Functional analysis of ATM variants in a high risk cohort provides insight into missing heritability


Early surveillance and prophylactic surgery for high risk women can address the pattern of ovarian cancer disease presentation, but neither is advised for the general population or even the majority of patients at moderate risk. Cancer genetic testing can be crucial in identifying people who would benefit from early surveillance and more thorough testing. In turn, improving cancer detection at an early stage when it is most treatable and possibly curable can significantly increase the survival of the most vulnerable patients. In diagnosing hereditary cancer and counselling patients with pedigrees suggestive of such a condition, variations of uncertain significance (VUS) continue to provide a difficulty.

In reaction to DNA double-strand breaks, the protein kinase ataxia telangiectasia mutated (ATM) plays a critical function. Ataxia Telangiectasia (AT), a rare genomic instability condition marked, among other things, by an increased risk of cancer, is brought on by both heterozygous and homozygous hereditary mutations in the ATM gene. The ATM gene is located on chromosome 11 and provides instructions for making the ATM protein, a key effector in the cellular response to DNA damage. The protein activates after the detection of damaged or broken DNA strands and activates enzymes that repair the broken DNA. Heterozygous germline ATM pathogenic variants are associated with an increased risk for developing a variety of cancers, including breast, colon, prostate, gastric, pancreatic, melanoma, and ovarian and possibly other cancers. The ATM gene is considered a moderate penetrance gene, meaning the risk of developing a malignancy in an individual who carries a pathogenic variant is two to four times that of the general population. The risks vary with the specific variant and are associated with family history. Due to the moderate penetrance of the ATM gene, patient counselling has proven difficult.

In a new study published in Cancer Genetics, Scott Baughan and Fatima Darwiche, led by Professor Michael Tainsky from the Wayne State University School of Medicine assessed several polymorphisms in the ATM gene that were chosen from a sample of high risk women with a personal history of ovarian cancer and negative genetic diagnosis in order to evaluate some of this limitation.

The research team created variant models and tested the function of these variations through a series of biochemical assays. Their innovative methodology can successfully identify variants that are probably to blame for missing heritability easier by combining functional investigations with carefully selected small cohorts.

Global analysis of the six variants of unknown significance via homology directed repair (HDR) assay and colony survival assay showed that several were defective in effecting DNA repair after damage. Given that ATM’s key role in the cell is as a protein kinase, the team proposed that impaired phosphorylation of one or more downstream targets of ATM in the DNA damage response pathway underlies the majority, if not all, of the variants that showed reduced function in the HDR and colony survival assays.

The authors studied the mechanistic impact of each of the six ATM VUS by examining several ATM phosphorylation targets. One variant, V2540I, showed similar activity in the HDR and colony survival assays to the negative assay controls (ATM knockdown and the known kinase dead variant S1981A). Reduced phosphorylation was also seen affecting several key ATM downstream targets, likely causing the impaired DNA damage response observed by the authors. Similarly, the authors observed reduced activity and defective phosphorylation for the variant S333F, though not as severe as V2540I. Given the abundance of phosphorylation targets for the ATM kinase, the authors were unable to find a mechanistic explanation for the decreased DNA repair efficacy conferred by the variants F1463C and S49C, though they propose several hypotheses to explain the phenomena, including impairment of activity relating to an unstudied target, additive, mild defects in phosphorylation across targets, or some other mechanism, such as a structural change affecting protein folding or interaction with other proteins. For the variant S49C, evidence for additive defects across many targets may be reflected in the dramatic decrease in CDC25A phosphorylation, a final stage event in the DNA damage response pathway.

In conclusion, the new study by the Tainsky lab team offers a novel, elegant method that can locate and examine the “missing” inherited mutations that elude doctors and produce false negative results in cancer gene testing panels, directly addressing the limitations of current variant assessment methods. The cost-benefit payoff of such studies shows that small-scale but rigorous in vitro examination of variants of uncertain significance can advance the cause of human health and increase the accuracy and utility of cancer genetic testing.


Baughan SL, Darwiche F, Tainsky MA. Functional analysis of ATM variants in a high risk cohort provides insight into missing heritability. Cancer Genetics. 2022;264:40-9.

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