Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

Chen

2022

Preprint

Spatially resolved transcriptomic analyses can reveal molecular insights underlying tissue structure and context-dependent cell-cell or cell-environment interaction. Due to the current technical limitation, obtaining genome-wide spatial transcriptome at single-cell resolution is challenging. Here we developed a new algorithm named iSpatial to derive spatial pattern of the entire transcriptome by integrating spatial transcriptomic and single-cell RNA-seq datasets. Compared to other existing methods, iSpatial has higher accuracy in predicting gene expression and their spatial distribution. Furthermore, it reduces false-positive and false-negative signals in the original datasets. By testing iSpatial with multiple spatial transcriptomic datasets, we demonstrate its wide applicability to datasets from different tissues and by different techniques. Thus, we provide a computational approach to reveal spatial organization of the entire transcriptome at single cell resolution. With numerous high-quality datasets available in the public domain, iSpatial provides a unique way for understanding the structure, function of complex tissues and disease processes.

Section: Resultsmentioning

confidence: 99%

“…The single cell resolution Stereo-seq data of mouse hemibrains is download from (https://db.cngb.org/stomics/mosta/) ( 34 ). We first transfer single cell level expression matrix to Seurat.…”

Section: Methodsmentioning

confidence: 99%

Accurate inference of genome-wide spatial expression with iSpatial

Chen

2022

Preprint

“…Stereo-seq library construction was described previously 14 . For the Stereo-seq library construction of the Syrian hamster infected by SARS-CoV-2, all the processes were performed in the ABSL-3 laboratory till the PCR products of cDNA were gained.…”

Section: Methodsmentioning

confidence: 99%

“…However, no reports have been published about the spatiotemporal landscape of SARS-CoV-2 clearance together with inflammation resolution and tissue repair. Here we applied our recently developed Stereo-seq 3 and droplet-based high-throughput scRNA-seq to the lungs of 45 hamsters infected with or without authentic SARS-CoV-2. A comprehensive spatiotemporal cellular and molecular atlas of the lung tissues was generated, covering whole lung lobes and the whole process from tissue damage and severe pneumonia to viral clearance and inflammation resolution.…”

Section: Introductionmentioning

confidence: 99%

“…We developed and applied a spatial transcriptomic sequencing technique with subcellular resolution and tissue-scale extensibility, i.e. , Stereo-seq 3 , together with single-cell RNA sequencing (scRNA-seq), to the entire lung lobes of 45 hamsters and obtained an elaborate map of the pulmonary spatiotemporal changes from acute infection, severe pneumonia to the late viral clearance and inflammation resolution. While SARS-CoV-2 infection caused massive damages to the hamster lungs, including naïve T cell infection and deaths related to lymphopenia, we identified a group of monocyte-derived proliferating Slamf9 + Spp1 + macrophages, which were SARS-CoV-2 infection-inducible and cell death-resistant, recruiting neutrophils to clear viruses together.…”

mentioning

confidence: 99%

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Spatiotemporal landscape of SARS-CoV-2 pulmonary infection reveals Slamf9⁺Spp1⁺ macrophages promoting viral clearance and inflammation resolution

Cong

Dong

Yang

et al. 2022

Preprint

Self Cite

While SARS-CoV-2 pathogenesis has been intensively investigated, the host mechanisms of viral clearance and inflammation resolution are still elusive because of the ethical limitation of human studies based on COVID-19 convalescents. Here we infected Syrian hamsters by authentic SARS-CoV-2 and built an ideal model to simulate the natural recovery process of SARS-CoV-2 infection from severe pneumonia. We developed and applied a spatial transcriptomic sequencing technique with subcellular resolution and tissue-scale extensibility, i.e., Stereo-seq, together with single-cell RNA sequencing (scRNA-seq), to the entire lung lobes of 45 hamsters and obtained an elaborate map of the pulmonary spatiotemporal changes from acute infection, severe pneumonia to the late viral clearance and inflammation resolution. While SARS-CoV-2 infection caused massive damages to the hamster lungs, including naive T cell infection and deaths related to lymphopenia, we identified a group of monocyte-derived proliferating Slamf9+Spp1+ macrophages, which were SARS-CoV-2 infection-inducible and cell death-resistant, recruiting neutrophils to clear viruses together. After viral clearance, the Slamf9+Spp1+ macrophages differentiated into Trem2+ and Fbp1+ macrophages, both responsible for inflammation resolution and replenishment of alveolar macrophages. The existence of this specific macrophage subpopulation and its descendants were validated by RNAscope in hamsters, immunofluorescence in hACE2 mice, and public human autopsy scRNA-seq data of COVID-19 patients. The spatiotemporal landscape of SARS-CoV-2 infection in hamster lungs and the identification of Slamf9+Spp1+ macrophages that is pivotal to viral clearance and inflammation resolution are important to better understand the critical molecular and cellular players of COVID-19 host defense and also develop potential interventions of COVID-19 immunopathology.

Single‐cell and spatial analyses reveal the association between gene expression of glutamine synthetase with the immunosuppressive phenotype of APOE+CTSZ+TAM in cancers

Wei

Chen

et al. 2023

Molecular Oncology

An immunosuppressive state is regulated by various factors in the tumor microenvironment (TME), including, but not limited to, metabolic plasticity of immunosuppressive cells and cytokines secreted by these cells. We used single‐cell RNA‐sequencing (scRNA‐seq) data and applied single‐cell flux estimation analysis to characterize the link between metabolism and cellular function within the hypoxic TME of colorectal (CRC) and lung cancer. In terms of metabolic heterogeneity, we found myeloid cells potentially inclined to accumulate glutamine but tumor cells inclined to accumulate glutamate. In particular, we uncovered a tumor‐associated macrophage (TAM) subpopulation, APOE+CTSZ+TAM, that was present in high proportions in tumor samples and exhibited immunosuppressive characteristics through upregulating the expression of anti‐inflammatory genes. The proportion of APOE+CTSZ+TAM and regulatory T cells (Treg) were positively correlated across CRC scRNA‐seq samples. APOE+CTSZ+TAM potentially interacted with Treg via CXCL16–CCR6 signals, as seen by ligand–receptor interactions analysis. Notably, glutamate‐to‐glutamine metabolic flux score and glutamine synthetase ( GLUL ) expression were uniquely higher in APOE+CTSZ+TAM, compared with other cell types within the TME. GLUL expression in macrophages was positively correlated with anti‐inflammatory score and was higher in high‐grade and invasive tumor samples. Moreover, spatial transcriptome and multiplex immunofluorescence staining of samples showed that APOE+CTSZ+TAM and Treg potentially colocalized in the tissue sections from CRC clinical samples. These results highlight the specific role and metabolic characteristic of the APOE+CTSZ+TAM subpopulation and provide a new perspective for macrophage subcluster‐targeted therapeutic interventions or metabolic checkpoint‐based cancer therapies.