Biology subjects

Noseda, M.

Publications and source records attributed to Noseda, M..

7 recordsLinked to original sources

bioRxiv2026

Multimodal Hypersampling of the adult human heart resolves tissue-specific cell states and disease-associated variants

Cardiovascular diseases often arise in anatomically specialised regions of the heart that remain poorly represented in existing single-cell and spatial atlas references. Here we profiled 28 regions of the adult human heart from 36 donors, combining paired single-nucleus RNA and chromatin accessibility assays with spatial transcriptomics. The resulting atlas integrates 1,059,175 expression profiles and 452,614 chromatin accessibility profiles, and defines spatial niches across the heart. In cardiac valves, we identify a valve fibroblast-macrophage niche that is polarised to the non-fibrosa surface and expands with age. Aortic stenosis genetic risk was enriched in inflammatory regulatory programmes of the Valve Fibroblast Immune cell state. In pulmonary veins, we define PITX2+ Myocardial Sleeve Cells, a region-restricted cardiomyocyte population in which a fine-mapped 4q25 atrial fibrillation variant intersects a cell type-specific open chromatin region. In coronary arteries, we resolve a RUNX1-marked synthetic smooth muscle layer in the subintima that provides a molecular identity for diffuse intimal thickening, a constitutive feature of the healthy vessel wall and a substrate for atherosclerosis, and show by perturbation in human smooth muscle cells that RUNX1 promotes cell-cycle entry while restraining inflammatory cytokine gene expression. Finally, allele-specific accessibility together with deep learning models fine-tuned to predict regulatory activity from DNA sequence identify cell type-specific regulatory effects at GWAS loci for atrial fibrillation, coronary artery disease and calcific aortic valve stenosis, including a variant whose Valve Fibroblast-specific effect on the polyamine transporter ATP13A3 is opposite in direction to the effect seen in bulk-tissue eQTL references that lack valve cells. Together with these cardiac sequence models and CardioSleuth, an AI-powered exploration engine for cardiac regulatory effects, this atlas links cardiac anatomy, gene regulation and disease genetics at single-cell resolution. By placing genetic risk in its precise cellular and anatomical context, it provides a foundation for mechanistic disease understanding, cell-state-specific therapeutic target nomination, and improved interpretation of inherited cardiovascular risk to inform future therapy and management.

Cell 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↗

bioRxiv2023

Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19

The most common cause of death due to COVID-19 remains respiratory failure. Yet, our understanding of the precise cellular and molecular changes underlying lung alveolar damage is limited. Here, we integrate single cell transcriptomic data of COVID-19 donor lungs with spatial transcriptomic data stratifying histopathological stages of diffuse alveolar damage (DAD). We identify changes in cellular composition across progressive DAD, including waves of molecularly distinct macrophages and depleted epithelial and endothelial populations throughout different types of tissue damage. Predicted markers of pathological states identify immunoregulatory signatures, including IFN-alpha and metallothionein signatures in early DAD, and fibrosis-related collagens in organised DAD. Furthermore, we predict a fibrinolytic shutdown via endothelial upregulation of SERPINE1/PAI-1. Cell-cell interaction analysis revealed macrophage-derived SPP1/osteopontin signalling as a key regulator during early DAD. These results provide the first comprehensive, spatially resolved atlas of DAD stages, highlighting the cellular mechanisms underlying pro-inflammatory and pro-fibrotic pathways across alveolar damage progression.

pathology↗

bioRxiv2023

Spatially resolved multiomics of human cardiac niches

A cells function is defined by its intrinsic characteristics and its niche: the tissue microenvironment in which it dwells. Here, we combine single-cell and spatial transcriptomic data to discover cellular niches within eight regions of the human heart. We map cells to micro-anatomic locations and integrate knowledge-based and unsupervised structural annotations. For the first time, we profile the cells of the human cardiac conduction system, revealing their distinctive repertoire of ion channels, G-protein coupled receptors, and cell interactions using a custom CellPhoneDB.org module. We show that the sinoatrial node is compartmentalised, with a core of pacemaker cells, fibroblasts and glial cells supporting paracrine glutamatergic signalling. We introduce a druggable target prediction tool, drug2cell, which leverages single-cell profiles and drug-target interactions, providing unexpected mechanistic insights into the chronotropic effects of drugs, including GLP-1 analogues. In the epicardium, we show enrichment of both IgG+ and IgA+ plasma cells forming immune niches which may contribute to infection defence. We define a ventricular myocardial-stress niche enriched for activated fibroblasts and stressed cardiomyocytes, cell states that are expanded in cardiomyopathies. Overall, we provide new clarity to cardiac electro-anatomy and immunology, and our suite of computational approaches can be deployed to other tissues and organs.

genomics↗

bioRxiv2021

Heterozygous transcriptional and nonsense decay signatures in blood outgrowth endothelial cells from patients with hereditary haemorrhagic telangiectasia

Frameshift and nonsense DNA variants represent the commonest causes of monogenic inherited diseases. They usually generate premature termination codon (PTC)-containing RNA transcripts that produce truncated proteins in recombinant systems, but endogenously are subject to nonsense mediated decay. To examine native consequences of these variants, we derived cells from pre-genotyped patients. Blood outgrowth endothelial cells (BOECs) were established from individuals with hereditary hemorrhagic telangiectasia (HHT) due to a heterozygous nonsense variant in ACVRL1, ENG or SMAD4 that each encode an endothelial cell-expressed protein mediating bone morphogenetic protein (BMP)/ transforming growth factor (TGF)-{beta} signalling. RNA sequencing alignments to PTC alleles varied from 8-23% of expected, and differed between same-donor replicates. Differential gene expression analyses were validated by single cell qRT-PCR, and identification of changes in wider, disease-specific BMP/TGF-{beta} pathway components. However, the most differentially expressed genes clustered to disease-independent terms for post translational protein modification (isopeptide bond; ubiquitin-like conjugation). They were the only terms meeting Benjamini significance after clustering Bonferroni-ranked, differentially expressed genes from the 5,013 meeting 10% intraassay coefficients of variation, and significance was robust to normalisation methods. Optimised pulse chase experiments supported perturbed wildtype protein maturation, but no PTC-truncated protein was identified. Unexpectedly, BOEC cultures with highest PTC persistence were discriminated in unsupervised hierarchical clustering of low GINI coefficient invariant housekeeper genes, and patterns were compatible with higher cellular stress. The findings support a model whereby PTCs are more of a burden in stressed cells, and lead us to conclude that overlooked and varying PTC burdens contribute to biological variability.

cell biology↗

bioRxiv2020

Lack of evidence of ACE2 expression and replicative infection by SARS-CoV-2 in human endothelial cells

A striking feature of severe COVID-19 is thrombosis in large as well as small vessels of multiple organs. This has led to the assumption that SARS-CoV-2 virus directly infects and damages the vascular endothelium. However, endothelial expression of ACE2, the cellular receptor for SARS-CoV-2, has not been convincingly demonstrated. Interrogating human bulk and single-cell transcriptomic data, we found ACE2 expression in endothelial cells to be extremely low or absent in vivo and not upregulated by exposure to inflammatory agents in vitro. Also, the endothelial chromatin landscape at the ACE2 locus showed presence of repressive and absence of activation marks, suggesting that the gene is inactive in endothelial cells. Finally, we failed to achieve infection and replication of SARS-CoV-2 in cultured human endothelial cells, which were permissive to productive infection by coronavirus 229E that uses CD13 as the receptor. Our data suggest that SARS-Cov-2 is unlikely to infect endothelial cells directly; these findings are consistent with a scenario where endothelial injury is indirectly caused by the infection of neighbouring epithelial cells and/or due to systemic effects mediated by immune cells, platelets, complement activation, and/or proinflammatory cytokines.

pathology↗

bioRxiv2020

Cells and gene expression programs in the adult human heart

Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and strategies to improve therapeutic opportunities require deeper understanding of the molecular processes of the normal heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavor. Here, using large-scale single cell and nuclei transcriptomic profiling together with state-of-the-art analytical techniques, we characterise the adult human heart cellular landscape covering six anatomical cardiac regions (left and right atria and ventricles, apex and interventricular septum). Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, revealing distinct subsets in the atria and ventricles indicative of diverse developmental origins and specialized properties. Further we define the complexity of the cardiac vascular network which includes clusters of arterial, capillary, venous, lymphatic endothelial cells and an atrial-enriched population. By comparing cardiac cells to skeletal muscle and kidney, we identify cardiac tissue resident macrophage subsets with transcriptional signatures indicative of both inflammatory and reparative phenotypes. Further, inference of cell-cell interactions highlight a macrophage-fibroblast-cardiomyocyte network that differs between atria and ventricles, and compared to skeletal muscle. We expect this reference human cardiac cell atlas to advance mechanistic studies of heart homeostasis and disease.

genomics↗