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Olazagoitia‐Garmendia A, Rojas‐Márquez H, Sebastian‐delaCruz M, Agirre‐Lizaso A, Ochoa A, Mendoza‐Gomez LM, Perugorria MJ, Bujanda L, Madrigal AH, Santin I, Castellanos‐Rubio A. m 6A Methylated Long Noncoding RNA LOC339803 Regulates Intestinal Inflammatory Response. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307928. [PMID: 38273714 PMCID: PMC10987157 DOI: 10.1002/advs.202307928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/20/2023] [Indexed: 01/27/2024]
Abstract
Cytokine mediated sustained inflammation increases the risk to develop different complex chronic inflammatory diseases, but the implicated mechanisms remain unclear. Increasing evidence shows that long noncoding RNAs (lncRNAs) play key roles in the pathogenesis of inflammatory disorders, while inflammation associated variants are described to affect their function or essential RNA modifications as N6-methyladenosine (m6A) methylation, increasing predisposition to inflammatory diseases. Here, the functional implication of the intestinal inflammation associated lncRNA LOC339803 in the production of cytokines by intestinal epithelial cells is described. Allele-specific m6A methylation is found to affect YTHDC1 mediated protein binding affinity. LOC339803-YTHDC1 interaction dictates chromatin localization of LOC339803 ultimately inducing the expression of NFκB mediated proinflammatory cytokines and contributing to the development of intestinal inflammation. These findings are confirmed using human intestinal biopsy samples from different intestinal inflammatory conditions and controls. Additionally, it is demonstrated that LOC339803 targeting can be a useful strategy for the amelioration of intestinal inflammation in vitro and ex vivo. Overall, the results support the importance of the methylated LOC339803 lncRNA as a mediator of intestinal inflammation, explaining genetic susceptibility and presenting this lncRNA as a potential novel therapeutic target for the treatment of inflammatory intestinal disorders.
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Affiliation(s)
- Ane Olazagoitia‐Garmendia
- Department of Biochemistry and Molecular BiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Henar Rojas‐Márquez
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Maialen Sebastian‐delaCruz
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Aloña Agirre‐Lizaso
- Department of Liver and Gastrointestinal DiseasesBiogipuzkoa Health Research InstituteDonostia University HospitalDonostia‐San Sebastian20014Spain
| | - Anne Ochoa
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Luis Manuel Mendoza‐Gomez
- Department of Biochemistry and Molecular BiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Biobizkaia Health Research InstituteBarakaldo48903Spain
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal DiseasesBiogipuzkoa Health Research InstituteDonostia University HospitalDonostia‐San Sebastian20014Spain
- Department of MedicineFaculty of Medicine and NursingUniversity of the Basque CountryUPV/EHUDonostia‐San Sebastián20014Spain
- CIBERehdInstituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - Luis Bujanda
- Department of Liver and Gastrointestinal DiseasesBiogipuzkoa Health Research InstituteDonostia University HospitalDonostia‐San Sebastian20014Spain
- Department of MedicineFaculty of Medicine and NursingUniversity of the Basque CountryUPV/EHUDonostia‐San Sebastián20014Spain
- CIBERehdInstituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - Alain Huerta Madrigal
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of MedicineMedicine FacultyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Gastroenterology DepartmentHospital Universitario de GaldakaoGaldakao48960Spain
| | - Izortze Santin
- Department of Biochemistry and Molecular BiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas CIBERDEMInstituto de Salud Carlos IIIMadrid28029Spain
| | - Ainara Castellanos‐Rubio
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas CIBERDEMInstituto de Salud Carlos IIIMadrid28029Spain
- IkerbasqueBasque Foundation for ScienceBilbao48011Spain
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2
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Hernangomez-Laderas A, Cilleros-Portet A, Martínez Velasco S, Marí S, Legarda M, González-García BP, Tutau C, García-Santisteban I, Irastorza I, Fernandez-Jimenez N, Bilbao JR. Sex bias in celiac disease: XWAS and monocyte eQTLs in women identify TMEM187 as a functional candidate gene. Biol Sex Differ 2023; 14:86. [PMID: 38072919 PMCID: PMC10712119 DOI: 10.1186/s13293-023-00572-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Celiac disease (CeD) is an immune-mediated disorder that develops in genetically predisposed individuals upon gluten consumption. HLA risk alleles explain 40% of the genetic component of CeD, so there have been continuing efforts to uncover non-HLA loci that can explain the remaining heritability. As in most autoimmune disorders, the prevalence of CeD is significantly higher in women. Here, we investigated the possible involvement of the X chromosome on the sex bias of CeD. METHODS We performed a X chromosome-wide association study (XWAS) and a gene-based association study in women from the CeD Immunochip (7062 cases, 5446 controls). We also constructed a database of X chromosome cis-expression quantitative trait loci (eQTLs) in monocytes from unstimulated (n = 226) and lipopolysaccharide (LPS)-stimulated (n = 130) female donors and performed a Summary-data-based MR (SMR) analysis to integrate XWAS and eQTL information. We interrogated the expression of the potentially causal gene (TMEM187) in peripheral blood mononuclear cells (PBMCs) from celiac patients at onset, on a gluten-free diet, potential celiac patients and non-celiac controls. RESULTS The XWAS and gene-based analyses identified 13 SNPs and 25 genes, respectively, 22 of which had not been previously associated with CeD. The X chromosome cis-eQTL analysis found 18 genes with at least one cis-eQTL in naïve female monocytes and 8 genes in LPS-stimulated female monocytes, 2 of which were common to both situations and 6 were unique to LPS stimulation. SMR identified a potentially causal association of TMEM187 expression in naïve monocytes with CeD in women, regulated by CeD-associated, eQTL-SNPs rs7350355 and rs5945386. The CeD-risk alleles were correlated with lower TMEM187 expression. These results were replicated using eQTLs from LPS-stimulated monocytes. We observed higher levels of TMEM187 expression in PBMCs from female CeD patients at onset compared to female non-celiac controls, but not in male CeD individuals. CONCLUSION Using X chromosome genotypes and gene expression data from female monocytes, SMR has identified TMEM187 as a potentially causal candidate in CeD. Further studies are needed to understand the implication of the X chromosome in the higher prevalence of CeD in women.
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Affiliation(s)
- Alba Hernangomez-Laderas
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Silvia Martínez Velasco
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Sergi Marí
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - María Legarda
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Bárbara Paola González-García
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Carlos Tutau
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Iñaki Irastorza
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain.
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain.
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain.
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
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Li XY, Wang JB, An HB, Wen MZ, You JX, Yang XT. Effect of SARS-CoV-2 infection on asthma patients. Front Med (Lausanne) 2022; 9:928637. [PMID: 35983093 PMCID: PMC9378965 DOI: 10.3389/fmed.2022.928637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundSARS-CoV-2 causes coronavirus disease 2019 (COVID-19), a new coronavirus pneumonia, and containing such an international pandemic catastrophe remains exceedingly difficult. Asthma is a severe chronic inflammatory airway disease that is becoming more common around the world. However, the link between asthma and COVID-19 remains unknown. Through bioinformatics analysis, this study attempted to understand the molecular pathways and discover potential medicines for treating COVID-19 and asthma.MethodsTo investigate the relationship between SARS-CoV-2 and asthma patients, a transcriptome analysis was used to discover shared pathways and molecular signatures in asthma and COVID-19. Here, two RNA-seq data (GSE147507 and GSE74986) from the Gene Expression Omnibus were used to detect differentially expressed genes (DEGs) in asthma and COVID-19 patients to find the shared pathways and the potential drug candidates.ResultsThere were 66 DEGs in all that were classified as common DEGs. Using a protein-protein interaction (PPI) network created using various bioinformatics techniques, five hub genes were found. We found that asthma has some shared links with the progression of COVID-19. Additionally, protein-drug interactions with common DEGs were also identified in the datasets.ConclusionWe investigated possible links between COVID-19 and asthma using bioinformatics databases, which might be useful in treating COVID-19 patients. More studies on populations affected by these diseases are needed to elucidate the molecular mechanism behind their association.
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Affiliation(s)
- Xin-yu Li
- Department of Interventional Therapy, Multidisciplinary Team of Vascular Anomalies, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- Department of Neurosurgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jing-bing Wang
- Department of Interventional Therapy, Multidisciplinary Team of Vascular Anomalies, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Hong-bang An
- Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Ming-zhe Wen
- Department of Interventional Therapy, Multidisciplinary Team of Vascular Anomalies, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jian-xiong You
- Department of Interventional Therapy, Multidisciplinary Team of Vascular Anomalies, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xi-tao Yang
- Department of Interventional Therapy, Multidisciplinary Team of Vascular Anomalies, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Xi-tao Yang,
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Spena S, Cairo A, Pappalardo E, Gorski MM, Garagiola I, Hassan S, Gualtierotti R, Peyvandi F. Genetic variants at the chromosomal region 2q21.3 underlying inhibitor development in patients with severe haemophilia A. Haemophilia 2022; 28:270-277. [PMID: 35182444 PMCID: PMC9306754 DOI: 10.1111/hae.14503] [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: 07/05/2021] [Revised: 01/19/2022] [Accepted: 01/23/2022] [Indexed: 11/29/2022]
Abstract
Introduction Inhibitor development affects about 30% of patients with severe haemophilia A (HA) and results from different environmental and genetic risk factors. Previously, we identified the missense variant rs3754689 in the LCT gene linked with this predisposition. Since rs3754689 variant is benign and is located in a conserved haplotype region, we hypothesized that the association signal captured by this variant is located in coinherited, neighbouring genes. Aim To identify novel genetic risk factors associated with inhibitor development in coding regions of R3HDM1, UBXN4, CXCR4, MCM6, DARS and miR128‐1 genes. Methods Targeted sequencing was performed in 246 severe HA patients (72 with and 174 without inhibitor): 181 previously and 65 newly enrolled. Results Forty‐one common and 152 rare variants passed the quality control. Logistic regression analysis of common variants identified rs3754689 and four additional variants (.011 < P < .047; FDR ranging .2‐.38). Logistic regression analysis performed only in the 220 Italian patients showed similar results (.004 < P < .05; FDR ranging .12‐.22). Three of these variants (rs3213892 and rs3816155 in the LCT intron 13 and rs961360 in the R3HDM1 intron10‐exon11 junction) may affect the expression of UBXN4 and R3HDM1, respectively. Rare variants did not show association with inhibitor development. Identified variants were not replicated in the multi‐ethnic SIPPET cohort of 230 severe HA patients. Conclusion Due to the limited sample size that may be responsible of the high FDR values, we could not confirm with certainty the analysed association. Further evaluation of the expression levels of analysed genes will confirm or not their role in inhibitor development.
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Affiliation(s)
- Silvia Spena
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, and Luigi Villa Foundation, Milan, Italy
| | - Andrea Cairo
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, and Luigi Villa Foundation, Milan, Italy
| | - Emanuela Pappalardo
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Marcin M Gorski
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Isabella Garagiola
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, and Luigi Villa Foundation, Milan, Italy
| | - Shermarke Hassan
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Roberta Gualtierotti
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, and Luigi Villa Foundation, Milan, Italy.,Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Flora Peyvandi
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, and Luigi Villa Foundation, Milan, Italy.,Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
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Hearing Function: Identification of New Candidate Genes Further Explaining the Complexity of This Sensory Ability. Genes (Basel) 2021; 12:genes12081228. [PMID: 34440402 PMCID: PMC8394865 DOI: 10.3390/genes12081228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022] Open
Abstract
To date, the knowledge of the genetic determinants behind the modulation of hearing ability is relatively limited. To investigate this trait, we performed Genome-Wide Association Study (GWAS) meta-analysis using genotype and audiometric data (hearing thresholds at 0.25, 0.5, 1, 2, 4, and 8 kHz, and pure-tone averages of thresholds at low, medium, and high frequencies) collected in nine cohorts from Europe, South-Eastern USA, Caucasus, and Central Asia, for an overall number of ~9000 subjects. Three hundred seventy-five genes across all nine analyses were tagged by single nucleotide polymorphisms (SNPs) reaching a suggestive p-value (p < 10−5). Amongst these, 15 were successfully replicated using a gene-based approach in the independent Italian Salus in the Apulia cohort (n = 1774) at the nominal significance threshold (p < 0.05). In addition, the expression level of the replicated genes was assessed in published human and mouse inner ear datasets. Considering expression patterns in humans and mice, eleven genes were considered particularly promising candidates for the hearing function: BNIP3L, ELP5, MAP3K20, MATN2, MTMR7, MYO1E, PCNT, R3HDM1, SLC9A9, TGFB2, and YTHDC2. These findings represent a further contribution to our understanding of the genetic basis of hearing function and its related diseases.
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Fukushi D, Inaba M, Katoh K, Suzuki Y, Enokido Y, Nomura N, Tokita Y, Hayashi S, Mizuno S, Yamada K, Wakamatsu N. R3HDM1 haploinsufficiency is associated with mild intellectual disability. Am J Med Genet A 2021; 185:1776-1786. [PMID: 33750005 DOI: 10.1002/ajmg.a.62173] [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: 11/04/2020] [Revised: 02/23/2021] [Accepted: 03/03/2021] [Indexed: 11/07/2022]
Abstract
R3HDM1 (R3H domain containing 1) is an uncharacterized RNA-binding protein that is highly expressed in the human cerebral cortex. We report the first case of a 12-year-old Japanese male with haploinsufficiency of R3HDM1. He presented with mild intellectual disability (ID) and developmental delay. He had a pericentric inversion of 46,XY,inv(2)(p16.1q21.3)dn with breakpoints in intron 19 of R3HDM1 (2q21.3) and the intergenic region (2p16.1). The R3HDM1 levels in his lymphoblastoid cells were reduced to approximately half that of the healthy controls. However, the expression of MIR128-1, in intron 18 of R3HDM1, was not affected via the pericentric inversion. Knockdown of R3HDM1 in mouse embryonic hippocampal neurons suppressed dendritic growth and branching. Notably, the Database of Genomic Variants reported the case of a healthy control with a 488-kb deletion that included both R3HDM1 and MIR128-1. miR-128 has been reported to inhibit dendritic growth and branching in mouse brain neurons, which directly opposes the novel functions of R3HDM1. These findings suggest that deleting both R3HDM1 and MIR128-1 alleviates the symptoms of the disease caused by loss-of-function mutations in R3HDM1 only. Thus, haploinsufficiency of R3HDM1 in the patient may be the cause of the mild ID due to the genetic imbalance between R3HDM1 and MIR128-1.
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Affiliation(s)
- Daisuke Fukushi
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Mie Inaba
- Department of Pediatrics, Central Hospital, Aichi Developmental Disability Center, Kasugai, Japan
| | - Kimiko Katoh
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Yasuyo Suzuki
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Yasushi Enokido
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Noriko Nomura
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Yoshihito Tokita
- Department of Disease Model, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Shin Hayashi
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Developmental Disability Center, Kasugai, Japan
| | - Kenichiro Yamada
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Nobuaki Wakamatsu
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan.,Department of Pathology and Host Defense, Faculty of Medicine, Kagawa University, Miki, Japan
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Hooikaas PJ, Damstra HG, Gros OJ, van Riel WE, Martin M, Smits YT, van Loosdregt J, Kapitein LC, Berger F, Akhmanova A. Kinesin-4 KIF21B limits microtubule growth to allow rapid centrosome polarization in T cells. eLife 2020; 9:62876. [PMID: 33346730 PMCID: PMC7817182 DOI: 10.7554/elife.62876] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/20/2020] [Indexed: 12/11/2022] Open
Abstract
When a T cell and an antigen-presenting cell form an immunological synapse, rapid dynein-driven translocation of the centrosome toward the contact site leads to reorganization of microtubules and associated organelles. Currently, little is known about how the regulation of microtubule dynamics contributes to this process. Here, we show that the knockout of KIF21B, a kinesin-4 linked to autoimmune disorders, causes microtubule overgrowth and perturbs centrosome translocation. KIF21B restricts microtubule length by inducing microtubule pausing typically followed by catastrophe. Catastrophe induction with vinblastine prevented microtubule overgrowth and was sufficient to rescue centrosome polarization in KIF21B-knockout cells. Biophysical simulations showed that a relatively small number of KIF21B molecules can restrict mirotubule length and promote an imbalance of dynein-mediated pulling forces that allows the centrosome to translocate past the nucleus. We conclude that proper control of microtubule length is important for allowing rapid remodeling of the cytoskeleton and efficient T cell polarization. The immune system is composed of many types of cells that can recognize foreign molecules and pathogens so they can eliminate them. When cells in the body become infected with a pathogen, they can process the pathogen’s proteins and present them on their own surface. Specialized immune cells can then recognize infected cells and interact with them, forming an ‘immunological synapse’. These synapses play an important role in immune response: they activate the immune system and allow it to kill harmful cells. To form an immunological synapse, an immune cell must reorganize its internal contents, including an aster-shaped scaffold made of tiny protein tubes called microtubules. The center of this scaffold moves towards the immunological synapse as it forms. This re-orientation of the microtubules towards the immunological synapse is known as 'polarization' and it happens very rapidly, but it is not yet clear how it works. One molecule involved in the polarization process is called KIF21B, a protein that can walk along microtubules, building up at the ends and affecting their growth. Whether KIF21B makes microtubules grow more quickly, or more slowly, is a matter of debate, and the impact microtubule length has on immunological synapse formation is unknown. Here, Hooikaas, Damstra et al. deleted the gene for KIF21B from human immune cells called T cells to find out how it affected their ability to form an immunological synapse. Without KIF21B, the T cells grew microtubules that were longer than normal, and had trouble forming immunological synapses. When the T cells were treated with a drug that stops microtubule growth, their ability to form immunological synapses was restored, suggesting a role for KIF21B. To explore this further, Hooikaas, Damstra et al. replaced the missing KIF21B gene with a gene that coded for a version of the protein that could be seen using microscopy. This revealed that, when KIF21B reaches the ends of microtubules, it stops their growth and triggers their disassembly. Computational modelling showed that cells find it hard to reorient their microtubule scaffolding when the individual tubes are too long. It only takes a small number of KIF21B molecules to shorten the microtubules enough to allow the center of the scaffold to move. Research has linked the KIF21B gene to autoimmune conditions like multiple sclerosis. Microtubules also play an important role in cell division, a critical process driving all types of cancer. Drugs that affect microtubule growth are already available, and a deeper understanding of KIF21B and microtubule regulation in immune cells could help to improve treatments in the future.
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Affiliation(s)
- Peter Jan Hooikaas
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Hugo Gj Damstra
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Oane J Gros
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Wilhelmina E van Riel
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Maud Martin
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Yesper Th Smits
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jorg van Loosdregt
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Florian Berger
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
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García-Santisteban I, Romero-Garmendia I, Cilleros-Portet A, Bilbao JR, Fernandez-Jimenez N. Celiac disease susceptibility: The genome and beyond. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 358:1-45. [PMID: 33707051 DOI: 10.1016/bs.ircmb.2020.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Celiac Disease (CeD) is an immune-mediated complex disease that is triggered by the ingestion of gluten and develops in genetically susceptible individuals. It has been known for a long time that the Human Leucocyte Antigen (HLA) molecules DQ2 and DQ8 are necessary, although not sufficient, for the disease development, and therefore other susceptibility genes and (epi)genetic events must participate in CeD pathogenesis. The advances in Genomics during the last 15 years have made CeD one of the immune-related disorders with the best-characterized genetic component. In the present work, we will first review the main Genome-Wide Association Studies (GWAS) carried out in the disorder, and emphasize post-GWAS discoveries, including diverse integrative strategies, SNP prioritization approaches, and insights into the Microbiome through the host Genomics. Second, we will explore CeD-related Epigenetics and Epigenomics, mostly focusing on the emerging knowledge of the celiac methylome, and the vast but yet under-explored non-coding RNA (ncRNA) landscape. We conclude that much has been done in the field although there are still completely unvisited areas in the post-Genomics of CeD. Chromatin conformation and accessibility, and Epitranscriptomics are promising domains that need to be unveiled to complete the big picture of the celiac Genome.
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Affiliation(s)
- Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain; Spanish Biomedical Research Center in Diabetes and associated Metabolic Disorders, CIBERDEM, Madrid, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain.
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9
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Fernandez-Jimenez N, Garcia-Etxebarria K, Plaza-Izurieta L, Romero-Garmendia I, Jauregi-Miguel A, Legarda M, Ecsedi S, Castellanos-Rubio A, Cahais V, Cuenin C, Degli Esposti D, Irastorza I, Hernandez-Vargas H, Herceg Z, Bilbao JR. The methylome of the celiac intestinal epithelium harbours genotype-independent alterations in the HLA region. Sci Rep 2019; 9:1298. [PMID: 30718669 PMCID: PMC6362130 DOI: 10.1038/s41598-018-37746-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/13/2018] [Indexed: 12/12/2022] Open
Abstract
The Human Leucocyte Antigen (HLA) locus and other DNA sequence variants identified in Genome-Wide Association (GWA) studies explain around 50% of the heritability of celiac disease (CD). However, the pathogenesis of CD could be driven by other layers of genomic information independent from sequence variation, such as DNA methylation, and it is possible that allele-specific methylation explains part of the SNP associations. Since the DNA methylation landscape is expected to be different among cell types, we analyzed the methylome of the epithelial and immune cell populations of duodenal biopsies in CD patients and controls separately. We found a cell type-specific methylation signature that includes genes mapping to the HLA region, namely TAP1 and HLA-B. We also performed Immunochip SNP genotyping of the same samples and interrogated the expression of some of the affected genes. Our analysis revealed that the epithelial methylome is characterized by the loss of CpG island (CGI) boundaries, often associated to altered gene expression, and by the increased variability of the methylation across the samples. The overlap between differentially methylated positions (DMPs) and CD-associated SNPs or variants contributing to methylation quantitative trait loci (mQTLs) is minimal. In contrast, there is a notable enrichment of mQTLs among the most significant CD-associated SNPs. Our results support the notion that DNA methylation alterations constitute a genotype-independent event and confirm its role in the HLA region (apart from the well-known, DQ allele-specific effect). Finally, we find that a fraction of the CD-associated variants could exert its phenotypic effect through DNA methylation.
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Affiliation(s)
- Nora Fernandez-Jimenez
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
| | - Koldo Garcia-Etxebarria
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
- Department of Gastrointestinal and Liver Diseases, Biodonostia Health Research Institute, Donostia, Basque Country, Spain
| | - Leticia Plaza-Izurieta
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
| | - Amaia Jauregi-Miguel
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
| | - Maria Legarda
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, 48903, Spain
| | - Szilvia Ecsedi
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
- Universite Côte d'Azur, INSERM, CNRS, iBV, Nice, France
| | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
- Spanish Biomedical Research Center in Diabetes and associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
| | - Davide Degli Esposti
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
- Irstea - Laboratoire d'écotoxicologie, UR "Milieux aquatiques, écologie et pollutions", Villeurbanne, France
| | - Iñaki Irastorza
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, 48903, Spain
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
- Department of Immunology, Virology and Inflammation; TGF beta and Immune Evasion Group; Cancer Research Center of Lyon; INSERM, CNRS, Centre Léon Bérard Hospital, Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain.
- Spanish Biomedical Research Center in Diabetes and associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
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10
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Del Prete E, Facchiano A, Liò P. Bioinformatics methodologies for coeliac disease and its comorbidities. Brief Bioinform 2018; 21:355-367. [PMID: 30452543 DOI: 10.1093/bib/bby109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/01/2018] [Accepted: 10/11/2018] [Indexed: 12/30/2022] Open
Abstract
Coeliac disease (CD) is a complex, multifactorial pathology caused by different factors, such as nutrition, immunological response and genetic factors. Many autoimmune diseases are comorbidities for CD, and a comprehensive and integrated analysis with bioinformatics approaches can help in evaluating the interconnections among all the selected pathologies. We first performed a detailed survey of gene expression data available in public repositories on CD and less commonly considered comorbidities. Then we developed an innovative pipeline that integrates gene expression, cell-type data and online resources (e.g. a list of comorbidities from the literature), using bioinformatics methods such as gene set enrichment analysis and semantic similarity. Our pipeline is written in R language, available at the following link: http://bioinformatica.isa.cnr.it/COELIAC_DISEASE/SCRIPTS/. We found a list of common differential expressed genes, gene ontology terms and pathways among CD and comorbidities and the closeness among the selected pathologies by means of disease ontology terms. Physicians and other researchers, such as molecular biologists, systems biologists and pharmacologists can use it to analyze pathology in detail, from differential expressed genes to ontologies, performing a comparison with the pathology comorbidities or with other diseases.
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Affiliation(s)
- Eugenio Del Prete
- Department of Sciences, University of Basilicata,Via dell'Ateneo Lucano, Potenza, Italy.,National Research Council, Institute of Food Science (CNR-ISA),Via Roma 64, Avellino, Italy.,Computer Laboratory, University of Cambridge, JJ Thomson Ave., Cambridge, UK
| | - Angelo Facchiano
- National Research Council, Institute of Food Science (CNR-ISA),Via Roma 64, Avellino, Italy
| | - Pietro Liò
- Computer Laboratory, University of Cambridge, JJ Thomson Ave., Cambridge, UK
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11
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Ho KWD, Wallace MR, Sibille KT, Bartley EJ, Cruz-Almeida Y, Glover TL, King CD, Goodin BR, Addison A, Edberg JC, Staud R, Bradley LA, Fillingim RB. Single Nucleotide Polymorphism in the COL11A2 Gene Associated with Heat Pain Sensitivity in Knee Osteoarthritis. Mol Pain 2018; 13:1744806917724259. [PMID: 28741447 PMCID: PMC5562334 DOI: 10.1177/1744806917724259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Pain is one of the most prominent symptoms of osteoarthritis. However, there is often discordance between the pain experienced by individuals with osteoarthritis and the degree of articular pathology. This suggests that individual differences, including genetic variability in the central processing of nociceptive stimuli, may impact the presentation of osteoarthritis. Here, we show that the single nucleotide polymorphism rs16868943 in the collagen gene COL11A2 is significantly associated with lowered heat pain tolerance on the arm in participants with knee osteoarthritis (P = 1.21 × 10−6, P = 0.0053 after Bonferroni correction, beta = −3.42). A total of 161 knee osteoarthritis participants were included and evaluated for heat, punctate and pressure pain sensitivity of the affected knee and the ipsilateral arm. Each participant was genotyped for 4392 single nucleotide polymorphisms in genes implicated in pain perception, inflammation and mood and tested for association with pain sensitivity. The minor A allele of single nucleotide polymorphism rs16868943 was significantly associated with lower arm heat pain tolerance after correction for age, gender, race, and study site. This single nucleotide polymorphism was also nominally associated with other measures of heat pain sensitivity, including lowered knee heat pain tolerance (P = 1.14 × 10−5, P = 0.05 after Bonferroni correction), lowered arm heat pain threshold (P = 0.0039, uncorrected) and lowered knee heat pain threshold (P = 0.003, uncorrected). Addition of genotypes from 91 participants without knee pain produced a significant interaction between knee osteoarthritis status and the rs16868943 single nucleotide polymorphism in heat pain tolerance (P = 1.71 × 10−5), such that rs16868943 was not associated with heat pain tolerance in participants without knee pain (P = 0.12, beta = 1.3). This is the first study to show genetic association with heat pain tolerance in individuals with osteoarthritis. The association is specific to participants who have already developed knee osteoarthritis, suggesting that the COL11A2 gene, which has previously been associated with familial osteoarthritis, may play a role in pain sensitization after the development of osteoarthritis.
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Affiliation(s)
| | - Margaret R Wallace
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL
| | - Kimberly T Sibille
- Department of Aging & Geriatric Research, University of Florida, Gainesville, FL
| | - Emily J Bartley
- Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, FL
| | - Yenisel Cruz-Almeida
- Department of Aging & Geriatric Research, University of Florida, Gainesville, FL
| | - Toni L Glover
- Pain Research & Intervention Center of Excellence, University of Florida, Gainesville, FL
| | - Christopher D King
- Department of Anesthesia, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH
| | - Burel R Goodin
- Department of Psychology, University of Alabama at Birmingham, Birmingham, AL
| | - Adriana Addison
- Division of Clinical Immunology & Rheumatotology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Jeffrey C Edberg
- Division of Clinical Immunology & Rheumatotology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Roland Staud
- Pain Research & Intervention Center of Excellence, University of Florida, Gainesville, FL
| | - Laurence A Bradley
- Division of Clinical Immunology & Rheumatotology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Roger B Fillingim
- Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, FL
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12
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Romero-Garmendia I, Garcia-Etxebarria K, Hernandez-Vargas H, Santin I, Jauregi-Miguel A, Plaza-Izurieta L, Cros MP, Legarda M, Irastorza I, Herceg Z, Fernandez-Jimenez N, Bilbao JR. Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease. Genes (Basel) 2018; 9:E245. [PMID: 29748492 PMCID: PMC5977185 DOI: 10.3390/genes9050245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to construct celiac co-expression patterns at a whole genome level and to identify transcription factors (TFs) that could drive the gliadin-related changes in coordination of gene expression observed in celiac disease (CD). Differential co-expression modules were identified in the acute and chronic responses to gliadin using expression data from a previous microarray study in duodenal biopsies. Transcription factor binding site (TFBS) and Gene Ontology (GO) annotation enrichment analyses were performed in differentially co-expressed genes (DCGs) and selection of candidate regulators was performed. Expression of candidates was measured in clinical samples and the activation of the TFs was further characterized in C2BBe1 cells upon gliadin challenge. Enrichment analyses of the DCGs identified 10 TFs and five were selected for further investigation. Expression changes related to active CD were detected in four TFs, as well as in several of their in silico predicted targets. The activation of TFs was further characterized in C2BBe1 cells upon gliadin challenge, and an increase in nuclear translocation of CAMP Responsive Element Binding Protein 1 (CREB1) and IFN regulatory factor-1 (IRF1) in response to gliadin was observed. Using transcriptome-wide co-expression analyses we are able to propose novel genes involved in CD pathogenesis that respond upon gliadin stimulation, also in non-celiac models.
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Affiliation(s)
- Irati Romero-Garmendia
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Koldo Garcia-Etxebarria
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Izortze Santin
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain.
| | - Amaia Jauregi-Miguel
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Leticia Plaza-Izurieta
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Marie-Pierre Cros
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Maria Legarda
- Pediatric Gastroenterology Unit, Cruces University Hospital, University of the Basque Country-(UPV/EHU) and Biocruces Health Research Institute, 48903 Barakaldo, Spain.
| | - Iñaki Irastorza
- Pediatric Gastroenterology Unit, Cruces University Hospital, University of the Basque Country-(UPV/EHU) and Biocruces Health Research Institute, 48903 Barakaldo, Spain.
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Nora Fernandez-Jimenez
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Jose Ramon Bilbao
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain.
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13
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Miraghazadeh B, Cook MC. Nuclear Factor-kappaB in Autoimmunity: Man and Mouse. Front Immunol 2018; 9:613. [PMID: 29686669 PMCID: PMC5900062 DOI: 10.3389/fimmu.2018.00613] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/12/2018] [Indexed: 12/21/2022] Open
Abstract
NF-κB (nuclear factor-kappa B) is a transcription complex crucial for host defense mediated by innate and adaptive immunity, where canonical NF-κB signaling, mediated by nuclear translocation of RelA, c-Rel, and p50, is important for immune cell activation, differentiation, and survival. Non-canonical signaling mediated by nuclear translocation of p52 and RelB contributes to lymphocyte maturation and survival and is also crucial for lymphoid organogenesis. We outline NF-κB signaling and regulation, then summarize important molecular contributions of NF-κB to mechanisms of self-tolerance. We relate these mechanisms to autoimmune phenotypes described in what is now a substantial catalog of immune defects conferred by mutations in NF-κB pathways in mouse models. Finally, we describe Mendelian autoimmune syndromes arising from human NF-κB mutations, and speculate on implications for understanding sporadic autoimmune disease.
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Affiliation(s)
- Bahar Miraghazadeh
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Acton, ACT, Australia
- Translational Research Unit, Canberra Hospital, Acton, ACT, Australia
| | - Matthew C. Cook
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Acton, ACT, Australia
- Translational Research Unit, Canberra Hospital, Acton, ACT, Australia
- Department of Immunology, Canberra Hospital, Acton, ACT, Australia
- *Correspondence: Matthew C. Cook,
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14
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Al-Aama JY, Shaik NA, Banaganapalli B, Salama MA, Rashidi O, Sahly AN, Mohsen MO, Shawoosh HA, Shalabi HA, Edreesi MA, Alharthi SE, Wang J, Elango R, Saadah OI. Whole exome sequencing of a consanguineous family identifies the possible modifying effect of a globally rare AK5 allelic variant in celiac disease development among Saudi patients. PLoS One 2017; 12:e0176664. [PMID: 28505210 PMCID: PMC5432167 DOI: 10.1371/journal.pone.0176664] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 04/14/2017] [Indexed: 12/20/2022] Open
Abstract
Celiac disease (CD), a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA and Non-HLA genes can explain up to 50% of CD’s heritability. In order to discover the missing heritability due to rare variants, we have exome sequenced a consanguineous Saudi family presenting CD in an autosomal recessive (AR) pattern. We have identified a rare homozygous insertion c.1683_1684insATT, in the conserved coding region of AK5 gene that showed classical AR model segregation in this family. Sequence validation of 200 chromosomes each of sporadic CD cases and controls, revealed that this extremely rare (EXac MAF 0.000008) mutation is highly penetrant among general Saudi populations (MAF is 0.62). Genotype and allelic distribution analysis have indicated that this AK5 (c.1683_1684insATT) mutation is negatively selected among patient groups and positively selected in the control group, in whom it may modify the risk against CD development [p<0.002]. Our observation gains additional support from computational analysis which predicted that Iso561 insertion shifts the existing H-bonds between 400th and 556th amino acid residues lying near the functional domain of adenylate kinase. This shuffling of amino acids and their H-bond interactions is likely to disturb the secondary structure orientation of the polypeptide and induces the gain-of-function in nucleoside phosphate kinase activity of AK5, which may eventually down-regulates the reactivity potential of CD4+ T-cells against gluten antigens. Our study underlines the need to have population-specific genome databases to avoid false leads and to identify true candidate causal genes for the familial form of celiac disease.
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Affiliation(s)
- Jumana Yousuf Al-Aama
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor Ahmad Shaik
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed A. Salama
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Omran Rashidi
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed N. Sahly
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed O. Mohsen
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Harbi A. Shawoosh
- Department of Pediatrics, King Fahd Armed Forces Hospital, Jeddah, Saudi Arabia
| | | | - Mohammad Al Edreesi
- Division of Gastroenterology, Department of Pediatrics, Dhahran Health Center, Saudi Aramco Medical Services Organization, Dhahran, Saudi Arabia
| | - Sameer E. Alharthi
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jun Wang
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ramu Elango
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (RE); (OIS)
| | - Omar I. Saadah
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- Division of Pediatric Gastroenterology, Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (RE); (OIS)
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