1
|
Lin H, Liao F, Liu J, Yang Z, Zhang J, Cheng J, Zhou H, Li S, Li L, Li Y, Zhuo Z, He J. Neuroblastoma susceptibility and association of N7-methylguanosine modification gene polymorphisms: multi-center case-control study. Pediatr Res 2024:10.1038/s41390-024-03318-w. [PMID: 38871802 DOI: 10.1038/s41390-024-03318-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 04/02/2024] [Accepted: 05/18/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Neuroblastoma (NB) is a common extracranial solid malignancy in children. The N7-methylguanosine (m7G) modification gene METTL1/WDR4 polymorphisms may serve as promising molecular markers for identifying populations susceptible to NB. METHODS TaqMan probes was usded to genotype METTL1/WDR4 single nucleotide polymorphisms (SNPs) in 898 NB patients and 1734 healthy controls. A logistic regression model was utilized to calculate the odds ratio (OR) and 95% confidence interval (CI), evaluating the association between genotype polymorphisms and NB susceptibility. The analysis was also stratified by age, sex, tumor origin site, and clinical stage. RESULTS Individual polymorphism of the METTL1/WDR4 gene investigated in this study did not show significant associations with NB susceptibility. However, combined genotype analysis revealed that carrying all 5 WDR4 protective genotypes was associated with a significantly lower NB risk compared to having 0-4 protective genotypes (AOR = 0.82, 95% CI = 0.69-0.96, P = 0.014). Further stratified analyses revealed that carrying 1-3 METTL1 risk genotypes, the WDR4 rs2156316 CG/GG genotype, the WDR4 rs2248490 CG/GG genotype, and having all five WDR4 protective genotypes were all significantly correlated with NB susceptibility in distinct subpopulations. CONCLUSIONS In conclusion, our findings suggest significant associations between m7G modification gene METTL1/WDR4 SNPs and NB susceptibility in specific populations. IMPACT Genetic variation in m7G modification gene is associated with susceptibility to NB. Single nucleotide polymorphisms in METTL1/WDR4 are associated with susceptibility to NB. Single nucleotide polymorphisms of METTL1/WDR4 can be used as a biomarker for screening NB susceptible populations.
Collapse
Affiliation(s)
- Huiran Lin
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
- Faculty of Medicine, Macau University of Science and Technology, Macau, 999078, China
| | - Fan Liao
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Jiabin Liu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Zhonghua Yang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Jiao Zhang
- Department of Pediatric Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jiwen Cheng
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, China
| | - Haixia Zhou
- Department of Hematology, The Key Laboratory of Pediatric Hematology and Oncology Diseases of Wenzhou, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Suhong Li
- Department of Pathology, Children Hospital and Women Health Center of Shanxi, Taiyuan, 030013, Shannxi, China
| | - Li Li
- Kunming Key Laboratory of Children Infection and Immunity, Yunnan Key Laboratory of Children's Major Disease Research, Yunnan Institute of Pediatrics Research, Yunnan Medical Center for Pediatric Diseases, Kunming Children's Hospital, Kunming, 650228, Yunnan, China
| | - Yong Li
- Department of Pediatric Surgery, Hunan Children's Hospital, Changsha, 410004, Hunan, China
| | - Zhenjian Zhuo
- Laboratory Animal Center, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China.
- Faculty of Medicine, Macau University of Science and Technology, Macau, 999078, China.
| |
Collapse
|
2
|
Xia X, Wang Y, Zheng JC. Internal m7G methylation: A novel epitranscriptomic contributor in brain development and diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:295-308. [PMID: 36726408 PMCID: PMC9883147 DOI: 10.1016/j.omtn.2023.01.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In recent years, N7-methylguanosine (m7G) methylation, originally considered as messenger RNA (mRNA) 5' caps modifications, has been identified at defined internal positions within multiple types of RNAs, including transfer RNAs, ribosomal RNAs, miRNA, and mRNAs. Scientists have put substantial efforts to discover m7G methyltransferases and methylated sites in RNAs to unveil the essential roles of m7G modifications in the regulation of gene expression and determine the association of m7G dysregulation in various diseases, including neurological disorders. Here, we review recent findings regarding the distribution, abundance, biogenesis, modifiers, and functions of m7G modifications. We also provide an up-to-date summary of m7G detection and profile mapping techniques, databases for validated and predicted m7G RNA sites, and web servers for m7G methylation prediction. Furthermore, we discuss the pathological roles of METTL1/WDR-driven m7G methylation in neurological disorders. Last, we outline a roadmap for future directions and trends of m7G modification research, particularly in the central nervous system.
Collapse
Affiliation(s)
- Xiaohuan Xia
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai 200072, China,Shanghai Frontiers Science Center of Nanocatalytic Medicine, Shanghai 200331, China,Corresponding author: Xiaohuan Xia, Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai 200065, China.
| | - Yi Wang
- Shanghai Frontiers Science Center of Nanocatalytic Medicine, Shanghai 200331, China,Translational Research Center, Shanghai Yangzhi Rehabilitation Hospital affiliated to Tongji University School of Medicine, Shanghai 201613, China
| | - Jialin C. Zheng
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai 200072, China,Shanghai Frontiers Science Center of Nanocatalytic Medicine, Shanghai 200331, China,Corresponding author: Jialin C. Zheng, Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai 200065, China.
| |
Collapse
|
3
|
Putscher E, Hecker M, Fitzner B, Boxberger N, Schwartz M, Koczan D, Lorenz P, Zettl UK. Genetic risk variants for multiple sclerosis are linked to differences in alternative pre-mRNA splicing. Front Immunol 2022; 13:931831. [PMID: 36405756 PMCID: PMC9670805 DOI: 10.3389/fimmu.2022.931831] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/12/2022] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Multiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system to which a genetic predisposition contributes. Over 200 genetic regions have been associated with increased disease risk, but the disease-causing variants and their functional impact at the molecular level are mostly poorly defined. We hypothesized that single-nucleotide polymorphisms (SNPs) have an impact on pre-mRNA splicing in MS. METHODS Our study focused on 10 bioinformatically prioritized SNP-gene pairs, in which the SNP has a high potential to alter alternative splicing events (ASEs). We tested for differential gene expression and differential alternative splicing in B cells from MS patients and healthy controls. We further examined the impact of the SNP genotypes on ASEs and on splice isoform expression levels. Novel genotype-dependent effects on splicing were verified with splicing reporter minigene assays. RESULTS We were able to confirm previously described findings regarding the relation of MS-associated SNPs with the ASEs of the pre-mRNAs from GSDMB and SP140. We also observed an increased IL7R exon 6 skipping when comparing relapsing and progressive MS patients to healthy subjects. Moreover, we found evidence that the MS risk alleles of the SNPs rs3851808 (EFCAB13), rs1131123 (HLA-C), rs10783847 (TSFM), and rs2014886 (TSFM) may contribute to a differential splicing pattern. Of particular interest is the genotype-dependent exon skipping of TSFM due to the SNP rs2014886. The minor allele T creates a donor splice site, resulting in the expression of the exon 3 and 4 of a short TSFM transcript isoform, whereas in the presence of the MS risk allele C, this donor site is absent, and thus the short transcript isoform is not expressed. CONCLUSION In summary, we found that genetic variants from MS risk loci affect pre-mRNA splicing. Our findings substantiate the role of ASEs with respect to the genetics of MS. Further studies on how disease-causing genetic variants may modify the interactions between splicing regulatory sequence elements and RNA-binding proteins can help to deepen our understanding of the genetic susceptibility to MS.
Collapse
Affiliation(s)
- Elena Putscher
- Rostock University Medical Center, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Michael Hecker
- Rostock University Medical Center, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Brit Fitzner
- Rostock University Medical Center, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Nina Boxberger
- Rostock University Medical Center, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Margit Schwartz
- Rostock University Medical Center, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Dirk Koczan
- Rostock University Medical Center, Institute of Immunology, Rostock, Germany
| | - Peter Lorenz
- Rostock University Medical Center, Institute of Immunology, Rostock, Germany
| | - Uwe Klaus Zettl
- Rostock University Medical Center, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| |
Collapse
|
4
|
Goris A, Vandebergh M, McCauley JL, Saarela J, Cotsapas C. Genetics of multiple sclerosis: lessons from polygenicity. Lancet Neurol 2022; 21:830-842. [PMID: 35963264 DOI: 10.1016/s1474-4422(22)00255-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 11/27/2022]
Abstract
Large-scale mapping studies have identified 236 independent genetic variants associated with an increased risk of multiple sclerosis. However, none of these variants are found exclusively in patients with multiple sclerosis. They are located throughout the genome, including 32 independent variants in the MHC and one on the X chromosome. Most variants are non-coding and seem to act through cell-specific effects on gene expression and splicing. The likely functions of these variants implicate both adaptive and innate immune cells in the pathogenesis of multiple sclerosis, provide pivotal biological insight into the causes and mechanisms of multiple sclerosis, and some of the variants implicated in multiple sclerosis also mediate risk of other autoimmune and inflammatory diseases. Genetics offers an approach to showing causality for environmental factors, through Mendelian randomisation. No single variant is necessary or sufficient to cause multiple sclerosis; instead, each increases total risk in an additive manner. This combined contribution from many genetic factors to disease risk, or polygenicity, has important consequences for how we interpret the epidemiology of multiple sclerosis and how we counsel patients on risk and prognosis. Ongoing efforts are focused on increasing cohort sizes, increasing diversity and detailed characterisation of study populations, and translating these associations into an understanding of the biology of multiple sclerosis.
Collapse
Affiliation(s)
- An Goris
- KU Leuven, Leuven Brain Institute, Department of Neurosciences, Laboratory for Neuroimmunology, Leuven, Belgium.
| | - Marijne Vandebergh
- KU Leuven, Leuven Brain Institute, Department of Neurosciences, Laboratory for Neuroimmunology, Leuven, Belgium
| | - Jacob L McCauley
- John P Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Janna Saarela
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway; Institute for Molecular Medicine Finland and Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Chris Cotsapas
- Departments of Neurology and Genetics, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
5
|
Alcina A, Fedetz M, Vidal-Cobo I, Andrés-León E, García-Sánchez MI, Barroso-Del-Jesus A, Eichau S, Gil-Varea E, Villar LM, Saiz A, Leyva L, Vandenbroeck K, Otaegui D, Izquierdo G, Comabella M, Urcelay E, Matesanz F. Identification of the genetic mechanism that associates L3MBTL3 to multiple sclerosis. Hum Mol Genet 2022; 31:2155-2163. [PMID: 35088080 PMCID: PMC9262392 DOI: 10.1093/hmg/ddac009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/19/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Multiple sclerosis (MS) is a complex and demyelinating disease of the central nervous system. One of the challenges of the post-GWAS era is to understand the molecular basis of statistical associations to reveal gene networks and potential therapeutic targets. The L3MBTL3 locus has been associated with MS risk by GWAS. To identify the causal variant of the locus, we performed fine mapping in a cohort of 3440 MS patients and 1688 healthy controls. The variant that best explained the association was rs6569648 (P = 4.13E-10, OR = 0.71, 95% CI = 0.64-0.79), which tagged rs7740107, located in intron 7 of L3MBTL3. The rs7740107 (A/T) variant has been reported to be the best expression and splice quantitative trait locus (eQTL and sQTL) of the region in up to 35 human GTEx tissues. By sequencing RNA from blood of 17 MS patients and quantification by digital qPCR, we determined that this eQTL/sQTL originated from the expression of a novel short transcript starting in intron 7 near rs7740107. The short transcript was translated into three proteins starting at different translation initiation codons. These N-terminal truncated proteins lacked the region where L3MBTL3 interacts with the transcriptional regulator RBPJ (Recombination Signal Binding Protein for Immunoglobulin Kappa J Region) which, in turn, regulates the Notch signaling pathway. Our data and other functional studies suggest that the genetic mechanism underlying the MS association of rs7740107 affects not only the expression of L3MBTL3 isoforms, but might also involve the Notch signaling pathway.
Collapse
Affiliation(s)
- 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
| | - 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
| | - Isabel Vidal-Cobo
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC) 18016 Granada, Spain
| | - Eduardo Andrés-León
- Bioinformatic Unit, Instituto de Parasitología y Biomedicina López Neyra (IPBLN-CSIC), Granada, Spain
| | - Maria-Isabel García-Sánchez
- UGC Neurología. Nodo Hospital Universitario Virgen Macarena, Biobanco del Sistema Sanitario Público de Andalucía, Sevilla, (Spain)
| | - Alicia Barroso-Del-Jesus
- Genomics Unit, Instituto de Parasitología y Biomedicina López Neyra (IPBLN-CSIC), Granada, Spain
| | - Sara Eichau
- UGC Neurología. Hospital Universitario Virgen Macarena, Sevilla, Spain
| | - 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
| | - Luisa-Maria Villar
- Departments of Immunology, Hospital Ramon y Cajal, (IRYCIS), Madrid, Spain
| | - Albert Saiz
- Servicio de Neurología, Hospital Clinic and Institut d'Investigació Biomèdica Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Laura Leyva
- Instituto de Investigación Biomédica de Málaga-IBIMA, UGC Neurología, Hospital Regional Universitario de Málaga, 29010 Málaga, 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
- Multiple Sclerosis Unit, Neurology Service, Vithas Nisa Hospital, 41950 Seville, Spain
| | - 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
| | - Elena Urcelay
- Lab. of Genetics of Complex Diseases, Hospital Clinico San Carlos, Instituto de Investigacion Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain
| | - 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
| |
Collapse
|