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Biology subjects

Bodnar, A.

Publications and source records attributed to Bodnar, A..

3 recordsLinked to original sources

Soluble, but not precursor EGF induces intracrine signaling of the EGFR

EGFR is a transmembrane receptor tyrosine kinase regulating growth and survival in epithelial tissues. Its ligand, the epidermal growth factor (EGF), is produced as a membrane-anchored precursor (preEGF) that is proteolytically cleaved to release soluble EGF (sEGF). EGFR overexpression can convert it from a physiological regulator into an oncogenic driver. Therapeutic strategies targeting EGFR include monoclonal antibodies (mAbs) and tyrosine kinase inhibitors (TKIs). Although mAbs such as cetuximab initially block EGFR activity, tumors often develop resistance. Recent findings indicate that sEGF can activate EGFR within intracellular vesicles, promoting intracrine signaling that sustains proliferation despite extracellular inhibition. Here, we investigated the mechanism of intracrine EGFR signaling in the Golgi apparatus using confocal microscopy, FRET and fluorescence correlation spectroscopy. sEGF, but not preEGF, bound and induced EGFR dimerization and phosphorylation. Erlotinib, a membrane permeable TKI, effectively blocked phosphorylation, whereas extracellular cetuximab did not. These findings imply sEGF-induced intracrine EGFR signaling in the Golgi. Our results may shed light on a potential resistance mechanism to antibody treatment.

biophysics↗

Building an epigenetic clock: Utilizing whole genome DNA methylation patterns to predict age in haddock, Melanogrammus aeglefinus

Age-based population models are a gold standard approach to estimate stock size and sustainable catch recommendations for effective fisheries management. Traditional ageing by counting annuli on their ear stones (otoliths), is labor-intensive, lethal, and can be inaccurate for long-lived fishes. In this study, we present an accurate, non-lethal epigenetic clock method for predicting age in haddock, Melanogrammus aeglefinus, one of the most valuable commercial fisheries in the north Atlantic Ocean. Pectoral fin tissue (n=140 individuals) was collected during Fall 2022 and Spring 2023 bottom trawl surveys in the Georges Bank-Gulf of Maine region, and whole-genome bisulfite sequencing was conducted to measure CpG loci DNA methylation levels. The most age-predictive loci were identified using a three-step modeling approach: a Bayesian generalized linear mixed model with length and sex as random factors followed by machine learning models with a 70/30 train-test split. The final model used 111 loci to predict age within 1-year at 93% accuracy. Hypo- and hyper-methylated age-related loci were found throughout the genome and were enriched in intragenic regions with functions related to immunity, transcriptional regulation, and signal transduction. This study provides an accurate, cost-effective, and scalable epigenetic tool for fisheries management to predict the age of haddock.

genomics↗

Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development

Mammalian nephrons originate from a population of nephron progenitor cells (NPCs), and it is known that NPCs transcriptomes change throughout nephrogenesis during healthy kidney development. To characterize chromatin accessibility and microRNA (miRNA) expression throughout this process, we collected NPCs from mouse kidneys at embryonic day 14.5 (E14.5) and postnatal day zero (P0) and assayed cells for transposase-accessible chromatin and small RNA expression. We observe 46,374 genomic regions of accessible chromatin, with 2,103 showing significant changes in accessibility between E14.5 and P0. In addition, we detect 1,104 known microRNAs, with 114 showing significant changes in expression. Genome-wide, changes in DNA accessibility and microRNA expression highlight biological processes like cellular differentiation, cell migration, extracellular matrix interactions, and developmental signaling pathways such as Notch. Furthermore, our data identify novel candidate cis-regulatory elements for Eya1 and Pax8, both genes with a role in NPC differentiation; we also associate expression-changing microRNAs, including let-7-5p, miR-125b-5p, miR-181a-2-3p, and miR-9-3p, with candidate cis-regulatory elements. Overall, our data characterize NPCs during kidney development and point out new candidate regulatory elements for genes and microRNA with key roles in nephrogenesis.

developmental biology↗