Phenotype/Genotype Associations in TET2-Driven Myeloid Neoplasms

TET2 is one of the most commonly mutated genes in myeloid neoplasia. The frequency of TET2 mutations (TET2^MUT) increases with age and they have been found in aging healthy controls, in whom their presence was associated with a subsequent risk of developing a myeloid neoplasm. The TET2 gene product is an enzyme that uses alpha-ketoglutarate (αKG) and vitamin C to hydroxylate 5-methylcytosine (5MC), leading to both passive demethylation during cell replication and active demethylation via base excision DNA repair enzymes.

Despite large studies, there is no consensus opinion as to the clinical impact of TET2 mutations and their mechanistic role in the pathogenesis of MDS. It is likely that the heterogeneity of TET2^MUT, their configuration, sub-clonal context and co-associated variables result in biological heterogeneity that precludes proper assessment of clinical impact. To address these issues we analyzed a cohort of 4974 patients with myeloid neoplasms using targeted deep sequencing of a panel of 60 genes found to be most frequently affected by somatic mutations in myeloid neoplasms. A total of 1861 TET2 alterations were identified as somatic in 1238 cases using various bioanalytic algorithms and sequencing of germline DNA where possible. Of these mutations, 80% were frame shift/stop codons (fs/sc) likely leading to various truncations, while 20% were missense (ms) mutations. While no hotspots for mutations were found, 53% were located in the proximity of the catalytic domain. The most recurrent ms alteration was p.Ile1873Thr, found in 2% of all TET2^MUT cases. Biallelic TE2^MUT were present in 45% of mutant cases; of which fs/sc alteration combinations were the most common (333/557; 60%), and an additional 9% were homozygous fs/sc variants. Biallelic ms mutations were present in 5% of biallelic cases (3% of homozygous ms configurations). Clinically, TET2^MUT were found in 17% of MDS patients, 65% of MDS/MPN, 12% of MPN, 21% of non-core binding factor pAML, and 26% of sAML, and were most frequently associated with normal cytogenetics (p<.001) and correlated with increased age (p=.001). Biallelic fs/sc TET2^MUT were most common in MDS/MPN (34%).

TET2^MUT tend to display a higher number of additional mutations than TET^WT (p<.001) cases, a trend that was also present comparing ancestral to secondary TET2^MUT carriers. In general, TET2^MUT were more associated with ASXL1 (p<.001), NPM1 (p<.001), and SRSF2 (p<.001) than were WT cases, whereas ETV6 (p<.001), IDH2 (p<.001), and TP53 (p<.001) were more common in TET2^WT cases. A TET2^MUT was most commonly associated with another TET2 alteration in 37% of MDS cases, followed by ASXL1 (17%), SF3B1 (13%) and SRSF2 (13%) mutations; in 54% of MDS/MPN cases, followed by SRSF2 (33%), ASXL1 (27%), and RUNX1 (13%) mutations); and in 40% of sAML, followed by ASXL1 (35%), RUNX1 (27%), and SRSF2 (22%) mutations. In contrast, in MPN, JAK2 (39%), TET2 (21%), and ASXL1 (16%) were the most common co-occurring mutations, and in pAML, NPM1 (71%), DNMT3A (48%), and TET2 (44%) co-occurred most commonly.

Analysis of clonal architecture including co-associated events revealed that 40% of TET2^MUT were dominant/possibly ancestral within the clonal hierarchy. In cases with a dominant TET2^MUT, the most commonly associated somatic events involved TET2 (18%), followed by SRSF2 (8%), ASXL1 (7%) and DNMT3A (6%). In those cases (26%) in which TET2 was not the dominant clone, SRSF2 (11%), ASXL1 (10%), DNMT3A (9%), and EZH2 (9%) were the most common early events. In 33% of TET2^MUTcases, the TET2^MUTclones were co-dominant with another TET2 (29%), SRSF2 (15%), DNMT3A (11%), or ASXL1 (9%).

TET2^MUT confers worse survival than WT cases (p<.001) in the population studied. No survival difference was seen between dominant and secondary TET2 mutations in total and within sub entities. Patients with multiple/homozygous TET2 mutations tend to have a worse prognosis than those with monoallelic TET2^MUT (p=.056). In MDS, MPN and MPN/MDS, patients with fs/sc mutations had worse survival than those with ms mutations (p=.05).

Our analyses demonstrate that TET2 lesions are strongly selected for in myeloid neoplasia and a gene dose effect may dictate biological and molecular features. While ancestral TET2 ancestral events do not determine the subsequent phenotype, subtypes of myeloid neoplasms appear to be associated with specific sets of secondary or tertiary sub-clonal events.