Computational repurposing of oncology drugs through off‐target drug binding interactions from pharmacological databases

PurposeSystematic repurposing of approved medicines for another indication may accelerate drug development in oncology. We present a strategy combining biomarker testing with drug repurposing to identify new treatments for patients with advanced cancer.MethodsTumours were sequenced with the Illumina TruSight Oncology 500 (TSO-500) platform or the FoundationOne CDx panel. Mutations were screened by two medical oncologists and pathogenic mutations were categorised referencing literature. Variants of unknown significance were classified as potentially pathogenic using plausible mechanisms and computational prediction of pathogenicity. Gain of function (GOF) mutations were evaluated through repurposing databases Probe Miner (PM), Broad Institute Drug Repurposing Hub (Broad Institute DRH) and TOPOGRAPH. GOF mutations were repurposing events if identified in PM, not indexed in TOPOGRAPH and excluding mutations with a known Food and Drug Administration (FDA)-approved biomarker. The computational repurposing approach was validated by evaluating its ability to identify FDA-approved biomarkers. The total repurposable genome was identified by evaluating all possible gene-FDA drug-approved combinations in the PM dataset.ResultsThe computational repurposing approach was accurate at identifying FDA therapies with known biomarkers (94%). Using next-generation sequencing molecular reports (n = 94), a meaningful percentage of patients (14%) could have an off-label therapeutic identified. The frequency of theoretical drug repurposing events in The Cancer Genome Atlas pan-cancer dataset was 73% of the samples in the cohort.ConclusionA computational drug repurposing approach may assist in identifying novel repurposing events in cancer patients with no access to standard therapies. Further validation is needed to confirm a precision oncology approach using drug repurposing. Repurposing identified Food and Drug Administration-approved drug-biomarker combinations with high sensitivity and specificity. In a real-world dataset, repurposing identified novel drug-biomarker combinations in patients who were ineligible for standard therapies or biomarker-matched trials. Preliminary functional validation was demonstrated for two drug-biomarker combinations. Using The Cancer Genome Atlas data, the potential scope of repurposing was identified. imag

Platelets kill intraerythrocytic malarial parasites and mediate survival to infection

Platelets play a critical role in the pathogenesis of malarial infections by encouraging the sequestration of infected red blood cells within the cerebral vasculature. But platelets also have well-established roles in innate protection against microbial infections. We found that purified human platelets killed Plasmodium falciparum parasites cultured in red blood cells. Inhibition of platelet function by aspirin and other platelet inhibitors abrogated the lethal effect human platelets exert on P. falciparum parasites. Likewise, platelet-deficient and aspirin-treated mice were more susceptible to death during erythrocytic infection with Plasmodium chabaudi. Both mouse and human platelets bind malarial-infected red cells and kill the parasite within. These results indicate a protective function for platelets in the early stages of erythrocytic infection distinct from their role in cerebral malaria

Mice That Are Congenic for the char2 Locus Are Susceptible to Malaria

A major advance has been made towards the positional cloning of char2 (a quantitative trait locus encoding resistance to Plasmodium chabaudi malaria). Mice congenic for the locus have been used to fine map the gene and to prove that char2 plays a significant role in the outcome of malarial infection, independently of other resistance loci

Improving prenatal diagnosis and management in Cumbria by telemedicine

Antenatal care involves the screening, diagnosis and monitoring of the “at-risk” fetus using ultrasound. When a problem is detected by an ultra-sonographer (e.g. a fetal anomaly or small sized baby), the mother is referred to a local specialist or the regional FM centre in Newcastle for confirmation of the diagnosis, counselling and management. At present, three consultant-led maternity units in Cumbria refer FM cases to Newcastle. This means that patients travel for 6 hours at their own expense. Telemedicine could help in reducing travel and improving access to consultants. This new service is aimed at establishing a videoconferencing infrastructure between the obstetric ultrasound department at West Cumberland Hospital and the Fetal Medicine (FM) centre in Newcastle. It is currently in its implementation stage

Platelets kill intraerythrocytic malarial parasites and mediate survival to infection

Platelets play a critical role in the pathogenesis of malarial infections by encouraging the sequestration of infected red blood cells within the cerebral vasculature. But platelets also have well-established roles in innate protection against microbial infections. We found that purified human platelets killed Plasmodium falciparum parasites cultured in red blood cells. Inhibition of platelet function by aspirin and other platelet inhibitors abrogated the lethal effect human platelets exert on P. falciparum parasites. Likewise, platelet-deficient and aspirin-treated mice were more susceptible to death during erythrocytic infection with Plasmodium chabaudi. Both mouse and human platelets bind malarial-infected red cells and kill the parasite within. These results indicate a protective function for platelets in the early stages of erythrocytic infection distinct from their role in cerebral malaria.4 page(s

Per una bibliografia sistematica della musica sacra a stampa dei secoli XVI e XVII. La banca dati

Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes (DEGs) between treatment groups based on RNA-Seq data. However, there is a lack of consensus on how to approach an optimal study design and choice of suitable software for the analysis. In this comparative study we evaluate the performance of three of the most frequently used software tools: Cufflinks-Cuffdiff2, DESeq and edgeR. A number of important parameters of RNA-Seq technology were taken into consideration, including the number of replicates, sequencing depth, and balanced vs. unbalanced sequencing depth within and between groups. We benchmarked results relative to sets of DEGs identified through either quantitative RT-PCR or microarray. We observed that edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives. Overall, DESeq or taking the intersection of DEGs from two or more tools is recommended if the number of false positives is a major concern in the study. In other circumstances, edgeR is slightly preferable for differential expression analysis at the expense of potentially introducing more false positives

Overview of the <i>E. coli</i> EC958 serum resistance genes.

<p>The circular diagram depicts the location of 56 serum resistance genes on the <i>E. coli</i> EC958 genome. The two outer rings containing blue and red arrows illustrate the CDS and serum resistance genes, respectively, on the forward and reverse strand of the genome. The inner red ring represents the logFC between the control and the test samples for each CDS. The three insets represent a close-up look at three regions on the genome with the graphs showing the location and relative number of each mutant found in the control (blue) and test (red) samples.</p