Genetic characterization of TET1, TET2, and TET3 alterations in myeloid malignancies

Abstract

IntroductionOur understanding of the molecular pathogenesis of myeloid malignancies, most notably acute myeloid leukemia (AML) and chronic myeloid leukemia (CML), has largely resulted from the identification and characterization of recurrent chromosomal translocations. 1 However, in many patients with myeloproliferative neoplasms (MPNs) and chronic myelomonocytic leukemia (CMML), recurrent clonal cytogenetic abnormalities are not observed. More recently, DNA resequencing studies of candidate genes, 2 gene families, 3,4 and the cancer genome 5 in MPN, CMML, and AML have identified somatic mutations in FLT3, 6 JAK2, [7][8][9][10][11][12][13]14,15 and the RAS family of oncogenes. 16 These discoveries demonstrate activation of signal transduction pathways is a common pathogenic event in myeloid malignancies and have led to the development of molecularly targeted therapies. However, with the exception of CML, these therapies have yet to substantively improve outcomes for patients with myeloid malignancies. 17,18 This may reflect insufficient target inhibition, or, alternatively, this may indicate incomplete dependence on these activated pathways resulting from the presence of additional somatic mutations with prognostic, therapeutic, and biologic relevance.The role of TET (Ten-Eleven Translocation) family gene members in hematopoietic transformation was thought to be restricted to the involvement of TET1 as a translocation partner MLL-translocated AML, until the recent identification of inactivating mutations in TET2 in MPN and MDS patients. 19 We therefore sought to evaluate a large set of MPN, CMML, and AML samples for somatic TET2 alterations. We sequenced all coding exons of TET2 in 408 paired tumor/normal samples and then assessed the frequency of somatic TET2 mutations in 606 patients with MPN, CMML, and AML. We also investigated whether deletion or epigenetic inactivation of TET2 are observed in MPN and evaluated MPN patients for somatic mutations in TET1 and TET3. Methods Copy number analysis of TET1, TET2, and TET3A total of 207 MPN tumor samples were analyzed using Affymetrix 250K StyI Arrays. 20 The JAK2V617F-mutant AML cell lines HEL and SET2 were analyzed using Affymetrix 6.0 SNP Arrays. Methylation-specific polymerase chain reactionMethylation of 2 CpG islands in the promoter region of TET2 was assessed in 37 MPN patients and 4 JAK2V617F-positive leukemia cell lines (SET2, MBO2, HEL, UKE1). Methylation-specific polymerase chain reaction was performed as previously described (primers are listed in supplemental Table 1). 21 StatisticsStatistical analyses were performed using MedCalc (MedCalc). Results and discussionSequence analysis of all coding exons of TET2 in 408 paired tumor/normal samples identified 8 frameshift, 12 nonsense, and 37 nonsynonymous alterations not present in dbSNP. Analysis of germ line DNA distinguished between 31 somatic missense mutations and 6 unannotated SNPs (Table 1; supplemental Figure 1); all unannotated SNPs were observed in matched normal tissue in at least 2 samples. Al...

Tet family proteins and 5-hydroxymethylcytosine in development and disease

“…hematopoietic cell proliferation and maturation (Abdel-Wahab et al, 2009;Albano et al, 2011;Chou et al, 2011;Euba et al, 2011;Figueroa et al, 2010;Pronier et al, 2011;Weissmann et al, 2011). Although Tet2 -/-mice appeared to develop normally overall, they displayed an abnormality in myeloid lineage differentiation and developed leukemia spontaneously Moran-Crusio et al, 2011;Quivoron et al, 2011).…”

“…By contrast, TET2, although only recently identified, is the most studied member of the Tet family genes in MDS and other types of leukemia. It has been reported as one of the most frequently mutated genes in myeloid malignancies (Abdel-Wahab et al, 2009;Albano et al, 2011;Chou et al, 2011;Euba et al, 2011;Figueroa et al, 2010;Weissmann et al, 2011). Whereas some of the mutation sites in TET2 correspond to residues within the catalytic domain and could thus impair catalytic activity, many mutations appear unrelated to enzymatic activity (Ko et al, 2010).…”

5-hydroxymethylcytosine

“…In 2009, sequencing of TET2 in some paired tumor/normal samples identified that gene mutations of TET2 occurred in myeloproliferative neoplasms (MPN), chronic myelomonocytic leukemia (CMML), and acute myeloid leukemia (AML). 54 Since then researches on TET2 and myeloid malignancies became more and more thorough. People showed that TET2 mutations were associated with myeloid malignancies compromising the TET2 catalytic activity.…”

Fumarate and Succinate Regulate Expression of Hypoxia-inducible Genes via TET Enzymes

“…There are three human TET isoenzymes. TET1 is highly expressed in embryonic stem cells, whereas TETs 2 and 3 are required for normal hematopoiesis (8,9). Mutations in TET2 are frequently found in acute myeloid leukemia (AML) and in several other hematological malignances (9 -12).…”