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Transcriptional regulation by NR5A2 couples cell differentiation and inflammation in the pancreas

Tissue-specific differentiation and inflammatory programmes are thought to independently contribute to disease. The orphan nuclear receptor NR5A2 is a key regulator of pancreas differentiation and SNPs in or near the human gene are associated with risk of pancreatic cancer. In mice, Nr5a2 heterozygosity sensitizes the pancreas to damage, impairs regeneration, and cooperates with mutant KRas in tumor progression. Through global transcriptomic analysis, we uncover a basal pre-inflammatory state in the pancreas of Nr5a2 heterozygous mice that is reminiscent of pancreatitis-induced inflammation and is conserved in histologically normal human pancreata with reduced NR5A2 mRNA expression. In Nr5a2+/- mice, Nr5a2 undergoes a dramatic transcriptional switch relocating from tissue-specific to inflammatory loci thereby promoting AP-1-dependent gene transcription. Importantly, deletion of c-Jun in the pancreas of these mice rescues the pre-inflammatory phenotype and the defective regenerative response to damage. These findings provide compelling evidence that the same transcriptional networks supporting homeostasis in normal tissue can be subverted to foster inflammation upon genetic or environmental constraints.

cancer biology

Dark selection for JAK/STAT-inhibitor resistance in chronic myelomonocytic leukemia

Acquired therapy resistance to cancer treatment is a common and serious clinical problem. The classic U-shape model for the emergence of resistance supposes that: (1) treatment changes the selective pressure on the treatment-naive tumour; (2) this shifting pressure creates a proliferative or survival difference between sensitive cancer cells and either an existing or de novo mutant; (3) the resistant cells then out-compete the sensitive cells and - if further interventions (like drug holidays or new drugs or dosage changes) are not pursued - take over the tumour: returning it to a state dangerous to the patient. The emergence of ruxolitinib resistance in chronic myelomonocytic leukemia (CMML) seems to challenge the classic model: we see the global properties of resistance, but not the drastic change in clonal architecture expected with the selection bottleneck. To study this, we explore three population-level models as alternatives to the classic model of resistance. These three effective models are designed in such a way that they are distinguishable based on limited experimental data on the time-progression of resistance in CMML. We also propose a candidate reductive implementation of the proximal cause of resistance to ground these effective theories. With these reductive implementations in mind, we also explore the impact of oxygen diffusion and spatial structure more generally on the dynamics of CMML in the bone marrow concluding that, even small fluctuations in oxygen availability can seriously impact the efficacy of ruxolitinib. Finally, we look at the ability of spatially distributed cytokine signaling feedback loops to produce a relapse in symptoms similar to what we observe in the clinic.

cancer biology

Oncogenic addiction to high 26S proteasome levels

Proteasomes are large intracellular complexes responsible for the degradation of cellular proteins. The altered protein homeostasis of cancer cells results in increased dependency on proteasome function. There are several different proteasome complexes that may be assembled in cells, with the 20S catalytic core common to them all. 20S proteasomes can function in isolation, or as part of larger complexes (26S) with regulatory particles (RP) such as the 19S that is needed for the targeting and processing of ubiquitinated substrates. Proteasome inhibitors target the catalytic barrel (20S) and thus this inhibition does not allow the deconvolution of the distinct roles of 20S vs. 26S proteasomes in cancer progression. We examined the degree of dependency of cancer cells specifically to the level of the 26S proteasome complex. We found that oncogenic transformation of human and mouse immortalized cells with mutant Ras induced a strong increase in the translation of the 26S proteasome subunits, giving rise to high 26S complex levels. We show that depletion of a single subunit of the 19S RP was sufficient to significantly reduce the 26S proteasome level and lower the cellular 26S/20S ratio. We further demonstrate that the accumulated 26S proteasome was essential for the viability of the transformed cells. Moreover, the viability of 20 different cancer cell lines, but not normal human fibroblasts, was severely compromised upon specific 26S proteasome suppression regardless of their p53 status. Suppression of 26S activated the UPR and Caspase-3, which at least partially explains the cell-killing effect. Morphologically, suppression of the 26S proteasome resulted in cytoplasm shrinkage and nuclear deformation. Thus, the tumor cell-specific addiction to high 26S proteasome levels sets the stage for future strategies in cancer therapy.

cancer biology

Targeting the Untargetable: Predicting Pramlintide Resistance Using a Neural Network Based Cellular Automata

De novo resistance is a major issue for the use of targeted anticancer drugs in the clinic. By integrating experimental data we have created a hybrid neural network/agent-based model to simulate the evolution and spread of resistance to the drug Pramlintide in cutaneous squamous cell carcinoma. Our model can eventually be used to predict patient responses to the drug and thus enable clinicians to make decisions regarding personalized, precision treatment regimes for patients.

cancer biology

Therapeutically advantageous secondary targets of abemaciclib identified by multi-omics profiling of CDK4/6 inhibitors

FDA approval of multiple drugs differing in chemical structures but targeting the same protein raises the question whether such drugs have sufficiently similar mechanisms of action to be considered functionally equivalent. In this paper we compare three recently approved inhibitors of the cyclin-dependent kinases CDK4/6 - palbociclib, ribociclib, and abemaciclib - that are becoming important therapies for the treatment of hormone-receptor positive breast and potentially other cancers. We find that transcriptional and proteomic changes induced by the three drugs differ significantly and that abemaciclib has unique cellular activities including induction of cell death (even in pRb-deficient cells), arrest in the G2 phase of the cell cycle, and reduced drug adaptation. These activities appear to arise from inhibition of kinases other than CDK4/6 including CDK2/Cyclin A/E and CDK1/Cyclin B.\n\nSIGNIFICANCEThe target profiles of most drugs are established relatively early in their development and are not systematically revisited at the time of approval. Scattered reports suggest that palbociclib, ribociclib, and abemaciclib differ in pharmacokinetics, dosing, and adverse effects but the three drugs are generally regarded as similar. Our finding that the drugs differ substantially in mechanism of action - abemaciclib retains activities of the earlier-generation drug alvocidib - suggests the potential for different uses in the clinic: in particular, abemaciclib may show activity in patients progressing on palbociclib or ribociclib. More generally, our approach relying on data from five distinct phenotypic and biochemical assays strongly suggests that a multi-faceted approach is necessary to get a reliable picture the target spectrum of kinase inhibitors.

cancer biology

The MYC antagonist MNT autoregulates its expression and supports proliferation in MAX deficient cells

MNT is a transcription factor of the MXD family. MNT-MAX dimers down-regulate genes by binding to E-box sequences, which can also be bound by MYC-MAX to activate transcription. MNT has been described as a modulator of MYC activity but little is known about MNT regulation and whether MNT has MAX-independent functions. Using a MAX deficient cell line and siRNA-mediated silencing of MAX, we show that in the absence of MAX, the total MNT levels are elevated and that MNT localizes both in the cytoplasm and the nucleus. In contrast, MNT is predominantly nuclear when MAX is expressed. MNT is required for optimal cell proliferation even in the absence of MAX, being the first report of a MAX-independent function of MNT. Interestingly, MNT forms homodimers and autoregulates its expression by repressing its own promoter. The tight MNT regulation and its activity in absence of MAX suggest its importance on cell homeostasis.

cancer biology

APR-246 reactivates mutant p53 by targeting cysteines 124 and 277

The TP53 tumor suppressor gene is frequently inactivated in human tumors by missense mutations in the DNA binding domain. TP53 mutations lead to protein unfolding, decreased thermostability and loss of DNA binding and transcription factor function. Pharmacological targeting of mutant p53 to restore its tumor suppressor function is a promising strategy for cancer therapy. The mutant p53 reactivating compound APR-246 (PRIMA-1Met) has been successfully tested in a phase I/IIa clinical trial. APR-246 is converted to the reactive electrophile methylene quinuclidinone (MQ), which binds covalently to p53 core domain. We identified cysteine 277 as a prime binding target for MQ in p53. Cys277 is also essential for MQ-mediated thermostabilization of wild-type, R175H and R273H mutant p53, while both Cys124 and Cys277 are required for APR-246-mediated functional restoration of R175H mutant p53 in living tumor cells. These findings may open opportunities for rational design of novel mutant p53-targeting compounds.

cancer biology

Combined Androgen Administration and HDAC Inhibition in Experimental Cancer Cachexia

PurposeThe common colon-26 mouse (C-26) model of experimental cachexia mimics recent late stage clinical failures of anabolic anti-cachexia therapy, and does not respond to the anabolic selective androgen receptor modulator (SARM) GTx-024. Based on the demonstrated anti-cachectic efficacy of the histone deacetylase inhibitor (HDACi) AR-42 in this model, we hypothesized that combined SARM/AR-42 would provide improved anti-cachectic efficacy.\n\nDesignIn the C-26 model, we determined a reduced efficacious dose of AR-42 which was combined with anabolic SARM therapy and evaluated for anti-cachectic efficacy. The effects of treatment and tumor burden on anabolic and catabolic signaling occurring in skeletal muscle were characterized using muscle performance parameters and RNA-seq.\n\nResultsAnabolic anti-cachexia therapy with diverse androgens had no impact on cachectic outcomes in the C-26 model. A reduced dose of the HDACi AR-42 alone provided limited anti-cachectic benefits, but when combined with the SARM GTx-024, significantly improved bodyweight (p<0.0001), hind limb muscle mass (p<0.05), and voluntary grip strength (p<0.0001) versus tumor-bearing controls. Reduced-dose AR-42 treatment suppressed the IL-6/GP130/STAT3 signaling axis without significantly impacting circulating cytokine levels. GTx-024-mediated {beta}-catenin target gene regulation was apparent in cachectic mice only when combined with AR-42.\n\nConclusionsCachectic signaling in the C-26 model is comprised of catabolic signaling insensitive to anabolic GTx-024 therapy and a blockade of GTx-024-mediated anabolic signaling. AR-42 treatment mitigates catabolic gene activation and restores anabolic responsiveness to GTx-024. Combining GTx-024, a clinically established anabolic therapy, with a low dose of AR-42, a clinically evaluated HDACi, represents a promising approach to improve anabolic response in cachectic patient populations.

cancer biology

Imaging-Genomics Study Of Head-Neck Squamous Cell Carcinoma: Associations Between Radiomic Phenotypes And Genomic Mechanisms Via Integration Of TCGA And TCIA

PurposeRecent data suggest that imaging radiomics features for a tumor could predict important genomic biomarkers. Understanding the relationship between radiomic and genomic features is important for basic cancer research and future patient care. For Head and Neck Squamous Cell Carcinoma (HNSCC), we perform a comprehensive study to discover the imaging-genomics associations and explore the potential of predicting tumor genomic alternations using radiomic features.\n\nMethodsOur retrospective study integrates whole-genome multi-omics data from The Cancer Genome Atlas (TCGA) with matched computed tomography imaging data from The Cancer Imaging Archive (TCIA) for the same set of 126 HNSCC patients. Linear regression analysis and gene set enrichment analysis are used to identify statistically significant associations between radiomic imaging features and genomic features. Random forest classifier is used to predict two key HNSCC molecular biomarkers, the status of human papilloma virus (HPV) and disruptive TP53 mutation, based on radiomic features.\n\nResultsWide-spread and statistically significant associations are discovered between genomic features (including miRNA expressions, protein expressions, somatic mutations, and transcriptional activities, copy number variations, and promoter region DNA methylation changes of pathways) and radiomic features characterizing the size, shape, and texture of tumor. Prediction of HPV and TP53 mutation status using radiomic features achieves an area under the receiver operating characteristics curve (AUC) of 0.71 and 0.641, respectively.\n\nConclusionOur analysis suggests that radiomic features are associated with genomic characteristics in HNSCC and provides justification for continued development of radiomics as biomarkers for relevant genomic alterations in HNSCC.

cancer biology

Accurate Discrimination of 23 Major Cancer Types via Whole Genome Somatic Mutation Patterns

The two strongest factors predicting a human cancers clinical behaviour are the primary tumours anatomic organ of origin and its histopathology. However, roughly 3% of the time a cancer presents with metastatic disease and no primary can be determined even after a thorough radiological survey. A related dilemma arises when a radiologically defined mass is sampled by cytology yielding cancerous cells, but the cytologist cannot distinguish between a primary tumour and a metastasis from elsewhere.\n\nHere we use whole genome sequencing (WGS) data from the ICGC/TCGA PanCancer Analysis of Whole Genomes (PCAWG) project to develop a machine learning classifier able to accurately distinguish among 23 major cancer types using information derived from somatic mutations alone. This demonstrates the feasibility of automated cancer type discrimination based on next-generation sequencing of clinical samples. In addition, this work opens the possibility of determining the origin of tumours detected by the emerging technology of deep sequencing of circulating cell-free DNA in blood plasma.

cancer biology

Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer

Pancreatic neuroendocrine tumors (pNETs) are uncommon cancers arising from pancreatic islet cells. Analysis of gene mutation, copy number and RNA expression of 57 sporadic pNETs showed that pNET genomes are dominated by aneuploidy. Remarkably, ~25% of pNETs had genomes characterized by recurrent loss of heterozygosity (LoH) of the same 10 chromosomes, accompanied by bi-allelic MEN1 inactivation, and these cases had generally poor clinical outcome. Another ~25% of all pNETs had chromosome 11 LoH and bi-allelic MEN1 inactivation, lacking the recurrent LoH pattern - these had universally good clinical outcome. Some level of aneuploidy was common, and overall ~80% of pNETs had LoH of [&ge;]1 chromosome. This aneuploidy led to changes in RNA expression at the level of whole chromosomes and allowed pathogenic germline variants (e.g. ATM) to be expressed unopposed, inactivating downstream tumor suppressor pathways. Some pNETs appear to utilize VHL gene methylation or mutation to activate pseudo-hypoxia. Contrary to expectation neither tumor morphology within well-differentiated pNETs nor single gene mutation had significant associations with clinical outcome, nor did expression of RNAs reflecting the activity of immune, differentiation, proliferative or tumor suppressor pathways. MEN1 was the only statistically significant recurrently mutated driver gene in pNETs. Only one pNET had clearly oncogenic and actionable SNVs (in PTEN and FLCN) confirmed by corroborating RNA expression changes. The two distinct patterns of aneuploidy described here, associated with markedly poor and good clinical outcome respectively, define a novel oncogenic mechanism and the first route to genomic precision oncology for this tumor type.

cancer biology

Evolutionary dynamics and molecular features of intra-tumor heterogeneity

The systematic assessment of intra-tumor heterogeneity is still limited and often unfeasible. In silico investigations of large tumor cohorts can be used to decipher how multiple clones emerge and organize into complex architectures. Here, we addressed this challenge by integrating mathematical modeling of cancer evolution with algorithmic inference of clonal phylogenies in 2,600 human tumors from 15 tumor types. Through numerical simulations, we could discriminate between observable and hidden intra-tumor heterogeneity, the latter characterized by clones that are missed by DNA sequencing of human samples. To overcome this limitation in human tumors, we show that population frequencies of detectable clones can be used to estimate the extent of hidden heterogeneity. Overall, simulated and human clonal architectures were highly concordant and showed that high numbers of clones invariably emerge through branching lineages. Interestingly, high numbers of alterations were not necessarily associated with high intra-tumor heterogeneity. Indeed, tumors with alterations in proliferation-associated genes exhibited high numbers of clonal mutations, but few clones. Instead, mutations of chromatin remodeling genes characterized tumors with high numbers of subclonal alterations and multiple clones. Our results identify evolutionary and genetic determinants of tumor clonal architectures to guide functional investigations of intra-tumor heterogeneity.

cancer biology

Continuous high-resolution in vivo imaging reveals tumor-specific dissemination in an embryonic zebrafish xenograft model

Mechanisms mediating tumor metastasis are crucial for diagnostic and therapeutic targeting. Here, we take advantage of a transparent embryonic zebrafish xenograft model (eZXM) to visualize and track injected human leukemic and breast cancer cells in real time using selective plane illumination microscopy (SPIM) for up to 30 hours. Injected cells exhibited disease-specific patterns of intravascular distribution with leukemic cells moving faster than breast cancer cells. While breast cancer cells predominantly adhered to nearby regions, about 30% invaded the avascularized tissue, reminiscent of their metastatic phenotype. Survival of the injected tumor cells was partly inhibited by the cellular innate immune system of the recipient embryos and leukemic cell dissemination was effectively inhibited by pharmacological ROCK1 blockade. These observations, and the ability to image several embryos simultaneously, support the use of eZXM and SPIM imaging as a functional screening platform to identify compounds that restricts cancer cell spread and invasion.

cancer biology

Targeting stromal remodeling and cancer stem cell plasticity to overcome chemoresistance in triple negative breast cancer

The cellular and molecular basis of stromal cell recruitment, activation and crosstalk in carcinomas is poorly understood, limiting the development of targeted anti-stromal therapies. In mouse models of triple negative breast cancer (TNBC), Hh ligand produced by neoplastic cells reprogrammed cancer-associated fibroblast (CAF) gene expression, driving tumor growth and metastasis. Hh-activated CAFs upregulated expression of FGF5 and production of fibrillar collagen, leading to FGFR and FAK activation in adjacent neoplastic cells, which then acquired a stem-like, drug-resistant phenotype. Treatment with smoothened inhibitors (SMOi) reversed these phenotypes. Stromal treatment of TNBC patient-derived xenograft (PDX) models with SMOi downregulated the expression of cancer stem cell markers and sensitized tumors to docetaxel, leading to markedly improved survival and reduced metastatic burden. In the phase I clinical trial EDALINE, 3 of 12 patients with metastatic TNBC derived clinical benefit from combination therapy with the SMOi Sonidegib and docetaxel chemotherapy, with one patient experiencing a complete response. Markers of pathway activity correlated with response. These studies identify Hh signaling to CAFs as a novel mediator of cancer stem cell plasticity and an exciting new therapeutic target in TNBC.\n\nSIGNIFICANCECompared to other breast cancer subtypes, TNBCs are associated with significantly worse patient outcomes. Standard of care systemic treatment for patients with non-BRCA1/2 positive TNBC is cytotoxic chemotherapy. However, the failure of 70% of treated TNBCs to attain complete pathological response reflects the relative chemoresistance of these tumors. New therapeutic strategies are needed to improve patient survival and quality of life. Here, we provide new insights into the dynamic interactions between heterotypic cells within a tumor. Specifically, we establish the mechanisms by which CAFs define cancer cell phenotype and demonstrate that the bidirectional CAF-cancer cell crosstalk can be successfully targeted in mice and humans using anti-stromal therapy.

cancer biology

Deimination of arginine at the C-terminal domain favors RNA polymerase II pause release

HighlightsO_LIPeptidyl arginine deiminase 2 (PADI2) citrullinates arginine1810 (cit1810) present at carboxy-terminal domain of RNA polymerase II (RNAP2-CTD).\nC_LIO_LIPADI2 and R1810 of RNAP2-CTD regulate transcription and proliferation of breast cancer cells.\nC_LIO_LIAbsence of cit1810 at RNAP2-CTD leads to RNAP2 accumulation at proximal promoter regions.\nC_LIO_LICit1810 at RNAP2-CTD facilitate interaction with P-TFEb complex.\nC_LI\n\nSUMMARYThe post-translational modification of key residues at the carboxy-terminal domain of RNA polymerase II (RNAP2-CTD), coordinates transcription, splicing, and RNA processing by modulating its capacity to act as a landing platform for a variety of protein complexes. Here, we identify a new modification at the CTD, the deimination of arginine and its conversion to citrulline by peptidyl arginine deiminase 2 (PADI2), an enzyme that has been associated with several diseases including cancer. We show that among PADI family members, only PADI2 citrullinates R1810 (Cit1810) at repeat 31 of the CTD. Depletion of PADI2 or loss of R1810 result in accumulation of RNAP2 at transcription start sites, reduced gene expression and inhibition of cell proliferation. Cit1810 is needed for interaction with the P-TEFb (positive transcription elongation factor b) kinase complex and for its recruitment to chromatin. In this way, CTD-Cit1810 favors RNAP2 pause release and efficient transcription in breast cancer cells.

cancer biology

The Neutrophil-to-Lymphocyte Ratio as a Prognostic Indicator in Head and Neck Cancer: A Systematic Review and Meta-Analysis

BackgroundThe aim of this systematic review and meta-analysis was to investigate the relationship between the Neutrophil-to-Lymphocyte Ratio (NLR) and prognosis in HNC.\n\nMethodsStudies were identified from Pubmed, Embase, Scopus, and the Cochrane Library. A systematic review and meta-analysis were performed to generate the pooled hazard ratios (HR) for overall survival (OS), disease free survival (DFS), and progression free survival (PFS).\n\nResultsOur analysis combined the results of over 6770 patients in 26 cohorts (25 studies). The pooled data demonstrated that an elevated NLR significantly predicted poorer OS, DFS, and PFS. Heterogeneity was found for OS, PFS, and marginally for DFS. Subgroup analysis in OS demonstrated that elevated NLR remained an indicator of poor prognosis.\n\nConclusionsElevated pretreatment NLR is a prognostic marker for HNC. It represents a simple and easily obtained marker that could be used to stratify groups of high-risk patients that might benefit from adjuvant therapy.

cancer biology

Venous Thromboembolism Risk in Head and Neck Cancer: Significance of the Preoperative Platelet-to-Lymphocyte Ratio

Abstract (250 limit)O_ST_ABSObjectiveC_ST_ABSWe aimed to investigate the association between the preoperative platelet-to-lymphocyte ratio (PLR) and venous thromboembolism (VTE) in head and neck cancer (HNC) patients undergoing major surgery.\n\nStudy DesignRetrospective cohort study\n\nSettingAcademic tertiary hospital from 2011 to 2017\n\nSubjects and MethodsPatients with confirmed HNC undergoing major surgery were included in this study. The preoperative PLR was recorded for all patients. Known VTE risk factors, including age, sex, smoking, BMI, prior VTE, and anticoagulation were also recorded. Risk factors were screened in univariate analysis using Wilcoxons rank sum test and {chi}2 test (Bonferroni corrected). Significant covariates were subsequently included in a multivariate regression model. Bootstrap techniques were used to obtain credible confidence intervals (CI).\n\nResultsThere were 306 patients enrolled with 7 cases of VTE (6 DVTs and 1 PE). On univariate analysis, length of stay (p = 0.0026), length of surgery (p = 0.0029), and PLR (p = 0.0002) were founded to have significant associations with VTE. A Receiver Operator Characteristic (ROC) curve was constructed, that yielded an AUROC of 0.905 (95% CI: 0.82 - 0.98). Using an optimized cutoff, the multivariate model showed that length of surgery ({beta} 95% CI: 0.0001 - 0.0006; p = 0.0056), and PLR ({beta} 95% CI: 5.3256 - 5.3868; p < 0.0001) were significant independent predictors of VTE.\n\nConclusionThis exploratory pilot study has shown that PLR offers a potentially accurate risk stratification measure as an adjunct to current tools in VTE risk prediction, without additional cost to health systems.\n\nOral PresentationThis data was presented as an oral presentation at the Annual American Academy of Otolaryngology - Head and Neck Surgery (AAO-HNSF) Meeting, 13th September 2017

cancer biology

Programming of macrophages by apoptotic cancer cells inhibits cancer progression through exosomal PTEN and PPARγ ligands

Apoptotic cell clearance by phagocytes is essential in tissue homeostasis. We demonstrated that conditioned medium (CM) from macrophages exposed to apoptotic cancer cells inhibits epithelial-mesenchymal transition (EMT), migration, and invasion of cancer cells with the acquisition of cancer-stem-like traits. Apoptotic 344SQ (ApoSQ) cell-induced PPAR{gamma} activity in macrophages caused increased PTEN levels, secreted in exosomes. ApoSQ-exposed CM from PTEN knockdown cells failed to enhance PTEN in recipient 344SQ cells, restore cellular polarity, and exert anti-EMT and anti-invasive effects. The CM which deficient of PPAR{gamma} ligands could not reverse the suppression of PPAR{gamma} activity and PTEN and consequently failed to the prevent EMT process. Moreover, single injection of ApoSQ cells inhibited lung metastasis in syngeneic mice with enhanced PPAR{gamma}/PTEN signaling both in tumor-associated macrophages and tumor cells. PPAR{gamma} antagonist GW9662 reversed PTEN signaling and anti-metastatic effect. Thus, apoptotic cancer cell therapy may offer a new strategy for the prevention of metastasis.

cancer biology