Biology subjects

Alonaizan, R.

Publications and source records attributed to Alonaizan, R..

5 recordsLinked to original sources

bioRxiv2026

Cardiac-immune microniches programme macrophage states in the regenerating heart

Adult zebrafish regenerate their hearts after injury, a process that requires macrophages, yet how local tissue microenvironments instruct macrophage states and function remains unclear. Here we combine single cell RNA sequencing with Visium and high-resolution MERFISH spatial transcriptomics to map the cardio-immune landscape of homeostatic and regenerating zebrafish hearts. We identify a mpeg1.1+ compartment comprising macrophages, dendritic, B and NK-like cells, and show that injury establishes a macrophage-centred immune environment with transcriptional programmes spanning resident surveillance, damage sensing, inflammation, antigen presentation, resolution and metabolic support. Communication-aware spatial modelling reveals that these states are not randomly distributed but organised into discrete structural-immune microniches across the injury region, each defined by stereotyped cellular compositions and ligand-receptor circuits. Within a fibroblast-macrophage microniche, we uncover an il34-csf1ra-egr1 axis in which col12a1a+ il34+ fibroblasts promote an egr1 pro-regenerative macrophage state that couples fibrosis, vascular integrity and epicardial signalling. We show that disruption of this axis by csf1ra loss of function reduces macrophage-, endothelial- and epicardial-rich microniches, amplifying fibroblast-driven domains that shift macrophages towards stress and long-sustained inflammatory programmes, thereby biasing early injury response towards a pro-fibrotic state. Our work establishes spatially defined cardio-immune microniches as key organisers of macrophage function and regenerative outcome, providing a mechanistic framework and actionable targets for reprogramming cardiac repair.

developmental biology↗

bioRxiv2025

A balanced circadian glycolytic rhythm drives cardiomyocyte cell cycle progression during fish heart regeneration.

The ability of heart tissue to repair itself after injury has fascinated scientists for decades1,2. Researchers have long studied the internal body clock, or circadian rhythm, for its role in coordinating daily cycles of metabolism and cell activity3,4, but its relevance to heart repair has remained unknown. This study explores, for the first time, whether natural daily rhythms influence heart regeneration--a process driven by cardiomyocyte proliferation. We discovered that DNA replication, mitosis, oxidative phosphorylation, and glycolysis follow a precise daily order in regenerating zebrafish hearts. Disrupting core clock gene expression abolishes the rhythms of glycolysis and mitosis, preventing cardiomyocyte cell cycle progression and regeneration. Insulin-resistant Astyanax mexicanus cavefish, which have adapted to dark caves, similarly show a loss of mitosis rhythm and cardiomyocyte cell cycle progression, which we find is caused by reduced glycolysis. Despite this reduction, glycolysis rhythm displays a larger amplitude in cavefish--a pattern recapitulated in insulin-resistant zebrafish. Insulin resistance resets metabolic rhythms to the morning, which is equally detrimental to regeneration. Here, we show that successful cardiac regeneration depends on synchronised clock and glucose rhythms, which together orchestrate the cell cycle events essential for cardiomyocyte proliferation and tissue repair.

physiology↗

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

microRNA-210 enhances cell survival and paracrine potential for cardiac cell therapy while targeting mitophagy.

The therapeutic potential of presumed cardiac progenitor cells (CPCs) in heart regeneration has garnered significant interest, yet clinical trials have revealed limited efficacy due to challenges in cell survival, retention, and expansion. Priming CPCs to survive the hostile hypoxic environment may be key to enhancing their regenerative capacity. We demonstrate that microRNA-210 (miR-210), known for its role in hypoxic adaptation, significantly improves CPC survival by inhibiting apoptosis through the downregulation of Casp8ap2, reduction of caspase activity, and decreased DNA fragmentation. Contrary to the expected induction of Bnip3-dependent mitophagy by hypoxia, miR-210 did not upregulate Bnip3, indicating a distinct anti-apoptotic mechanism. Instead, miR-210 reduced markers of mitophagy and increased mitochondrial biogenesis and oxidative metabolism, suggesting a role in metabolic reprogramming. Furthermore, miR-210 enhanced the secretion of paracrine growth factors from CPCs, which promoted in vitro endothelial cell proliferation and cardiomyocyte survival. These findings elucidate the multifaceted role of miR-210 in CPC biology and its potential to enhance cell-based therapies for myocardial repair by promoting cell survival, metabolic adaptation, and paracrine signalling.

developmental biology↗

bioRxiv2024

Transcriptomic analysis of adult mouse cardiac stromal cells using single-cell qRT-PCR

Fate mapping studies have challenged the longstanding view of the adult mammalian heart as a post-mitotic organ, suggesting limited cardiomyocyte renewal. This has spurred efforts to identify cardiac progenitor cell (CPC) populations, but their contribution to cardiac regeneration has been found to be minimal compared to cardiomyocyte proliferation. Despite this, CPC transplantation has shown therapeutic potential through paracrine signalling. The identity of CPCs remains unclear due to overlapping characteristics with other cardiac stromal cell populations such as fibroblasts, mesenchymal cells, and pericytes. This study sought to optimise the isolation of CPCs by developing a cardiac collagenase-trypsin (CT) protocol, which was compared to the established method of isolating cardiosphere-derived cells (CDCs). The CT protocol resulted in a higher cell yield and reduced expansion time, with both CTs and CDCs showing superior survival potential under serum starvation compared to commercially acquired cardiac fibroblasts (CFs). Single-cell qRT-PCR analysis revealed that CTs and CDCs share a similar gene expression profile, distinct from CFs, characterised by the enrichment of cardiogenic transcription factors. Notably, CTs exhibited higher expression of Tcf21 and lower Tbx5, suggesting an epicardial-derived fibroblast phenotype, whereas Tbx5 was enriched in CDCs and CFs. Additionally, CTs showed an enrichment of macrophage-associated genes Mrc1 and Csf1r, possibly due to the transdifferentiation of macrophages to or from a fibroblast phenotype in a subset of CTs. The study concludes that CTs represent a robust and efficient source of CPCs with therapeutic potential and offers insights into the complex identity of cardiac stromal cells.

developmental biology↗