Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis

Abstract

A significant fraction of sudden death in children and young adults is due to myocarditis, an inflammatory disease of the heart, most often caused by viral infection. Here we used integrated single-cell and spatial transcriptomics to create a high-resolution, spatially resolved map of reovirus-induced myocarditis in neonatal murine hearts. We assayed hearts collected at three timepoints after reovirus infection and studied the temporal, spatial, and cellular heterogeneity of host-virus interactions. We further assayed the intestine, the primary site of reovirus infection to establish a full chronology of molecular events that ultimately lead to myocarditis. We implemented targeted enrichment of viral transcripts to establish the cellular targets of the virus in the intestine and the heart. Our data give insight into the cell-type specificity of innate immune responses, and into the transcriptional states of inflamed cardiac cells that recruit circulating immune cells, including cytotoxic T cells which induce pyroptosis in the myocarditic tissue. Analyses of spatially restricted gene expression in myocarditic regions and the border zone around those regions identified immune-mediated cell-type specific injury and stress responses. Overall, we observe a dynamic and complex network of cellular phenotypes and cell-cell interactions associated with viral myocarditis.

Single cell and spatial transcriptomic analyses reveal microglia-plasma cell crosstalk in the brain during Trypanosoma brucei infection

“…The integration of scRNAseq with spatial transcriptomics enable us to characterise cellular and tissue responses to infections on regional and global scales. This has been successfully applied to characterise local immune responses to Mycobacterium tuberculosis 12 and M. leprae 13 and in the heart during viral myocarditis 14 . However, to our knowledge, similar approaches have not been implemented to study tissue responses to protozoan parasites.…”

In situ polyadenylation enables spatial mapping of the total transcriptome

“…To test the performance and versatility of STRS, we applied it to two distinct mouse tissue types: injured hindlimb muscle 5 and virally infected heart tissue 4 . We quantified the percentage of unique molecules (UMIs) as a function of RNA biotype (GENCODE M28 annotations; Fig 1b ).…”

“…We performed hybridization-based enrichment of viral fragments on the Visium and STRS libraries for reovirus-infected hearts using the xGen Hybridization and Wash Kit (IDT; 1080577) 4 . In this approach, a panel of 5’-biotinylated oligonucleotides was used for capture and pulldown of target molecules of interest, which were then PCR amplified and sequenced.…”

“…Previously published spatial RNA-sequencing data were downloaded from Gene Expression Omnibus (GEO) and are available under the following accession numbers; regenerating skeletal muscle 5 GSE161318, infected heart tissue 4 GSE189636. Spatial Total RNA-Sequencing data generated in this study can be found on GEO under the accession number GSE200481.…”

Integrative single cell and spatial transcriptomic analysis reveal reciprocal microglia-plasma cell crosstalk in the mouse brain during chronicTrypanosoma bruceiinfection

“…The integration of scRNAseq with spatial transcriptomics enable us to characterise cellular and tissue responses to infections on regional and global scales. This has been successfully applied to characterise local immune responses to Mycobacterium tuberculosis (Carow et al, 2019) and M. leprae (Ma et al, 2021) and in the heart during viral myocarditis (Mantri et al, 2021). However, to our knowledge, similar approaches have not been implemented to study tissue responses to protozoan parasites.…”