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Huang X, Liang W, Yang R, Jin L, Zhao K, Chen J, Shang X, Zhou Y, Wang X, Yu H. Variations in the LINGO2 and GLIS3 Genes and Gene-Environment Interactions Increase Gestational Diabetes Mellitus Risk in Chinese Women. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11596-11605. [PMID: 38888423 DOI: 10.1021/acs.est.4c03221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Gestational diabetes mellitus (GDM) has been found to be a common complication in pregnant women, known to escalate the risk of negative obstetric outcomes. In our study, we genotyped 1,566 Chinese pregnant women for two single nucleotide polymorphisms (SNPs) in the LINGO2 gene and one SNP in the GLIS3 gene, utilizing targeted next-generation sequencing. The impact of two interacting genes, and the interaction of genes with the environment─including exposure to particulate matter (PM2.5), ozone (O3), and variations in prepregnancy body mass index (BMI)─on the incidence of GDM were analyzed using logistic regression. Our findings identify the variants LINGO2 rs10968576 (P = 0.022, OR = 1.224) and rs1412239 (P = 0.018, OR = 1.231), as well as GLIS3 rs10814916 (P = 0.028, OR = 1.172), as risk mutations significantly linked to increased susceptibility to GDM. Further analysis underscores the crucial role of gene-gene and gene-environment interactions in the development of GDM among Chinese women (P < 0.05). Particularly, the individuals carrying the rs10968576 G-rs1412239 G-rs10814916 C haplotype exhibit increased susceptibility to GDM during the prepregnancy period when interacting with PM2.5, O3, and BMI (P = 8.004 × 10-7, OR = 1.206; P = 6.3264 × 10-11, OR = 1.280; P = 9.928 × 10-7, OR = 1.334, respectively). In conclusion, our research emphasizes the importance of the interaction between specific gene variations─LINGO2 and GLIS3─and environmental factors in influencing GDM risk. Notably, we found significant associations between these gene variations and GDM risk across various environmental exposure periods.
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Affiliation(s)
- Xiao Huang
- Department of Immunology, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi 563000, China
| | - Weiwei Liang
- Department of Immunology, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi 563000, China
| | - Runqiu Yang
- Department of Immunology, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi 563000, China
| | - Lei Jin
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory of Reproductive Health, Peking University, Beijing 100091, China
| | - Kai Zhao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Juan Chen
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Xuejun Shang
- Department of Urology, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210023, China
| | - Yuanzhong Zhou
- School of Public Health, Key Laboratory of Maternal & Child Health and Exposure Science of Guizhou Higher Education Institutes, Zunyi Medical University, Zunyi 563000, China
| | - Xin Wang
- Department of Immunology, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi 563000, China
| | - Hongsong Yu
- Department of Immunology, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi 563000, China
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Lee J, Cho K, Weigel KA, White HM, Do C, Choi I. Identification of genomic regions and genes associated with subclinical ketosis in periparturient dairy cows. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2024; 66:567-576. [PMID: 38975580 PMCID: PMC11222121 DOI: 10.5187/jast.2023.e97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/16/2023] [Accepted: 09/12/2023] [Indexed: 07/09/2024]
Abstract
Subclinical ketosis (SCK) is a prevalent metabolic disorder that occurs during the transition to lactation period. It is defined as a high blood concentration of ketone bodies (beta-hydroxybutyric acid f ≥ 1.2 mmol/L) within the first few weeks of lactation, and often presents without clinical signs. SCK is mainly caused by negative energy balance (NEB). The objective of this study is to identify single nucleotide polymorphisms (SNPs) associated with SCK using genome-wide association studies (GWAS), and to predict the biological functions of proximal genes using gene-set enrichment analysis (GSEA). Blood samples were collected from 112 Holstein cows between 5 and 18 days postpartum to determine the incidence of SCK. Genomic DNA extracted from both SCK and healthy cows was examined using the Illumina Bovine SNP50K BeadChip for genotyping. GWAS revealed 194 putative SNPs and 163 genes associated with those SNPs. Additionally, GSEA showed that the genes retrieved by Database for Annotation, Visualization, and Integrated Discovery (DAVID) belonged to calcium signaling, starch and sucrose, immune network, and metabolic pathways. Furthermore, the proximal genes were found to be related to germ cell and early embryo development. In summary, this study proposes several feasible SNPs and genes associated with SCK through GWAS and GSEA. These candidates can be utilized in selective breeding programs to reduce the genetic risk for SCK and subfertility in high-performance dairy cows.
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Affiliation(s)
- Jihwan Lee
- Dairy Science Division, National Institute
of Animal Science, RDA, Cheon 31000, Korea
| | - KwangHyeon Cho
- Department of Beef and Dairy Science,
Korea National College of Agriculture and Fisheries, Jeonju
54874, Korea
| | - Kent A. Weigel
- Department of Animal and Dairy Sciences,
University of Wisconsin, Madison 53706, USA
| | - Heather M. White
- Department of Animal and Dairy Sciences,
University of Wisconsin, Madison 53706, USA
| | - ChangHee Do
- Department of Animal and Dairy Sciences,
Chungnam National University, Daejeon 34134, Korea
| | - Inchul Choi
- Department of Animal and Dairy Sciences,
Chungnam National University, Daejeon 34134, Korea
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3
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Hu JJ, Zhang YB, Zheng SF, Chen GR, Lin YX, Kang DZ, Lin ZY, Yao PS. The causal relationship between circulating biomarkersand the risk of bipolar disorder: A two-sample Mendelian randomization study. J Psychiatr Res 2023; 164:66-71. [PMID: 37327502 DOI: 10.1016/j.jpsychires.2023.05.070] [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: 01/12/2023] [Revised: 03/27/2023] [Accepted: 05/25/2023] [Indexed: 06/18/2023]
Abstract
OBJECTIVE To identify susceptible biomarkers for the development of bipolar disorder (BD), we conducted a Mendelian Randomization (MR) design to screen circulating proteins for the potential risk of bipolar disorder systematically. METHODS We performed a two-sample Mendelian randomization (MR) analysis to estimate the causality of 4782 human circulating proteins on the risk of bipolar disorder. 376 circulating biomarkers were selected in MR estimation (4406 circulating proteins with less than 3 SNPs were excluded) with 5368 European descents. GWAS meta-analysis of the potential role of all-cause bipolar disorder arose from the Psychiatric Genomics Consortium (41,917 cases, 371,549 controls). RESULTS After IVW and sensitivity analysis, 4 circulating proteins having causal effects on bipolar disorder were identified. ISG15, as a key player in the innate immune response, decreased the risk of bipolar disorder causally (OR = 0.92, 95% CI = 0.89-0.94, P = 1.46e-09). Furthermore, MLN decreased the risk of bipolar disorder causally (OR = 0.94, 95% CI = 0.91-0.97, P = 1.04e-04). In addition, SFTPC (OR = 0.91, 95% CI = 0.86-0.96, P = 4.47e-04) and VCY (OR = 0.86, 95% CI = 0.77-0.96, P = 8.55e-03) presented a suggestive association with bipolar disorder. CONCLUSIONS Our findings indicated that ISG15 and MLN showed evidence of causality in bipolar disorder and provided a promising target for the diagnosis and treatment of diseases.
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Affiliation(s)
- Jiao-Jiao Hu
- Department of Neurosurgery, Neurosurgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian, China
| | - Yi-Bin Zhang
- Department of Neurosurgery, Neurosurgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian, China
| | - Shu-Fa Zheng
- Department of Neurosurgery, Neurosurgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian, China
| | - Guo-Rong Chen
- Department of Neurosurgery, Neurosurgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian, China
| | - Yuan-Xiang Lin
- Department of Neurosurgery, Neurosurgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian, China; Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian, China
| | - De-Zhi Kang
- Department of Neurosurgery, Neurosurgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian, China; Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian, China; Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian, China.
| | - Zhang-Ya Lin
- Department of Neurosurgery, Neurosurgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian, China; Department of Pain, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
| | - Pei-Sen Yao
- Department of Neurosurgery, Neurosurgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, Fujian, China.
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Banerjee S, Simonetti FL, Detrois KE, Kaphle A, Mitra R, Nagial R, Söding J. Tejaas: reverse regression increases power for detecting trans-eQTLs. Genome Biol 2021; 22:142. [PMID: 33957961 PMCID: PMC8101255 DOI: 10.1186/s13059-021-02361-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 04/22/2021] [Indexed: 12/18/2022] Open
Abstract
Trans-acting expression quantitative trait loci (trans-eQTLs) account for ≥70% expression heritability and could therefore facilitate uncovering mechanisms underlying the origination of complex diseases. Identifying trans-eQTLs is challenging because of small effect sizes, tissue specificity, and a severe multiple-testing burden. Tejaas predicts trans-eQTLs by performing L2-regularized “reverse” multiple regression of each SNP on all genes, aggregating evidence from many small trans-effects while being unaffected by the strong expression correlations. Combined with a novel unsupervised k-nearest neighbor method to remove confounders, Tejaas predicts 18851 unique trans-eQTLs across 49 tissues from GTEx. They are enriched in open chromatin, enhancers, and other regulatory regions. Many overlap with disease-associated SNPs, pointing to tissue-specific transcriptional regulation mechanisms.
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Affiliation(s)
- Saikat Banerjee
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, 37077, Germany.
| | - Franco L Simonetti
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, 37077, Germany
| | - Kira E Detrois
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, 37077, Germany.,Georg-August University, Göttingen, 37075, Germany
| | - Anubhav Kaphle
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, 37077, Germany.,Georg-August University, Göttingen, 37075, Germany
| | | | | | - Johannes Söding
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, 37077, Germany. .,Campus-Institut Data Science (CIDAS), University of Göttingen, Göttingen, 37073, Germany. .,Cluster of Excellence "Multiscale Bioimaging" (MBExC), University of Göttingen, Göttingen, 37075, Germany.
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5
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An B, Xu L, Xia J, Wang X, Miao J, Chang T, Song M, Ni J, Xu L, Zhang L, Li J, Gao H. Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle. BMC Genet 2020; 21:32. [PMID: 32171250 PMCID: PMC7071762 DOI: 10.1186/s12863-020-0837-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/04/2020] [Indexed: 01/08/2023] Open
Abstract
Background Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and cannon bone size (CS). We performed genome-wide association studies (GWAS) of these traits over the course of three growth stages (6, 12 and 18 months after birth) using three statistical models, single-trait GWAS, multi-trait GWAS and LONG-GWAS. The Illumina Bovine HD 770 K BeadChip was used to identify genomic single nucleotide polymorphisms (SNPs) in 1217 individuals. Results In total, 19, 29, and 10 significant SNPs were identified by the three models, respectively. Among these, 21 genes were promising candidate genes, including SOX2, SNRPD1, RASGEF1B, EFNA5, PTBP1, SNX9, SV2C, PKDCC, SYNDIG1, AKR1E2, and PRIM2 identified by single-trait analysis; SLC37A1, LAP3, PCDH7, MANEA, and LHCGR identified by multi-trait analysis; and P2RY1, MPZL1, LINGO2, CMIP, and WSCD1 identified by LONG-GWAS. Conclusions Multiple association analysis was performed for six growth traits at each growth stage. These findings offer valuable insights for the further investigation of potential genetic mechanism of growth traits in Simmental beef cattle.
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Affiliation(s)
| | | | - Jiangwei Xia
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310000, China
| | - Xiaoqiao Wang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Jian Miao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Meihua Song
- Zhuang Yuan Veterinary Station of Qixia city, Yantai, 265300, China
| | - Junqing Ni
- Heibei Livestock Breeding Workstation, Shijiazhuang, 050061, China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China.
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6
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Rigau M, Juan D, Valencia A, Rico D. Intronic CNVs and gene expression variation in human populations. PLoS Genet 2019; 15:e1007902. [PMID: 30677042 PMCID: PMC6345438 DOI: 10.1371/journal.pgen.1007902] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 12/17/2018] [Indexed: 11/19/2022] Open
Abstract
Introns can be extraordinarily large and they account for the majority of the DNA sequence in human genes. However, little is known about their population patterns of structural variation and their functional implication. By combining the most extensive maps of CNVs in human populations, we have found that intronic losses are the most frequent copy number variants (CNVs) in protein-coding genes in human, with 12,986 intronic deletions, affecting 4,147 genes (including 1,154 essential genes and 1,638 disease-related genes). This intronic length variation results in dozens of genes showing extreme population variability in size, with 40 genes with 10 or more different sizes and up to 150 allelic sizes. Intronic losses are frequent in evolutionarily ancient genes that are highly conserved at the protein sequence level. This result contrasts with losses overlapping exons, which are observed less often than expected by chance and almost exclusively affect primate-specific genes. An integrated analysis of CNVs and RNA-seq data showed that intronic loss can be associated with significant differences in gene expression levels in the population (CNV-eQTLs). These intronic CNV-eQTLs regions are enriched for intronic enhancers and can be associated with expression differences of other genes showing long distance intron-promoter 3D interactions. Our data suggests that intronic structural variation of protein-coding genes makes an important contribution to the variability of gene expression and splicing in human populations.
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Affiliation(s)
- Maria Rigau
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - David Juan
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Daniel Rico
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
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7
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Han HG, Moon HW, Jeon YJ. ISG15 in cancer: Beyond ubiquitin-like protein. Cancer Lett 2018; 438:52-62. [DOI: 10.1016/j.canlet.2018.09.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 09/06/2018] [Indexed: 01/08/2023]
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Choi S, Lee S, Kim Y, Hwang H, Park T. HisCoM-GGI: Hierarchical structural component analysis of gene-gene interactions. J Bioinform Comput Biol 2018; 16:1840026. [PMID: 30567476 DOI: 10.1142/s0219720018400267] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although genome-wide association studies (GWAS) have successfully identified thousands of single nucleotide polymorphisms (SNPs) associated with common diseases, these observations are limited for fully explaining "missing heritability". Determining gene-gene interactions (GGI) are one possible avenue for addressing the missing heritability problem. While many statistical approaches have been proposed to detect GGI, most of these focus primarily on SNP-to-SNP interactions. While there are many advantages of gene-based GGI analyses, such as reducing the burden of multiple-testing correction, and increasing power by aggregating multiple causal signals across SNPs in specific genes, only a few methods are available. In this study, we proposed a new statistical approach for gene-based GGI analysis, "Hierarchical structural CoMponent analysis of Gene-Gene Interactions" (HisCoM-GGI). HisCoM-GGI is based on generalized structured component analysis, and can consider hierarchical structural relationships between genes and SNPs. For a pair of genes, HisCoM-GGI first effectively summarizes all possible pairwise SNP-SNP interactions into a latent variable, from which it then performs GGI analysis. HisCoM-GGI can evaluate both gene-level and SNP-level interactions. Through simulation studies, HisCoM-GGI demonstrated higher statistical power than existing gene-based GGI methods, in analyzing a GWAS of a Korean population for identifying GGI associated with body mass index. Resultantly, HisCoM-GGI successfully identified 14 potential GGI, two of which, (NCOR2 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>×</mml:mo></mml:math> SPOCK1) and (LINGO2 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>×</mml:mo></mml:math> ZNF385D) were successfully replicated in independent datasets. We conclude that HisCoM-GGI method may be a valuable tool for genome to identify GGI in missing heritability, allowing us to better understand the biological genetic mechanisms of complex traits. We conclude that HisCoM-GGI method may be a valuable tool for genome to identify GGI in missing heritability, allowing us to better understand biological genetic mechanisms of complex traits. An implementation of HisCoM-GGI can be downloaded from the website ( http://statgen.snu.ac.kr/software/hiscom-ggi ).
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Affiliation(s)
- Sungkyoung Choi
- Department of Pharmacology, Yonsei University College of Medicine, 50-1 Yonsei-ro Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Sungyoung Lee
- Center for Precision Medicine, Seoul National University Hospital, 71 Daehak-ro Jongno-gu, Seoul 03082, Republic of Korea
| | - Yongkang Kim
- Department of Statistics, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul 08826, Republic of Korea.,Department of Psychology, McGill University, 2001 Avenue McGill College, Montreal, Quebec H3A 1G1, Canada
| | - Heungsun Hwang
- Department of Psychology, McGill University, 2001 Avenue McGill College, Montreal, Quebec H3A 1G1, Canada
| | - Taesung Park
- Department of Statistics, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul 08826, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul 08826, Republic of Korea
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9
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Mizoguchi T, Minakuchi H, Ishisaka M, Tsuruma K, Shimazawa M, Hara H. Behavioral abnormalities with disruption of brain structure in mice overexpressing VGF. Sci Rep 2017; 7:4691. [PMID: 28680036 PMCID: PMC5498671 DOI: 10.1038/s41598-017-04132-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 05/10/2017] [Indexed: 01/01/2023] Open
Abstract
VGF nerve growth factor inducible (VGF) is a neuropeptide induced by nerve growth factor and brain-derived neurotrophic factor. This peptide is involved in synaptic plasticity, neurogenesis, and neurite growth in the brain. Patients with depression and bipolar disorder have lower-than-normal levels of VGF, whereas patients with schizophrenia and other cohorts of patients with depression have higher-than-normal levels. VGF knockout mice display behavioral abnormalities such as higher depressive behavior and memory dysfunction. However, it is unclear whether upregulation of VGF affects brain function. In the present study, we generated mice that overexpress VGF and investigated several behavioral phenotypes and the brain structure. These adult VGF-overexpressing mice showed (a) hyperactivity, working memory impairment, a higher depressive state, and lower sociality compared with wild-type mice; (b) lower brain weight without a change in body weight; (c) increased lateral ventricle volume compared with wild-type mice; and (d) striatal morphological defects. These results suggest that VGF may modulate a variety of behaviors and brain development. This transgenic mouse line may provide a useful model for research on mental illnesses.
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Affiliation(s)
- Takahiro Mizoguchi
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Hiroko Minakuchi
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Mitsue Ishisaka
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Kazuhiro Tsuruma
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Masamitsu Shimazawa
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Hideaki Hara
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan.
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10
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Guénard F, Bouchard-Mercier A, Rudkowska I, Lemieux S, Couture P, Vohl MC. Genome-Wide Association Study of Dietary Pattern Scores. Nutrients 2017; 9:E649. [PMID: 28644415 PMCID: PMC5537769 DOI: 10.3390/nu9070649] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/07/2017] [Accepted: 06/21/2017] [Indexed: 01/08/2023] Open
Abstract
Dietary patterns, representing global food supplies rather than specific nutrients or food intakes, have been associated with cardiovascular disease (CVD) incidence and mortality. The contribution of genetic factors in the determination of food intakes, preferences and dietary patterns has been previously established. The current study aimed to identify novel genetic factors associated with reported dietary pattern scores. Reported dietary patterns scores were derived from reported dietary intakes for the preceding month and were obtained through a food frequency questionnaire and genome-wide association study (GWAS) conducted in a study sample of 141 individuals. Reported Prudent and Western dietary patterns demonstrated nominal associations (p < 1 × 10-5) with 78 and 27 single nucleotide polymorphisms (SNPs), respectively. Among these, SNPs annotated to genes previously associated with neurological disorders, CVD risk factors and obesity were identified. Further assessment of SNPs demonstrated an impact on gene expression levels in blood for SNPs located within/near BCKDHB (p = 0.02) and the hypothalamic glucosensor PFKFB3 (p = 0.0004) genes, potentially mediated through an impact on the binding of transcription factors (TFs). Overrepresentations of glucose/energy homeostasis and hormone response TFs were also observed from SNP-surrounding sequences. Results from the current GWAS study suggest an interplay of genes involved in the metabolic response to dietary patterns on obesity, glucose metabolism and food-induced response in the brain in the adoption of dietary patterns.
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Affiliation(s)
- Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), School of Nutrition, Laval University, Québec, QC G1V 0A6, Canada.
| | - Annie Bouchard-Mercier
- Institute of Nutrition and Functional Foods (INAF), School of Nutrition, Laval University, Québec, QC G1V 0A6, Canada.
| | - Iwona Rudkowska
- Endocrinology and Nephrology Unit, Centre de recherche du CHU de Québec, Laval University, Québec, QC G1V 4G2, Canada.
| | - Simone Lemieux
- Institute of Nutrition and Functional Foods (INAF), School of Nutrition, Laval University, Québec, QC G1V 0A6, Canada.
| | - Patrick Couture
- Institute of Nutrition and Functional Foods (INAF), Endocrinology and Nephrology Unit, Centre de recherche du CHU de Québec, Laval University, Québec, QC G1V 4G2, Canada.
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), School of Nutrition, Laval University, Québec, QC G1V 0A6, Canada.
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11
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Genomic structural variations for cardiovascular and metabolic comorbidity. Sci Rep 2017; 7:41268. [PMID: 28120895 PMCID: PMC5264603 DOI: 10.1038/srep41268] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 12/19/2016] [Indexed: 12/19/2022] Open
Abstract
The objective of this study was to identify genes targeted by both copy number and copy-neutral changes in the right coronary arteries in the area of advanced atherosclerotic plaques and intact internal mammary arteries derived from the same individuals with comorbid coronary artery disease and metabolic syndrome. The artery samples from 10 patients were screened for genomic imbalances using array comparative genomic hybridization. Ninety high-confidence, identical copy number variations (CNVs) were detected. We also identified eight copy-neutral changes (cn-LOHs) > 1.5 Mb in paired arterial samples in 4 of 10 individuals. The frequencies of the two gains located in the 10q24.31 (ERLIN1) and 12q24.11 (UNG, ACACB) genomic regions were evaluated in 33 paired arteries and blood samples. Two patients contained the gain in 10q24.31 (ERLIN1) and one patient contained the gain in 12q24.11 (UNG, ACACB) that affected only the blood DNA. An additional two patients harboured these CNVs in both the arteries and blood. In conclusion, we discovered and confirmed a gain of the 10q24.31 (ERLIN1) and 12q24.11 (UNG, ACACB) genomic regions in patients with coronary artery disease and metabolic comorbidity. Analysis of DNA extracted from blood indicated a possible somatic origin for these CNVs.
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Ashenhurst JR, Harden KP, Corbin WR, Fromme K. Alcohol-related genes show an enrichment of associations with a persistent externalizing factor. JOURNAL OF ABNORMAL PSYCHOLOGY 2016; 125:933-945. [PMID: 27505405 DOI: 10.1037/abn0000194] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Research using twins has found that much of the variability in externalizing phenotypes-including alcohol and drug use, impulsive personality traits, risky sex, and property crime-is explained by genetic factors. Nevertheless, identification of specific genes and variants associated with these traits has proven to be difficult, likely because individual differences in externalizing are explained by many genes of small individual effect. Moreover, twin research indicates that heritable variance in externalizing behaviors is mostly shared across the externalizing spectrum rather than specific to any behavior. We use a longitudinal, "deep phenotyping" approach to model a general externalizing factor reflecting persistent engagement in a variety of socially problematic behaviors measured at 11 assessment occasions spanning early adulthood (ages 18 to 28). In an ancestrally homogenous sample of non-Hispanic Whites (N = 337), we then tested for enrichment of associations between the persistent externalizing factor and a set of 3,281 polymorphisms within 104 genes that were previously identified as associated with alcohol-use behaviors. Next, we tested for enrichment among domain-specific factors (e.g., property crime) composed of residual variance not accounted for by the common factor. Significance was determined relative to bootstrapped empirical thresholds derived from permutations of phenotypic data. Results indicated significant enrichment of genetic associations for persistent externalizing, but not for domain-specific factors. Consistent with twin research findings, these results suggest that genetic variants are broadly associated with externalizing behaviors rather than unique to specific behaviors. (PsycINFO Database Record
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