(s)
- Ruxandra Neatu
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle-Upon-Tyne NE1 3BZ, UK
| | - Ifeanyi Enekwa
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
| | - Dean J. Thompson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
| | - Edward C. Schwalbe
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
| | - Giorgio Fois
- Institue of General Physiology, University of Ulm, Albert-Einstein-Allee 11, D89081 Ulm, Germany
| | - Gina Abdelaal
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
| | - Stephany Veuger
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
| | - Manfred Frick
- Institue of General Physiology, University of Ulm, Albert-Einstein-Allee 11, D89081 Ulm, Germany
| | - Peter Braubach
- Institute of Pathology, MHH Hannover, 30625 Hannover, Germany
| | - Sterghios A. Moschos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
- Correspondence:
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Lillehoj EP, Luzina IG, Atamas SP. Mammalian Neuraminidases in Immune-Mediated Diseases: Mucins and Beyond. Front Immunol 2022; 13:883079. [PMID: 35479093 PMCID: PMC9035539 DOI: 10.3389/fimmu.2022.883079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/21/2022] [Indexed: 12/28/2022] Open
Abstract
Mammalian neuraminidases (NEUs), also known as sialidases, are enzymes that cleave off the terminal neuraminic, or sialic, acid resides from the carbohydrate moieties of glycolipids and glycoproteins. A rapidly growing body of literature indicates that in addition to their metabolic functions, NEUs also regulate the activity of their glycoprotein targets. The simple post-translational modification of NEU protein targets-removal of the highly electronegative sialic acid-affects protein folding, alters protein interactions with their ligands, and exposes or covers proteolytic sites. Through such effects, NEUs regulate the downstream processes in which their glycoprotein targets participate. A major target of desialylation by NEUs are mucins (MUCs), and such post-translational modification contributes to regulation of disease processes. In this review, we focus on the regulatory roles of NEU-modified MUCs as coordinators of disease pathogenesis in fibrotic, inflammatory, infectious, and autoimmune diseases. Special attention is placed on the most abundant and best studied NEU1, and its recently discovered important target, mucin-1 (MUC1). The role of the NEU1 - MUC1 axis in disease pathogenesis is discussed, along with regulatory contributions from other MUCs and other pathophysiologically important NEU targets.
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Affiliation(s)
- Erik P. Lillehoj
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Irina G. Luzina
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Research Service, Baltimore Veterans Affairs (VA) Medical Center, Baltimore, MD, United States
| | - Sergei P. Atamas
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
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Moss BJ, Ryter SW, Rosas IO. Pathogenic Mechanisms Underlying Idiopathic Pulmonary Fibrosis. ANNUAL REVIEW OF PATHOLOGY 2022; 17:515-546. [PMID: 34813355 DOI: 10.1146/annurev-pathol-042320-030240] [Citation(s) in RCA: 169] [Impact Index Per Article: 84.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The pathogenesis of idiopathic pulmonary fibrosis (IPF) involves a complex interplay of cell types and signaling pathways. Recurrent alveolar epithelial cell (AEC) injury may occur in the context of predisposing factors (e.g., genetic, environmental, epigenetic, immunologic, and gerontologic), leading to metabolic dysfunction, senescence, aberrant epithelial cell activation, and dysregulated epithelial repair. The dysregulated epithelial cell interacts with mesenchymal, immune, and endothelial cells via multiple signaling mechanisms to trigger fibroblast and myofibroblast activation. Recent single-cell RNA sequencing studies of IPF lungs support the epithelial injury model. These studies have uncovered a novel type of AEC with characteristics of an aberrant basal cell, which may disrupt normal epithelial repair and propagate a profibrotic phenotype. Here, we review the pathogenesis of IPF in the context of novel bioinformatics tools as strategies to discover pathways of disease, cell-specific mechanisms, and cell-cell interactions that propagate the profibrotic niche.
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Affiliation(s)
- Benjamin J Moss
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA; ,
| | - Stefan W Ryter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA;
| | - Ivan O Rosas
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA; ,
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Wu X, Li W, Luo Z, Chen Y. The minor T allele of the MUC5B promoter rs35705950 associated with susceptibility to idiopathic pulmonary fibrosis: a meta-analysis. Sci Rep 2021; 11:24007. [PMID: 34907291 PMCID: PMC8671516 DOI: 10.1038/s41598-021-03533-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/06/2021] [Indexed: 11/09/2022] Open
Abstract
MUC5B promoter rs35705950 T/G gene polymorphism has been associated with the risk of IPF, but the influence of this relationship varies among different populations. In the past 2 years, there were new clinical studies with different results, but none of them reached unified conclusions. Therefore, this study further included the latest case-control studies, integrated their results and carried out meta-analysis on them to draw reliable conclusions. PubMed, EMBASE, CNKI, Wanfang database and VIP Chinese science were searched by a computer to collect the related literatures of MUC5B gene polymorphism and IPF susceptibility published before June 15, 2021. The first author, year of publication, diagnostic criteria and gene frequency were extracted after screened them. Forest plot was drawn and the trial sequential analysis (TSA) was carried out to confirm the stability of the meta-analysis results. Registration number: CRD42021272940. A total of 24 case-control studies (13 studies on the Caucasian, 7 studies on the Asian and 4 studies on the mixed population), and a total of 6749 IPF patients and 13,898 healthy controls were included in this study. The T vs.G, TT vs. GG, GT vs. GG, GT + TT vs. GG and TT vs. GG + GT genetic models of MUC5B promoter rs35705950 T/G polymorphism were associated with IPF risk in all populations, and the effect values were ([OR] 4.12, 95% CI [3.64, 4.67]), ([OR] 10.12, 95% CI [7.06, 14.49]), ([OR] 4.84, 95% CI [3.85, 6.08]), ([OR] 4.84, 95% CI [3.79, 6.19]) and ([OR] 5.11, 95% CI [4.02, 6.49]), respectively. The results of TSA confirmed the stability of the results. Subgroup analysis showed that T vs.G, TT vs. GG, GT vs. GG, GT + TT vs. GG and TT vs. GG + GT genetic models of MUC5B polymorphism were associated with IPF risk in Caucasian population. The effect values were ([OR] 4.50, 95% CI [3.93, 5.16]), ([OR] 10.98, 95% CI [7.59, 15.89]), ([OR] 6.27, 95% CI [5.37, 7.32]), ([OR] 6.30, 95% CI [5.19, 7.64]) and ([OR] 5.15, 95% CI [4.01, 6.61]), respectively. Similar results were also found in Asian and mixed populations. The association strength of the minor T allele in the Caucasian was more significant than that of the Asian population ([OR] 4.50 vs. [OR] 2.39), and the association strength of all genetic models carrying "T" was more significant than that of the Asian population ([OR] 10.98 vs. [OR] 4.29). In Caucasian, Asian and mixed populations, T minor allele carriers were more likely to be susceptible to pulmonary fibrosis, and TT genotype carriers were more likely to be susceptible to IPF than GT genotype carriers. The association between IPF and Caucasian population with minor T allele and all "T" genetic model was more significant than that of Asian population.
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Affiliation(s)
- Xiaozheng Wu
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China
| | - Wen Li
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China
| | - Zhenliang Luo
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China
| | - Yunzhi Chen
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China.
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Kishore A, Petrek M. Roles of Macrophage Polarization and Macrophage-Derived miRNAs in Pulmonary Fibrosis. Front Immunol 2021; 12:678457. [PMID: 34489932 PMCID: PMC8417529 DOI: 10.3389/fimmu.2021.678457] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022] Open
Abstract
This mini-review summarizes the current evidence for the role of macrophage activation and polarization in inflammation and immune response pertinent to interstitial lung disease, specifically pulmonary fibrosis. In the fibrosing lung, the production and function of inflammatory and fibrogenic mediators involved in the disease development have been reported to be regulated by the effects of polarized M1/M2 macrophage populations. The M1 and M2 macrophage phenotypes were suggested to correspond with the pro-inflammatory and pro-fibrogenic signatures, respectively. These responses towards tissue injury followed by the development and progression of lung fibrosis are further regulated by macrophage-derived microRNAs (miRNAs). Besides cellular miRNAs, extracellular exosomal-miRNAs derived from M2 macrophages have also been proposed to promote the progression of pulmonary fibrosis. In a future perspective, harnessing the noncoding miRNAs with a key role in the macrophage polarization is, therefore, suggested as a promising therapeutic strategy for this debilitating disease.
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Affiliation(s)
- Amit Kishore
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia.,Accuscript Consultancy, Ludhiana, India
| | - Martin Petrek
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia.,Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia.,Departments of Experimental Medicine, and Immunology, University Hospital Olomouc, Olomouc, Czechia
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Michalski JE, Schwartz DA. Genetic Risk Factors for Idiopathic Pulmonary Fibrosis: Insights into Immunopathogenesis. J Inflamm Res 2021; 13:1305-1318. [PMID: 33447070 PMCID: PMC7801923 DOI: 10.2147/jir.s280958] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
Idiopathic pulmonary fibrosis is an etiologically complex interstitial lung disease characterized by progressive scarring of the lungs with a subsequent decline in lung function. While much of the pathogenesis of IPF still remains unclear, it is now understood that genetic variation accounts for at least one-third of the risk of developing the disease. The single-most validated and most significant risk factor, genetic or otherwise, is a gain-of-function promoter variant in the MUC5B gene. While the functional impact of these IPF risk variants at the cellular and tissue levels are areas of active investigation, there is a growing body of evidence that these genetic variants may influence disease pathogenesis through modulation of innate immune processes.
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Affiliation(s)
- Jacob E Michalski
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - David A Schwartz
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
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10
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Lou HQ, Huang CX, Li GY, Li P, Zhang SM, Li HG, Han L, Bao MH. The Association between MUC5B Rs35705950 and Risks of Idiopathic Interstitial Pneumonia, Systemic Sclerosis Interstitial Lung Disease, and Familial Interstitial Pneumonia: A Meta-Analysis. IRANIAN JOURNAL OF PUBLIC HEALTH 2020; 49:2240-2250. [PMID: 34178730 PMCID: PMC8215073 DOI: 10.18502/ijph.v49i12.4801] [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] [Indexed: 11/24/2022]
Abstract
Background: Interstitial lung disease (ILD) is a category of chronic lung diseases with more than 200 subtypes. Idiopathic interstitial pneumonia (IIP), systemic sclerosis (SSc) ILD, and familial interstitial pneumonia (FIP) are three major groups of lung diseases with different causes or with unknown causes. Mucin5B (MUC5B) belongs to the mucin family, which contribute to the lubricating and viscoelastic properties of the whole saliva, normal lung mucus, and cervical mucus. The association between MUC5B rs35705950 and ILDs risks has been widely studied. However, the results were inconclusive and inconsistent. Methods: In the present meta-analysis, the database PubMed, Embase, Cochrane Central Register of Controlled Trials, CNKI and Chinese Biomedical Literature Database were searched till Aug 20th, 2018. Overall 16 publications with 28 studies, 76345 cases and 18402 controls were included. Results: The results indicated a significant increase of overall IIP risk for TT genotype and T allele of the rs35705950 in all genetic models (TT vs GG, OR=9.11; TT vs GT+TT, OR=5.80; GT+TT vs GG, OR=4.34; T vs G, OR=4.03. P<0.0001). Subgroup analysis by subtypes of IIP revealed higher risks of TT genotype and T allele for IPF and iNSIP (P<0.05). A significant increase of FIP risk was also found for the TT genotype and T allele of the rs35705950 (TT vs GG, OR=17.08; GT+TT vs GG, OR=6.02; T vs G, OR=1.64.P<0.05). Conclusion: No significant relations existed between the rs35705950 and SSc-ILD risks. MUC5B rs35705950 might be a predictor for the susceptibility of IIP and FIP.
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Affiliation(s)
- Huai-Qing Lou
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China.,Department of Pharmacology, School of Pharmaceutical Science, Changsha Medical University, Changsha, 410219, China.,Department of Physiology, School of Basic Medical Science, Central South University, Changsha, Hunan, 410007, China
| | - Chun-Xia Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Changsha Medical University, Changsha, Hunan, 410007, China
| | - Guang-Yi Li
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China
| | - Ping Li
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China
| | - Shou-Ming Zhang
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China
| | - Hai-Gang Li
- Department of Pharmacology, School of Pharmaceutical Science, Changsha Medical University, Changsha, 410219, China
| | - Li Han
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China.,Department of Physiology, School of Basic Medical Science, Central South University, Changsha, Hunan, 410007, China
| | - Mei-Hua Bao
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China.,Department of Pharmacology, School of Pharmaceutical Science, Changsha Medical University, Changsha, 410219, China
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Dagneaux L, Owen AR, Bettencourt JW, Barlow JD, Amadio PC, Kocher JP, Morrey ME, Sanchez-Sotelo J, Berry DJ, van Wijnen AJ, Abdel MP. Human Fibrosis: Is There Evidence for a Genetic Predisposition in Musculoskeletal Tissues? J Arthroplasty 2020; 35:3343-3352. [PMID: 32593486 PMCID: PMC7842876 DOI: 10.1016/j.arth.2020.05.070] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Pathologic fibrosis is characterized by dysregulation of gene expression with excessive extracellular matrix production. The genetic basis for solid organ fibrosis is well described in the literature. However, there is a paucity of evidence for similar processes in the musculoskeletal (MSK) system. The purpose of this review is to provide an overview of existing evidence of genetic predisposition to pathologic fibrosis in the cardiac, pulmonary, and MSK systems, and to describe common genetic variants associated with these processes. METHODS A comprehensive search of several databases from 2000 to 2019 was conducted using relevant keywords in the English language. Genes reported as involved in idiopathic fibrotic processes in the heart, lung, hand, shoulder, and knee were recorded by 2 independent authors. RESULTS Among 2373 eligible studies, 52 studies investigated genetic predisposition in terms of variant analysis with the following organ system distribution: 36 pulmonary studies (69%), 15 hand studies (29%), and 1 knee study (2%). Twenty-two percent of gene variants identified were associated with both pulmonary and MSK fibrosis (ie, ADAM, HLA, CARD, EIF, TGF, WNT, and ZNF genes). Genetic variants known to be involved in the MSK tissue development or contractility properties in muscle were identified in the pulmonary fibrosis. CONCLUSION Despite shared genetic variations in both the lung and hand, there remains limited information about genetic variants associated with fibrosis in other MSK regions. This finding establishes the necessity of further studies to elucidate the genetic determinants involved in the knee, shoulder, and other joint fibrotic pathways. LEVEL OF EVIDENCE Level III.
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Affiliation(s)
- Louis Dagneaux
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN
| | - Aaron R. Owen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN
| | | | | | - Peter C. Amadio
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN
| | - Jean P. Kocher
- Department of Bioinformatics, Mayo Clinic, Rochester, MN
| | - Mark E. Morrey
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN
| | | | - Daniel J. Berry
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN
| | | | - Matthew P. Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN,Reprint requests: Matthew P. Abdel, MD, Department of Orthopedic Surgery, Mayo Clinic, 200 First Street S.W., Rochester, MN 55905
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Shi X, Ma Y, Li H, Yu H. Association between FCGR2A rs1801274 and MUC5B rs35705950 variations and pneumonia susceptibility. BMC MEDICAL GENETICS 2020; 21:71. [PMID: 32252656 PMCID: PMC7137230 DOI: 10.1186/s12881-020-01005-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/19/2020] [Indexed: 12/22/2022]
Abstract
Background Herein, we collected currently published data to comprehensively evaluate the impact of the FCGR2A (Fc fragment of IgG receptor IIa) rs1801274 and MUC5B (mucin 5B, oligomeric mucus/gel-forming) rs35705950 variations on susceptibility to pneumonia diseases. Methods We retrieved case-control studies from three online databases and applied the statistical approach of meta-analysis for a series of pooling analyses. Results A total of fourteen case-control studies were included for FCGR2A rs1801274; while thirty-one case-control studies were included for MUC5B rs35705950. No significant difference between pneumonia cases and controls for FCGR2A rs1801274 was found. However, MUC5B rs35705950 was significantly associated with pneumonia susceptibility in the whole population under the genetic models of allelic T vs. G [OR (odds ratio) =3.78], carrier T vs. G (OR = 3.31), TT vs. GG (OR = 13.66), GT vs. GG (OR = 4.78), GT + TT vs. GG (OR = 5.05), and TT vs. GG + GT (OR = 6.47) (all P < 0.001, Bonferroni-adjusted P < 0.006; false discovery rate-adjusted P < 0.0010). Furthermore, we observed a similar positive result for subgroup analyses of “Caucasian”, “Asian”, “population-based control”, and “idiopathic pulmonary fibrosis”. Conclusions MUC5B rs35705950, but not FCGR2A rs1801274, increases susceptibility to clinical pneumonia, especially to idiopathic pulmonary fibrosis, in both the Caucasian and Asian populations.
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Affiliation(s)
- Xueshu Shi
- Nursing Division, The second affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300150, P.R. China
| | - Yue Ma
- Endoscopic Skull Base Surgery Center, Tianjin Huanhu Hospital, No 6, JiZhao Road, Jinnan District, Tianjin, 300350, P.R. China
| | - Haiyan Li
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin Huanhu Hospital, Tianjin, 300350, P.R. China
| | - Huanxin Yu
- Endoscopic Skull Base Surgery Center, Tianjin Huanhu Hospital, No 6, JiZhao Road, Jinnan District, Tianjin, 300350, P.R. China.
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13
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Telomere shortening in blood leukocytes of patients with posttraumatic stress disorder. J Psychiatr Res 2019; 111:83-88. [PMID: 30685566 DOI: 10.1016/j.jpsychires.2019.01.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/14/2019] [Accepted: 01/21/2019] [Indexed: 01/09/2023]
Abstract
Telomeres are protective fragments on chromosome ends involved in maintaining genome stability, preventing chromosomal fusions, regulation of cell division. It was shown that telomere attrition rate is accelerated in age-related diseases, as well as in response to physiological and psychosocial stress. The aim of this study was to evaluate relative leukocyte telomere length (LTL) in patients with post traumatic stress disorder (PTSD), as well as to investigate association of functional SNPs of telomerase TERC and TERT genes with LTL and PTSD. The relative LTL was measured by multiplex quantitative PCR method; genotyping of TERC rs12696304, TERT rs7726159 and rs2736100 was performed by PCR with sequence specific primers. Comparison of LTL in diseased and healthy subjects showed that PTSD patients had shorter average LTL than controls. Also, the frequency and the carriage rate of the TERT rs2736100*T allele was higher in PTSD patients compared to controls. Overall our results are in line with previous research in different populations. Furthermore, we have demonstrated that rs2736100 of TERT gene was significantly associated with PTSD and the minor allele of this polymorphism may be considered as a risk factor for PTSD in the Armenian population.
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14
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Fibrosis: Lessons from OMICS analyses of the human lung. Matrix Biol 2018; 68-69:422-434. [PMID: 29567123 DOI: 10.1016/j.matbio.2018.03.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 12/30/2022]
Abstract
In recent decades there has been a significant shift in our understanding of idiopathic pulmonary fibrosis (IPF), a progressive and lethal disorder. While initially much of the mechanistic understanding was derived from hypotheses generated from animal models of disease, in recent decades new insights derived from humans with IPF have taken precedence. This is mainly because of the establishment of large collections of IPF lung tissues and patient cohorts, and the emergence of high throughput profiling technologies collectively termed 'omics' technologies based on their shared suffix. In this review we describe impacts of 'omics' analyses of human IPF samples on our understanding of the disease. In particular, we discuss the results of genomics and transcriptomics studies, as well as proteomics, epigenomics and metabolomics. We then describe how these findings can be integrated in a modified paradigm of human idiopathic pulmonary fibrosis, that introduces the 'hallmarks of aging' as a central theme in the IPF lung. This allows resolution of all the disparate cellular and molecular features in IPF, from the central role of epithelial cells, through the dramatic phenotypic alterations observed in fibroblasts and the numerous aberrations that inflammatory cells exhibit. We end with reiterating a call for renewed efforts to collect and analyze carefully characterized human tissues, in ways that would facilitate implementation of novel technologies for high resolution single cell omics profiling.
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15
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Kaur A, Mathai SK, Schwartz DA. Genetics in Idiopathic Pulmonary Fibrosis Pathogenesis, Prognosis, and Treatment. Front Med (Lausanne) 2017; 4:154. [PMID: 28993806 PMCID: PMC5622313 DOI: 10.3389/fmed.2017.00154] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/07/2017] [Indexed: 12/14/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF), the most common form of idiopathic interstitial pneumonia (IIP), is characterized by irreversible scarring of the lung parenchyma and progressive decline in lung function leading to eventual respiratory failure. The prognosis of IPF is poor with a median survival of 3–5 years after diagnosis and no curative medical therapies. Although the pathogenesis of IPF is not well understood, there is a growing body of evidence that genetic factors contribute to disease risk. Recent studies have identified common and rare genetic variants associated with both sporadic and familial forms of pulmonary fibrosis, with at least one-third of the risk for developing fibrotic IIP explained by common genetic variants. The IPF-associated genetic loci discovered to date are implicated in diverse biological processes, including alveolar stability, host defense, cell–cell barrier function, and cell senescence. In addition, some common variants have also been associated with distinct clinical phenotypes. Better understanding of how genetic variation plays a role in disease risk and phenotype could identify potential therapeutic targets and inform clinical decision-making. In addition, clinical studies should be designed controlling for the genetic backgrounds of subjects, since clinical outcomes and therapeutic responses may differ by genotype. Further understanding of these differences will allow the development of personalized approaches to the IPF management.
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Affiliation(s)
- Amarpreet Kaur
- Department of Medicine, University of Colorado Denver School of Medicine, Aurora, CO, United States
| | - Susan K Mathai
- Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver School of Medicine, Aurora, CO, United States
| | - David A Schwartz
- Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver School of Medicine, Aurora, CO, United States
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Piñero J, Bravo À, Queralt-Rosinach N, Gutiérrez-Sacristán A, Deu-Pons J, Centeno E, García-García J, Sanz F, Furlong LI. DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. Nucleic Acids Res 2016; 45:D833-D839. [PMID: 27924018 PMCID: PMC5210640 DOI: 10.1093/nar/gkw943] [Citation(s) in RCA: 1423] [Impact Index Per Article: 177.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/29/2016] [Accepted: 10/18/2016] [Indexed: 12/12/2022] Open
Abstract
The information about the genetic basis of human diseases lies at the heart of precision medicine and drug discovery. However, to realize its full potential to support these goals, several problems, such as fragmentation, heterogeneity, availability and different conceptualization of the data must be overcome. To provide the community with a resource free of these hurdles, we have developed DisGeNET (http://www.disgenet.org), one of the largest available collections of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific literature. DisGeNET data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotype-phenotype relationships. The information is accessible through a web interface, a Cytoscape App, an RDF SPARQL endpoint, scripts in several programming languages and an R package. DisGeNET is a versatile platform that can be used for different research purposes including the investigation of the molecular underpinnings of specific human diseases and their comorbidities, the analysis of the properties of disease genes, the generation of hypothesis on drug therapeutic action and drug adverse effects, the validation of computationally predicted disease genes and the evaluation of text-mining methods performance.
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Affiliation(s)
- Janet Piñero
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), C/Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Àlex Bravo
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), C/Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Núria Queralt-Rosinach
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), C/Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Alba Gutiérrez-Sacristán
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), C/Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Jordi Deu-Pons
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), C/Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Emilio Centeno
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), C/Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Javier García-García
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), C/Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), C/Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Laura I Furlong
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), C/Dr Aiguader 88, E-08003 Barcelona, Spain
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