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Biology subjects

Willey, J. C.

Publications and source records attributed to Willey, J. C..

3 recordsLinked to original sources

Microcystin-LR aerosol exposure increases inflammatory drivers of asthma, Evidence of an NF-κB amplification mechanism

Microcystin-LR (MC-LR) is one of a large family of cyanotoxins which are naturally produced by cyanobacteria within harmful algal blooms occurring in bodies of water globally. Early findings of the toxicity of such blooms stemmed from fatalities of livestock drinking from affected water. Since then, various toxins have been identified such as the microcystins. Microcystin-LR has been studied as a representative congener due to its abundance and toxicity. While there have been extensive studies of microcystin-LR by oral route exposure, we have turned our attention to inhalation route exposure due to the recent findings of microcystin-containing lake and sea-spray aerosol. We have shown inflammatory outcomes in the airways of mice and in human cell culture models after microcystin aerosol exposure, and have found a consistent molecular patterns similar to those of Type 1/Type 17 driven neutrophilic asthma. Here we address the hypothesis that MC-LR will increase the inflammatory mediators of neutrophilic asthma leading to worsening symptoms. This is tested and characterized in both in vitro and in vivo models. We found that asthma symptoms and molecular signatures of inflammation are both worsened by MC-LR exposure in a mouse model of neutrophilic asthma. We found that 3D human airway cell culture models reconstructed from asthmatic donor cells are similarly affected, however healthy donor cells are nearly unaltered by comparison. Aggregating these findings with RNA sequencing data from all models, we developed a hypothetical molecular mechanism which relies on MC-LR mediated amplification of existing inflammatory signaling. We test this in a human reporter cell line of NF-{kappa}B activity and further demonstrate the mechanism by inhibitor testing. This study sheds light on the risk to asthmatic patients living near or recreating on affected bodies of water. Beyond asthma, we believe this study provides crucial insight into the findings over the last 40 years concerning disparate outcomes of MC-LR exposure as the result of exposure will be dependent on the signaling state of the tissue upon exposure.

molecular biology↗

Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samples

Clinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE) tissue or cell block cytology samples in oncology panel sequencing to identify mutations that can predict patient response to targeted therapy. To understand the technical error due to FFPE processing, a robustly characterized normal cell line was used to create FFPE samples with four different pre-tissue processing formalin fixation times. A total of 96 FFPE sections were then distributed to different laboratories for targeted sequencing analysis by four oncopanels, and variants resulting from technical error were identified. Tissue sections that failed more frequently showed low cellularity, lower than recommended library preparation DNA input, or target sequencing depth. Importantly, sections from block surfaces were more likely to show FFPE-specific errors, akin to "edge effects" seen in histology, and the depth of formalin damage was related to fixation time. To assure reliable results, we recommend avoiding the block surface portion and restricting mutation detection to genomic regions of high confidence.

cancer biology↗

Advancing quality-control for NGS measurement of actionable mutations in circulating tumor DNA

The primary objective of the FDA-led Sequencing and Quality Control Phase 2 (SEQC2) project is to develop standard analysis protocols and quality control metrics for use in DNA testing to enhance scientific research and precision medicine. This study reports a targeted next generation sequencing (NGS) method that enables more accurate detection of actionable mutations in circulating tumor DNA (ctDNA) clinical specimens. This advancement was enabled by designing a synthetic internal standard spike-in for each actionable mutation target, suitable for use in NGS following hybrid-capture enrichment and unique molecular index (UMI) or non-UMI library preparation. When mixed with contrived ctDNA reference samples, internal standards enabled calculation of technical error rate, limit of blank, and limit of detection for each variant at each nucleotide position, in each sample. True positive mutations with variant allele fraction too low for detection by current practice were detected with this method, thereby increasing sensitivity.

genomics↗