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Multi-modal Single Cell Profiling of COVID – 19 PBMC Samples

Multi-modal Single Cell Profiling of COVID – 19 PBMC Samples:

Integration of Molecular Profiles with Clinical Parameters and Disease Progression

Prof. Bertie Göttgens and Dr. Nicola Wilson – Stem Cell Institute, University of Cambridge, UK

In collaboration with Prof. Ken Smith – Addenbrooke’s hospital, University of Cambridge, UK

Simply Put

The University of Cambridge and its affiliated hospitals have mobilised diverse teams to help the international fight against COVID-19. Due to the complex and unpredictable response of the immune system to the COVID-19 virus, it is of vital importance to investigate the impact of this disease on all the immune cells present in our blood. These types of investigations will hopefully provide us with a better ability to predict how the symptoms will progress in different patients and potentially lead to the development of better treatment regimes. In order to gain a better understanding of how the immune system responds in different COVID-19 patients, we will be comparing samples from patients with different severities of disease along with healthy donor samples.
The immune system is made up of many different types of cells which interact with one another as well as with the rest of the blood system. For this reason, we take advantage of the rapidly advancing technologies which allow a detailed characterisation of the molecular features and the physical properties of thousands of individual cells at the same time. By undertaking this project, we hope to identify therapeutic targets, markers that provide information on personalising the treatment of individual patients, as well as a map of cellular interactions driving disease severity and variability to aid future drug discovery efforts.

Description

In response to the global COVID-19 pandemic, Addenbrooke’s hospital – the teaching hospital of the University of Cambridge medical school – has gathered its resources in patient care and medical research. The infrastructure has been set up, that will enable a multitude of clinical research, alongside the critical patient care required for COVID-19 patients admitted to the hospital in April and May 2020.

Upon admission to Addenbrooke’s hospital, 200 patients will be enrolled in the NIHR BioResource COVID19 cohort, and complex biochemical, flow cytometry, a genomic and molecular analysis will be undertaken. The analysis includes collecting peripheral blood mononuclear cells (PBMC), where multiple aliquots for each of those 200 patients will be stored away. Samples will be linked to Addenbrooke’s electronic medical record system allowing the collection of comprehensive clinical data. Once patient outcomes are known, a subset of these samples will be defrosted and subjected to a battery of further tests, which will include single-cell genomics analysis as outlined below.

This project focuses on single-cell profiling for peripheral blood mononuclear cells (PBMC) taken from COVID-19 patients to establish full single-cell transcriptome, protein expression for 225 proteins, B-cell receptor, and T-cell receptor rearrangement status.

PBMCs from 80 individual patients will be profiled. 40 of those patients will have progressed to more severe disease, while the other 40 showed no progression. For 10 of the 40 patients that progressed to a more severe stage of the disease, two additional (sequential) samples will be taken to monitor changes in PBMCs associated with severe symptoms. Therefore, this setup entails profiling a total of 100 PBMC samples (80 admission samples and 2×10 disease progression samples).

The single-cell analysis will be performed using the latest multi-modal molecular profiling technology. Importantly, additional vials of viable PBMCs will be kept in storage for possible future analysis of further data types, including open chromatin.

The strategy outlined above will permit deep datamining of the single-cell data against all the clinical and immunological parameters, including patient outcomes. Possible discoveries may include new gene or protein signatures expressed at the time of hospital admission that can predict subsequent disease outcomes, which would allow the future focussing of clinical resources on the most at-risk patients. Moreover, gene/protein signatures associated with poor disease outcome may also highlight biological pathways to be targeted by existing drugs, thus providing new treatment options for this patient group. Finally, analysis of BCR and TCR receptor status will allow future investigations into how the immune system responds to COVID-19 and reveal what types of immune responses are associated with good/poor patient outcomes, providing essential clues for the design of successful immune- modulatory treatment regimens.

The research groups of Sarah Teichmann (Head of Cellular Genetics, Wellcome Sanger Institute) and John Marioni (European Bioinformatics Institute) will support initial data processing and analysis.

All raw and processed genomic data will be freely available to the global community fighting the COVID-19 pandemic.

Results

This project has been a combined effort across three medical centres within the UK (Newcastle, Cambridge and London). The funds provided by the Aging Biology Foundation Europe supported the research undertaken at the Cambridge site.

The project has taken advantage of single-cell multi-omics techniques, in which transcriptomic analysis, cell surface phenotype and lymphocyte antigen receptor characterisation, all at a single cell resolution, were combined.

The results of the research have been submitted in January 2021 to a peer reviewed journal. 

In this article the authors highlight how this multi-omic analysis of PBMCs has contributed to the characterisation of the cellular immune response in the peripheral blood to COVID-19 across a range of disease severities and to this end has provided several insights into COVID-19: 

  1. a new non-classical monocyte state that sequesters platelets and replenishes the alveolar macrophage pool; 
  2. platelet activation accompanied by early priming towards megakaryopoiesis in immature haematopoietic stem/progenitor cells accompanied by the expansion of megakaryocyte-primed progenitors;
  3. increased clonally expanded CD8+ effector:effector memory T cells, and proliferating CD4+ and CD8+ T cells in patients with more severe disease; 
  4. relative increase of IgA plasmablasts in asymptomatic stages that switches to expansion of IgG plasmablasts and plasma cells, accompanied with higher incidence of BCR sharing, as disease severity increases.

In the meantime, to ensure the availability of data and the analysis, a pre-print has been submitted to medrxiv and a user-friendly web portal made available. The processed data is available to download from Array Express using accession number E565 MTAB-10026 and all data analysis scripts are available at the GitHub.