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An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases.
Transcribed enhancer maps can reveal nuclear interactions underpinning each cell type and connect specific cell types to diseases. Using a 5' single-cell RNA sequencing approach, we defined transcription start sites of enhancer RNAs and other classes of coding and noncoding RNAs in human CD4+ T cells, revealing cellular heterogeneity and differentiation trajectories. Integration of these datasets with single-cell chromatin profiles showed that active enhancers with bidirectional RNA transcription are highly cell type-specific and that disease heritability is strongly enriched in these enhancers. The resulting cell type-resolved multimodal atlas of bidirectionally transcribed enhancers, which we linked with promoters using fine-scale chromatin contact maps, enabled us to systematically interpret genetic variants associated with a range of immune-mediated diseases.
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Single-cell RNA-seq reveals the immune profile changes in patients with diarrhoeal-irritable bowel syndrome.
BACKGROUND: Diarrhea-predominant irritable bowel syndrome (IBS-D) is characterized by recurrent abdominal pain and chronic diarrhea. T lymphocytes, which play a crucial role in gut inflammation and immune responses, may significantly contribute to the pathophysiology of IBS-D. However, the exact mechanisms by which T lymphocytes affect IBS-D remain unclear. The precise pathways and interactions involved in IBS-D are still to be determined. METHODS: We conducted single-cell RNA sequencing on blood samples from 4 IBS-D patients and 4 healthy controls. Following data preprocessing, we conducted subsequence bioinformatics analysis. Additionally, serum and colon tissue samples from IBS-D rat models were analyzed using ELISA and three-parameter fluorescence to further elucidate the T lymphocytes landscape associated with IBS-D. RESULTS: A total of 45,649 cells were classified into four distinct cell types. Among them, T lymphocytes were further subdivided into 20 unique clusters. Novel markers that were highly expressed in T lymphocytes were identified. Dysregulation of HIF-1α pathway, NF-kappa B pathway, and IL-17 signaling pathway, were observed through trajectory analysis. Additionally, single-cell regulatory network inference and clustering analysis revealed the FOS signaling pathway as a potential therapeutic target for IBS-D. Furthermore, we detected abnormally elevated levels of PLK3 and NFKBIZ in the serum and colon tissues of the IBS-D rat model. Our study mapped the communication atlas of T lymphocytes that may influence the pathophysiology of IBS-D. CONCLUSIONS: This study uncovers novel molecular features and identifies potential therapeutic targets of T lymphocytes in IBS-D, thereby advancing our understanding of the disease and expanding treatment options.
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Molecularly defined and spatially resolved cell atlas of the whole mouse brain.
In mammalian brains, millions to billions of cells form complex interaction networks to enable a wide range of functions. The enormous diversity and intricate organization of cells have impeded our understanding of the molecular and cellular basis of brain function. Recent advances in spatially resolved single-cell transcriptomics have enabled systematic mapping of the spatial organization of molecularly defined cell types in complex tissues1-3, including several brain regions (for example, refs. 1-11). However, a comprehensive cell atlas of the whole brain is still missing. Here we imaged a panel of more than 1,100 genes in approximately 10 million cells across the entire adult mouse brains using multiplexed error-robust fluorescence in situ hybridization12 and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating multiplexed error-robust fluorescence in situ hybridization and single-cell RNA sequencing data. Using this approach, we generated a comprehensive cell atlas of more than 5,000 transcriptionally distinct cell clusters, belonging to more than 300 major cell types, in the whole mouse brain with high molecular and spatial resolution. Registration of this atlas to the mouse brain common coordinate framework allowed systematic quantifications of the cell-type composition and organization in individual brain regions. We further identified spatial modules characterized by distinct cell-type compositions and spatial gradients featuring gradual changes of cells. Finally, this high-resolution spatial map of cells, each with a transcriptome-wide expression profile, allowed us to infer cell-type-specific interactions between hundreds of cell-type pairs and predict molecular (ligand-receptor) basis and functional implications of these cell-cell interactions. These results provide rich insights into the molecular and cellular architecture of the brain and a foundation for functional investigations of neural circuits and their dysfunction in health and disease.
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Single-cell RNA-seq and pathological phenotype reveal the functional atlas and precise roles of Sox30 in testicular cell development and differentiation.
Sox30 has recently been demonstrated to be a key regulator of spermatogenesis. However, the precise roles of Sox30 in the testis remain largely unclear. Here, the specific functions of Sox30 in testicular cells were determined by single-cell sequencing and confirmed via pathological analyses. Sox30 loss appears to damage all testicular cells to different extents. Sox30 chiefly drives the differentiation of primary spermatocytes. Sox30 deficiency causes spermatocyte arrest at the early phase of meiosis I, with nearly no normally developing second spermatocytes and three new spermatocyte -subclusters emerging. In addition, Sox30 seems to play important roles in the mature phenotypes of Sertoli and Leydig cells, and the proliferation and differentiation of spermatogonia. The developmental trajectory of germ cells begins with spermatogonia and splits into two different spermatocyte branches, with Sox30-null spermatocytes and wild-type spermatocytes placed at divergent ends. An opposite developmental trajectory of spermatocyte subclusters is observed, followed by incomplete development of spermatid subclusters in Sox30-null mice. Sox30 deficiency clearly alters the intercellular cross-talk of major testicular cells and dysregulates the transcription factor networks primarily involved in cell proliferation and differentiation. Mechanistically, Sox30 appears to have similar terminal functions that are involved mainly in spermatogenic development and differentiation among major testicular cells, and Sox30 performs these similar crucial roles through preferential regulation of different signalling pathways. Our study describes the exact functions of Sox30 in testicular cell development and differentiation and highlights the primary roles of Sox30 in the early meiotic phase of germ cells.
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Single-cell transcriptional atlas reveals distinct immune-chondrocyte crosstalk mechanisms in temporomandibular joint osteoarthritis induced by different types of occlusal disorder.
Temporomandibular joint (TMJ) osteoarthritis (OA) is a progressive degenerative disease in which the intricate mechanisms of the condyle cartilage damage are yet to be disclosed. A detailed characterization of cellular composition and signal networks involved in the pathogenesis is in need. This study, for the first time, identified chondrocytes heterogeneity and subchondral immune microenvironments based on single-cell transcriptomes of the mouse mandibular condyle, and provided insights into the cellular and signaling basis of the homeostasis of the condyle and pathogenesis of TMJOA by healthy-to-diseased comparisons. The differentially expressed gene pattern distinguished 8 chondrocyte subsets and 9 immune cell types in the condyle. Close interactions were found between these cell populations, with enhanced communication between chondrocytes and immune cell subsets in the condyles subjected to anterior premature contact (APC) model or unilateral anterior crossbite (UAC) model. The single-cell transcriptomic changes suggested predominant roles of neutrophils in immune-chondrocyte interactions in these occlusal disorder models. Neutrophils-derived TNF-α signaling was inferred to be the most greatly enhanced information flow in the condyle of the APC model, while increased Thbs1-Sdc4 signaling in mediating neutrophils-to-chondrocytes interactions was indicated in the UAC-model condyle, with predominant BSP signaling. Interfering in these signaling by drug administration demonstrated therapeutic potential for the APC- or UAC-induced TMJOA.
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Individual cell types in C. elegans age differently and activate distinct cell-protective responses.
Aging is characterized by a global decline in physiological function. However, by constructing a complete single-cell gene expression atlas, we find that Caenorhabditis elegans aging is not random in nature but instead is characterized by coordinated changes in functionally related metabolic, proteostasis, and stress-response genes in a cell-type-specific fashion, with downregulation of energy metabolism being the only nearly universal change. Similarly, the rates at which cells age differ significantly between cell types. In some cell types, aging is characterized by an increase in cell-to-cell variance, whereas in others, variance actually decreases. Remarkably, multiple resilience-enhancing transcription factors known to extend lifespan are activated across many cell types with age; we discovered new longevity candidates, such as GEI-3, among these. Together, our findings suggest that cells do not age passively but instead react strongly, and individualistically, to events that occur during aging. This atlas can be queried through a public interface.
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Metagenomic and single-cell RNA-Seq survey of the Helicobacter pylori-infected stomach in asymptomatic individuals.
Helicobacter pylori colonization of the gastric niche can persist for years in asymptomatic individuals. To deeply characterize the host-microbiota environment in H. pylori-infected (HPI) stomachs, we collected human gastric tissues and performed metagenomic sequencing, single-cell RNA-Seq (scRNA-Seq), flow cytometry, and fluorescent microscopy. HPI asymptomatic individuals had dramatic changes in the composition of gastric microbiome and immune cells compared with noninfected individuals. Metagenomic analysis uncovered pathway alterations related to metabolism and immune response. scRNA-Seq and flow cytometry data revealed that, in contrast to murine stomachs, ILC2s are virtually absent in the human gastric mucosa, whereas ILC3s are the dominant population. Specifically, proportion of NKp44+ ILC3s out of total ILCs were highly increased in the gastric mucosa of asymptomatic HPI individuals, and correlated with the abundance of selected microbial taxa. In addition, CD11c+ myeloid cells and activated CD4+ T cells and B cells were expanded in HPI individuals. B cells of HPI individuals acquired an activated phenotype and progressed into a highly proliferating germinal-center stage and plasmablast maturation, which correlated with the presence of tertiary lymphoid structures within the gastric lamina propria. Our study provides a comprehensive atlas of the gastric mucosa-associated microbiome and immune cell landscape when comparing asymptomatic HPI and uninfected individuals.
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Single-cell RNA-seq uncovers lineage-specific regulatory alterations of fibroblasts and endothelial cells in ligamentum flavum hypertrophy.
BACKGROUND: Lumbar spinal stenosis (LSS) represents a major global healthcare burden resulting in back pain and disorders of the limbs among the elderly population. The hypertrophy of ligamentum flavum (HLF), marked by fibrosis and inflammation, significantly contributes to LSS. Fibroblasts and endothelial cells are two important cells in the pathological process of ligamentum flavum (LF) fibrosis and inflammation. These two cells exhibit heterogeneity in various fibrotic diseases, yet their heterogeneity in LF fibrosis remains poorly defined. METHODS: Using single-cell RNA-seq, we examined the alterations of fibroblasts, endothelial cells, and key genes in the hypertrophic LF, aiming to establish a comprehensive single-cell atlas of LF to identify high-priority targets for pharmaceutical treatment of LSS. RESULTS: Here, we find there are five distinct subpopulations of LF fibroblasts: secretory-papillary, secretory-reticular, mesenchymal, pro-inflammatory, and unknown. Importantly, in HLF, the proportion of mesenchymal fibroblast subpopulations increases significantly compared to normal LF (NLF), reflecting their close association with the pathogenesis of HLF. Furthermore, critical target genes that might be involved in HLF and fibrosis, such as MGP, ASPN, OGN, LUM, and CTSK, are identified. In addition, we also investigate the heterogeneity of endothelial cells and highlight the critical role of AECs subpopulation in LF fibrosis. CONCLUSION: This study will contribute to our understanding of the pathogenesis of HLF and offer possible targets for the treatment of fibrotic diseases.
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Single-cell RNA-seq reveals breast cancer heterogeneity and identifies TCP1 as a therapeutic target in breast cancer.
Breast cancer is composed of diverse cell populations, and this intratumoral heterogeneity profoundly affects clinical behavior. Here, we leveraged single cell RNA sequencing (scRNA-seq) of 68 breast cancer specimens to dissect tumor heterogeneity at high resolution. Unsupervised clustering identified all major cell types of the tumor microenvironment (TME)-including malignant epithelial cells, fibroblasts, T cells, macrophages, endothelial cells, and others-with striking variability in their proportions across molecular subtypes. For example, a BRCA1-mutant triple-negative breast cancer (TNBC) sample showed dense immune infiltration, whereas an estrogen receptor (ER)-positive tumor was mostly epithelial, consistent with known subtype differences in immunogenicity. We applied inference of copy number variations (inferCNV) to distinguish malignant epithelial cells, identifying ~90,000 tumor cells with significant copy-number aberrations enriched for cancer hallmark pathways. Re-clustering of these malignant cells revealed five discrete subpopulations. Notably, a KRT17-positive subcluster displayed the highest stemness score and a distinctive ETS-family transcription factor (ERG) regulon, suggesting a stem-like phenotype. Using The Cancer Genome Atlas (TCGA) cohort, we found that genes upregulated in this KRT17+ subpopulation, particularly NFKBIA, PDLIM4, and TCP1 stratified patient survival. An 8-gene risk signature derived from the KRT17 program segregated patients into high- and low-risk groups with markedly different outcomes. High-risk tumors were characterized by an immunosuppressive TME enriched in M2-like macrophages, whereas low-risk tumors more often harbored lymphocyte-predominant infiltrates. Focusing on TCP1, a chaperonin subunit upregulated in high-risk tumors, we demonstrate that TCP1 knockdown in breast cancer cell lines substantially impairs cell migration (~50% reduction in wound closure) and invasion (P < 0.01). These findings reveal functionally distinct malignant cell states within breast cancer and identify TCP1 as a promising therapeutic target to disrupt aggressive, stem-like tumor cell programs, ultimately guiding more personalized treatment strategies.
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Cytocipher determines significantly different populations of cells in single-cell RNA-seq data.
MOTIVATION: Identification of cell types using single-cell RNA-seq is revolutionizing the study of multicellular organisms. However, typical single-cell RNA-seq analysis often involves post hoc manual curation to ensure clusters are transcriptionally distinct, which is time-consuming, error-prone, and irreproducible. RESULTS: To overcome these obstacles, we developed Cytocipher, a bioinformatics method and scverse compatible software package that statistically determines significant clusters. Application of Cytocipher to normal tissue, development, disease, and large-scale atlas data reveals the broad applicability and power of Cytocipher to generate biological insights in numerous contexts. This included the identification of cell types not previously described in the datasets analysed, such as CD8+ T cell subtypes in human peripheral blood mononuclear cells; cell lineage intermediate states during mouse pancreas development; and subpopulations of luminal epithelial cells over-represented in prostate cancer. Cytocipher also scales to large datasets with high-test performance, as shown by application to the Tabula Sapiens Atlas representing >480 000 cells. Cytocipher is a novel and generalizable method that statistically determines transcriptionally distinct and programmatically reproducible clusters from single-cell data. AVAILABILITY AND IMPLEMENTATION: The software version used for this manuscript has been deposited on Zenodo (https://doi.org/10.5281/zenodo.8089546), and is also available via github (https://github.com/BradBalderson/Cytocipher).