Biology subjects

Carter, R. D.

Publications and source records attributed to Carter, R. D..

4 recordsLinked to original sources

bioRxiv2025

Absence of a prolonged macrophage and B cell response inhibits heart regeneration in the Mexican cavefish

A balanced immune response after cardiac injury is crucial to successful heart regeneration, but knowledge of what distinguishes a regenerative from a scarring response is still limited. The Mexican cavefish provides a unique comparative model to study heart regeneration and scarring within a single species. Surface-dwelling fish are capable of heart regeneration whereas their cave-dwelling Pachon counterparts lack this ability, similar to the human heart. Using single-cell transcriptomics and immune perturbations, we find significant differences in the immune response between the two populations. Unlike the transient response in the scarring Pachon, the regenerative surface fish heart generates an unexpected functionally active prolonged innate and adaptive immune response at the late stages of regeneration. Inhibiting the overall prolonged immune response impairs regeneration and cardiomyocyte proliferation. Further characterisation of specific cell types shows that late-present macrophages are phagocytic, and their depletion disrupts regeneration but not cardiomyocyte proliferation while inhibiting B cells impairs regeneration by reducing cardiomyocyte proliferation. This B cell response is conserved in zebrafish. Our findings reveal critical immune mechanisms distinguishing regenerative and non-regenerative responses, offering insights for potential therapeutic strategies to enhance heart repair.

developmental biology↗

bioRxiv2025

A cluster of RNA Polymerase II molecules is stably associated with an active gene

In eukaryotic nuclei, transcription is associated with the clustering of RNA Polymerase II (RNAPII) molecules. The mechanisms underlying cluster formation, their interactions with genes, and their impact on transcriptional activity remain heavily debated. Here, we take advantage of the naturally occurring increase in transcriptional activity during Zygotic Genome Activation (ZGA) in Drosophila melanogaster embryos to characterize the functional roles of RNAPII clusters in a developmental context. Using single-molecule tracking and lattice light-sheet microscopy, we find that RNAPII cluster formation depends on transcription initiation, and that cluster lifetimes depend on transcriptional activity when not constrained by interphase duration. We show that single clusters are stably associated with active gene loci during transcription and that cluster intensities are strongly correlated with transcriptional output. Collectively, our data and simulations on cluster formation kinetics show that RNAPII clusters reflect local accumulations of transcriptionally engaged polymerases and do not form through higher-order mechanisms such as phase separation.

biophysics↗

bioRxiv2024

Multiomics-based assessment of 2D and 3D human iPSC-cardiomyocyte models of insulin resistance demonstrate metabolic and contractile dysfunction that recapitulates diabetic cardiomyopathy.

In type II diabetes (T2DM), the heart is exposed to hyperglycaemia, hyperlipidaemia, and hyperinsulinaemia, leading to insulin resistance and metabolic dysfunction, culminating in diabetic cardiomyopathy (DbCM). Human-centric models of DbCM are needed to provide mechanistic insights and therapeutic targets in a translationally relevant setting. We hypothesised that culturing human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) in an "insulin resistance" (IR) media, and assessing this using a systems biology approach, would offer a comprehensive evaluation of dysregulated pathways, establishing their suitability as a model of DbCM. Culturing hiPSC-CMs in 2D or 3D as engineered heart tissue (EHT) in IR media induced insulin resistance and activated numerous pathways implicated in DbCM, including metabolic remodelling, mitochondrial dysfunction, extracellular matrix remodelling, and endoplasmic reticulum stress. Pathways involved in fatty acid oxidation were upregulated, while those involved in glucose metabolism were downregulated, which was validated using radioisotope flux measurements. Adaptation to hypoxia, a key component of post-ischaemic remodelling, was blunted in the 2D IR hiPSC-CMs. Combining proteomic and transcriptomic analyses in the IR 3D EHT revealed significant enrichment of DbCM pathways, with subnetworks enriched for several metabolic and diabetes-related pathways. Additionally, IR 3D EHT displayed impaired relaxation, mimicking the diastolic dysfunction observed in T2DM patients. In conclusion, culturing hiPSC-CM in 2D or 3D in an IR media activates multiple mechanisms implicated in the development of DbCM, with IR 3D EHT also recapitulating the diastolic dysfunction present in patients with T2DM.

molecular biology↗

bioRxiv2022

AICAR prevents doxorubicin-induced heart failure in rats by ameliorating cardiac atrophy and improving fatty acid oxidation

Doxorubicin (DOX) is a widely used chemotherapeutic agent that can cause serious cardiotoxic side effects, leading to functional cardiac decline and ultimately, congestive heart failure (HF). Impaired mitochondrial function and energetics are thought to be key factors driving progression into HF. We have previously shown in a rat model of chronic intravenous DOX-administration that heart failure with reduced ejection fraction correlates with mitochondrial loss and dysfunction. Adenosine monophosphate-dependent kinase (AMPK) is a cellular energy sensor, regulating mitochondrial biogenesis and oxidative metabolism, including fatty acid oxidation. We hypothesized that AMPK activation could restore mitochondrial number and function and therefore be a novel cardioprotective strategy for the prevention of DOX-HF. We therefore set out to assess whether 5-aminoimidazole-4-carboxamide 1-{beta}-D-ribofuranoside (AICAR), an activator of AMPK, could prevent cardiac functional decline in this clinically relevant rat model of DOX-HF. In line with our hypothesis, AICAR improved cardiac systolic function. We show that this could be due to normalisation of substrate supply to the heart, as AICAR prevented DOX-induced dyslipidaemia. AICAR furthermore improved cardiac mitochondrial fatty acid oxidation, despite no increase in mitochondrial number. In addition, we found that AICAR prevented excessive myocardial atrophy, and RNAseq analysis showed that this may be due to normalisation of protein synthesis pathways, which are impaired in DOX-treated rat hearts. Taken together, these results show promise for use of AICAR as a cardioprotective agent in DOX-HF to both preserve cardiac mass and improve cardiac function.

biochemistry↗