Molecular Profiling of COVID-19 Autopsies Uncovers Novel Disease Mechanisms
Authors: Pujadas Elisabet , Beaumont Michael , Shah Hardik , Schrode Nadine , Francoeur Nancy , Shroff Sanjana , Bryce Clare , Grimes Zachary , Gregory Jill , Donnelly Ryan , Fowkes Mary E. , Beaumont Kristin , Sebra Robert , Cordon-Cardo Carlos 
Published: April 2021

Background

Current understanding of COVID-19 pathophysiology is limited by disease heterogeneity, complexity, and a paucity of studies evaluating patient tissues with advanced molecular tools.

Methods

Autopsy tissues from two COVID-19 patients, one of whom died after a month-long hospitalization with multi-organ involvement while the other died after a few days of respiratory symptoms, were evaluated using multi-scale RNASeq methods (bulk, single-nuclei, and spatial RNASeq next-generation sequencing) to provide unprecedented molecular resolution of COVID-19 induced damage.

Findings

Comparison of infected/uninfected tissues revealed four major regulatory pathways. Effectors within these pathways could constitute novel therapeutic targets, including the complement receptor C3AR1, calcitonin-like receptor or decorin. Single-nuclei RNA sequencing of olfactory bulb and prefrontal cortex highlighted remarkable diversity of coronavirus receptors. Angiotensin I converting enzyme 2 was rarely expressed, while Basignin showed diffuse expression, and alanyl aminopeptidase was associated with vascular/mesenchymal cell types. Comparison of lung and lymph node tissues from patients with different symptomatology with Digital Spatial Profiling resulted in distinct molecular phenotypes.

Interpretation

COVID-19 is a far more complex and heterogeneous disease than initially anticipated. Evaluation of COVID-19 rapid autopsy tissues with advanced molecular techniques can identify pathways and effectors at play in individual patients, measure the staggering diversity of receptors in specific brain areas and other well-defined tissue compartments at the single-cell level, and help dissect differences driving diverging clinical courses among patients. Extension of this approach to larger datasets will substantially advance the understanding of the mechanisms behind COVID-19 pathophysiology.

Funding

No external funding was used in this study.

Research in context

Evidence before this study

Information regarding changes seen in COVID-19 has accumulated very rapidly over a short period of time. Studies often rely on examination of normal samples and model systems, or are limited to peripheral blood or small biopsies when dealing with tissues collected from patients infected with SARS-CoV-2. For that reason, autopsy studies have become an important source of insights into the pathophysiology of severe COVID-19 disease, highlighting the emerging role of hyperinflammatory and hypercoagulable syndromes. Studies of autopsy tissues, however, are usually limited to histopathologic and immunohistochemical evaluation. The next frontier in understanding COVID-19 mechanisms of disease will require generation of highly dimensional, patient-specific datasets that can help dissect this complex and heterogeneous disease.

Added value of this study

Our work illustrates how high-resolution molecular and spatial profiling of COVID-19 patient tissues collected during rapid autopsies can serve as a hypothesis-generating tool to identify key mediators driving the pathophysiology of COVID-19 for diagnostic and therapeutic target testing. Here we employ bulk RNA sequencing to identify key regulators of COVID-19 and list specific mediators for further study as potential diagnostic and therapeutic targets. We use single-nuclei RNA sequencing to highlight the diversity and heterogeneity of coronavirus receptors within the brain, suggesting that it will be critical to expand the focus from ACE2 to include other receptors, such as BSG and ANPEP, and we perform digital spatial profiling of lung and lymph node tissue to compare two patients with different clinical courses and symptomatology.

Implications of all the available evidence

COVID-19 is a far more heterogeneous and complex disease than initially anticipated. Advanced molecular tools can help identify specific pathways and effectors driving the pathophysiology of COVID-19 and lead to novel biomarkers and therapeutic targets in a patient-specific manner. Larger studies representing the diversity of clinical presentations and pre-existing conditions will be needed to capture the full complexity of this disease.