1
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Saquib M, Agnihotri P, Biswas S. Interrelated grid of non-coding RNA: An important aspect in Rheumatoid Arthritis pathogenesis. Mol Biol Rep 2023:10.1007/s11033-023-08543-w. [PMID: 37294467 DOI: 10.1007/s11033-023-08543-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
Inflammation and autoimmunity are the root cause of rheumatoid arthritis, a destructive disease of joints. Multiple biomolecules are involved in the pathogenesis of RA and are related to various events of molecular biology. RNA is a versatile biomolecule, playing numerous roles at structural, functional, and regulatory stages to maintain cellular homeostasis. The involvement of RNA (coding/non-coding) in disease development and progression has left a wide whole to fill with newer approaches. Non-coding RNAs belong to the housekeeping and regulatory categories and both have their specific roles, and their alteration causes specific implications in disease pathogenesis. Housekeeping RNAs, rRNA, tRNA and regulatory RNA, micro-RNA, circular RNA, piRNA and long non-coding RNA were found to be important regulators of inflammation. They work at the pre-and post-transcriptional levels and were found to be more intriguing to study their regulatory impact on disease pathogenesis. The review addresses a question on how the non-coding RNA gets involved in early RA pathogenesis and can be utilized to know their targets to understand the disease better and make way towards the unresolved mystery of RA development.
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Affiliation(s)
- Mohd Saquib
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prachi Agnihotri
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sagarika Biswas
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Integrative and Functional Biology Department CSIR- Institute of Genomics & Integrative Biology, Mall Road, Delhi, 110 007, India.
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2
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Tyagi N, Mehla K, Gupta D. Deciphering novel common gene signatures for rheumatoid arthritis and systemic lupus erythematosus by integrative analysis of transcriptomic profiles. PLoS One 2023; 18:e0281637. [PMID: 36928613 PMCID: PMC10019710 DOI: 10.1371/journal.pone.0281637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/24/2023] [Indexed: 03/18/2023] Open
Abstract
Rheumatoid Arthritis (RA) and Systemic Lupus Erythematosus (SLE) are the two highly prevalent debilitating and sometimes life-threatening systemic inflammatory autoimmune diseases. The etiology and pathogenesis of RA and SLE are interconnected in several ways, with limited knowledge about the underlying molecular mechanisms. With the motivation to better understand shared biological mechanisms and determine novel therapeutic targets, we explored common molecular disease signatures by performing a meta-analysis of publicly available microarray gene expression datasets of RA and SLE. We performed an integrated, multi-cohort analysis of 1088 transcriptomic profiles from 14 independent studies to identify common gene signatures. We identified sixty-two genes common among RA and SLE, out of which fifty-nine genes (21 upregulated and 38 downregulated) had similar expression profiles in the diseases. However, antagonistic expression profiles were observed for ACVR2A, FAM135A, and MAPRE1 genes. Thirty genes common between RA and SLE were proposed as robust gene signatures, with persistent expression in all the studies and cell types. These gene signatures were found to be involved in innate as well as adaptive immune responses, bone development and growth. In conclusion, our analysis of multicohort and multiple microarray datasets would provide the basis for understanding the common mechanisms of pathogenesis and exploring these gene signatures for their diagnostic and therapeutic potential.
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Affiliation(s)
- Neetu Tyagi
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Kusum Mehla
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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3
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Loarce-Martos J, Calvo Sanz L, Garrote-Corral S, Ballester González R, Pariente Rodríguez R, Rita CG, García-Soidan A, Bachiller-Corral J, Roy Ariño G. Myositis autoantibodies detected by line blot immunoassay: clinical associations and correlation with antibody signal intensity. Rheumatol Int 2023; 43:1101-1109. [PMID: 36763166 DOI: 10.1007/s00296-023-05279-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/15/2023] [Indexed: 02/11/2023]
Abstract
The aim of this study is to assess the relationship between myositis specific (MSA) and myositis associated (MAA) antibodies and diagnosis (including idiopathic inflammatory myopathies [IIM] and other systemic autoimmune diseases [SAID]), and to explore the impact of antibody signal intensity in diagnostic accuracy. We retrospectively reviewed all the serum samples obtained from patients tested for MSA/MAA by line immunoassay (LIA) between 01/01/2018 and 31/12/2020 in Ramón y Cajal University Hospital (Spain). Clinical true positive (CTP) MSAs and MAAs were defined as those patients with IIM or SAID with phenotypes expected of that MSA/MAA. Patients who did not have a phenotype compatible with that antibody were classified as clinical false positive (CFP). One hundred and thirty positive samples were analysed. Forty-six patients (33.38%) were classified as IIM, forty-two (32.3%) as SAID and forty-two (32.3%) as non-IIM/SAID. Among these 130 patients, 164 MSA/MAA were detected. Eighty-five (51.8%) positive MSA/MAA were classified as CTP, and seventy-nine (48.2%) as CFP. Strongly positive antibodies were more frequently CTP (35/47, 74.5%) than weak positives (54/68, 36.8%), (p ˂ 0.001). Antibodies classified as CTP had a higher signal intensity than CFP (36.77 AU vs 20.00 AU, CI95% 7.79-22.09, p ˂ 0.001). The probability of a CFP was associated to negative ANA, low ANA titer, and multiple positive MSA/MAA (p ˂ 0.001). In this study, we confirmed that CFP results using LIA are frequent, and are associated with low signal intensity MSA/MAA, negative ANA, lower titer ANA, and with multiple positive samples.
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Affiliation(s)
- Jesús Loarce-Martos
- Department of Rheumatology, Hospital Universitario Ramón y Cajal, Madrid, Spain.
| | - Laura Calvo Sanz
- Department of Rheumatology, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | | | | | | | | | - Ana García-Soidan
- Department of Immunology, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | | | - Garbiñe Roy Ariño
- Department of Immunology, Hospital Universitario Ramón y Cajal, Madrid, Spain
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Rahman N, Begum S, Khan A, Afridi SG, Khayam Sahibzada MU, Atwah B, Alhindi Z, Khan H. An insight in Salmonella typhi associated autoimmunity candidates' prediction by molecular mimicry. Comput Biol Med 2022; 148:105865. [PMID: 35843194 DOI: 10.1016/j.compbiomed.2022.105865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/26/2022] [Accepted: 07/09/2022] [Indexed: 12/11/2022]
Abstract
Autoimmune diseases develop when the immune system targets healthy cells and tissues of an individual. In developing countries, S. typhi (a gram-negative pathogenic bacteria) remains a major public health issue. This study aimed to employ bioinformatics analyses to determine the 3D structural-based molecular mimicry and sequence of S. typhi and human host proteins. In addition, to classify possible antigenic microbial peptides homologous to human peptides and comprehend the molecular basis of S. typhi-related autoimmune disorders. Protein sequences were obtained from the NCBI database, and redundancy was removed using the CD-HIT tool. The BLASTp comparative sequence analysis was followed for molecular mimicry identification of human and S. typhi protein sequences. The PathDIP database was utilized to simulate essential physical relationships between proteins and curated pathways for metabolic processes. Subsequently, the IEDB database was used to find cross-reactive MHC class-II binding epitopes that could trigger an autoimmune reaction. SPARKS-X computational biology resource was also used to determine the structural homology between human and S. typhi peptides. The BLASTp study showed that S. typhi and the human host have several proteins holding considerable sequence similarities based on a set threshold of e ≤ 10-6 and bit score ≥100. The PathDIP putatively identified that these proteins enriched in a total of 68 metabolic pathways by a significant P-value (P < 0.005). The PSORTb analysis predicted that 26 out of these proteins are cytosolic, 1 predicted to be periplasmic protein, and 1 predicted to be localized in the cytoplasmic membrane. IEDB data analysis predicted many S.typhi and human homologs epitopes as a good binder of human HLA, i.e. DRB1*01:01, DPA1*03:01/DPB1*04:02, and DQA1*01:02/DQB1*06:02 with IC50 < 50 nM. Finally, the docking data demonstrated that homolog lead epitopes promisingly interact with HLA and immune TLR4 receptors by exhibiting the best docking scores and molecular interactions. The analyses ultimately identified several potential candidate proteins and peptides that could cause S.typhi infection-mediated autoimmune diseases in humans.
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Affiliation(s)
- Noor Rahman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Sara Begum
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan.
| | - Sahib Gul Afridi
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | | | - Banan Atwah
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Zain Alhindi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan.
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Al-Mustanjid M, Mahmud SMH, Akter F, Rahman MS, Hossen MS, Rahman MH, Moni MA. Systems biology models to identify the influence of SARS-CoV-2 infections to the progression of human autoimmune diseases. INFORMATICS IN MEDICINE UNLOCKED 2022; 32:101003. [PMID: 35818398 PMCID: PMC9259025 DOI: 10.1016/j.imu.2022.101003] [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: 02/17/2022] [Revised: 06/25/2022] [Accepted: 06/25/2022] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been circulating since 2019, and its global dominance is rising. Evidences suggest the respiratory illness SARS-CoV-2 has a sensitive affect on causing organ damage and other complications to the patients with autoimmune diseases (AD), posing a significant risk factor. The genetic interrelationships and molecular appearances between SARS-CoV-2 and AD are yet unknown. We carried out the transcriptomic analytical framework to delve into the SARS-CoV-2 impacts on AD progression. We analyzed both gene expression microarray and RNA-Seq datasets from SARS-CoV-2 and AD affected tissues. With neighborhood-based benchmarks and multilevel network topology, we obtained dysfunctional signaling and ontological pathways, gene disease (diseasesome) association network and protein-protein interaction network (PPIN), uncovered essential shared infection recurrence connectivities with biological insights underlying between SARS-CoV-2 and AD. We found a total of 77, 21, 9, 54 common DEGs for SARS-CoV-2 and inflammatory bowel disorder (IBD), SARS-CoV-2 and rheumatoid arthritis (RA), SARS-CoV-2 and systemic lupus erythematosus (SLE) and SARS-CoV-2 and type 1 diabetes (T1D). The enclosure of these common DEGs with bimolecular networks revealed 10 hub proteins (FYN, VEGFA, CTNNB1, KDR, STAT1, B2M, CD3G, ITGAV, TGFB3). Drugs such as amlodipine besylate, vorinostat, methylprednisolone, and disulfiram have been identified as a common ground between SARS-CoV-2 and AD from drug repurposing investigation which will stimulate the optimal selection of medications in the battle against this ongoing pandemic triggered by COVID-19.
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Affiliation(s)
- Md Al-Mustanjid
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - S M Hasan Mahmud
- Department of Computer Science, American International University-Bangladesh, Dhaka, 1229, Bangladesh
| | - Farzana Akter
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Shazzadur Rahman
- Department of Computer Science & Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Sajid Hossen
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia-7003, Bangladesh
| | - Mohammad Ali Moni
- Department of Computer Science and Engineering, Pabna Science & Technology University, Pabna, 6600, Bangladesh
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6
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Kong X, Diao S, Xu H, Sun J, Ma B. Association between miRNA-499 gene polymorphism and autoimmune diseases: A meta-analysis. PLoS One 2022; 17:e0266265. [PMID: 35358276 PMCID: PMC8970500 DOI: 10.1371/journal.pone.0266265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/17/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction The association between miRNA-499 rs3746444 and a variety of autoimmune diseases has been reported. However, these results were contradictory and just focused on one or two autoimmune diseases. The present study aims to examine the possible association between rs3746444 polymorphism and the risk of autoimmune diseases. Methods The studies that evaluated the association between miRNA-499 gene polymorphism and autoimmune diseases were retrieved. Five different genetic models were used to evaluate the association. The random-effects model was used to pool the effect sizes. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to estimate the associations. Stratification analyses were performed by ethnicity and type of autoimmune diseases. False-positive report probability (FPRP) was performed for determining noteworthy associations. Results Seventeen articles (twenty studies) involving 4,376 cases and 4,991 controls were identified and included in our meta-analysis. The pooled ORs of all eligible case-control studies indicated a significant association between miRNA-499 gene polymorphism and autoimmune diseases: (T vs. C: OR = 0.877; 95% CI: 0.774, 0.993; P = 0.039). Stratified analysis indicated a significant association across both Caucasian (TT vs. TC+CC: OR = 0.779; 95% CI: 0.622, 0.976; P = 0.030) and Asian (T vs. C: OR = 0.895; 95% CI: 0.808, 0.992; P = 0.035) populations. There was also a significant association in Behcet’s disease, rheumatoid arthritis, systemic lupus erythematosus, and ulcerative colitis populations. Conclusions Our meta-analysis suggested that the miRNA-499 rs3746444 polymorphism was associated with an elevated risk of autoimmune diseases in the overall analysis as well as Caucasian and Asian populations.
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Affiliation(s)
- Xiangjian Kong
- Department of Cardiology, The Affiliated Hospital of Binzhou Medical University, Binzhou, Shandong, China
| | - Shuling Diao
- Department of Cardiology, The Affiliated Hospital of Binzhou Medical University, Binzhou, Shandong, China
| | - Huipu Xu
- Department of Cardiology, The Affiliated Hospital of Binzhou Medical University, Binzhou, Shandong, China
| | - Junming Sun
- Department of Cardiology, The Affiliated Hospital of Binzhou Medical University, Binzhou, Shandong, China
| | - Baoxin Ma
- Second Department of Cardiology, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- * E-mail:
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Abstract
The last decade has seen an enormous increase in long non-coding RNA (lncRNA) research within rheumatology. LncRNAs are arbitrarily classed as non-protein encoding RNA transcripts that exceed 200 nucleotides in length. These transcripts have tissue and cell specific patterns of expression and are implicated in a variety of biological processes. Unsurprisingly, numerous lncRNAs are dysregulated in rheumatoid conditions, correlating with disease activity and cited as potential biomarkers and targets for therapeutic intervention. In this chapter, following an introduction into each condition, we discuss the lncRNAs involved in rheumatoid arthritis, osteoarthritis and systemic lupus erythematosus. These inflammatory joint conditions share several inflammatory signalling pathways and therefore not surprisingly many commonly dysregulated lncRNAs are shared across these conditions. In the interest of translational research only those lncRNAs which are strongly conserved have been addressed. The lncRNAs discussed here have diverse roles in regulating inflammation, proliferation, migration, invasion and apoptosis. Understanding the molecular basis of lncRNA function in rheumatology will be crucial in fully determining the inflammatory mechanisms that drive these conditions.
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Lari A, Pourbadie HG, Sharifi-Zarchi A, Akhtari M, Samimi LN, Jamshidi A, Mahmoudi M. Dysregulation of ribosome-related genes in ankylosing spondylitis: a systems biology approach and experimental method. BMC Musculoskelet Disord 2021; 22:789. [PMID: 34521416 PMCID: PMC8442383 DOI: 10.1186/s12891-021-04662-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 08/31/2021] [Indexed: 11/10/2022] Open
Abstract
Background Ankylosing spondylitis (AS) is an autoimmune rheumatic disease. Few candidate gene associations have been reported for AS and the current understanding of its pathogenesis remains still poor. Thus, the exact mechanism of AS is needed to urgently be disclosed. The purpose of this study was to identify candidate genes involving in AS disease. Methods and results GSE25101 publicly available microarray and GSE117769 RNA-seq datasets of AS patients were obtained for bioinformatics analyses. Gene set enrichment analysis showed that in the microarray dataset, the ribosome pathway was significantly up-regulated in AS compared with controls. Furthermore, some ribosomal components demonstrated overexpression in patients in the RNA-seq dataset. To confirm the findings, 20 AS patients and 20 matching controls were selected from the Rheumatology Research Center clinic, Shariati Hospital. PBMCs were separated from whole blood and RNA contents were extracted. Following the results of datasets analysis, the expression level of rRNA5.8S pseudogene, rRNA18S pseudogene, RPL23, RPL7, and RPL17 genes were measured through real-time PCR. Our findings showed dysregulation of rRNA5.8S and rRNA18S pseudogenes, and also the RPL17 gene in patients. Conclusion Considering that genes involved in ribosome biogenesis contributed to some AS-associated biological processes as well as diseases that have comorbidities with AS, our results might advance our understanding of the pathological mechanisms of ankylosing spondylitis. Supplementary Information The online version contains supplementary material available at 10.1186/s12891-021-04662-2.
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Affiliation(s)
- Arezou Lari
- Systems Biomedicine Unit, Pasteur Institute of Iran, Tehran, Iran.,Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, PO-BOX: 1411713137, Kargar Ave, Tehran, Iran
| | | | - Ali Sharifi-Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Maryam Akhtari
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, PO-BOX: 1411713137, Kargar Ave, Tehran, Iran.,Inflammation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Leila Nejatbakhsh Samimi
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, PO-BOX: 1411713137, Kargar Ave, Tehran, Iran
| | - Ahmadreza Jamshidi
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, PO-BOX: 1411713137, Kargar Ave, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, PO-BOX: 1411713137, Kargar Ave, Tehran, Iran. .,Inflammation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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Glavaški M, Velicki L. Shared Molecular Mechanisms of Hypertrophic Cardiomyopathy and Its Clinical Presentations: Automated Molecular Mechanisms Extraction Approach. Life (Basel) 2021; 11:life11080785. [PMID: 34440529 PMCID: PMC8398249 DOI: 10.3390/life11080785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 12/30/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiovascular disease with a prevalence of 1 in 500 people and varying clinical presentations. Although there is much research on HCM, underlying molecular mechanisms are poorly understood, and research on the molecular mechanisms of its specific clinical presentations is scarce. Our aim was to explore the molecular mechanisms shared by HCM and its clinical presentations through the automated extraction of molecular mechanisms. Molecular mechanisms were congregated by a query of the INDRA database, which aggregates knowledge from pathway databases and combines it with molecular mechanisms extracted from abstracts and open-access full articles by multiple machine-reading systems. The molecular mechanisms were extracted from 230,072 articles on HCM and 19 HCM clinical presentations, and their intersections were found. Shared molecular mechanisms of HCM and its clinical presentations were represented as networks; the most important elements in the intersections’ networks were found, centrality scores for each element of each network calculated, networks with reduced level of noise generated, and cooperatively working elements detected in each intersection network. The identified shared molecular mechanisms represent possible mechanisms underlying different HCM clinical presentations. Applied methodology produced results consistent with the information in the scientific literature.
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Affiliation(s)
- Mila Glavaški
- Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, 21000 Novi Sad, Serbia;
- Correspondence: or
| | - Lazar Velicki
- Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, 21000 Novi Sad, Serbia;
- Institute of Cardiovascular Diseases Vojvodina, Put Doktora Goldmana 4, 21204 Sremska Kamenica, Serbia
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Pellenz FM, Dieter C, Lemos NE, Bauer AC, Souza BMD, Crispim D. Association of TYK2 polymorphisms with autoimmune diseases: A comprehensive and updated systematic review with meta-analysis. Genet Mol Biol 2021; 44:e20200425. [PMID: 33949620 PMCID: PMC8097517 DOI: 10.1590/1678-4685-gmb-2020-0425] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/09/2021] [Indexed: 12/05/2022] Open
Abstract
Autoimmune diseases are characterized by the loss of self-tolerance, leading to
immune-mediated tissue destruction and chronic inflammation. Tyrosine kinase 2
(TYK2) protein plays a key role in immunity and apoptosis pathways. Studies have
reported associations between single nucleotide polymorphisms (SNPs) in the
TYK2 gene and autoimmune diseases; however, results are
still inconclusive. Thus, we conducted a systematic review followed by
meta-analysis. A literature search was performed to find studies that
investigated associations between TYK2 SNPs and autoimmune
diseases (multiple sclerosis, systemic lupus erythematosus, Crohn’s disease,
ulcerative colitis, psoriasis, rheumatoid arthritis, type 1 diabetes, and
inflammatory bowel disease). Pooled odds ratios (OR) with 95 % CI were
calculated using random (REM) or fixed (FEM) effects models in the Stata 11.0
Software. Thirty-four articles were eligible for inclusion in the meta-analyses,
comprising 9 different SNPs: rs280496, rs280500, rs280523, rs280519, rs2304256,
rs12720270, rs12720356, rs34536443, and rs35018800. Meta-analysis results showed
the minor alleles of rs2304256, rs12720270, rs12720356, rs34536443, and
rs35018800 SNPs were associated with protection against autoimmune diseases.
Moreover, the A allele of the rs280519 SNP was associated with risk for systemic
lupus erythematosus. Our meta-analyses demonstrated that the rs2304256,
rs12720270, rs12720356, rs34536443, rs35018800, and rs280519 SNPs in the
TYK2 gene are associated with different autoimmune
diseases.
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Affiliation(s)
- Felipe Mateus Pellenz
- Hospital de Clínicas de Porto Alegre, Serviço de Endocrinologia, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| | - Cristine Dieter
- Hospital de Clínicas de Porto Alegre, Serviço de Endocrinologia, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| | - Natália Emerim Lemos
- Hospital de Clínicas de Porto Alegre, Serviço de Endocrinologia, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| | - Andrea Carla Bauer
- Hospital de Clínicas de Porto Alegre, Serviço de Endocrinologia, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil.,Hospital de Clínicas de Porto Alegre, Serviço de Nefrologia, Porto Alegre, RS, Brazil
| | - Bianca Marmontel de Souza
- Hospital de Clínicas de Porto Alegre, Serviço de Endocrinologia, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| | - Daisy Crispim
- Hospital de Clínicas de Porto Alegre, Serviço de Endocrinologia, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
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11
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Li Z, Liu Y, Jia A, Cui Y, Feng J. Cerebrospinal fluid cells immune landscape in multiple sclerosis. J Transl Med 2021; 19:125. [PMID: 33766068 PMCID: PMC7995713 DOI: 10.1186/s12967-021-02804-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
Background Multiple Sclerosis (MS) is a potentially devastating autoimmune neurological disorder, which characteristically induces demyelination of white matter in the brain and spinal cord. Methods In this study, three characteristics of the central nervous system (CNS) immune microenvironment occurring during MS onset were explored; immune cell proportion alteration, differential gene expression profile, and related pathways. The raw data of two independent datasets were obtained from the ArrayExpress database; E-MTAB-69, which was used as a derivation cohort, and E-MTAB-2374 which was used as a validation cohort. Differentially expressed genes (DEGs) were identified by the false discovery rate (FDR) value of < 0.05 and |log2 (Fold Change)|> 1, for further analysis. Then, functional enrichment analyses were performed to explore the pathways associated with MS onset. The gene expression profiles were analyzed using CIBERSORT to identify the immune type alterations involved in MS disease. Results After verification, the proportion of five types of immune cells (plasma cells, monocytes, macrophage M2, neutrophils and eosinophils) in cerebrospinal fluid (CSF) were revealed to be significantly altered in MS cases compared to the control group. Thus, the complement and coagulation cascades and the systemic lupus erythematosus (SLE) pathways may play critical roles in MS. We identified NLRP3, LILRB2, C1QB, CD86, C1QA, CSF1R, IL1B and TLR2 as eight core genes correlated with MS. Conclusions Our study identified the change in the CNS immune microenvironment of MS cases by analysis of the in silico data using CIBERSORT. Our data may assist in providing directions for further research as to the molecular mechanisms of MS and provide future potential therapeutic targets in treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02804-7.
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Affiliation(s)
- Zijian Li
- Department of Neurology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, Liaoning, 110004, China
| | - Yongchao Liu
- Department of Neurology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, Liaoning, 110004, China
| | - Aili Jia
- Department of Neurology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, Liaoning, 110004, China
| | - Yueran Cui
- Department of Neurology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, Liaoning, 110004, China
| | - Juan Feng
- Department of Neurology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, Liaoning, 110004, China.
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Guo J, Han B, Wang J, Zhang L, Chen N, Sun W, Gao Y. The differential expression and potential roles of circular RNAs in children with anti-NMDA receptor encephalitis. J Neuroimmunol 2020; 348:577381. [PMID: 32911360 DOI: 10.1016/j.jneuroim.2020.577381] [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: 07/19/2020] [Revised: 08/27/2020] [Accepted: 08/29/2020] [Indexed: 10/23/2022]
Abstract
To explore the role of circular RNAs (circRNAs) in pediatric anti-N-methyl-d-aspartate (NMDA) receptor encephalitis, we assessed the profiles of circRNAs and mRNAs in blood leukocytes from anti-NMDA receptor encephalitis patients and healthy controls using microarray analysis. 1196 circRNAs and 719 mRNAs (change ≥2, p < .05) were dysregulated in anti-NMDA receptor encephalitis patients, relative to healthy controls, based on microarray data. Further bioinformatic analysis demonstrated that the host genes of dysregulated circRNAs are primarily associated with receptor internalization. In conclusion, circRNAs may be implicated in the pathogenesis of pediatric anti-NMDA receptor encephalitis.
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Affiliation(s)
- Jiamin Guo
- Department of Pediatrics, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China; Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong first Medical University, Jinan, Shandong, 250021, China
| | - Bo Han
- Department of Pediatrics, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China; Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong first Medical University, Jinan, Shandong, 250021, China.
| | - Jing Wang
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong first Medical University, Jinan, Shandong, 250021, China
| | - Li Zhang
- Department of Pediatrics, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Na Chen
- Department of Pediatrics, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China; Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong first Medical University, Jinan, Shandong, 250021, China
| | - Wenxiu Sun
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong first Medical University, Jinan, Shandong, 250021, China
| | - Yuxing Gao
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong first Medical University, Jinan, Shandong, 250021, China
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Abstract
PURPOSE OF REVIEW Rheumatoid arthritis (RA) is a prototypic autoimmune disease manifesting as chronic inflammation of the synovium and leading to acceleration of cardiovascular disease and shortening of life expectancy. The basic defect causing autoimmunity has remained elusive, but recent insights have challenged the notion that autoantigen is the core driver. RECENT FINDINGS Emerging data have added metabolic cues involved in the proper maintenance and activation of immune cells as pathogenic regulators. Specifically, studies have unveiled metabolic pathways that enforce T cell fate decisions promoting tissue inflammation; including T cell tissue invasiveness, T cell cytokine release, T cell-dependent macrophage activation and inflammatory T cell death. At the center of the metabolic abnormalities lies the mitochondria, which is consistently underperforming in RA T cells. The mitochondrial defect results at least partially from insufficient DNA repair and leads to lipid droplet accumulation, formation of invasive membrane ruffles, inflammasome activation and pyroptotic T cell death. SUMMARY T cells in patients with RA, even naïve T cells never having been involved in inflammatory lesions, have a unique metabolic signature and the changes in intracellular metabolites drive pathogenic T cell behavior. Recognizing the role of metabolic signals in cell fate decisions opens the possibility for immunomodulation long before the end stage synovial inflammation encountered in clinical practice.
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Biassoni R, Di Marco E, Squillario M, Barla A, Piccolo G, Ugolotti E, Gatti C, Minuto N, Patti G, Maghnie M, d'Annunzio G. Gut Microbiota in T1DM-Onset Pediatric Patients: Machine-Learning Algorithms to Classify Microorganisms as Disease Linked. J Clin Endocrinol Metab 2020; 105:5871462. [PMID: 32692360 DOI: 10.1210/clinem/dgaa407] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
Abstract
AIMS The purpose of this work is to find the gut microbial fingerprinting of pediatric patients with type 1 diabetes. METHODS The microbiome of 31 children with type 1 diabetes at onset and of 25 healthy children was determined using multiple polymorphic regions of the 16S ribosomal RNA. We performed machine-learning analyses and metagenome functional analysis to identify significant taxa and their metabolic pathways content. RESULTS Compared with healthy controls, patients showed a significantly higher relative abundance of the following most important taxa: Bacteroides stercoris, Bacteroides fragilis, Bacteroides intestinalis, Bifidobacterium bifidum, Gammaproteobacteria and its descendants, Holdemania, and Synergistetes and its descendants. On the contrary, the relative abundance of Bacteroides vulgatus, Deltaproteobacteria and its descendants, Parasutterella and the Lactobacillus, Turicibacter genera were significantly lower in patients with respect to healthy controls. The predicted metabolic pathway more associated with type 1 diabetes patients concerns "carbon metabolism," sugar and iron metabolisms in particular. Among the clinical variables considered, standardized body mass index, anti-insulin autoantibodies, glycemia, hemoglobin A1c, Tanner stage, and age at onset emerged as most significant positively or negatively correlated with specific clusters of taxa. CONCLUSIONS The relative abundance and supervised analyses confirmed the importance of B stercoris in type 1 diabetes patients at onset and showed a relevant role of Synergistetes and its descendants in patients with respect to healthy controls. In general the robustness and coherence of the showed results underline the relevance of studying the microbioma using multiple polymorphic regions, different types of analysis, and different approaches within each analysis.
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Affiliation(s)
- Roberto Biassoni
- Molecular Diagnostics, Analysis Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Eddi Di Marco
- Molecular Diagnostics, Analysis Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | | | - Gianluca Piccolo
- Pediatric Clinic Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Elisabetta Ugolotti
- Molecular Diagnostics, Analysis Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Cinzia Gatti
- Molecular Diagnostics, Analysis Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Nicola Minuto
- Pediatric Clinic Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Giuseppa Patti
- Department of Pediatrics, IRCCS Istituto Giannina Gaslini, University of Genoa, Genoa, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University Of Genoa, Genoa, Italy
| | - Mohamad Maghnie
- Pediatric Clinic Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Pediatrics, IRCCS Istituto Giannina Gaslini, University of Genoa, Genoa, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University Of Genoa, Genoa, Italy
| | - Giuseppe d'Annunzio
- Pediatric Clinic Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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15
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Li X, Yang Y, Sun G, Dai W, Jie X, Du Y, Huang R, Zhang J. Promising targets and drugs in rheumatoid arthritis: a module-based and cumulatively scoring approach. Bone Joint Res 2020; 9:501-514. [PMID: 32922758 PMCID: PMC7468554 DOI: 10.1302/2046-3758.98.bjr-2019-0301.r1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AIMS Rheumatoid arthritis (RA) is a systematic autoimmune disorder, characterized by synovial inflammation, bone and cartilage destruction, and disease involvement in multiple organs. Although numerous drugs are employed in RA treatment, some respond little and suffer from severe side effects. This study aimed to screen the candidate therapeutic targets and promising drugs in a novel method. METHODS We developed a module-based and cumulatively scoring approach that is a deeper-layer application of weighted gene co-expression network (WGCNA) and connectivity map (CMap) based on the high-throughput datasets. RESULTS Four noteworthy RA-related modules were identified, revealing the immune- and infection-related biological processes and pathways involved in RA. HLA-DMA, HLA-DMB, HLA-DPA1, HLA-DPB1, HLA-DQB1, HLA-DRA, HLA-DRB1, BLNK, BTK, CD3D, CD4, IL2RG, INPP5D, LCK, PTPRC, RAC2, SYK, and VAV1 were recognized as the key hub genes with high connectivity in gene regulation networks and gene pathway networks. Moreover, the long noncoding RNAs (lncRNAs) in the RA-related modules, such as FAM30A and NEAT1, were identified as the indispensable interactors with the hub genes. Finally, candidate drugs were screened by developing a cumulatively scoring approach based on the selected modules. Niclosamide and the other compounds of T-type calcium channel blocker, IKK inhibitor, and PKC activator, HIF activator, and proteasome inhibitor, which harbour the similar gene signature with niclosamide, were promising drugs with high specificity and broad coverage for the RA-related modules. CONCLUSION This study provides not only the promising targets and drugs for RA but also a novel methodological insight into the target and drug screening.Cite this article: Bone Joint Res 2020;9(8):501-514.
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Affiliation(s)
- Xingyan Li
- Department of Bone and Joint Surgery, The Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yejing Yang
- Department of Bone and Joint Surgery, The Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Guili Sun
- Department of Nutriology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wanwu Dai
- Department of Bone and Joint Surgery, The Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xuri Jie
- Department of Hematology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yongjun Du
- Department of Bone and Joint Surgery, The Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Runjie Huang
- Second Clinical College, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaming Zhang
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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16
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Langley MR, Yoon H, Kim HN, Choi CI, Simon W, Kleppe L, Lanza IR, LeBrasseur NK, Matveyenko A, Scarisbrick IA. High fat diet consumption results in mitochondrial dysfunction, oxidative stress, and oligodendrocyte loss in the central nervous system. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165630. [PMID: 31816440 PMCID: PMC7982965 DOI: 10.1016/j.bbadis.2019.165630] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/14/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
Abstract
Metabolic syndrome is a key risk factor and co-morbidity in multiple sclerosis (MS) and other neurological conditions, such that a better understanding of how a high fat diet contributes to oligodendrocyte loss and the capacity for myelin regeneration has the potential to highlight new treatment targets. Results demonstrate that modeling metabolic dysfunction in mice with chronic high fat diet (HFD) consumption promotes loss of oligodendrocyte progenitors across the brain and spinal cord. A number of transcriptomic and metabolomic changes in ER stress, mitochondrial dysfunction, and oxidative stress pathways in HFD-fed mouse spinal cords were also identified. Moreover, deficits in TCA cycle intermediates and mitochondrial respiration were observed in the chronic HFD spinal cord tissue. Oligodendrocytes are known to be particularly vulnerable to oxidative damage, and we observed increased markers of oxidative stress in both the brain and spinal cord of HFD-fed mice. We additionally identified that increased apoptotic cell death signaling is underway in oligodendrocytes from mice chronically fed a HFD. When cultured under high saturated fat conditions, oligodendrocytes decreased both mitochondrial function and differentiation. Overall, our findings show that HFD-related changes in metabolic regulators, decreased mitochondrial function, and oxidative stress contribute to a loss of myelinating cells. These studies identify HFD consumption as a key modifiable lifestyle factor for improved myelin integrity in the adult central nervous system and in addition new tractable metabolic targets for myelin protection and repair strategies.
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Affiliation(s)
- Monica R Langley
- Department of Physical Medicine & Rehabilitation, Rehabilitation Medicine Research Center, Mayo Clinic, Rochester, MN 55905, USA
| | - Hyesook Yoon
- Department of Physical Medicine & Rehabilitation, Rehabilitation Medicine Research Center, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Ha Neui Kim
- Department of Physical Medicine & Rehabilitation, Rehabilitation Medicine Research Center, Mayo Clinic, Rochester, MN 55905, USA
| | - Chan-Il Choi
- Department of Physical Medicine & Rehabilitation, Rehabilitation Medicine Research Center, Mayo Clinic, Rochester, MN 55905, USA
| | - Whitney Simon
- Department of Physical Medicine & Rehabilitation, Rehabilitation Medicine Research Center, Mayo Clinic, Rochester, MN 55905, USA
| | - Laurel Kleppe
- Department of Physical Medicine & Rehabilitation, Rehabilitation Medicine Research Center, Mayo Clinic, Rochester, MN 55905, USA
| | - Ian R Lanza
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA; Department of Endocrinology, Mayo Clinic, Rochester, MN 55905, USA
| | - Nathan K LeBrasseur
- Department of Physical Medicine & Rehabilitation, Rehabilitation Medicine Research Center, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Aleksey Matveyenko
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA; Department of Endocrinology, Mayo Clinic, Rochester, MN 55905, USA
| | - Isobel A Scarisbrick
- Department of Physical Medicine & Rehabilitation, Rehabilitation Medicine Research Center, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA.
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17
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Weighted Gene Coexpression Network Analysis Identified MicroRNA Coexpression Modules and Related Pathways in Type 2 Diabetes Mellitus. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:9567641. [PMID: 31915515 PMCID: PMC6935443 DOI: 10.1155/2019/9567641] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/04/2019] [Accepted: 11/11/2019] [Indexed: 12/31/2022]
Abstract
Objective Type 2 diabetes mellitus (T2DM) is a metabolic disease with high incidence, which has seriously affected human life and health. MicroRNA, a short-chain noncoding RNA, plays an important role in T2DM. Identification of meaningful microRNA modules and the role of microRNAs provide a basis for searching potential biomarkers of T2DM. Materials and Methods In this study, three newly diagnosed patients with T2DM and three controls were selected for Whole Peripheral Blood RNA Sequencing to establish a microRNA library. Weighted gene coexpression network analysis (WGCNA) was applied to construct coexpression modules and to detect the trait-related microRNA modules; then, KEGG enrichment analysis was performed to predict the biological function of the interest modules, and candidate hub microRNAs were screened out by the value of module membership (MM) and protein-protein interaction (PPI) network. Result Four microRNA modules (blue, brown, magenta, and turquoise) were highly associated with the T2DM; the number of miRNAs in these modules ranged from 41 to 469. The Fc gamma R-mediated phagocytosis pathway, Rap1 signaling pathway, MAPK signaling pathway, and Lysosome pathway were common pathways in three of the four modules. RPS27A, UBC, and RAC1 were the top three proteins in our study; their corresponding RNAs were miR-1271-5p, miR-130a-3p, miR-130b-3p, and miR-574-3p. Conclusion In summary, this study identified blood miRNAs in human T2DM using RNA sequencing. The findings may be the foundation for understanding the potential role of miRNAs in T2DM.
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18
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Testori A, Lasorsa VA, Cimmino F, Cantalupo S, Cardinale A, Avitabile M, Limongelli G, Russo MG, Diskin S, Maris J, Devoto M, Keavney B, Cordell HJ, Iolascon A, Capasso M. Exploring Shared Susceptibility between Two Neural Crest Cells Originating Conditions: Neuroblastoma and Congenital Heart Disease. Genes (Basel) 2019; 10:genes10090663. [PMID: 31480262 PMCID: PMC6771154 DOI: 10.3390/genes10090663] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/12/2019] [Accepted: 08/26/2019] [Indexed: 12/13/2022] Open
Abstract
In the past years, genome wide association studies (GWAS) have provided evidence that inter-individual susceptibility to diverse pathological conditions can reveal a common genetic architecture. Through the analysis of congenital heart disease (CHD) and neuroblastoma (NB) GWAS data, we aimed to dissect the genetic susceptibility shared between these conditions, which are known to arise from neural crest cell (NCC) migration or development abnormalities, via identification and functional characterization of common regions of association. Two loci (2q35 and 3q25.32) harbor single nucleotide polymorphisms (SNPs) that are associated at a p-value < 10-3 with conotruncal malformations and ventricular septal defect respectively, as well as with NB. In addition, the lead SNP in 4p16.2 for atrial septal defect and the lead SNP in 3q25.32 for tetralogy of Fallot are less than 250 Kb distant from the lead SNPs for NB at the same genomic regions. Some of these shared susceptibility loci regulate the expression of relevant genes involved in NCC formation and developmental processes (such as BARD1, MSX1, and SHOX2) and are enriched in several epigenetic markers from NB and fetal heart cell lines. Although the clinical correlation between NB and CHD is unclear, our exploration of a possible common genetic basis between NB and a subset of cardiac malformations can help shed light on their shared embryological origin and pathogenetic mechanisms.
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Affiliation(s)
- Alessandro Testori
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Vito A Lasorsa
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Flora Cimmino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Sueva Cantalupo
- IRCCS SDN, Istituto di Ricerca Diagnostica e Nucleare, 80143 Naples, Italy
| | - Antonella Cardinale
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Marianna Avitabile
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Giuseppe Limongelli
- Division of Cardiology, Università degli Studi della Campania "Luigi Vanvitelli" - AO dei Colli, Presidio Monaldi, 80121 Naples, Italy
| | - Maria Giovanna Russo
- Division of Cardiology, Università degli Studi della Campania "Luigi Vanvitelli" - AO dei Colli, Presidio Monaldi, 80121 Naples, Italy
| | - Sharon Diskin
- Division of Oncology and Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Maris
- Division of Oncology and Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcella Devoto
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Translational and Precision Medicine, University of Rome "La Sapienza", 00185 Rome, Italy
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bernard Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M20 4BX, UK
| | - Heather J Cordell
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy.
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy.
- IRCCS SDN, Istituto di Ricerca Diagnostica e Nucleare, 80143 Naples, Italy.
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19
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Identification of a Shared Microbiomic and Metabolomic Profile in Systemic Autoimmune Diseases. J Clin Med 2019; 8:jcm8091291. [PMID: 31450824 PMCID: PMC6780636 DOI: 10.3390/jcm8091291] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/17/2019] [Accepted: 08/21/2019] [Indexed: 12/12/2022] Open
Abstract
Dysbiosis has been described in systemic autoimmune diseases (SADs), including systemic lupus erythematosus (SLE), Sjögren’s syndrome (SjS), and primary anti-phosholipid syndrome (PAPS), however the biological implications of these associations are often elusive. Stool and plasma samples from 114 subjects, including in SLE (n = 27), SjS (n = 23), PAPs (n = 11) and undifferentiated connective tissue (UCTD, n = 26) patients, and geographically-matched healthy controls (HCs, n = 27), were collected for microbiome (16s rRNA gene sequencing) and metabolome (high-performance liquid chromatography coupled to mass spectrometry) analysis to identify shared characteristics across diseases. Out of 130 identified microbial genera, a subset of 29 bacteria was able to differentiate study groups (area under receiver operating characteristics (AUROC) = 0.730 ± 0.025). A fair classification was obtained with a subset of 41 metabolic peaks out of 254 (AUROC = 0.748 ± 0.021). In both models, HCs were well separated from SADs, while UCTD largely overlapped with the other diseases. In all of the SADs pro-tolerogenic bacteria were reduced, while pathobiont genera were increased. Metabolic alterations included two clusters comprised of: (a) members of the acylcarnitine family, positively correlating with a Prevotella-enriched cluster and negatively correlating with a butyrate-producing bacteria-enriched cluster; and (b) phospholipids, negatively correlating with butyrate-producing bacteria. These findings demonstrate a strong interaction between intestinal microbiota and metabolic function in patients with SADs.
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20
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Tellefsen S, Morthen MK, Richards SM, Lieberman SM, Rahimi Darabad R, Kam WR, Sullivan DA. Sex Effects on Gene Expression in Lacrimal Glands of Mouse Models of Sjögren Syndrome. Invest Ophthalmol Vis Sci 2019; 59:5599-5614. [PMID: 30481277 PMCID: PMC6262646 DOI: 10.1167/iovs.18-25772] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Purpose Sjögren syndrome is an autoimmune disease that occurs primarily in women, and is associated with lacrimal gland inflammation and aqueous-deficient dry eye. We hypothesize that sex-associated differences in lacrimal gland gene expression are very important in promoting lymphocyte accumulation in this tissue and contribute to the onset, progression, and/or severity of the inflammatory disease process. To test our hypothesis, we explored the nature and extent of sex-related differences in gene expression in autoimmune lacrimal glands. Methods Lacrimal glands were collected from age-matched, adult, male and female MRL/MpJ-Tnfrsf6lpr (MRL/lpr) and nonobese diabetic/LtJ (NOD) mice. Glands were processed for the analysis of differentially expressed mRNAs by using CodeLink Bioarrays and Affymetrix GeneChips. Data were evaluated with bioinformatics and statistical software. Results Our results show that sex significantly influences the expression of thousands of genes in lacrimal glands of MRL/lpr and NOD mice. The immune nature of this glandular response is very dependent on the Sjögren syndrome model. Lacrimal glands of female, as compared with male, MRL/lpr mice contain a significant increase in the expression of genes related to inflammatory responses, antigen processing, and chemokine pathways. In contrast, it is the lacrimal tissue of NOD males, and not females, that presents with a significantly greater expression of immune-related genes. Conclusions These data support our hypothesis that sex-related differences in gene expression contribute to lacrimal gland disease in Sjögren syndrome. Our findings also suggest that factors in the lacrimal gland microenvironment are critically important in mediating these sex-associated immune effects.
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Affiliation(s)
- Sara Tellefsen
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, Massachusetts, United States.,Department of Medical Biochemistry, Oslo University Hospital/Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mathias Kaurstad Morthen
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, Massachusetts, United States.,Department of Medical Biochemistry, Oslo University Hospital/Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Stephen M Richards
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, Massachusetts, United States.,Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Scott M Lieberman
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
| | - Raheleh Rahimi Darabad
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, Massachusetts, United States.,Department of Clinical Anesthesia, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Wendy R Kam
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - David A Sullivan
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
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21
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Xu F, Jin L, Jin Y, Nie Z, Zheng H. Long noncoding RNAs in autoimmune diseases. J Biomed Mater Res A 2018; 107:468-475. [PMID: 30478988 DOI: 10.1002/jbm.a.36562] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022]
Abstract
With the completion of the human genome project and further development of high-throughput genomic technologies, interest in long noncoding RNAs (lncRNAs), which are defined as non-protein-coding RNAs at least 200 nucleotides in length, has strongly increased, and lncRNAs have become a major research direction. Increasing evidence demonstrates that lncRNAs are closely related to human growth and development and to disease occurrence via various mechanisms. lncRNAs also play crucial roles in the differentiation and activation of immune cells, and their relationships with human autoimmune diseases have received increasing attention. The development of biotechnology has led to the gradual discovery of many potential lncRNA functions. In this review, we discuss various lncRNAs that have been implicated in different human autoimmune diseases, focusing on their clinical applications as potential biomarkers and therapeutic targets in the pathologies of diverse human autoimmune diseases. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 468-475, 2019.
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Affiliation(s)
- Fei Xu
- Department of Microbiology and Immunology, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Lei Jin
- Department of Inspection and Quarantine, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Yueling Jin
- Department of Inspection and Quarantine, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Zhiyan Nie
- Department of Microbiology and Immunology, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Hong Zheng
- Department of Microbiology and Immunology, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
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Aguirre-Plans J, Piñero J, Menche J, Sanz F, Furlong LI, Schmidt HHHW, Oliva B, Guney E. Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology. Pharmaceuticals (Basel) 2018; 11:E61. [PMID: 29932108 PMCID: PMC6160959 DOI: 10.3390/ph11030061] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/15/2018] [Accepted: 06/19/2018] [Indexed: 01/13/2023] Open
Abstract
The past decades have witnessed a paradigm shift from the traditional drug discovery shaped around the idea of “one target, one disease” to polypharmacology (multiple targets, one disease). Given the lack of clear-cut boundaries across disease (endo)phenotypes and genetic heterogeneity across patients, a natural extension to the current polypharmacology paradigm is to target common biological pathways involved in diseases via endopharmacology (multiple targets, multiple diseases). In this study, we present proximal pathway enrichment analysis (PxEA) for pinpointing drugs that target common disease pathways towards network endopharmacology. PxEA uses the topology information of the network of interactions between disease genes, pathway genes, drug targets and other proteins to rank drugs by their interactome-based proximity to pathways shared across multiple diseases, providing unprecedented drug repurposing opportunities. Using PxEA, we show that many drugs indicated for autoimmune disorders are not necessarily specific to the condition of interest, but rather target the common biological pathways across these diseases. Finally, we provide high scoring drug repurposing candidates that can target common mechanisms involved in type 2 diabetes and Alzheimer’s disease, two conditions that have recently gained attention due to the increased comorbidity among patients.
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Affiliation(s)
- Joaquim Aguirre-Plans
- Research Programme on Biomedical Informatics, the Hospital del Mar Medical Research Institute and Pompeu Fabra University, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Janet Piñero
- Research Programme on Biomedical Informatics, the Hospital del Mar Medical Research Institute and Pompeu Fabra University, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Jörg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria.
| | - Ferran Sanz
- Research Programme on Biomedical Informatics, the Hospital del Mar Medical Research Institute and Pompeu Fabra University, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Laura I Furlong
- Research Programme on Biomedical Informatics, the Hospital del Mar Medical Research Institute and Pompeu Fabra University, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Harald H H W Schmidt
- Department of Pharmacology and Personalised Medicine, CARIM, FHML, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands.
| | - Baldo Oliva
- Research Programme on Biomedical Informatics, the Hospital del Mar Medical Research Institute and Pompeu Fabra University, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Emre Guney
- Research Programme on Biomedical Informatics, the Hospital del Mar Medical Research Institute and Pompeu Fabra University, Dr. Aiguader 88, 08003 Barcelona, Spain.
- Department of Pharmacology and Personalised Medicine, CARIM, FHML, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands.
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