Biology subjects

Baxter, R.

Publications and source records attributed to Baxter, R..

7 recordsLinked to original sources

bioRxiv2026

ATP11A and ATP11C are plasma membrane phosphatidylserine flippases in in vitro human megakaryocytes.

Thrombotic diseases are the major worldwide cause of cardiovascular death. Platelets prevent blood loss following injury (haemostasis), but inappropriate and excessive platelet activation can lead to thrombosis. Platelet activation must be tightly controlled. Pro-coagulant platelets expose phosphatidylserine (PS), enabling coagulation complex assembly, enhancing thrombin generation and thrombosis. PS is normally restricted to the inner leaflet of the plasma membrane by flippase (aminophospholipid translocase) activity. However, the flippase protein(s) responsible for this crucial activity in platelets remains unidentified. The P4 ATPases ATP11A and ATP11C, regulated by their obligatory partner CDC50A, flip PS at the plasma membrane in a range of different cell types. To investigate platelet flippases, human induced pluripotent stem cells (hiPSCs) were forward-programmed into CD41+/CD42+ megakaryocytes, the platelet precursor. Wildtype (WT) forward-programmed megakaryocytes showed similar flippase activity to human platelets with internalisation of NBD-PS that could be inhibited by high cytosolic Ca2+ or N-ethylmaleimide (NEM). We then generated CDC50A, ATP11A or ATP11C single knockout and ATP11A/11C double knockout (DKO) hiPSCs using CRISPR-Cas9. CDC50A-KO, ATP11A-KO, ATP11C-KO and DKO hiPSC clones successfully formed CD41a+/CD42a+ mature megakaryocytes. CDC50A-KO megakaryocytes bound Annexin V when unstimulated and had no remaining NEM-sensitive flippase activity indicating the involvement of a P4-ATPase. Although ATP11A-KO and ATP11C-KO megakaryocytes had similar flippase activity to WT clones, DKO clones had inhibited NBD-PS internalisation compared to WT and had no remaining NEM-sensitive flippase activity. This indicates that the CDC50A-regulated P4-ATPases ATP11A and ATP11C act together at the megakaryocyte plasma membrane and are responsible for PS flippase activity and therefore likely responsible in human platelets.

cell biology↗

bioRxiv2024

Chronic inorganic nitrate supplementation does not improve metabolic health and worsens disease progression in mice with diet-induced obesity.

Inorganic nitrate (NO3-) has been proposed to be of therapeutic use as a dietary supplement in obesity and related conditions including the Metabolic Syndrome (MetS), type-II diabetes and metabolic dysfunction associated steatotic liver disease (MASLD). Administration of NO3- to endothelial nitric oxide synthase-deficient mice reversed aspects of MetS, however the impact of NO3- supplementation in diet-induced obesity is not well understood. Here we investigated the whole-body metabolic phenotype and cardiac and hepatic metabolism in mice fed a high-fat high-sucrose (HFHS) diet for up to 12-months of age, supplemented with 1 mM NaNO3 (or NaCl) in their drinking water. HFHS-feeding was associated with a progressive obesogenic and diabetogenic phenotype, which was not ameliorated by NO3-. Furthermore, HFHS-fed mice supplemented with NO3- showed elevated levels of cardiac fibrosis, and accelerated progression of MASLD including development of hepatocellular carcinoma in comparison with NaCl-supplemented mice. NO3- did not enhance mitochondrial {beta}-oxidation capacity in any tissue assayed and did not suppress hepatic lipid accumulation, suggesting it does not prevent lipotoxicity. We conclude that NO3- is ineffective in preventing the metabolic consequences of an obesogenic diet and may instead be detrimental to metabolic health against the background of HFHS-feeding. This is the first report of an unfavorable effect of long-term nitrate supplementation in the context of the metabolic challenges of overfeeding, warranting urgent further investigation into the mechanism of this interaction. New & NoteworthyInorganic nitrate has been suggested to be of therapeutic benefit in obesity-related conditions as it increases nitric oxide bioavailability, enhances mitochondrial {beta}-oxidation and reverses Metabolic Syndrome in eNOS-/- mice. However, we here show that over 12 months, nitrate was ineffective in preventing metabolic consequences in high-fat high-sucrose fed mice, and worsened aspects of metabolic health, impairing cholesterol handling, increasing cardiac fibrosis, and exacerbating steatotic liver disease progression, with acceleration to hepatocellular carcinoma.

physiology↗

bioRxiv2024

Development of Retinotopic Feedback: Layer 6 Pyramids to Lateral Geniculate Principal Cells

The development of many feedforward pathways in the brain, from sensory inputs to neocortex, have been studied and modeled extensively, but the development of feedback connections, which tend to occur after the development of feedforward pathways, have received less attention. The abundance of feedback connections within neocortex and between neocortex and thalamus suggests that understanding feedback connections is crucial to understanding connectivity and signal processing in the brain. It is well known that many neural layers are arranged topologically with respect to sensory input, and many neural models impose a symmetry of connections between layers, commonly referred to as reciprocal connectivity. Here, we are concerned with how such reciprocal, feedback connections develop so that the topology of the sensory input is preserved. We focus on feedback connections from layer 6 of visual area V1 to primary neurons in the Lateral Geniculate Nucleus (LGN). The proposed model is based on the hypothesis that feedback connections from V1-L6 to LGN use voltage-activated T-channels to appropriately establish and modify synapses in spite of unavoidable temporal delays. We also hypothesize that developmental spindling relates to synaptogenesis and memory consolidation.

neuroscience↗

bioRxiv2023

Network-based prioritisation and validation of novel regulators of vascular smooth muscle cell proliferation in disease

Aberrant vascular smooth muscle cell (VSMC) homeostasis and proliferation are hallmarks of vascular diseases causing heart attack and stroke. To elucidate molecular determinants governing VSMC proliferation, we reconstructed gene regulatory networks from single cell transcriptomics and epigenetic profiling. We find progressive activation of enhancers at disease-relevant loci in VSMCs that dont respond to injury and proliferation-predisposed cells. Our analysis suggests that while many transcription factors are shared, their target loci differ between VSMC states. Comparison of rewiring between VSMC subsets and in silico perturbation analysis prioritised novel regulators, including RUNX1 and the network target TIMP1. We experimentally validated that the pioneer factor RUNX1 increased VSMC responsiveness and show that TIMP1 feeds back to promote VSMC proliferation through CD74-mediated STAT3 signalling. Both RUNX1 and the TIMP1-CD74 axis were expressed in hVSMCs, at low frequency in normal arteries and increased in disease, suggesting clinical significance and potential as novel vascular disease targets.

molecular biology↗

bioRxiv2023

The endoplasmic reticulum stress sensor IRE1 regulates collagen secretion through the enforcement of the proteostasis factor P4HB/PDIA1 contributing to liver damage and fibrosis

Collagen is one the most abundant proteins and the main cargo of the secretory pathway, contributing to hepatic fibrosis and cirrhosis due to excessive deposition of extracellular matrix. Here we investigated the possible contribution of the unfolded protein response, the main adaptive pathway that monitors and adjusts the protein production capacity at the endoplasmic reticulum, to collagen biogenesis and liver disease. Genetic ablation of the ER stress sensor IRE1 reduced liver damage and diminished collagen deposition in models of liver fibrosis triggered by carbon tetrachloride (CCl4) administration or by high fat diet. Proteomic and transcriptomic profiling identified the prolyl 4-hydroxylase (P4HB, also known as PDIA1), which is known to be critical for collagen maturation, as a major IRE1-induced gene. Cell culture studies demonstrated that IRE1 deficiency results in collagen retention at the ER and altered secretion, a phenotype rescued by P4HB overexpression. Taken together, our results collectively establish a role of the IRE1/P4HB axis in the regulation of collagen production and its significance in the pathogenesis of various disease states.

cell biology↗

bioRxiv2021

Low-coverage reduced representation sequencing reveals subtle within-island genetic structure in Aldabra giant tortoises

Aldabrachelys gigantea (Aldabra giant tortoise) is one of only two giant tortoise species left in the world and survives as a single wild population of over 100,000 individuals on Aldabra Atoll, Seychelles. Despite this large current population size, the species faces an uncertain future because of its extremely restricted distribution range and high vulnerability to the projected consequences of climate change. Captive-bred A. gigantea are increasingly used in rewilding programs across the region, where they are introduced to replace extinct giant tortoises in an attempt to functionally resurrect degraded island ecosystems. However, there has been little consideration of the current levels of genetic variation and differentiation within and among the islands on Aldabra. As previous microsatellite studies were inconclusive, we combined low-coverage and double digest restriction associated DNA (ddRAD) sequencing to analyze samples from 33 tortoises (11 from each main island). Using 5,426 variant sites within the tortoise genome, we detected patterns of population structure within two of the three studied islands, but no differentiation between the islands. These unexpected results highlight the importance of using genome-wide genetic markers to capture higher-resolution genetic structure to inform future management plans, even in a seemingly panmictic population. We show that low-coverage ddRAD sequencing provides an affordable alternative approach to conservation genomic projects of non-model species with large genomes.

ecology↗

bioRxiv2021

Compositional Data Analysis using Kernels in Mass Cytometry Data

MotivationCell type abundance data arising from mass cytometry experiments are compositional in nature. Classical association tests do not apply to the compositional data due to their non-Euclidean nature. Existing methods for analysis of cell type abundance data suffer from several limitations for high-dimensional mass cytometry data, especially when the sample size is small. ResultsWe proposed a new multivariate statistical learning methodology, Compositional Data Analysis using Kernels (CODAK), based on the kernel distance covariance (KDC) framework to test the association of the cell type compositions with important predictors (categorical or continuous) such as disease status. CODAK scales well for high-dimensional data and provides satisfactory performance for small sample sizes (n < 25). We conducted simulation studies to compare the performance of the method with existing methods of analyzing cell type abundance data from mass cytometry studies. The method is also applied to a high-dimensional dataset containing different subgroups of populations including Systemic Lupus Erythematosus (SLE) patients and healthy control subjects. Availability and ImplementationCODAK is implemented using R. The codes and the data used in this manuscript are available on the web at http://github.com/GhoshLab/CODAK/. Supplementary informationSupplementary Materials.pdf.

bioinformatics↗