Bioinformatic and functional analysis of TGFBR1 polymorphisms

Objectives The transforming growth factor-beta (TGFB) pathway has substantial impact on cellular functions, cell proliferation, and apoptosis. We used bioinformatics, gene expression, and cell biological assays to evaluate the functionality of frequent Inherited germline polymorphisms in the TGFB receptor 1 (TGFBR1). Methods In an exploratory (n=55) and confirmatory (n=106) study, we analyzed the TGFB1 pathway after incubation with TGF beta 1 ligand and after exposure to X-rays in peripheral blood human mononuclear cells. Expression of TGFB pathway genes was assessed by real-time PCR, and cellular viability was analyzed by flow cytometry. A total of six polymorphisms including the deletion variant ( 6A) were identified to tag currently known common genetic variations in TGFBR1 and were analyzed in relation to the phenotypes. Results In accordance with a negative feedback mechanism, incubations with the ligand TGF beta 1 was followed by up-regulation of the intracellular SMAD7 and down-regulation of the SMAD3 mRNA molecules. The TGFBR1 6A deletion variant attenuated the suppression of SMAD3 in response to TGF beta 1 (P=0.02, in both studies). Moreover, cells harboring 6A were more sensitive toward cytotoxic effects of irradiation (P=0.001 after adjustment for age and sex). Cells were particularly prone toward radiation toxicity when carrying, in addition to 6A, the variant allele of rs11568785, which exhibits a strong genetic selection signature. Conclusion The 6A deletion and the linked rs11568785 polymorphisms seem to attenuate TGFB signaling. This should be considered not only for clinical-epidemiological studies on cancer susceptibility but may also be relevant for side effects from drugs or radiotherapy. Pharmacogenetics and Genomics 19:249-259 (C) 2009 Wolters Kluwer Health vertical bar Lippincott Williams & Wilkins.