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He J, Li Q, Zhang Q. rvTWAS: identifying gene-trait association using sequences by utilizing transcriptome-directed feature selection. Genetics 2024; 226:iyad204. [PMID: 38001381 DOI: 10.1093/genetics/iyad204] [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: 10/20/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
Toward the identification of genetic basis of complex traits, transcriptome-wide association study (TWAS) is successful in integrating transcriptome data. However, TWAS is only applicable for common variants, excluding rare variants in exome or whole-genome sequences. This is partly because of the inherent limitation of TWAS protocols that rely on predicting gene expressions. Our previous research has revealed the insight into TWAS: the 2 steps in TWAS, building and applying the expression prediction models, are essentially genetic feature selection and aggregations that do not have to involve predictions. Based on this insight disentangling TWAS, rare variants' inability of predicting expression traits is no longer an obstacle. Herein, we developed "rare variant TWAS," or rvTWAS, that first uses a Bayesian model to conduct expression-directed feature selection and then uses a kernel machine to carry out feature aggregation, forming a model leveraging expressions for association mapping including rare variants. We demonstrated the performance of rvTWAS by thorough simulations and real data analysis in 3 psychiatric disorders, namely schizophrenia, bipolar disorder, and autism spectrum disorder. We confirmed that rvTWAS outperforms existing TWAS protocols and revealed additional genes underlying psychiatric disorders. Particularly, we formed a hypothetical mechanism in which zinc finger genes impact all 3 disorders through transcriptional regulations. rvTWAS will open a door for sequence-based association mappings integrating gene expressions.
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Affiliation(s)
- Jingni He
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary T2N 1N4, Canada
| | - Qing Li
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary T2N 1N4, Canada
| | - Qingrun Zhang
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary T2N 1N4, Canada
- Department of Mathematics and Statistics, University of Calgary, Calgary T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary T2N 1N4, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary T2N 1N4, Canada
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Tesfaye M, Chatterjee S, Zeng X, Joseph P, Tekola-Ayele F. Impact of depression and stress on placental DNA methylation in ethnically diverse pregnant women. Epigenomics 2021; 13:1485-1496. [PMID: 34585950 DOI: 10.2217/epi-2021-0192] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aim: To investigate the association between placental genome-wide methylation at birth and antenatal depression and stress during pregnancy. Methods: We examined the association between placental genome-wide DNA methylation (n = 301) and maternal depression and stress assessed at six gestation periods during pregnancy. Correlation between DNA methylation at the significantly associated CpGs and expression of nearby genes in the placenta was tested. Results: Depression and stress were associated with methylation of 16 CpGs and two CpGs, respectively, at a 5% false discovery rate. Methylation levels at two of the CpGs associated with depression were significantly associated with expression of ADAM23 and CTDP1, genes implicated in neurodevelopment and neuropsychiatric diseases. Conclusion: Placental epigenetic changes linked to antenatal depression suggest potential fetal brain programming. Clinical trial registration number: NCT00912132 (ClinicalTrials.gov).
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Affiliation(s)
- Markos Tesfaye
- Section of Sensory Science & Metabolism (SenSMet), National Institute on Alcohol Abuse & Alcoholism & National Institute of Nursing Research, National Institutes of Health, Bethesda, MD 20892, USA.,Department of Psychiatry, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Suvo Chatterjee
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892-7004, USA
| | - Xuehuo Zeng
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paule Joseph
- Section of Sensory Science & Metabolism (SenSMet), National Institute on Alcohol Abuse & Alcoholism & National Institute of Nursing Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fasil Tekola-Ayele
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892-7004, USA
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Fries GR, Li Q, McAlpin B, Rein T, Walss-Bass C, Soares JC, Quevedo J. The role of DNA methylation in the pathophysiology and treatment of bipolar disorder. Neurosci Biobehav Rev 2016; 68:474-488. [PMID: 27328785 DOI: 10.1016/j.neubiorev.2016.06.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 06/03/2016] [Accepted: 06/12/2016] [Indexed: 12/31/2022]
Abstract
Bipolar disorder (BD) is a multifactorial illness thought to result from an interaction between genetic susceptibility and environmental stimuli. Epigenetic mechanisms, including DNA methylation, can modulate gene expression in response to the environment, and therefore might account for part of the heritability reported for BD. This paper aims to review evidence of the potential role of DNA methylation in the pathophysiology and treatment of BD. In summary, several studies suggest that alterations in DNA methylation may play an important role in the dysregulation of gene expression in BD, and some actually suggest their potential use as biomarkers to improve diagnosis, prognosis, and assessment of response to treatment. This is also supported by reports of alterations in the levels of DNA methyltransferases in patients and in the mechanism of action of classical mood stabilizers. In this sense, targeting specific alterations in DNA methylation represents exciting new treatment possibilities for BD, and the 'plastic' characteristic of DNA methylation accounts for a promising possibility of restoring environment-induced modifications in patients.
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Affiliation(s)
- Gabriel R Fries
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA.
| | - Qiongzhen Li
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA
| | - Blake McAlpin
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA
| | - Theo Rein
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstraße 2-10, 80804, Munich, Germany
| | - Consuelo Walss-Bass
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA; Neuroscience Graduate Program, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA
| | - Jair C Soares
- Center of Excellence on Mood Disorders, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Joao Quevedo
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA; Center of Excellence on Mood Disorders, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA; Neuroscience Graduate Program, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA; Laboratory of Neurosciences, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
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Nestler EJ, Peña CJ, Kundakovic M, Mitchell A, Akbarian S. Epigenetic Basis of Mental Illness. Neuroscientist 2015; 22:447-63. [PMID: 26450593 DOI: 10.1177/1073858415608147] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Psychiatric disorders are complex multifactorial illnesses involving chronic alterations in neural circuit structure and function as well as likely abnormalities in glial cells. While genetic factors are important in the etiology of most mental disorders, the relatively high rates of discordance among identical twins, particularly for depression and other stress-related syndromes, clearly indicate the importance of additional mechanisms. Environmental factors such as stress are known to play a role in the onset of these illnesses. Exposure to such environmental insults induces stable changes in gene expression, neural circuit function, and ultimately behavior, and these maladaptations appear distinct between developmental versus adult exposures. Increasing evidence indicates that these sustained abnormalities are maintained by epigenetic modifications in specific brain regions. Indeed, transcriptional dysregulation and the aberrant epigenetic regulation that underlies this dysregulation is a unifying theme in psychiatric disorders. Here, we provide a progress report of epigenetic studies of the three major psychiatric syndromes, depression, schizophrenia, and bipolar disorder. We review the literature derived from animal models of these disorders as well as from studies of postmortem brain tissue from human patients. While epigenetic studies of mental illness remain at early stages, understanding how environmental factors recruit the epigenetic machinery within specific brain regions to cause lasting changes in disease susceptibility and pathophysiology is revealing new insight into the etiology and treatment of these conditions.
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Affiliation(s)
- Eric J Nestler
- Departments of Neuroscience and Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Catherine J Peña
- Departments of Neuroscience and Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marija Kundakovic
- Departments of Neuroscience and Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda Mitchell
- Departments of Neuroscience and Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Schahram Akbarian
- Departments of Neuroscience and Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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