The Karolinska KI/K COVID-19 Immune Atlas: An open resource for immunological research and educational purposes

Abstract

The Karolinska KI/K COVID-19 Immune Atlas project was conceptualized in March 2020 as a part of the academic research response to the developing SARS-CoV-2 pandemic. The aim was to rapidly provide a curated dataset covering the acute immune response towards SARS-CoV-2 infection in humans, as it occurred during the first wave. The Immune Atlas was built as an open resource for broad research and educational purposes. It contains a presentation of the response evoked by different immune and inflammatory cells in defined naïve patient-groups as they presented with moderate and severe COVID-19 disease. The present Resource Article describes how the Karolinska KI/K COVID-19 Immune Atlas allow scientists, students, and other interested parties to freely explore the nature of the immune response towards human SARS-CoV-2 infection in an online setting.

Keywords: COVID-19; Karolinska KI/K COVID-19 Immune Atlas; SARS-CoV-2; biobank; immune atlas; immune response.

FIGURE 1

Structure of the Immune Atlas web interface, patient cohort, and flow cytometry panels used for immunophenotyping. A, Overview of the head menu of the Immune Atlas. Below the toolbar appears the different immune cell populations studied from peripheral blood of defined groups of COVID‐19 patients and healthy controls. B, Under the section “Project”, the item “Cohort” provides clinical information of the patients included in the Immune Atlas project. C, Under the section “Project”, the item “Panels” provides details on the flow cytometry panels used to immunophenotype each of the cellular populations

FIGURE 2

Interactive exploration of immune cell counting and immunophenotyping results. A, From the head menu “Atlas” (1), by selecting the immune cell population of interest (here “NK cells”) (2), and the corresponding level of detail (here total or specific subsets of NK cells) (3), analytic results (4), and group comparisons (5) are available. Several graphical representations can be chosen (here “Box plot”) (6), where interactive statistics appear when pointing at the comparison of interest (7). B, When selecting a specific cell subset (1), “Percentages” and mean fluorescence intensity (“MFI”) from the flow cytometry analysis are available (2), for the groups of interest (here “Heathy controls” vs “Severe” COVID‐19 patients) (3), and can be visualized (here “Volcano plots”) (4), with interactive statistics (5). C, Other graphical representations are available such as “Radar chart” displaying all investigated markers for the selected cell subset (left) as well as related statistics (right)

FIGURE 3

Overview of the immune cell subsets and corresponding immunophenotyping results. Radar charts display immunophenotyping profiles related to each immune cell subset for the following immune cell populations: (A) T cells, (B) unconventional T cells, (C) B cells, (D) granulocytes, (E) ILCs, (F) DC and monocytes. Here, three patient groups are compared (tool bar at the bottom left; percentages for all cells except for DC and monocytes where MFI are displayed)

FIGURE 4

Interactive exploration of results from analysis of soluble factors. By selecting “Soluble factor” from the head menu (1), results from proteomic analyses are available for exploration. Comparisons of interest can be selected (2), where results are displayed as volcano plots and the search for a specific protein can be performed (3), or selected directly from the plot (4). In both cases, the corresponding details on results and statistics are interactively displayed in the right panel (5)