1Multi-omics project research on germ-free mice.Source: STOmics DB (ID: STT0000129 )

The gut microbiota influences host immunity and metabolism, and changes in its composition and function have been implicated in several non-communicable diseases. Here, comparing germ-free (GF) and specific pathogen-free (SPF) mice using spatial transcriptomics, single-cell RNA sequencing, and targeted bile acid metabolomics across multiple organs, we systematically assessed how the gut microbiota's absence affected organ morphology, immune homeostasis, bile acid, and lipid metabolism. Through integrated analysis, we detect marked aberration in B, myeloid, and T/NK cells, altered mucosal zonation and nutrient uptake, and significant shifts in bile acid profiles in feces, liver, and circulation, with the alternate synthesis pathway predominant in GF mice, and pronounced changes in bile acid enterohepatic circulation.Particularly, autophagy-driven lipid droplet breakdown in ileum epithelium and the liver's zinc finger and BTB domain containing protein (ZBTB20)- Lipoprotein lipase (LPL) axis are key to plasma lipid homeostasis in GF mice. Our results unveil the complexity of microbiota-host interactions in the crosstalk between commensal gut bacteria and the host.

2Exploring the Cellular and Molecular Basis of Murine Cardiac Development through Spatiotemporal Transcriptome SequencingSource: STOmics DB (ID: STT0000062 )

Spatial transcriptomics is a powerful tool that combines molecular data with spatial information, enabling a deeper understanding of tissue morphology and cellular interactions. In this study, we employed state-of-the-art spatial transcriptome sequencing technology to investigate the development of the mouse heart and establish a comprehensive spatiotemporal cell atlas of early murine cardiac development. Through the analysis of this atlas, we elucidated the spatial organization of cardiac cellular lineages and their interactions during development. Notably, we observed dynamic changes in gene expression within major cell lineages, including fibroblasts and cardiomyocytes. Furthermore, we identified critical genes such as IGF2, H19, and TCAP that may be associated with the loss of regeneration ability during development. Additionally, we predicted potential transcription factors, including TCF12 and Plagl1, that are likely involved in losing regeneration during early heart developing stage. Moreover, we successfully identified marker genes, such as Adamts8 and Bmp10, that can distinguish between the left and right atria. Our study provides novel insights into murine cardiac development and offers a valuable resource for future investigations in the field of heart research.

3Single cell resolved spatial immune repertoire unveils spatial heterogeneity of lymphoid aggregates in perturbed tissues[st]Source: STOmics DB (ID: STT0000123 )

T cells and B cells mediate antigen-specific inflammation. Tracing T cell and B cell clonal activity through heritable receptor sequences could provide significant insights on immune surveillance and regulation, while current available tools could not provide clonal information at single cell resolution with spatial distribution simultaneously. To break through this, we developed an ultra-sensitive T/B cell receptor sequencing strategy based on stereo-seq. Thus, we yielded a spatially resolved immune repertoire atlas at single cell resolution and observed heterogenic LAs with varied clonal activity in perturbed tissues. Specifically, 50um-2000um micro aggregates formed in a kidney cancer for T and B cell clonal expansion. Intratumoral tertiary lymphoid structure (TLS) primed significantly higher proportion of mutated B/plasma clones over peritumoral TLS in lung cancer. In inflammatory bowel disease, immigrant B/plasma cells matured in the plasma cell aggregates within the lamina propria, instead of the submucosal TLS, to mediate locoregional inflammation. Collectively, our study provides an effective approach to profile spatial immune repertoire at single cell resolution with paired TCR/BCR chains, allowing us to decipher T/B cell clonal activities crossing perturbed tissues.

4Spatially resolved multi-omics analytics of pituitary plasticity in mammalsSource: STOmics DB (ID: STT0000021 )

The plasticity of pituitary hormone production regulates the neuroendocrine adaptation of puberty, reproduction and homeostatic metabolism. However, the anatomical structures, functional cell populations and regulatory networks in the adult pituitary are still not fully elucidated. Here, we integrate omics data of the single-nucleus RNA and ATAC sequencing, high-resolution spatial transcriptomics, and metabolomics to investigate the molecular features of cell diversity and plasticity in anterior pituitaries from adult human, monkey and mouse. Our results reveal the comprehensive cell composition, novel anatomical and molecular features of hormonal cells, stromal cells, stem and progenitor cells. Analysis of differentially expressed genes along pseudotime trajectory, RNA velocity and transcription factor activity unveil the critical regulatory network for cell fate determination and functions, including Axon guidance and Hippo pathways. The importance of endoplasmic reticulum stress and unfolded protein response in the regulation of hormone production and oxidative stress is identified. Consistently, enrichment of potent antioxidants such as spermine and glutathione are detected in mouse hormonal cells. Furthermore, the putative receptor-ligand interactions reveal regulatory relationships between diverse cells, suggesting the pituitary stem cell niche comprising stromal cells expressing extracellular matrix proteins and growth factors. Our findings systematically illustrate the cellular and mechanistic basis of mammalian pituitary plasticity.

5Public Datasets of STOmicsSource: STOmics DB (ID: STT0000124 )

Browse and obtain STOmics public datasets for further exploration needs.

6Microbiota-mediated shaping of mouse spleen structure and immune function characterized by scRNA-seq and Stereo-seqSource: STOmics DB (ID: STT0000089 )

Gut microbes exhibit complex interactions with their hosts and shape an organism immune system throughout its lifespan. As the largest secondary lymphoid organ, the spleen has a wide range of immunological functions. To explore the role of microbiota in regulating and shaping the spleen, we employ scRNA-seq and Stereo-seq technologies based on germ-free (GF) mice to detect differences in tissue size, anatomical structure, cell types, functions, and spatial molecular characteristics. We identify 18 cell types, 9 subtypes of T cells, and 7 subtypes of B cells. Gene differential expression analysis reveals that the absence of microorganisms results in alterations in erythropoiesis within the red pulp region and congenital immune deficiency in the white pulp region. Stereo-seq results demonstrate a clear hierarchy of immune cells in the spleen, including marginal zone (MZ) macrophages, MZ B cells, follicular B cells and T cells, distributed in a well-defined pattern from outside to inside. However, this hierarchical structure is disturbed in GF mice. Ccr7 and Cxcl13 chemokines are specifically expressed in the spatial locations of T cells and B cells, respectively. We speculate that the microbiota may mediate the structural composition or partitioning of spleen immune cells by modulating the expression levels of chemokines.

7Fate Determination of Cancer-associated Fibroblast Drives Polarized Immunity in Cancer-stroma BoundarySource: STOmics DB (ID: STT0000036 )

The exciting responding rate to anti-PD1 treatment makes dMMR colorectal cancer (CRC) an outstanding model to explore the mechanism underlying immunotherapy sensitivity. This study provides a spatial transcriptomic landscape of CRC tumor at 50 μm resolution and highlights the plasticity of the cancer-stroma boundary immunity. It demonstrates the utility of high-resolution spatial transcriptome to study the cellular components and molecular pattern in the microscopic boundary, in which cancer cells co-opt stromal cells to alter the boundary immunity.

8Spatial transcriptomic landscape unveils immunoglobin-associated senescence as a hallmark of agingSource: STOmics DB (ID: STT0000039 )

To systematically characterize the loss of tissue integrity and organ dysfunction resulting from aging, we produced an in-depth spatial transcriptomic profile of nine tissues in male mice during aging. We showed that senescence-sensitive spots (SSSs) colocalized with elevated entropy in organizational structure and that the aggregation of immunoglobulin-expressing cells is a characteristic feature of the microenvironment surrounding SSSs. Immunoglobulin G (IgG) accumulated across the aged tissues in both male and female mice, and a similar phenomenon was observed in human tissues, suggesting the potential of the abnormal elevation of immunoglobulins as an evolutionarily conserved feature in aging. Furthermore, we observed that IgG could induce a pro-senescent state in macrophages and microglia, thereby exacerbating tissue aging, and that targeted reduction of IgG mitigated aging across various tissues in male mice. This study provides a high-resolution spatial depiction of aging and indicates the pivotal role of immunoglobulin-associated senescence during the aging process.

9stereo-seq data of primary lung and liver organoidSource: STOmics DB (ID: STT0000115 )

Spatial transcriptomics technologies have demonstrated exceptional performance in characterizing brain and visceral organ tissues, as well as brain and retinal organoids. However, it has not yet been proven whether spatial transcriptomics can effectively characterize primary tissue-derived organoids, as the standardized tissue sectioning or slicing methods are not applicable for such organoids. Herein, we present a technique for organoid-spatially resolved transcriptomics based on organoid lamination. Primary mouse lung and liver-derived organoids were used in this study. The organoids were formulated using the droplet-engineering method, and laminated using a homemade device with weight compression. This technique preserved most cells in individual organoids while maintaining delicate epithelium structures in laminated domains that can be recognized through visual segmentation. The mouse lung and liver organoids were resolved comprising various cell types, including alveolar cells, damage-associated transient progenitor cells, basal cells, macrophages, endothelial cells, fibroblasts, hepatocytes, and hepatic stellate cells. The distribution and count of cells were confirmed using immunohistology and identified with spatial transcriptomic features. This study reports first the automated and integrated spatial transcriptomics method for primary organoids. It has the potential to standardize and rapidly characterize primary tissue-derived organoids

10Single-cell and spatiotemporal transcriptomic reveals the effects of microorganisms on immunity and metabolism in mouse liverSource: STOmics DB (ID: STT0000034 )

The gut-liver axis is a complex bidirectional communication pathway between the intestine and the liver in which microorganisms and their metabolites from the intestine flow through the portal vein to the liver and influence liver function. In a sterile environment, the phenotype or function of the liver is altered, yet there are few studies on the specific cellular and molecular effects of microorganisms on the liver. Towards this aim, we constructed single-cell and spatial transcriptomic (ST) profiles of germ-free (GF) and specific pathogen-free (SPF) mice livers. The single cell RNA sequencing (scRNA-seq) found that the proportion of the vast majority of immune cells in GF mice was significantly reduced, especially natural killer T (NKT) cells, IgA plasma cells (IgAs), and Kupffer cells (KCs). The spatial enhanced resolution omics-sequencing (Stereo-seq) confirmed that microorganisms mediated the accumulation of Kupffer cells in the periportal zone. We also unexpectedly found that IgA plasma cells were more numerous and concentrated in the periportal vein in sections from SPF mice, while they were fewer and scattered in GF mice. ST technology also enables precise zonation of liver lobules into eight layers and three patterns based on gene expression level in each layer, allowing us to further investigate the effects of microbes on gene zonation patterns and functions. Furthermore, the untargeted metabolism experiments in the liver discovered that propionic acid levels were significantly lower in GF mice and may be related to the control of genes involved in bile acid and fatty acid metabolism. In conclusion, the combined study of scRNA-seq, Stereo-seq, and untargeted metabolomics revealed immune system defects as well as altered bile acid and lipid metabolic processes at the single-cell and spatial levels in the livers of GF mice. This study has great value for understanding host-microbiota interactions.