Piwi proteins and their associated piRNAs are essential for preserving the self-renewal property of mammalian germ stem cells. Their highly conserved role in CpG island DNA methylation and chromatin modifications in germ stem cells has long been associated with transposon silencing but recent reports hint at protein coding regions being targets for Piwi-mediated epigenetic changes as well. Interestingly, the expression of PIWI family members is not restricted to the germline, and certain members have also been implicated in tumorigenesis in cases of adenocarcinomas, gliomas, and sarcomas. The following review discusses our knowledge of the function of Piwi proteins and piRNAs in suppressing transposable elements while maintaining the self-renewing population of germ stem cells. We also highlight the somatic function of Piwi as an epigenetic modifier. Furthermore, we summarize the recently uncovered involvement of Piwi proteins and piRNAs in various cancers. Stem Cells

Homeobox genes are known to be key factors in leukemogenesis. Although the TALE family homeodomain factor Meis1 has been linked to malignancy, a role for MEIS2 is less clear. Here, we demonstrate that MEIS2 is expressed at high levels in patients with AML1-ETO-positive acute myeloid leukemia and that growth of AML1-ETO-positive leukemia depends on MEIS2 expression. In mice, MEIS2 collaborates with AML1-ETO to induce acute myeloid leukemia. MEIS2 binds strongly to the Runt domain of AML1-ETO, indicating a direct interaction between these transcription factors. High expression of MEIS2 impairs repressive DNA binding of AML1-ETO, inducing increased expression of genes such as the druggable proto-oncogene YES1. Collectively, these data describe a pivotal role for MEIS2 in AML1-ETO-induced leukemia.

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...

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Homeobox genes are key regulators in normal and malignant hematopoiesis. The human Vent-like homeobox gene VENTX, a putative homolog of the Xenopus laevis Xvent-2 gene, was shown to be highly expressed in normal myeloid cells and in patients with acute myeloid leukemia. We now demonstrate that constitutive expression of VENTX suppresses expression of genes responsible for terminal erythroid differentiation in normal CD34+ stem and progenitor cells. Transplantation of bone marrow progenitor cells retrovirally engineered to express VENTX caused massive expansion of primitive erythroid cells and partly acute erythroleukemia in transplanted mice. The leukemogenic potential of VENTX was confirmed in the AML1-ETO transplantation model, as in contrast to AML1-ETO alone co-expression of AML1-ETO and VENTX induced acute myeloid leukemia, partly expressing erythroid markers, in all transplanted mice. VENTX was highly expressed in patients with primary human erythroleukemias and knockdown of VENTX in the erythroleukemic HEL cell line significantly blocked cell growth. In summary, these data indicate that VENTX is able to perturb erythroid differentiation and to contribute to myeloid leukemogenesis when co-expressed with appropriate AML oncogenes and point to its potential significance as a novel therapeutic target in AML.

There is high interest in understanding the mechanisms that drive self-renewal of stem cells. HOXB4 is one of the few transcription factors that can amplify long-term repopulating hematopoietic stem cells in a controlled way. Here we show in mice that this characteristic of HOXB4 depends on a proline-rich sequence near the N terminus, which is unique among HOX genes and highly conserved in higher mammals. Deletion of this domain substantially enhanced the oncogenicity of HOXB4, inducing acute leukemia in mice. Conversely, insertion of the domain into Hoxa9 impaired leukemogenicity of this homeobox gene. These results indicate that proline-rich stretches attenuate the potential of stem cell active homeobox genes to acquire oncogenic properties.

Piwi proteins belong to a class of proteins which were shown to be critically involved in the maintenance of the self-renewal property of stem cells in lower organisms. Furthermore, it was shown that they preserve genomic integrity through epigenetic silencing of transposable elements via CpG methylation and repressive histone modifications such as H3K9me3 in close interaction with a novel class of non-coding RNA called piRNA. So far there are neither precise data on the function of Piwi proteins in human acute myeloid leukemia, nor are there reports on expression of piRNAs in this disease. In a first step we tested PIWIL gene expression levels in normal human hematopoietic cells and leukemic patient samples by qRT-PCR. Among the family of human PIWI genes, PIWIL4 showed the highest expression level and was ubiquitously expressed in normal hematopoietic stem/progenitors, mature lymphoid and myeloid cells. Importantly, PIWIL4 showed aberrantly high expression in more than 72% of the AML patients (n=68; p< 0.0001) compared to normal CD34+ bone marrow (BM) and total BM cells (n=3). Notably, in nine of the ten MLL-AF9 rearranged AML patients, PIWIL4 was 64-fold higher expressed compared to normal CD34+ BM (p<0.0001) and 8-fold higher compared to inv(16), PML-RARa or cytogenetically normal AML patients (p<0.0001). To further validate this finding we analysed gene expression data performed on CD34+ human cord blood cells transduced with MLL-AF9 (n=9) vs AML-ETO (n=6) vs MYH11 (n=3): of note, PIWIL4 showed a 6 fold increase in expression in the MLL-AF9 transduced cells compared to the other experimental arms. Stable knockdown of PIWIL4 in the MLL rearranged AML cell lines MV4-11 (MLL-AF4) and THP-1 (MLL-AF9) significantly impaired growth in vitro (n=3) reducing proliferation and clonogenic growth by 83%/93% and 91%/93%, respectively. In addition, depletion of PIWIL4 delayed onset of leukemia in NSG mice transplanted with MV4-11/ THP-1 cells transduced with shPIWIL4 compared to the scrambled control (shRNA: AML onset 48/62d after transplantation vs. 30/30 days in the scrambled control; n=4/8 per arm; p< 0.0001/p<0.001). ChIP-seq analysis revealed that depletion of PIWIL4 in the THP1 cell line results in a marked global reduction in repressive H3K9me3 marks and in an increase in activating H3K4me3 marks as compared to cells transduced with the scrambled control. RNA-seq analyses revealed over 2500 differentially expressed genes upon PIWIL4 depletion with 60% of the genes being upregulated compared to the scrambled control (p<0.05). Among them genes involved in cell cycle such as RB1, P21, TGFB1 as well as epigenetic modifiers such as SETDB1, HDAC1,2 and demethylating enzyme TDG were differentially expressed. RB1 and EED, a protein necessary for PRC2 complex function, displayed an increase in expression and loss of H3K9me3 modifications on their promoters upon knockdown of PIWIL4. To prove piRNA expression in human AML and to test any association between PIWIL4 expression and piRNA signatures, microarray analyses covering 23,677 piRNAs was performed on the MLL-AF9 rearranged THP-1 cell line, of which 14193 piRNAs showed expression levels higher than 4 (arbitrary log2 scale). PIWIL4 knockdown induced differential expression of 981 piRNAs (p≤0.01, fold change ≥2), of which 527 were downregulated and 454 upregulated. Thus, collectively, we could show for the first time that PIWIL4 expression is deregulated in human AML, affects leukemic growth, shapes epigenetic marks and impacts piRNA expression in this disease. Disclosures: No relevant conflicts of interest to declare.

DNA methylation patterns are highly deregulated in human acute myeloid leukemia (AML) cases and stratify AML patient samples into different subgroup. AML1-ETO is the most commonly occurring fusion gene in AML and these AML cases exhibit an aberrant and distinct methylation pattern. So far, the underlying mechanisms for this are only poorly understood. The TET1 dioxygenase has recently emerged as an important epigenetic modifier: by catalyzing the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) TET1 plays an important role in active demethylation, thereby regulating a variety of biological processes. It was linked to tumorigenesis based on the observation that its expression is frequently deregulated in solid cancer. However, the role of TET1 in AML1-ETO+ (AE+)human AML cases is yet unexplored. Using quantitative real time (qRT)- PCR we now show that AE+ AML is characterized by high and aberrant expression of TET1: the gene was significantly higher expressed in the majority of AE+ patients (n=7, p<0.01) compared to other AML subtypes such as inv(16) (n=11), PML-RARα+ (n=31), cytogenetically normal (CN)-AML patients (n=33) and CD34+ normal BM cells (n=4). This observation was consistent with published cDNA microarray data on large patient cohorts (Haferlach et al., JCO 2010, p<0.008 t-test, p<0.01 Anova) and recently published transcriptome data (TCGA) of AML patients. In contrast to TET1, TET2 and TET3 did not show significant higher expression in AE+ patients compared to other AML subtypes. In line with patient data, TET1 was highest expressed in the AE+ AML cell line KASUMI-1 and SKNO-1 compared to other AML cell lines (p<0.05 and n=3). Compared to normal CD34+ and myeloid (CD33+, CD15+ and CD14+) cells (n=3), TET1 was 10-fold and 16-fold higher expressed in AE+ patient samples (n= 7). Aberrant expression of TET1 in AE+ leukemic cells was associated with hypomethylation of its promoter and enrichment for H3K4me3 euchromatic marks at its promoter as determined by LC/MS and ChIP-qPCR respectively. Knockdown (KD) of TET1 mRNA using two short hairpin RNAs (shRNAs) in AE+ AML cell lines impaired their cell growth and clonogenicity by over 50% in vitro (n=3 and p<0.01). shRNA mediated depletion of TET1 did not impact the cell growth and clonogenicity of the TET1 negative cell line RAJI, ruling out off target effects of the shRNAs (n=3). In mice, KD of Tet1 in leukemic bone marrow cells expressing the truncated leukemogenic AML1-ETO9a (AE9a) fusion, dramatically inhibited cell growth (>60% compared to scrambled, n=3, p<0.01), clonogenicity (>50-70% reduction in primary CFCs, p<0.01, n=3) and importantly delayed onset of leukemia in vivo (median survival 35 days for scr vs 80 days for shRNA mice, n=4/arm, p<0.03). Tet1-knock-out c-kit+ hematopoietic stem and progenitor cells (HSPCs) transduced with AE9a showed reduced primary colony formation and impaired serial replanting capacity in vitro compared to AE9a transduced Tet1-wild-type HSPCs (>50% and >70%, respectively; p<0.001, n=3). Global analysis of 5hmC and 5mC levels using hMeDIP/MeDIP-seq performed on TET1 depleted KASUMI-1 cells revealed lower global 5hmC levels and increase in 5mC as compared to cells transduced with scrambled control (n=2). 3324 promoter regions lost 5hmC and gained 5mC upon TET1 depletion (-5kTSS, Fold enrichment cut off <2-fold, q-value<1e5). Recent studies have shown that PARP activity induces TET1 expression by regulating its promoter epigenetically. We could show that aberrant TET1 expression could be antagonized by the PARP inhibitor olaparib in AE+ leukemic cell lines. Furthermore, olaparib treatment decreased 5hmC levels and reduced cell growth and clonogenicity of human AE+ cell lines and of the murine AE9a+ leukemic cell line in vitro (n=3, p<0.01). In conclusion, our data indicates that aberrant TET1 expression contributes to the growth of AE+ AML by maintaining the 5-hydroxymethylome and that the PARP inhibitor olaparib can at least partially antagonize the oncogenic effect of TET in AML. Disclosures Mulaw: NuGEN: Honoraria. Buske:Celltrion, Inc.: Consultancy, Honoraria.