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Functional consequences of PRPF39 on distant genes and cisplatin sensitivity.

ABSTRACT: Variation in gene expression has been found to be important in disease susceptibility and pharmacogenomics. Local and distant expression quantitative trait loci (eQTLs) have been identified via genome-wide association study (GWAS); yet the functional analysis of these variants has been challenging. The aim of this study was to unravel the functional consequence of a gene with a local SNP with evidence for local and distant regulatory roles in cellular sensitivity to cisplatin, one of the most widely used chemotherapeutic drugs. To this end, we measured cellular susceptibility to cisplatin in 176 HapMap lymphoblastoid cell lines derived from Yoruba individuals from Ibadan, Nigeria. The 276 cytotoxicity-associated SNPs at the suggestive threshold of P ? 0.0001 were significantly enriched for eQTLs. Of these SNPs, we found one intronic SNP, rs17115814, that had a significant relationship with the expression level of its host gene, PRPF39 (P= 0.0007), and a significant correlation with the expression of over 100 distant transcripts (P ? 0.0001). Successful knockdown of PRPF39 expression using siRNA resulted in a significant increase in cisplatin resistance. We then measured the expression of 61 downstream targets after PRPF39 knockdown and found 53 gene targets had significant (P ? 0.05) expression changes. Included in the list of genes that significantly changed after PRPF39 knockdown were MAP3K4 and TFPD2, two important signaling genes previously shown to be relevant in cisplatin response. Thus, modulation of a local target gene identified through a GWAS was followed by a downstream cascade of gene expression changes resulting in greater resistance to cisplatin.

SUBMITTER: Stark AL

PROVIDER: S-EPMC3441128 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature

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Functional consequences of PRPF39 on distant genes and cisplatin sensitivity.

Stark Amy L AL Delaney Shannon M SM Wheeler Heather E HE Im Hae Kyung HK Dolan M Eileen ME

Human molecular genetics 20120705 19

Variation in gene expression has been found to be important in disease susceptibility and pharmacogenomics. Local and distant expression quantitative trait loci (eQTLs) have been identified via genome-wide association study (GWAS); yet the functional analysis of these variants has been challenging. The aim of this study was to unravel the functional consequence of a gene with a local SNP with evidence for local and distant regulatory roles in cellular sensitivity to cisplatin, one of the most wi ...[more]

PMID: 22773733

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Project description:BackgroundThe ubiquitin(Ub)-proteasome pathway is implicated in the regulation of a variety of cellular functions and plays a major role in stress response in eukaryotic cells, by targeting misfolded and damaged proteins for degradation. In addition, in the presence of DNA damage, the Ub-proteasome system regulates proteins involved in sensing, repairing, and/or tolerating the damage. Antitumor agents such as cisplatin can activate the pathway, but the role of specific pathway components in cell sensitivity/response to the drug is not known. Since platinum compounds represent clinically relevant antitumor agents and a major limitation to their use is the development of drug resistance, there is an urgent need for identifying targets for improving their efficacy.ResultsIn the present study, we performed a genome-wide screening for sensitivity to cisplatin using non-essential haploid deletion mutants of the fission yeast Schizosaccharomyces pombe, belonging to a collection of haploid strains constructed through homologous recombination. Using this approach, we identified three Ub-proteasome mutants exhibiting hypersensitivity to cisplatin (ubp16, ubc13 and pmt3) and ten mutants (including ufd2, beta7 20S, rpt6/let1) resistant to the drug. In addition, the importance of lub1 gene emerged from the comparison between the present screening and gene expression profile data previously obtained in fission yeast.ConclusionsThe factors identified in the present study allowed us to highlight most finely the close relationship between the Ub-proteasome system and DNA damage response mechanisms, thus establishing a comprehensive framework of regulators likely relevant also in higher eukaryotes. Our results provide the proof of principle of the involvement of specific genes modulated by cisplatin treatment in cell response to the drug, suggesting their potential role as targets for modulating cisplatin sensitivity. In this regard, the prospective identification of novel targets for modulation of cisplatin sensitivity in an eukaryotic model organism appears particularly intriguing towards the discovery of strategies to overcome cisplatin resistance in human tumors.

Project description:Many differentially methylated genes have been identified in prostate cancer (PCa), primarily using candidate gene-based assays. Recently, several global DNA methylation profiles have been reported in PCa, however, each of these has weaknesses in terms of ability to observe global DNA methylation alterations in PCa. We hypothesize that there remains unidentified aberrant DNA methylation in PCa, which may be identified using higher resolution assay methods. We used the newly developed Illumina HumanMethylation450 BeadChip in PCa (n = 19) and adjacent normal tissues (n = 4) and combined these with gene expression data for identifying new DNA methylation that may have functional consequences in PCa development and progression. We also confirmed our methylation results in an independent data set. Two aberrant DNA methylation genes were validated among an additional 56 PCa samples and 55 adjacent normal tissues. A total 28,735 CpG sites showed significant differences in DNA methylation (FDR adjusted P<0.05), defined as a mean methylation difference of at least 20% between PCa and normal samples. Furthermore, a total of 122 genes had more than one differentially methylated CpG site in their promoter region and a gene expression pattern that was inverse to the direction of change in DNA methylation (e.g. decreased expression with increased methylation, and vice-versa). Aberrant DNA methylation of two genes, AOX1 and SPON2, were confirmed via bisulfate sequencing, with most of the respective CpG sites showing significant differences between tumor samples and normal tissues. The AOX1 promoter region showed hypermethylation in 92.6% of 54 tested PCa samples in contrast to only three out of 53 tested normal tissues. This study used a new BeadChip combined with gene expression data in PCa to identify novel differentially methylated CpG sites located within genes. The newly identified differentially methylated genes may be used as biomarkers for PCa diagnosis.

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Functional consequences of PRPF39 on distant genes and cisplatin sensitivity.

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Functional consequences of PRPF39 on distant genes and cisplatin sensitivity.

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