TET1 promotes growth of T-cell acute lymphoblastic leukemia and can be antagonized via PARP inhibition

Abstract

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological cancer characterized by skewed epigenetic patterns, raising the possibility of therapeutically targeting epigenetic factors in this disease. Here we report that among different cancer types, epigenetic factor TET1 is highly expressed in TALL and is crucial for human TALL cell growth in vivo. Tet1 knockout mice and knockdown in human T-cells did not perturb normal T-cell proliferation, indicating that TET1 expression is dispensable for normal T-cell growth. The promotion of leukemic growth by TET1 was depending on its catalytic property to maintain global 5hydroxymethylcytosine (5hmC) marks, thereby regulating cell cycle, DNA repair genes and TALL associated oncogenes. Furthermore, overexpression of the Tet1 catalytic domain was sufficient to augment global 5hmC levels and leukemic growth of TALL cells in vivo. We demonstrate that PARP enzymes, which are highly expressed in TALL patients, participate in establishing H3K4me3 marks at the TET1 promoter and that PARP1 interacts with the TET1 protein. Importantly, the growth related role of TET1 in TALL could be antagonized by the clinically approved PARP inhibitor Olaparib, which abrogated TET1 expression, induced loss of 5hmC marks and antagonized leukemic growth of TALL cells, opening a therapeutic avenue for this disease. 10 transplantation (Fig. S2H). Moreover, in a published microarray analysis of TALL cell lines transplanted into xenografts, a similar increase in TET1 expression was observed (Fig. S2I), suggesting that high TET1 expression is associated with leukemic growth in vivo. Indeed, forced expression of Tet1-CD in TALL cell lines significantly augmented leukemic growth in vitro and in vivo (Fig. 3D-E). These data clearly suggest that the growth-promoting role of TET1 in TALL is at least partly dependent on its enzymatic activity. TET1 depletion induces loss of 5hmC marks at promoters and gene bodies of genes involved in cell cycle, DNA repair and NOTCH pathway Next we analyzed 5hmC levels in TALL cells via Intracellular fluorescence (IF) in our knockdown, rescue and overexpression experiments. IF-flow cytometry for 5hmC marks in TET1 depleted JURKAT cells, primary TALL patients and TET1 knockout bulk TALL cell lines revealed a significant decrease in global 5hmC levels (Fig. 4A-B and Fig. S3A-B) and increase in 5mC levels (Fig. S3C). Conversely, overexpression of Tet1-CD in TET1 depleted cells or wild type TALL cells induced a global increase in 5hmC levels (Fig. 4C-D). Furthermore, we performed hydroxymethylated DNA immunoprecipitation (hMeDIP)-seq in TET1 depleted JURKAT cells. In hMeDIP-seq, TET1 depletion resulted in more than a 59% reduction of global 5hmC enrichment at the promoter (-5kbTSS), gene body (GB) and intergenic regions compared to scrambled control (referred to as TET1 dependent 5hmC or T1-5hmC regions from here) (Fig. 4E-F). In detail, a total of 2,404 and 6,115 5hmC enriched promoters and GB were observed in the scrambled arm, respectively, out of which more th...

DNA Methylation in T-Cell Acute Lymphoblastic Leukemia: In Search for Clinical and Biological Meaning

“…TET1 protein has been reported to have dual roles in hematological malignances depending on the cellular lineage. In B-cell malignances it is postulated to act as a tumor suppressor [ 56 ], while in T-ALL it has been shown to carry growth-promoting potential when upregulated [ 57 ]. This gene is highly expressed in the majority of T-ALL patients and in many T-ALL cell lines.…”

“…This gene is highly expressed in the majority of T-ALL patients and in many T-ALL cell lines. The higher expression of TET1 is more frequently observed in adolescent and young adult patients [ 57 ]. In pediatric T-ALL patients, higher TET1 expression was found in intermediate and in high risk groups than in the standard risk group [ 57 ].…”

“…The higher expression of TET1 is more frequently observed in adolescent and young adult patients [ 57 ]. In pediatric T-ALL patients, higher TET1 expression was found in intermediate and in high risk groups than in the standard risk group [ 57 ]. The oncogenic role of TET1 protein in T-ALL was confirmed by Bamezai et al in 2020 [ 57 ].…”

“…In pediatric T-ALL patients, higher TET1 expression was found in intermediate and in high risk groups than in the standard risk group [ 57 ]. The oncogenic role of TET1 protein in T-ALL was confirmed by Bamezai et al in 2020 [ 57 ]. The group used shRNA to deplete TET1 in human T-ALL cell lines and in patient derived T-ALL cells transplanted to immunocompromised mice to investigate TET1 function in T-ALL development.…”

“…They performed hydroxymethylated DNA immunoprecipitation followed by deep sequencing (hMe-DIP)-seq in TET1 depleted JURKAT cells and revealed that downregulation of TET1 resulted in 5hmC decrease at genes associated with cell cycle, DNA repair and oncogenic pathways. What is more, depletion of TET1 was demonstrated to increase DNA damage, as shown by comet assays in cell lines and primary patient T-ALL cells [ 57 ]. In the same study the authors demonstrated that TET1 gets upregulated in response to exposure of T-ALL cell lines to radiation inducing DNA damage.…”