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Delineating significant genome-wide associations of variants with antipsychotic and antidepressant treatment response: implications for clinical pharmacogenomics.

ABSTRACT: BACKGROUND:Genome-wide association studies (GWAS) have significantly contributed to the association of many clinical conditions and phenotypic characteristics with genomic variants. The majority of these genomic findings have been deposited to the GWAS catalog. So far, findings uncovering associations of single nucleotide polymorphisms (SNPs) with treatment efficacy in mood disorders are encouraging, but not adequate. METHODS:Statistical, genomic, and literature information was retrieved from EBI's GWAS catalog, while we also searched for potential clinical information/clinical guidelines in well-established pharmacogenomics databases regarding the assessed drug-SNP correlations of the present study. RESULTS:Here, we provide an overview of significant genome-wide associations of SNPs with the response to commonly prescribed antipsychotics and antidepressants. Up to date, this is the first study providing novel insight in previously reported pharmacogenomics associations for antipsychotic/antidepressant treatment. We also show that although there are published CPIC guidelines for antidepressant agents, as well as the FDA labels include genome-based drug prescription information for both antipsychotic and antidepressant treatments, there are no specific clinical guidelines for the assessed drug-SNP correlations of this study. CONCLUSIONS:Our present findings suggest that more effort should be implemented towards identifying GWA-significant antipsychotic and antidepressant pharmacogenomics correlations. Moreover, additional functional studies are required in order to characterise the potential role of the assessed SNPs as biomarkers for the response of patients to antipsychotic/antidepressant treatment.

SUBMITTER: Koromina M

PROVIDER: S-EPMC6964087 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Delineating significant genome-wide associations of variants with antipsychotic and antidepressant treatment response: implications for clinical pharmacogenomics.

Koromina Maria M Koutsilieri Stefania S Patrinos George P GP

Human genomics 20200115 1

<h4>Background</h4>Genome-wide association studies (GWAS) have significantly contributed to the association of many clinical conditions and phenotypic characteristics with genomic variants. The majority of these genomic findings have been deposited to the GWAS catalog. So far, findings uncovering associations of single nucleotide polymorphisms (SNPs) with treatment efficacy in mood disorders are encouraging, but not adequate.<h4>Methods</h4>Statistical, genomic, and literature information was re ...[more]

PMID: 31941550

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Project description:Abstract Background: Schizophrenia is a lifelong debilitating mental illness often characterized by hallucinations, delusions, and disorganized thought and behavior. Currently, antipsychotic medications serve as the best treatment option for schizophrenia, but clinical responses to antipsychotic medications are highly variable. Therefore, the demand for reliable biological predictors is high. A glutamate and N-methyl-d-asparate (NMDA) receptor hypofunction model based on pharmacologic and genetic studies have been suggested as an approach to study the pharmacogenetics of antipsychotic medications. Previous studies have shown clozapine (CLZ) displaces NMDAR antagonists and enhances NMDAR mediated neurotransmission. Previously, our group (Taylor et al, 2016) investigated 8 SNPs in the NMDAR subunit gene GRIN2B with response to CLZ and one marker (rs1072388) was nominally significant. Taylor et al (in press) more recently found the glycine transporter 1 gene (SLC6A9, rs16831558) exhibited an allele dose-dependent improvement in the positive symptoms of CC-homozygotes compared to T-allele carriers (Puncorrected = .008, Pcorrected = .08). In our current study, we examined the GRIN2A receptor gene that was genome-wide significant in the GWAS of schizophrenia by Ripke et al (2014). A SNP marker from GRIN2A (rs992266789) and one from the glutamate receptor ionotropic delta 2 (GRID2, rs1875705) were selected for our association study of CLZ treatment response. Methods: We investigated rs9922678 and rs1875705 in relation to CLZ treatment response in a prospective study consisting of 170 Caucasian patients treated with CLZ for 6 months. Treatment response was evaluated using the 18-item Brief Psychiatric Rating Scale (BPRS), using either responder vs nonresponder status or continuous change scores. Baseline score was included as a covariate. All statistical analyses were performed using IBM SPSS. Results: No significant association was observed for rs9922678 and rs1875705 with BPRS total score and responder vs nonresponder status under genotypic, allelic, and additive models. Conclusion: Although no significant results were obtained from our current study, there is still strong neurobiological evidence suggesting involvement of the glutamate system in CLZ action. Additional glutamate system genes and multiple markers should be investigated. Further studies with greater sample size are required before firm conclusions can be drawn. In addition, it would be helpful to investigate other phenotypes such as cognition and tardive dyskinesia because glutamate neurotransmission also plays a role in these areas.

Project description:Cancer patients show large individual variation in their response to chemotherapeutic agents. Gemcitabine (dFdC) and AraC, two cytidine analogues, have shown significant activity against a variety of tumors. We previously used expression data from a lymphoblastoid cell line-based model system to identify genes that might be important for the two drug cytotoxicity. In the present study, we used that same model system to perform a genome-wide association (GWA) study to test the hypothesis that common genetic variation might influence both gene expression and response to the two drugs. Specifically, genome-wide single nucleotide polymorphisms (SNPs) and mRNA expression data were obtained using the Illumina 550K(R) HumanHap550 SNP Chip and Affymetrix U133 Plus 2.0 GeneChip, respectively, for 174 ethnically-defined "Human Variation Panel" lymphoblastoid cell lines. Gemcitabine and AraC cytotoxicity assays were performed to obtain IC(50) values for the cell lines. We then performed GWA studies with SNPs, gene expression and IC(50) of these two drugs. This approach identified SNPs that were associated with gemcitabine or AraC IC(50) values and with the expression regulation for 29 genes or 30 genes, respectively. One SNP in IQGAP2 (rs3797418) was significantly associated with variation in both the expression of multiple genes and gemcitabine and AraC IC(50). A second SNP in TGM3 (rs6082527) was also significantly associated with multiple gene expression and gemcitabine IC50. To confirm the association results, we performed siRNA knock down of selected genes with expression that was associated with rs3797418 and rs6082527 in tumor cell and the knock down altered gemcitabine or AraC sensitivity, confirming our association study results. These results suggest that the application of GWA approaches using cell-based model systems, when combined with complementary functional validation, can provide insights into mechanisms responsible for variation in cytidine analogue response.

Dataset Information

Delineating significant genome-wide associations of variants with antipsychotic and antidepressant treatment response: implications for clinical pharmacogenomics.

Publications

Delineating significant genome-wide associations of variants with antipsychotic and antidepressant treatment response: implications for clinical pharmacogenomics.

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