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.

SUMMARY The pathogenesis of idiopathic pulmonary fibrosis (IPF), an intractable interstitial lung disease, is unclear. Recessive mutations in some genes implicated in Hermansky-Pudlak syndrome (HPS) cause HPS-associated interstitial pneumonia (HPSIP), a clinical entity that is similar to IPF. We previously reported that HPS1−/−embryonic stem cell-derived 3D lung organoids showed fibrotic changes. Here, we show that the introduction of all HPS mutations associated with HPSIP promotes fibrotic changes in lung organoids, while the deletion of HPS8, which is not associated with HPSIP, does not. Genome-wide expression analysis revealed the upregulation of interleukin-11 (IL-11) in epithelial cells from HPS mutant fibrotic organoids. IL-11 was detected predominantly in type 2 alveolar epithelial cells in end-stage IPF, but was expressed more broadly in HPSIP. Finally, IL-11 induced fibrosis in WT organoids, while its deletion prevented fibrosis in HPS4−/− organoids, suggesting IL-11 as a therapeutic target. hPSC-derived 3D lung organoids are, therefore, a valuable resource to model fibrotic lung disease.

SUMMARY D-type cyclins form complexes with cyclin dependent kinases (CDK4/6), and promote cell cycle progression. Although cyclin D functions appear largely tissue specific, we demonstrate that cyclin D3 has unique functions in lymphocyte development and cannot be replaced by cyclin D2, which is also expressed during blood differentiation. We show that only combined deletion of p27Kip1 and Rb is sufficient to rescue the development of Ccnd3−/− thymocytes. Furthermore, we show that a small molecule targeting the kinase function of cyclin D3:CDK4/6 inhibits both cell cycle entry in human T cell acute lymphoblastic leukemia (T-ALL) and disease progression in animal models of T-ALL. These studies identify unique functions for cyclin D3:CDK4/6 complexes and suggest potential therapeutic protocols for this devastating blood tumor.