Biallelic TET2 Inactivation in Myeloid Neoplasia: From Clonal Hierarchy to Clinical Phenotypes
Authors: Awada Hassan , Nagata Yasunobu , Goyal Abhinav , Asad Mohammad Fahad B. , Patel Bhumika J. , Hirsch Cassandra M. , Kuzmanovic Teodora , Adema Vera , Aly Mai , Przychodzen Bartlomiej P. , Guan Yihong , Shen Wenyi , Williams Louis , Nazha Aziz , Abazeed Mohamed , Sekeres Mikkael A. , Radivoyevitch Tomas , Haferlach Torsten , Jha Babal K. , Visconte Valeria , Maciejewski Jaroslaw P. 
Published: October 2019

Abstract
Genomic data has led to the identification of bio-markers of morphological features and disease sub-entities in myeloid neoplasia (MN). Somatic TET2 mutations (TET2MT) are frequently found in MN, particularly in chronic myelomonocytic leukemia (CMML). TET2MT 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 TET2MT 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 TET2MT in patients with MN. Of these, 40% of the patients harbored biallelic TET2MT (biTET2MT). 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 biTET2MT, 13 hemizygous TET2MT and 3 homozygous TET2MT, i.e. UPD) and 919 were biTET2- (96 monoallelicTET2MT and 823 wild type). TET2 hits were ancestral lesions in 72% of biTET2ivs. 38% in biTET2- cases (P<.0001). When the 1stTET2 hit was ancestral in biTET2i, the most common subsequent hit was a 2ndTET2MT, followed by SRSF2MT, ASXL1MT, KRASMT/NRASMT and DNMT3AMT. Truncation mutations (frameshift or nonsense variants) were found in 83% of biTET2ivs. 65% of biTET2- cases (P=.02). A second TET2 hit in biTET2MT cases significantly increases the accrual of additional truncating changes. Furthermore, biTET2i were significantly enriched for additional hits in SRSF2MT (33%; P<.0001) and KRASMT/NRASMT (16%; P=.03) while biTET2- for TP53MT (11%; P=.03). SRSF2MT was also found to be significantly associated with biTET2i when compared to monoallelicTET2MT (P=.02). In contrast, biTET2i cases showed absence of SRSF2MT 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 SRSF2MT or KRASMT/NRASMT, 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.

Disclosures
Nazha: MEI: Consultancy. Sekeres:Celgene: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Opsona: Membership on an entity's Board of Directors or advisory committees; Opsona: Membership on an entity's Board of Directors or advisory committees. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Maciejewski:Ra Pharmaceuticals, Inc: Consultancy; Alexion Pharmaceuticals, Inc.: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Ra Pharmaceuticals, Inc: Consultancy; Alexion Pharmaceuticals, Inc.: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Apellis Pharmaceuticals: Consultancy; Apellis Pharmaceuticals: Consultancy.