Functional Analysis of Promoter Variants in Genes Involved in Sex Steroid Action, DNA Repair and Cell Cycle Control

Abstract

Genetic variants affecting the regulation of gene expression are among the main causes of human diversity. The potential importance of regulatory polymorphisms is underscored by results from Genome Wide Association Studies, which have already implicated such polymorphisms in the susceptibility to complex diseases such as breast cancer. In this study, we re-sequenced the promoter regions of 24 genes involved in pathways related to breast cancer including sex steroid action, DNA repair, and cell cycle control in 60 unrelated Caucasian individuals. We constructed haplotypes and assessed the functional impact of promoter variants using gene reporter assays and electrophoretic mobility shift assays. We identified putative functional variants within the promoter regions of estrogen receptor 1 (ESR1), ESR2, forkhead box A1 (FOXA1), ubiquitin interaction motif containing 1 (UIMC1) and cell division cycle 7 (CDC7). The functional polymorphism on CDC7, rs13447455, influences CDC7 transcriptional activity in an allele-specific manner and alters DNA–protein complex formation in breast cancer cell lines. Moreover, results from the Breast Cancer Association Consortium show a marginal association between rs13447455 and breast cancer risk (p=9.3x10-5), thus warranting further investigation. Furthermore, our study has helped provide methodological solutions to some technical difficulties that were encountered with gene reporter assays, particularly regarding inter-clone variability and statistical consistency.

DICER1‐associated embryonal rhabdomyosarcoma and adenosarcoma of the gynecologic tract: Pathology, molecular genetics, and indications for molecular testing

“…As a second step, in vitro and in vivo assays may shed more light on the effect of the VUS. There are several in vitro assays that can be used to test the functional consequences of variants, such as minigene assays for splicing altering variants 103,104 or gene reporter assays for promotor variants 105,106 . In addition, the analysis of RNA extracted from normal/tumor tissue may aid in testing the consequences of the alteration, for example if it affects the splicing or behaves as a LOF.…”

Significance of the lncRNAs MALAT1 and ANRIL in occurrence and development of glaucoma

“…SNPs can induce changes in transcription rate, genetic stability, and cellular function, making individuals predisposed to diseases. For example, rs13447455 at the promoter of CDC7 altered the structure of a DNA‐protein complex in breast cancer cells, 72 and functional polymorphism of the lncRNA TUG1 was associated with ischemic stroke risk. 73 The mature MALAT1 transcript is highly stable in organisms, 74 and its stability is altered in disease state.…”

Residential PM2.5 exposure and the nasal methylome in children

“…Differential DNAm of MEIS1 , IRX2 , and GRIK3 are known epigenetic biomarkers of lung cancer (however, it is worth noting that MEIS1 and IRX2 were hyper rather than hypo-methylated as is observed in cancer studies; GRIK3 is hypomethylated in our study as well as in carcinogenesis) ( Pradhan et al, 2013 ; Rauch et al, 2012 ). AGAP1 controls cancer cell invasion, ( Tsutsumi et al, 2020 ) and U1MC1 is involved in recognition and repair of DNA lesions ( Hamdi et al, 2019 ). However, it is important to note that, given the overlaps between inflammatory pathways and those in carcinogenesis ( Greten and Grivennikov, 2019 ), the pollution-related differential methylation of genes associated with cancer in the airways in our study may simply reflect alterations in inflammatory processes, including pathways involved in tissue homeostasis and repair that do not necessarily give rise to carcinogenesis.…”