2980 Introduction: Oncolytic replication-selective adenoviruses and adenoviral vectors have potential therapeutic use in pancreatic cancer. Understanding the mechanisms behind the interaction between adenovirus and chemotherapy may enable more efficacious combination regimens to be delivered. Methods: The human pancreatic cancer cell lines MiaPaCa2, Suit2 and Hs766t, and the murine cell line Panc02, were screened for sensitivity to adenovirus (Ad5) and the E1A-CR2 deletion mutant dl 922/947 in combination with the cytotoxic drugs 5-fluorouracil (5-FU) and gemcitabine; dl312 (E1-deleted) was used as a control. Cell death was measured using cell death assay and isobolograms used to evaluate synergy. CAR expression, using a monoclonal antibody to human CAR, and infectability by Ad-GFP were assessed by FACS analysis. Results: Supra-additive effects on cell death of combination treatment with Ad5 or dl922/947 and either gemcitabine or 5-FU were seen in all 4 cell lines tested.Gemcitabine increased sensitivity of the cells to Ad5 by 3600-fold in MiaPaCa2, 1200-fold in Suit 2, 11,500-fold in Hs766t and 3000-fold in Panc02. Ad5 increased sensitivity to 5-FU with increases of 5000-fold in MiaPaca2, 99000-fold in Suit2, 6900-fold in Hs766t, and 240-fold in Panc02. Synergistic effects were also seen with dl922/947. Viral replication was supported in all the cell lines; administration of chemotherapy did not increase viral replication. All cell lines were infectable by Ad-GFP in a dose-dependent manner. The least infectable human cell line was Hs766t (16% cells infected) and the most infectable was MiaPaCa2 (48% cells infected). An increase in infectability with adenovirus was seen after chemotherapy in all the cell lines tested. Increases in infectability of up to 4-fold in Hs766t, 2-fold in MiaPaCa2, 10-fold in Panc02 and 5-fold in Suit2 cells were seen with both agents. Baseline CAR expression was similar in Suit2 and MiaPaCa2 cells after 24 hours in culture with Hs766t reaching the same levels after 72 hours in culture. Using the same conditions as described for infectivity, an increase in the level of CAR expression was seen in MiaPaCa2 cells and Hs766t cells following the administration of gemcitabine and 5-FU, but not in Suit2 cells. Conclusions: Synergy between adenovirus and chemotherapy is observed in pancreatic cancer cell lines. Chemotherapy increases infectability by adenovirus, although modulation of CAR expression is not the only mechanism for this. An increase in viral replication is not seen with chemotherapy. Other cellular changes, including cell cycle analysis, are currently being explored.
Plasmodium falciparum causes the most severe form of malaria and affects 3.2 million people annually. Due to the increasing incidence of resistance to existing drugs, there is a growing need to discover new and more effective drugs against malaria. Despite the global importance of P. falciparum, vast majority of its proteins are uncharacterized experimentally. Application of newer approaches using several "omics" data has become successful for exploring the biological interactions underlying cellular processes. Till date not many system level study has been published using P. falciparum protein protein interaction. Hence, the purpose of this study is to develop a standardized pipeline for structural, functional, and topographical analysis of large scale protein protein interaction network (PPIN) in order to identify proteins important for network topology and integrity. Here, P. falciparum PPIN has been utilized as a model for better understanding of the molecular mechanisms of survival and pathogenesis of malaria parasite. Various graph theoretical approaches were implemented to identify highly interacting hub and central proteins that are crucial for network integrity. Further, potential network perturbing proteins via an in-silico knock-out (KO) analysis to isolate important interacting proteins (IIPs), which in principle, can elicit significant impact on the global and local environments of the P. falciparum interaction network. 177 hubs and 132 central proteins were identified from the malarial (proteins: 1607; interactions: 4750) PPI networks. Using the in-silico knock-out exercise 131 and 99 global and local network perturbing proteins were also identified. Finally, 271 proteins from P. falciparum were shortlisted as important interacting proteins (IIPs), which not only play crucial role in intra-pathogen network integrity, stage specificity but also interact with various human proteins involved in multiple metabolic pathways within the host cell. These IIPs could be used as potential drug targets in malarial research. Graph theoretical analysis of PPIN can be a very useful approach to identify proteins that are important for regulation of the interactions required for an organism's survival. Important interacting proteins (IIPs) identified using P. falciparum PPIN provides a useful dataset containing probable candidates for future drug target analysis.
Thoracic cancer examines the epidemiology, aetiology, and role of screening and prevention in the reduction of deaths from lung cancer, the majority caused by cigarette smoking. The pathology and genetics of lung cancer, with particular note of the driver mutations, are followed by the symptoms and signs of the disease. Appropriate investigations are described to stage the tumour. The optimum treatment for localised non-small cell lung cancer (NSCLC) is surgical resection, followed in some cases by adjuvant chemotherapy. However, most cases present with disease too advanced for surgery, and for these chemotherapy and radiotherapy are appropriate. Metastatic NSCLC can be treated with platinum based doublet chemotherapy with modest palliative benefits. Metastatic NSCLC with specific driver mutations are amenable to control by targeted therapy. Locally advanced NSCLC is often treated with similar chemotherapy and radiotherapy, ideally administered concurrently, to achieve symptom relief but also improved survival rates. Short course simple radiotherapy offers symptom relief in patients not fit for chemotherapy. Patients with localised NSCLC who are not fit for surgery, may benefit from radical radiotherapy, particularly stereotactic radiotherapy. Small cell lung cancer (SCLC) is characterised by almost universal systemic spread, so that surgery is rarely appropriate. Staging is similar to NSCLC, and chemotherapy is the mainstay of treatment, usually cisplatin or carboplatin combined with etoposide. When possible, this is combined with concurrent thoracic irradiation covering all radiological sites of disease. Prophylactic cranial irradiation reduces the risk of CNS disease. Malignant pleural mesothelioma is caused by occupational asbestos exposure. Symptoms and signs, investigation and staging, and management are discussed. Thymic tumours, their pathology, presenting symptoms including paraneoplastic syndromes, investigation, staging and treatment are reviewed.
Abstract Anti‐angiogenic and anti‐stromal therapies are being developed for the treatment of cancer. Elucidation of the factors involved in tumour angiogenesis, in particular, the VEGF‐VEGFR pathway, has enabled new targeted therapies to be developed. Bevacizumab and the multi‐targeted receptor tyrosine kinase inhibitors have shown clinical efficacy when given in combination with conventional cytotoxic therapy. Other agents include endogenous inhibitors of apoptosis, matrix metalloproteinase inhibitors, and integrin antagonists, which are in the early phases of clinical development. Angiogenic inhibitors may synergize with conventional cytotoxic therapy and radiotherapy in decreasing tumour growth.
Abstract Background Microbiome analysis is becoming a standard component in many scientific studies, but also requires extensive quality control of the 16S rRNA gene sequencing data prior to analysis. In particular, when investigating low-biomass microbial environments such as human skin, contaminants distort the true microbiome sample composition and need to be removed bioinformatically. We introduce MicrobIEM, a novel tool to bioinformatically remove contaminants using negative controls. Results We benchmarked MicrobIEM against five established decontamination approaches in four 16S rRNA amplicon sequencing datasets: three serially diluted mock communities (10 8 –10 3 cells, 0.4–80% contamination) with even or staggered taxon compositions and a skin microbiome dataset. Results depended strongly on user-selected algorithm parameters. Overall, sample-based algorithms separated mock and contaminant sequences best in the even mock, whereas control-based algorithms performed better in the two staggered mocks, particularly in low-biomass samples (≤ 10 6 cells). We show that a correct decontamination benchmarking requires realistic staggered mock communities and unbiased evaluation measures such as Youden’s index. In the skin dataset, the Decontam prevalence filter and MicrobIEM’s ratio filter effectively reduced common contaminants while keeping skin-associated genera. Conclusions MicrobIEM’s ratio filter for decontamination performs better or as good as established bioinformatic decontamination tools. In contrast to established tools, MicrobIEM additionally provides interactive plots and supports selecting appropriate filtering parameters via a user-friendly graphical user interface. Therefore, MicrobIEM is the first quality control tool for microbiome experts without coding experience.
SUMMARY Efflux is a common mechanism of resistance to antibiotics. We show that efflux itself promotes accumulation of antibiotic-resistance mutations (ARM). This phenomenon was initially discovered in a bacterial swarm where the linked phenotypes of high efflux and high mutation frequencies spatially segregated to the swarm edge, driven there by motility. We uncovered and validated a global regulatory network that connects high efflux to downregulation of specific DNA repair pathways even in non-swarming states. The efflux-DNA repair link was corroborated in a clinical ‘resistome’ database: genomes with mutations that increase efflux exhibit a significant increase in ARMs. Accordingly, efflux inhibitors decreased evolvability to antibiotic resistance. Swarms also revealed how bacterial populations serve as reservoir of ARMs even in absence of antibiotic selection pressure. High efflux at the edge births mutants that, despite compromised fitness, survive there because of reduced competition. This finding is relevant to biofilms where efflux activity is high.
Abstract Cancer of unknown primary origin (CUP) is classically associated with rapid progression and poor prognosis. If review of the available radiological and pathological information favours a particular tumour type, site-specific chemotherapy can be instituted; otherwise, empirical combination chemotherapy is recommended. Many patients present with advanced disease and poor performance status. The introduction of dedicated multidisciplinary team (MDT) care for CUP, including an MDT with palliative care and oncology input, is designed to diagnose patients earlier and identify patients suitable for treatment earlier in their disease pathway. Furthermore, developments in imaging, immunohistochemistry, and molecular profiling may lead to improvements in identifying the site of origin or targets suitable for treatment. This is a case of a patient who presented with a raised CA125 and multiple liver metastases and responded to chemotherapy regimens with activity in ovarian cancer. Although an unusual case of CUP, the principles of diagnosis and management of CUP are well illustrated.
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