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Pugsley K, Namipashaki A, Bellgrove MA, Hawi Z. Evaluating the regulatory function of non-coding autism-associated single nucleotide polymorphisms on gene expression in human brain tissue. Autism Res 2024; 17:467-481. [PMID: 38323502 DOI: 10.1002/aur.3101] [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: 09/11/2023] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
Common variants account for most of the estimated heritability associated with autism spectrum disorder (autism). Although several replicable single nucleotide polymorphisms (SNPs) for the condition have been detected using genome-wide association study (GWAS) methodologies, their pathophysiological relevance remains elusive. Examining this is complicated, however, as all detected loci are situated within non-coding regions of the genome. It is therefore likely that they possess roles of regulatory function as opposed to directly affecting gene coding sequences. To bridge the gap between SNP discovery and mechanistic insight, we applied a comprehensive bioinformatic pipeline to functionally annotate autism-associated polymorphisms and their non-coding linkage disequilibrium (i.e., non-randomly associated) partners. We identified 82 DNA variants of probable regulatory function that may contribute to autism pathogenesis. To validate these predictions, we measured the impact of 11 high-confidence candidates and their GWAS linkage disequilibrium partners on gene expression in human brain tissue from Autistic and non-Autistic donors. Although a small number of the surveyed variants exhibited measurable influence on gene expression as determined via quantitative polymerase chain reaction, these did not survive correction for multiple comparisons. Additionally, no significant genotype-by-diagnosis effects were observed for any of the SNP-gene associations. We contend that this may reflect an inability to effectively capture the modest, neurodevelopmental-specific impact of individual variants on biological dysregulation in available post-mortem tissue samples, as well as limitations in the existing autism GWAS data.
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Affiliation(s)
- Kealan Pugsley
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Atefeh Namipashaki
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Mark A Bellgrove
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Ziarih Hawi
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
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Hou Y, Zhou M, Li Y, Tian T, Sun X, Chen M, Xu W, Lu M. Risk SNP-mediated LINC01614 upregulation drives head and neck squamous cell carcinoma progression via PI3K/AKT signaling pathway. Mol Carcinog 2022; 61:797-811. [PMID: 35687049 DOI: 10.1002/mc.23422] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 11/11/2022]
Abstract
As potential biomarkers and therapeutic targets, long noncoding RNAs (lncRNAs) are involved in the tumorigenesis of various tumors. Genetic variation in long noncoding regions can lead to lncRNA dysfunction and even cancer. Nevertheless, studies on the association between lncRNA-associated single-nucleotide polymorphisms (SNPs) and the risk of head and neck squamous cell carcinoma (HNSCC) remain inadequate. Here, we aimed to explore the association between SNPs in LINC01614 and HNSCC risk, and the potential role of LINC01614 in tumorigenesis. In this study, we found that rs16854802 A > G (odds ratio [OR] = 1.42, 95% confidence interval [CI]: 1.22-1.77, p < 0.001) and rs3113503 G > C (OR = 1.38, 95% CI: 1.15-1.64, p < 0.001) in LINC01614 increased the risk of HNSCC in the Chinese population. Functional bioinformatic analysis and luciferase reporter assay revealed that rs3113503 G > C variant disrupted the binding of miRNA-616-3p to LINC01614, which resulted in the increased expression of LINC01614. Further analysis of the TCGA database demonstrated that the upregulated LINC01614 in HNSCC cancer tissues was associated with poor prognostic in HNSCC patients. In vitro experiments showed that knockdown of LINC01614 inhibited the proliferation, invasion, and migration ability of HNSCC cells. Mechanistically, allele C of rs3113503 in LINC01614 was more effective than allele G in activating the PI3K/AKT signaling pathway. Moreover, the reduced expression of LINC01614 also inhibited the activation of the PI3K/AKT signaling pathway. In summary, our findings revealed that the risk SNP rs3113503 G > C in LINC01614 altered the binding to miR-616-3p, which led to increased LINC01614 expression and promoted HNSCC progression by activating the PI3K/AKT signaling pathway.
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Affiliation(s)
- Yaxuan Hou
- Department of Epidemiology and Biostatistics, and The Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meng Zhou
- Department of Epidemiology and Biostatistics, and The Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuncheng Li
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Tian
- Department of Epidemiology and Biostatistics, and The Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xun Sun
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Mo Chen
- Department of Epidemiology and Biostatistics, and The Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Guidance Center for Social Psychological Service, Wuhan Mental Health Center, Huazhong University of Science and Technology, Wuhan, China
| | - Wenmao Xu
- Department of Epidemiology and Biostatistics, and The Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Public Health, Wuhan No. 1 Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Meixia Lu
- Department of Epidemiology and Biostatistics, and The Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Dark C, Williams C, Bellgrove MA, Hawi Z, Bryson-Richardson RJ. Functional validation of CHMP7 as an ADHD risk gene. Transl Psychiatry 2020; 10:385. [PMID: 33159045 PMCID: PMC7648633 DOI: 10.1038/s41398-020-01077-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/14/2020] [Accepted: 10/22/2020] [Indexed: 12/27/2022] Open
Abstract
Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder of childhood with a strong genetic component. Despite the success of mapping ADHD risk loci, little work has been done to experimentally verify the contribution of these loci to ADHD phenotypes. Meta-analysis of four genome-wide association studies in ADHD suggested CHMP7 as a predisposing gene for ADHD. A DNA variant (rs2294123) mapped to CHMP7 has been shown (via bioinformatic analysis) to have a high likelihood for functionality and correlate with reduced transcript levels. We used CRISPR-Cas9 genome editing to generate a chmp7 zebrafish model for ADHD. chmp7+/- fish showed comparable reductions in mRNA levels to individuals homozygous for the CHMP7 ADHD risk allele. These fish displayed significant hyperactivity over a 24-h period at 6 days post-fertilisation compared to chmp7+/+, but this effect did not persist into juvenile and adulthood stages. In addition, chmp7+/- fish had significantly smaller total brain volumes than chmp7+/+ fish. Finally, the hyperactivity at 6 days post-fertilisation was significantly reduced through the application of methylphenidate, a mainstay pharmacological treatment for ADHD. Overall, this study highlights an important role for CHMP7 in the neurodevelopment of ADHD, and demonstrates the utility of zebrafish for modelling the functional effects of genes conferring risk to ADHD.
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Affiliation(s)
- Callum Dark
- grid.1002.30000 0004 1936 7857School of Biological Sciences, Faculty of Science, Monash University, Clayton, Australia
| | - Caitlin Williams
- grid.1002.30000 0004 1936 7857School of Biological Sciences, Faculty of Science, Monash University, Clayton, Australia
| | - Mark A. Bellgrove
- grid.1002.30000 0004 1936 7857Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Australia
| | - Ziarih Hawi
- grid.1002.30000 0004 1936 7857Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Australia
| | - Robert J. Bryson-Richardson
- grid.1002.30000 0004 1936 7857School of Biological Sciences, Faculty of Science, Monash University, Clayton, Australia
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Bhat V, Joober R, Sengupta SM. How Environmental Factors Can Get Under the Skin: Epigenetics in Attention-Deficit/Hyperactivity Disorder. J Am Acad Child Adolesc Psychiatry 2017; 56:278-280. [PMID: 28335869 DOI: 10.1016/j.jaac.2016.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/21/2016] [Accepted: 01/30/2017] [Indexed: 10/19/2022]
Affiliation(s)
- Venkat Bhat
- University of Toronto and the University Health Network, Toronto, Ontario, Canada.
| | - Ridha Joober
- McGill University, Montreal, Quebec, Canada and the Douglas Mental Health University Institute, Montreal
| | - Sarojini M Sengupta
- McGill University, Montreal, Quebec, Canada and the Douglas Mental Health University Institute, Montreal
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Integrative transcriptomic meta-analysis of Parkinson's disease and depression identifies NAMPT as a potential blood biomarker for de novo Parkinson's disease. Sci Rep 2016; 6:34579. [PMID: 27680512 PMCID: PMC5041099 DOI: 10.1038/srep34579] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/15/2016] [Indexed: 02/06/2023] Open
Abstract
Emerging research indicates that depression could be one of the earliest prodromal symptoms or risk factors associated with the pathogenesis of Parkinson’s disease (PD), the second most common neurodegenerative disorder worldwide, but the mechanisms underlying the association between both diseases remains unknown. Understanding the molecular networks linking these diseases could facilitate the discovery of novel diagnostic and therapeutics. Transcriptomic meta-analysis and network analysis of blood microarrays from untreated patients with PD and depression identified genes enriched in pathways related to the immune system, metabolism of lipids, glucose, fatty acids, nicotinamide, lysosome, insulin signaling and type 1 diabetes. Nicotinamide phosphoribosyltransferase (NAMPT), an adipokine that plays a role in lipid and glucose metabolism, was identified as the most significant dysregulated gene. Relative abundance of NAMPT was upregulated in blood of 99 early stage and drug-naïve PD patients compared to 101 healthy controls (HC) nested in the cross-sectional Parkinson’s Progression Markers Initiative (PPMI). Thus, here we demonstrate that shared molecular networks between PD and depression provide an additional source of biologically relevant biomarkers. Evaluation of NAMPT in a larger prospective longitudinal study including samples from other neurodegenerative diseases, and patients at risk of PD is warranted.
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Dalvie S, Koen N, McGregor N, O'Connell K, Warnich L, Ramesar R, Nievergelt CM, Stein DJ. Toward a Global Roadmap for Precision Medicine in Psychiatry: Challenges and Opportunities. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:557-564. [PMID: 27636104 DOI: 10.1089/omi.2016.0110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mental disorders represent a major public health burden worldwide. This is likely to rise in the next decade, with the highest increases predicted to occur in low- and middle-income countries. Current psychotropic medication treatment guidelines focus on uniform approaches to the treatment of heterogeneous disorders and achieve only partial therapeutic success. Developing a global precision medicine approach in psychiatry appears attractive, given the value of this approach in other fields of medicine, such as oncology and infectious diseases. In this horizon scanning analysis, we review the salient opportunities and challenges for precision medicine in psychiatry over the next decade. Variants within numerous genes involved in a range of pathways have been implicated in psychotropic drug response and might ultimately be used to guide choice of pharmacotherapy. Multipronged approaches such as multi-omics (genomics, proteomics, metabolomics) analyses and systems diagnostics together with high-throughput sequencing and genotyping technologies hold promise for identifying precise and targeted treatments in mental disorders. To date, however, the vast majority of pharmacogenomics work has been undertaken in high-income countries on a relatively small proportion of the global population, and many other challenges face the field. Opportunities and challenges for establishing a global roadmap for precision medicine in psychiatry are discussed in this article.
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Affiliation(s)
- Shareefa Dalvie
- 1 Department of Psychiatry and Mental Health, University of Cape Town , Cape Town, South Africa .,2 MRC/UCT Human Genetics Research Unit, Division of Human Genetics, University of Cape Town , Cape Town, South Africa
| | - Nastassja Koen
- 1 Department of Psychiatry and Mental Health, University of Cape Town , Cape Town, South Africa .,3 Medical Research Council (MRC) Unit on Anxiety and Stress Disorders , Cape Town, South Africa
| | - Nathaniel McGregor
- 4 Department of Genetics, Stellenbosch University , Tygerberg, South Africa .,5 Department of Psychiatry, Stellenbosch University , Tygerberg, South Africa
| | - Kevin O'Connell
- 4 Department of Genetics, Stellenbosch University , Tygerberg, South Africa
| | - Louise Warnich
- 4 Department of Genetics, Stellenbosch University , Tygerberg, South Africa
| | - Raj Ramesar
- 2 MRC/UCT Human Genetics Research Unit, Division of Human Genetics, University of Cape Town , Cape Town, South Africa
| | - Caroline M Nievergelt
- 6 Department of Psychiatry, University of California San Diego , San Diego, California.,7 Veteran Affairs (VA) San Diego Center of Excellence for Stress and Mental Health , San Diego, California
| | - Dan J Stein
- 1 Department of Psychiatry and Mental Health, University of Cape Town , Cape Town, South Africa .,3 Medical Research Council (MRC) Unit on Anxiety and Stress Disorders , Cape Town, South Africa
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