1
|
Sentis G, Loukogiannaki C, Malissovas N, Nikolopoulos D, Manolakou T, Flouda S, Grigoriou M, Banos A, Boumpas DT, Filia A. A network-based approach reveals long non-coding RNAs associated with disease activity in lupus nephritis: key pathways for flare and potential biomarkers to be used as liquid biopsies. Front Immunol 2023; 14:1203848. [PMID: 37475860 PMCID: PMC10355154 DOI: 10.3389/fimmu.2023.1203848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Objective A blood-based biomarker is needed to assess lupus nephritis (LN) disease activity, minimizing the need for invasive kidney biopsies. Long non-coding RNAs (lncRNAs) are known to regulate gene expression, appear to be stable in human plasma, and can serve as non-invasive biomarkers. Methods Transcriptomic data of whole blood samples from 74 LN patients and 20 healthy subjects (HC) were analyzed to identify differentially expressed (DE) lncRNAs associated with quiescent disease and flares. Weighted gene co-expression network analysis (WGCNA) was performed to uncover lncRNAs with a central role (hub lncRNAs) in regulating key biological processes that drive LN disease activity. The association of hub lncRNAs with disease activity was validated using RT-qPCR on an independent cohort of 15 LN patients and 9 HC. cis- and trans-targets of validated lncRNAs were explored in silico to examine potential mechanisms of their action. Results There were 444 DE lncRNAs associated with quiescent disease and 6 DE lncRNAs associated with flares (FDR <0.05). WGCNA highlighted IFN signaling and B-cell activity/adaptive immunity as the most significant processes contributing to nephritis activity. Four disease-activity-associated lncRNAs, namely, NRIR, KLHDC7B-DT, MIR600HG, and FAM30A, were detected as hub genes and validated in an independent cohort. NRIR and KLHDC7B-DT emerged as potential key regulators of IFN-mediated processes. Network analysis suggests that FAM30A and MIR600HG are likely to play a central role in the regulation of B-cells in LN through cis-regulation effects and a competing endogenous RNA mechanism affecting immunoglobulin gene expression and the IFN-λ pathway. Conclusions The expression of lncRNAs NRIR, KLHDC7B-DT, FAM30A, and MIR600HG were associated with disease activity and could be further explored as blood-based biomarkers and potential liquid biopsy on LN.
Collapse
Affiliation(s)
- George Sentis
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Catherine Loukogiannaki
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Nikos Malissovas
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Dionysis Nikolopoulos
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Theodora Manolakou
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Sofia Flouda
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Maria Grigoriou
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
- 1st Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Aggelos Banos
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Dimitrios T. Boumpas
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Anastasia Filia
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
- 1st Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| |
Collapse
|
2
|
Gil-Varea E, Fedetz M, Eixarch H, Spataro N, Villar LM, Urcelay E, Saiz A, Fernández Ó, Leyva L, Ramió-Torrentà L, Vandenbroeck K, Otaegui D, Castillo-Triviño T, Izquierdo G, Malhotra S, Bosch E, Navarro A, Alcina A, Montalban X, Matesanz F, Comabella M. A New Risk Variant for Multiple Sclerosis at 11q23.3 Locus Is Associated with Expansion of CXCR5+ Circulating Regulatory T Cells. J Clin Med 2020; 9:jcm9030625. [PMID: 32110891 PMCID: PMC7141122 DOI: 10.3390/jcm9030625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 12/22/2022] Open
Abstract
Genome-wide association studies and meta-analysis have contributed to the identification of more than 200 loci associated with multiple sclerosis (MS). However, a proportion of MS heritability remains unknown. We aimed to uncover new genetic variants associated with MS and determine their functional effects. For this, we resequenced the exons and regulatory sequences of 14 MS risk genes in a cohort of MS patients and healthy individuals (n = 1070) and attempted to validate a selection of signals through genotyping in an independent cohort (n = 5138). We identified three new MS-associated variants at C-X-C motif chemokine receptor 5 (CXCR5), Ts translation elongation factor, mitochondrial (TSFM) and cytochrome P450 family 24 subfamily A member 1 (CYP24A1). Rs10892307 resulted in a new signal at the CXCR5 region that explains one of the associations with MS within the locus. This polymorphism and three others in high linkage disequilibrium mapped within regulatory regions. Of them, rs11602393 showed allele-dependent enhancer activity in the forward orientation as determined by luciferase reporter assays. Immunophenotyping using peripheral blood mononuclear cells from MS patients associated the minor allele of rs10892307 with increased percentage of regulatory T cells expressing CXCR5. This work reports a new signal for the CXCR5 MS risk locus and points to rs11602393 as the causal variant. The expansion of CXCR5+ circulating regulatory T cells induced by this variant could cause its MS association.
Collapse
Affiliation(s)
- Elia Gil-Varea
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (E.G.-V.); (H.E.); (S.M.); (X.M.)
| | - Maria Fedetz
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), 18016 Granada, Spain; (M.F.); (A.A.)
| | - Herena Eixarch
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (E.G.-V.); (H.E.); (S.M.); (X.M.)
| | - Nino Spataro
- Genetics Laboratory, UDIAT-Centre Diagnòstic, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, 08208 Sabadell, Spain;
| | - Luisa María Villar
- Departments of Immunology and Neurology, Multiple Sclerosis Unit, Hospital Ramon y Cajal, (IRYCIS), 28034 Madrid, Spain;
| | - Elena Urcelay
- Lab. of Genetics of Complex Diseases, Hospital Clinico San Carlos, Instituto de Investigacion Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain;
| | - Albert Saiz
- Servicio de Neurología, Hospital Clinic and Institut d’Investigació Biomèdica Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain;
| | - Óscar Fernández
- Unidad de Gestión Clínica de Neurociencias, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Regional Universitario de Málaga, Universidad de Málaga, 29010 Málaga, Spain; (Ó.F.); (L.L.)
| | - Laura Leyva
- Unidad de Gestión Clínica de Neurociencias, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Regional Universitario de Málaga, Universidad de Málaga, 29010 Málaga, Spain; (Ó.F.); (L.L.)
| | - Lluís Ramió-Torrentà
- Girona Neuroimmunology and Multiple Sclerosis Unit, Neurology Department, Dr. Josep Trueta University Hospital, Neurodegeneration and Neuroinflammation Group, Girona Biomedical Research Institute (IdIBGi), Department of Medical Sciences, Faculty of Medicine, University of Girona, 17190 Girona, Spain;
| | - Koen Vandenbroeck
- Inflammation & Biomarkers Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - David Otaegui
- Neurosciences Area, Biodonostia Health Research Institute, 20014 San Sebastián, Spain;
| | | | - Guillermo Izquierdo
- Departamento de Neurología, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain;
| | - Sunny Malhotra
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (E.G.-V.); (H.E.); (S.M.); (X.M.)
| | - Elena Bosch
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain; (E.B.); (A.N.)
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 43200 Reus, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain; (E.B.); (A.N.)
- Centre de Regulació Genòmica (CRG), 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Antonio Alcina
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), 18016 Granada, Spain; (M.F.); (A.A.)
| | - Xavier Montalban
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (E.G.-V.); (H.E.); (S.M.); (X.M.)
- Center for Multiple Sclerosis, St. Michael’s Hospital, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Fuencisla Matesanz
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), 18016 Granada, Spain; (M.F.); (A.A.)
- Correspondence: (F.M.); (M.C.); Tel.: +34-958-181-668 (F.M.); +34-932-746-834 (M.C.); Fax: +34-932-746-084 (M.C.)
| | - Manuel Comabella
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (E.G.-V.); (H.E.); (S.M.); (X.M.)
- Correspondence: (F.M.); (M.C.); Tel.: +34-958-181-668 (F.M.); +34-932-746-834 (M.C.); Fax: +34-932-746-084 (M.C.)
| |
Collapse
|
3
|
Smagina I, Lunev K, Elchaninova S. Association between vitamin D status and CYP27b1 and CYP24A1 gene polymorphisms in patients with multiple sclerosis in the Altai region. Zh Nevrol Psikhiatr Im S S Korsakova 2020; 120:61-66. [DOI: 10.17116/jnevro202012007261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
4
|
Hao S, Wang R, Zhang Y, Zhan H. Prediction of Alzheimer's Disease-Associated Genes by Integration of GWAS Summary Data and Expression Data. Front Genet 2019; 9:653. [PMID: 30666269 PMCID: PMC6330278 DOI: 10.3389/fgene.2018.00653] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia. It is the fifth leading cause of death among elderly people. With high genetic heritability (79%), finding the disease's causal genes is a crucial step in finding a treatment for AD. Following the International Genomics of Alzheimer's Project (IGAP), many disease-associated genes have been identified; however, we do not have enough knowledge about how those disease-associated genes affect gene expression and disease-related pathways. We integrated GWAS summary data from IGAP and five different expression-level data by using the transcriptome-wide association study method and identified 15 disease-causal genes under strict multiple testing (α < 0.05), and four genes are newly identified. We identified an additional 29 potential disease-causal genes under a false discovery rate (α < 0.05), and 21 of them are newly identified. Many genes we identified are also associated with an autoimmune disorder.
Collapse
Affiliation(s)
- Sicheng Hao
- College of Computer and Information Science, Northeastern University, Boston, MA, United States
| | - Rui Wang
- College of Computer and Information Science, Northeastern University, Boston, MA, United States
| | - Yu Zhang
- Department of Neurosurgery, Heilongjiang Province Land Reclamation Headquarters General Hospital, Harbin, China
| | - Hui Zhan
- College of Electronic Engineering, Heilongjiang University, Harbin, China
| |
Collapse
|
5
|
Squires KE, Montañez-Miranda C, Pandya RR, Torres MP, Hepler JR. Genetic Analysis of Rare Human Variants of Regulators of G Protein Signaling Proteins and Their Role in Human Physiology and Disease. Pharmacol Rev 2018; 70:446-474. [PMID: 29871944 DOI: 10.1124/pr.117.015354] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Regulators of G protein signaling (RGS) proteins modulate the physiologic actions of many neurotransmitters, hormones, and other signaling molecules. Human RGS proteins comprise a family of 20 canonical proteins that bind directly to G protein-coupled receptors/G protein complexes to limit the lifetime of their signaling events, which regulate all aspects of cell and organ physiology. Genetic variations account for diverse human traits and individual predispositions to disease. RGS proteins contribute to many complex polygenic human traits and pathologies such as hypertension, atherosclerosis, schizophrenia, depression, addiction, cancers, and many others. Recent analysis indicates that most human diseases are due to extremely rare genetic variants. In this study, we summarize physiologic roles for RGS proteins and links to human diseases/traits and report rare variants found within each human RGS protein exome sequence derived from global population studies. Each RGS sequence is analyzed using recently described bioinformatics and proteomic tools for measures of missense tolerance ratio paired with combined annotation-dependent depletion scores, and protein post-translational modification (PTM) alignment cluster analysis. We highlight selected variants within the well-studied RGS domain that likely disrupt RGS protein functions and provide comprehensive variant and PTM data for each RGS protein for future study. We propose that rare variants in functionally sensitive regions of RGS proteins confer profound change-of-function phenotypes that may contribute, in newly appreciated ways, to complex human diseases and/or traits. This information provides investigators with a valuable database to explore variation in RGS protein function, and for targeting RGS proteins as future therapeutic targets.
Collapse
Affiliation(s)
- Katherine E Squires
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
| | - Carolina Montañez-Miranda
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
| | - Rushika R Pandya
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
| | - Matthew P Torres
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
| | - John R Hepler
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
| |
Collapse
|
6
|
Chen XL, Zhang ML, Zhu L, Peng ML, Liu FZ, Zhang GX, Wang LM, Zhao J. Vitamin D receptor gene polymorphisms and the risk of multiple sclerosis: An updated meta-analysis. Microb Pathog 2017; 110:594-602. [DOI: 10.1016/j.micpath.2017.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 06/22/2017] [Accepted: 08/01/2017] [Indexed: 10/19/2022]
|
7
|
Abstract
Although many genome-wide association studies have been performed, the identification of disease polymorphisms remains important. It is now suspected that many rare disease variants induce the association signal of common variants in linkage disequilibrium (LD). Based on recent development of genetic models, the current study provides explanations of the existence of rare variants with high impacts and common variants with low impacts. Disease variants are neither necessary nor sufficient due to gene–gene or gene–environment interactions. A new method was developed based on theoretical aspects to identify both rare and common disease variants by their genotypes. Common disease variants were identified with relatively small odds ratios and relatively small sample sizes, except for specific situations in which the disease variants were in strong LD with a variant with a higher frequency. Rare disease variants with small impacts were difficult to identify without increasing sample sizes; however, the method was reasonably accurate for rare disease variants with high impacts. For rare variants, dominant variants generally showed better Type II error rates than recessive variants; however, the trend was reversed for common variants. Type II error rates increased in gene regions containing more than two disease variants because the more common variant, rather than both disease variants, was usually identified. The proposed method would be useful for identifying common disease variants with small impacts and rare disease variants with large impacts when disease variants have the same effects on disease presentation.
Collapse
|