Now showing items 1-20 of 4197

    • Silencing microRNA-330-5p increases MMP1 expression and promotes an invasive phenotype in oesophageal adenocarcinoma

      Bibby, Becky A; Miranda, Cecelia S; Reynolds, John V; Cawthorne, Christopher J; Maher, Stephen G; Cancer Biology and Therapeutics Lab, School of Life Sciences, University of Hull, Hull (2019)
      BACKGROUND: Many patients diagnosed with oesophageal adenocarcinoma (OAC) present with advanced disease and approximately half present with metastatic disease. Patients with localised disease, who are managed with curative intent, frequently undergo neoadjuvant chemoradiotherapy. Unfortunately, ~?70% of patients have little or no response to chemoradiotherapy. We previously identified miR-330-5p as being the most significantly downregulated microRNA in the pre-treatment OAC tumours of non-responders to treatment, but that loss of miR-330-5p had a limited impact on sensitivity to chemotherapy and radiation in vitro. Here, we further examined the impact of miR-330-5p loss on OAC biology. METHODS: miR-330-5p was suppressed in OE33 OAC cells following stable transfection of a vector-driven anti-sense RNA. Whole transcriptome digital RNA-Seq was employed to identify miR-330-5p regulated genes, and qPCR was used for validation. Protein expression was assessed by protein array, Western blotting and zymography. Invasive potential was measured using a transwell assay system. Tumour xenograft growth profile studies were performed in immunocompromised CD1 mice. RESULTS: In OE33 cells, suppression of miR-330-5p significantly altered expression of 42 genes, and several secreted proteases. MMP1 gene expression and protein secretion was significantly enhanced with miR-330-5p suppression. This corresponded to enhanced collagen invasion in vitro. In vivo, OE33-derived tumour xenografts with miR-330-5p suppression grew faster than controls. CONCLUSIONS: Loss of miR-330-5p expression in OAC tumours may influence tumour cell invasive capacity, tumour growth and therapeutic sensitivity via alterations to the tumour microenvironment.
    • Exploring Shared Susceptibility between Two Neural Crest Cells Originating Conditions: Neuroblastoma and Congenital Heart Disease

      Testori, A; Lasorsa, VA; Cimmino, F; Cantalupo, S; Cardinale, A; Avitabile, M; Limongelli, G; Russo, MG; Diskin, S; Maris, J; et al. (2019)
      In the past years, genome wide association studies (GWAS) have provided evidence that inter-individual susceptibility to diverse pathological conditions can reveal a common genetic architecture. Through the analysis of congenital heart disease (CHD) and neuroblastoma (NB) GWAS data, we aimed to dissect the genetic susceptibility shared between these conditions, which are known to arise from neural crest cell (NCC) migration or development abnormalities, via identification and functional characterization of common regions of association. Two loci (2q35 and 3q25.32) harbor single nucleotide polymorphisms (SNPs) that are associated at a p-value < 10-3 with conotruncal malformations and ventricular septal defect respectively, as well as with NB. In addition, the lead SNP in 4p16.2 for atrial septal defect and the lead SNP in 3q25.32 for tetralogy of Fallot are less than 250 Kb distant from the lead SNPs for NB at the same genomic regions. Some of these shared susceptibility loci regulate the expression of relevant genes involved in NCC formation and developmental processes (such as BARD1, MSX1, and SHOX2) and are enriched in several epigenetic markers from NB and fetal heart cell lines. Although the clinical correlation between NB and CHD is unclear, our exploration of a possible common genetic basis between NB and a subset of cardiac malformations can help shed light on their shared embryological origin and pathogenetic mechanisms.
    • Oncogenic MYC amplifies mitotic perturbations

      Littler, Samantha; Sloss, O; Geary, B; Pierce, A; Whetton, Anthony D; Taylor, Stephen S; Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, 555 Wilmslow Road, Manchester M20 4GJ, UK (2019)
      The oncogenic transcription factor MYC modulates vast arrays of genes, thereby influencing numerous biological pathways including biogenesis, metabolism, proliferation, apoptosis and pluripotency. When deregulated, MYC drives genomic instability via several mechanisms including aberrant proliferation, replication stress and ROS production. Deregulated MYC also promotes chromosome instability, but less is known about how MYC influences mitosis. Here, we show that deregulating MYC modulates multiple aspects of mitotic chromosome segregation. Cells overexpressing MYC have altered spindle morphology, take longer to align their chromosomes at metaphase and enter anaphase sooner. When challenged with a variety of anti-mitotic drugs, cells overexpressing MYC display more anomalies, the net effect of which is increased micronuclei, a hallmark of chromosome instability. Proteomic analysis showed that MYC modulates multiple networks predicted to influence mitosis, with the mitotic kinase PLK1 identified as a central hub. In turn, we show that MYC modulates several PLK1-dependent processes, namely mitotic entry, spindle assembly and SAC satisfaction. These observations thus underpin the pervasive nature of oncogenic MYC and provide a mechanistic rationale for MYC's ability to drive chromosome instability.
    • Emerging Epigenetic Therapeutic Targets in Acute Myeloid Leukemia

      Wingelhofer, Bettina; Somervaille, Tim CP; Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, University of Manchester, Manchester (2019)
      Acute myeloid leukemia (AML) is a genetically heterogeneous malignancy for which treatment options have been largely limited to cytotoxic chemotherapy for the past four decades. Next-generation sequencing and other approaches have identified a spectrum of genomic and epigenomic alterations that contribute to AML initiation and maintenance. The key role of epigenetic modifiers and the reversibility of epigenetic changes have paved the way for evaluation of a new set of drug targets, and facilitated the design of novel candidate treatment strategies. More recently, seven new targeted therapies have been FDA-approved demonstrating successful implementation of the past decades' research. In this review, we will summarize the most recent advances in targeted therapeutics designed for a focused group of key epigenetic regulators in AML, outline their mechanism of action and their current status in clinical development. Furthermore, we will discuss promising new approaches for epigenetic targeted treatment in AML which are currently being tested in pre-clinical trials.
    • Extreme Incidence of Skin Cancer in Kidney and Liver Transplant Recipients Living with High Sun Exposure

      Plasmeijer, EI; Jiyad, Z; Way, M; Marquart, L; Miura, K; Campbell, S; Isbel, N; Fawcett, J; Ferguson, LE; Davis, M; et al. (2019)
    • The Milk Protein Alpha-Casein Suppresses Triple Negative Breast Cancer Stem Cell Activity Via STAT and HIF-1alpha Signalling Pathways in Breast Cancer Cells and Fibroblasts

      Garner, K, E, L; Hull, NJ; Sims, AH; Lamb, R; Clarke, Robert B; Faculty of Biology, Medicine and Health, Michael Smith Building, University of Manchester, Dover Street, Manchester, M13 9PT, UK. (2019)
      Triple negative breast cancer (TNBC) is the most lethal breast cancer subtype. Extended periods of lactation protect against breast cancer development, but the mechanisms underlying this protection are unknown. We examined the effects of the milk protein alpha-casein over expression in the triple negative MDA-MB-231 breast cancer cell line. The effects of recombinant alpha-casein added exogenously to MDA-MB-231 breast cancer cells, and immortalised human fibroblasts were also investigated. We used transcriptional reporters to understand the signalling pathways downstream of alpha-casein in breast cancer cells and these fibroblasts that were activated by breast cancer cells. To extend our findings to the clinical setting, we analysed public gene expression datasets to further understand the relevance of these signalling pathways in triple negative breast cancer cells and patient samples. Finally, we used small molecular inhibitors to target relevant pathways and highlight these as potential candidates for the treatment of TN breast cancer. High levels of alpha-casein gene expression were predictive of good prognosis across 263 TNBC patient tumour samples. Alpha-casein over expression or exogenous addition reduces cancer stem cell (CSC) activity. HIF-1alpha was identified to be a key downstream target of alpha-casein, in both breast cancer cells and activated fibroblasts, and STAT transcription factors to be upstream of HIF-1alpha. Interestingly, HIF-1alpha is regulated by STAT3 in breast cancer cells, but STAT1 is the regulator of HIF-1alpha in activated fibroblasts. In analysis of 573 TNBC patient samples, alpha-casein expression, inversely correlated to HIF-1alpha, STAT3 and STAT1. STAT1 and STAT3 inhibitors target HIF-1alpha signalling in activated fibroblasts and MDA-MB-231 breast cancer cells respectively, and also abrogate CSC activities. Our findings provide an explanation for the protective effects of lactation in TNBC. Clinical data correlates high alpha-casein expression with increased recurrence-free survival in TNBC patients. Mechanistically, alpha-casein reduces breast cancer stem cell activity in vitro, and STAT3 and STAT1 were identified as regulators of pro-tumorigenic HIF-1alpha signalling in breast cancer cells and fibroblasts respectively.
    • Validated imaging biomarkers as decision-making tools in clinical trials and routine practice: current status and recommendations from the EIBALL* subcommittee of the European Society of Radiology (ESR)

      de Souza, NM; Achten, E; Alberich-Bayarri, A; Bamberg, F; Boellaard, R; Clement, O; Fournier, L; Gallagher, F; Golay, X; Heussel, CP; et al. (q)
      Observer-driven pattern recognition is the standard for interpretation of medical images. To achieve global parity in interpretation, semi-quantitative scoring systems have been developed based on observer assessments; these are widely used in scoring coronary artery disease, the arthritides and neurological conditions and for indicating the likelihood of malignancy. However, in an era of machine learning and artificial intelligence, it is increasingly desirable that we extract quantitative biomarkers from medical images that inform on disease detection, characterisation, monitoring and assessment of response to treatment. Quantitation has the potential to provide objective decision-support tools in the management pathway of patients. Despite this, the quantitative potential of imaging remains under-exploited because of variability of the measurement, lack of harmonised systems for data acquisition and analysis, and crucially, a paucity of evidence on how such quantitation potentially affects clinical decision-making and patient outcome. This article reviews the current evidence for the use of semi-quantitative and quantitative biomarkers in clinical settings at various stages of the disease pathway including diagnosis, staging and prognosis, as well as predicting and detecting treatment response. It critically appraises current practice and sets out recommendations for using imaging objectively to drive patient management decisions.
    • Identification of Resistance Pathways Specific to Malignancy Using Organoid Models of Pancreatic Cancer

      Ponz-Sarvise, M; Corbo, V; Tiriac, H; Engle, DD; Frese, Kristopher K; Oni, TE; Hwang, CI; Ohlund, D; Chio, IIC; Baker, LA; et al. (2019)
      PURPOSE: KRAS is mutated in the majority of pancreatic ductal adenocarcinoma. MAPK and PI3K-AKT are primary KRAS effector pathways, but combined MAPK and PI3K inhibition has not been demonstrated to be clinically effective to date. We explore the resistance mechanisms uniquely employed by malignant cells. EXPERIMENTAL DESIGN: We evaluated the expression and activation of receptor tyrosine kinases in response to combined MEK and AKT inhibition in KPC mice and pancreatic ductal organoids. Additionally, we sought to determine the therapeutic efficacy of targeting resistance pathways induced by MEK and AKT inhibition in order to identify malignant-specific vulnerabilities. RESULTS: Combined MEK and AKT inhibition modestly extended the survival of KPC mice and increased Egfr and ErbB2 phosphorylation levels. Tumor organoids, but not their normal counterparts, exhibited elevated phosphorylation of ERBB2 and ERBB3 after MEK and AKT blockade. A pan-ERBB inhibitor synergized with MEK and AKT blockade in human PDA organoids, whereas this was not observed for the EGFR inhibitor Erlotinib. Combined MEK and ERBB inhibitor treatment of human organoid orthotopic xenografts was sufficient to cause tumor regression in short-term intervention studies. CONCLUSIONS: Analyses of normal and tumor pancreatic organoids revealed the importance of ERBB activation during MEK and AKT blockade primarily in the malignant cultures. The lack of ERBB hyperactivation in normal organoids suggests a larger therapeutic index. In our models pan-ERBB inhibition was synergistic with dual inhibition of MEK and AKT and the combination of a pan-ERBB inhibitor with MEK antagonists showed the highest activity both in vitro and in vivo.
    • Circulating tumour cells and hypercoagulability: a lethal relationship in metastatic breast cancer

      Kirwan, Cliona C; Descamps, T; Castle, John; Division of Cancer Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, Manchester Cancer Research Centre, University of Manchester, Wilmslow Road, Manchester, M20 4GJ, UK (2019)
      PURPOSE: Circulating tumour cells (CTCs) are a marker of poor prognosis and are associated with increased risk of venous thromboembolism in metastatic breast cancer (MBC). We aimed to determine if the presence of CTCs and plasma markers of hypercoagulability [thrombin-antithrombin III (TAT), fibrinogen and D-dimer] are biomarkers of survival in MBC. METHODS/PATIENTS: In a prospective study of MBC patients, CTC (CellSearch¨) enumeration and plasma TAT, fibrinogen and D-dimer measured prior to commencement of treatment for disease progression were correlated to overall survival. RESULTS: At study completion, of 50 MBC patients recruited (median age 59 years, range 36-82), 40 patients had died (median survival 417 days, range 58-2141). CTCs (³?1/7.5 ml) were identified in 16 patients (median number of cells per 7.5 ml, 3 (range 1-31) and were associated with systemic hypercoagulability (medians TAT: 8.1 vs. 5.2 ng/ml, p?=?0.03; fibrinogen: 4.3 vs. 3.1 g/l, p?=?0.03; D-dimer: 1327 vs. 683 ng/ml, p?=?0.0001). At 1 year, of 16 patients with ³?1 CTC, 7 had died (44%), compared to 5 of 26 (19%) patients in the no-CTC group. The presence of ³?1 CTC was associated with a trend for reduced overall survival (median 455 days vs. 614 days, p?=?0.15). Plasma TAT inversely correlated with survival and was significantly higher in patients dying within 1 year (median 9.8 vs. 5.2 ng/ml, p?=?0.004) whilst D-dimer showed a trend for reduced 1-year survival (median 1211 vs. 817 ng/ml, p?=?0.06). MBC patients with combined high D-dimer (³?895 ng/ml) and CTC positivity (³?1/7.5 ml whole peripheral blood) had significantly reduced survival (p?=?0.04). CONCLUSIONS: The correlation between CTCs, hypercoagulability and reduced survival in MBC suggests the coagulation system supports tumour cell metastasis and is, therefore, a potential therapeutic target.
    • Impact of dose and duration of therapy on dexamethasone pharmacokinetics in childhood acute lymphoblastic leukaemia-a report from the UKALL 2011 trial

      Jackson, RK; Liebich, M; Berry, P; Errington, J; Liu, Jizhong; Parker, Catriona; Moppett, J; Samarasinghe, S; Hough, R; Rowntree, C; et al. (2019)
      INTRODUCTION: The use of dexamethasone in acute lymphoblastic leukaemia therapy contributes to short- and long-term toxicities. The UKALL 2011 randomised trial investigated whether a more intense dexamethasone dose (10 mg/m2/d x 14d, short vs 6 mg/m2/d x 28d, standard) would lead to a more rapid cytoreduction and reduced adverse effects associated with longer durations of steroids in induction. The impact of dose and duration on dexamethasone pharmacokinetics was investigated. METHODS: Blood samples were obtained on one of the first three and last three days of induction dexamethasone dosing at time points up to 8 h after oral administration. Plasma dexamethasone levels were quantified in 1084 plasma samples obtained from 174 children and a population pharmacokinetic model developed. RESULTS: Drug exposure varied significantly between patients, with a >12-fold variation in AUC0-12h values and a marked overlap in dexamethasone exposures between dose levels. Intuitively, AUC0-12h was significantly higher with short dosing (10 mg/m2/d), but cumulative exposure was significantly higher with standard dosing over 28 days, after a higher cumulative dose. Concomitant rasburicase administration was associated with a 60% higher dexamethasone clearance. Day 8 bone marrow response was comparable between dosing arms, but those with <5% blast count exhibited a greater mean dexamethasone exposure than those with >5%. No statistical differences were observed between arms in terms of steroid-related toxicity or minimal residual disease at the end of induction. CONCLUSION: The potential significance of dexamethasone AUC0-12h on early response and higher cumulative exposure on the standard arm suggest that duration of therapy and exposure may be more important factors than absolute dose from a clinical pharmacology perspective.
    • Skin ageing continues long after ultraviolet radiation damage

      Earnshaw, CH; Nagore, E; Roeck, K; Schneider, S; Budden, T; Craig, Sarah; Griffiths, C; Furney, S; Krutmann, J; Viros, Amaya; et al. (2019)
    • RUNX transcription factors: orchestrators of development

      Mevel, R; Draper, JE; Lie-a-ling, Michael; Kouskoff, Valerie; Lacaud, Georges; Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Alderley Edge, Macclesfield SK10 4TG, (2019)
      RUNX transcription factors orchestrate many different aspects of biology, including basic cellular and developmental processes, stem cell biology and tumorigenesis. In this Primer, we introduce the molecular hallmarks of the three mammalian RUNX genes, RUNX1, RUNX2 and RUNX3, and discuss the regulation of their activities and their mechanisms of action. We then review their crucial roles in the specification and maintenance of a wide array of tissues during embryonic development and adult homeostasis.
    • Small-Molecule Inhibition of UBE2T/FANCL-Mediated Ubiquitylation in the Fanconi Anemia Pathway

      Cornwell, MJ; Thomson, Graeme J; Coates, J; Belotserkovskaya, R; Waddell, Ian D; Jackson, SP; Galanty, Y; The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry , University of Cambridge , Cambridge CB2 1QN , United Kingdom (2019)
      The Fanconi anemia pathway orchestrates the repair of DNA interstrand cross-links and stalled replication forks. A key step in this pathway is UBE2T and FANCL-dependent monoubiquitylation of the FANCD2-FANCI complex. The Fanconi anemia pathway represents an attractive therapeutic target, because activation of this pathway has been linked to chemotherapy resistance in several cancers. However, to date, very few selective inhibitors of ubiquitin conjugation pathways are known. By using a high-throughput screen-compatible assay, we have identified a small-molecule inhibitor of UBE2T/FANCL-mediated FANCD2 monoubiquitylation that sensitizes cells to the DNA cross-linking agent, carboplatin.
    • Comparative fitness analysis of D-cycloserine resistant mutants reveals both fitness-neutral and high-fitness cost genotypes

      Evangelopoulos, D; Prosser, GA; Rodgers, A; Dagg, BM; Khatri, B; Ho, MM; Gutierrez, MG; Cortes, T; de, Carvalho, LPS; Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK (2019)
      Drug resistant infections represent one of the most challenging medical problems of our time. D-cycloserine is an antibiotic used for six decades without significant appearance and dissemination of antibiotic resistant strains, making it an ideal model compound to understand what drives resistance evasion. We therefore investigated why Mycobacterium tuberculosis fails to become resistant to D-cycloserine. To address this question, we employed a combination of bacterial genetics, genomics, biochemistry and fitness analysis in vitro, in macrophages and in mice. Altogether, our results suggest that the ultra-low rate of emergence of D-cycloserine resistance mutations is the dominant biological factor delaying the appearance of clinical resistance to this antibiotic. Furthermore, we also identified potential compensatory mechanisms able to minimize the severe fitness costs of primary D-cycloserine resistance conferring mutations.
    • Sortilin targeted therapy in breast cancer with elevated progranulin expression

      Berger, K; Rhost, S; Hughes, E; Harrison, Hannah; Rafnsdottir, S; Jacobsson, H; Gregersson, P; Magnusson, Y; Fitzpatrick, P; Andersson, D; et al. (2019)
      Background: A major challenge concerning breast cancer therapy is the occasional lack of effects using drugs that target cancer cells unspecifically. One possible explanation for this treatment failure is the existence of the small subpopulation of breast cancer stem cells that are believed to be more resistant towards conventional therapy and possesses the ability to drive tumor formation and disease progression. Cytokines secreted by nearby cells and other factors in the surrounding tumor microenvironment further stimulate the cancer cells, contributing to a heterogeneous and potentially more treatment resistant tumor. Thus, a more specific treatment approach targeting the breast cancer stem cell niche is crucial in preventing disease recurrences. In a cytokine screen, we identified progranulin as one of the main compounds secreted from cells exposed to hypoxia, leading to cancer stem cell propagation. Progranulin is involved in biological processes such as wound healing, inflammation and cancer progression. Progranulin and its receptor sortilin are known to be highly expressed in subgroups of breast cancer and are further associated with a clinically aggressive phenotype. Methods/Results: By carrying out a number of in vitro and in vivo like screening assays, we demonstrate that progranulin influences the stem cell population in breast cancer and is responsible for spreading a cancer stem cell promoting signal to normoxic tumor areas. In breast cancer, progranulin induces a dedifferentiation process in the receiving cancer cells and expression of cancer stem cell markers together with an EMT-associated gene expression profile, leading to cancer stem cell expansion. By using siRNA and pharmacological inhibition of sortilin, we show that sortilin is a functional receptor of progranulin and is responsible for driving progranulin induced breast cancer stem cell propagation. Supporting the role of progranulin in cancer progression, administration of progranulin in immunocompromised mice induce lung metastasis in our breast cancer xenograft models. The use of different approaches for blocking sortilin, such as sortilin inhibitors, down-modulators or sortilin-targeted antibodies can prevent this dedifferentiation process, both in vitro and in vivo, making the tumor cells less aggressive and metastatic. Conclusion: Targeting progranulin through its associated receptors is a potential therapeutic strategy for the treatment of patients with breast tumors having elevated progranulin or sortilin expression. By inhibiting the secretion based breast cancer progression, we could possibly block the formation of metastasis and cancer cell infiltration.
    • Osteoblasts contribute to a protective niche that supports melanoma cell proliferation and survival

      Ferguson, J; Wilcock, DJ; McEntegart, S; Badrock, AP; Levesque, M; Dummer, R; Wellbrock, Claudia; Smith, M P; Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester (2019)
      Melanoma is the deadliest form of skin cancer; a primary driver of this high level of morbidity is the propensity of melanoma cells to metastasize. When malignant tumours develop distant metastatic lesions the new local tissue niche is known to impact on the biology of the cancer cells. However, little is known about how different metastatic tissue sites impact on frontline targeted therapies. Intriguingly, melanoma bone lesions have significantly lower response to BRAF or MEK inhibitor therapies. Here, we have investigated how the cellular niche of the bone can support melanoma cells by stimulating growth and survival via paracrine signalling between osteoblasts and cancer cells. Melanoma cells can enhance the differentiation of osteoblasts leading to increased production of secreted ligands, including RANKL. Differentiated osteoblasts in turn can support melanoma cell proliferation and survival via the secretion of RANKL that elevates the levels of the transcription factor MITF, even in the presence of BRAF inhibitor. By blocking RANKL signalling, either via neutralizing antibodies, genetic alterations or the RANKL receptor inhibitor SPD304, the survival advantage provided by osteoblasts could be overcome.
    • Peripheral PD-1+CD56+ T-cell frequencies correlate with outcome in stage IV melanoma under PD-1 blockade

      Bochem, J; Zelba, H; Amaral, T; Spreuer, J; Soffel, D; Eigentler, T; Wagner, NB; Uslu, U; Terheyden, P; Meier, F; et al. (2019)
      Immune checkpoint blockade with anti-PD-1 antibodies is showing great promise for patients with metastatic melanoma and other malignancies, but despite good responses by some patients who achieve partial or complete regression, many others still do not respond. Here, we sought peripheral blood T-cell biomarker candidates predicting treatment outcome in 75 stage IV melanoma patients treated with anti-PD-1 antibodies. We investigated associations with clinical response, progression-free survival (PFS) and overall survival (OS). Univariate analysis of potential biological confounders and known biomarkers, and a multivariate model, was used to determine statistical independence of associations between candidate biomarkers and clinical outcomes. We found that a lower than median frequency of peripheral PD-1+CD56+ T-cells was associated with longer OS (p = 0.004), PFS (p = 0.041) and superior clinical benefit (p = 0.009). However, neither frequencies of CD56-CD4+ nor CD56-CD8+ T-cells, nor of the PD-1+ fraction within the CD4 or CD8 subsets was associated with clinical outcome. In a multivariate model with known confounders and biomarkers only the M-category (HR, 3.11; p = 0.007) and the frequency of PD-1+CD56+ T-cells (HR, 2.39; p = 0.028) were identified as independent predictive factors for clinical outcome under PD-1 blockade. Thus, a lower than median frequency of peripheral blood PD-1+CD56+ T-cells prior to starting anti-PD-1 checkpoint blockade is associated with superior clinical response, longer PFS and OS of stage IV melanoma patients.
    • First person - Andrew Porter

      Porter, Andrew P; Cell Signalling Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield SK10 4TG, UK. (2019)
      First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Andrew Porter is first author on ‘The interaction between CASK and the tumour suppressor Dlg1 regulates mitotic spindle orientation in mammalian epithelia’, published in JCS. Andrew is a postdoc in the lab of Prof. Angeliki Malliri at the Cancer Research UK Manchester Institute, investigating how abnormal mitotic events – spindle misorientation, centriole defects and chromosomal instability – contribute to tumourigenesis.
    • Machine learning and data mining frameworks for predicting drug response in cancer: an overview and a novel in silico screening process based on association rule mining

      Vougas, K; Sakellaropoulos, T; Kotsinas, A; Foukas, GP; Ntargaras, A; Koinis, F; Polyzos, A; Myrianthopoulos, V; Zhou, H; Narang, S; et al. (2019)
      A major challenge in cancer treatment is predicting the clinical response to anti-cancer drugs on a personalized basis. The success of such a task largely depends on the ability to develop computational resources that integrate big "omic" data into effective drug-response models. Machine learning is both an expanding and an evolving computational field that holds promise to cover such needs. Here we provide a focused overview of: 1) the various supervised and unsupervised algorithms used specifically in drug response prediction applications, 2) the strategies employed to develop these algorithms into applicable models, 3) data resources that are fed into these frameworks and 4) pitfalls and challenges to maximize model performance. In this context we also describe a novel in silico screening process, based on Association Rule Mining, for identifying genes as candidate drivers of drug response and compare it with relevant data mining frameworks, for which we generated a web application freely available at: https://compbio.nyumc.org/drugs/. This pipeline explores with high efficiency large sample-spaces, while is able to detect low frequency events and evaluate statistical significance even in the multidimensional space, presenting the results in the form of easily interpretable rules. We conclude with future prospects and challenges of applying machine learning based drug response prediction in precision medicine.
    • Lost or forgotten: the nuclear cathepsin protein isoforms in cancer

      Soond, SM; Kozhevnikova, MV; Frolova, AS; Savvateeva, LV; Plotnikov, EY; Townsend, Paul A; Han, YP; Zamyatnin, AA; Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Trubetskaya str. 8-2, Moscow, 119991, Russian Federation (2019)
      While research into the role of cathepsins has been progressing at an exponential pace over the years, research into their respective isoform proteins has been less frenetic. In view of the functional and biological potential of such protein isoforms in model systems for cancer during their initial discovery, much later they have offered a new direction in the field of cathepsin basic and applied research. Consequently, the analysis of such isoforms has laid strong foundations in revealing other important regulatory aspects of the cathepsin proteins in general. In this review article, we address these key aspects of cathepsin isoform proteins, with particular emphasis on how they have shaped what is now known in the context of nuclear cathepsin localization and what potential these hold as nuclear-based therapeutic targets in cancer.