Biology subjects

Pyke, C.

Publications and source records attributed to Pyke, C..

5 recordsLinked to original sources

bioRxiv2023

Encompassing view of spatial and single-cell RNA-seq renews the role of the microvasculature in human atherosclerosis

Atherosclerosis is a pervasive contributor to cardiovascular diseases including ischemic heart disease and stroke. Despite the advance and success of effective lipid lowering-therapies and hypertensive agents, the residual risk of an atherosclerotic event remains high and improving disease understanding and development of novel therapeutic strategies has proven to be challenging. This is largely due to the complexity of atherosclerosis with a spatial interplay of multiple cell types within the vascular wall. Here, we generated an integrative high-resolution map of human atherosclerotic plaques by combining single-cell RNA-seq from multiple studies and novel spatial transcriptomics data from 12 human specimens to gain insights into disease mechanisms. Comparative analyses revealed cell-type and atherosclerosis-specific expression changes and associated alterations in cell-cell communication. We highlight the possible recruitment of lymphocytes via different endothelial cells of the vasa vasorum, the migration of vascular smooth muscle cells towards the lumen to become fibromyocytes, and cell-cell communication in the plaque, indicating an intricate cellular interplay within the adventitia and the subendothelial space in human atherosclerosis.

bioinformatics↗

bioRxiv2023

A Benchmark of state-of-the-art Deconvolution Methods in Spatial Transcriptomics: Insights from Cardiovascular Disease and Chronic Kidney Disease

A major challenge in sequencing based spatial transcriptomics (ST) is resolution limitations. Tissue sections are divided into hundreds-to thousands of spots, where each spot invariably contains a mixture of cell types. Methods have been developed to deconvolute the mixed transcriptional signal into its constituents. While ST is becoming essential for drug discovery especially in Cardiometabolic diseases, to date no deconvolution benchmark has been performed on these types of tissues and diseases. However, the three methods Cell2location, RCTD and spatialDWLS have previously been shown to perform well in brain tissue and simulated data. Here, we compare these methods to assess best performance when using human data from Cardiovascular Disease (CVD) data and Chronic Kidney Disease (CKD) from patients at different pathological states, evaluated using expert annotation. In this benchmark, we found that all three methods performed comparably well in deconvoluting verifiable cell types including smooth muscle cells and macrophages in vascular samples and podocytes in kidney samples. RCTD shows the best performance accuracy scores in CVD samples while Cell2location on average achieved the highest performance across test experiments. While all three methods had similar accuracies Cell2location need less reference data to converge at the expense of higher computational intensity. Finally, we also report that RCTD has the fastest computational time and the simplest workflow requiring fewer computational dependencies. In conclusion, we find that each method has particular advantages, and the optimal choice depends on the use case.

bioinformatics↗

bioRxiv2023

Human HYPOMAP: A comprehensive spatio-cellular map of the human hypothalamus

The hypothalamus is a brain region that plays a key role in coordinating fundamental biological functions. However, our understanding of the underlying cellular components and circuitry, have, until recently, emerged primarily from rodent studies. Here, we combine a single-nucleus sequencing database of 433,369 human hypothalamic cells, with spatial transcriptomics, to present a comprehensive spatio-cellular transcriptional map of the human hypothalamus, the HYPOMAP. Analysing hypothalamic leptin melanocortin pathway neuronal populations that play a role in appetite control, we identify spatially distinct populations of arcuate nucleus POMC and AGRP neurons, and their receptors MC3R and MC4R. Next, we map the cells expressing incretin receptors, targets of the new generation of anti-obesity medications, and uncover transcriptionally distinct GLP1R and GIPR-expressing cellular populations. Finally, out of the 458 hypothalamic cell types in HYPOMAP, we find 182 neuronal clusters are significantly enriched in expression of BMI GWAS genes. This enrichment is driven by 375 effector genes, with rare deleterious variants in 6 of these; MC4R, PCSK1, POMC, CALCR, BSN and CORO1A, the last of which has previously not been linked to obesity; being significantly associated with changes in BMI at the population level. Thus, the HYPOMAP provides a detailed atlas of the human hypothalamus in a spatial context, and serves as an important resource to identify novel druggable targets for treating a wide range of conditions, including reproductive, circadian, and metabolic disorders.

neuroscience↗

bioRxiv2023

Ccn2 deficiency causes smooth muscle cell de-differentiation and severe atherosclerosis in hyperlipidemic mice

Cellular communication network factor 2 (CCN2/CTGF) is a matricellular protein with an established role in fibrotic diseases and cancers, and therapies targeting CCN2 is currently in Phase II and III clinical trials for idiopathic pulmonary fibrosis, pancreatic cancer and Duchenne Muscular Dystrophy. Recent studies have highlighed a protective role of CCN2 in aortic aneurysm disease, but its role in atherosclerosis remains to be investigated. We identified arteries as having the highest relative expression of CCN2 across 54 human tissues. In aortas, CCN2 was among the highest expressed genes, and in situ hybridization of human internal thoracic arteries revealed vascular smooth muscle cells (SMCs) as its principal source. Hypothesizing a role for CCN2 in SMC phenotype maintenance and athero-protection, we investigated inducible Ccn2 knockout (Ccn2{Delta}/{Delta}) mice in normo- and hyper-lipidemic settings. Induction of hyperlipidemia by single intravenous injection of 1{middle dot}1011 viral genomes of rAAV8-D377Y-mPcsk9 combined with 24 weeks of western type diet resulted in severe enlargement (3-5-fold increase of relative aorta mass compared to wildtype littermates, p < 0.0001) and whitening of Ccn2{Delta}/{Delta} aortas. Oil Red O-staining of en face prepared thoracic aortas showed a marked increase in atherosclerosis in Ccn2{Delta}/{Delta} mice as compared to wildtype littermates (75% vs. 10% Oil Red O-positive aortic area, p < 0.0001). Transcriptomic profiling of cultivated SMCs derived from aortas of normolipidemic mice showed signatures of dedifferentiation (reduced expression of e.g. Myocd, Acta2 and Myh11) and modulation toward a synthetic, pro-inflammatory phenotype of Ccn2{Delta}/{Delta} SMCs. These effects were verified in vivo and in CCN2-silenced human aortic SMCs. Taken together, we find that CCN2 plays a critical athero-protective role in artery tissues, likely through maintaining SMCs in a differentiated, contractile phenotype.

pathology↗

bioRxiv2021

A survey of the mouse hindbrain in the fed and fasted state using single-nucleus RNA sequencing

ObjectiveThe area postrema (AP) and the nucleus tractus solitaris (NTS), located in the hindbrain, are key nuclei that sense and integrate peripheral nutritional signals and, consequently, regulate feeding behaviour. While single cell transcriptomics have been used in mice to reveal the gene expression profile and heterogeneity of key hypothalamic populations, similar in-depth studies have not yet been performed in the hindbrain. MethodsUsing single-nucleus RNA sequencing, we provide a detailed survey of 16,034 cells within the AP and NTS of the mouse, in the fed and fasted state. ResultsOf these, 8910 are neurons that group into 30 clusters, with 4289 coming from mice fed ad libitum and 4621 from overnight fasted mice. 7124 nuclei are from non-neuronal cells, including oligodendrocytes, astrocytes and microglia. Interestingly, we identified that the oligodendrocyte population was particularly transcriptionally sensitive to an overnight fast. The receptors GLP1R, GIPR, GFRAL and CALCR, which bind GLP1, GIP, GDF15 and amylin respectively, are all expressed in the hindbrain and are major targets for anti-obesity therapeutics. We characterise the transcriptomes of these four populations and show that their gene expression profiles are not dramatically altered by an overnight fast. Notably, we find that roughly half of cells that express GIPR are oligodendrocytes. Additionally, we profile POMC expressing neurons within the hindbrain and demonstrate that 84% of POMC neurons express either PCSK1, PSCK2 or both, implying that melanocortin peptides are likely produced by these neurons. ConclusionWe provide a detailed single-cell level characterisation of AP and NTS cells expressing receptors for key anti-obesity drugs that are either already approved for human use or are in clinical trials. This resource will help delineate the mechanisms underlying the effectiveness of these compounds, and also prove useful in the continued search for other novel therapeutic targets.

neuroscience↗