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Shi Y, Cheng Y, Wang W, Tang L, Li W, Zhang L, Yuan Z, Zhu F, Duan Q. YANK2 activated by Fyn promotes glioma tumorigenesis via the mTOR-independent p70S6K activation pathway. Sci Rep 2024; 14:10507. [PMID: 38714727 PMCID: PMC11076283 DOI: 10.1038/s41598-024-61157-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/02/2024] [Indexed: 05/10/2024] Open
Abstract
Glioma, particularly glioblastomas (GBM), is incurable brain tumor. The most targeted receptor tyrosine kinase (RTKs) drugs did not bring benefit to GBM patients. The mechanism of glioma growth continues to be explored to find more effective treatment. Here, we reported that Ser/Thr protein kinase YANK2 (yet another kinase 2) is upregulated in glioma tissues and promotes the growth and proliferation of glioma in vitro and in vivo. Further, we confirmed that oncogene Fyn directly activated YANK2 through phosphorylation its Y110, and Fyn-mediated YANK2 phosphorylation at Y110 site promotes glioma growth by increasing its stability. Finally, YANK2 was proved to be a novel upstream kinase of p70S6K and promotes glioma growth by directly phosphorylating p70S6K at T389. Taken together, we found a new mTOR-independent p70S6K activation pathway, Fyn-YANK2-p70S6K, which promotes glioma growth, and YANK2 is a potential oncogene and serves as a novel therapeutic target for glioma.
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Affiliation(s)
- Yue Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yue Cheng
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Department of Clinical Laboratory, Zhengzhou Eighth People's Hospital, Zhengzhou, Henan, China
| | - Wei Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Liu Tang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Wensheng Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Liyuan Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Zheng Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Feng Zhu
- Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, Henan, China.
- Medical and Industry Crossover Research Institute of Medical College, Henan University, Kaifeng, 475000, Henan, China.
| | - Qiuhong Duan
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
- Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, Henan, China.
- Medical and Industry Crossover Research Institute of Medical College, Henan University, Kaifeng, 475000, Henan, China.
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Braz CU, Passamonti MM, Khatib H. Characterization of genomic regions escaping epigenetic reprogramming in sheep. ENVIRONMENTAL EPIGENETICS 2023; 10:dvad010. [PMID: 38496251 PMCID: PMC10944287 DOI: 10.1093/eep/dvad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 03/19/2024]
Abstract
The mammalian genome undergoes two global epigenetic reprogramming events during the establishment of primordial germ cells and in the pre-implantation embryo after fertilization. These events involve the erasure and re-establishment of DNA methylation marks. However, imprinted genes and transposable elements (TEs) maintain their DNA methylation signatures to ensure normal embryonic development and genome stability. Despite extensive research in mice and humans, there is limited knowledge regarding environmentally induced epigenetic marks that escape epigenetic reprogramming in other species. Therefore, the objective of this study was to examine the characteristics and locations of genomic regions that evade epigenetic reprogramming in sheep, as well as to explore the biological functions of the genes within these regions. In a previous study, we identified 107 transgenerationally inherited differentially methylated cytosines (DMCs) in the F1 and F2 generations in response to a paternal methionine-supplemented diet. These DMCs were found in TEs, non-repetitive regions, and imprinted and non-imprinted genes. Our findings suggest that genomic regions, rather than TEs and imprinted genes, have the propensity to escape reprogramming and serve as potential candidates for transgenerational epigenetic inheritance. Notably, 34 transgenerational methylated genes influenced by paternal nutrition escaped reprogramming, impacting growth, development, male fertility, cardiac disorders, and neurodevelopment. Intriguingly, among these genes, 21 have been associated with neural development and brain disorders, such as autism, schizophrenia, bipolar disease, and intellectual disability. This suggests a potential genetic overlap between brain and infertility disorders. Overall, our study supports the concept of transgenerational epigenetic inheritance of environmentally induced marks in mammals.
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Affiliation(s)
- Camila U Braz
- Department of Animal Sciences, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition, Universit’a Cattolica del Sacro Cuore, Piacenza, 29122, Italy
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI 53706, USA
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Hettema JM, van den Oord EJCG, Zhao M, Xie LY, Copeland WE, Penninx BWJH, Aberg KA, Clark SL. Methylome-wide association study of anxiety disorders. Mol Psychiatry 2023; 28:3484-3492. [PMID: 37542162 PMCID: PMC10838347 DOI: 10.1038/s41380-023-02205-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023]
Abstract
Anxiety Disorders (ANX) such as panic disorder, generalized anxiety disorder, and phobias, are highly prevalent conditions that are moderately heritable. Evidence suggests that DNA methylation may play a role, as it is involved in critical adaptations to changing environments. Applying an enrichment-based sequencing approach covering nearly 28 million autosomal CpG sites, we conducted a methylome-wide association study (MWAS) of lifetime ANX in 1132 participants (618 cases/514 controls) from the Netherlands Study of Depression and Anxiety. Using epigenomic deconvolution, we performed MWAS for the main cell types in blood: granulocytes, T-cells, B-cells and monocytes. Cell-type specific analyses identified 280 and 82 methylome-wide significant associations (q-value < 0.1) in monocytes and granulocytes, respectively. Our top finding in monocytes was located in ZNF823 on chromosome 19 (p = 1.38 × 10-10) previously associated with schizophrenia. We observed significant overlap (p < 1 × 10-06) with the same direction of effect in monocytes (210 sites), T-cells (135 sites), and B-cells (727 sites) between this Discovery MWAS signal and a comparable replication dataset from the Great Smoky Mountains Study (N = 433). Overlapping Discovery-Replication MWAS signal was enriched for findings from published GWAS of ANX, major depression, and post-traumatic stress disorder. In monocytes, two specific sites in the FZR1 gene showed significant replication after Bonferroni correction with an additional 15 nominally replicated sites in monocytes and 4 in T-cells. FZR1 regulates neurogenesis in the hippocampus, and its knockout leads to impairments in associative fear memory and long-term potentiation in mice. In the largest and most extensive methylome-wide study of ANX, we identified replicable methylation sites located in genes of potential relevance for brain mechanisms of psychiatric conditions.
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Affiliation(s)
- John M Hettema
- Department of Psychiatry & Behavioral Sciences, Texas A&M University, College Station, TX, USA
| | - Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Min Zhao
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Lin Y Xie
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Brenda W J H Penninx
- Department of Psychiatry, VU University Medical Center / GGZ inGeest, Amsterdam, 1081 HV, the Netherlands
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Shaunna L Clark
- Department of Psychiatry & Behavioral Sciences, Texas A&M University, College Station, TX, USA.
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Screening of Hub Genes in Hepatocellular Carcinoma Based on Network Analysis and Machine Learning. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:7300788. [PMID: 36479313 PMCID: PMC9722289 DOI: 10.1155/2022/7300788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/11/2022] [Accepted: 11/01/2022] [Indexed: 11/30/2022]
Abstract
Hepatocellular carcinoma (LIHC) is the fifth common cancer worldwide, and it requires effective diagnosis and treatment to prevent aggressive metastasis. The purpose of this study was to construct a machine learning-based diagnostic model for the diagnosis of liver cancer. Using weighted correlation network analysis (WGCNA), univariate analysis, and Lasso-Cox regression analysis, protein-protein interactions network analysis is used to construct gene networks from transcriptome data of hepatocellular carcinoma patients and find hub genes for machine learning. The five models, including gradient boosting, random forest, support vector machine, logistic regression, and integrated learning, were to identify a multigene prediction model of patients. Immunological assessment, TP53 gene mutation and promoter methylation level analysis, and KEGG pathway analysis were performed on these groups. Potential drug molecular targets for the corresponding hepatocellular carcinomas were obtained by molecular docking for analysis, resulting in the screening of 2 modules that may be relevant to the survival of hepatocellular carcinoma patients, and the construction of 5 diagnostic models and multiple interaction networks. The modes of action of drug-molecule interactions that may be effective against hepatocellular carcinoma core genes CCNA2, CCNB1, and CDK1 were investigated. This study is expected to provide research ideas for early diagnosis of hepatocellular carcinoma.
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Guo L, Ni Z, Wei G, Cheng W, Huang X, Yue W. Epigenome-wide DNA methylation analysis of whole blood cells derived from patients with GAD and OCD in the Chinese Han population. Transl Psychiatry 2022; 12:465. [PMID: 36344488 PMCID: PMC9640561 DOI: 10.1038/s41398-022-02236-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 10/14/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
Abstract
Generalized anxiety disorder (GAD) and obsessive-compulsive disorder (OCD) had high comorbidity and affected more than 44 million people around the world leading to a huge burden on health and economy. Here, we conducted an epigenome-wide DNA methylation study employing 93 patients with GAD, 65 patients with OCD, and 302 health controls, to explore epigenetic alterations associated with the onset and differences of GAD and OCD. We identified multiple differentially methylated positions (DMPs) and regions (DMRs): three DMP genes included RIOK3 (cg21515243, p = 8.00 × 10-10), DNASE2 (cg09379601, p = 1.10 × 10-9), and PSMB4 (cg01334186, p = 3.70 × 10-7) and two DMR genes USP6NL (p = 4.50 × 10-4) and CPLX1 (p = 6.95 × 10-4) were associated with the onset of GAD and OCD; three DMPs genes included LDLRAP1 (cg21400344, p = 4.40 × 10-12), ACIN1 (cg23712970, p = 2.98×10-11), and SCRT1 (cg25472897, p = 5.60 × 10-11) and three DMR genes WDR19 (p = 3.39 × 10-3), SYCP1 (p = 6.41 × 10-3), and FAM172A (p = 5.74 × 10-3) were associated with the differences between GAD and OCD. Investigation of epigenetic age and chronological age revealed a different epigenetic development trajectory of GAD and OCD. Conclusively, our findings which yielded robust models may aid in distinguishing patients from healthy controls (AUC = 0.90-0.99) or classifying patients with GAD and OCD (AUC = 0.89-0.99), and may power the precision medicine for them.
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Affiliation(s)
- Liangkun Guo
- grid.459847.30000 0004 1798 0615Institute of Mental Health, Peking University Sixth Hospital, Beijing, 100191 China ,grid.459847.30000 0004 1798 0615National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191 China ,grid.506261.60000 0001 0706 7839NHC Key Laboratory of Mental Health, & Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191 China
| | - Zhaojun Ni
- grid.459847.30000 0004 1798 0615Institute of Mental Health, Peking University Sixth Hospital, Beijing, 100191 China ,grid.459847.30000 0004 1798 0615National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191 China ,grid.506261.60000 0001 0706 7839NHC Key Laboratory of Mental Health, & Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191 China
| | - Guiming Wei
- Department of Neurology, Shandong Daizhuang Hospital, 272051 Jining, Shandong China
| | - Weiqiu Cheng
- grid.5510.10000 0004 1936 8921NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Xuebing Huang
- Institute of Mental Health, Peking University Sixth Hospital, Beijing, 100191, China. .,National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China. .,NHC Key Laboratory of Mental Health, & Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191, China.
| | - Weihua Yue
- Institute of Mental Health, Peking University Sixth Hospital, Beijing, 100191, China. .,National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China. .,NHC Key Laboratory of Mental Health, & Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191, China. .,PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China. .,Chinese Institute for Brain Research, Beijing, 102206, China.
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Cheng Y, Wang Y, Zhang W, Yin J, Dong J, Liu J. Relationship between intestinal flora, inflammation, BDNF gene polymorphism and generalized anxiety disorder: A clinical investigation. Medicine (Baltimore) 2022; 101:e28910. [PMID: 35866837 PMCID: PMC9302347 DOI: 10.1097/md.0000000000028910] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
INTRODUCTION Understanding factors related to generalized anxiety disorder pathogenesis is critical for elucidating the mechanism and preventing its establishment. Intestinal flora and hereditary factors such as brain-derived neurotrophic factor (BDNF) gene polymorphism may have a role in the development of generalized anxiety disorder. This work explored the relationship between intestinal flora, inflammatory changes and BDNF gene polymorphisms and the occurrence of generalized anxiety disorder. METHODS Forty-eight patients with generalized anxiety disorder and 57 healthy people were included in the study. As the disease group and control group, the polymorphisms of rs10767664 and rs7124442 of the BDNF gene, differences in the distribution of intestinal flora, and changes in inflammatory and immune indicators were analyzed. RESULTS The distribution of BDNF gene alleles, genotypes and haplotypes in the disease group were different from those in the control group. The levels of TNF-α (P = .000), interleukin-4 (P = .000), interleukin-10 (P = .043) and IgG (P = .008) in patients with generalized anxiety disorder in the disease group were different from those in the control group. The distribution of gut microbes in patients with generalized anxiety disorder in the disease group was different from that in the control group. CONCLUSION The onset of generalized anxiety disorder is related to BDNF gene polymorphism, and is accompanied by changes in intestinal flora and inflammatory immune status in the body.
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Affiliation(s)
- Yuanyuan Cheng
- Shandong Mental Health Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Qingdao Mental Health Center, Qingdao University, Qingdao, Shandong, China
| | - Yue Wang
- Hiser Medicine Center of Qingdao, Qingdao, Shandong, China
| | - Wen Zhang
- Binzhou People's Hospital, Binzhou, Shandong, China
| | - Junbo Yin
- Qingdao Mental Health Center, Qingdao University, Qingdao, Shandong, China
| | - Jicheng Dong
- Qingdao Mental Health Center, Qingdao University, Qingdao, Shandong, China
| | - Jintong Liu
- Shandong Mental Health Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Department of Psychiatry and Mental Health, School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- *Correspondence: Jintong Liu, Shangdong Mental Health Center, Cheeloo College of Medicine, Shandong University, 49 Wenhua East Road, Jinan, Shandong 250014, China (e-mail: )
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Manu DM, Mwinyi J, Schiöth HB. Challenges in Analyzing Functional Epigenetic Data in Perspective of Adolescent Psychiatric Health. Int J Mol Sci 2022; 23:ijms23105856. [PMID: 35628666 PMCID: PMC9147258 DOI: 10.3390/ijms23105856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 12/10/2022] Open
Abstract
The formative period of adolescence plays a crucial role in the development of skills and abilities for adulthood. Adolescents who are affected by mental health conditions are at risk of suicide and social and academic impairments. Gene–environment complementary contributions to the molecular mechanisms involved in psychiatric disorders have emphasized the need to analyze epigenetic marks such as DNA methylation (DNAm) and non-coding RNAs. However, the large and diverse bioinformatic and statistical methods, referring to the confounders of the statistical models, application of multiple-testing adjustment methods, questions regarding the correlation of DNAm across tissues, and sex-dependent differences in results, have raised challenges regarding the interpretation of the results. Based on the example of generalized anxiety disorder (GAD) and depressive disorder (MDD), we shed light on the current knowledge and usage of methodological tools in analyzing epigenetics. Statistical robustness is an essential prerequisite for a better understanding and interpretation of epigenetic modifications and helps to find novel targets for personalized therapeutics in psychiatric diseases.
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Wang H, Wu Y, Fang R, Sa J, Li Z, Cao H, Cui Y. Time-Varying Gene Network Analysis of Human Prefrontal Cortex Development. Front Genet 2020; 11:574543. [PMID: 33304381 PMCID: PMC7701309 DOI: 10.3389/fgene.2020.574543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 10/19/2020] [Indexed: 11/13/2022] Open
Abstract
The prefrontal cortex (PFC) constitutes a large part of the human central nervous system and is essential for the normal social affection and executive function of humans and other primates. Despite ongoing research in this region, the development of interactions between PFC genes over the lifespan is still unknown. To investigate the conversion of PFC gene interaction networks and further identify hub genes, we obtained time-series gene expression data of human PFC tissues from the Gene Expression Omnibus (GEO) database. A statistical model, loggle, was used to construct time-varying networks and several common network attributes were used to explore the development of PFC gene networks with age. Network similarity analysis showed that the development of human PFC is divided into three stages, namely, fast development period, deceleration to stationary period, and recession period. We identified some genes related to PFC development at these different stages, including genes involved in neuronal differentiation or synapse formation, genes involved in nerve impulse transmission, and genes involved in the development of myelin around neurons. Some of these genes are consistent with findings in previous reports. At the same time, we explored the development of several known KEGG pathways in PFC and corresponding hub genes. This study clarified the development trajectory of the interaction between PFC genes, and proposed a set of candidate genes related to PFC development, which helps further study of human brain development at the genomic level supplemental to regular anatomical analyses. The analytical process used in this study, involving the loggle model, similarity analysis, and central analysis, provides a comprehensive strategy to gain novel insights into the evolution and development of brain networks in other organisms.
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Affiliation(s)
- Huihui Wang
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Yongqing Wu
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Ruiling Fang
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Jian Sa
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Zhi Li
- Department of Hematology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Hongyan Cao
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, United States
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Ciuculete DM, Voisin S, Kular L, Jonsson J, Rask-Andersen M, Mwinyi J, Schiöth HB. meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes. Clin Epigenetics 2020; 12:99. [PMID: 32616021 PMCID: PMC7333393 DOI: 10.1186/s13148-020-00884-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Little is known about how genetics and epigenetics interplay in depression. Evidence suggests that genetic variants may change vulnerability to depression by modulating DNA methylation (DNAm) and non-coding RNA (ncRNA) levels. Therefore, the aim of the study was to investigate the effect of the genetic variation, previously identified in the largest genome-wide association study for depression, on proximal DNAm and ncRNA levels. RESULTS We performed DNAm quantitative trait locus (meQTL) analysis in two independent cohorts (total n = 435 healthy individuals), testing associations between 102 single-nucleotide polymorphisms (SNPs) and DNAm levels in whole blood. We identified and replicated 64 SNP-CpG pairs (padj. < 0.05) with meQTL effect. Lower DNAm at cg02098413 located in the HACE1 promoter conferred by the risk allele (C allele) at rs1933802 was associated with higher risk for depression (praw = 0.014, DNAm = 2.3%). In 1202 CD14+ cells sorted from blood, DNAm at cg02088412 positively correlated with HACE1 mRNA expression. Investigation in postmortem brain tissue of adults diagnosed with major depressive disorder (MDD) indicated 1% higher DNAm at cg02098413 in neurons and lower HACE1 mRNA expression in CA1 hippocampus of MDD patients compared with healthy controls (p = 0.008 and 0.012, respectively). Expression QTL analysis in blood of 74 adolescent revealed that hsa-miR-3664-5p was associated with rs7117514 (SHANK2) (padj. = 0.015, mRNA difference = 5.2%). Gene ontology analysis of the miRNA target genes highlighted implication in neuronal processes. CONCLUSIONS Collectively, our findings from a multi-tissue (blood and brain) and multi-layered (genetic, epigenetic, transcriptomic) approach suggest that genetic factors may influence depression by modulating DNAm and miRNA levels. Alterations at HACE1 and SHANK2 loci imply potential mechanisms, such as oxidative stress in the brain, underlying depression. Our results deepened the knowledge of molecular mechanisms in depression and suggest new epigenetic targets that should be further evaluated.
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Affiliation(s)
- Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, Husargatan 3, 753124, Uppsala, Sweden.
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, 3011, Australia
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 171 76, Stockholm, Sweden
| | - Jörgen Jonsson
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, Husargatan 3, 753124, Uppsala, Sweden
| | - Mathias Rask-Andersen
- Department of Immunology, Genetic and Pathology, Uppsala University, Uppsala, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, Husargatan 3, 753124, Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, Husargatan 3, 753124, Uppsala, Sweden.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
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Strickland SL, Reddy JS, Allen M, N'songo A, Burgess JD, Corda MM, Ballard T, Wang X, Carrasquillo MM, Biernacka JM, Jenkins GD, Mukherjee S, Boehme K, Crane P, Kauwe JS, Ertekin‐Taner N. MAPT haplotype-stratified GWAS reveals differential association for AD risk variants. Alzheimers Dement 2020; 16:983-1002. [PMID: 32400971 PMCID: PMC7983911 DOI: 10.1002/alz.12099] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/26/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022]
Abstract
INTRODUCTION MAPT H1 haplotype is implicated as a risk factor for neurodegenerative diseases including Alzheimer's disease (AD). METHODS Using Alzheimer's Disease Genetics Consortium (ADGC) genome-wide association study (GWAS) data (n = 18,841), we conducted a MAPT H1/H2 haplotype-stratified association to discover MAPT haplotype-specific AD risk loci. RESULTS We identified 11 loci-5 in H2-non-carriers and 6 in H2-carriers-although none of the MAPT haplotype-specific associations achieved genome-wide significance. The most significant H2 non-carrier-specific association was with a NECTIN2 intronic (P = 1.33E-07) variant, and that for H2 carriers was near NKX6-1 (P = 1.99E-06). The GABRG2 locus had the strongest epistasis with MAPT H1/H2 variant rs8070723 (P = 3.91E-06). Eight of the 12 genes at these loci had transcriptome-wide significant differential expression in AD versus control temporal cortex (q < 0.05). Six genes were members of the brain transcriptional co-expression network implicated in "synaptic transmission" (P = 9.85E-59), which is also enriched for neuronal genes (P = 1.0E-164), including MAPT. DISCUSSION This stratified GWAS identified loci that may confer AD risk in a MAPT haplotype-specific manner. This approach may preferentially enrich for neuronal genes implicated in synaptic transmission.
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Affiliation(s)
| | - Joseph S. Reddy
- Department of Health Sciences ResearchMayo ClinicJacksonvilleFloridaUSA
| | - Mariet Allen
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | | | | | - Travis Ballard
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | - Xue Wang
- Department of Health Sciences ResearchMayo ClinicJacksonvilleFloridaUSA
| | | | | | | | | | | | - Paul Crane
- University of WashingtonSeattleWashingtonUSA
| | | | - Nilüfer Ertekin‐Taner
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
- Department of NeurologyMayo ClinicJacksonvilleFloridaUSA
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Peedicayil J. The Potential Role of Epigenetic Drugs in the Treatment of Anxiety Disorders. Neuropsychiatr Dis Treat 2020; 16:597-606. [PMID: 32184601 PMCID: PMC7060022 DOI: 10.2147/ndt.s242040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/14/2020] [Indexed: 12/14/2022] Open
Abstract
There is increasing evidence that abnormalities in epigenetic mechanisms of gene expression contribute to the pathogenesis of anxiety disorders (ADs). This article discusses the role of epigenetic mechanisms of gene expression in the pathogenesis of ADs. It also discusses the data so far obtained from preclinical and clinical trials on the use of epigenetic drugs for treating ADs. Most drug trials investigating the use of epigenetic drugs for treating ADs have used histone deacetylase inhibitors (HDACi). HDACi are showing favorable results in both preclinical and clinical drug trials for treating ADs. However, at present the mode of action of HDACi in ADs is not clear. More work needs to be done to elucidate how epigenetic dysregulation contributes to the pathogenesis of ADs. More work also needs to be done on the mode of action of HDACi in alleviating the signs and symptoms of ADs.
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Affiliation(s)
- Jacob Peedicayil
- Department of Pharmacology & Clinical Pharmacology, Christian Medical College, Vellore, India
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12
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Lin E, Tsai SJ. Gene-Environment Interactions and Role of Epigenetics in Anxiety Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1191:93-102. [PMID: 32002924 DOI: 10.1007/978-981-32-9705-0_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Several environmental risk factors such as early adverse childhood experiences, stress, and stressful life events are associated with anxiety disorders. Current approaches such as epigenetics and gene-environment interactions were used to identify candidate biomarkers for anxiety disorders to assess determinants of disease. In this chapter, in relation to gene-environment interactions, a variety of association studies regarding anxiety disorders were surveyed. We then showed supporting results from recent association studies such as human studies and animal models in terms of the epigenetic contribution to disease susceptibility to anxiety disorders. At last, future directions and limitations are highlighted. With the advances in multi-omics technologies, innovative ideas regarding disease prevention and drug responsiveness in anxiety disorders require further research in epigenetics and gene-environment interactions.
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Affiliation(s)
- Eugene Lin
- Department of Biostatistics, University of Washington, Seattle, WA, USA.,Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan. .,Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan. .,Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan.
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13
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Ciuculete DM, Voisin S, Kular L, Welihinda N, Jonsson J, Jagodic M, Mwinyi J, Schiöth HB. Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression. Epigenetics 2019; 15:646-663. [PMID: 31852353 PMCID: PMC7574381 DOI: 10.1080/15592294.2019.1700628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Unrecognized depression during adolescence can result in adult suicidal behaviour. The aim of this study was to identify, replicate and characterize DNA methylation (DNAm) shifts in depression aetiology, using a longitudinal, multi-tissue (blood and brain) and multi-layered (genetics, epigenetics, transcriptomics) approach. We measured genome-wide blood DNAm data at baseline and one-year follow-up, and imputed genetic variants, in 59 healthy adolescents comprising the discovery cohort. Depression and suicidal symptoms were determined using the Development and Well-Being Assessment (DAWBA) depression band, Montgomery-Åsberg Depression Rating Scale-Self (MADRS-S) and SUicide Assessment Scale (SUAS). DNAm levels at follow-up were regressed against depression scores, adjusting for sex, age and the DNAm residuals at baseline. Higher methylation levels of 5% and 13% at cg24627299 within the MET gene were associated with higher depression scores (praw<1e-4) and susceptibility for suicidal symptoms (padj.<0.005). The nearby rs39748 was discovered to be a methylation and expression quantitative trait locus in blood cells. mRNA levels of hepatocyte growth factor (HGF) expression, known to strongly interact with MET, were inversely associated with methylation levels at cg24627299, in an independent cohort of 1180 CD14+ samples. In an open-access dataset of brain tissue, lower methylation at cg24627299 was found in 45 adults diagnosed with major depressive disorder compared with matched controls (padj.<0.05). Furthermore, lower MET expression was identified in the hippocampus of depressed individuals compared with controls in a fourth, independent cohort. Our findings reveal methylation changes at MET in the pathology of depression, possibly involved in downregulation of HGF/c-MET signalling the hippocampal region.
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Affiliation(s)
- Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University , Footscray, Australian
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Nipuni Welihinda
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Jörgen Jonsson
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University , Moscow, Russia
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