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Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and therapeutic strategies require a deeper understanding of the molecular processes involved in the healthy heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavour. Here, using state-of-the-art analyses of large-scale single-cell and single-nucleus transcriptomes, we characterize six anatomical adult heart regions. Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, and reveal distinct atrial and ventricular subsets of cells with diverse developmental origins and specialized properties. We define the complexity of the cardiac vasculature and its changes along the arterio-venous axis. In the immune compartment, we identify cardiac-resident macrophages with inflammatory and protective transcriptional signatures. Furthermore, analyses of cell-to-cell interactions highlight different networks of macrophages, fibroblasts and cardiomyocytes between atria and ventricles that are distinct from those of skeletal muscle. Our human cardiac cell atlas improves our understanding of the human heart and provides a valuable reference for future studies. Single-cell and single-nucleus RNA sequencing are used to construct a cellular atlas of the human heart that will aid further research into cardiac physiology and disease.

The function of a cell is defined by its intrinsic characteristics and its niche: the tissue microenvironment in which it dwells. Here we combine single-cell and spatial transcriptomics data to discover cellular niches within eight regions of the human heart. We map cells to microanatomical locations and integrate knowledge-based and unsupervised structural annotations. We also profile the cells of the human cardiac conduction system 1 . The results revealed their distinctive repertoire of ion channels, G-protein-coupled receptors (GPCRs) and regulatory networks, and implicated FOXP2 in the pacemaker phenotype. We show that the sinoatrial node is compartmentalized, with a core of pacemaker cells, fibroblasts and glial cells supporting glutamatergic signalling. Using a custom CellPhoneDB.org module, we identify trans-synaptic pacemaker cell interactions with glia. We introduce a druggable target prediction tool, drug2cell, which leverages single-cell profiles and drug–target interactions to provide 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 that may contribute to infection defence. Overall, we provide new clarity to cardiac electro-anatomy and immunology, and our suite of computational approaches can be applied to other tissues and organs. Single-cell and spatial transcriptomic analysis of eight human heart tissues reveals the cellular profiles and tissue architecture of niches including the cardiac conduction system, and a new tool, drug2cell, identifies drug target expression.

Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To (re)define tissue architecture of lung and airways, we profiled five proximal-to-distal locations of healthy human lungs in depth using multi-omic single cell/nuclei and spatial transcriptomics (queryable at lungcellatlas.org ). Using computational data integration and analysis, we extend beyond the suspension cell paradigm and discover macro and micro-anatomical tissue compartments including previously unannotated cell types in the epithelial, vascular, stromal and nerve bundle micro-environments. We identify and implicate peribronchial fibroblasts in lung disease. Importantly, we discover and validate a survival niche for IgA plasma cells in the airway submucosal glands (SMG). We show that gland epithelial cells recruit B cells and IgA plasma cells, and promote longevity and antibody secretion locally through expression of CCL28, APRIL and IL-6. This new ‘gland-associated immune niche’ has implications for respiratory health. Multi-omics profiling of 45 human lung samples highlights 80 different cell types along the proximal to distal axis of the lung with certain cell types showing enrichment for disease-associated genes. An immune niche for IgA-expressing plasma cells within airway submucosal glands (SMG) is also identified.

BackgroundThe prediction of a difficult cholecystectomy has traditionally been based on certain pre-operative clinical and imaging factors. Most of the previous literature reported small patient cohorts and have not used an objective measure of operative difficulty. The aim of this study was to develop a pre-operative score to predict difficult cholecystectomy, as defined by a validated intra-operative difficulty grading scale.MethodTwo cohorts from prospectively maintained databases of patients who underwent laparoscopic cholecystectomy were analysed: the CholeS Study (8755 patients) and a single surgeon series (4089 patients). Factors potentially predictive of difficulty were correlated to the Nassar intra-operative difficulty scale. A multivariable binary logistic regression analysis was then used to identify factors that were independently associated with difficult laparoscopic cholecystectomy, defined as operative difficulty grades 3 to 5. The resulting model was then converted to a risk score, and validated on both internal and external datasets.ResultIncreasing age and ASA classification, male gender, diagnosis of CBD stone or cholecystitis, thick-walled gallbladders, CBD dilation, use of pre-operative ERCP and non-elective operations were found to be significant independent predictors of difficult cases. A risk score based on these factors returned an area under the ROC curve of 0.789 (95% CI 0.773–0.806, p < 0.001) on external validation, with 11.0% versus 80.0% of patients classified as low versus high risk having difficult surgeries.ConclusionWe have developed and validated a pre-operative scoring system that uses easily available pre-operative variables to predict difficult laparoscopic cholecystectomies. This scoring system should assist in patient selection for day case surgery, optimising pre-operative surgical planning (e.g. allocation of the procedure to a suitably trained surgeon) and counselling patients during the consent process. The score could also be used to risk adjust outcomes in future research.

Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define additional heterogeneity and novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. First, we have generated a single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data set from 5 different locations of the human lung and airways. Second, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN). Competing Interest Statement In the past three years, SAT has received remuneration for consulting and Scientific Advisory Board Membership from Genentech, Roche, Biogen, GlaxoSmithKline, Foresite Labs and Qiagen. SAT is a co-founder, board member and holds equity in Transition Bio.

Autism is a highly heritable neurodevelopmental condition that manifests across a wide phenotypic spectrum. Rare and loss-of-function mutations strongly predispose to autism and co-occurring developmental and intellectual disabilities in over 10% of autistic individuals. Understanding whether these variants converge on specific regional brain circuits or widely alter human brain development is crucial to understanding the etiology of profound autism. To date, transcriptomic atlases have mainly implicated the developing cerebral cortex, yet other brain areas have received relatively little attention. Here, we present a single-cell resolution spatial transcriptomic atlas of 250 autism susceptibility genes during human brain development. Profiling over 10 million cells across the midgestation forebrain, we found convergence of these genes across a small number of regional programs. The developing thalamus showed the most prevalent expression of autism susceptibility genes, followed by germinal zones throughout the brain. Within the thalamus, excitatory neurons showed the most enriched expression, which varied across thalamic nuclei harboring distinct circuits. Across the germinal zones, neural progenitors in the medial ganglionic eminences that generate parvalbumin- and somatostanin-positive interneurons showed highest expression. Our findings reveal the prevalent expression of autism associated genes beyond the developing cerebral cortex and implicate the developing human thalamus as a major hub of autism susceptibility.

The primary function of the thyroid gland is the synthesis and release of thyroid hormones, which are essential for health from embryogenesis to adulthood. Thyroid disorders occur frequently and include congenital hypothyroidism, which occurs due to aberrant thyroid development (thyroid dysgenesis) or impaired hormone synthesis and is particularly prevalent in trisomy 21 (T21). In contrast, thyroid carcinoma, an acquired disorder, is the most common endocrine malignancy in both paediatric and adult populations. Understanding the molecular basis of thyroid dysgenesis and paediatric thyroid carcinoma remains challenging, and requires an improved understanding of foetal thyroid development. To address this, we generated a comprehensive spatiotemporal atlas of the human thyroid during the first and second trimesters of pregnancy. Profiling over 200,000 cells with single-cell sequencing revealed key cell types involved in thyroid gland development, including the hormone-producing thyrocytes. We discovered that foetal thyroid follicular cells are heterogeneous epithelial populations consisting of two main functional subtypes (fTFC1, fTFC2), with fTFC2 expressing increased levels of PAX8, and spatial transcriptomics revealed subtype co-occurrence within individual follicles. While both fTFC1 and fTFC2 persist in adult thyroid, fTFC2 is a minor population amongst additional PAX8-positive follicular cell subsets. We observed thyroid dysgenesis in T21 age-matched specimens, and T21 thyrocytes showed transcriptional signatures of cytoskeletal disorganisation and altered interactions with the extracellular matrix, as well as compensatory activation of metabolic stress gene programs and upregulation of thyroid biosynthetic genes. In line with the altered proportions of fTFC2 in healthy foetal and adult thyroid, papillary thyroid cancer in children is transcriptionally enriched for the fTFC2 signature compared to that in adults. All together, these findings reveal thyrocyte heterogeneity across the lifespan and provide insights into thyroid development in health and disease, informing potential therapeutic interventions.

Combinations of transcription factors (TFs) regulate gene expression and determine cell fate. Much effort has been devoted to understanding TF activity in different tissues and how tissue-specificity is achieved. However, ultimately gene regulation occurs at the single cell level and the recent explosion in the availability of single cell gene expression data now makes it possible to understand TF activity at this granular level of resolution. Here, we leverage a large collection of Human Cell Atlas (HCA) single cell data to explore TF activity by examining cell-type and tissue-specific sets of target genes, or regulons. We compile a regulon atlas, CellRegulon, and map the activity of TFs in an extensive set of healthy adult and foetal tissues spanning hundreds of cell types. Using CellRegulon, we describe dynamic patterns of co-regulation, associate TF-modules with different cellular functions and characterise the distribution of active TFs and TF families across cell types. We show that CellRegulon can link disease gene expression signatures to cell types and TFs relevant to the disease. Finally, using a newly generated multiome dataset of the adult lung, we show how CellRegulon can be extended into an enhancer-gene regulatory network (eGRN) to improve cell-type associations with genetic risk loci for diseases, such as childhood onset asthma, COPD and IPF, and to identify high risk gene modules. Our database for easy download and interactive exploration allows researchers to understand key gene modules activated at cell type transitions and will therefore be valuable for tasks such as cell type engineering (https://www.cellregulondb.org).

The human reproductive tract plays an essential role in species perpetuation. Its development involves complex processes of sex specification, tissue patterning and morphogenesis, which, if disrupted, can cause lifelong health issues, including infertility. Here, we generated an extensive single-cell and spatial multi-omic atlas of the human reproductive tract during prenatal development, which allowed us to answer questions that smaller-scale, organ-focused experiments could not address before. We identified potential regulators of sexual dimorphism in reproductive organs, pinpointing novel genes involved in urethral canalisation of the penis, with relevance to hypospadias. By combining histological features with gene expression data, we defined the transcription factors and cell signalling events required for the regionalisation of the Müllerian and Wolffian ducts. This led to a refinement of how the HOX code is established in the distinct reproductive organs, including increased expression of thoracic HOX genes in the rostral mesenchyme of the fallopian tube and epididymis. Our study further revealed that the epithelial regionalisation of the fallopian tube and epididymis required for sperm maturation in adulthood is established early in development. In contrast, later events in gestation or postnatally are necessary for the regionalisation of the uterocervical canal epithelium. By mapping sex-specific reproductive tract regionalisation and differentiation at the cellular level, our study offers valuable insights into the causes and potential treatments of reproductive disorders.