Biology subjects

Richardson, L.

Publications and source records attributed to Richardson, L..

At least 19 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↗

bioRxiv2026

A Functional Genetic Atlas of Parkin Resolves Variants of Uncertain Significance and Predicts Parkinson's Disease Age at Onset

Autosomal recessive mutations in the Parkin gene (PRKN) cause early-onset Parkinsons disease (PD). Parkin functions as a ubiquitin E3 ligase acting downstream of the PINK1 kinase to promote phosphorylated ubiquitin at sites of mitochondrial damage. Yet the functional effects of most PRKN gene variants remain unknown. Here we use a pooled cellular assay measuring phosphorylated ubiquitin accumulation to quantify the activity of [~]9,200 PRKN missense and nonsense variants. Our screen identifies thousands of loss- and gain-of-function variants, including activating variants mainly residing at autoinhibitory interfaces. Functional scores accurately distinguish known PD pathogenic and benign variants, and enable reclassification of 173/184 variants of uncertain significance (VUS). When combined into biallelic genotype scores, these data predict the age at disease onset in patients, revealing a quantitative link between Parkin activity and clinical manifestation. Our results provide a comprehensive functional genetic map of Parkin and demonstrate the power of multiplexed assays of variant effects (MAVEs) for variant interpretation and precision medicine in PD.

genetics↗

bioRxiv2026

Prenatal Exposure to Bacterial Extracellular Vesicles Influences Fetal Gut Immunity and Immune Programming

BackgroundThe fetal immune system undergoes pivotal development during gestation, preparing for postnatal antigenic challenges. Bacterial extracellular vesicles (bEVs), bioactive particles shed by bacteria, are emerging as modulators of host immunity. However, their role in shaping fetal intestinal immune development remains largely unexplored. ObjectivesThis study aimed to investigate the effects of bEV exposure on lymphoid and myeloid populations in the fetal murine gut, focusing on their role in priming intestinal immunity, promoting differentiation, and modulating immune cell phenotypes in both normal and germ-free (GF) environments. Materials and MethodsWe used a murine model to evaluate the immune-modulating effects of bEVs during fetal development. bEVs were isolated from bacterial cultures and introduced into the amniotic sac of embryonic day 15.5 (E15.5) fetuses through intra-amniotic injection. Fetal and neonatal mice were either raised under conventional conditions (normal environment, NE) or in germ-free (GF) environments to assess microbiota-dependent effects. Immune profiling of fetal (E17) and postnatal (4 weeks) gut tissues was performed using high-dimensional mass cytometry (CyTOF) in both conventionally housed and germ-free (GF) mice. Clustering and differential expression analyses identified lymphoid and myeloid subpopulations, including progenitors, antigen-presenting cells, and intestinal stem cells (ISCs). secondary immune challenge (LPS or TSST-1) was conducted in postnatal bEV-primed mice to assess immune memory responses. ResultsbEV exposure significantly increased the prevalence of CD45- CD24+ CD44+ ISCs, promoting intestinal renewal and defense via differentiation into Paneth and tuft cells. These ISCs exhibited potential antigen-presenting capabilities through MHC expression. CD45+ lymphoid progenitors were upregulated, highlighting their role in early differentiation pathways. Myeloid progenitors, particularly monocyte-dendritic progenitor subsets, showed a bias toward antigen-presenting phenotypes.Germ-free models revealed heightened sensitivity to bEVs, with pronounced activation of progenitors and a reduction in exhaustion markers. Interestingly, macrophage and neutrophil populations displayed dose-dependent modulation, with low bEV concentrations promoting their expansion and higher doses leading to reduced incidence. Our findings suggest that bEVs act as immune priming agents in the fetal gut, promoting progenitor expansion and differentiation while preparing the intestine for postnatal challenges. Differences in responses between NE and GF models emphasize the importance of environmental influences, including microbiota, on bEV-mediated immune modulation. ConclusionbEVs play a pivotal role in shaping fetal intestinal immunity by priming lymphoid and myeloid progenitors and enhancing ISC function. These results open potential avenues for leveraging bEVs in immunomodulation and vaccine strategies. Future studies should explore the functional responses of bEV-primed cells and their translational relevance in humans.

developmental biology↗

bioRxiv2026

P-glycoprotein exofection between fetal and maternal cells as a mechanism of intercellular material transfer at the feto maternal interface

Cells can recover lost protein functions through a process we term exofection, in which extracellular vesicles deliver functional molecular cargo to recipient cells and transiently reprogram their activity. Here we show that exosomes derived from fetal chorion trophoblast cells (CTCs) restore P-glycoprotein (P-gp) efflux transporter function in inflammation-impaired maternal decidual cells (DECs) at the feto-maternal interface. CTCs maintain high P-gp expression under inflammatory stress, whereas DECs exhibit marked downregulation of transporter genes and proteins. Proteomic analysis revealed that CTC-derived exosomes package P-gp as a stable cargo that enters DECs through clathrin- and heparan sulfate-dependent uptake pathways. Delivery of CTC exosomes reinstated P-gp abundance and efflux capacity in LPS-stimulated or P-gp-deficient DECs, as shown by calcein efflux and immunofluorescence assays. In pregnant P-gp knockout mice, exosome treatment restored systemic clearance of the P-gp substrate tacrolimus and improved pharmacokinetic parameters. These findings establish exofection as a naturally occurring mechanism of transporter rescue at the feto-maternal interface, where fetal exosomes compensate for inflammation-induced maternal loss of efflux capacity. By restoring P-gp-mediated barrier function, exofection provides a protective strategy that limits the accumulation of xenobiotics and cytokines in maternal tissues and safeguards the fetus. This work reveals a previously unrecognized form of intercellular communication with broad implications for fetal protection, placental biology, cellular engineering, and the delivery of therapeutic proteins. One Sentence SummaryExofection is identified as a novel mechanism of transient cellular engineering via exosome-mediated functional protein delivery between cells.

developmental biology↗

bioRxiv2025

nf-core/proteinfamilies: A scalable pipeline for the generation of protein families

The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterised sequences with the few experimentally characterised ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates protein nascent families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage can scale approximately linearly with input size, while the biological benchmarks showed that the generated protein families closely resemble manually curated families found in widely used databases.

bioinformatics↗

bioRxiv2025

Genetic and plastic effects on trait variability in two major tree species: insights from common garden experiments across Europe

Phenotypic plasticity and genetic adaptation are key mechanisms that enable species to respond to changing environments. Tree traits do not vary independently but rather in coordination. However, our understanding of whether functional traits are governed by the same mechanism is far from complete. Thus, we aim at assessing the drivers of trait variability of sessile oak and European beech provenances across their distribution ranges. We estimated growth-related and leaf morphological traits from 9 and 11 provenances of oak and beech, respectively, grown in four different common gardens distributed across their respective distribution areas. Overall, phenotypic plasticity played a dominant role in explaining individual trait variability. For most oak traits, variation among provenances and genetically based plasticity were correlated with the climate of origin, whereas fewer significant associations were found for beech. In oak, climate-transfer distance analyses revealed that traits such as DBH, height, specific leaf area, and long-term growth responses to summer temperature decreased when provenances were moved away from their local precipitation regime. In beech, significant climate-transfer distances were fewer and primarily related to temperature-related parameters. These results suggest that natural selection and local adaptation may play a secondary but notable role. The pattern of multi-trait phenotypes indicates that resource-use strategies among provenances covary with the temperatures of origin in both species. The limited genetic responses in beech could hinder its survival if it reaches the boundaries of trait plasticity, while oak may better adjust through adaptation. Our study contributes to a better understanding of the interplay between genetic adaptation and phenotypic plasticity in long-lived forest trees.

ecology↗

bioRxiv2025

PIMENTO: A PrIMEr infereNce TOolkit to facilitate large-scale calling of amplicon sequence variants

The identification of amplicon sequence variants from DNA metabarcoding data is a common method for revealing the taxonomic makeup of environmental samples, and for allowing comparative studies between similar datasets. A significant hurdle to the large-scale calling of amplicon sequence variants from publicly available nucleotide datasets is the heterogeneous presence of primer sequences in reads, the removal of which is a necessary pre-processing step for this form of analysis. Furthermore, as the details of the experimental primers are rarely captured in the metadata associated with the sequence records, there is a need for a method that can automatically infer the presence and identity of primers in sequencing data. In this work, we introduce PIMENTO, a Python package which uses a dual-strategy approach for identifying primers that are present in sequencing reads to enable their removal, and therefore facilitate amplicon sequence variant calling at scale.

bioinformatics↗

bioRxiv2025

Biome-specific genome catalogues reveal functional potential of shallow sequencing

The use of 16S rRNA metabarcoding for functional prediction is limited by several biases. Shallow shotgun sequencing is a cost-effective and taxonomically high-resolution alternative to 16S rRNA metabarcoding, but the low sequencing depth limits functional inference. Our BioSIFTR tool maps shallow shotgun sequencing reads against single-biome databases and extrapolates into their precalculated functional profiles. We used three datasets from red junglefowl, mice, and human gut, containing matched deep shotgun metagenomic and 16S rRNA metabarcoding data for taxonomic and functional benchmarking. An additional human gut deep shotgun sequencing data set was subsampled to 1 M reads and analysed with BioSIFTR to replicate previously obtained results. BioSIFTR taxonomic and functional profiles closely agree with the results of the full deep sequencing data in all biomes. We also replicated differences in the human gut microbiome between high and low trimethylamine N-oxide producing participants, using only < 2 % of the original deep sequencing data. The BioSIFTR tool is a powerful approach which approximates the functional information of a deep-sequenced metagenome while using only a fraction of the data. Shallow shotgun sequencing combined with BioSIFTR could be a stand-in replacement for 16S rRNA metabarcoding with an increased taxonomic and functional resolution, and lower bias. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/659887v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@8ca365org.highwire.dtl.DTLVardef@13b466dorg.highwire.dtl.DTLVardef@8cad19org.highwire.dtl.DTLVardef@1b853fa_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

The role of MEGF10 in myoblast fusion and hypertrophic response to overload of skeletal muscle

Biallelic mutations in multiple EGF domain protein 10 (MEGF10) gene cause EMARDD (early myopathy, areflexia, respiratory distress and dysphagia) in humans, a severe recessive myopathy, associated with reduced numbers of PAX7 positive satellite cells. To better understand the role of MEGF10 in satellite cells, we overexpressed human MEGF10 in mouse H-2kb-tsA58 myoblasts and found that it inhibited fusion. Addition of purified extracellular domains of human MEGF10, with (ECD) or without (EGF) the N-terminal EMI domain to H-2kb-tsA58 myoblasts, showed that the ECD was more effective at reducing myoblast adhesion and fusion by day 7 of differentiation, yet promoted adhesion of myoblasts to non-adhesive surfaces, highlighting the importance of the EMI domain in these behaviours. We additionally tested the role of Megf10 in vivo using transgenic mice with reduced (Megf10+/-) or no (Megf10-/-) Megf10. We found that the extensor digitorum longus muscle had fewer Pax7 positive satellite cell nuclei and was less able to undergo hypertrophy in response to muscle overload concomitant with a lower level of satellite cell activation. Taken together, our data suggest that MEGF10 may promote satellite cell adhesion and survival and prevent premature fusion helping to explain its role in EMARDD.

cell biology↗

bioRxiv2024

Single Cell Integration Characterises Metaplasia in Inflammatory Intestinal Diseases

The gastrointestinal (GI) tract consists of connected organs, from the oral cavity to rectum, which function to ensure efficient nutrient uptake and barrier immunity. Diseases of the GI tract affect millions worldwide and as such there are now over 25 published single cell RNA-sequencing (scRNAseq) datasets surveying the GI tract, profiling specific anatomical regions, cell lineages, ages and diseases. To consolidate these efforts, we harmonised and integrated scRNAseq datasets across the whole GI tract from developing and adult human tissues, as well as newly generated data from preterm gut. We uniformly processed 385 samples from 189 healthy controls using a newly developed automated QC approach (scAutoQC). In total, our healthy reference contains [~]1.1 million cells which we annotated to a total of 137 fine-grained cell states. We anchor 13 published and 1 unpublished GI disease datasets covering gastric and colorectal (CRC) cancers, celiac disease, ulcerative colitis (UC) and Crohns disease (CD) to this reference, taking our atlas to a total of 1.6 million cells. We provide our atlas as a valuable resource to the community (available at gutcellatlas.org). Using this resource, we discover epithelial cell metaplasia arising from stem cells across intestinal inflammatory diseases (celiac, UC and CD) and CRC with transcriptional similarity to cells of the gastric and Brunners glands. Whilst previously linked to mucosal healing, we now implicate these cells in inflammation through recruitment of immune cells including T cells and neutrophils, and through direct interactions with T cells. Overall, we discover a shift in paradigm whereby changes in stem cells during inflammation lead to altered mucosal tissue architecture, which in turn contributes to ongoing inflammation. These findings highlight that in addition to barrier function, epithelial cells actively contribute to progression of inflammation which may be a function applicable to other tissues and diseases.

genomics↗

bioRxiv2024

Early life milk diets shape infant gut microbiota: evidence of microbial plasticity in response to breast and formula milk.

In early life, diet plays a key role in shaping the infant microbiota, yet the impact of breast milk and formula on microbial ecosystems at different stages of infant development remains poorly understood. Here, we performed static batch culture experiments using infant faecal samples at ages 1, 12 and 18 months of age, supplemented with either breast milk or formula for 48 hours. We further removed small metabolites (e.g. small carbohydrates, proteins and lipids) from breast and formula milk through dialysis and also added this to the static batch cultures with faecal samples from each infant. Our results show that the one-month-old faecal microbiota exhibited the greatest sensitivity to dietary intervention, with significant changes in microbial composition, metabolites and lipids, particularly in response to formula supplementation. In contrast, the microbiota at 12 months displayed increased stability, while the 18-month-old infant samples were the most resilient to different dietary supplementation. We also observed that triglyceride (TG46:1) was produced in the youngest infant samples but consumed by the older infant microbiota, suggesting a shift in metabolic interactions as the gut microbiota diversifies with age. Metabolite profiles linked to KEGG pathways further indicated the older infants diverse microbiotas had greater functional capacity in comparison to the one-month-old infant, particularly in response to breast milk. Fewer overall metabolic pathways were affected when the infant samples were grown in formula. Collectively, our data underscores the importance of early life diet in shaping microbiota profiles, with more stable microbial dynamics in more mature gut ecosystems, in response to dietary changes which are also associated with downstream functional (i.e. metabolite/lipid) readouts. Notably, the removal of small metabolites from breast milk by dialysis highlighted the potential role of milk lipids in promoting growth of foundational microbiota members like Bifidobacterium. Our data, along with further studies, are required to probe the mechanisms by which specific nutrients, particularly lipids, modulate microbial composition and support infant health during the first 2 years of life.

microbiology↗

bioRxiv2024

A multiomic atlas of human early skeletal development

Bone and joint formation in the developing skeleton rely on co-ordinated differentiation of progenitors in the nascent developing limbs and joints. The cell states, epigenetic processes and key regulatory factors underlying their lineage commitment to osteogenic and other mesenchymal populations during ossification and joint formation remain poorly understood and are largely unexplored in human studies. Here, we apply paired single-nuclei transcriptional and epigenetic profiling of 336,000 droplets, in addition to spatial transcriptomics, to construct a comprehensive atlas of human bone, cartilage and joint development in the shoulder, hip, knee and cranium from 5 to 11 post-conception weeks. Spatial mapping of cell clusters to our highly multiplexed in situ sequencing (ISS) data using our newly developed tool ISS-Patcher revealed new cellular mechanisms of zonation during bone and joint formation. Combined modelling of chromatin accessibility and RNA expression allowed the identification of the transcriptional and epigenetic regulatory landscapes that drive differentiation of mesenchymal lineages including osteogenic and chondrogenic lineages, and novel chondrocyte cell states. In particular, we define regionally distinct limb and cranial osteoprogenitor populations and trajectories across the fetal skeleton and characterise differential regulatory networks that govern intramembranous and endochondral ossification. We also introduce SNP2Cell, a tool to link cell-type specific regulatory networks to numerous polygenic traits such as osteoarthritis. We also conduct in silico perturbations of genes that cause monogenic craniosynostosis and implicate potential pathogenic cell states and disease mechanisms involved. This work forms a detailed and dynamic regulatory atlas of human fetal skeletal maturation and advances our fundamental understanding of cell fate determination in human skeletal development.

developmental biology↗

bioRxiv2024

Multiomic analysis reveals developmental dynamics of the human heart in health and disease

Developmental dynamics involve the specification of diverse cell types and their spatial organization into multicellular niches. Here, we combine single-cell and spatial multiomics to define 19 distinct tissue niches in the developing heart, leading to the development of a context-aware, resolution-agnostic niche classification tool (TissueTypist). Applying high-resolution spatial profiling to the developing sinoatrial node, we resolve three pacemaker cell subtypes arrayed along a linear axis. First trimester subpopulations, such as the pacemaker cells in the sinus horn and sinoatrial node head region, display neuro-attractant programmes and interact with parasympathetic neurons via interactions including Semaphorin-Plexin signalling. Temporal trajectories map maturation of atrial and ventricular cardiomyocytes, uncovering a lipid-metabolic switch and potential key regulators of cell type identity. In the ventricle, we identify cellular and transcriptional gradients along both pseudotime and transmural axes, offering new molecular insights into myocardial compaction and maturation. Comparative profiling of euploid and trisomy 21 hearts shows a depletion of compact cardiomyocytes and heightened apoptosis, validated in isogenic-matched trisomy 21 and euploid iPSC-derived cardiomyocytes. This implicates disrupted myocardial growth may be a mechanism for Downs syndrome-associated congenital heart disease. Overall, we deliver a spatially resolved framework of human cardiac development, enabling systematic exploration of developmental niches in health and disease.

developmental biology↗

bioRxiv2024

High-resolution atlas of the developing human heart and the great vessels

The human heart and adjoining great vessels consist of multiple cell types essential for life, yet many remain uncharacterised molecularly during development. Here, we performed a high-resolution profiling of the developing heart and great vessels between 4 and 20 post-conception weeks using single-cell and spatial transcriptomics defining 63 cell types with distinct identity and location-specific signatures. We reveal previously unreported molecular identities in cell types, including the pericardium and the ductus arteriosus. In the cardiomyocytes, we identify signatures of the trabeculated-compact, and right-left axes of ventricular cardiomyocytes. In vessels, we distinguish the constituents belonging to either coronary or great vessels. We confirm our transcriptional findings spatially, revealing nuanced signatures with specific zonation patterns and validating this atlas as a curated transcriptional reference for future studies. We leverage the temporal scope of the presented atlas to build CMageR, a predictive pipeline for scRNA-seq combining cardiac cell annotation with a transcriptional cardiac clock of single-cell developmental age for each cell type. Our cardiomyocyte clock captures dynamic biology, revealing core functional changes and novel markers of maturity during the first and second trimester. Finally, we benchmark in vitro models, suggesting a transcriptional right-chamber bias in stem cell derived cardiomyocytes with the oldest model age-matched to 12 post-conception weeks. Collectively, our work provides a high-resolution atlas of human cardiac development to enhance our understanding of function in development, health, and disease, and a foundation for building a rich reference to benchmark and improve in vitro models.

developmental biology↗

bioRxiv2024

Unlocking the soundscape of coral reefs with artificial intelligence

Passive acoustic monitoring can offer insights into the state of coral reef ecosystems at low-costs and over extended temporal periods. Comparison of whole soundscape properties can rapidly deliver broad insights from acoustic data, in contrast to the more detailed but time-consuming analysis of individual bioacoustic signals. However, a lack of effective automated analysis for whole soundscape data has impeded progress in this field. Here, we show that machine learning (ML) can be used to unlock greater insights from reef soundscapes. We showcase this on a diverse set of tasks using three biogeographically independent datasets, each containing fish community, coral cover or depth zone classes. We show supervised learning can be used to train models that can identify ecological classes and individual sites from whole soundscapes. However, we report unsupervised clustering achieves this whilst providing a more detailed understanding of ecological and site groupings within soundscape data. We also compare three different approaches for extracting feature embeddings from soundscape recordings for input into ML algorithms: acoustic indices commonly used by soundscape ecologists, a pretrained convolutional neural network (P-CNN) trained on 5.2m hrs of YouTube audio and a CNN trained on individual datasets (T-CNN). Although the T-CNN performs marginally better across the datasets, we reveal that the P-CNN is a powerful tool for identifying marine soundscape ecologists due to its strong performance, low computational cost and significantly improved performance over acoustic indices. Our findings have implications for soundscape ecology in any habitat. Author SummaryArtificial intelligence has the potential to revolutionise bioacoustic monitoring of coral reefs. So far, a limited set of work has used machine learning to train detectors for specific sounds such as individual fish species. However, building detectors is a time-consuming process that involves manually annotating large amounts of audio followed by complicated model training, this must then be repeated all over again for any new dataset. Instead, we explore machine learning techniques for whole soundscape analysis, which compares the acoustic properties of raw recordings from the entire habitat. We identify multiple machine learning methods for whole soundscape analysis and rigorously test these using datasets from Indonesia, Australia and French Polynesia. Our key findings show use of a neural network pretrained on 5.2m hours of unrelated YouTube audio offers a powerful tool to produce compressed representations of reef audio data, conserving the datas key properties whilst being executable on a standard personal laptop. These representations can then be used to explore patterns in reef soundscapes using "unsupervised machine learning", which is effective at grouping similar recordings periods together and dissimilar periods apart. We show these groupings hold relationships with ground truth ecological data, including coral coverage, the fish community and depth.

ecology↗

bioRxiv2024

Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age

The immune system comprises multiple cell lineages and heterogeneous subsets found in blood and tissues throughout the body. While human immune responses differ between sites and over age, the underlying sources of variation remain unclear as most studies are limited to peripheral blood. Here, we took a systems approach to comprehensively profile RNA and surface protein expression of over 1.25 million immune cells isolated from blood, lymphoid organs, and mucosal tissues of 24 organ donors aged 20-75 years. We applied a multimodal classifier to annotate the major immune cell lineages (T cells, B cells, innate lymphoid cells, and myeloid cells) and their corresponding subsets across the body, leveraging probabilistic modeling to define bases for immune variations across donors, tissue, and age. We identified dominant tissue-specific effects on immune cell composition and function across lineages for lymphoid sites, intestines, and blood-rich tissues. Age-associated effects were intrinsic to both lineage and site as manifested by macrophages in mucosal sites, B cells in lymphoid organs, and T and NK cells in blood-rich sites. Our results reveal tissue-specific signatures of immune homeostasis throughout the body and across different ages. This information provides a basis for defining the transcriptional underpinnings of immune variation and potential associations with disease-associated immune pathologies across the human lifespan.

immunology↗

bioRxiv2023

A spatial human thymus cell atlas mapped to a continuous tissue axis

T cells develop from circulating precursors, which enter the thymus and migrate throughout specialised sub-compartments to support maturation and selection. This process starts already in early fetal development and is highly active until the involution of the thymus in adolescence. To map the micro-anatomical underpinnings of this process in pre- vs. post-natal states, we undertook a spatially resolved analysis and established a new quantitative morphological framework for the thymus, the Cortico-Medullary Axis. Using this axis in conjunction with the curation of a multimodal single-cell, spatial transcriptomics and high-resolution multiplex imaging atlas, we show that canonical thymocyte trajectories and thymic epithelial cells are highly organised and fully established by post-conception week 12, pinpoint TEC progenitor states, find that TEC subsets and peripheral tissue genes are associated with Hassalls Corpuscles and uncover divergence in the pace and drivers of medullary entry between CD4 vs. CD8 T cell lineages. These findings are complemented with a holistic toolkit for spatial analysis and annotation, providing a basis for a detailed understanding of T lymphocyte development.

immunology↗

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↗