The clinical and functional effects of TERT variants in myelodysplastic syndrome

Abstract

Germline pathogenic TERT variants are associated with short telomeres and an increased risk of developing myelodysplastic syndrome (MDS) among patients with a telomere biology disorder. We identified TERT rare variants in 41 of 1514 MDS patients (2.7%) without a clinical diagnosis of a telomere biology disorder who underwent allogeneic transplantation. Patients with a TERT rare variant had shorter telomere length (P < .001) and younger age at MDS diagnosis (52 vs 59 years, P = .03) than patients without a TERT rare variant. In multivariable models, TERT rare variants were associated with inferior overall survival (P = .034) driven by an increased incidence of nonrelapse mortality (NRM; P = .015). Death from a noninfectious pulmonary cause was more frequent among patients with a TERT rare variant. Most variants were missense substitutions and classified as variants of unknown significance. Therefore, we cloned all rare missense variants and quantified their impact on telomere elongation in a cell-based assay. We found that 90% of TERT rare variants had severe or intermediate impairment in their capacity to elongate telomeres. Using a homology model of human TERT bound to the shelterin protein TPP1, we inferred that TERT rare variants disrupt domain-specific functions, including catalysis, protein-RNA interactions, and recruitment to telomeres. Our results indicate that the contribution of TERT rare variants to MDS pathogenesis and NRM risk is underrecognized. Routine screening for TERT rare variants in MDS patients regardless of age or clinical suspicion may identify clinically inapparent telomere biology disorders and improve transplant outcomes through risk-adapted approaches.

Graphical abstract

Figure 1.

TERT variants in MDS and NHL. (A) Classification approach of nonsynonymous TERT coding variants identified in the MDS and NHL cohorts. (B) Frequency of TERT common and TERT rare variants within the MDS and NHL cohorts. (C) Domain distribution of TERT variants within the MDS cohort. TERT common variants (n = 180) and rare variants (n = 41, R1086H in 2 patients) are located above and below the coding region, respectively. The size of each ball is proportional to the number of patients with that variant. TERT rare variants are colored in red and TERT common variants in blue.

Figure 2.

Association of TERT variants with telomere length and age at MDS diagnosis. (A) Pretransplant whole blood relative telomere length by TERT variant status. (B) Age at MDS diagnosis by TERT variant status. TERT variant groups are labeled: no TERT variant (black), TERT common variant (gray), and TERT rare variant (red). (C) Variant allele fraction distribution of TERT variants, germline SNPs (black), and myeloid mutations (blue). (D) Variant allele fraction distribution of TERT rare variants as a function of the proportion of blood lymphocytes. Linear regression slope with P value is shown.

Figure 3.

Transplant outcomes by TERT rare variant status. (A) Kaplan-Meier curve for overall survival. (B) Cumulative incidence curves for nonrelapse mortality. (C) Cumulative incidence curves for relapse. Patients with a TERT rare variant are colored in red and patients without a TERT rare variant are colored in green. (D) Multivariable models of overall survival, NRM, and relapse.

Figure 4.

Functional characterization of TERT rare variants. (A) Cell-based telomere elongation assay in isogenic bulk K562 cell lines with doxycycline-inducible TERT expression. TERT expression throughout the experiment is shown for control conditions: luciferase, TERT^WT, TERT^V694M. hTERT band (∼127 kDa) is labeled with an arrow, and the asterisk corresponds to a nonspecific band seen in all conditions. (B) Telomere length measurements by terminal restriction fragment analysis and qPCR (ddCT represents RTL) for luciferase (green), TERT^WT (blue), and TERT^V694M (red). (C) Telomere elongation capacity of TERT rare variants normalized to TERT^WT are shown in ranked order grouped by structural domain. Control conditions are colored in black and TERT rare variants in red.

Figure 5.

Structural analysis of TERT rare variants. (A) Human TERT homology model. The ring, formed by the TRBD, RTD, and CTE domain, is colored in purple and the TEN domain in green. Panels B, C, D, and E show the TERT rare variants within the RTD (enzymatic core and IFD regions), TRBD, TEN, and CTE domains (including the FVYL pocket), respectively. R622 belongs to the RTD but is displayed in panel C because of its proximity to the TRBD. The side-chains for the residues mutated in the MDS rare variants (crimson carbon atoms) and the catalytic residues in the active site (yellow carbon atoms) are shown in stick representation. The modeled regions of TERC are in orange, whereas the DNA substrate is depicted in black.