This web page was produced as an assignment for an undergraduate course at Davidson College.
Understanding the dangerous effects that COVID-19 has on the human immune system could be the key to fighting it
Scientists seek to better understand the biological makeup of humans through the study of their immune system. More specifically research of the immune system is approached through the investigation of the effects that specific illnesses have on the body. This understanding can then be applied to create effective treatments for individuals who suffer from such diseases. At the forefront of this immunology research is the exploration of COVID-19, as the cause of the current global pandemic. In order to investigate the landscape of the immune system for specific diseases such as COVID-19, scientists can utilize a handful of techniques such as single cell RNA sequencing (Xu et al. 2020). Such methods in past research have already characterized certain elements of the human immune response to COVID-19, including increased levels of cytokines in the blood during severe COVID-19 recovery, which in turn can cause deadly cytokine storms in the body (Hojyo et al. 2020). However, overall, the pathogenesis mechanisms, which underlie COVID-19, still remain mostly unclear.
To further investigate the landscape of COVID-19, Xu et al. analyzed 20059 peripheral immune cells across three healthy controls (HC), five mild COVID-19 infection patients, and eight severe COVID-19 infection patients. Utilizing single cell RNA sequencing (scRNA-seq) and subsequent clustering analysis ten major cells types were identified: T cells, NK cells, B Cells, monocyte, myeloid DCs, plasmacytoid DCs, plasma cells, megakaryocyte, cycling cells, and erythrocyte (Xu et al. 2020). However, erythrocytes were not included in further results of this study and cycling cells were further clustered into cycling T, cycling PC, and cycling NK cells. This analysis determined there to be a significantly large increase in monocyte/T cell ratios in COVID-19 patients compared to healthy controls, showing one way that this infection greatly influences the makeup of immune cells in the blood.
Since there was this noticeable increase in monocytes associated with COVID-19, myeloid cells were reclustered for further investigation. Five distinct cell types were identified: CD14+ classic monocyte, CD14+CD16+ intermediate monocytes, CD16+ non-classical monocytes, DC1, and DC2 (Xu et al. 2020). The proportions of these cell types varied significantly from the severe cases to the mild and control cases. Compared to mild and control cases, severe infection had a significant increase in the proportion of CD14+ monocytes, but a significant decrease in CD16+ non-classical monocytes, CD14+CD16+, and DC2. UMAP projection patterns of just CD14+ monocytes showed altered transcriptome features between the COVID-19 patients and healthy controls. GO analysis of differentially expressed genes (DEGs) associated severe COVID-19 infection to the upregulation of response to virus, neutrophil activation, and energy metabolism pathways along with the downregulation of monocyte functions such as decreased cytokine secretion/chemokine production and antigen processing/presentation. More broadly, this upregulation reflects the immune response to infection while this downregulation demonstrates COVID-19 immune paralysis.
As a respiratory disease, COVID-19 causes activation of bronchoalveolar lavage fluid (BALF) monocyte-macrophages, especially in severe infection. Thus, the authors studied paired samples of BALF and blood cells of two mild COVID-19 patients and five severe COVID-19 patients. Integration analysis of these BALF and circulating myeloid cells recognized differential expression, which indicated blood-toward-BALF circulation as expected of recruitment of peripheral monocytes to inflammatory tissues (Xu et al. 2020). Transcriptome analysis of these paired samples resulted in a high number of DEGs, which when paired with GO analysis connects, show broad activation of multiple immune pathways in BALF monocyte-macrophages, including response to cytokines, neutrophil activation and leukocyte migration. More specifically, pathways in BALF monocyte-macrophages relevant to severe COVID were especially upregulated while pathways related to alveoli macrophages functions were downregulated. Moreover, cytokine and chemokine levels in monocyte-macrophages were found to be highly expressed in BALFs but not their blood sample counterparts, suggesting monocyte-macrophages to be immune silent in blood cells. It was also observed that there was a relatively higher level of anti-inflammatory cytokines, but not pro-inflammatory cytokines, in BALFs from severe than mild COVID-19 cases, signifying that excess pro-inflammatory cytokines is not the cause of cytokine storms associated with severe COVID-19.
To look further at potential immune responses, the authors next clustered NK and T cells. UMAPs show innate like T cell proportions to be significantly lower in severe than mild cases while the proportions of several CD4+ subsets significantly increased (Xu et al. 2020). Paired T cell receptor (TCR) clonotype analysis further revealed increased clonal expansion in severe COVID infections in CD4+ but not CD8+ T cell subsets, showing preferential activation of CD4+ T cell responses. Looking more specifically at T cells and their movement from blood to BALFs in COVID patients, the researchers noticed that a lot of BALF cells could be traced back to their paired blood samples especially in severe infection. Transcriptome analysis also showed T cells to have heightened expression in BALF cells, which is likely caused by the increased chemokines in BALFs identified earlier.
While each piece of this study only answers a small portion of the questions researchers have about COVID-19 during the current global pandemic, each piece unearthed helps to put together an immune cell landscape for this disease. Doing so is incredibly important in order to construct and perfect effective treatment in order to save the lives of those who fall to severe infection. While its broad investigation is the strength of this study, its inability to investigate further some of its own discoveries is also a weakness. Moving forward the role of anti-inflammatory cytokines, in the context of the research presented here, should be explored in order to understand how inhibiting local cytokine storms could be an effective COVID-19 infection treatment.
Mimi Ughetta is a Genomics Major at Davidson College in Davidson, NC. Contact her at miughetta@davidson.edu.
References:
Hojyo S., M. Uchida, K. Tanaka, R. Hasebe, Y. Tanaka, et al., 2020 How COVID-19 induces cytokine storm with high mortality. Inflammation and Regeneration 40. https://pubmed.ncbi.nlm.nih.gov/33014208/
Viktor Forgacs, (2020). https://unsplash.com/photos/FcDqdJUM6B4
Xu, G., Qi, F., Li, H. et al. The differential immune responses to COVID-19 in peripheral and lung revealed by single-cell RNA sequencing. Cell Discov 6, 73 (2020). https://pubmed.ncbi.nlm.nih.gov/33101705/
Back to home page here.
© Copyright 2020 Department of Biology, Davidson College, Davidson, NC 28036.
