Deep spatial profiling of COVID19 brains reveals neuroinflammation by compartmentalized local immune cell interactions and targets for intervention

Abstract

COVID-19 causes neurological symptoms that can be potentially life-threatening in up to 67 % of the patients. The underlying pathophysiological mechanisms of COVID-19 associated encephalopathy, the involved immune cells, their spatial distribution and their cellular interactions during disease remain largely unclear. In this study, we performed a 38-biomarker imaging mass cytometry analysis of the brain stem from 25 patients and additional controls to understand the local immune response during SARS-CoV-2 infection at a spatially resolved, high-dimensional single-cell level. Importantly, utilizing an unbiased image segmentation and cell classification pipeline, we observed a significant immune activation in the central nervous system (CNS) and identified novel context-specific CD8 T cell and microglial clusters. Spatially resolved single-cell analysis identified distinct phenotypes of T cells and microglial clusters, their presence in specific anatomical regions and their cellular interactions. Our analysis further highlights microglial nodules and perivascular immune cell clusters as key sites of the local immune response. It also demonstrates that disease-associated neuroinflammation is associated with severe axonal damage as a structural basis for the neurologic deficits. Finally, we identified compartment- and cluster-specific immune checkpoints that can be used for future therapeutic interventions.

Efficacy of GC-376 against SARS-CoV-2 virus infection in the K18 hACE2 transgenic mouse model

“…Similar results were observed with Iba1 IHC, showing similar staining patterns in the organs from the high dose challenge groups but lower staining overall in G6 (low dose/GC-376) when compared against its control G5 (low dose/vehicle) (Fig. 6, panels [21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40]. Findings were overall consistent with the extent of inflammatory reaction and lesions observed by HE.…”

“…The widespread virus colonization of neurons and associated meningoencephalitis observed in mice, partially explains the neurological deficits observed COVID-19 patients 37,38 . Various infective mechanisms and paths can be exploited by the virus to reach the central nervous system.…”

“…Reduced virus involvement in the brain is important considering the neurologic features observed in COVID-19 patients where disorientation, poorly organized movements and confusion among other neurological symptoms have been observed 36 . Additionally, COVID-19 neurological symptoms can be potentially life threatening in around 65% of the cases 37 . A positive effect of GC-376 was also supported by the histopathological examinations and analysis of markers of cellular infiltration (CD3 and Iba1).…”

“…Mild increase in macrophages were observed in G4, G3 and G5 NT at 2 dpc invading lamina propria and olfactory epithelium (arrowheads and inserts) (33,35). No increase in Iba1+ staining was observed in G6 and G1 NT at 2 dpc (36)(37)39). Mild-moderate increase in perivascular macrophages was observed in G4, G3, and G5 brains at 5 dpc accompanied by marked increased in staining of resident microglial cells within areas of intense virus antigen positivity (arrowheads) (38,40).…”

The spatio-temporal landscape of lung pathology in SARS-CoV-2 infection

“…bronchoalveolar lavage fluid 17 have brought to light major changes in the immune system such as excessive neutrophil activation 18 , lymphopenia 3 , and aberrant adaptive immune system responses 2 among the most prominent changes. However, thorough analysis of infected tissue and immune system in a spatial context has only recently started 4,[19][20][21] and is currently lacking for most infected organs, including the lung. While most COVID-19 patients with severe disease develop ARDS, administering routine clinical supportive care as for other ARDS does not entirely aid in patient recovery.…”