Biology subjects

Bradley, E. J.

Publications and source records attributed to Bradley, E. J..

3 recordsLinked to original sources

bioRxiv2025

Comparative circadian transcriptome analysis reveals dampened and phase-advanced rhythms in sun-exposed human skin

BackgroundDaily molecular rhythms modulate skin physiology. However, the effects of chronic sun exposure on these rhythms remain unstudied. ObjectivesThis study aimed to identify and compare rhythmic genes and pathways in photoprotected and chronically photoexposed human skin in vivo. MethodsTwenty healthy White women, aged 51-63, with moderate-severe photoageing of the dorsal forearm were recruited. Skin biopsies (3mm) were taken from photoprotected (upper buttock) and photoexposed (dorsal forearm) skin of each individual at noon, 6PM, midnight, and 6AM, across a 24-hour cycle. Skin biopsies were analysed by RNA sequencing. Cosinor analysis identified cycling genes along with their amplitudes and peak expression phases. Nested models were used to identify genes that were differentially rhythmic between the photoprotected and photoexposed sites. Phase set and gene set analyses identified pathways enriched among rhythmic transcripts or altered between the two sites. ResultsIn the photoprotected buttock skin, 1546 genes (12%) met the criteria for cycling. In photoexposed forearm skin, the number was reduced to 959 (8%). As a group, transcripts that cycled in both sites had overall higher amplitude in photoprotected skin (p < 2.2e-16). Peak expression times for these transcripts showed a pronounced bimodal distribution and were clustered in the early morning and mid-afternoon. Distributions of peak times were significantly different between photoexposed and photoprotected skin (p < 0.00025), with peak times advanced in photoexposed skin. We identified 480 genes with significantly different rhythmic properties between the skin sites. Genes involved in DNA repair, MYC targets, E2F and G2M checkpoint pathways were enriched among those that showed higher amplitude oscillations in photoprotected skin. Genes involved in epithelial mesenchymal transition and apical junction pathways showed higher amplitude oscillations in photoexposed skin. ConclusionsTemporal rhythms have a marked influence on skin molecular physiology and are altered in photoaged skin. Temporally advanced cycling patterns and a reduced number of rhythmic genes in photoexposed as compared to photoprotected skin suggest that chronic UV exposure may disrupt and/or reprogram circadian output rhythms to further alter skin physiology.

cell biology↗

bioRxiv2023

Novel in-silico predicted matrikines are differential mediators of in vitro and in vivo cellular metabolism

The exogenous application of small peptides can beneficially affect clinical skin appearance (wrinkles) and architecture (collagen and elastic fibre deposition and epidermal thickness). However, the discovery of new bioactive peptides has not been underpinned by any guiding hypothesis. As endogenous extracellular matrix (ECM)-derived peptides produced during tissue remodelling can act as molecular signals influencing cell metabolism, we hypothesised that protease cleavage site prediction could identify putative novel matrikines with beneficial activities. Here, we present an in silico to in vivo discovery pipeline, which enables the prediction and characterisation of peptide matrikines which differentially influence cellular metabolism in vitro. We use this pipeline to further characterise a combination of two novel ECM peptide mimics (GPKG and LSVD) which act in vitro to enhance the transcription of ECM organisation and cell proliferation genes and in vivo to promote epithelial and dermal remodelling. This pipeline approach can both identify new matrikines and provide insights into the mechanisms underpinning tissue homeostasis and repair.

cell biology↗

bioRxiv2021

Unbiased and UMI-informed sequencing of cell-free miRNAs at single-nucleotide resolution

Terminal nucleotidyl transferases are enzymes that add non-templated nucleotides to RNA molecules. In the case of microRNAs, this process was shown to be functionally relevant for their maturation process and generation of isomiRs with non-canonical mRNA targets. Deconvolution of these posttranscriptional modifications is challenging in particular for extracellular miRNAs that are considered as a target for minimally-invasive diagnostics. Massively parallel RNA sequencing is the only method that can truthfully reveal isomiR diversity in biological samples and determine relative quantities. Improvements aside, current small RNA sequencing strategies remain imprecise. We developed IsoSeek that diverges from these methods by making use of randomized 5- and 3-adapters combined with a 10N unique molecular identifier (UMI). Using synthetic miRNA and isomiR spike-in sets and testing depletion and RNA competition strategies in 7 sequencing rounds of >100 samples, we rigorously optimized and validated the technical accuracy of the IsoSeek method. In genetically-altered HEK293, we characterized the terminal uridylase (TUT4/TUT7) dependent miRNA uridylome and discovered extensive uridylation of disease-associated miRNAs. Notably, 3-uridylated isomiR profiles of plasma extracellular vesicles (EVs) rely on UMI-correction. Thus, IsoSeek advances our knowledge of cell-free miRNAs and supports development into non-invasive biomarkers.

genomics↗