T cell acute lymphoblastic leukemia (T-ALL) is a hematological malignancy with dismal overall prognosis, exhibiting up to a 25% relapse rate, mainly due to the absence of non-cytotoxic targeted therapy options. Despite the fact that drugs targeting the function of key epigenetic factors have been approved in the context of hematopoietic disorders1 and the recent identification of mutations affecting chromatin modulators in a variety of leukemias2,3, “epigenetic” drugs are not currently used for TALL treatment. Recently, we described a tumor suppressor role of the polycomb repressive complex 2 (PRC2) in this tumor4. Here we sought out to delineate the role of histone 3 lysine 27 (H3K27) demethylases, JMJD3 and UTX. We show that JMJD3 is essential for initiation and maintenance of disease, as it controls important oncogenic gene targets through the modulation of H3K27 methylation. In contrast, UTX acts a tumor suppressor and frequently genetically inactivated in T-ALL. Moreover, we demonstrate that the small molecule inhibitor GSKJ45 affects T-ALL growth, by targeting JMJD3 activity. These findings show that two proteins with similar enzymatic function can play opposing roles in the context of the same disease and pave the way for the use of a new category of epigenetic inhibitors in hematopoietic malignancies.

SUMMARY While transcriptional regulation of stem cell pluripotency and differentiation has been extensively studied, only a small number of studies have addressed the roles for post-translational modifications in these processes. A key mechanism of post-translational modification is ubiquitination by the ubiquitin-proteasome system (UPS). Here we map, using shotgun proteomics, the ubiquitinated protein landscape during ES cell differentiation and induced pluripotency. Moreover, using UPS-targeted RNAi screens, we identify novel regulators of pluripotency and differentiation. We focus on two of these proteins, the deubiquitinating enzyme, Psmd14, and the E3 ligase, Fbxw7, and characterize their importance in ES cell pluripotency and cellular reprogramming. This is the first global characterization of the UPS as a key regulator of stem cell pluripotency, opening the way for future studies that focus on specific UPS enzymes or ubiquitinated substrates.

Although the majority of acute myeloid leukemia (AML) patients initially respond to chemotherapy, many patients subsequently relapse; the mechanistic basis for AML persistence following chemotherapy has not been delineated. Recurrent somatic mutations in DNA methyltransferase 3A (DNMT3A), most frequently at arginine 882 (DNMT3Amut), are observed in AML1–3 and in individuals with clonal hematopoiesis in the absence of leukemic transformation4,5. DNMT3Amut AML patients have an inferior outcome when treated with standard-dose daunorubicin-based induction chemotherapy6,7, suggesting that DNMT3Amut cells persist and drive relapse8. Here we show that Dnmt3amut induces hematopoietic stem cell (HSC) expansion, cooperates with Flt3ITD and Npm1c to induce AML in vivo, and promotes resistance to anthracycline chemotherapy. In AML patients, DNMT3AR882 mutations predict for minimal residual disease (MRD), underscoring their role in AML chemoresistance. DNMT3Amut cells show impaired nucleosome eviction and chromatin remodeling in response to anthracyclines, resulting from attenuated recruitment of histone chaperone SPT-16 following anthracycline exposure. This defect leads to an inability to sense and repair DNA torsional stress, which results in increased mutagenesis. Our studies identify a critical role for DNMT3AR882 mutations in driving AML chemoresistance, and highlight the importance of chromatin remodeling in response to cytotoxic chemotherapy.

Colorectal cancer (CRC) is a leading cause of death, yet facile preclinical models that mimic the natural stages of CRC progression are lacking. Through the orthotopic engraftment of colon organoids we describe a broadly usable immunocompetent CRC model that recapitulates the entire adenoma-adenocarcinoma-metastasis axis in vivo. The engraftment procedure takes less than 5 minutes, shows efficient tumor engraftment in 2/3 mice, and can be achieved using organoids derived from GEMMs, wild type organoids engineered ex vivo, or from patient-derived human CRC organoids. In this model, we describe the genotype and time-dependent progression of CRCs from adenocarcinoma (6 weeks), to local disseminated disease (11–12 weeks) and spontaneous metastasis (>20 weeks). Further, we use the system to show that loss of dysregulated Wnt signaling is critical for the progression of disseminated CRCs. Thus, our approach provides a fast and flexible means to produce tailored CRC mouse models for genetic studies and pre-clinical investigation.