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5-fluorouracil (5-FU) is a successful and broadly used anti-cancer therapeutic. A major mechanism of action of 5-FU is thought to be through thymidylate synthase (TYMS) inhibition resulting in dTTP depletion and activation of the DNA damage response. This suggests that 5-FU should synergize with other DNA damaging agents. However, we found that combinations of 5-FU and oxaliplatin or irinotecan failed to display any evidence of synergy in clinical trials, and resulted in sub-additive killing in a panel of colorectal cancer (CRC) cell lines. In seeking to understand this antagonism, we unexpectedly found that an RNA damage response during ribosome biogenesis dominates the drug’s efficacy in tumor types for which 5-FU shows clinical benefit. 5-FU has an inherent bias for RNA incorporation, and blocking this greatly reduced drug-induced lethality, indicating that accumulation of damaged RNA is more deleterious than the lack of new RNA synthesis. Using 5-FU metabolites that specifically incorporate into either RNA or DNA revealed that CRC cell lines and patient-derived colorectal cancer organoids are inherently more sensitive to RNA damage. This difference held true in cell lines from other tissues in which 5-FU has shown clinical utility, whereas cell lines from tumor tissues that lack clinical 5-FU responsiveness typically showed greater sensitivity to the drug’s DNA damage effects. Analysis of changes in the phosphoproteome and ubiquitinome shows RNA damage triggers the selective ubiquitination of multiple ribosomal proteins leading to autophagy-dependent rRNA catabolism and proteasome-dependent degradation of ubiquitinated ribosome proteins. Further, RNA damage response to 5-FU is selectively enhanced by compounds that promote ribosome biogenesis, such as KDM2A inhibitors. These results demonstrate the presence of a strong RNA damage response linked to apoptotic cell death, with clear utility of combinatorially targeting this response in cancer therapy.

Tumour heterogeneity is thought to be a major barrier to successful cancer treatment due to the presence of drug resistant clonal lineages. However, identifying the characteristics of such lineages that underpin resistance to therapy has remained challenging. Here, we utilise clonal transcriptomics with WILD-seq;Cancer begins when a cell multiplies again and again to form a tumour. By the time that tumour measures a centimetre across, it can contain upwards of a hundred million cells. And even though they all came from the same ancestor, they are far from identical. The tumour's family tree has many branches, and each one responds differently to treatment. If some are susceptible to a drug the cells die, the tumour shrinks, and the therapy will appear to be successful. But, if even a small number of cancer cells survive, they will regrow, often more persistently, causing a relapse. Identifying resistant cells, their characteristics, and how to kill them has been challenging due to a lack of good animal models. One way to keep track of a cancer family tree is to insert so-called genetic barcodes into the ancestral cells. As the tumour grows, the cells will pass the barcodes to their descendants. Scientists do this by using viruses that naturally paste their genes into the cells they infect. Applying this technique to an animal model of cancer could reveal which genes allow some cells to survive, and how to overcome them. Wild, Cannell et al. developed a genetic barcoding system called WILD-seq and used it to track all the cells in a mouse tumour. The mice received the same drugs used to treat patients with breast cancer. By scanning the genetic barcodes using recently developed single cell sequencing technologies, Wild, Cannell et al. were able to identify and count each type of cancer cell and work out which genes they were using. This revealed which cells the standard treatment could not kill and exposed their genetic weaknesses. Wild, Cannell et al. used this information to target the cells with a drug currently used to treat leukaemia. The drug identified by this new genetic barcoding approach is already licensed for use in humans. Further investigation could reveal whether it might help to shrink breast tumours that do not respond to standard therapy. Similar experiments could uncover more information about how other types of tumour evolve too.

IntroductionVasculogenic mimicry (VM), the process of tumor cell trans-differentiation to endow endothelial-like characteristics supportingde novovessel formation, is associated with poor prognosis in several tumor types, including small cell lung cancer (SCLC). In genetically engineered mouse models (GEMMs) of SCLC, NOTCH and MYC co-operate to drive a neuroendocrine (NE) to non-NE phenotypic switch and co-operation between NE and non-NE cells is required for metastasis. Here, we define the phenotype of VM-competent cells and molecular mechanisms underpinning SCLC VM using circulating tumor cell-derived explant (CDX) models and GEMMs.MethodsWe analysed perfusion within VM vessels and their association with NE and non-NE phenotypes using multiplex immunohistochemistry in CDX and GEMMs. VM-proficient cell subpopulations inex vivocultures were molecularly profiled by RNA sequencing and mass spectrometry. We evaluated their 3D structure and defined collagen-integrin interactions.ResultsWe show that VM vessels are present in 23/25 CDX models and in 2 GEMMs. Perfused VM vessels support tumor growth and only Notch-active non-NE cells are VM-competentin vivoandex vivo, expressing pseudohypoxia, blood vessel development and extracellular matrix (ECM) organization signatures. On Matrigel, VM-primed non-NE cells re-model ECM into hollow tubules in an integrin β1-dependent process.ConclusionsWe identify VM as an exemplar of functional heterogeneity and plasticity in SCLC and these findings take significant steps towards understanding the molecular events that enable VM. These results support therapeutic co-targeting of both NE and non-NE cells to curtail SCLC progression and to improve SCLC patient outcomes in future.

SUMMARY RNA-binding proteins (RBPs) play critical roles in regulating gene expression by modulating splicing, RNA stability, and protein translation. Stimulus-induced alterations in RBP function contribute to global changes in gene expression, but identifying which RBPs are responsible for the observed changes remains an unmet need. Here, we present Transite, a computational approach that systematically infers RBPs influencing gene expression through changes in RNA stability and degradation. As a proof of principle, we apply Transite to RNA expression data from human patients with non-small-cell lung cancer whose tumors were sampled at diagnosis or after recurrence following treatment with platinum-based chemotherapy. Transite implicates known RBP regulators of the DNA damage response and identifies hnRNPC as a new modulator of chemotherapeutic resistance, which we subsequently validated experimentally. Transite serves as a framework for the identification of RBPs that drive cell-state transitions and adds additional value to the vast collection of publicly available gene expression datasets., In Brief Krismer et al. present a computational approach to identify RNA-binding proteins (RBPs) that modulate post-transcriptional control of gene expression using RNA expression data as inputs. By applying this approach to publicly available patient datasets, they identify and experimentally confirm that the RBP hnRNPC contributes to chemotherapy resistance in lung cancer., Graphical Abstract

Summary Accurate measurement of clonal genotypes, mutational processes, and replication states from individual tumor-cell genomes will facilitate improved understanding of tumor evolution. We have developed DLP+, a scalable single-cell whole-genome sequencing platform implemented using commodity instruments, image-based object recognition, and open source computational methods. Using DLP+, we have generated a resource of 51,926 single-cell genomes and matched cell images from diverse cell types including cell lines, xenografts, and diagnostic samples with limited material. From this resource we have defined variation in mitotic mis-segregation rates across tissue types and genotypes. Analysis of matched genomic and image measurements revealed correlations between cellular morphology and genome ploidy states. Aggregation of cells sharing copy number profiles allowed for calculation of single-nucleotide resolution clonal genotypes and inference of clonal phylogenies and avoided the limitations of bulk deconvolution. Finally, joint analysis over the above features defined clone-specific chromosomal aneuploidy in polyclonal populations., Graphical Abstract, Highlights • Scaled method and resource of > 50K single-cell whole genomes from diverse cell types • Clonal merging can resolve clone specific mutations to single-nucleotide level • Image analysis of single cells permits correlation of morphology and genome features • Clonal replication states and rare aneuploidy patterns of single cells measured, A high-throughput method for amplication-free single-cell whole-genome sequencing can be scaled up to analyze tens of thousands of cells from different tissues and clinical sample types and identifies replication states, aneuploidies, and subclonal mutations.

Summary Expression of the Myc oncoprotein is downregulated in response to stress signals to allow cells to cease proliferation and escape apoptosis, but the mechanisms involved in this process are poorly understood. Cell cycle arrest in response to DNA damage requires downregulation of Myc via a p53-independent signaling pathway. Here we have used siRNA screening of the human kinome to identify MAPKAPK5 (MK5, PRAK) as a negative regulator of Myc expression. MK5 regulates translation of Myc, since it is required for expression of miR-34b and miR-34c that bind to the 3′UTR of MYC . MK5 activates miR-34b/c expression via phosphorylation of FoxO3a, thereby promoting nuclear localization of FoxO3a and enabling it to induce miR-34b/c expression and arrest proliferation. Expression of MK5 in turn is directly activated by Myc, forming a negative feedback loop. MK5 is downregulated in colon carcinomas, arguing that this feedback loop is disrupted during colorectal tumorigenesis.

In response to DNA damage, cells activate a complex, kinase-based signaling network that consist of two components--a rapid phosphorylation-driven signaling cascade that results in immediate inhibition of Cdk/cyclin complexes to arrest the cell cycle along with recruitment of repair machinery to damaged DNA, followed by a delayed transcriptional response that promotes cell cycle arrest through the induction of Cdk inhibitors, such as p21. In recent years a third layer of complexity has emerged that involves post-transcriptional control of mRNA stability, splicing, and translation as a critical part of the DNA damage response. Here, we describe recent work implicating DNA damage-dependent modification of RNA-binding proteins that are responsible for some of these mRNA effects, highlighting recent work on post-transcriptional regulation of the cell cycle checkpoint protein/apoptosis inducer Gadd45a by the checkpoint kinase MAPKAP Kinase-2.

Over the past 8 years several lines of compelling evidence have indicated that microRNAs are critical downstream effectors of classic oncogene/tumour suppressor networks. The archetypal examples of oncogene and tumour suppressor microRNAs are the miR-17-92 (oncomir 1) polycistron and miR-34 respectively. Whilst the involvement of these two opposing families of microRNAs in oncogenesis has been known for some time, the mRNA targets through which they exert their phenotypes are only just beginning to be uncovered. Moreover, several recent reports have demonstrated that the relevant physiological targets of certain individual microRNAs are actually fairly limited, with repression of just one or two major targets sufficient to explain the observed phenotype. In this review we will discuss the emerging role of microRNAs in tumourigenesis with a specific focus on miR-34c-dependent regulation of Myc.

UVB-induced lesions in mammalian cellular DNA can, through the process of mutagenesis, lead to carcinogenesis. However, eukaryotic cells have evolved complex mechanisms of genomic surveillance and DNA damage repair to counteract the effects of UVB radiation. We show that following UVB DNA damage, there is an overall inhibition of protein synthesis and translational reprogramming. This reprogramming allows selective synthesis of DDR proteins, such as ERCC1, ERCC5, DDB1, XPA, XPD, and OGG1 and relies on upstream ORFs in the 5′ untranslated region of these mRNAs. Experiments with DNA-PKcs-deficient cell lines and a specific DNA-PKcs inhibitor demonstrate that both the general repression of mRNA translation and the preferential translation of specific mRNAs depend on DNA-PKcs activity, and therefore our data establish a link between a key DNA damage signaling component and protein synthesis.

MicroRNAs (miRNAs) are noncoding RNAs that base pair imperfectly to homologous regions in target mRNAs and negatively influence the synthesis of the corresponding proteins. Repression is mediated by a number of mechanisms, one of which is the direct inhibition of protein synthesis. Surprisingly, previous studies have suggested that two mutually exclusive mechanisms exist, one acting at the initiation phase of protein synthesis and the other at a postinitiation event. Here, we resolve this apparent dichotomy by demonstrating that the promoter used to transcribe the mRNA influences the type of miRNA-mediated translational repression. Transcripts derived from the SV40 promoter that contain let-7 target sites in their 3′ UTRs are repressed at the initiation stage of translation, whereas essentially identical mRNAs derived from the TK promoter are repressed at a postinitiation step. We also show that there is a miR-34 target site within the 3′ UTR of c- myc mRNA and that promoter dependency is also true for this endogenous 3′ UTR. Overall, these data establish a link between the nuclear history of an mRNA and the mechanism of miRNA-mediated translational regulation in the cytoplasm.

We show that a common polymorphic variant in the ERCC5 5′ untranslated region (UTR) generates an upstream ORF (uORF) that affects both the background expression of this protein and its ability to be synthesized following exposure to agents that cause bulky adduct DNA damage. Individuals that harbor uORF1 have a marked resistance to platinum-based agents, illustrated by the significantly reduced progression-free survival of pediatric ependymoma patients treated with such compounds. Importantly, inhibition of DNA-PKcs restores sensitivity to platinum-based compounds by preventing uORF1-dependent ERCC5 expression. Our data support a model in which a heritable 5′ noncoding mRNA element influences individuals’ responses to platinum-based chemotherapy.

Nutrition during early mammalian development permanently influences health of the adult, including increasing the risk of type 2 diabetes and coronary heart disease. However, the molecular mechanisms underlying such programming are poorly defined. Here we demonstrate that programmed changes in miRNA expression link early-life nutrition to long-term health. Specifically, we show that miR-483-3p is upregulated in adipose tissue from low-birth-weight adult humans and prediabetic adult rats exposed to suboptimal nutrition in early life. We demonstrate that manipulation of miR-483-3p levels in vitro substantially modulates the capacity of adipocytes to differentiate and store lipids. We show that some of these effects are mediated by translational repression of growth/differentiation factor-3, a target of miR-483-3p. We propose that increased miR-483-3p expression in vivo, programmed by early-life nutrition, limits storage of lipids in adipose tissue, causing lipotoxicity and insulin resistance and thus increasing susceptibility to metabolic disease., This work was funded by the BBSRC (project grants BB/F-15364/1 and BB/F-14279/1). SEO is a British Heart Foundation Senior Fellow (FS/09/029/27902), MB is an MRC Senior Fellow and AEW is a BBSRC Professorial Fellow. KS and SEO are members of the MRC Centre for Obesity and Related Metabolic Diseases (MRC-CORD), which also provided a studentship for MW. KS is a member of the European Union COST Action BM0602.

DNA damage activates a signalling network that blocks cell-cycle progression, recruits DNA repair factors and/or triggers senescence or programmed cell death. Alterations in chromatin structure are implicated in the initiation and propagation of the DNA damage response. Here we further investigate the role of chromatin structure in the DNA damage response by monitoring ionizing-radiation-induced signalling and response events with a high-content multiplex RNA-mediated interference screen of chromatin-modifying and -interacting genes. We discover that an isoform of Brd4, a bromodomain and extra-terminal (BET) family member, functions as an endogenous inhibitor of DNA damage response signalling by recruiting the condensin II chromatin remodelling complex to acetylated histones through bromodomain interactions. Loss of this isoform results in relaxed chromatin structure, rapid cell-cycle checkpoint recovery and enhanced survival after irradiation, whereas functional gain of this isoform compacted chromatin, attenuated DNA damage response signalling and enhanced radiation-induced lethality. These data implicate Brd4, previously known for its role in transcriptional control, as an insulator of chromatin that can modulate the signalling response to DNA damage.

Over the past 8 years several lines of compelling evidence have indicated that microRNAs are critical downstream effectors of classic oncogene/tumour suppressor networks. The archetypal examples of oncogene and tumour suppressor microRNAs are the miR-17-92 (oncomir 1) polycistron and miR-34 respectively. Whilst the involvement of these two opposing families of microRNAs in oncogenesis has been known for some time, the mRNA targets through which they exert their phenotypes are only just beginning to be uncovered. Moreover, several recent reports have demonstrated that the relevant physiological targets of certain individual microRNAs are actually fairly limited, with repression of just one or two major targets sufficient to explain the observed phenotype. In this review we will discuss the emerging role of microRNAs in tumourigenesis with a specific focus on miR-34c-dependent regulation of Myc.

miRNAs (microRNAs) are short non-coding RNAs that regulate gene expression post-transcriptionally. They generally bind to the 3′-UTR (untranslated region) of their target mRNAs and repress protein production by destabilizing the mRNA and translational silencing. The exact mechanism of miRNA-mediated translational repression is yet to be fully determined, but recent data from our laboratory have shown that the stage of translation which is inhibited by miRNAs is dependent upon the promoter used for transcribing the target mRNA. This review focuses on understanding how miRNA repression is operating in light of these findings and the questions that still remain.

Depression of myocardial function during severe sepsis, which currently accounts for approx. 200,000 deaths/year in the United States (1), is characterized by a decrease in contractility and a poor response to fluid therapy (2). Since the md-1980s it has been recognized that the decreased cardiac function, which undoubtedly contributes to the overall pathophysiology of the septic state, does not arise from factors that are intrinsic to the myocardium, but instead results from the presence of circulating myocardial depressant factors (3, 4). Since much of the massive inflammation and multi-organ dysfunction in sepsis result from the secretion of various cytokines, it was long suspected that these proteins were also responsible, at least in part, for the observed myocardial dysfunction, although their identification, and the molecular basis for their effects on myocyte function were poorly understood. Pathan and colleagues recently showed that the cytokine IL-6 is a major factor responsible for modulating myocardial depression in children with meningococcal septicemia (5). In this issue of Critical Care Medicine, Pathan et al., use an in-vitro cardiac myocyte cell culture system to investigate the signaling pathways (and potential drug targets) that modulate and/or are modulated by IL-6 (new article). They report that the stress activated p38 mitogen activated protein kinase (p38 MAPK) pathway controls IL-6-induced myocardial depression and that this can be reversed using a specific chemical inhibitor of this kinase (SB203580). The authors go on to look at gene expression changes in a small cohort of pediatric patients with meningococcal sepsis and find a number of differences between septic patients and healthy controls. Amongst the genes that show differential expression are a number of upstream and downstream regulators of p38 MAPK signaling indicating that this pathway is deregulated in this cohort of patients. However, the mechanism by which such a large group of genes involved in p38 MAPK signaling could be deregulated remains to be determined. In addition to the work of Pathan et al., are a number of observations that link p38 MAPK and one of it’s downstream kinases, MK2 (MAPKAPK2) to the control of IL-6 biosynthesis (6). For example, during LPS-induced inflammation p38 MAPK activates MK2, which in turn controls IL-6 production by stabilizing the IL-6 messenger RNA (7). Therefore the p38 MAPK/MK2 pathway appears to lie both upstream and downstream of IL-6 in inflammation and sepsis. These observations are of obvious clinical relevance since p38 MAPK and its downstream effectors are under intense scrutiny as viable drug targets for the treatment of a number of diseases from colitis to cancer (6, 8, 9). The current study further highlights the potential utility of p38 MAPK inhibitors in the specific management of sepsis-associated cardiac dysfunction. p38 MAPK, however, activates a variety of downstream effectors that affect a wide variety of other cellular responses during sepsis in addition to cytokine secretion and myocardial contractility, including effects on apoptosis and neutrophil function (10, 11). In this regard, drugs that target the specific components of the p38 MAPK pathway that are central to its IL-6 effects, such as MK2 or its substrates, may also show promise in the clinical treatment of sepsis by preventing IL-6 production thus inhibiting myocardial depression, while having fewer effects on other p38 MAPK-dependent responses. In this regard emerging new drugs targeting IL-6 itself, such as IL-6 blocking monoclonal antibodies (12), may also show utility in this setting. Importantly the utility of these drugs will not be limited to myocardial dysfunction in sepsis since the p38 MAPK/MK2/IL6 pathway appears to be a major determinant of response to chemotherapy in certain cancers (13, 14). For example, p38 MAPK-dependent IL-6 secretion from thymic endothelial cells mediates drug resistance and relapse in a mouse model of Burkitt’s lymphoma (15). Therefore new drugs targeting the p38 MAPK-MK2-IL-6 signaling pathway may have a broader utility in cancer treatment as well as for the treatment of conditions where chronic inflammation is a major driving force of the diseased state, such as sepsis. If such drugs prove useful, it will be yet another example of how agents that were developed to limit the pathology of inflammation, such as cyclooxygenase inhibitors, can have a double life in clinical oncology. That indeed would be quite a lot of heart to salvage.

A fundamental limitation in the ability to devise new therapeutic strategies for manipulating the DNA damage response to treat cancer is the identification of synthetic lethal interactions that function in tumors in vivo. We recently identified the stress activated p38MAPK/MK2 pathway as a critical component of the DNA damage response network in tumor cells in vitro. When treated with genotoxic chemotherapy, MK2 is essential for the survival of tumor cell lines that lack functional p53, but is dispensable in p53-proficient cells. A critical function of MK2 in p53-deficient cells is the post-transcriptional regulation of gene expression, namely the stabilization of the mRNA of cell cycle regulators such as Gadd45α. Intriguingly, MK2 also plays an essential role in the biosynthesis of inflammatory cytokines, including IL-1, IL-6 and TNFα that are key signaling components in the tumor microenvironment. These MK2-regulated cytokines are likely to play important roles in promoting tumor development, as many cancers arise in setting of chronic inflammation, as well as in the creation of chemo-resistant niches where therapeutic resistance develops. The fact that p53 is commonly lost in tumors suggests that the therapeutic targeting of MK2 may be a useful strategy to enhance destruction of tumors by genotoxic chemotherapy. To explore the role of the p38MAPK/MK2 pathway in the integration of the DNA damage response and cytokine signaling during tumor development and chemotherapeutic response in vivo, we have generated a novel mouse model in which Cre-mediated recombination can be used to create MK2-proficient and deficient tumors within a single animal. This strategy allows direct comparison of MK2 synthetic lethality with genetic mutations that promote tumor development and with the tumor response to DNA damaging chemotherapy in a novel internally controlled setting in vivo. Furthermore, this approach potentially allows tumor autonomous signaling events after DNA damage to be distinguished from signaling events within the stromal microenvironment. Using this approach in a murine autochthonous model of non-small-cell lung cancer (NSCLC) we demonstrate that synthetic lethality between p53 and MK2 can successfully be exploited for enhanced chemo-sensitization of tumors to DNA damaging chemotherapy in vivo. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B66. Citation Format: Sandra Morandell, H.-Christian Reinhardt, Ian G. Cannell, Michael B. Yaffe. A novel cre-versible approach for identifying synthetic lethal interactions in the DNA damage response in vivo. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B66.