Transcriptomic Changes Associated with Rare Germline Missense ATM Variants in Chronic Lymphocytic Leukaemia

Abstract

Background Germline pathogenic variants in ATM gene are associated with risk of chronic lymphocytic leukaemia (CLL) and poorer prognosis. However, genetic testing is revealing a large number of rare germline missense variants of uncertain significance (VUS) in ATM whose clinical value is unclear. In this study, we evaluated the impact of ATM germline missense variants on the CLL transcriptome. Methods The genetic germline and transcriptome data from 237 CLL cases were obtained from public CLL datasets (EGAD00001001464, EGAD0000100146612). Only rare (minor allele frequency < 0.5%) missense ATM germline variants annotated as VUS by Clinvar and Varsome databases and with pathogenic prediction by SIFT/PolyPhen were studied. The transcriptome analysis was carried out using the DEseq2, 3D RNA-seq and Enrichr tools. Adjusted p value (padj) < 0.15 was considered significant. Results Of the analysed dataset, 9 (3.8%) CLL cases carried rare germline missense predicted pathogenic VUS in ATM. Further analysis was performed within subgroups of patients based on their IGHV mutational status, as preliminary cluster analysis showed distinct gene expression profiles for these subgroups. In the IGHV mutated (m-IGHV) subgroup, six cases carried germline missense ATM VUS(s) (G204R, R717W, D817N, V1671G, T1871I, L2293R, L2293V), four had solo del(11q) and 77 were without any somatic and/or germline disruption in genes associated with DNA damage response (DDR), nor did they carry mutations in a panel of 10 recurrently mutated genes (TP53, SF3B1, BIRC3, NOTCH1, XPO1, EGR2, POT1, NFKBIE, RPS15, FBXW7) associated with inferior prognosis in CLL. In patients with unmutated IGHV (u-IGHV), three cases had ATM VUS (N796H, P1376S, D2870N), including one with concurrent del(11q), 7 had only del(11q), and 20 were without any somatic and/or germline disruption in DDR and CLL-associated genes. Transcriptome analysis of m-IGHV patients with germline missense ATM predicted pathogenic VUS revealed that the highest enrichment scores belonged to mitotic spindle signaling, reactive oxygen species pathway, cholesterol homeostasis, peroxisome, fatty acid metabolism, Wnt/β-catenin signaling, response to UV radiation and oxidative phosphorylation, and genes enriched in targets of MYC, E2F, RUNX1 and CREB1 transcription factors. Analysis of m-IGHV patients with del(11q) revealed similar gene enrichment in mitotic spindle signaling, hypoxia and in the targets of MYC, RUNX1 and CREB1 as in the m-IGHV cohort with ATM VUS, but additionally, genes enriched in TNF-α signaling via NF-κB, apoptosis, and IFN-γ response were detected. Furthermore, two m-IGHV cases had biallelic disruption of TP53; analysis of these patients revealed differentially expressed genes involved in apoptosis, cholesterol homeostasis, oxidative phosphorylation, and targets of MYC and E2F. Analysis of u-IGHV patients with germline missense ATM VUS showed no significant results compared to cases without DDR/CLL gene aberrations, probably due to the low number of cases. Enrichment of genes involved in the p53 pathway, cholesterol homeostasis and MYC targets was observed in u-IGHV patients with only del(11q). Evaluation of another independent CLL cohort is currently underway. Conclusions This preliminary analysis showed a similar impact of rare germline ATM VUS on the CLL transcriptome as del(11q), at least in m-IGHV CLL, which was characterized by differentially expressed genes involved in mitotic spindle and oxidative stress signaling and targets of MYC, RUNX1 and CREB1 transcription factors. These data highlight the need for further investigation and validation of detected transcriptomic changes in a larger cohort, which is ongoing. Grant support: MH CZ - DRO (FNOl, 00098892), IGA LF UP_2022_011