1
|
An X, Zhao S, Fang J, Li Q, Yue C, Jing C, Zhang Y, Zhang J, Zhou J, Chen C, Qu H, Ma Q, Lin Q. Identification of genetic susceptibility for Chinese migraine with depression using machine learning. Front Neurol 2024; 15:1418529. [PMID: 39144710 PMCID: PMC11322385 DOI: 10.3389/fneur.2024.1418529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/11/2024] [Indexed: 08/16/2024] Open
Abstract
Background Migraine is a common primary headache that has a significant impact on patients' quality of life. The co-occurrence of migraine and depression is frequent, resulting in more complex symptoms and a poorer prognosis. The evidence suggests that depression and migraine comorbidity share a polygenic genetic background. Objective The aim of this study is to identify related genetic variants that contribute to genetic susceptibility to migraine with and without depression in a Chinese cohort. Methods In this case-control study, 263 individuals with migraines and 223 race-matched controls were included. Eight genetic polymorphism loci selected from the GWAS were genotyped using Sequenom's MALDI-TOF iPLEX platform. Results In univariate analysis, ANKDD1B rs904743 showed significant differences in genotype and allele distribution between migraineurs and controls. Furthermore, a machine learning approach was used to perform multivariate analysis. The results of the Random Forest algorithm indicated that ANKDD1B rs904743 was a significant risk factor for migraine susceptibility in China. Additionally, subgroup analysis by the Boruta algorithm showed a significant association between this SNP and migraine comorbid depression. Migraineurs with depression have been observed to have worse scores on the Beck Anxiety Inventory (BAI) and the Migraine Disability Assessment Scale (MIDAS). Conclusion The study indicates that there is an association between ANKDD1B rs904743 and susceptibility to migraine with and without depression in Chinese patients.
Collapse
Affiliation(s)
- Xingkai An
- Department of Neurology and Department of Neuroscience, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen, China
- Xiamen Key Laboratory of Brain Center, Xiamen, China
- Xiamen Medical Quality Control Center for Neurology, Xiamen, China
- Fujian Provincial Clinical Research Center for Brain Diseases, Fuzhou, China
- Xiamen Clinical Research Center for Neurological Diseases, Xiamen, China
| | - Shanshan Zhao
- Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jie Fang
- Department of Neurology and Department of Neuroscience, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen, China
- Xiamen Key Laboratory of Brain Center, Xiamen, China
- Xiamen Medical Quality Control Center for Neurology, Xiamen, China
- Fujian Provincial Clinical Research Center for Brain Diseases, Fuzhou, China
- Xiamen Clinical Research Center for Neurological Diseases, Xiamen, China
| | - Qingfang Li
- Department of Neurology and Department of Neuroscience, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Cen Yue
- Department of Neurology and Department of Neuroscience, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen, China
- Xiamen Key Laboratory of Brain Center, Xiamen, China
- Xiamen Medical Quality Control Center for Neurology, Xiamen, China
- Fujian Provincial Clinical Research Center for Brain Diseases, Fuzhou, China
- Xiamen Clinical Research Center for Neurological Diseases, Xiamen, China
| | - Chuya Jing
- Department of Neurology and Department of Neuroscience, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen, China
- Xiamen Key Laboratory of Brain Center, Xiamen, China
- Xiamen Medical Quality Control Center for Neurology, Xiamen, China
- Fujian Provincial Clinical Research Center for Brain Diseases, Fuzhou, China
- Xiamen Clinical Research Center for Neurological Diseases, Xiamen, China
| | - Yidan Zhang
- Department of Neurology and Department of Neuroscience, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen, China
- Xiamen Key Laboratory of Brain Center, Xiamen, China
- Xiamen Medical Quality Control Center for Neurology, Xiamen, China
- Fujian Provincial Clinical Research Center for Brain Diseases, Fuzhou, China
- Xiamen Clinical Research Center for Neurological Diseases, Xiamen, China
| | - Jiawei Zhang
- Department of Neurology and Department of Neuroscience, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen, China
- Xiamen Key Laboratory of Brain Center, Xiamen, China
- Xiamen Medical Quality Control Center for Neurology, Xiamen, China
- Fujian Provincial Clinical Research Center for Brain Diseases, Fuzhou, China
- Xiamen Clinical Research Center for Neurological Diseases, Xiamen, China
| | - Jie Zhou
- Department of Neurology and Department of Neuroscience, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen, China
- Xiamen Key Laboratory of Brain Center, Xiamen, China
- Xiamen Medical Quality Control Center for Neurology, Xiamen, China
- Fujian Provincial Clinical Research Center for Brain Diseases, Fuzhou, China
- Xiamen Clinical Research Center for Neurological Diseases, Xiamen, China
| | - Caihong Chen
- Department of Neurology and Department of Neuroscience, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen, China
- Xiamen Key Laboratory of Brain Center, Xiamen, China
- Xiamen Medical Quality Control Center for Neurology, Xiamen, China
- Fujian Provincial Clinical Research Center for Brain Diseases, Fuzhou, China
- Xiamen Clinical Research Center for Neurological Diseases, Xiamen, China
| | - Hongli Qu
- Department of Neurology and Department of Neuroscience, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen, China
- Xiamen Key Laboratory of Brain Center, Xiamen, China
- Xiamen Medical Quality Control Center for Neurology, Xiamen, China
- Fujian Provincial Clinical Research Center for Brain Diseases, Fuzhou, China
- Xiamen Clinical Research Center for Neurological Diseases, Xiamen, China
| | - Qilin Ma
- Department of Neurology and Department of Neuroscience, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen, China
- Xiamen Key Laboratory of Brain Center, Xiamen, China
- Xiamen Medical Quality Control Center for Neurology, Xiamen, China
- Fujian Provincial Clinical Research Center for Brain Diseases, Fuzhou, China
- Xiamen Clinical Research Center for Neurological Diseases, Xiamen, China
| | - Qing Lin
- Department of Neurology and Department of Neuroscience, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen, China
- Xiamen Key Laboratory of Brain Center, Xiamen, China
- Xiamen Medical Quality Control Center for Neurology, Xiamen, China
- Fujian Provincial Clinical Research Center for Brain Diseases, Fuzhou, China
- Xiamen Clinical Research Center for Neurological Diseases, Xiamen, China
| |
Collapse
|
2
|
Costantino F, Breban M. Family studies: A useful tool to better understand spondyloarthritis. Joint Bone Spine 2023; 90:105588. [PMID: 37201576 DOI: 10.1016/j.jbspin.2023.105588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/12/2023] [Indexed: 05/20/2023]
Abstract
Spondyloarthritis (SpA) is an immune-mediated disease characterized by a high heritability, reflected by strong familial aggregation. Therefore, family studies are a powerful tool for elucidating the genetic basis of SpA. First, they helped to assess the relative importance of genetic and environmental factors and established the polygenic character of the disease. Family-based designs were also historically used to identify genetic factors of susceptibility through linkage analyses. In SpA, three whole-genome linkage studies were published in the 1990's, unfortunately with few consistent results. After having been put aside for several years in favour of case-control GWAS, there is a renewed interest in family-based designs in particular to detect rare variant associations. This review aims at summarizing what family studies have brought to the field of SpA genetics, from genetic epidemiology studies to the most recent rare variant analyses. It also highlights the potential interest of family history of SpA to help diagnosis and detection of patients at high risk to develop the disease.
Collapse
Affiliation(s)
- Félicie Costantino
- Rheumatology Department, AP-HP, Ambroise-Paré Hospital, 92100 Boulogne-Billancourt, France; Infection & Inflammation, UMR 1173, Inserm, UVSQ/Université Paris Saclay, 78180 Montigny-Le-Bretonneux, France; Laboratory of Excellence INFLAMEX, Université Paris-Centre, Paris, France.
| | - Maxime Breban
- Rheumatology Department, AP-HP, Ambroise-Paré Hospital, 92100 Boulogne-Billancourt, France; Infection & Inflammation, UMR 1173, Inserm, UVSQ/Université Paris Saclay, 78180 Montigny-Le-Bretonneux, France; Laboratory of Excellence INFLAMEX, Université Paris-Centre, Paris, France
| |
Collapse
|
3
|
Mahdinejad-Yazdi M, Sobhan MR, Dastgheib SA, Bahrami R, Shaker SH, Mirjalili H, Sadeghizadeh-Yazdi J, Zare-Shehneh M, Neamatzadeh H. A meta-analysis for association of TNF-α -308G>A polymorphism with susceptibility to Ankylosing Spondylitis. J Orthop 2021; 26:79-87. [PMID: 34349398 DOI: 10.1016/j.jor.2021.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/11/2021] [Indexed: 01/13/2023] Open
Abstract
Objective We performed a meta-analysis of all eligible studies on the association of TNF-α -308G>A polymorphism with risk of Ankylosing spondylitis (AS). Methods A comprehensive literature research was performed in online databases. Results A total of 28 studies with 4489 cases and 5919 controls were included. Pooled ORs showed a significant association between TNF-α -308G>A polymorphism and risk of AS. Moreover, stratified analysis by ethnicity showed a significant association between TNF-α -308G>A polymorphism and AS risk in Asians, Caucasians and Mixed populations, but not in Chinese population. Conclusion This meta-analysis suggested that the TNF-α -308G>A polymorphism was associated with AS risk.
Collapse
Affiliation(s)
| | - Mohammad Reza Sobhan
- Department of Orthopedics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Seyed Alireza Dastgheib
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Bahrami
- Neonatal Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Hossein Shaker
- Department of Emergency Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Mirjalili
- Department of Emergency Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Jalal Sadeghizadeh-Yazdi
- Department of Food Science and Technology, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Masoud Zare-Shehneh
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hossein Neamatzadeh
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Mother and Newborn Health Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| |
Collapse
|
4
|
Costantino F, Mambu Mambueni H, Said-Nahal R, Garchon HJ, Breban M. What Have We Learned From Family-Based Studies About Spondyloarthritis? Front Genet 2021; 12:671306. [PMID: 34149813 PMCID: PMC8209510 DOI: 10.3389/fgene.2021.671306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/12/2021] [Indexed: 01/31/2023] Open
Abstract
Spondyloarthritis (SpA) is a chronic inflammatory disorder with a high familial aggregation, emphasizing the existence of genetic susceptibility factors. In the last decades, family-based studies have contributed to better understand the genetic background of SpA, in particular by showing that the most likely model of transmission is oligogenic with multiplicative effects. Coexistence of different SpA subtypes within families also highlighted the complex interplay between all subtypes. Several whole-genome linkage analyses using sib-pairs or multiplex families were performed in the 1990s to try to identify genetic susceptibility factors besides HLA-B27. Unfortunately, no consistent results were obtained and family-based studies have been progressively set aside in favor of case-control designs. In particular, case-control genome-wide association studies allowed the identification of more than 40 susceptibility regions. However, all these loci explain only a small fraction of disease predisposition. Several hypotheses have been advanced to account for this unexplained heritability, including rare variants involvement, leading to a renewed interest in family-based designs, which are probably more powerful in the detection of such variants. In this review, our purpose is to summarize what has been learned to date regarding SpA genetics from family-based studies, with a special focus on recent identification of rare associated variants through next-generation sequencing studies.
Collapse
Affiliation(s)
- Félicie Costantino
- UVSQ, Inserm U1173, Infection et inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Montigny-le-Bretonneux, France.,Rheumatology Division, Ambroise Paré Hospital, Boulogne-Billancourt, France
| | - Hendrick Mambu Mambueni
- UVSQ, Inserm U1173, Infection et inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Montigny-le-Bretonneux, France
| | - Roula Said-Nahal
- UVSQ, Inserm U1173, Infection et inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Montigny-le-Bretonneux, France.,Rheumatology Division, Ambroise Paré Hospital, Boulogne-Billancourt, France
| | - Henri-Jean Garchon
- UVSQ, Inserm U1173, Infection et inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Montigny-le-Bretonneux, France.,Genetics Division, Ambroise Paré Hospital, Boulogne-Billancourt, France
| | - Maxime Breban
- UVSQ, Inserm U1173, Infection et inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Montigny-le-Bretonneux, France.,Rheumatology Division, Ambroise Paré Hospital, Boulogne-Billancourt, France
| |
Collapse
|
5
|
Yang G, Yin Y, Tan Z, Liu J, Deng X, Yang Y. Whole-exome sequencing identified a novel heterozygous mutation of SALL1 and a new homozygous mutation of PTPRQ in a Chinese family with Townes-Brocks syndrome and hearing loss. BMC Med Genomics 2021; 14:24. [PMID: 33478437 PMCID: PMC7819242 DOI: 10.1186/s12920-021-00871-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/07/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Previous studies have revealed that mutations of Spalt Like Transcription Factor 1 (SALL1) are responsible for Townes-Brocks syndrome (TBS), a rare genetic disorder that is characterized by an imperforate anus, dysplastic ears, thumb malformations and other abnormalities, such as hearing loss, foot malformations, renal impairment with or without renal malformations, genitourinary malformations, and congenital heart disease. In addition, the protein tyrosine phosphatase receptor type Q (PTPRQ) gene has been identified in nonsyndromic hearing loss patients with autosomal recessive or autosomal dominant inherited patterns. METHODS A Chinese family with TBS and hearing loss was enrolled in this study. The proband was a two-month-old girl who suffered from congenital anal atresia with rectal perineal fistula, ventricular septal defect, patent ductus arteriosus, pulmonary hypertension (PH), and finger deformities. The proband's father also had external ear deformity with deafness, toe deformities and PH, although his anus was normal. Further investigation found that the proband's mother presented nonsyndromic hearing loss, and the proband's mother's parents were consanguine married. Whole-exome sequencing and Sanger sequencing were applied to detect the genetic lesions of TBS and nonsyndromic hearing loss. RESULTS Via whole-exome sequencing and Sanger sequencing of the proband and her mother, we identified a novel heterozygous mutation (ENST00000251020: c.1428_1429insT, p. K478QfsX38) of SALL1 in the proband and her father who presented TBS phenotypes, and we also detected a new homozygous mutation [ENST00000266688: c.1057_1057delC, p. L353SfsX8)] of PTPRQ in the proband's mother and uncle, who suffered from nonsyndromic hearing loss. Both mutations were located in the conserved sites of the respective protein and were predicted to be deleterious by informatics analysis. CONCLUSIONS This study confirmed the diagnosis of TBS at the molecular level and expanded the spectrum of SALL1 mutations and PTPRQ mutations. Our study may contribute to the clinical management and genetic counselling of TBS and hearing loss.
Collapse
Affiliation(s)
- Guangxian Yang
- Department of Cardiothoracic Surgery, Hunan Children's Hospital, No. 86 Ziyuan Road, Changsha, Hunan Province, 410007, China.
| | - Yi Yin
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiping Tan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jian Liu
- Department of Cardiothoracic Surgery, Hunan Children's Hospital, No. 86 Ziyuan Road, Changsha, Hunan Province, 410007, China
| | - Xicheng Deng
- Department of Cardiothoracic Surgery, Hunan Children's Hospital, No. 86 Ziyuan Road, Changsha, Hunan Province, 410007, China
| | - Yifeng Yang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| |
Collapse
|
7
|
Costantino F, Breban M, Garchon HJ. Genetics and Functional Genomics of Spondyloarthritis. Front Immunol 2018; 9:2933. [PMID: 30619293 PMCID: PMC6305624 DOI: 10.3389/fimmu.2018.02933] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
Spondyloarthritis (SpA) is a chronic inflammatory disorder with high heritability but with complex genetics. It encompasses several entities that share common clinical features. Most of the genetic studies in SpA have been restricted to ankylosing spondylitis (AS), the prototypical form of SpA. However, there is growing evidence of shared genetic background between all the SpA subtypes and also with some other immune-mediated diseases. The most important part of SpA heritability comes from the HLA-B27 allele in the major histocompatibility complex (MHC) that explains around 25% of the attributable heredity. Several other loci outside of the MHC have been shown to be involved in the disease. However, all these non-MHC loci explain only a small additional fraction of disease predisposition. Thus, a substantial fraction of SpA genetic basis remains poorly understood. Gene expression profiling is a complementary approach to elucidate the underlying mechanisms and pathways that drive the disease. Several expression profiling studies have been undertaken in SpA. However, results have been quite disappointing with little overlap between the studies largely due to the small sample sizes, resulting in limited power to discover small effects. In this review, we summarize current knowledge on genetic findings concerning SpA and we describe strategic approaches for identification of additional variants, with a focus on rare variants in familial forms. We also provide an overview of gene expression studies in SpA and discuss the possibilities offered by high-throughput RNA sequencing technologies, in particular in sorted cells. Finally, issues in establishing molecular mechanisms underlying genetic association hits and potential translational applications will be addressed.
Collapse
Affiliation(s)
- Félicie Costantino
- UMR 1173 INSERM/Versailles Saint-Quentin-en-Yvelines University, Montigny le Bretonneux, France.,Rheumatology Division Ambroise Paré Hospital (AP-HP), Boulogne-Billancourt, France
| | - Maxime Breban
- UMR 1173 INSERM/Versailles Saint-Quentin-en-Yvelines University, Montigny le Bretonneux, France.,Rheumatology Division Ambroise Paré Hospital (AP-HP), Boulogne-Billancourt, France
| | - Henri-Jean Garchon
- UMR 1173 INSERM/Versailles Saint-Quentin-en-Yvelines University, Montigny le Bretonneux, France.,Genetics Division Ambroise Paré Hospital (AP-HP), Boulogne-Billancourt, France
| |
Collapse
|