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Chordoma is a primary bone cancer with no approved therapy1. The identification of therapeutic targets in this disease has been challenging due to the infrequent occurrence of clinically actionable somatic mutations in chordoma tumors2,3. Here we describe the discovery of therapeutically targetable chordoma dependencies via genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling. These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation. In other cancer types, transcriptional CDK inhibitors have been observed to downregulate highly expressed, enhancer-associated oncogenic transcription factors4,5. In chordoma, we find that T is associated with a 1.5-Mb region containing ‘super-enhancers’ and is the most highly expressed super-enhancer-associated transcription factor. Notably, transcriptional CDK inhibition leads to preferential and concentration-dependent downregulation of cellular brachyury protein levels in all models tested. In vivo, CDK7/12/13-inhibitor treatment substantially reduces tumor growth. Together, these data demonstrate small-molecule targeting of brachyury transcription factor addiction in chordoma, identify a mechanism of T gene regulation that underlies this therapeutic strategy, and provide a blueprint for applying systematic genetic and chemical screening approaches to discover vulnerabilities in genomically quiet cancers. A combination of genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling enables the discovery of therapeutically targetable tumor dependencies in rare tumors.

Small-molecule probes can illuminate biological processes and aid in the assessment of emerging therapeutic targets by perturbing biological systems in a manner distinct from other experimental approaches. Despite the tremendous promise of chemical tools for investigating biology and disease, small-molecule probes were unavailable for most targets and pathways as recently as a decade ago. In 2005, the U.S. National Institutes of Health launched the decade-long Molecular Libraries Program with the intent of innovating in and broadening access to small-molecule science. This Perspective describes how novel small-molecule probes identified through the program are enabling the exploration of biological pathways and therapeutic hypotheses not otherwise testable. These experiences illustrate how small-molecule probes can help bridge the chasm between biological research and the development of medicines, but also highlight the need to innovate the science of therapeutic discovery.

Plasticity of the cell state has been proposed to drive resistance to multiple classes of cancer therapies, thereby limiting their effectiveness. A high-mesenchymal cell state observed in human tumours and cancer cell lines has been associated with resistance to multiple treatment modalities across diverse cancer lineages, but the mechanistic underpinning for this state has remained incompletely understood. Here we molecularly characterize this therapy-resistant high-mesenchymal cell state in human cancer cell lines and organoids and show that it depends on a druggable lipid-peroxidase pathway that protects against ferroptosis, a non-apoptotic form of cell death induced by the build-up of toxic lipid peroxides. We show that this cell state is characterized by activity of enzymes that promote the synthesis of polyunsaturated lipids. These lipids are the substrates for lipid peroxidation by lipoxygenase enzymes. This lipid metabolism creates a dependency on pathways converging on the phospholipid glutathione peroxidase (GPX4), a selenocysteine-containing enzyme that dissipates lipid peroxides and thereby prevents the iron-mediated reactions of peroxides that induce ferroptotic cell death. Dependency on GPX4 was found to exist across diverse therapy-resistant states characterized by high expression of ZEB1, including epithelial-mesenchymal transition in epithelial-derived carcinomas, TGFβ-mediated therapy-resistance in melanoma, treatment-induced neuroendocrine transdifferentiation in prostate cancer, and sarcomas, which are fixed in a mesenchymal state owing to their cells of origin. We identify vulnerability to ferroptic cell death induced by inhibition of a lipid peroxidase pathway as a feature of therapy-resistant cancer cells across diverse mesenchymal cell-state contexts.

Changes in cellular gene expression in response to small-molecule or genetic perturbations have yielded signatures that can connect unknown mechanisms of action (MoA) to ones previously established. We hypothesized that differential basal gene expression could be correlated with patterns of small-molecule sensitivity across many cell lines to illuminate the actions of compounds whose MoA are unknown. To test this idea, we correlated the sensitivity patterns of 481 compounds with ~19,000 basal transcript levels across 823 different human cancer cell lines and identified selective outlier transcripts. This process yielded many novel mechanistic insights, including the identification of activation mechanisms, cellular transporters, and direct protein targets. We found that ML239, originally identified in a phenotypic screen for selective cytotoxicity in breast cancer stem-like cells, most likely acts through activation of fatty acid desaturase 2 (FADS2). These data and analytical tools are available to the research community through the Cancer Therapeutics Response Portal.

Identifying genetic alterations that prime a cancer cell to respond to a particular therapeutic agent can facilitate the development of precision cancer medicines. Cancer cell-line (CCL) profiling of small-molecule sensitivity has emerged as an unbiased method to assess the relationships between genetic or cellular features of CCLs and small-molecule response. Here, we developed annotated cluster multidimensional enrichment analysis to explore the associations between groups of small molecules and groups of CCLs in a new, quantitative sensitivity dataset. This analysis reveals insights into small-molecule mechanisms of action, and genomic features that associate with CCL response to small-molecule treatment. We are able to recapitulate known relationships between FDA-approved therapies and cancer dependencies and to uncover new relationships, including for KRAS-mutant cancers and neuroblastoma. To enable the cancer community to explore these data, and to generate novel hypotheses, we created an updated version of the Cancer Therapeutic Response Portal (CTRP v2). Significance: We present the largest CCL sensitivity dataset yet available, and an analysis method integrating information from multiple CCLs and multiple small molecules to identify CCL response predictors robustly. We updated the CTRP to enable the cancer research community to leverage these data and analyses. Cancer Discov; 5(11); 1210–23. ©2015 AACR. See related commentary by Gray and Mills, p. 1130. This article is highlighted in the In This Issue feature, p. 1111

While acute myeloid leukemia (AML) comprises many disparate genetic subtypes, one shared hallmark is the arrest of leukemic myeloblasts at an immature and self-renewing stage of development. Therapies that overcome differentiation arrest represent a powerful treatment strategy. We leveraged the observation that the majority of AML, despite their genetically heterogeneity, share in the expression of HoxA9, a gene normally downregulated during myeloid differentiation. Using a conditional HoxA9 model system, we performed a high-throughput phenotypic screen and defined compounds that overcame differentiation blockade. Target identification led to the unanticipated discovery that inhibition of the enzyme dihydroorotate dehydrogenase (DHODH) enables myeloid differentiation in human and mouse AML models. In vivo, DHODH inhibitors reduced leukemic cell burden, decreased levels of leukemia-initiating cells, and improved survival. These data demonstrate the role of DHODH as a metabolic regulator of differentiation and point to its inhibition as a strategy for overcoming differentiation blockade in AML.

A new web portal helps connect scientists and coordinate scientific efforts to address the challenges of the developing world.

Nat. Chem. Biol. 11, 536–541 (2015); published online 21 July 2015; corrected after print 16 September 2015. In the version of this Commentary initially published, there were several errors in the author list and author affiliations. Bryan Roth was incorrectly listed as “Brian Roth” and his correct affiliations are: The National Institute of Mental Health Psychoactive Active Drug Screening Program (NIMH PDSP), Department of Pharmacology, The University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

Methods for protein labeling have enabled significant advances in understanding protein function. However, currently available methods have disadvantages that limit their utility. Protein fusions, such as those with green fluorescent protein (GFP), provide a high level of specificity, but the large size of the tag can interfere with protein function. Peptide labels, including aptamers, are generally less disruptive, but the peptide tags now available either have lower specificity or rely on relatively unstable noncovalent interactions. In the February issue of Nature Methods, Chen et al. describe a method based on the specific, covalent labeling of peptide tags that combines the advantages of both approaches.

The gout space is heating up, but is there sufficient room in the market to accommodate multiple new therapeutics?

The U.K.-based Institute of Cancer Research and Cancer Research Technology Ltd. are collaborating with Janssen to target an undisclosed step in the unfolded protein response in multiple myeloma. Previous results from the U.K. team have suggested the kinase domain of IRE1 as a potential target in the pathway.

A Dana-Farber–led team has found that MYCN amplification provides a marker for sensitivity to BET bromodomain inhibition in neuroblastomas. GSK is using the marker as one criterion to select patients for a Phase I trial of its BET bromodomain inhibitor in cancer.

A Boston-based team and a group led by Roche's Genentech unit have each identified new kinase regulators of WNT signaling—YES1 and RIPK4, respectively—that provide two new, druggable targets. Each team will now look for the cancer subtypes most likely to respond to inhibitors of these kinases.

An Institute of Cancer Research team has developed a computational algorithm that hones in on cancer targets with the desired mix of biological validation and druggability. The approach could help prioritize targets.

A Memorial Sloan-Kettering team has conducted one of the first large-scale screens of a small molecule library in neuronal cells obtained by differentiating patient-derived iPS cells. Separately, a partnership led by Roche and the University of Oxford is aiming to establish a repository of iPS cells from 500 patients with diabetes or various neurological diseases.

A Dundee-UNC team has created a computational algorithm that mines medicinal chemistry literature to predict new ligands that bind specific combinations of GPCRs. Ex Scientia was spun out of Dundee to commercialize the technology.

A trio of papers has provided new hints on how best to use activators of PKM2, a target involved in cancer cell metabolism. Astex is using its findings to steer an early stage PKM2 program, whereas Agios is remaining mum on the direction of its PKM2 program.

UCSF and Mount Sinai researchers have used whole-organism screening in a Drosophila cancer model to identify and optimize a multitargeted kinase inhibitor with activity in a mouse model of medullary thyroid carcinoma. An undisclosed pharma is negotiating to license the IP.

Two groups have developed platforms that could improve the identification of cancer drug combinations. A UNC team is using chemical proteomics to rationally design kinase inhibitor combinations that block resistance pathways, whereas MIT researchers are screening for combinations that are synergistic when dosed sequentially.

Two groups have come to the conclusion that breakthroughs in translational medicine require collecting large-scale data on patients, including outcomes and making those data available to translational researchers. Sage Bionetworks launched a portal through which users can contribute their own health and genomic data for research and a report from the U.S. National Academy of Sciences is calling for the creation of a national infrastructure for accessing and analyzing open-source patient data.

A Brigham and Women's Hospital team has identified an enzyme that regulates white adipose plasticity, whereas a University of Cambridge team has identified a secreted protein that activates brown fat. Testing the potential of these new targets for boosting or activating calorie-burning brown fat will require developing lead therapeutic molecules.

Phenotypic screening for drug discovery is making a comeback, but not everybody is embracing it. Some pharmas, such as Novartis and GSK, are placing a bet on phenotypic screening, whereas others, such as Genentech, are staying focused on target-based screening.

Swedish researchers have used an in vitro screen to evaluate the target selectivity of a panel of small molecule PARP inhibitors. The findings could eventually lead to next-generation PARP inhibitors that have a better therapeutic index than inhibitors currently in the cancer clinic.

A U.S.–South Korean team has identified the molecular target of the antifibrotic and anti-inflammatory small molecule halofuginone. The findings could help guide the design of next-generation analogs with improved pharmacological profiles and help select specific indications to pursue.

Japanese researchers have developed a method for creating large libraries of N-methylated peptide macrocycles. PeptiDream Inc. has exclusively licensed the technology and set up collaborations with six pharmas.

NCI and University of Tokyo researchers have developed a fluorescent probe that can be sprayed onto tissue during surgery to detect small metastases. The researchers plan to validate the method in fresh surgical tissue from ovarian cancer patients in preparation for an IND.

As Laurie Glimcher was preparing to take over as dean of Weill Cornell, SciBX caught up with her to discuss research priorities for academic medical centers, the most effective models for promoting industry–academic partnerships and the potential for NYC to emerge as a biopharma hub.

Eli Lilly is rolling out its Open Innovation Drug Discovery platform to cast a wide net for finding innovative molecules from external investigators in the company's core disease focus areas. The pharma has also joined a public-private partnership being led by the Structural Genomics Consortium to identify IP-free molecules against epigenetic targets.

Harvard and the Shanghai Institute of Organic Chemistry have identified a small molecule called spautin-1 that blocks the prosurvival autophagy pathway in cancer cells. Based on the findings, Harvard, Roche and BioBay have partnered to develop spautin-1 derivatives.

A St. Jude team has used a disease subtype screening approach to identify 5-fluorouracil as a potential treatment for the brain cancer ependymoma, where no therapeutic has worked. The researchers plan to start a Phase I trial to confirm proof of principle for the subtype approach to drug finding.

Epizyme believes it has produced the first evidence for in vivo efficacy for a histone methyltransferase inhibitor. Although the biotech thinks its animal findings have implications for an entire class of new drugs, it will aim to begin human studies in a small but aggressive subset of acute leukemias.

The biotech and its academic collaborators designed what looked to be a promising small molecule inhibitor of the SKP2 ubiquitin ligase complex. But the company concluded it would be difficult to optimize the cancer compound and now is setting its sights on undisclosed targets outside the ubiquitin pathway.

A University of North Carolina team has documented a large jump in small molecule drug discovery in U.S. academia, with the number of dedicated centers more than doubling in the last six years. Key challenges include funding and establishing the value created for industry.

An international team looking to target subsets of squamous cell lung cancer has identified mutations in DDR2 that drive 3%–4% of cases. The researchers are aiming to start a Phase II trial with Bristol-Myers's Sprycel, a marketed kinase inhibitor that blocks DDR2.

Two U.S. academic groups have identified RAR-related orphan receptor inhibitors that block production of proinflammatory Th17 cells and decrease the severity of multiple sclerosis in mice. Independently, Merck and biotech partner Lycera are targeting one of these receptors for RA, psoriasis and other autoimmune diseases.