Polymorphisms in human heat shock factor-1 and analysis of potential biological consequences

The stress-activated transcription factor, heat shock factor-1 (HSF1), regulates many genes including cytoprotective heat shock proteins (HSPs). We hypothesized that polymorphisms in HSF1 may alter the level or function of HSF1 protein accounting for interindividual viability in disease susceptibility or prognosis. We searched for exomic variants in HSF1 by querying human genome databases and directly sequencing DNA from 80 anonymous genomic DNA samples. Overall, HSF1 sequence was highly conserved, with no common variations. We found 31 validated deviations from a reference sequence in the dbSNP database and an additional 5 novel variants by sequencing, with allele frequencies that were 0.06 or less. Of these 36, 2 were in 5′-untranslated region (5′UTR), 10 in 3′UTR, and 24 in the coding region. The potential effects of 5′UTR on secondary structure, protein structure/function, and 3′UTR targets of microRNAs were analyzed using RNAFold, PolyPhen-2, SIFT, and MicroSNiper. One of the 5′UTR variants was predicted to strengthen secondary structure. Eight of 3′UTR variants were predicted to modify microRNA target sequences. Eight of the coding region variants were predicted to modify HSF1 structure/function. Reducing HSF1 levels in A549 cells using short hairpin RNA (shRNA) increased sensitivity to heat-induced killing demonstrating the impact that genetic variants that reduce HSF1 levels might have. Using the pmirGLO expression system, we found that the wild-type HSF1 3′UTR suppressed translation of a firefly luciferase reporter plasmid by 65 %. Introducing two of four 3′UTR single nucleotide polymorphisms (SNPs) increased HSF1 3′UTR translational suppression by 27–44 % compared with the wild-type HSF1 3′UTR sequence while a third SNP reduced suppression by 25 %. HSF1 variants may alter HSF1 protein levels or function with potential effects on cell functions, including sensitivity to stress.