SummaryA functional genomics study revealed that the activity of acetyl-CoA synthetase 2 (ACSS2) contributes to cancer cell growth under low-oxygen and lipid-depleted conditions. Comparative metabolomics and lipidomics demonstrated that acetate is used as a nutritional source by cancer cells in an ACSS2-dependent manner, and supplied a significant fraction of the carbon within the fatty acid and phospholipid pools. ACSS2 expression is upregulated under metabolically stressed conditions and ACSS2 silencing reduced the growth of tumor xenografts. ACSS2 exhibits copy-number gain in human breast tumors, and ACSS2 expression correlates with disease progression. These results signify a critical role for acetate consumption in the production of lipid biomass within the harsh tumor microenvironment.

Synthetic lethality occurs when the inhibition of two genes is lethal while the inhibition of each single gene is not. It can be harnessed to selectively treat cancer by identifying inactive genes in a given cancer and targeting their synthetic lethal (SL) partners. We present a data-driven computational pipeline for the genome-wide identification of SL interactions in cancer by analyzing large volumes of cancer genomic data. First, we show that the approach successfully captures known SL partners of tumor suppressors and oncogenes. We then validate SL predictions obtained for the tumor suppressor VHL. Next, we construct a genome-wide network of SL interactions in cancer and demonstrate its value in predicting gene essentiality and clinical prognosis. Finally, we identify synthetic lethality arising from gene overactivation and use it to predict drug efficacy. These results form a computational basis for exploiting synthetic lethality to uncover cancer-specific susceptibilities.

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Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer-related mortality. Despite significant advances made in the treatment of other cancers, current chemotherapies offer little survival benefit in this disease. Pancreaticoduodenectomy offers patients the possibility of a cure, but most will die of recurrent or metastatic disease. Hence, preventing metastatic disease in these patients would be of significant benefit. Using principal component analysis (PCA), we identified a LOX/hypoxia signature associated with poor patient survival in resectable patients. We found that LOX expression is upregulated in metastatic tumors from Pdx1-Cre KrasG12D/+ Trp53R172H/+ (KPC) mice and that inhibition of LOX in these mice suppressed metastasis. Mechanistically, LOX inhibition suppressed both migration and invasion of KPC cells. LOX inhibition also synergized with gemcitabine to kill tumors and significantly prolonged tumor-free survival in KPC mice with early-stage tumors. This was associated with stromal alterations, including increased vasculature and decreased fibrillar collagen, and increased infiltration of macrophages and neutrophils into tumors. Therefore, LOX inhibition is able to reverse many of the features that make PDAC inherently refractory to conventional therapies and targeting LOX could improve outcome in surgically resectable disease.

BackgroundEnhanced macromolecule biosynthesis is integral to growth and proliferation of cancer cells. Lipid biosynthesis has been predicted to be an essential process in cancer cells. However, it is unclear which enzymes within this pathway offer the best selectivity for cancer cells and could be suitable therapeutic targets.ResultsUsing functional genomics, we identified stearoyl-CoA desaturase (SCD), an enzyme that controls synthesis of unsaturated fatty acids, as essential in breast and prostate cancer cells. SCD inhibition altered cellular lipid composition and impeded cell viability in the absence of exogenous lipids. SCD inhibition also altered cardiolipin composition, leading to the release of cytochrome C and induction of apoptosis. Furthermore, SCD was required for the generation of poly-unsaturated lipids in cancer cells grown in spheroid cultures, which resemble those found in tumour tissue. We also found that SCD mRNA and protein expression is elevated in human breast cancers and predicts poor survival in high-grade tumours. Finally, silencing of SCD in prostate orthografts efficiently blocked tumour growth and significantly increased animal survival.ConclusionsOur data implicate lipid desaturation as an essential process for cancer cell survival and suggest that targeting SCD could efficiently limit tumour expansion, especially under the metabolically compromised conditions of the tumour microenvironment.Electronic supplementary materialThe online version of this article (doi:10.1186/s40170-016-0146-8) contains supplementary material, which is available to authorized users.

While synthetic lethality (SL) holds promise in developing effective cancer therapies, SL candidates found via experimental screens often have limited translational value. Here we present a data-driven approach, ISLE (identification of clinically relevant synthetic lethality), that mines TCGA cohort to identify the most likely clinically relevant SL interactions (cSLi) from a given candidate set of lab-screened SLi. We first validate ISLE via a benchmark of large-scale drug response screens and by predicting drug efficacy in mouse xenograft models. We then experimentally test a select set of predicted cSLi via new screening experiments, validating their predicted context-specific sensitivity in hypoxic vs normoxic conditions and demonstrating cSLi’s utility in predicting synergistic drug combinations. We show that cSLi can successfully predict patients’ drug treatment response and provide patient stratification signatures. ISLE thus complements existing actionable mutation-based methods for precision cancer therapy, offering an opportunity to expand its scope to the whole genome.

The APC tumour suppressor gene is the most commonly mutated gene in colorectal cancer (CRC). Loss of Apc in intestinal stem cells (ISCs) drives aberrant Wnt signalling and adenoma formation in mice 1 . We previously showed that a reduction in WNT-ligand secretion increases the ability of Apc-mutant ISCs to colonise a crypt (fixation) and accelerate tumourigenesis 2 . Here, we investigate key mechanistic processes whereby Apc-mutant cells gain a clonal advantage over wild-type counterparts to achieve fixation. We find that Apc-mutant cells are enriched for transcripts encoding several secreted Wnt antagonists, with Notum being the most highly expressed. Indeed, conditioned medium from Apc-mutant cells suppresses the growth of wild-type organoids in a Notum-dependent manner. Furthermore, Notum-secreting mutant clones actively inhibit the proliferation of surrounding wild-type crypt cells and drive their differentiation, thereby outcompeting them from the niche. Importantly, genetic or pharmacological inhibition of Notum is sufficient to abrogate the expansion of Apcmutant cells and their ability to form intestinal adenomas. Taken together, we demonstrate Notum as a key mediator during the early stages of mutation fixation, which can be targeted to restore wild-type cell competition and thus, offer novel preventative strategies for high-risk patients. MainThe colonic epithelium displays one of the highest mutation rates of all tissues 3,4 , with lossof-function mutations in the APC tumour suppressor considered a key early event in colorectal cancer (CRC) initiation 5 . For a mutation to be maintained within a crypt, it needs to become "fixed", by mutant cells outcompeting wild-type intestinal stem cells (ISC) from the crypt 6,7 .Previous studies revealed that Apc loss (or Kras activation) confer a clonal advantage to ISCs 7,8, increasing their probability of fixation/winning within the crypt and, in the case of Apc mutation, driving adenoma formation. Even though APC-deficient clones have an increased probability of "winning", they can still be stochastically eliminated from the ISC pool i.e. lose.This suggests uncovering the molecular mechanisms by which APC-deficient cells outcompete wild-type cells could lead to novel chemo-preventative approaches.APC is a negative regulator of Wnt signalling that functions as an integral part of the destruction complex, which directs the phosphorylation and degradation of β-catenin 9 . Since Apc-mutant tumours exhibit constitutive Wnt-pathway activation, we first sought to identify genes differentially upregulated in Apc-mutant cells relative to the normal intestinal epithelium.For this, we performed transcriptomic analysis of tumours that develop in VillinCre ER ;Apc fl/+ (hereafter VilCre ER ;Apc fl/+ ) mice following the sporadic loss of the remaining copy of Apc 10 , akin to human CRC 11 . As expected, Wnt-target genes were highly upregulated in these Apcmutant tumours (Extended Data Fig. 1a). The most highly upregulated gene was Notum (Fig. 1a), which encodes a secreted WNT...

Ezrin plays an important role in pseudopodial extension in Fos-transformed Rat-1 fibroblasts, and maintains cell shape in normal Rat-1 cells. The increased expression, hyperphosphorylation and subcellular redistribution of ezrin upon fibroblast transformation coupled with its roles in cell shape and motility suggest a critical role for ezrin in oncogenic transformation.