ETV6 Mutations in Myeloid Neoplasia: Unraveling Clinical Features and Molecular Signatures
Authors: Kewan Tariq , Ladel Luisa , Kiwan Ahmad , Mendez Lourdes M 
Published: December 2024

Introduction

The ETS variant transcription factor 6 (ETV6) has a crucial role in normal hematopoiesis. Autosomal dominant germline mutations (ETV6GL) are responsible for familial thrombocytopenia and associated with increased risk of hematologic malignancies by an unclear mechanism. Although rare, somatic mutations of ETV6 (ETV6SM) have been reported in 2-3% of patients (pts) with myeloid malignancies. In this study, we analyzed the prevalence, clinical, and molecular profile of ETV6GL and ETV6SM among pts with myeloid neoplasia (MN).

Methods

We reviewed all the cases with available targeted next generation sequencing (NGS) between 2016 and 2024 in the Yale New Haven Health network. All Identified variants were searched in ClinVAR and COSMIC databases and assigned as ETV6GL or ETV6 SM if ever reported. ETV6GL were further classified into benign/likely benign (B/LB), pathogenic/ likely pathogenic (P/LP) and variants of undetermined significance (VUS). According to our molecular pathology pipeline, somatic variants were classified into three levels: level-1 (pathogenic), level-2 (likely pathogenic), and level-3 (variants of undetermined significance). Clinical and molecular features for pts with ETV6SM, ETV6GL (P/LP and VUS variants), and ETV6 wild-type (ETV6WT) were compared. The clonal burdens for ETV6GL VUS variants were compared with general population allelic frequency if available.

Results

Overall, 2978 pts with available molecular data were included of whom 82 (2.8%) had ETV6 variants: 23 (27%) ETV6SM, 52 (61%) ETV6GL, 17 (20%) reported as both ETV6SM/ ETV6GL, and 27 (32%) previously unreported ETV6 variants. Of the 82 pts, 84% had MN as follows: 36% MDS, 25% AML, 19% MPN, 12% CMML, and 9% CCUS. The median age of the pts with MN was 74 (37-87) and 35% were female. The median platelet count was 123 (3-1352 x109/L). Normal karyotype (45%), complex karyotype (9%), and -7/deletion 7q (9%) were the most frequent cytogenetics.

The frequency of ETV6SM among MN pts was 30.4% (21/69). MDS (57%) and MPN (29%) were the most common diagnosis associated with ETV6SM. The median platelet count was 155 (5-1352 x 109/L). In terms of variants, 18 (86%) were missense and 3 (24%) were nonsense (all p. Arg359*). The median variable allele frequency (VAF) of ETV6SM was 43% (range: 3-51%). Comparing ETV6SM vs. ETV6WT), the most frequently occurring co-mutations were ASXL1MT (33% vs. 9%, p&lt;0.001), KRASMT/NRASMT (24% vs. 6%, p&lt;0.001), SETBP1MT (19% vs. 1%) and DNMT3AMT (19% vs. 11%, p&lt;0.001).

ETV6GL were classified as: B/LB (n=20, 47%), P/LP (n=10, 23%), and VUS (n=13, 30%). The frequency of ETV6GL (P/LP and VUS) among MN pts was 10 (43%) and 13 (57%). Median platelet count of pts with P/LP and VUS ETV6GL was 195 and 143 x109/L, respectively. The type of P/LP ETV6GL mutations (n) were nonsense (4), missense (4), frameshift (1), and splicing site (1). The median VAF of ETV6GL was 47%. ASXL1MT (70% vs. 9%, p&lt;0.001), SRSF2MT (40% vs. 9%, 0.001) and KRASMT/NRASMT (30% vs. 6%, p=0.001), were the most common co-mutations within the ETV6GL P/LP cohort (compared to ETV6WT and other ETV6MT). Compared to other cases, VUS cases had high frequency of TP53MT (23% vs. 9%, p=0.074) and KRASMT/NRASMT (15% vs. 6%, p=0.132). Allelic burden of p.Arg39Gln ETV6GL (n=2, 0.0006) was higher than the general population (0.00002).

Of the new previously unreported variants, 9/23 were Level-2: 4 frameshift, 2 missense, 2 splicing sites, and 1 nonsense MT. Interestingly, only one developed MDS while 4 had AML (2 APML), 3 had MPN and one had CCUS. The median platelet count was 99 (13-1243 x109/L). Most of the remaining variants (10/23) were Level-3 missense MT and only one was a frameshift deletion.

We then analyzed serial molecular profiles of 13 pts with P/LP ETV6SM & GL to characterize clonal evolution and of these, 38% (5) pts were found to have acquired new mutations compared to the baseline molecular profile; 3 acquired RASMT and 2 acquired new SETBP1MT. In one case, an MDS pt acquired new SETBP1MT (VAF:19.6%) on top of 2 NRASMT (21+22%), 2 TET2MT (24+26%), EZH2MT (92%), and ETV6MT (21%). Of the remaining 8 pts, 2 had RASMT and 3 had both RASMT and SETBP1MT at time of diagnosis which did not change over time.

Conclusion

In our study, ETV6SM occurred rarely among pts with MN. Pts with ETV6 SM & GL have a distinct molecular signature and are significantly associated with ASXL1MT, RASMT, and SETBP1MT, with the latter two being potentially acquired prospectively.