Abstract 57: Patients with germline ATM mutations develop clonal hematopoiesis characterized by co-occurrence of multiple somatic ATM alterations
Authors: Decker Brennan , Kou Angela A. , Janovitz Tyler , Mata Douglas A. , Sokol Ethan S. , Jin Dexter X. , Tukachinsky Hanna , Vergilio Jo-Anne , Elvin Julia A. , Oxnard Geoffrey R. 
Published: June 2022

BACKGROUND The DNA repair gene ATM is remarkable for its roles across the spectrum of neoplastic biology, including inherited risk of multiple malignancies, somatic tumor biology, and clonal hematopoiesis (CH). We hypothesized that comparison of liquid biopsy (LB) versus tumor tissue (TT) from germline ATM pathogenic mutation carriers (gATM+) might offer additional insights into the role of ATM in CH.

METHODS 34,825 LB samples and 384,847 TT specimens were sequenced for up to 324 genes during routine clinical care and analyzed for all classes of genomic alterations (Frampton 2013, Woodhouse 2020). Individual variants were assessed for germline versus somatic origin using the validated somatic-germline zygosity algorithm (Sun 2018).

RESULTS Germline ATM mutations were observed in 0.9% (113/12,217) of LB and 0.8% (3,029/384,847) of TT (P&lt;0.001). Up to 27 ATM mutations were identified per gATM+ sample, with a range of 1-27 in LB and 1-8 in TT. Co-occurrence of 3+ ATM mutations in a single sample was 18-fold higher among gATM+ subjects undergoing LB versus TT (23.9% vs. 1.2%, P&lt;0.001). In LB, the incidence of 3+ ATM mutations increased with age for all groups, but the frequency in gATM+ subjects diverged as patient age advanced. In the age 80+ subgroup, 57.1% (28/49) of gATM+ subjects had 3+ ATM mutations, compared to 3.3% (133/4,055) of gATM− subjects (P&lt;0.001). A significant difference was maintained after correcting for the contribution of the germline ATM mutation to the total number of ATM mutations in gATM+ subjects. We hypothesized that multiple ATM variants per sample could be caused by high TMB or positive selection for multiple subclonal hits in the ATM gene. In TT, observation of 3+ ATM mutations was associated with high TMB in 80.5% (513/637) of cases. In contrast, 88.5% (555/627) of LB samples with 3+ ATM mutations had low TMB (Pdiff&lt;0.001), a pattern consistent with positive selection in LB. LB from gATM+ cases with 3+ ATM mutations all had one variant with ~50% variant allele fraction (VAF), while 80.0% (546/682) of the co-mutations had VAF &lt;1%. Co-mutations included 32.0% (793/2,485) truncating alterations and 68.1% (1,692/2,485) missense alterations. Low VAF missense co-mutations were clustered in the FAT and PIKKc domains, which are known pathogenic missense mutation hotspots. This distribution suggests that some missense alterations within these hotspots that are currently classified as VUS are under positive selection and therefore warrant consideration for reclassification.

CONCLUSION The finding of numerous ATM mutations under positive selection in gATM+ subjects was specific to LB, increased in incidence with age, and co-mutations tended to have low VAF. All these features are consistent with polyclonal hematopoiesis (polyCH) involving ATM co-mutations in gATM+ subjects. Additional investigation is needed to extend our understanding of this phenomenon.

Citation Format: Brennan Decker, Angela A. Kou, Tyler Janovitz, Douglas A. Mata, Ethan S. Sokol, Dexter X. Jin, Hanna Tukachinsky, Jo-Anne Vergilio, Julia A. Elvin, Geoffrey R. Oxnard. Patients with germline ATM mutations develop clonal hematopoiesis characterized by co-occurrence of multiple somatic ATM alterations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 57.