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Chen S, Tang D, Deng L, Xu S. Asian-European differentiation of schizophrenia-associated genes driven by admixture and natural selection. iScience 2024; 27:109560. [PMID: 38638564 PMCID: PMC11024917 DOI: 10.1016/j.isci.2024.109560] [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: 08/22/2023] [Revised: 12/29/2023] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
The European-centered genome-wide association studies of schizophrenia (SCZ) may not be well applied to non-European populations. We analyzed 1,592 reported SCZ-associated genes using the public genome data and found an overall higher Asian-European differentiation on the SCZ-associated variants than at the genome-wide level. Notable examples included 15 missense variants, a regulatory variant SLC5A10-rs1624825, and a damaging variant TSPAN18-rs1001292. Independent local adaptations in recent 25,000 years, after the Asian-European divergence, could have contributed to such genetic differentiation, as were identified at a missense mutation LTN1-rs57646126-A in Asians, and a non-risk allele ZSWIM6-rs72761442-G in Europeans. Altai-Neanderthal-derived alleles may have opposite effects on SCZ susceptibility between ancestries. Furthermore, adaptive introgression was detected on the non-risk haplotype at 1q21.2 in Europeans, while in Asians it was observed on the SCZ risk haplotype at 3p21.31 which is also potentially ultra-violet protective. This study emphasizes the importance of including more representative Asian samples in future SCZ studies.
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Affiliation(s)
- Sihan Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Die Tang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lian Deng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
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Kwon S, Safer J, Nguyen DT, Hoksza D, May P, Arbesfeld JA, Rubin AF, Campbell AJ, Burgin A, Iqbal S. Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573913. [PMID: 38260256 PMCID: PMC10802383 DOI: 10.1101/2024.01.02.573913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics technologies have enabled the detection and generation of variants at an unprecedented scale. However, efficient tools and resources are needed to link these two disparate data types - to "map" variants onto protein structures, to better understand how the variation causes disease and thereby design therapeutics. Here we present the Genomics 2 Proteins Portal (G2P; g2p.broadinstitute.org/): a human proteome-wide resource that maps 19,996,443 genetic variants onto 42,413 protein sequences and 77,923 structures, with a comprehensive set of structural and functional features. Additionally, the G2P portal generalizes the capability of linking genomics to proteins beyond databases by allowing users to interactively upload protein residue-wise annotations (variants, scores, etc.) as well as the protein structure to establish the connection. The portal serves as an easy-to-use discovery tool for researchers and scientists to hypothesize the structure-function relationship between natural or synthetic variations and their molecular phenotype.
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3
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Chen Z, Luo S, Liu ZG, Deng YC, He SL, Liu XR, Yi YH, Wang J, Gao LD, Li BM, Wu ZJ, Ye ZL, Liang DH, Bian WJ, Liao WP. CELSR1 variants are associated with partial epilepsy of childhood. Am J Med Genet B Neuropsychiatr Genet 2022; 189:247-256. [PMID: 36453712 DOI: 10.1002/ajmg.b.32916] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/25/2022] [Accepted: 07/26/2022] [Indexed: 02/01/2023]
Abstract
CELSR1 gene, encoding cadherin EGF LAG seven-pass G-type receptor 1, is mainly expressed in neural stem cells during the embryonic period. It plays an important role in neurodevelopment. However, the relationship between CELSR1 and disease of the central nervous system has not been defined. In this study, we performed trios-based whole-exome sequencing in a cohort of 356 unrelated cases with partial epilepsy without acquired causes and identified CELSR1 variants in six unrelated cases. The variants included one de novo heterozygous nonsense variant, one de novo heterozygous missense variant, and four compound heterozygous missense variants that had one variant was located in the extracellular region and the other in the cytoplasm. The patients with biallelic variants presented severe epileptic phenotypes, whereas those with heterozygous variants were associated with a mild epileptic phenotype of benign epilepsy with centrotemporal spikes (BECTS). These variants had no or low allele frequency in the gnomAD database. The frequencies of the CELSR1 variants in this cohort were significantly higher than those in the control populations. The evidence from ClinGen Clinical-Validity Framework suggested a strong association between CELSR1 variants and epilepsy. These findings provide evidence that CELSR1 is potentially a candidate pathogenic gene of partial epilepsy of childhood.
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Affiliation(s)
- Zheng Chen
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China.,Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sheng Luo
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Zhi-Gang Liu
- Department of Pediatrics, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, China
| | - Yan-Chun Deng
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Su-Li He
- Department of Pediatrics, Shantou Chaonan Minsheng Hospital, Shantou, China
| | - Xiao-Rong Liu
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Yong-Hong Yi
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Jie Wang
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Liang-Di Gao
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Bing-Mei Li
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Zhi-Jun Wu
- Department of Neurology, Second Hospital of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Zi-Long Ye
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - De-Hai Liang
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Wen-Jun Bian
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Wei-Ping Liao
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
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Li C, Liang X, Cheng S, Wen Y, Pan C, Zhang H, Chen Y, Zhang J, Zhang Z, Yang X, Meng P, Zhang F. A multi-environments-gene interaction study of anxiety, depression and self-harm in the UK Biobank cohort. J Psychiatr Res 2022; 147:59-66. [PMID: 35026594 DOI: 10.1016/j.jpsychires.2022.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 12/26/2021] [Accepted: 01/03/2022] [Indexed: 12/22/2022]
Abstract
The effects of gene-by-environment (G×E) interactions on complex diseases are significant, especially the superimposed effects of multiple environmental factors. However, research on the multi-environments-gene interactions of anxiety, depression, and self-harm is still limited. This study included white individuals (N = 66,041-74,482) from the UK Biobank. We fitted all environmental factors to a single environmental score (ES), and the estimated ES was used to calculate the multiplicative interaction effects between ES and genome-wide SNPs. Heritability was stratified by minor allele frequency (MAF) and linkage disequilibrium (LD). Our research found 10 loci with significant interaction effects, such as rs114830993 (PRICKLE2, P = 2.30 × 10-8), rs151323364 (ASTN2, P = 2.71 × 10-10) and rs536631793 (SYN3, P = 4.09 × 10-8). In addition, we found that G×E heritability has a significant contribution to the depression of Patient Health Questionnaire-9 (PHQ-9) scores (h2G×E (female) = 6.1%, h2G×E (male) = 8.7%). Our research supported the important influence of multi-environments-gene interactions on anxiety, depression, and self-harm and provided clues for the prevention and etiological research of them.
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Affiliation(s)
- Chun'e Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xiao Liang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chuyu Pan
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Huijie Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yujing Chen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jingxi Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Zhen Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Peilin Meng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.
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Muk T, Stensballe A, Dmytriyeva O, Brunse A, Jiang PP, Thymann T, Sangild PT, Pankratova S. Differential Brain and Cerebrospinal Fluid Proteomic Responses to Acute Prenatal Endotoxin Exposure. Mol Neurobiol 2022; 59:2204-2218. [PMID: 35064541 DOI: 10.1007/s12035-022-02753-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/17/2022] [Indexed: 12/12/2022]
Abstract
Chorioamnionitis (CA) is a risk factor for preterm birth and is associated with neurodevelopmental delay and cognitive disorders. Prenatal inflammation-induced brain injury may resolve during the immediate postnatal period when rapid brain remodeling occurs. Cerebrospinal fluid (CSF) collected at birth may be a critical source of predictive biomarkers. Using pigs as a model of preterm infants exposed to CA, we hypothesized that prenatal lipopolysaccharide (LPS) exposure induces proteome changes in the CSF and brain at birth and postnatally. Fetal piglets (103 days gestation of full-term at 117 days) were administered intra-amniotic (IA) lipopolysaccharide (LPS) 3 days before preterm delivery by caesarian section. CSF and brain tissue were collected on postnatal Days 1 and 5 (P1 and P5). CSF and hippocampal proteins were profiled by LC-MS-based quantitative proteomics. Neuroinflammatory responses in the cerebral cortex, periventricular white matter and hippocampus were evaluated by immunohistochemistry, and gene expression was evaluated by qPCR. Pigs exposed to LPS in utero showed changes in CSF protein levels at birth but not at P5. Complement protein C3, hemopexin, vasoactive intestinal peptide, carboxypeptidase N subunit 2, ITIH1, and plasminogen expression were upregulated in the CSF, while proteins associated with axon growth and synaptic functions (FGFR1, BASP1, HSPD1, UBER2N, and RCN2), adhesion (talin1), and neuronal survival (Atox1) were downregulated. Microglia, but not astrocytes, were activated by LPS at P5 in the hippocampus but not in other brain regions. At this time, marginal increases in complement protein C3, LBP, HIF1a, Basp1, Minpp1, and FGFR1 transcription indicated hippocampal proinflammatory responses. In conclusion, few days exposure to endotoxin prenatally induce proteome changes in the CSF and brain at birth, but most changes resolve a few days later. The developing hippocampus has high neuronal plasticity in response to perinatal inflammation. Changes in CSF protein expression at birth may predict later structural brain damage in preterm infants exposed to variable types and durations of CA-related inflammation in utero.
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Affiliation(s)
- Tik Muk
- Section of Comparative Pediatrics and Nutrition, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Oksana Dmytriyeva
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Anders Brunse
- Section of Comparative Pediatrics and Nutrition, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ping-Ping Jiang
- Section of Comparative Pediatrics and Nutrition, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Thymann
- Section of Comparative Pediatrics and Nutrition, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Per Torp Sangild
- Section of Comparative Pediatrics and Nutrition, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark.,Department of Paediatrics, Odense University Hospital, Odense, Denmark
| | - Stanislava Pankratova
- Section of Comparative Pediatrics and Nutrition, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, 1870, Frederiksberg C, Denmark.
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