Journal: Nature cardiovascular research

Article Title: Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis.

doi: 10.1038/s44161-022-00138-1

Figure Lengend Snippet: Fig. 1 | Single-cell and spatial transcriptomics of cardiac and ileum tissue of reovirus-infected neonatal mice. a, Experiment and analysis workflow. Four- day-old neonatal mice weighing 3 g per pup were infected (per os) with reovirus T1L. Neonatal mice infected with 1× PBS were used as mock controls. Ileum tissue (1 dpi and 4 dpi) and heart tissues (4 dpi, 7 dpi and 10 dpi) were assayed and used for scRNA-seq and spatial transcriptomics. b, UMAP plot of 31,684 single-cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi (one animal per condition), clustered by gene expression and colored by cell type (left). UMAP plots showing cardiac cell type clusters across samples for the heart scRNA-seq data (right). c, 8,243 spatial transcriptomes of cardiac tissue sections from mock-infected and reovirus-infected mice at 4 dpi and 7 dpi (one animal per condition). H&E-stained image of reovirus-infected myocarditic

Article Snippet: UMAP plot showing the expression of myocyte-specific genes that are upregulated in the border zone of myocarditic regions (right). g, High-resolution Slide-seq spatial transcriptomics map of cardiac ventricular tissue from reovirus infected mice at 7 dpi colored by Slide-seq bead clusters.

Techniques: Infection, Gene Expression, Staining

Journal: Nature cardiovascular research

Article Title: Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis.

doi: 10.1038/s44161-022-00138-1

Figure Lengend Snippet: Fig. 3 | Cytotoxic T cells recruited by inflamed endothelial cells induce pyroptosis in myocarditic tissue. a, UMAP plot of 9,786 single-cell endothelial cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi colored by endothelial cell subtype clusters (phenotypes) (top) and condition (bottom). b, Heat map showing top five differentially expressed genes (two-sided Wilcoxon test, log fold change > 1.0 and P < 0.01) for endothelial cell subtypes. c, UMAP plot showing the expression of genes upregulated in Cxcl9-high endothelial cells. d, Spatial transcriptomic maps of cardiac tissue from reovirus infected hearts at 7 dpi showing gene module scores calculated for four GO terms enriched in Cxcl9-high endothelial cells. e, UMAP plot of 2,205 single-cell T cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi colored by T cell subtype clusters (top) and condition (bottom). f, Heat map showing top five differentially expressed genes (two-sided Wilcoxon test, log fold change > 1.0 and P < 0.01) for T cell subtypes. g, UMAP plot showing the expression of genes upregulated in cytotoxic T cells from myocarditic heart at 7 dpi. h, Spatial transcriptomics maps of cardiac tissue from reovirus infected hearts at 7 dpi

Article Snippet: UMAP plot showing the expression of myocyte-specific genes that are upregulated in the border zone of myocarditic regions (right). g, High-resolution Slide-seq spatial transcriptomics map of cardiac ventricular tissue from reovirus infected mice at 7 dpi colored by Slide-seq bead clusters.

Techniques: Infection, Expressing

Journal: Nature cardiovascular research

Article Title: Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis.

doi: 10.1038/s44161-022-00138-1

Figure Lengend Snippet: Fig. 4 | Myocarditic regions and the border zone have distinct transcriptomic profiles and cell-type-specific signatures. a, Spatial transcriptomics map of cardiac tissue section from reovirus-infected mice at 7 dpi colored by spot clusters representing transcriptionally distinct tissue regions. b, Spatial transcriptomics maps of cardiac tissue sections from reovirus-infected mice at 7 dpi showing the expression of differentially expressed genes of interest in the myocarditic and the border zone. c, Changes in average predicted cell type proportions across the infected ventricle, for cell types enriched in the myocarditic region and the border zone. d, UMAP plot of 502 single-cell cardiomyocyte cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi colored by myocyte cell subtype (phenotypes) (left) and condition (right). e, Heat map showing the top five differentially expressed genes (two-sided Wilcoxon test, log fold change > 1.0 and P < 0.01) for cardiomyocyte cell subtypes. f, Venn diagram showing myocyte-specific genes

Article Snippet: UMAP plot showing the expression of myocyte-specific genes that are upregulated in the border zone of myocarditic regions (right). g, High-resolution Slide-seq spatial transcriptomics map of cardiac ventricular tissue from reovirus infected mice at 7 dpi colored by Slide-seq bead clusters.

Techniques: Infection, Expressing

Journal: MedComm

Article Title: Neuro‐Immune Crosstalk: Molecular Mechanisms, Biological Functions, Diseases, and Therapeutic Targets

doi: 10.1002/mco2.70497

Figure Lengend Snippet: Timeline of key milestones in neuroimmunology research. This timeline outlines major discoveries that have shaped the field of neuroimmunology. During the 1950s to 1970s, a series of foundational studies established the concept of “immune privilege” in the brain. Since the late 20th century, growing evidence has revealed bidirectional communication between the central nervous system (CNS) and the immune system, including active immune surveillance by the CNS and crucial regulatory roles of immune cells in neurogenesis and neural protection. In recent years, the integration of cutting‐edge technologies—such as single‐cell multiomics, tissue clearing, and organoid models—has enabled precise dissection of neuro‐immune interactions and facilitated the development of individualized interventions, ushering the field into a new era of mechanistic and translational research. Abbreviations : PNS, parasympathetic nervous system; SNS, sympathetic nervous system.

Article Snippet: To overcome these challenges, researchers have developed cutting‐edge tools, including: (1) high‐resolution spatial multiomics platforms (e.g., integrated spatial transcriptomics‐proteomics) for spatiotemporal mapping of neuro‐immune interactions to construct comprehensive “neuro‐immune connectomes”; (2) optimized organoid coculture systems, particularly brain–immune cell interaction models; and (3) advanced in vivo imaging techniques (e.g., two‐photon microscopy coupled with specific reporter systems) for real‐time observation of neuro‐immune processes.

Techniques: Dissection, Clinical Proteomics

Journal: MedComm

Article Title: Neuro‐Immune Crosstalk: Molecular Mechanisms, Biological Functions, Diseases, and Therapeutic Targets

doi: 10.1002/mco2.70497

Figure Lengend Snippet: Key technologies in neuroimmunology research. Advanced technologies hold great potential for deciphering neuro‐immune interactions, yet each category possesses distinct advantages and limitations. Single‐cell multiomics enables high‐resolution dissection of cellular heterogeneity but is costly and involves complex data analysis. Spatiotemporal and intravital imaging allows real‐time dynamic monitoring of cellular activities but is constrained by limited imaging depth and phototoxicity. Tissue clearing techniques facilitate 3D visualization of thick specimens but may compromise fluorescence signals and antigen integrity. Viral and synthetic biology tools provide precise genetic manipulation capabilities yet carry risks of immunogenicity and off‐target effects. Humanized and organoid models better recapitulate human physiology but often lack authentic microenvironmental contexts and involve complex culture systems. In vivo visualization and modulation technologies offer high physiological relevance, though invasive procedures and technical challenges remain substantial obstacles.

Article Snippet: To overcome these challenges, researchers have developed cutting‐edge tools, including: (1) high‐resolution spatial multiomics platforms (e.g., integrated spatial transcriptomics‐proteomics) for spatiotemporal mapping of neuro‐immune interactions to construct comprehensive “neuro‐immune connectomes”; (2) optimized organoid coculture systems, particularly brain–immune cell interaction models; and (3) advanced in vivo imaging techniques (e.g., two‐photon microscopy coupled with specific reporter systems) for real‐time observation of neuro‐immune processes.

Techniques: Dissection, Imaging, Fluorescence, Immunopeptidomics, In Vivo