Clinical application of a cancer genomic profiling assay to guide precision medicine decisions

AIM: Develop and apply a comprehensive and accurate next-generation sequencing based assay to help clinicians to match oncology patients to therapies. MATERIALS and METHODS: The performance of the CANCERPLEX(R) assay was assessed using DNA from well-characterized routine clinical formalin-fixed paraffin-embedded (FFPE) specimens and cell lines. RESULTS: The maximum sensitivity of the assay is 99.5% and its accuracy is virtually 100% for detecting somatic alterations with an allele fraction of as low as 10%. Clinically actionable variants were identified in 93% of patients (930 of 1000) who underwent testing. CONCLUSION: The test\u27s capacity to determine all of the critical genetic changes, tumor mutation burden, microsatellite instability status and viral associations has important ramifications on clinical decision support strategies, including identification of patients who are likely to benefit from immune checkpoint blockage therapies

Virology under the microscope—a call for rational discourse

Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns – conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we – a broad group of working virologists – seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology

Molecular mechanisms of diaphragm development: implications for congenital diaphragmatic hernia

Thesis (Ph.D.)--Boston UniversityPLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at [email protected]. Thank you.Congenital abnormalities of the diaphragm, specifically congenital diaphragmatic hernia (CDH), affect 1 in 3,000 live births and are associated with substantial morbidity and mortality. Evidence in humans and animal models support genetic causation. The etiology of most cases, however, remains unknown, though is likely polygenic in the majority. Another impediment to uncovering CDH etiology is that collection of human specimens at the onset of diaphragm development (4 weeks gestation) is not feasible. Identification of key transcriptional programs involved in normal diaphragm development is needed to gain a more comprehensive understanding of the genetic etiology of CDH. As an initial step, unique transcriptome-wide data sets are generated from laser-captured mouse embryonic diaphragms at three key time-points of diaphragm development. These data sets provide the first unbiased perspective on genes and signaling pathways active during early and late diaphragm morphogenesis. Moreover, using a curated list of known CDR-associated genes as "baits", the normal expression data sets are filtered for identification of biologically relevant CDH candidate genes. By this approach, 27 novel CDH candidate genes are described, among which, pre-B cell leukemia transcription factor 1 (Pbxl) is selected to validate the prioritization approach. Diaphragm defects resembling the human CDH phenotype, never previously appreciated, are observed among Pbxl mutant mice at E15.5. Secondly, a human family containing several affected individuals with CDH is used for gene discovery. A multiplatform analysis approach, coupled with external filtering with the normal diaphragm expression data, provide a mechanism for identification of candidate modifier loci. This integrative strategy, which identifies a FOG2 deletion and several potential modifiers of the CDH phenotype, is described. The design of a customized diagnostic/discovery capture array for next-generation sequencing of a large CDH patient cohort uses the set of CDR-candidate genes identified herein.2031-01-0

Invasive fungal infections in liver diseases

Patients with liver diseases, including decompensated cirrhosis, alcohol-associated hepatitis, and liver transplant recipients are at increased risk of acquiring invasive fungal infections (IFIs). These infections carry high morbidity and mortality. Multiple factors, including host immune dysfunction, barrier failures, malnutrition, and microbiome alterations, increase the risk of developing IFI. Candida remains the most common fungal pathogen causing IFI. However, other pathogens, including Aspergillus, Cryptococcus, Pneumocystis, and endemic mycoses, are being increasingly recognized. The diagnosis of IFIs can be ascertained by the direct observation or isolation of the pathogen (culture, histopathology, and cytopathology) or by detecting antigens, antibodies, or nucleic acid. Here, we provide an update on the epidemiology, pathogenesis, diagnosis, and management of IFI in patients with liver disease and liver transplantation

Short-term diesel exhaust inhalation in a controlled human crossover study is associated with changes in DNA methylation of circulating mononuclear cells in asthmatics

Background: Changes in DNA methylation have been associated with traffic-related air pollution in observational studies, but the specific mechanisms and temporal dynamics therein have not been explored in a controlled study of asthmatics. In this study, we investigate short-term effects of diesel exhaust inhalation on DNA methylation levels at CpG sites across the genome in circulating blood in asthmatics. Methods A double-blind crossover study of filtered air and diesel exhaust exposures was performed on sixteen non-smoking asthmatic subjects. Blood samples were collected pre-exposure, and then 6 and 30 hours post-exposure. Peripheral blood mononuclear cell DNA methylation was interrogated using the Illumina Infinium HumanMethylation450 Array. Exposure-related changes in DNA methylation were identified. In addition, CpG sites overlapping with Alu or LINE1 repetitive elements and candidate microRNA loci were also analyzed. Results DNA methylation at 2827 CpG sites were affected by exposure to diesel exhaust but not filtered air; these sites enriched for genes involved in protein kinase and NFkB pathways. CpG sites with significant changes in response to diesel exhaust exposure primarily became less methylated, with a site residing within GSTP1 being among the significant hits. Diesel exhaust-associated change was also found for CpG sites overlapping with Alu and LINE1 elements as well as for a site within miR-21. Conclusion Short-term exposure to diesel exhaust resulted in DNA methylation changes at CpG sites residing in genes involved in inflammation and oxidative stress response, repetitive elements, and microRNA. This provides plausibility for the role of DNA methylation in pathways by which airborne particulate matter impacts gene expression and offers support for including DNA methylation analysis in future efforts to understand the interactions between environmental exposures and biological systems.Medicine, Department ofMolecular Medicine and Therapeutics, Centre forPopulation and Public Health (SPPH), School ofMedicine, Faculty ofNon UBCReviewedFacult