The relationship of SARS-CoV-2 pulmonary infection and severity of disease is not fully understood. Here we show analysis of autopsy specimens from 24 patients who succumbed to SARS-CoV-2 infection using a combination of different RNA and protein analytical platforms to characterize inter-patient and intra-patient heterogeneity of pulmonary virus infection. There is a spectrum of high and low virus cases associated with duration of disease. High viral cases have high activation of interferon pathway genes and a predominant M1-like macrophage infiltrate. Low viral cases are more heterogeneous likely reflecting inherent patient differences in the evolution of host response, but there is consistent indication of pulmonary epithelial cell recovery based on napsin A immunohistochemistry and RNA expression of surfactant and mucin genes. Using a digital spatial profiling platform, we find the virus corresponds to distinct spatial expression of interferon response genes demonstrating the intra-pulmonary heterogeneity of SARS-CoV-2 infection.
COVID-19 , Host Microbial Interactions , Interferons/metabolism , Lung , Adult , Aged , Aged, 80 and over , Aspartic Acid Endopeptidases/metabolism , Autopsy , COVID-19/immunology , COVID-19/metabolism , Epithelial Cells/metabolism , Epithelial Cells/pathology , Epithelial Cells/virology , Female , Humans , Immunity , Immunohistochemistry , In Situ Hybridization , Interferons/genetics , Lung/pathology , Lung/virology , Macrophages/immunology , Male , Middle Aged , Mucins/genetics , Mucins/metabolism , Surface-Active Agents/metabolism , Transcriptome , Viral Load
The relationship of SARS-CoV-2 lung infection and severity of pulmonary disease is not fully understood. We analyzed autopsy specimens from 24 patients who succumbed to SARS-CoV-2 infection using a combination of different RNA and protein analytical platforms to characterize inter- and intra- patient heterogeneity of pulmonary virus infection. There was a spectrum of high and low virus cases that was associated with duration of disease and activation of interferon pathway genes. Using a digital spatial profiling platform, the virus corresponded to distinct spatial expression of interferon response genes and immune checkpoint genes demonstrating the intra-pulmonary heterogeneity of SARS-CoV-2 infection.
A family of mammalian protocadherin (Pcdh) proteins is encoded by three closely linked gene clusters (alpha, beta, and gamma). Multiple alpha and gamma Pcdh mRNAs are expressed in distinct patterns in the nervous system and are generated by alternative pre-mRNA splicing between different "variable" exons and three "constant" exons within each cluster. We show that each Pcdh variable exon is preceded by a promoter and that promoter choice determines which variable exon is included in a Pcdh mRNA. In addition, we provide evidence that alternative splicing of variable exons within a gene cluster occurs via a cis-splicing mechanism. However, virtually every variable exon can engage in trans-splicing with constant exons from another cluster, albeit at a far lower level.
Alternative Splicing/genetics , Cadherins/genetics , Promoter Regions, Genetic/genetics , RNA Precursors/metabolism , Alleles , Animals , Exons/genetics , Humans , Mice , Protein Isoforms/genetics , Protein Precursors/chemistry , Protein Precursors/genetics , RNA Precursors/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Reverse Transcriptase Polymerase Chain Reaction , Trans-Splicing/genetics , Transcription, Genetic
