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Cerebrospinal fluid (CSF) is a clear fluid surrounding and nourishing the brain and spinal cord. Molecular profiling of the CSF is a common diagnostic approach for central nervous system (CNS) diseases, including infectious diseases, autoimmune disorders, brain hemorrhage and traumatic brain injury, CNS tumors, and Alzheimer’s disease1–10. Rodent models are critical for investigating CNS disease mechanisms and therapeutics, however, both collecting CSF and injecting materials into CSF in small animals are technically challenging and often result in high rates of postoperative mortality. Here, we present an easy-to-practice and cost-effective protocol with minimum instrument requirements to access the CSF in live rodents for collection and infusion purposes. By introducing a metal needle tool bent at a unique angle and length, we could steadily reach the CSF via the foramen magnum. Compared with prior methods, this protocol requires neither the operator to discern the changes in resistance from solid tissues while puncturing the needle, nor surgical opening of the skin and muscle covering the rodent neck. Using this method, we frequently obtain 5-15 μL of CSF from mice and 70-120 μL from rats to enable diverse downstream analyses including mass spectrometry. Due to the minimal invasiveness, this procedure allows iterative CSF collection from the same animal every few days – a major improvement over prior protocols that require extensive surgical operations. Moreover, we demonstrate that this method could be used for injecting desired solutions including dyes into mouse CSF with high success rates. Our method shortens the time required for CSF collection or injection to 3-5 minutes. Notably, we could reach near 100% postoperative recovery rates in both mice and rats even with repetitive collections. Together, we establish an efficient and minimally-invasive protocol for collecting CSF and inoculating reagents into the CSF in live rodents to enable various longitudinal studies at the forefronts of CNS investigation.

The characterization of cancer genomes has provided insight into somatically altered genes across tumors, transformed our understanding of cancer biology, and enabled tailoring of therapeutic strategies. However, the function of most cancer alleles remains mysterious, and many cancer features transcend their genomes. Consequently, tumor genomic characterization does not influence therapy for most patients. Approaches to understand the function and circuitry of cancer genes provide complementary approaches to elucidate both oncogene and non-oncogene dependencies. Emerging work indicates that the diversity of therapeutic targets engendered by non-oncogene dependencies is much larger than the list of recurrently mutated genes. Here we describe a framework for this expanded list of cancer targets, providing novel opportunities for clinical translation.

Ferroptosis—an iron-dependent, non-apoptotic cell death process—is involved in various degenerative diseases and represents a targetable susceptibility in certain cancers1. The ferroptosis-susceptible cell state can either pre-exist in cells that arise from certain lineages or be acquired during cell-state transitions2–5. However, precisely how susceptibility to ferroptosis is dynamically regulated remains poorly understood. Here we use genome-wide CRISPR–Cas9 suppressor screens to identify the oxidative organelles peroxisomes as critical contributors to ferroptosis sensitivity in human renal and ovarian carcinoma cells. Using lipidomic profiling we show that peroxisomes contribute to ferroptosis by synthesizing polyunsaturated ether phospholipids (PUFA-ePLs), which act as substrates for lipid peroxidation that, in turn, results in the induction of ferroptosis. Carcinoma cells that are initially sensitive to ferroptosis can switch to a ferroptosis-resistant state in vivo in mice, which is associated with extensive downregulation of PUFA-ePLs. We further find that the pro-ferroptotic role of PUFA-ePLs can be extended beyond neoplastic cells to other cell types, including neurons and cardiomyocytes. Together, our work reveals roles for the peroxisome–ether-phospholipid axis in driving susceptibility to and evasion from ferroptosis, highlights PUFA-ePL as a distinct functional lipid class that is dynamically regulated during cell-state transitions, and suggests multiple regulatory nodes for therapeutic interventions in diseases that involve ferroptosis. The cellular organelles peroxisomes contribute to the sensitivity of cells to ferroptosis by synthesizing polyunsaturated ether phospholipids, and changes in the abundances of these lipids are associated with altered sensitivity to ferroptosis during cell-state transitions.

Ferroptosis is an iron-dependent cell death modality driven by oxidative phospholipid damage. In contrast to apoptosis, which enables organisms to eliminate targeted cells purposefully at specific times, ferroptosis appears to be a vulnerability of cells that otherwise use high levels of polyunsaturated lipids to their advantage. Cells in this high polyunsaturated lipid state generally have safeguards that mitigate ferroptotic risk. Since its recognition, ferroptosis has been implicated in degenerative diseases in tissues including kidney and brain, and is a targetable vulnerability in multiple cancers—each likely characterized by the high polyunsaturated lipid state with insufficient or overwhelmed ferroptotic safeguards. In this Perspective, we present progress towards defining the essential roles and key mediators of lipid peroxidation and ferroptosis in disease contexts. Moreover, we discuss gaps in our understanding of ferroptosis, and list key challenges that have thus far limited the full potential of targeting ferroptosis for improving human health.

Glutathione peroxidase 4 (GPX4) utilizes glutathione (GSH) to detoxify lipid peroxidation and plays an essential role in inhibiting ferroptosis. As a selenoprotein, GPX4 protein synthesis is highly inefficient and energetically costly. How cells coordinate GPX4 synthesis with nutrient availability remains unclear. In this study, we perform integrated proteomic and functional analyses to reveal that SLC7A11-mediated cystine uptake promotes not only GSH synthesis, but also GPX4 protein synthesis. Mechanistically, we find that cyst(e)ine activates mechanistic/mammalian target of rapamycin complex 1 (mTORC1) and promotes GPX4 protein synthesis at least partly through the Rag-mTORC1-4EBP signaling axis. We show that pharmacologic inhibition of mTORC1 decreases GPX4 protein levels, sensitizes cancer cells to ferroptosis, and synergizes with ferroptosis inducers to suppress patient-derived xenograft tumor growth in vivo. Together, our results reveal a regulatory mechanism to coordinate GPX4 protein synthesis with cyst(e)ine availability and suggest using combinatorial therapy of mTORC1 inhibitors and ferroptosis inducers in cancer treatment., Glutathione peroxidase 4 (GPX4) inhibits ferroptosis, but protein synthesis is inefficient and costly. Here, the authors reveal that cystine uptake promotes GPX4 synthesis by activating mTORC1 and show that cancer cells are sensitized to ferroptosis by mTORC1 inhibition.

Scientific concern about veterinary antibiotics (VAs) residues in the aquatic environment has increased in recent years. However, little is known about the underlying molecular mechanism of antioxidative stress caused by VAs in fish. In this study, zebrafish larvae were exposed to two representatives of VAs, chlortetracycline (CTC) and oxytetracycline (OTC), for 48 h. The oxidative stress responses and possible molecular mechanism of action were investigated. The results showed that the activities of CAT, SOD and GPx were significantly inhibited and the contents of GSH and MDA increased after CTC exposure. Moreover, SOD and CAT activity were parallel to their mRNA and protein levels. Under OTC exposure, CAT and GST activity were inhibited, while GPx activity was induced, and MDA content decreased significantly. After treatment with CTC and OTC, glucose levels and Nrf2 mRNA and protein levels in zebrafish larvae were significantly downregulated. Further molecular docking and molecular dynamics simulations revealed that CTC and OTC are capable of docking into the binding pocket of zebrafish PI3K, an important molecule in the activation of Nrf2, and can form stable interactions through hydrogen bonds. The overall results indicated that CTC and OTC significantly induced oxidative stress responses in zebrafish larvae, and both CTC and OTC act as inhibitors of PI3K to inhibit the activation of the Nrf2/ARE signaling pathway, thus reducing the antioxidant capacity of fish.

Despite considerable efforts to identify cancer metabolic alterations that might unveil druggable vulnerabilities, systematic characterizations of metabolism as it relates to functional genomic features and associated dependencies remain uncommon. To further understand the metabolic diversity of cancer, we profiled 225 metabolites in 928 cell lines from more than 20 cancer types in the Cancer Cell Line Encyclopedia (CCLE) using liquid chromatography–mass spectrometry (LC-MS). This resource enables unbiased association analysis linking the cancer metabolome to genetic alterations, epigenetic features and gene dependencies. Additionally, by screening barcoded cell lines, we demonstrated that aberrant ASNS hypermethylation sensitizes subsets of gastric and hepatic cancers to asparaginase therapy. Finally, our analysis revealed distinct synthesis and secretion patterns of kynurenine, an immune-suppressive metabolite, in model cancer cell lines. Together, these findings and related methodology provide comprehensive resources that will help clarify the landscape of cancer metabolism. Systematic metabolite profiling across cancer cell lines uncovers patterns associated with genetic and epigenetic features and reveals dysregulated metabolic states that can be exploited for anticancer therapy

Clear-cell carcinomas (CCCs) are a histological group of highly aggressive malignancies commonly originating in the kidney and ovary. CCCs are distinguished by aberrant lipid and glycogen accumulation and are refractory to a broad range of anti-cancer therapies. Here we identify an intrinsic vulnerability to ferroptosis associated with the unique metabolic state in CCCs. This vulnerability transcends lineage and genetic landscape, and can be exploited by inhibiting glutathione peroxidase 4 (GPX4) with small-molecules. Using CRISPR screening and lipidomic profiling, we identify the hypoxia-inducible factor (HIF) pathway as a driver of this vulnerability. In renal CCCs, HIF-2α selectively enriches polyunsaturated lipids, the rate-limiting substrates for lipid peroxidation, by activating the expression of hypoxia-inducible, lipid droplet-associated protein (HILPDA). Our study suggests targeting GPX4 as a therapeutic opportunity in CCCs, and highlights that therapeutic approaches can be identified on the basis of cell states manifested by morphological and metabolic features in hard-to-treat cancers., Clear-cell carcinomas are aggressive tumours characterised by high accumulation of lipids and glycogen. Here, the authors report that these cancers have a common vulnerability to GPX4 inhibition-induced ferroptosis and using CRISPR screen and lipodomic profiling, they identify HIF-2α- HILPDA axis promotes ferroptosis via enrichment of PUFA lipids.

A residual height trajectory algorithm of complex surface plane envelope is proposed for NC grinding of complex surface. Firstly, based on the differential geometric relationship between the grinding wheel end plane and the workpiece surface, the properties of the plane enveloping surface are analyzed; secondly, the residual height based on the space vector is calculated; Secondly, the algorithm is proposed by using the tangent characteristics of the contour line of the equal residual height; Finally, the tool path of the ellipsoid convex surface is calculated, and the characteristics of the two different tool paths are compared and analyzed, and it is proved that the proposed method is effective The tool path has higher machining efficiency at the residual height.

Sodium p-perfluorous nonenoxybenzene sulfonate (OBS), a novel alternative to perfluorooctanesulfonate (PFOS), is widely used in industry as a surfactant, firefighting foam and photographic material. The occurrence of OBS in the aquatic environment has been recently reported, but little information is available on its accumulation and toxic effects in aquatic organisms. In this study, zebrafish larvae (3 d post-fertilization) were subjected to OBS (10, 100 μg/L) and PFOS (10 μg/L) for a period of 48 h, followed by a 24 h of depuration period. The bioconcentration and depuration kinetics, oxidative stress and possible molecular mechanisms of OBS and PFOS were investigated in zebrafish larvae. Our results showed that the uptake and depuration of both OBS and PFOS fitted well with a first-order kinetic model. The uptake rate constant of OBS was similar to that of PFOS, but the depuration rate constant was much higher than PFOS with a half-life of 69.7–85 h for OBS and 222.2 h for PFOS. The calculated BCFs of OBS and PFOS were 238.0–242.5 and 644.2, respectively. In our acute toxicity assay, the enhanced expression of Nrf2 protein accompanied by the upregulation of CAT and SOD protein expressions indicated OBS and PFOS induced oxidative stress in zebrafish larvae, and the Nrf2-ARE signaling pathway was involved in this process. Collectively, OBS has a lower bioconcentration potential than PFOS, but its toxic effect on oxidative stress was comparable to PFOS in zebrafish larvae.

Polyunsaturated phospholipids are essential for multiple cellular functions; however, their uncontrolled peroxidation leads to ferroptosis. Here we describe photochemical activation of membrane lipid peroxidation (PALP), which uses localized laser pulses to induce lipid peroxidation photochemically. While PALP bypasses enzymatic requirements for lipid peroxidation, the resulting BODIPY-C11-based signal is largely correlated with local polyunsaturated phospholipid concentration on membranes. This technique enables non-invasive reporting of lipid unsaturation levels and sensitivity to ferroptosis in live cells.

Ferroptosis is widely involved in degenerative diseases in various tissues including kidney, liver and brain, and is a targetable vulnerability in clear-cell carcinomas and therapy-resistant cancers. Accumulation of phospholipid hydroperoxides in cellular membranes is recognized as the hallmark and rate-limiting step of ferroptosis; however, the enzymes contributing to lipid peroxidation remain poorly characterized. Using genome-wide, CRISPR/Cas9-mediated suppressor screens, we identify cytochrome P450 oxidoreductase (POR) as a contributor to ferroptotic cell death in cancer cells exhibiting inherent and induced susceptibility to ferroptosis. By genetic depletion of POR in cancer cells, we reveal that POR contributes to ferroptosis across a wide range of lineages and cell-states, and in response to distinct mechanisms of ferroptosis induction. Using systematic lipidomic profiling, we further map POR’s activity to the lipid peroxidation step in ferroptosis. Hence, our work suggests POR as a key mediator of ferroptosis and a potential druggable target for developing anti-ferroptosis therapeutics.

Summary Ferroptosis is an emerging cancer suppression strategy. However, how to select cancer patients for treating with ferroptosis inducers remains challenging. Here, we develop photochemical activation of membrane lipid peroxidation (PALP), which uses targeted lasers to induce localized polyunsaturated fatty acyl (PUFA)-lipid peroxidation for reporting ferroptosis sensitivity in cells and tissues. PALP captured by BODIPY-C11 can be suppressed by lipophilic antioxidants and iron chelation, and is dependent on PUFA-lipid levels. Moreover, we develop PALPv2, for studying lipid peroxidation on selected membranes along the z axis in live cells using two-photon microscopes. Using PALPv1, we detect PUFA-lipids in multiple tissues, and validate a PUFA-phospholipid reduction during muscle aging as previously reported. Patterns of PALPv1 signals across multiple cancer cell types in vitro and in vivo are concordant with their ferroptosis susceptibility and PUFA-phospholipid levels. We envision that PALP will enable rapid stratification of ferroptosis sensitivity in cancer patients and facilitate PUFA-lipid research.

In this study, we outline a regulatory network that involves the p53 tumor suppressor family and the Wnt pathway acting together with the TGF-β pathway in mesendodermal differentiation of mouse and human embryonic stem cells. Knockout of all three members, p53, p63, and p73, shows that the p53 family is essential for mesendoderm specification during exit from pluripotency in embryos and in culture. Wnt3 and its receptor Fzd1 are direct p53 family target genes in this context, and induction of Wnt signaling by p53 is critical for activation of mesendodermal differentiation genes. Globally, Wnt3-activated Tcf3 and nodal-activated Smad2/3 transcription factors depend on each other for co-occupancy of target enhancers associated with key differentiation loci. Our results therefore highlight an unanticipated role for p53 family proteins in a regulatory network that integrates essential Wnt-Tcf and nodal-Smad inputs in a selective and interdependent way to drive mesendodermal differentiation of pluripotent cells.

Ferroptosis-an iron-dependent, non-apoptotic cell death process-is involved in various degenerative diseases and represents a targetable susceptibility in certain cancers

TGF-β receptors phosphorylate SMAD2 and SMAD3 transcription factors, which then form heterotrimeric complexes with SMAD4 and cooperate with context-specific transcription factors to activate target genes. Here we provide biochemical and structural evidence showing that binding of SMAD2 to DNA depends on the conformation of the E3 insert, a structural element unique to SMAD2 and previously thought to render SMAD2 unable to bind DNA. Based on this finding, we further delineate TGF-β signal transduction by defining distinct roles for SMAD2 and SMAD3 with the forkhead pioneer factor FOXH1 as a partner in the regulation of differentiation genes in mouse mesendoderm precursors. FOXH1 is prebound to target sites in these loci and recruits SMAD3 independently of TGF-β signals, whereas SMAD2 remains predominantly cytoplasmic in the basal state and set to bind SMAD4 and join SMAD3:FOXH1 at target promoters in response to Nodal TGF-β signals. The results support a model in which signal-independent binding of SMAD3 and FOXH1 prime mesendoderm differentiation gene promoters for activation, and signal-driven SMAD2:SMAD4 binds to promoters that are preloaded with SMAD3:FOXH1 to activate transcription.

Epithelial-to-mesenchymal transitions (EMTs) are phenotypic plasticity processes that confer migratory and invasive properties to epithelial cells during development, wound-healing, fibrosis and cancer1–4. EMTs are driven by SNAIL, ZEB and TWIST transcription factors5,6 together with microRNAs that balance this regulatory network7,8. Transforming growth factor β (TGF-β) is a potent inducer of developmental and fibrogenic EMTs4,9,10. Aberrant TGF-β signalling and EMT are implicated in the pathogenesis of renal fibrosis, alcoholic liver disease, non-alcoholic steatohepatitis, pulmonary fibrosis and cancer4,11. TGF-β depends on RAS and mitogen-activated protein kinase (MAPK) pathway inputs for the induction of EMTs12–19. Here we show how these signals coordinately trigger EMTs and integrate them with broader pathophysiological processes. We identify RAS-responsive element binding protein 1 (RREB1), a RAS transcriptional effector20,21, as a key partner of TGF-β-activated SMAD transcription factors in EMT. MAPK-activated RREB1 recruits TGF-β-activated SMAD factors to SNAIL. Context-dependent chromatin accessibility dictates the ability of RREB1 and SMAD to activate additional genes that determine the nature of the resulting EMT. In carcinoma cells, TGF-β–SMAD and RREB1 directly drive expression of SNAIL and fibrogenic factors stimulating myofibroblasts, promoting intratumoral fibrosis and supporting tumour growth. In mouse epiblast progenitors, Nodal–SMAD and RREB1 combine to induce expression of SNAIL and mesendoderm-differentiation genes that drive gastrulation. Thus, RREB1 provides a molecular link between RAS and TGF-β pathways for coordinated induction of developmental and fibrogenic EMTs. These insights increase our understanding of the regulation of epithelial plasticity and its pathophysiological consequences in development, fibrosis and cancer. RAS and TGF-β pathways regulate distinct modes of epithelial-to-mesenchymal transition via RAS-responsive element binding protein 1.

SUMMARYKidney cancers are characterized by extensive metabolic reprogramming and resistance to a broad range of anti-cancer therapies. By interrogating the Cancer Therapeutics Response Portal compound sensitivity dataset, we show that cells of clear-cell renal cell carcinoma (ccRCC) possess a lineage-specific vulnerability to ferroptosis that can be exploited by inhibiting glutathione peroxidase 4 (GPX4). Using genome-wide CRISPR screening and lipidomic profiling, we reveal that this vulnerability is driven by the HIF-2α–HILPDA pathway by inducing a polyunsaturated fatty acyl (PUFA)-lipid-enriched cell state that is dependent on GPX4 for survival and susceptible to ferroptosis. This cell state is developmentally primed by the HNF-1β–1-Acylglycerol-3-Phosphate O-Acyltransferase 3 (AGPAT3) axis in the renal lineage. In addition to PUFA metabolism, ferroptosis is facilitated by a phospholipid flippase TMEM30A involved in membrane topology. Our study uncovers an oncogenesis-associated vulnerability, delineates the underlying mechanisms and suggests targeting GPX4 to induce ferroptosis as a therapeutic opportunity in ccRCC.HIGHLIGHTSccRCC cells exhibit strong susceptibility to GPX4 inhibition-induced ferroptosisThe GPX4-dependent and ferroptosis-susceptible state in ccRCC is associated with PUFA-lipid abundanceThe HIF-2α–HILPDA axis promotes the selective deposition of PUFA-lipids and ferroptosis susceptibilityAGPAT3 selectively synthesizes PUFA-phospholipids and primes renal cells for ferroptosis

Metastatic seeding by disseminated cancer cells principally occurs in perivascular niches. Here, we show that mechanotransduction signaling triggered by the pericyte-like spreading of disseminated cancer cells on host tissue capillaries is critical for metastatic colonization. Disseminated cancer cells employ cell adhesion molecule L1 (L1CAM) to spread on capillaries and activate the mechanotransduction effectors Yes-associated protein (YAP) and myocardin-related transcription factor (MRTF). This L1CAM-mediated spreading is robust enough to displace resident pericytes, which also use L1CAM for perivascular spreading. L1CAM activates YAP by engaging β1 integrin and integrin linked kinase (ILK). L1CAM-YAP signaling enables the outgrowth of metastasis-initiating cells both immediately upon their infiltration of target organs and after they exit from a period of dormancy. Our results identify an important step in the initiation of metastatic colonization, define its molecular constituents, and provide an explanation for the widespread association of L1CAM with metastatic relapse in the clinic.

Smad transcription factors activated by TGF-β or by BMP receptors form trimeric complexes with Smad4 to target specific genes for cell fate regulation. The CAGAC motif has been considered as the main binding element for Smad2/3/4, whereas Smad1/5/8 have been thought to preferentially bind GC-rich elements. However, chromatin immunoprecipitation analysis in embryonic stem cells showed extensive binding of Smad2/3/4 to GC-rich cis-regulatory elements. Here, we present the structural basis for specific binding of Smad3 and Smad4 to GC-rich motifs in the goosecoid promoter, a nodal-regulated differentiation gene. The structures revealed a 5-bp consensus sequence GGC(GC)|(CG) as the binding site for both TGF-β and BMP-activated Smads and for Smad4. These 5GC motifs are highly represented as clusters in Smad-bound regions genome-wide. Our results provide a basis for understanding the functional adaptability of Smads in different cellular contexts, and their dependence on lineage-determining transcription factors to target specific genes in TGF-β and BMP pathways., Smad transcription factors are part of the TGF-β signal transduction pathways and are recruited to the genome by cell lineage-defining factors. Here, the authors identify specific Smad binding GC-rich motifs and provide structural information showing Smad3 and Smad4 bound to these motifs.

To meet their metabolic needs, starved cells first activate autophagy, but activation in parallel of the general amino acid control pathway increases amino acid uptake, leading to reactivation of mTOR and down-regulation of autophagy., Organisms have evolved elaborate mechanisms to adjust intracellular nutrient levels in response to fluctuating availability of exogenous nutrients. During starvation, cells can enhance amino acid uptake and synthesis through the general amino acid control (GAAC) pathway, whereas nonessential cellular contents are recycled by autophagy. How these two pathways are coordinated in response to starvation is currently unknown. Here we show that the GAAC pathway couples exogenous amino acid availability with autophagy. Starvation caused deactivation of mTOR, which then activated autophagy. In parallel, serum/glutamine starvation activated the GAAC pathway, which up-regulated amino acid transporters, leading to increased amino acid uptake. This elevated the intracellular amino acid level, which in turn reactivated mTOR and suppressed autophagy. Knockdown of activating transcription factor 4, the major transcription factor in the GAAC pathway, or of SLC7A5, a leucine transporter, caused impaired mTOR reactivation and much higher levels of autophagy. Thus, the GAAC pathway modulates autophagy by regulating amino acid uptake and mTOR reactivation during serum/glutamine starvation.

In the version of this Article originally published, the authors inadvertently included the term 'pericytic mimicry' in relation to ref. 54. This has now been corrected by inserting an additional reference at position 51 and amending the text in the Discussion relating to 'pericytic mimicry', ref. 54 and pericyte-like spreading. The original refs 51-70 have also been renumbered. Furthermore, Fig. 8l has been amended to remove the term 'pericyte mimicry' that the authors had included inadvertently during figure preparation. These corrections have been made in the online versions of the Article.

SummaryHow organ-specific metastatic traits arise in primary tumors remains unknown. Here, we show a role of the breast tumor stroma in selecting cancer cells that are primed for metastasis in bone. Cancer-associated fibroblasts (CAFs) in triple-negative (TN) breast tumors skew heterogeneous cancer cell populations toward a predominance of clones that thrive on the CAF-derived factors CXCL12 and IGF1. Limiting concentrations of these factors select for cancer cells with high Src activity, a known clinical predictor of bone relapse and an enhancer of PI3K-Akt pathway activation by CXCL12 and IGF1. Carcinoma clones selected in this manner are primed for metastasis in the CXCL12-rich microenvironment of the bone marrow. The evidence suggests that stromal signals resembling those of a distant organ select for cancer cells that are primed for metastasis in that organ, thus illuminating the evolution of metastatic traits in a primary tumor and its distant metastases.

Aberrant Wnt signaling can drive cancer development. In many cancer types, the genetic basis of Wnt pathway activation remains incompletely understood. Here, we report recurrent somatic mutations of the Drosophila melanogaster tumor suppressor-related gene FAT1 in glioblastoma (20.5%), colorectal cancer (7.7%), and head and neck cancer (6.7%). FAT1 encodes a cadherin-like protein, which we found is able to potently suppress cancer cell growth in vitro and in vivo by binding β-catenin and antagonizing its nuclear localization. Inactivation of FAT1 via mutation therefore promotes Wnt signaling and tumorigenesis and affects patient survival. Taken together, these data strongly point to FAT1 as a tumor suppressor gene driving loss of chromosome 4q35, a prevalent region of deletion in cancer. Loss of FAT1 function is a frequent event during oncogenesis. These findings address two outstanding issues in cancer biology: the basis of Wnt activation in non-colorectal tumors and the identity of a 4q35 tumor suppressor.

TGF-β signaling can be pro-tumorigenic or tumor suppressive. We investigated this duality in pancreatic ductal adenocarcinoma (PDA), which, with other gastrointestinal cancers, exhibits frequent inactivation of the TGF-β mediator Smad4. We show that TGF-β induces an epithelial-mesenchymal transition (EMT), generally considered a pro-tumorigenic event. However, in TGF-β-sensitive PDA cells, EMT becomes lethal by converting TGF-β-induced Sox4 from an enforcer of tumorigenesis into a promoter of apoptosis. This is the result of an EMT-linked remodeling of the cellular transcription factor landscape, including the repression of the gastrointestinal lineage-master regulator Klf5. Klf5 cooperates with Sox4 in oncogenesis and prevents Sox4-induced apoptosis. Smad4 is required for EMT but dispensable for Sox4 induction by TGF-β. TGF-β-induced Sox4 is thus geared to bolster progenitor identity, whereas simultaneous Smad4-dependent EMT strips Sox4 of an essential partner in oncogenesis. Our work demonstrates that TGF-β tumor suppression functions through an EMT-mediated disruption of a lineage-specific transcriptional network.

The newly emergent human coronavirus HKU1 (HCoV-HKU1) was first identified in Hong Kong in 2005. Infection by HCoV-HKU1 occurs worldwide and causes syndromes such as the common cold, bronchitis, and pneumonia. The CoV main protease (M pro ), which is a key enzyme in viral replication via the proteolytic processing of the replicase polyproteins, has been recognized as an attractive target for rational drug design. In this study, we report the structure of HCoV-HKU1 M pro in complex with a Michael acceptor, inhibitor N3. The structure of HCoV-HKU1 provides a high-quality model for group 2A CoVs, which are distinct from group 2B CoVs such as severe acute respiratory syndrome CoV. The structure, together with activity assays, supports the relative conservation at the P1 position that was discovered by sequencing the HCoV-HKU1 genome. Combined with structural data from other CoV M pro s, the HCoV-HKU1 M pro structure reported here provides insights into both substrate preference and the design of antivirals targeting CoVs.

Leptomeningeal metastasis represents a rare but fatal outcome of disseminated cancer. Although much has been learned through observational studies, retrospective analyses and case reports, understanding of the molecular mechanisms underlying this complication has lagged behind that of other metastatic sites. To this end, we have created interrogable mouse models of breast and lung cancer that separate the molecular characteristics required for cancer cell access to the leptomeningeal space from those characteristics needed for cancer cell survival within the CSF. These models are both histologically and transcriptomally distinct from parenchymal metastases. Transcriptomal profiling of these diverse models representing breast and lung cancers in both xenograft and syngeneic systems has identified a distinct set of genes or “signature” differentially expressed by cells competent to seed and grow within the leptomeninges. This signature provides evidence that circulating cancer cells exploit the innate immune system to bypass the blood-CSF-barrier and gain access to and survive within the spinal fluid. These gene products are detectable in CSF from patients with cytology- or MRI-proven leptomeningeal metastasis. Genetic or pharmacologic blockade of select genes within this signature inhibits seeding of the leptomeninges by circulating tumor cells and inhibits growth of cancer cells within this space. This work demonstrates that leptomeningeal metastases are the result of distinct alterations in gene expression apart from those characterizing parenchymal metastases. Further, these models provide evidence that diverse primary tumors employ a conserved mechanism to arrive and survive within the CSF. Finally, this conserved gene signature shows great promise as a therapeutic target for this morbid complication of cancer.

Metastasis frequently develops years after the removal of a primary tumor, from a minority of disseminated cancer cells that survived as latent entities through unknown mechanisms. We isolated latency competent cancer (LCC) cells from early stage human lung and breast carcinoma cell lines and defined the mechanisms that suppress outgrowth, support long-term survival, and maintain tumor-initiating potential in these cells during the latent metastasis stage. LCC cells show stem-cell-like characteristics and express SOX2 and SOX9 transcription factors, which are essential for their survival in host organs under immune surveillance and for metastatic outgrowth under permissive conditions. Through expression of the WNT inhibitor DKK1, LCC cells self-impose a slow-cycling state with broad downregulation of ULBP ligands for NK cells and evasion of NK-cell-mediated clearance. By expressing a Sox-dependent stem-like state and actively silencing WNT signaling, LCC cells can enter quiescence and evade innate immunity to remain latent for extended periods.

Drug resistance invariably limits the clinical efficacy of targeted therapy with kinase inhibitors against cancer. Here we show that targeted therapy with BRAF, ALK or EGFR kinase inhibitors induces a complex network of secreted signals in drug-stressed human and mouse melanoma and human lung adenocarcinoma cells. This therapy-induced secretome stimulates the outgrowth, dissemination and metastasis of drug-resistant cancer cell clones and supports the survival of drug-sensitive cancer cells, contributing to incomplete tumour regression. The tumour-promoting secretome of melanoma cells treated with the kinase inhibitor vemurafenib is driven by downregulation of the transcription factor FRA1. In situ transcriptome analysis of drug-resistant melanoma cells responding to the regressing tumour microenvironment revealed hyperactivation of several signalling pathways, most prominently the AKT pathway. Dual inhibition of RAF and the PI(3)K/AKT/mTOR intracellular signalling pathways blunted the outgrowth of the drug-resistant cell population in BRAF mutant human melanoma, suggesting this combination therapy as a strategy against tumour relapse. Thus, therapeutic inhibition of oncogenic drivers induces vast secretome changes in drug-sensitive cancer cells, paradoxically establishing a tumour microenvironment that supports the expansion of drug-resistant clones, but is susceptible to combination therapy.

We molecularly dissected leptomeningeal metastasis, or spread of cancer to the cerebrospinal fluid (CSF), which is a frequent and fatal condition mediated by unknown mechanisms. We selected lung and breast cancer cell lines for the ability to infiltrate and grow in CSF, a remarkably acellular, mitogen-poor metastasis microenvironment. Complement component 3 (C3) was upregulated in four leptomeningeal metastatic models and proved necessary for cancer growth within the leptomeningeal space. In human disease, cancer cells within the CSF produced C3 in correlation with clinical course. C3 expression in primary tumors was predictive of leptomeningeal relapse. Mechanistically, we found that cancer-cell-derived C3 activates the C3a receptor in the choroid plexus epithelium to disrupt the blood-CSF barrier. This effect allows plasma components, including amphiregulin, and other mitogens to enter the CSF and promote cancer cell growth. Pharmacologic interference with C3 signaling proved therapeutically beneficial in suppressing leptomeningeal metastasis in these preclinical models.

Leptomeningeal metastasis represents a rare but fatal outcome of disseminated cancer. Although much has been learned through observational studies, retrospective analyses and case reports, understanding of the molecular mechanisms underlying this complication has been hampered by lack of a mouse model. Therefore, our objective was to create an interrogable mouse model that separates the molecular characteristics required for cancer cell access to the leptomeningeal space from those characteristics needed for cancer cell survival within the CSF. To accomplish this, human and mouse cancer cell lines were subjected to multiple rounds of in vivo selection. First, the cells were selected for survival within the leptomeninges: Parental cell lines were directly injected into the CSF via the cisterna magna and tumor cell growth was monitored with bioluminescent imaging. Cancer cells were collected from the basilar meninges and expanded in culture. After three rounds of this selection, the cells were designated “LeptoR3”. Second, the cells were selected for characteristics allowing for cancer cells to access the leptomeningeal space. The triple-selected “LeptoR3” cells were disseminated hematogenously via intracardiac injection. Mice were monitored for development of leptomeningeal metastases with bioluminescent imaging. After development of leptomeningeal mestastasis, these cells were collected, designated “LeptoIC” and expanded in culture. Finally, the Lepto IC, Lepto R3 and parental cell lines were subjected to gene expression profiling by RNASeq. The transcriptomal profiles of these cell lines demonstrate that leptomeningeal metastases employ a distinct array of genes to gain access to the leptomeningeal space and to survive once there. These mouse models represent a powerful tool for the molecular dissection of leptomeningeal metastasis.