title: Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.
abstract: Using the relative expression levels of two SNP alleles of a gene in the same sample is an effective approach for identifying cis-acting regulatory SNPs (rSNPs). In the current study, we established a process for systematic screening for cis-acting rSNPs using experimental detection of AI as an initial approach. We selected 160 expressed candidate genes that are involved in cancer and anticancer drug resistance for analysis of AI in a panel of cell lines that represent different types of cancers and have been well characterized for their response patterns against anticancer drugs. Of these genes, 60 contained heterozygous SNPs in their coding regions, and 41 of the genes displayed imbalanced expression of the two cSNP alleles. Genes that displayed AI were subjected to bioinformatics-assisted identification of rSNPs that alter the strength of transcription factor binding. rSNPs in 15 genes were subjected to electrophoretic mobility shift assay, and in eight of these genes (APC, BCL2, CCND2, MLH1, PARP1, SLIT2, YES1, XRCC1) we identified differential protein binding from a nuclear extract between the SNP alleles. The screening process allowed us to zoom in from 160 candidate genes to eight genes that may contain functional rSNPs in their promoter regions.
authors.affiliation: Molecular Medicine, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
authors.forename: Lili
authors.initials: L
authors.lastname: Milani
authors.forename: Manu
authors.initials: M
authors.lastname: Gupta
authors.forename: Malin
authors.initials: M
authors.lastname: Andersen
authors.forename: Sumeer
authors.initials: S
authors.lastname: Dhar
authors.forename: Mårten
authors.initials: M
authors.lastname: Fryknäs
authors.forename: Anders
authors.initials: A
authors.lastname: Isaksson
authors.forename: Rolf
authors.initials: R
authors.lastname: Larsson
authors.forename: Ann-Christine
authors.initials: AC
authors.lastname: Syvänen
mesh_terms: D022981:Allelic Imbalance; D045744:Cell Line, Tumor; D019295:Computational Biology; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D024202:Electrophoretic Mobility Shift Assay; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors