The BCL2 family plays important roles in acute myeloid leukemia (AML). Venetoclax, a selective BCL2 inhibitor, has received FDA approval for the treatment of AML. However, drug resistance ensues after prolonged treatment, highlighting the need for a greater understanding of the underlying mechanisms. Using a genome-wide CRISPR/Cas9 screen in human AML, we identifi ed genes whose inactivation sensitizes AML blasts to venetoclax. Genes involved in mitochondrial organization and function were signifi cantly depleted throughout our screen, including the mitochondrial chaperonin CLPB. We demonstrated that CLPB is upregulated in human AML, it is further induced upon acquisition of venetoclax resistance, and its ablation sensitizes AML to venetoclax. Mechanistically, CLPB maintains the mitochondrial cristae structure via its interaction with the cristae-shaping protein OPA1, whereas its loss promotes apoptosis by inducing cristae remodeling and mitochondrial stress responses. Overall, our data suggest that targeting mitochondrial architecture may provide a promising approach to circumvent venetoclax resistance. SIGNIFICANCE: A genome-wide CRISPR/Cas9 screen reveals genes involved in mitochondrial biological processes participate in the acquisition of venetoclax resistance. Loss of the mitochondrial protein CLPB leads to structural and functional defects of mitochondria, hence sensitizing AML cells to apoptosis. Targeting CLPB synergizes with venetoclax and the venetoclax/azacitidine combination in AML in a p53-independent manner.

Highlights d A machine learning (ML) workflow is designed to predict drug response in cancer patients d Deep neural networks (DNNs) surpass current ML algorithms in drug response prediction d DNNs predict drug response and survival in various large clinical cohorts d DNNs capture intricate biological interactions linked to specific drug response pathways

and data mining frameworks for predicting drug response in cancer: An overview and a novel in silico screening process based on association rule mining.

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The NSD2 p.E1099K (EK) mutation is observed in 10% of acute lymphoblastic leukemia (ALL) samples with enrichment at relapse indicating a role in clonal evolution and drug resistance. To discover mechanisms that mediate clonal expansion, we engineered B-ALL cell lines (Reh, 697) to overexpress wildtype (WT) and EK NSD2, but observed no differences in proliferation, clonal growth, or chemosensitivity. To address whether NSD2 EK acts collaboratively with other pathways, we used shRNAs to knockdown expression of NSD2 in B-ALL cell lines heterozygous for NSD2 EK (RS4;11, RCH-ACV, SEM). Knockdown resulted in decreased proliferation in all lines, decreased clonal growth in RCH-ACV, and increased sensitivity to cytotoxic chemotherapeutic agents, although the pattern of drug sensitivity varied among cell lines implying that the oncogenic properties of NSD2 mutations are likely cell context specific and rely on cooperative pathways. Knockdown of both Type II and REIIBP EK isoforms had a greater impact than knockdown of Type II alone, suggesting that both SET containing EK isoforms contribute to phenotypic changes driving relapse. Furthermore, in vivo models using both cell lines and patient samples revealed dramatically enhanced proliferation of NSD2 EK compared to WT and reduced sensitivity to 6-mercaptopurine in the relapse sample relative to diagnosis. Finally, EK-mediated changes in chromatin state and transcriptional output differed dramatically among cell lines further supporting a cell context specific role of NSD2 EK. These results demonstrate a unique role of NSD2 EK in mediating clonal fitness through pleiotropic mechanisms dependent on the genetic and epigenetic landscape. IMPLICATIONSNSD2 p.E1099K mutation leads to drug resistance and a clonal advantage in childhood B-ALL.

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31Planar cell polarity (PCP) and neural tube defects (NTDs) are linked, with a subset of NTD 32 patients found to harbour mutations in PCP genes, but there is limited data on whether these 33 mutations disrupt PCP signaling in vivo. The core PCP gene Van Gogh (Vang), Vangl1/2 in 34 mammals, is the most specific for PCP. We thus addressed potential causality of NTD-35 associated Vangl1/2 mutations, from either mouse or human patients, in Drosophila allowing 36 intricate analysis of the PCP pathway. Introducing the respective mammalian mutations into 37 Drosophila Vang revealed defective phenotypic and functional behaviors, with changes to 38 Vang localization, post-translational modification, and mechanistic function, such as its 39 ability to interact with PCP effectors. Our findings provide mechanistic insight into how 40 different mammalian mutations contribute to developmental disorders and strengthen the 41 link between PCP and NTD. Importantly, analyses of the human mutations revealed that 42 each is a causative factor for the associated NTD.43 108 Wnt/Frizzled-PCP pathway. Besides the four-pass trans-membrane protein Vang (Vangl1 109 and Vangl2 in mammals, see above), which was -like all other core PCP factors -originally 110 discovered in Drosophila (Taylor et al., 1998), a.k.a. strabismus/stbm (Wolff and Rubin, 111 1998), they include the atypical cadherin Flamingo (Fmi; Celsr in mammals), the seven-pass 112 transmembrane protein Frizzled (Fz; Fzd in vertebrates with several family members), and 113 the cytoplasmic proteins Dishevelled (Dsh; Dvl in mammals), Diego (Dgo; Inversin/Diversin 114 in vertebrates), and Prickle (Pk). The pathway is synonymous with the asymmetric

Dysregulation of kinase signaling pathways favors tumor cell survival and therapy resistance in cancer. Here, we reveal a posttranslational regulation of kinase signaling and nuclear receptor activity via deubiquitination in T cell acute lymphoblastic leukemia (T-ALL). We observed that the ubiquitin-specific protease 11 (USP11) is highly expressed and associates with poor prognosis in T-ALL. USP11 ablation inhibits leukemia progression in vivo, sparing normal hematopoiesis. USP11 forms a complex with USP7 to deubiquitinate the oncogenic lymphocyte cell–specific protein-tyrosine kinase (LCK) and enhance its activity. Impairment of LCK activity leads to increased glucocorticoid receptor (GR) expression and glucocorticoids sensitivity. Genetic knockout of USP7 improved the antileukemic efficacy of glucocorticoids in vivo. The transcriptional activation of GR target genes is orchestrated by the deubiquitinase activity and mediated via an increase in enhancer-promoter interaction intensity. Our data unveil how dysregulated deubiquitination controls leukemia survival and drug resistance, suggesting previously unidentified therapeutic combinations toward targeting leukemia.