Biology subjects

Baxter, M.

Publications and source records attributed to Baxter, M..

8 recordsLinked to original sources

bioRxiv2025

Hypercholesterolaemia promotes epigenetic memory in hematopoietic stem cells that persists after lipid lowering and causes systemic immunometabolic dysfunction mediated by macrophage metabolic reprogramming

In patients with atherosclerotic cardiovascular disease (ASCVD) lowering LDL cholesterol (LDL-C) reduces the risk of adverse cardiovascular events. However, these patients remain at continued risk of adverse cardiovascular events despite achieving optimal LDL-C lowering. We hypothesised that this residual risk is mediated by epigenetic programming of haematopoietic stem cells (HSC) which persists after cholesterol levels are lowered and results in sustained effects on innate immune cell metabolism, that is not resolved by cholesterol lowering. We found that exposure to high cholesterol (HC) in vivo induced long-term metabolic changes in macrophages differentiated ex vivo from bone marrow, leading to a pro-inflammatory profile; these changes persisted in vivo despite cholesterol lowering. HSC from HC mice had altered chromatin accessibility that persisted after cholesterol lowering and was also present in bone marrow monocytes and tissue resident macrophages. HC provoked RUNX1-dependent downregulation of stearoyl-CoA desaturase (SCD) which reduced mono-unsaturated fatty acid (MUFA) availability for OxPhos in murine and human monocytes and macrophages. Supplementation with MUFA restored OxPhos capacity and promoted a shift towards a less pro-inflammatory macrophage phenotype in HC-trained BMDM. Bone marrow chimera and lineage tracking studies revealed that prior exposure of HSC to HC conferred adverse systemic metabolic effects on normocholesterolemic mice, with increased adipose tissue mass and increased migration of macrophages derived from HC-exposed HSC into adipose tissue, resulting in increased adipose tissue inflammation and systemic glucose intolerance. These findings indicate that HC results in long-lasting immuno-epigenetic memory in HSC which is refractory to lipid lowering, and provide strong evidence that exposure to HC can have prolonged consequences that require new therapeutic approaches, beyond cholesterol lowering.

immunology↗

bioRxiv2025

REnformer, a single-cell ATAC-seq predicting model to investigate open chromatin sites

Genome regulatory elements are fundamental to cellular identity and cell type specific gene expression. Understanding how the underlying genetic code is differentially utilised by different cell types is central to understanding human health and disease. To better understand how DNA encodes genome regulatory elements such as promoters, enhancers, and boundary elements, we leverage the Enformer gene expression and epigenetic prediction model. We used transfer learning with high quality single cell ATAC datasets to develop REnformer, a model to predict chromatin accessibility. By introducing a bench-mark for comparing performances against Enformer model, REnformer significantly outperformed Enformer in terms of higher prediction outcomes and lower error rates in all extensive analyses shown; introducing these benchmarks allowed us, and possible future works, to fairly compare such models. We further tested REnformer by predicting the effects of a well characterised -thalassemia variant and found that the prediction aligned with the observed change in genome regulatory element, previously validated. We conclude that REnformer is and can be a state-of-the-art tool to predict cell type specific regulatory elements, and interrogate the effect of genome variation in health and disease.

bioinformatics↗

bioRxiv2025

The 18S rRNA methyltransferase, BUD23, is required for appropriate lipid and mitochondrial metabolism

Efficient energy metabolism is essential for health and its dysregulation drives cardiometabolic disease. Delivery of regulatory control through translation and ribosome function is emerging as important. Here, we identify the rRNA methyltransferase BUD23 as a potent regulator of cellular and systemic energy homeostasis. Adipocyte-specific deletion of BUD23 in mice regulates lipid and mitochondrial metabolism resulting in a pronounced lean phenotype and resistance to diet-induced obesity. Mechanistically, BUD23 modulates translation initiation and efficiency of mRNAs with specific features - including short 5 UTR length and GC-rich post-initiation codon usage - characteristic of mitochondrial and lipogenic proteins. Genetic analyses and Mendelian randomisation support a role for BUD23 in human cardiometabolic traits and disease burden. Together, our findings uncover a conserved translational control mechanism that regulates energy state, from cellular metabolism through to human cardiometabolic health.

cell biology↗

bioRxiv2024

Glial cell derived pathway directs regenerating optic nerve axons toward the CNS midline

After optic nerve injury, several retinal ganglion cell (RGC) intrinsic signaling pathways have been shown to enhance RGC survival and RGC axonal growth. In contrast, few extrinsic cues have been identified that guide regenerating RGC axons toward and across the optic chiasm. Here, we use live-cell imaging in larval zebrafish to show that regrowing RGC axons initiate growth toward the midline and extend along a trajectory similar to their original projection. From a candidate genetic screen, we identify the glycosyltransferase Lh3 (also referred to as Plod3) to be required to direct regrowing RGC axons toward the midline during active regeneration. Moreover, we show that transgenic lh3 expression in sox10+ presumptive olig2+ oligodendrocytes located near the optic chiasm restores directed axonal growth in lh3 mutants. Finally, we find that mutants in collagen 18a1 (col18a1), a putative Lh3 substrate, display RGC axonal misguidance phenotypes similar to lh3 mutants, suggesting that lh3 may act through col18a1 during regeneration. Combined, these data identify lh3 as part of a glial derived molecular pathway critical for guiding in vivo regenerating RGC axons toward and across the optic chiasm.

neuroscience↗

bioRxiv2024

Serotonin neuromodulation directs optic nerve regeneration

Optic nerve (ON) regeneration in mammalian systems is limited by an overshadowing dominance of inhibitory factors. This has severely hampered the identification of pro- regenerative pathways. Here, we take advantage of the regenerative capacity of larval zebrafish to identify pathways that promote ON regeneration. From a small molecule screen, we identified modulators of serotonin (5-HT) signaling that inhibit ON regeneration. We find several serotonin type-1 receptor genes are expressed in RGC neurons during regeneration and that inhibiting 5- HT1 receptors or components of the 5-HT pathway selectively impedes ON regeneration. We show that 5-HT1 receptor signaling is dispensable during ON development yet is critical for regenerating axons to emerge from the injury site. Blocking 5-HT receptors once ON axons have crossed the chiasm does not inhibit regeneration, suggesting a selective role for 5-HT receptor signaling early during ON regeneration. Finally, we show that agonist-mediated activation of 5-HT1 receptors leads to enhanced and ectopic axonal regrowth. Combined, our results provide evidence for mechanisms through which serotonin-dependent neuromodulation directs ON regeneration in vivo. Summary Statement5-HT1 receptors selectively promote early optic nerve regrowth in zebrafish but are dispensable during development. Serotonin receptor-dependent modulation instructs regenerating optic nerve axons toward the brain in vivo.

developmental biology↗

bioRxiv2024

Deciphering cis-regulatory elements using REgulamentary

With the boom in Genome-Wide Association Studies (GWAS), it has become apparent that many disease-associated genetic variants lie in the non-coding regions of the genome. In order to prioritise these variants and disentangle their functional significance, it is important to be able to accurately classify cis-regulatory elements within these non-coding regions of the genome. Historically, the classification of cis-regulatory elements relied purely on the presence of characteristic histone marks, with recent advancements in their classification using more sophisticated Hidden Markov Model (HMM)-based approaches. The limitation of the HMM-based approaches is that the output of these models is an arbitrary chromatin state, which then requires the user to manually assign these states to a particular class of cis-regulatory elements. Here we present a new tool, REgulamentary, which enables de novo genome-wide annotation of cis-regulatory elements in a cell-type specific manner. We benchmarked REgulamentary against GenoSTAN, the most popular existing published chromatin annotation and regulatory element identification tool, to demonstrate the advancements REgulamentary can provide in assigning chromatin states. Finally, as an example of REgulamentarys utility in solving complex disease trait loci, we applied REgulamentary to published GWAS data to demonstrate how this tool can be used to prioritise likely causal variants.

bioinformatics↗

bioRxiv2022

Thyroid hormone and ALK5 inhibitor improve maturation of human pluripotent stem cell derived hepatocytes

Hepatocytes derived from human pluripotent stem cells (PSCs) hold great promise for modeling human liver disease, in vitro hepatotoxicity testing, and future cellular therapy. However, current protocols generate hepatocyte-like cells (HLCs) that resemble fetal hepatocytes, and thus do not accurately recapitulate the molecular identity and functions of the adult liver. To address this, we compared the transcriptomes of human fetal and adult liver to PSC-derived HLCs during progressive stages of in vitro differentiation. This revealed that during the final stages of in vitro differentiation the hepatic transcription factors HNF4A and CEBPA were sub-optimally expressed. Computational analyses predicted that ALK5i II (TGF-{beta} receptor inhibitor) and thyroid hormone (T3) would be able to rectify this and improve HLC maturation. We next show that application of these molecules during hepatocyte differentiation indeed increases CEBPA and HNF4A mRNA and protein expression, and that these HLCs show enhanced albumin secretion, a 25-fold increase in CYP3A4 activity, and 10 to 100-fold increased expression of mature hepatic markers. We demonstrate that this improved maturation is effective across different cell lines and HLC differentiation protocols, and exemplifies that our approach provides a tractable template for identifying and targeting additional factors that that will fully mature human liver cells from human pluripotent stem cells.

developmental biology↗

bioRxiv2021

Circadian clock function does not require the histone methyltransferase MLL3

AO_SCPLOWBSTRACTC_SCPLOWThe circadian clock controls the physiological function of tissues through the regulation of thousands of genes in a cell-type specific manner. The core cellular circadian clock is a transcription-translation negative feedback loop, which can recruit epigenetic regulators to facilitate temporal control of gene expression. Histone methyltransferase, mixed lineage leukemia gene 3 (MLL3) was reported to be required for maintenance of circadian oscillations in cultured cells. Here, we test the role of MLL3 in circadian organisation in whole animals. Using mice expressing catalytically inactive MLL3, we show that MLL3 methyltransferase activity is in fact not required for circadian oscillations in vitro in a range of tissues, nor for maintenance of circadian behavioural rhythms in vivo. In contrast to a previous report, loss of MLL3-dependent methylation did not affect global levels of H3K4 methylation in liver, indicating substantial compensation from other methyltransferases. Further, we found little evidence of genomic repositioning of H3K4me3 marks. We did, however, observe repositioning of H3K4me1 from intronic regions to intergenic regions and gene promoters, however there were no changes in H3K4me1 mark abundance around core circadian clock genes. Output functions of the circadian clock, such as control of inflammation, were largely intact in MLL3-methyltransferase deficient mice, although some gene specific changes were observed, with sexually dimorphic loss of circadian regulation of specific cytokines. Taken together, these observations call for a major reassessment of the inter-relationship between the circadian clock and MLL3-directed histone methylation, and a deeper examination of other epigenetic mechanisms which may facilitate circadian clock function. SO_SCPLOWIGNIFICANCEC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSTATEMENTC_SCPLOWA highly cited paper published in PNAS previously reported an essential role for the histone methyltransferase MLL3 in maintaining circadian oscillations in cultured cells. We tested the role of MLL3 in vivo and in primary tissues showing that MLL3 in fact plays no role in organising the core circadian clock, and has no functional impact on whole animal circadian behaviour. However, in further analysis, we newly discover a role for MLL3 in conferring circadian control to components of the inflammatory response, doing so in a sexually dimorphic manner. As the MLL family of histone methyltransferases are being targeted by pharmaceuticals for cancer, it is important to understand how methyltransferases may be driving circadian rhythms in gene expression.

molecular biology↗