Biomedical subjects

Kaylene J Simpson

Publications and source records attributed to Kaylene J Simpson.

3 recordsLinked to original sources

PubMed2026

RAD54L coordinates the nucleolar DNA damage response to maintain rDNA stability.

The nucleolus is organized around actively transcribed ribosomal RNA genes (rDNA), where high RNA polymerase I (Pol I) activity creates intrinsic susceptibility to replication stress and DNA damage. Here, we identify the DNA translocase RAD54L as a critical regulator of the nucleolar DNA damage response (nDDR) to rDNA double-strand breaks (DSBs) and replication stress. We show that RAD54L localizes to the nucleolus under basal conditions and is recruited to nucleolar caps following CRISPR-Cas9-induced rDNA-DSBs to promote repair. RAD54L loss results in persistent RAD51 foci, increased nucleolar γH2AX, and micronuclei formation, indicating defective resolution of rDNA lesions and genome instability. Under baseline conditions and replication stress induced by the Pol I transcription inhibitor CX-5461, RAD54L limits the accumulation of ssDNA and coordinates nDDR signaling. We further show that rDNA-DSBs induce RNA polymerase II-dependent RNA-DNA hybrids (R-loops) at intergenic rDNA regions, which facilitate nucleolar reorganization and cap formation and repair factor recruitment. Together, these findings establish RAD54L as a key regulator that coordinates replication stress response and rDNA repair, maintaining rDNA stability and genome integrity.

DNA, Ribosomal↗

PubMed2026

From complexity to clarity: Building dashboards for hit selection in high throughput screens.

High throughput screening produces large, complex datasets that are difficult to interrogate without programming expertise, making hit selection time-consuming and inflexible. While instrument software and commercial tools offer partial solutions, they often lack adaptability or require costly infrastructure. Interactive dashboards provide an effective alternative by enabling dynamic filtering and integrated visualization within a single interface. Here, we present simple R Markdown-based templates for creating customizable, modular dashboards for screen data analysis. Built using the flexdashboard and crosstalk R packages, and HTML widgets, these lightweight, easy-to-build HTML dashboards require no complex installation process or installation of licensed software. They support linked visualizations, threshold-based filtering (e.g., Z-score, p-value, fold change), and interactive data exploration and are shared as a standalone HTML file. This framework enables rapid, flexible hit selection across diverse high throughput screening applications and is designed for users with basic R experience.

High-Throughput Screening Assays↗

PubMed2025

Genome-wide analysis of host-encoded microRNAs modulating SARS-CoV-2 infection.

Viruses exploit cellular machinery to complete their replication cycle. Furthering our understanding of this process provides insight into the mechanism of virus replication and potential targets for antiviral therapeutics. Genome-wide CRISPR screens have identified cellular pathways important in the SARS-COV-2 infection process, including vesicular traffic, lipid homeostasis and PI3K signalling. Functional genomics-driven analysis of host-encoded microRNAs (miRNAs) impacting SARS-CoV-2 infection would provide further unbiased and discovery-driven insight into the host-pathogen interface. Here we present findings from genome-wide complementary miRNA mimic and inhibitor screens performed in a bio-safety level (BSL)-4 laboratory using a combination of high-throughput robotics, high-content imaging and novel data analysis pipelines. This dataset has identified both miRNA promoters and inhibitors of SARS-CoV-2 replication which may be used by researchers to further explore therapeutic targets against SARS-CoV-2 and the host factors influencing COVID pathogenesis.

MicroRNAs↗