Publications
94 results found
Frampton AE, Krell J, Mato Prado M, et al., 2016, Prospective validation of microRNA signatures for detecting pancreatic malignant transformation in endoscopic-ultrasound guided fine-needle aspiration biopsies, Oncotarget, Vol: 7, ISSN: 1949-2553
Background: Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease. Novel biomarkers are required to aid treatment decisions and improve patient outcomes. MicroRNAs (miRNAs) are potentially ideal diagnostic biomarkers, as they are stable molecules, and tumour and tissue specific. Results: Logistic regression analysis revealed an endoscopic-ultrasound fine-needle aspiration (EUS-FNA) 2-miRNA classifier (miR-21 + miR-155) capable of distinguishing benign from malignant pancreatic lesions with a sensitivity of 81.5% and a specificity of 85.7% (AUC 0.930). Validation FNA cohorts confirmed both miRNAs were overexpressed in malignant disease, while circulating miRNAs performed poorly.Methods: Fifty-five patients with a suspicious pancreatic lesion on cross-sectional imaging were evaluated by EUS-FNA. At echo-endoscopy, the first part of the FNA was sent for cytological assessment and the second part was used for total RNA extraction. Candidate miRNAs were selected after careful review of the literature and expression was quantified by qRT-PCR. Validation was performed on an independent cohort of EUS-FNAs, as well as formalin-fixed paraffin embedded (FFPE) and plasma samples.Conclusions: We provide further evidence for using miRNAs as diagnostic biomarkers for pancreatic malignancy. We demonstrate the feasibility of using fresh EUS-FNAs to establish miRNA-based signatures unique to pancreatic malignant transformation and the potential to enhance risk stratification and selection for surgery.
Krell J, Stebbing J, Carissimi C, et al., 2016, TP53 regulates miRNA association with AGO2 to remodel the miRNA-mRNA interaction network, GENOME RESEARCH, Vol: 26, Pages: 331-341, ISSN: 1088-9051
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- Citations: 45
Pardo OE, Munro CE, Castellano L, et al., 2016, miR-515-5p controls cancer cell migration through MARK4 regulation, EMBO Reports, Vol: 17, Pages: 570-584, ISSN: 1469-221X
Here we show that miR-515-5p inhibits cancer cell migration and metastasis. RNA-seqanalyses of both estrogen receptor-positive and negative breast cancer cells overexpressingmiR-515-5p reveals down-regulation of NRAS, FZD4, CDC42BPA, PIK3C2Band MARK4 mRNAs. We demonstrate that miR-515-5p inhibits MARK4 directly 3’UTRinteraction and that MARK4 knockdown mimics the effect of miR-515-5p on breast andlung cancer cell migration. MARK4 over-expression rescues the inhibitory effects of miR-515-5p, suggesting miR-515-5p mediates this process through MARK4 down-regulation.Furthermore, miR-515-5p expression is reduced in metastases compared to primarytumours derived from both in vivo xenografts and samples from patients with breastcancer. Conversely, miR-515-5p overexpression prevents tumour cell dissemination ina mouse metastatic model. Moreover, high miR-515-5p and low MARK4 expressioncorrelate with increased breast and lung cancer patients’ survival, respectively. Takentogether, these data demonstrate the importance of miR-515-5p/MARK4 regulation incell migration and metastasis across two common cancers.
Jacob J, Favicchio R, Karimian N, et al., 2015, LMTK3 escapes tumour suppressor miRNAs via sequestration of DDX5., Cancer Letters, Vol: 372, Pages: 137-146, ISSN: 1872-7980
Lemur tyrosine kinase-3 (LMTK3) plays an important role in cancer progression and is associated with breast, lung, gastric and colorectal cancer. MicroRNAs (miRNAs) are small endogenous non-coding RNAs that typically repress target genes at post-transcriptional level and have an important role in tumorigenesis. By performing a miRNA expression profile, we identified a subset of miRNAs modulated by LMTK3. We show that LMTK3 induces miR-34a, miR-196-a2 and miR-182 levels interacting with DEAD-box RNA helicase p68 (DDX5). LMTK3 binds via DDX5 to the pri-miRNA of these three mature miRNAs, thereby sequestrating them from further processing. Ectopic expression of miR-34a and miR-182 in LMTK3-overexpressing cell lines (MCF7-LMTK3 and MDA-MB-231-LMTK3) inhibits breast cancer proliferation, invasion and migration. Interestingly, miR-34a and miR-182 directly bind to the 3'UTR of LMTK3 mRNA and consequently inhibit both its stability and translation, acting as tumour suppressor-like miRNAs. In aggregate, we show that LMTK3 is involved in miRNA biogenesis through modulation of the Microprocessor complex, inducing miRNAs that target LMTK3 itself.
Krell J, Stebbing J, Carissimi C, et al., 2015, TP53 regulates miRNA association with AGO2 to remodel the miRNA-mRNA interaction network., Genome Research, ISSN: 1549-5469
DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq we show that the DNA-damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs whose cellular abundance or differential association with AGO2 is regulated by TP53 are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.
Nguyen VTM, Barozzi I, Faronato M, et al., 2015, Differential epigenetic reprogramming in response to specific endocrine therapies promotes cholesterol biosynthesis and cellular invasion, Nature Communications, Vol: 6, Pages: 1-15, ISSN: 2041-1723
Endocrine therapies target the activation of the oestrogen receptor alpha (ERa) via distinctmechanisms, but it is not clear whether breast cancer cells can adapt to treatment usingdrug-specific mechanisms. Here we demonstrate that resistance emerges via drug-specificepigenetic reprogramming. Resistant cells display a spectrum of phenotypical changes withinvasive phenotypes evolving in lines resistant to the aromatase inhibitor (AI). Orthogonalgenomics analysis of reprogrammed regulatory regions identifies individual drug-inducedepigenetic states involving large topologically associating domains (TADs) and the activationof super-enhancers. AI-resistant cells activate endogenous cholesterol biosynthesis (CB)through stable epigenetic activation in vitro and in vivo. Mechanistically, CB sparks theconstitutive activation of oestrogen receptors alpha (ERa) in AI-resistant cells, partly via thebiosynthesis of 27-hydroxycholesterol. By targeting CB using statins, ERa binding is reducedand cell invasion is prevented. Epigenomic-led stratification can predict resistance to AI in asubset of ERa-positive patients.
Cathcart P, Lucchesi W, Ottaviani S, et al., 2015, Noncoding RNAs and the control of signalling via nuclear receptor regulation in health and disease, BEST PRACTICE & RESEARCH CLINICAL ENDOCRINOLOGY & METABOLISM, Vol: 29, Pages: 529-543, ISSN: 1521-690X
Frampton AE, Krell J, Gall TMH, et al., 2015, miR-15b and miR-17 Are Tumor-derived Plasma MicroRNAs Dysregulated in Colorectal Neoplasia, Annals of Surgery, Vol: 262, Pages: e61-e61, ISSN: 0003-4932
Frampton AE, Krell J, Jamieson NB, et al., 2015, microRNAs with prognostic significance in pancreatic ductal adenocarcinoma: A meta-analysis, European Journal of Cancer, Vol: 51, Pages: 1389-1404, ISSN: 1879-0852
BackgroundReports have described the prognostic relevance of microRNAs (miRNAs) in patients treated for pancreatic ductal adenocarcinoma (PDAC). However, many of these include small numbers of patients. To increase statistical power and improve translation, we performed a systematic review and meta-analysis to determine a pooled conclusion. We examined the impact of miRNAs on overall survival (OS) and disease-free survival (DFS) in PDAC.MethodsEligible studies were identified and quality assessed using multiple search strategies (last search December 2014). Data were collected from studies correlating clinical outcomes with dysregulated tumoural or blood miRNAs. Studies were pooled, and combined hazard ratios (HRs) with 95% confidence intervals (CIs) were used to estimate strength of the associations.ResultsTwenty studies involving 1525 patients treated for PDAC were included. After correcting for publication bias, OS was significantly shortened in patients with high tumoural miR-21 (adjusted HR = 2.48; 1.96–3.14). This result persisted when only studies adjusting for adjuvant chemotherapy were combined (adjusted HR = 2.72; 1.91–3.89). High miR-21 also predicted reduced DFS (adjusted HR = 3.08; 1.78–5.33). Similarly, we found significant adjusted HRs for poor OS for high miR-155, high miR-203, and low miR-34a; and unadjusted HRs for high miR-222 and high miR-10b. The small number of studies, limited number of miRNAs and paucity of multivariate analyses are the limitations of our study.ConclusionsThis is the first rigorous pooled analysis assessing miRNAs as prognostic biomarkers in PDAC. Tumoural miR-21 overexpression emerged as an important predictor of poor prognosis after PDAC resection independent of other clinicopathologic factors, including adjuvant chemotherapy use.
Roca-Alonso L, Castellano L, Mills A, et al., 2015, Myocardial MiR-30 downregulation triggered by doxorubicin drives alterations in beta-adrenergic signaling and enhances apoptosis, Cell Death & Disease, Vol: 6, ISSN: 2041-4889
The use of anthracyclines such as doxorubicin (DOX) has improved outcome in cancer patients, yet associated risks ofcardiomyopathy have limited their clinical application. DOX-associated cardiotoxicity is frequently irreversible and typicallyprogresses to heart failure (HF) but our understanding of molecular mechanisms underlying this and essential for development ofcardioprotective strategies remains largely obscure. As microRNAs (miRNAs) have been shown to play potent regulatory roles inboth cardiovascular disease and cancer, we investigated miRNA changes in DOX-induced HF and the alteration of cellularprocesses downstream. Myocardial miRNA profiling was performed after DOX-induced injury, either via acute application toisolated cardiomyocytes or via chronic exposure in vivo, and compared with miRNA profiles from remodeled hearts followingmyocardial infarction. The miR-30 family was downregulated in all three models. We describe here that miR-30 act regulating theβ-adrenergic pathway, where preferential β1- and β2-adrenoceptor (β1AR and β2AR) direct inhibition is combined with Giα-2targeting for fine-tuning. Importantly, we show that miR-30 also target the pro-apoptotic gene BNIP3L/NIX. In aggregate, wedemonstrate that high miR-30 levels are protective against DOX toxicity and correlate this in turn with lower reactive oxygenspecies generation. In addition, we identify GATA-6 as a mediator of DOX-associated reductions in miR-30 expression. Inconclusion, we describe that DOX causes acute and sustained miR-30 downregulation in cardiomyocytes via GATA-6. miR-30overexpression protects cardiac cells from DOX-induced apoptosis, and its maintenance represents a potential cardioprotectiveand anti-tumorigenic strategy for anthracyclines.
Miller HC, Kidd M, Castellano L, et al., 2015, Molecular genetic findings in small bowel neuroendocrine neoplasms: a review of the literature, INTERNATIONAL JOURNAL OF ENDOCRINE ONCOLOGY, Vol: 2, Pages: 143-150, ISSN: 2045-0869
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- Citations: 1
Lombardo Y, de Giorgio A, Coombes CR, et al., 2015, Mammosphere Formation Assay from Human Breast Cancer Tissues and Cell Lines, JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, ISSN: 1940-087X
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- Citations: 67
Krell J, Stebbing J, Frampton AE, et al., 2015, The role of TP53 in miRNA loading onto AGO2 and in remodelling the miRNA-mRNA interaction network, LANCET, Vol: 385, Pages: 15-15, ISSN: 0140-6736
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- Citations: 3
Frampton AE, Castellano L, Colombo T, et al., 2015, Integrated molecular analysis to investigate the role of microRNAs in pancreatic tumour growth and progression, LANCET, Vol: 385, Pages: 37-37, ISSN: 0140-6736
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- Citations: 8
Castellano L, Rizzi E, Krell J, et al., 2015, The germline of the malaria mosquito produces abundant miRNAs, endo-siRNAs, piRNAs and 29-nt small RNAs, Bmc Genomics, Vol: 16
Britton D, Zen Y, Selzer S, et al., 2014, Quantification of pancreatic cancer proteome & phosphorylome: Indicates molecular events likely contributing to cancer & activation status of drug targets, 105th Annual Meeting of the American-Association-for-Cancer-Research (AACR), Publisher: AMER ASSOC CANCER RESEARCH, ISSN: 0008-5472
Ottaviani S, de Giorgio A, Harding V, et al., 2014, Noncoding RNAs and the control of hormonal signaling via nuclear receptor regulation, JOURNAL OF MOLECULAR ENDOCRINOLOGY, Vol: 53, Pages: R61-R70, ISSN: 0952-5041
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- Citations: 8
Tan GC, Chan E, Molnar A, et al., 2014, 5 ' isomiR variation is of functional and evolutionary importance, Nucleic Acids Research, Vol: 42, Pages: 9424-9435, ISSN: 1362-4962
We have sequenced miRNA libraries from human embryonic,neural and foetal mesenchymal stem cells.We report that the majority of miRNA genes encodemature isomers that vary in size by one ormore bases at the 3 and/or 5 end of the miRNA.Northern blotting for individual miRNAs showed thatthe proportions of isomiRs expressed by a singlemiRNA gene often differ between cell and tissuetypes. IsomiRs were readily co-immunoprecipitatedwith Argonaute proteins in vivo and were active inluciferase assays, indicating that they are functional.Bioinformatics analysis predicts substantial differencesin targeting between miRNAs with minor 5differences and in support of this we report that a 5isomiR-9–1 gained the ability to inhibit the expressionof DNMT3B and NCAM2 but lost the ability toinhibit CDH1 in vitro. This result was confirmed bythe use of isomiR-specific sponges. Our analysis ofthe miRGator database indicates that a small percentageof human miRNA genes express isomiRs asthe dominant transcript in certain cell types and analysisof miRBase shows that 5 isomiRs have replacedcanonical miRNAs many times during evolution. Thisstrongly indicates that isomiRs are of functional importanceand have contributed to the evolution ofmiRNA genes.INT
Roca-Alonso L, Castellano L, Mills A, et al., 2014, Myocardial miR-30 down-regulation caused by doxorubicin alters the beta-adrenergic system and mitochondrial death pathways, CARDIOVASCULAR RESEARCH, Vol: 103, ISSN: 0008-6363
de Giorgio A, Castellano L, Krell J, et al., 2014, Crosstalk-induced loss of miR-126 promotes angiogenesis, ONCOGENE, Vol: 33, Pages: 3634-3635, ISSN: 0950-9232
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- Citations: 11
Krell J, Frampton AE, Mirnezami R, et al., 2014, Growth Arrest-Specific Transcript 5 Associated snoRNA Levels Are Related to p53 Expression and DNA Damage in Colorectal Cancer, PLOS One, Vol: 9, ISSN: 1932-6203
Background: The growth arrest-specific transcript 5 gene (GAS5) encodes a long noncoding RNA (lncRNA) and hosts anumber of small nucleolar RNAs (snoRNAs) that have recently been implicated in multiple cellular processes and cancer.Here, we investigate the relationship between DNA damage, p53, and the GAS5 snoRNAs to gain further insight into thepotential role of this locus in cell survival and oncogenesis both in vivo and in vitro.Methods: We used quantitative techniques to analyse the effect of DNA damage on GAS5 snoRNA expression and to assessthe relationship between p53 and the GAS5 snoRNAs in cancer cell lines and in normal, pre-malignant, and malignanthuman colorectal tissue and used biological techniques to suggest potential roles for these snoRNAs in the DNA damageresponse.Results: GAS5-derived snoRNA expression was induced by DNA damage in a p53-dependent manner in colorectal cancercell lines and their levels were not affected by DICER. Furthermore, p53 levels strongly correlated with GAS5-derived snoRNAexpression in colorectal tissue.Conclusions: In aggregate, these data suggest that the GAS5-derived snoRNAs are under control of p53 and that they havean important role in mediating the p53 response to DNA damage, which may not relate to their function in the ribosome.We suggest that these snoRNAs are not processed by DICER to form smaller snoRNA-derived RNAs with microRNA (miRNA)-like functions, but their precise role requires further evaluation. Furthermore, since GAS5 host snoRNAs are often used asendogenous controls in qPCR quantifications we show that their use as housekeeping genes in DNA damage experimentscan lead to inaccurate results.
Gall TMH, Jacob J, Frampton AE, et al., 2014, Reduced dissemination of circulating tumor cells with no-touch isolation surgical technique in patients with pancreatic cancer, JAMA Surgery, Vol: 149, Pages: 482-485, ISSN: 2168-6254
Roca-Alonso L, Castellano L, Mills A, et al., 2014, Myocardial miR-30 down-regulation triggered by doxorubicin drives alterations in the beta-adrenergic pathway and enhances apoptosis, EUROPEAN JOURNAL OF HEART FAILURE, Vol: 16, Pages: 115-115, ISSN: 1388-9842
Frampton AE, Giovannetti E, Jamieson NB, et al., 2014, A microRNA meta-signature for pancreatic ductal adenocarcinoma, EXPERT REVIEW OF MOLECULAR DIAGNOSTICS, Vol: 14, Pages: 267-271, ISSN: 1473-7159
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- Citations: 25
Britton D, Zen Y, Quaglia A, et al., 2014, Quantification of Pancreatic Cancer Proteome and Phosphorylome: Indicates Molecular Events Likely Contributing to Cancer and Activity of Drug Targets, PLOS One, Vol: 9, ISSN: 1932-6203
Objective: LC-MS/MS phospho-proteomics is an essential technology to help unravel the complex molecular events thatlead to and propagate cancer. We have developed a global phospho-proteomic workflow to determine activity of signalingpathways and drug targets in pancreatic cancer tissue for clinical application.Methods: Peptides resulting from tryptic digestion of proteins extracted from frozen tissue of pancreatic ductaladenocarcinoma and background pancreas (n = 12), were labelled with tandem mass tags (TMT 8-plex), separated by strongcation exchange chromatography, then were analysed by LC-MS/MS directly or first enriched for phosphopeptides usingIMAC and TiO2, prior to analysis. In-house, commercial and freeware bioinformatic platforms were used to identify relevantbiological events from the complex dataset.Results: Of 2,101 proteins identified, 152 demonstrated significant difference in abundance between tumor and non-tumortissue. They included proteins that are known to be up-regulated in pancreatic cancer (e.g. Mucin-1), but the majority werenew candidate markers such as HIPK1 & MLCK. Of the 6,543 unique phosphopeptides identified (6,284 uniquephosphorylation sites), 635 showed significant regulation, particularly those from proteins involved in cell migration (Rhoguanine nucleotide exchange factors & MRCKa) and formation of focal adhesions. Activator phosphorylation sites on FYN,AKT1, ERK2, HDAC1 and other drug targets were found to be highly modulated ($2 fold) in different cases highlightingtheir predictive power.Conclusion: Here we provided critical information enabling us to identify the common and unique molecular events likelycontributing to cancer in each case. Such information may be used to help predict more bespoke therapy suitable for anindividual case.
Frampton AE, Castellano L, Colombo T, et al., 2014, MicroRNAs Cooperatively Inhibit a Network of Tumor Suppressor Genes to Promote Pancreatic Tumor Growth and Progression, GASTROENTEROLOGY, Vol: 146, Pages: 268-+, ISSN: 0016-5085
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- Citations: 132
Maftouh M, Avan A, Funel N, et al., 2014, MIR-211 MODULATES GEMCITABINE ACTIVITY THROUGH DOWNREGULATION OF RIBONUCLEOTIDE REDUCTASE AND INHIBITS THE INVASIVE BEHAVIOR OF PANCREATIC CANCER CELLS, 15th International Symposium on Purine and Pyrimidine Metabolism in Man, Publisher: TAYLOR & FRANCIS INC, Pages: 384-393, ISSN: 1525-7770
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- Citations: 54
Gall TMH, Frampton AE, Krell J, et al., 2013, Cell-free DNA for the detection of pancreatic, liver and upper gastrointestinal cancers: has progress been made?, FUTURE ONCOLOGY, Vol: 9, Pages: 1861-1869, ISSN: 1479-6694
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- Citations: 5
Pinho FG, Frampton AE, Nunes J, et al., 2013, Downregulation of microRNA-515-5p by the Estrogen Receptor Modulates Sphingosine Kinase 1 and Breast Cancer Cell Proliferation, CANCER RESEARCH, Vol: 73, Pages: 5936-5948, ISSN: 0008-5472
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- Citations: 64
de Giorgio A, Krell J, Harding V, et al., 2013, Emerging Roles of Competing Endogenous RNAs in Cancer: Insights from the Regulation of PTEN, MOLECULAR AND CELLULAR BIOLOGY, Vol: 33, Pages: 3976-3982, ISSN: 0270-7306
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- Citations: 62
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