Biology subjects

Brown, B. A.

Publications and source records attributed to Brown, B. A..

3 recordsLinked to original sources

bioRxiv2023

Single-cell RNA sequencing reveals microenvironment context-specific routes for epithelial-mesenchymal transition in pancreas cancer cells

In the PDAC tumor microenvironment, multiple factors initiate the epithelial-mesenchymal transition (EMT) that occurs heterogeneously among transformed ductal cells, but it is unclear if different drivers promote EMT through common or distinct signaling pathways. Here, we use single-cell RNA sequencing (scRNA-seq) to identify the transcriptional basis for EMT in pancreas cancer cells in response to hypoxia or EMT-inducing growth factors. Using clustering and gene set enrichment analysis, we find EMT gene expression patterns that are unique to the hypoxia or growth factor conditions or that are common between them. Among the inferences from the analysis, we find that the FAT1 cell adhesion protein is enriched in epithelial cells and suppresses EMT. Further, the receptor tyrosine kinase AXL is preferentially expressed in hypoxic mesenchymal cells in a manner correlating with YAP nuclear localization, which is suppressed by FAT1 expression. AXL inhibition prevents EMT in response to hypoxia but not growth factors. Relationships between FAT1 or AXL expression with EMT were confirmed through analysis of patient tumor scRNA-seq data. Further exploration of inferences from this unique dataset will reveal additional microenvironment context-specific signaling pathways for EMT that may represent novel drug targets for PDAC combination therapies.

cancer biology↗

bioRxiv2023

Analytical performance and concordance with next-generation sequencing of a rapid multiplexed dPCR panel for the detection of actionable DNA and RNA biomarkers in non-small cell lung cancer

BackgroundOver the last ten years, the discovery and FDA approval of targeted therapies for lung cancer has significantly improved patient survival rates. However, despite these improved survival rates, only 68% of patients receive molecular testing that results in assignment of targeted therapy 1,2. Barriers to timely access to biomarker information include no testing ordered3,high nucleic acid input requirements, and problematic turnaround time (TAT) by NGS (> 14 days)4. Here we report the analytical performance and concordance with next-generation sequencing (NGS) of a highly-multiplexed research use only (RUO) panel using digital PCR (dPCR). The HDPCR NSCLC panel reports the status for variants (SNV, indels, and fusions) in eight actionable genes using amplitude modulation and multi-spectral encoding in dPCR5. MethodsThe panels analytical sensitivity and reactivity were determined using DNA and RNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue spiked with plasmid DNA or in-vitro transcribed RNA. Concordance was established on 106 FFPE samples previously characterized using the Oncomine Precision Assay(R) or pathology results. Discordant resolution was resolved with Archer Fusionplex(R) and Variantplex(R) panels. ResultsThe analytical sensitivity, reported as estimated mutant allele fraction (MAF), for DNA targets (EGFR exon 19 deletions, EGFR exon 20 insertions, EGFR S768I, EGFR L858R, EGFR T790M, EGFR L861Q, BRAF V600E, EGFR G719X, ERBB2 exon 20 insertions and KRAS G12C) ranged from 0.8% - 4.9% with 40 ng of DNA input, and 2.4% to 10.9% with 15 ng of DNA input. For RNA fusion targets (ALK, RET, ROS, NTRK 1/2/3, and MET exon 14 skipping), the analytical sensitivity ranged from 24 - 150 copies with 5 ng of total RNA input. The population prevalence-based coverage ranged from 89.2% to 100.0% across targets and >99.0% in aggregate. The accuracy of the assay was >97% with respect to the comparator method.

cancer biology↗

bioRxiv2022

A histone methylation-MAPK signaling axis drives durable epithelial-mesenchymal transition in hypoxic pancreas cancer

Here, we show that hypoxia drives especially long-lasting epithelial-mesenchymal transition (EMT) in pancreatic ductal adenocarcinoma (PDAC) primarily through a positive-feedback histone methylation-MAPK signaling axis. We find that transformed cells preferentially undergo EMT in hypoxic tumor regions in multiple model systems and that hypoxia drives a cell-autonomous EMT in PDAC cells which, unlike EMT in response to growth factors, can last for weeks. We further demonstrate that hypoxia reduces histone demethylase KDM2A activity, suppresses PP2 family phosphatase expression, and activates MAPKs to post-translationally stabilize histone methyltransferase NSD2, leading to an H3K36me2-dependent EMT in which hypoxia-inducible factors play only a supporting role. This mechanism can be antagonized in vivo by combinations of MAPK inhibitors that may be effective in multi-drug therapies designed to target EMT.

cancer biology↗