Single-cell analysis of approximately 800,000 immune cells from 130 individuals identifies differences in the immune response associated with disease severity
Visualisation of an antibody expression landscape in COVID-19, shown as a rotating network. Cells are coloured by antibody class produced, and cells producing the same antibodies cluster together into raspberry-like structures.
An interesting feature of the COVID-19 pandemic is the vast range in severity of the symptoms experienced by people infected with SARS-CoV-2; from asymptomatic carriers and mild coughs to severe respiratory distress and need for ventilators. Understanding why different people have such varied experiences could be of great benefit to the development of new treatments and might enable prediction as to whether newly infected patients are more likely to develop severe disease. Menna Clatworthy’s group, in the University of Cambridge Molecular Immunity Unit that is housed at the LMB, has taken part in the largest study of its type to investigate differences in the immune response that could explain this variation.
To do this, a large team of researchers from Newcastle University, the University of Cambridge, the Wellcome Sanger Institute, and EBI collaborated to analyse blood samples taken from 130 people at three different UK centres. This involved single-cell RNA sequencing of approximately 800,000 individual immune cells and measurements of thousands of parameters, including detailed analysis of cell surface proteins and immune receptors. Importantly, this is one of the only such studies to include people who were infected with SARS-CoV-2 asymptomatically, allowing investigation of differences in the immune response across the full range of experienced symptoms.
In asymptomatic carriers of SARS-CoV-2, the team found that IgA antibody-producing cells in the blood were preserved or expanded – this type of antibody is found at important barriers such as the nose and lungs, whereas these cells were lost in those who got sick. This suggests that an effective antibody defence at key barriers is likely to be an important feature that determines the fate of infected individuals.
Patients with mild symptoms had raised levels of anti-viral helper T cells and antibody-producing B cells in the bloodstream. Contrastingly, these were lost in severe disease cases, where the team saw an increase in monocytes and killer T cells (high levels of which can lead to lung inflammation), and raised levels of platelet-producing cells, which help blood to form clots. These findings could explain how the immune response in severe disease can lead to increased risk of clotting and respiratory distress due to inflammation in the lungs.
By studying the immune responses in people from three UK centres (Newcastle, Cambridge, and London), the team was able to examine regional differences and surprisingly found a relationship between the antibody response and the city the patient came from, hinting that this part of the immune response might be tailored to different variants of the virus.
This is one of the most detailed studies of immune responses to COVID-19 to date and begins to help us understand why some people get really sick while others fight off the virus without even knowing they have it. The finding that effective antibody responses in the nose and lungs may be important for a robust defence could be used to allow screening of individuals who have been infected to predict who might be more likely to succumb to severe disease. The study also suggests that it could also be possible to develop new treatments against severe disease by reducing platelet production or the number of killer T cells and thereby reducing lung inflammation.
The work was funded by UKRI MRC, Wellcome Trust, NIHR, the Lister Institute of Preventative Medicine, the Aging Biology Foundation, ERC, Versus Arthritis, Cancer Research UK, EMBL, Chan Zuckerberg Initiative, BBSRC, EPSRC, The Jikei University School of Medicine, BMA Foundation, Action Medical Research, German Research Foundation, the UK Coronavirus Immunology Consortium, and Barbour Foundation.
Personal perspectives of COVID-19 research
We are accompanying Insights on Research that cover COVID-19 research with interviews with the scientists who carried out the work, to give some perspective of the experiences of transitioning to COVID-19 research and working at the LMB during the height of the ongoing pandemic. One member of Menna’s group who led the B cell analysis for this study, Kelvin Tuong, describes how he ended up doing this work and what it was like working on this project.
What is your normal research focus?
Single-cell analysis of immune cells such as macrophages and B cells in organs such as the kidneys and prostate.
Why did you change focus to work on COVID-linked research?
I was already working primarily on a number of B cell-related projects that used the same sets of skills and it was a natural extension to apply these skillsets to the COVID project.
Moreover, I was serendipitously developing a single-cell BCR (B cell receptor)-sequencing analysis software package over Christmas of 2019, which I’ve named dandelion, because I wanted to improve my capabilities with BCR sequencing analysis and there was a general shortage of publicly available tools to do the analysis.
When the pandemic started, Menna and her clinical colleagues worked hard to source some samples for a separate pilot COVID-19 related project during the first wave, and I was able to quickly adapt dandelion to analyse the results promptly. We showcased the data and dandelion during a Human Cell Atlas Special Meeting on COVID-19, which then led to us being approached to help with the BCR analysis by the Newcastle team.
How might this research make a difference to the pandemic outcome?
Our dataset is one of the largest and most comprehensive COVID-19 related datasets that’s currently available and is the one of the few (if any) that actually included asymptomatic individuals as part of the cohort. This was significant as it revealed trends that were not known before; for example, asymptomatics appeared to have an intact antibody sub-class most commonly found in mucosal barrier tissues (IgA2), whereas symptomatic COVID patients showed significant reductions across the board. It is exciting to speculate that this may lead to new therapeutics to try and promote or recover this humoral response in individuals to better cope with the infection, or as a screening tool to triage patients due to low levels of the aforementioned antibody sub-class as this might mean that they are going to end up having a bad response to the virus.
What has your experience in the lab been like during the pandemic?
Like many others, I have worked from home for almost the entirety of 2020. While working arrangements certainly became more flexible, it was challenging to separate work from rest because my resting spot and working spot were the same. Perhaps because of this I ended up looking more productive than usual and this had a knock-on effect of increasing my workload even further. While I think I’ve handled this generally well, I think this is not sustainable in the long term and I’m beginning to feel the effects of burnout; I’m very much looking forward to when I can go back to lab and have more normal interactions with work and colleagues, and also a proper holiday that does not involve sitting at home doing nothing.
What next? Will your involvement in COVID research continue or are you returning to your normal research focus?
My involvement in COVID research will likely continue for a while more. There’s data coming through from patients infected by the B1.1.7 strain in the UK, COVID-19 patients with renal failure, and international collaborations to consolidate the publicly available BCR repertoire data.
Single-cell multi-omics analysis of the immune response in COVID-19. Stephenson, E., Reynolds, G., Botting, RA., Calero-Nieto, FJ., Morgan, MD., Tuong, ZK., Bach, K., Sungnak, W., Worlock, KB., Yoshida, M., Kumasaka, N., Kania, K., Engelbert, J., Olabi, B., Stremenova Spegarova, J., Wilson, NK., Mende, N., Jardine, L., Gardner, LCS., Goh, I., Horsfall, D., McGrath, J., Webb, S., Mather, MW., Lindeboom, RGH., Dann, E., Huang, N., Polanski, K., Prigmore, E., Gothe, F., Scott, J., Payne, RP., Baker, KF., Hanrath, AT., Schim van der Loeff, ICD., Barr, AS., Sanchez-Gonzalez, A., Bergamaschi, L., Mescia, F., Barnes, JL., Kilich, E., de Wilton, A., Saigal, A., Saleh, A., Janes, SM., Smith, CM., Gopee, N., Wilson, C., Coupland, P., Coxhead, JM., Kiselev, VY., van Dongen, S., Bacardit, J., King, HW., CITIID-NIHR COVID-19 BioResource Collaboration, Rostron, AJ., Simpson, AJ., Hambleton, S., Laurenti, E., Lyons, PA., Meyer, KB., Nikolić, MZ., Duncan, CJA., Smith, KGC., Teichmann, SA., Clatworthy, MR., Marioni, JC., Göttgens, B., Haniffa, M. Nature Medicine https://doi.org/10.1038/s41591-021-01329-2
Menna’s group page
Muzlifah Haniffa’s page
Bertie Göttgens’ page
Sarah Teichmann’s page
John Marioni’s page
LMB joins the fight against COVID-19