Biology subjects

Cabrera, K.

Publications and source records attributed to Cabrera, K..

3 recordsLinked to original sources

bioRxiv2024

The Dlk1-Dio3 noncoding RNA cluster coordinately regulates mitochondrial respiration and chromatin structure to establish proper cell state for muscle differentiation

The coordinate regulation of metabolism and epigenetics to establish cell state-specific gene expression patterns during lineage progression is a central aspect of cell differentiation, but the factors that regulate this elaborate interplay are not well-defined. The imprinted Dlk1-Dio3 noncoding RNA (ncRNA) cluster has been associated with metabolism in various progenitor cells, suggesting it functions as a regulator of metabolism and cell state. Here, we directly demonstrate that the Dlk1-Dio3 ncRNA cluster coordinates mitochondrial respiration and chromatin structure to maintain proper cell state. Stable muscle cell lines were generated harboring two distinct deletions in the proximal promoter region resulting in either greatly upregulated or downregulated expression of the entire Dlk1-Dio3 ncRNA cluster. Both mutant lines displayed impaired muscle differentiation along with altered mitochondrial respiration and genome-wide changes in chromatin accessibility and histone methylation. Global gene expression patterns and pathway analyses indicated a reprogramming of myogenic cell state creating a differentiated-like phenotype in proliferating myoblasts. Our results strongly suggest the Dlk1-Dio3 ncRNA locus is a nodal regulator coordinating metabolic activity and the epigenome to maintain proper cell state in the myogenic lineage. Summary statementMuscle cell state is regulated by the imprinted Dlk1-Dio3 noncoding RNA locus through its coordinate control of mitochondrial activity and histone modifications.

developmental 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

Drosophila immune priming to Enterococcus faecalis relies on immune tolerance rather than resistance

Most multicellular organisms, including fruit flies, possess an innate immune response, but lack an adaptive immune response. Even without adaptive immunity, "immune priming" allows organisms to survive a second infection more effectively after an initial, non-lethal infection. We used Drosophila melanogaster to study the transcriptional program that underlies priming. Using an insect-derived strain of Gram-positive Enterococcus faecalis, we found a low dose infection enhances survival of a subsequent high dose infection. The enhanced survival in primed animals does not correlate with a decreased bacterial load, implying that the organisms tolerate, rather than resist the infection. We measured the transcriptome associated with immune priming in the fly immune organs: the fat body and hemocytes. We found many genes that were only upregulated in re-infected flies. In contrast, there are very few genes that either remained transcriptionally active throughout the experiment or more efficiently re-activated upon reinfection. Measurements of priming in immune deficient mutants revealed IMD signaling is largely dispensable for responding to a single infection, but needed to fully prime; while Toll signaling is required to respond to a single infection, but dispensable for priming. Overall, we found a primed immune response to E. faecalis relies on immune tolerance rather than bacterial resistance and drives a unique transcriptional response.

immunology↗