The immune response to SARS-CoV-2infection in tissue: A multi-omic spatial investigation

Pugh, Matthew R ORCID: 0000-0002-6324-661X (2024). The immune response to SARS-CoV-2infection in tissue: A multi-omic spatial investigation. University of Birmingham. Ph.D.

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Abstract

The SARS-CoV-2 virus primarily infects the lung and can induce a localised and systemic immune response, which in some patients, can be fatal. The virus can also infect other non-respiratory tissues such as the placenta. SARS-CoV-2 infection in the placenta is associated with fetal compromise and intra-uterine death. Whilst much work has been done to describe the systemic immune response to SARS-CoV-2 infection, little has been done to describe the immune response in primary tissue. Adopting a multi-modal, spatial profiling approach on fixed tissue specimens from post- mortem and pathology archives, I describe the characteristics of the immune response in COVID-19 lung tissue and COVID-19 placentitis. Multi-modal approaches contributing towards this deep phenotypic characterisation included bulk and spatial transcriptomics, multiplex immunohistochemistry, single-plex immunohistochemistry and RNAscope, enabling robust cross-validation.

Lung tissues from 8 post mortem COVID-19 patients were analysed and compared to diseased and normal controls. On histological assessment, the lungs of COVID-19 patients invariably showed diffuse alveolar damage, with varying degrees of fibrosis, vasculitis, thrombosis and secondary infection. SARS-CoV-2 virus was predominantly detected in early-stage disease within the epithelium and a small proportion of macrophages. Macrophages were the predominant immune cells, with less numerous infiltrations of granulocytes and lymphocytes. The immediate virus microenvironment was enriched for immune evasive PDL1 expressing macrophages and deplete of lymphocytes. Whilst virus was apparently cleared in later stage disease, the immune infiltrate appeared to increase. Collagens were upregulated in the interstitium of COVID-19 lungs, in particular collagen VI. Serum pro-collagen VI was measured in the serum of a cohort of living patients with variable severity COVID-19. Increased serum pro-collagen VI was associated with severe disease and poor outcome.

Placentas from 13 SARS-CoV-2 positive mothers histologically showed chronic histiocytic intervillositis (CHI) and massive peri-villous fibrin deposition (MPVFD) in most cases, with a small subset showing chronic villitis. Trophoblastic SARS-CoV-2 infection and intra-uterine death was exclusively associated with CHI/MPVFD. Trophoblastic SARS-CoV-2 infection, compared to diseased and normal controls, was associated with prominent M1 macrophage infiltration and enrichment for CD4+ T-cells and B-cells. Macrophages showed CXCL10 expression which is associated with immune cell recruitment and fibrin deposition. The immediate immune microenvironment showed enrichment for CD4+ T-cells and PDL1 expressing macrophages. Interferon responses were transcriptomically blunted in viral rich regions of the placenta. A subset of placentas from SARS-CoV-2 infected with CHI morphology showed no evidence of virus, which may represent viral clearance akin to lung infection.

In summary, both diseases are characterised by florid localised immune responses with prominent innate and adaptive immune cell infiltrates and marked alterations in tissue architecture. There are competing antiviral and immune evasive responses present in both infected tissue, which ultimately lead to the observed pathological changes. The changes observed in lung and placenta can be used to infer novel prognosticators and treatments. Specifically, the elevated collagen VI signature observed in post-mortem lung translates into a novel serum-based prognosticator for mortality in hospitalised COVID-19 patients. Furthermore, the observed upregulation of CXCL10 in macrophages in COVID-19 placentitis could represent a novel therapeutic target.
Overall, the study demonstrates how spatial profiling techniques can be harnessed to understand complex phenomena in fixed archival tissue, inferring data of clinical relevance.

Type of Work:

Thesis (Doctorates > Ph.D.)

Award Type:

Doctorates > Ph.D.

Supervisor(s):