Project description:Background. Ageing is one of the main risk factors of cardiovascular disease. Pericytes are capillary-associated mural cells involved in the maintenance and stability of the vascular network. In the heart, the consequences of ageing on cardiac pericytes are unknown. Methods. In this study, we have combined single nucleus RNA sequencing and histological analysis to determine the effects of ageing on cardiac pericytes. Furthermore, we have conducted in vivo and in vitro analysis of RGS5 loss of function and finally have perfomed pericytes-fibroblasts co-culture studies to understand the effect of RGS5 loss of function in pericytes on the neighbouring fibroblasts. Results. We showed that ageing reduces the pericyte area and coverage. Single nucleus RNA sequencing analysis further revealed that the expression of the Regulator of G protein signalling 5 (Rgs5) is reduced in old cardiac pericytes. In vivo and in vitro studies showed that the deletion of RGS5 induces morphological changes and a pro-fibrotic gene expression signature characterized by the expression of different extracellular matrix components and growth factors like TGFB2 and PDGFB in pericytes. Indeed, the culture of fibroblasts with the supernatant of RGS5 deficient pericytes induced their activation characterized by the increased expression of α smooth muscle actin in a TFGβ2 dependent mechanism. Conclusions. Our results identify RGS5 as a crucial regulator of pericyte function during cardiac ageing. The deletion of RGS5 causes cardiac dysfunction and induces myocardial fibrosis, one of the hallmarks of cardiac ageing.
Project description:Aging is a major risk factor for impaired cardiovascular health. The aging myocardium is characterized by microcirculatory and diastolic dysfunction and increased susceptibility to arrhythmias. Nerves align with vessels during development. However, the impact of aging on the cardiac neuro-vascular interface is entirely unknown. Here, we report that aging reduces nerve density specifically in the left ventricle and dysregulates vascular-derived neuro-regulatory genes. Aging leads to a down-regulation of miR-145 and de-repression of the neuro-repulsive factor Semaphorin-3A. miR-145 deletion, which increased Sema3a expression, or endothelial Sema3a overexpression reduced axon density, thus mimicking the observed aged heart phenotype. Removal of senescent cells, which accumulated with chronological age in parallel to the decline in nerve density, rescued age-induced denervation, reduced Sema3a expression, preserved heart rate variability and reduced electrical instability. These data suggest that senescence-associated regulation of neuro-regulatory genes is associated with reduced nerve density and, thereby, contributes to age-associated cardiac dysfunction.
Project description:Here we provide snRNA-seq datasets from heart failure patients with reduced ejection fraction and snRNA-SEQ of the corresponding LAD mouse model (permanent ligation of the left anterior descending artery)
Project description:Single-cell transcriptomics has emerged as a powerful technology for understanding cardiovascular diseases, providing valuable insights into transcriptomic changes linked to heart failure, both with and without preserved ejection fraction. However, significant gaps persist in our understanding of the molecular mechanisms underlying these different types of heart failure, and we continue to seek innovative approaches to tackle the challenges posed by the increasing scale and complexity of single-cell datasets in identifying meaningful gene signatures. The integration of machine learning, particularly deep neural networks, has shown immense promise in addressing these challenges by learning transcriptional patterns from single-cell transcriptomic data, reconstructing expression profiles, and effectively classifying cells. Recent advancements in explainable artificial intelligence enhanced the interpretation of these models by attributing importance scores, such as Shapley values. However, methods for identifying differentially regulated gene contribution scores have not yet been integrated. In this study, we introduce a novel method to identify differentially explained genes (DXGs) based on importance scores derived from custom-built neural networks capable of classifying heart failure subtypes at the single-cell level. We highlight the superiority of DXGs in identifying heart failure-relevant pathways, presenting them in a format comparable to traditional differential expression analyses. Using this method, we identify novel signatures providing new insights into the molecular basis of heart failure and offering a robust foundation for future research and therapeutic exploration.
Project description:Brown adipocyte-specific ChREBP knockout were generated by crossing mice with a floxed exon1a in the Mlxipl gene with Ucp1-Cre mice. These ChREBPflox/flox Ucp1-Cre+ (Cre+) mice and ChREBP-expressing control (Cre-) mice were studied under various conditions of BAT activation. Housing at room temperature (22°C, RT) was chosen as a control condition when BAT is mildly activated. Cold-exposure (6°C) was carried out for 1 day (acute cold ), as an early stage when proliferative processes of BAT adaptation are not yet taking place, or for 10 days (chronic cold) when BAT is fully expanded.
Project description:We characterized single-cell transcriptional profiles of the cardiac non-myocyte cell pool in C57BL/6J mice. The cell preparation we sequenced consisted of metabolically active, nucleated non-myocyte cells from heart ventricles of female and male mice which were depleted of endothelial cells. The goals of this experiment included examining cellular diversity, identifying markers of understudied cell populations, exploring functional roles of different cell types, and characterizing sexual dimorphism in cardiac gene expression.
Project description:Single-nucleus RNA-seq-2 method that allows deep characterization of nuclei isolated from frozen archived tissues. We have used this approach to characterize the transcriptional profile of individual hepatocytes with different levels of ploidy. This method has the potential to explore archived samples, for instance to study the development and progression of disease in complex tissues. To illustrate the potential of this method, we have deeply characterized the cellular heterogeneity driven by spatial distribution and different levels of ploidy in the young adult mouse liver.
Project description:We performed 3' single-cell RNA-seq using the 10X Genomics Chromium (version 1 chemistry) system on ~19,000 undifferentiated human IPSCs to explore the cellular heterogeneity of a seemingly homogeneous cell population.
Project description:Using 6-months, 16-months, and 24-months old mice of a inducible expression of human a-syn constructs based Parkinson mouse model, we produced a single nucleus RNA dataset by cutting 0mm Bregma to -5mm Bregma. The Chromium 3’ Single Cell Library Kit (10x Genomics) was used and Sequencing was performed on a NovaSeq 6000.
Project description:In dogs, a species for which markers of cell populations are often limiting, we sought to evaluate in an unbiased way the heterogeneity of cell subpopulations in the bronchoalveolar lavage fluid of healthy dogs, by single-cell RNA-sequencing.