Clonal Architecture Analysis of TET2 Mutations in Myelodysplastic Neoplasms
Authors: Zhang Yudi , Wang Wei , Jiang Lingxu , Liu Xiaozhen , Yu Huchu , Tong Hongyan 
Published: December 2024

Purpose: TET2 is one of the most frequently mutated genes in both myelodysplasia neoplasms (MDS) and clonal hematopoiesis of indeterminate potential (CHIP). We hypothesized that MDS originating from CHIP with mutated TET2 had ancestral TET2 hits and differs from other MDS subjects. Therefore, we conducted clonal architecture analyses of TET2 to reveal the heterogeneity of TET2 in MDS.
Methods: Data from 551 newly-diagnosed de novo MDS seen at our center were collected. All the MDS subjects were underwent comprehensive pre-treatment examinations including bone marrow and hematological analyses, cytogenetic, and the next-generation sequencing (NGS). For external validation, data from primary MDS patients from the IWG-PM cohort were used (https://www.cbioportal.org/). Variant allele frequency (VAF) of mutations were ranked and we used a cutoff of at least a 5% difference between VAFs to identify ancestral and sub-clonal mutations. The last follow-up was on April 30, 2024 with a median follow-up of survivors 39 months. The study was conducted under the approval of the Ethics Committee of the First Affiliated Hospital of Zhejiang University and in accordance with the Declaration of Helsinki.
Results: 480 (87.1%) subjects had one or more mutation(s) and TET2 was the second common mutation. A total of 140 TET2 mutations were identified in 114 (20.7%) subjects, among them 32% were missense, 24% were frameshifts, 22% were nonsense and 22% were other variants. The most common base-pair change was a cytosine-to-thymine (C-T) transition (26.7%), followed by guanine-to-adenine transition (G-A; 18.5%). Of TETMT subjects, 32 (28%) had more than one TET2 mutations, those subjects could be either TET2 biallelic or biclonal.
MDS with TET2MTwere older than those with TET2WT (64 vs 60y, P &lt;0.001). Among TET2MT subjects, those with C-T transition were older (66 vs 64y, P &lt;0.001) while those with G-A transition (59 vs 65y, P &lt;0.001) were younger than other TET2MT subjects. MDS with biallelic or biclonal TET2MT had older age (69y vs 63y, P &lt;0.001) and lower hemoglobin concentrations (72 vs 86g/L, P &lt;0.001) compared those with single TET2MT.
Among 93 TET2MTsubjects who had 2 or more mutations, 52 (56%) TET2MT were first hit (ancestral clone) and 41 (44%) were secondary hit (subclone). MDS with ancestral TET2MT were related with younger age (62 vs 67y, P &lt;0.001), higher monocyte counts (0.36 vs 0.21× 10E+9/L, P=0.05), lower IPSSM risks (P=0.04), more G-A transitions (P=0.02) and were more frequently in MDS-non-EB subtypes (P=0.01). When TET2 was the first hit, the most common second mutation is another TET2 mutation followed by ASXL1, U2AF1, RUNX1, SF3B1, SRSF2 and TP53. When TET2 was the secondary hit, the most frequently dominant clone was ASXL1, RUNX1, STAG2 and ZRSR2.
Overall, TET2MT had no impact on survival. However, MDS with biallelic or biclonal TET2MT had significantly briefer survival than those with single TET2MT (15 vs 49months, P=0.01) and MDS with secondary TET2MT had significantly briefer survival than those with ancestral TET2MT (13 vs 49months, P=0.01). We also examined the impacts of additional mutations on survival in TET2MTcases. When TET2 was the first hit, subjects with co-mutated RUNX1 had worse survival and when TET2 was the secondary hit, subjects with co-mutated DNMT3A and TP53 had worse survival. Secondary TET2 was still an independent risk viable after adjusting for IPSS-R risk categories (HR=1.67 [95%CI 1.10-2.56]; P=0.02). However, when the age was adjusted, the clonal architecture of TET2 loss the prognostic value.
In IWG-PM cohort, 630 (28.3%) of 2223 primary MDS harbored TET2 mutation. MDS with TET2MT had older age than MDS with TET2WT (75 vs 71y, P&lt;0.001). In 586 cases with 2 or more mutations, 333 (57%) TET2MT were first hit and 253 (43%) were secondary hit. MDS with ancestral TET2MT were related with higher monocyte counts (0.44 vs 0.32× 10E+9/L, P&lt;0.001), lower IPSSR (P=0.03) and IPSSM risks (P&lt;0.01). MDS with secondary TET2MT had shorter survival than those with ancestral TET2MT (40 vs 56months, P=0.05).
Conclusion: We demonstrated the heterogeneity of TET2 mutation in MDS. In summary, biallelic TET2 had significantly worse prognosis. MDS with ancestral TET2 hit may identified a subprop derive from CHIP. Those subjects were more likely to had lower risk and better prognosis.