Biallelic TET2 Inactivation in Myeloid Neoplasia: From Clonal Hierarchy to Clinical Phenotypes

Genomic data has led to the identification of bio-markers of morphological features and disease sub-entities in myeloid neoplasia (MN). Somatic TET2 mutations (TET2^MT) are frequently found in MN, particularly in chronic myelomonocytic leukemia (CMML). TET2^MT are mostly loss-of-function and hypomorphic hits leading to inactivation of TET2 protein. In fact, impaired TET2 activity skews the differentiation of hematopoietic stem cells toward proliferating myeloid precursors favoring myeloid tumorigenesis. However, the contribution of TET2^MT to clinico-hematological features in MN has been controversial, possibly due to studies containing too few patients relative to the combinatorial diversity of co-occurring lesions.

We recently reported on the clonal architecture of TET2^MT in patients with MN. Of these, 40% of the patients harbored biallelic TET2^MT (biTET2^MT). Further analysis showed a frequent occurrence of biallelic TET2 inactivation (biTET2ⁱ). To date, only a few studies have investigated the clinical consequences of biTET2ⁱ in MN. We hypothesized that the presence of biTET2ⁱ identifies a group of patho-morphological features that independently define a distinct MN subtype. To test our hypothesis, we studied correlations between mutational configuration, clinico-hematological/morphological features and survival outcomes in cases that were biTET2ⁱvs. not (biTET2^-), combining whole exome and targeted deep sequencing, SNP-arrays and conventional cytogenetics.

Among 1,001 clinically annotated MN patients, 82 were biTET2ⁱ (66 biTET2^MT, 13 hemizygous TET2^MT and 3 homozygous TET2^MT, i.e. UPD) and 919 were biTET2^- (96 monoallelicTET2^MT and 823 wild type). TET2 hits were ancestral lesions in 72% of biTET2ⁱvs. 38% in biTET2^- cases (P<.0001). When the 1^stTET2 hit was ancestral in biTET2ⁱ, the most common subsequent hit was a 2^ndTET2^MT, followed by SRSF2^MT, ASXL1^MT, KRAS^MT/NRAS^MT and DNMT3A^MT. Truncation mutations (frameshift or nonsense variants) were found in 83% of biTET2ⁱvs. 65% of biTET2^- cases (P=.02). A second TET2 hit in biTET2^MT cases significantly increases the accrual of additional truncating changes. Furthermore, biTET2ⁱ were significantly enriched for additional hits in SRSF2^MT (33%; P<.0001) and KRAS^MT/NRAS^MT (16%; P=.03) while biTET2^- for TP53^MT (11%; P=.03). SRSF2^MT was also found to be significantly associated with biTET2ⁱ when compared to monoallelicTET2^MT (P=.02). In contrast, biTET2ⁱ cases showed absence of SRSF2^MT in the absence of monocytosis. We then assessed associations of biTET2ⁱ with specific genotype/phenotype. Clinical analyses revealed that cases with biTET2ⁱ compared to cases with biTET2^- were older (91% ≥60 years vs. 74%, P=.0004) and more commonly had normal karyotype (65% vs. 45%; P=.0007). BiTET2ⁱ were enriched in patients with CMML1/2 (44% vs. 9%; P<.0001), and predominantly in lower-risk cases (62% vs. 47% in biTET2^-; P=.003). While a second TET2 hit occurred frequently, biTET2ⁱ did not portend faster progression but rather associated with monocytic differentiation, consistent with its prevalence in CMML. In addition, among biTET2ⁱ with SRSF2^MT or KRAS^MT/NRAS^MT, CMML was diagnosed in 70% (P=.001) and 77% (P=.01) of the cases, respectively, significantly higher than what was seen in the biTET2ⁱ population (44%). In biTET2^- cases, leukopenia (81%; P<.0001), neutropenia (52%; P=.008), pancytopenia (27%; P=.008) and increased marrow blast percentages (≥5% in 33%; P=.01) were more prevalent than in biTET2ⁱ cases, which in return co-segregated with monocytosis (84%; P<.0001), marrow hypercellularity (cellularity >70% in 67%; P<.0001) and marked myeloid dysplasia (68%; P=.0003). Given our observation of a highly significant (P<.0001) relationship between biTET2ⁱ, CMML diagnosis and/or monocytosis, we also evaluated patients without frank diagnosis of CMML (CMML^-) and compared biTET2ⁱvs.biTET2^- for associations with monocytosis and myeloid dysplasia, two hallmarks of CMML. Increased monocyte counts among CMML^-cases were significantly overrepresented in biTET2ⁱ cases (72%; P=.03) vs.biTET2^- (55%) as was myeloid dysplasia (72% vs. 46%; P=.0001). Lastly, biTET2ⁱ as a sole hit or in combination with other hits did not influence survival outcomes.

In sum, biTET2ⁱ invariantly associates with distinct morphological and clinical phenotype. It may thus represent an early diagnostic marker of morphologic MN sub-entities.