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Single-cell and spatial RNA sequencing reveal the spatiotemporal trajectories of fruit senescence.

ABSTRACT: The senescence of fruit is a complex physiological process, with various cell types within the pericarp, making it highly challenging to elucidate their individual roles in fruit senescence. In this study, a single-cell expression atlas of the pericarp of pitaya (Hylocereus undatus) is constructed, revealing exocarp and mesocarp cells undergoing the most significant changes during the fruit senescence process. Pseudotime analysis establishes cellular differentiation and gene expression trajectories during senescence. Early-stage oxidative stress imbalance is followed by the activation of resistance in exocarp cells, subsequently senescence-associated proteins accumulate in the mesocarp cells at late-stage senescence. The central role of the early response factor HuCMB1 is unveiled in the senescence regulatory network. This study provides a spatiotemporal perspective for a deeper understanding of the dynamic senescence process in plants.

SUBMITTER: Li X

PROVIDER: S-EPMC11006883 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature

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Single-cell and spatial RNA sequencing reveal the spatiotemporal trajectories of fruit senescence.

Li Xin X Li Bairu B Gu Shaobin S Pang Xinyue X Mason Patrick P Yuan Jiangfeng J Jia Jingyu J Sun Jiaju J Zhao Chunyan C Henry Robert R

Nature communications 20240410 1

The senescence of fruit is a complex physiological process, with various cell types within the pericarp, making it highly challenging to elucidate their individual roles in fruit senescence. In this study, a single-cell expression atlas of the pericarp of pitaya (Hylocereus undatus) is constructed, revealing exocarp and mesocarp cells undergoing the most significant changes during the fruit senescence process. Pseudotime analysis establishes cellular differentiation and gene expression trajector ...[more]

PMID: 38600080

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Project description:BackgroundHeart failure (HF) represents one of healthcare's biggest challenges. Although rarely noticed, aging is a crucial risk factor for cardiovascular disease. Our study aims to reveal aging's role in HF by integrating single-cell RNA-sequencing (scRNA-seq) and bulk RNA-sequencing databases.MethodsWe collected HF heart sample data from the Gene Expression Omnibus database and senescence gene data from CellAge. The FindCluster () package was used for cell cluster analysis. Differentially expressed genes (DEG) were identified operating the FindMarkers function. Cell activity score calculation was performed using the AUCell package. UpSetR plotted the intersection between DEGs of active cell types, bulk data DEGs, and genes associated with aging. Using the DGIdb database gene-drug interaction data, we search for potential targeted therapeutics based on common senescence genes.ResultsThe scRNA-seq data revealed myocardial heterogeneity in HF tissues. A series of crucial common senescence genes were found. The senescence gene expression profile hints at an intriguing connection between monocytes and HF. After analyzing the DEGs in the bulk dataset, the DEGs in scRNA-seq, the DEGs in each active cell type, and senescence genes, we identified ten genes as common senescence genes present in HF. Correlation analysis of transcriptomics, proteomics, and ceRNA was performed to provide ideas for future studies individually. Moreover, we discovered that common senescence genes and potential therapeutic drugs interact among different cell types. Further research is needed on the expression pattern of senescence genes and molecular regulation in HF.ConclusionsIn summary, we identified the functional significance of the senescence gene in HF using integrated data. It is possible that this more profound understanding of how senescence contributes to the development of HF will aid in unraveling the mechanisms that promote the disease and provide hints for developing therapeutics.

Project description:BackgroundGastric cancer is a highly aggressive malignancy characterized by a complex tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs), which are a key component of the TME, exhibit significant heterogeneity and play crucial roles in tumor progression. Therefore, a comprehensive understanding of CAFs is essential for developing novel therapeutic strategies for gastric cancer.MethodsThis study investigates the characteristics and functional information of CAF subtypes and explores the intercellular communication between CAFs and malignant epithelial cells (ECs) in gastric cancer by analyzing single-cell sequencing data from 24 gastric cancer samples. CellChat was employed to map intercellular communication, and Seurat was used to integrate single-cell sequencing data with spatial transcriptome data to reconstruct a comprehensive single-cell spatial map. The spatial relationship between apCAFs and cancer cells was analyzed using multicolor immunohistochemistry.ResultsCells were categorized into nine distinct categories, revealing a positive correlation between the proportions of epithelial cells (ECs) and fibroblasts. Furthermore, six fibroblast subpopulations were identified: inflammatory (iCAFs), pericytes, matrix (mCAFs), antigen-presenting (apCAFs), smooth muscle cells (SMCs), and proliferative CAFs (pCAFs). Each of these subpopulations was linked to various biological processes and immune responses. Malignant ECs exhibited heightened intercellular communication, particularly with CAF subpopulations, through specific ligand-receptor interactions. High-density regions of CAF subpopulations displayed spatial exclusivity, with pericytes serving as a source for iCAFs, mCAFs, and apCAFs. Notably, malignant ECs and apCAFs showed increased interactions, with certain ligand-receptor pairs potentially impacting the prognosis of gastric cancer. Multiplex immunohistochemistry (mIHC) confirmed the close spatial proximity of apCAFs to cancer cells in gastric cancer.ConclusionOur study provided a comprehensive characterization of CAF heterogeneity in gastric cancer and revealed the intricate intercellular networks within the TME. The identified CAF subpopulations and their interactions with malignant cells could serve as potential therapeutic targets.

Dataset Information

Single-cell and spatial RNA sequencing reveal the spatiotemporal trajectories of fruit senescence.

Publications

Single-cell and spatial RNA sequencing reveal the spatiotemporal trajectories of fruit senescence.

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