Preprint A multimodal atlas of COVID-19 severity identifies hallmarks of dysregulated immunity, 2025, Slowikowski et al.

[SNT Gatchaman]

A multimodal atlas of COVID-19 severity identifies hallmarks of dysregulated immunity

Spoiler: Authors

Kamil Slowikowski; Pritha Sen; Christopher V Cosgriff; Jessica Tantivit; Tom Eisenhaure; Thomas J LaSalle; Kasidet Manakongtreecheep; Alice Tirard; Benjamin Y Arnold; Ana Pacheco-Navarro; Emily Yu-Ann Yang; Miguel Reyes; Anna Gonye; Irena Gushterova; Brian Russo; Maricarmen Rojas-Lopez; Nihaarika Sharma; Molly F Thomas; Tatyana Sharova; Dennie Frederick; Kendall Lavin-Parsons; Brendan Lilley; Brenna McKaig; Carl Lodenstein; Hargun Khanna; Kyle Kays; Nicole Charland; Neal Smith; Swetha Ramesh; Toni M Delorey; Devan Phillips; Liat Amir-Zilberstein; Eric M Brown; Maura Benson; Sung-Moo Park; Betsabeh K Tusi; Vladislav Pokatayev; Cody Hecht; Novalia Pishesha; Ann E Woolley; Lisa Cosimi; Orit Rozenblatt-Rosen; Lloyd Bod; Paul C Blainey; Aviv Regev; Jacques Deguine; Ramnik Xavier; Deborah Hung; Genevieve M Boland; Roby P Bhattacharyya; Paul J Utz; Marcia B Goldberg; Michael K Mansour; Michael R Filbin; Moshe Sade-Feldman; Nir Hacohen; Alexandra-Chloe Villani

The alpha-variant wave of the COVID-19 pandemic provided a unique opportunity to study, at single-cell resolution, how near-universal exposure to the same pathogen can lead to either effective or dysfunctional immune responses in humans. Although single-cell RNA-sequencing studies have characterized immune cellular features of COVID-19, they have not shown how tocilizumab treatment changes these features at single-cell resolution, or which features might persist into convalescence.

In this study, we analyzed 2.5 million circulating immune cells from 428 patients across time points (840 PBMC samples), encompassing three contemporaneous SARS-CoV-2 cohorts: acutely infected patients across five WHO disease severity levels and three time points, patients from the first randomized control trial to study the efficacy of tocilizumab in the management of COVID-19, and convalescent patients three months after infection. We used linear modeling to integrate multiple data types — including single-cell RNA-seq, CITE-seq, TCR and BCR sequencing, viral load measurements, viral neutralization assays, detection of 75 autoantibodies, HLA genotype data, and serum proteomics covering 1,463 targets — to derive the most comprehensive view to-date of the biological features of COVID-19 disease severity.

Our findings show that myeloid-derived suppressor cells (MDSCs) act as a key immunologic pivot point in severe COVID-19. Myeloid dysfunction, which is marked by impaired antigen presentation, drives a non-productive adaptive immune response, as reflected by reduced expression of B and T cell gene programs involved in antigen recognition, immune synapse formation, and cytotoxicity.

Severe disease is also linked to autoantibodies targeting type I interferons, influenced by specific HLA-DQB1 allelic variants, and strongly correlated with serum IL-6 levels. Tocilizumab treatment eliminates CLU-expressing MDSCs and ISG-positive myeloid subsets, restores antigen presentation, and reactivates productive adaptive immunity. These changes align with improved clinical outcomes and better clinical laboratory measures, including reduced CRP. While many immunologic abnormalities in acute severe COVID-19 resolve during convalescence 3-months post-infection, we observed persistently high ICOS expression in regulatory T cells, potentially linking acute infection to chronic post-COVID syndromes.

Overall, we define distinct innate and adaptive host immune responses associated with acute, IL-6-responsive, and convalescent SARS-CoV-2 infection. Our multimodal and high-dimensional dataset with curated clinical metadata provides a foundational and clinically relevant resource for modeling host immune response biology in health and disease.

Web | PDF | Preprint: MedRxiv | Open Access

 

[Hutan]

While many immunologic abnormalities in acute severe COVID-19 resolve during convalescence 3-months post-infection, we observed persistently high ICOS expression in regulatory T cells, potentially linking acute infection to chronic post-COVID syndromes.

ICOS? - see later in the post
The paper is mostly about severe disease. I don't think they identified any patients as having PASC, so discussion about PASC tend to be noting what they found in their severe and convalescent patients and comparing that with what studies of PASC have found.



Histones

When analyzed at the cell lineage level, only 18 genes were differentially expressed, 14 of which were in the MNP lineage (Figure 8 E), and most of the genes were related (Table S26). Several histone genes (HIST1H1D, HIST1H1C, HIST1H1E, HIST2H2AC) were elevated three months after infection in all four lineages (CD8 T cells, CD4 T cells, B cells, MNPs) (Figure 8 I, J, K). Some of these genes were also associated with severe disease in acute infection (Figure 8 L).

While certain histone genes were uniquely associated with acute infection or convalescence, HIST1H1C and HIST2H2AC were induced in both (Figure S21 A, B, C). Notably, HIST1H1C transcription was also elevated in the blood in a study of 48 patients with PASC (Post-Acute Sequelae of COVID-19)55, and the encoded H1C protein has been shown to inhibit influenza virus replication56. Our results show that specific histone genes are transcriptionally induced during acute infection, associated with disease severity, and remain elevated in circulating immune cells during convalescence.

In convalescent patients, we also observed a persistent elevation of HIST1H1C expression across all immune cell lineages, which was also found to be elevated in patients with PASC 55. Eukaryotic histones have ancient evolutionary history with viruses101, and the SARS-CoV-2 protein ORF8 mimics a histone H3 motif102, suggesting a possible mechanism for viral interference with host chromatin regulation. Furthermore, H1C has been shown to bind dendritic cells and induce cytokine storm103, as well as mediate immune evasion by down-regulating MHC-I expression104.

ICOS

In the Treg cells from convalescent donors (c-CD4-6), we found higher expression of ICOS (FC = 3, P = 2e-6, FDR = 0.02) (Figure 8 M, N), but we did not find this in the Tregs from acute donors (Figure 8 O). However, ICOS was associated with worse severity in all CD4 T cells from acute patients (FC = 1.75, P = 2e-6, FDR = 2e-4, Table S6). ICOS is known to regulate immune tolerance and autoimmunity, and it may play a role in both post-acute sequelae and the immune response during recurrent infection57

Patients who were sampled three months after clearing SARS-CoV-2 infection had relatively subtle cellular abundance changes compared to what was observed in acute infection. The major sepsis-associated transcriptional hallmarks (e.g., repressed HLA, TCR, and BCR genes) were not observed in convalescent patients, indicating that these are molecular signals specific to acute infection and severe illness. However, we found that convalescent patients have persistent elevated expression of histone genes (e.g., HIST1H1C) in all immune cell types and elevated expression of ICOS in CD4 Tregs.

We also found that Tregs from convalescent patients have persistently higher ICOS expression, a co-stimulatory molecule known to be elevated in autoimmune diseases57. Although we saw most acuity-associated immune alterations resolve three months into convalescence, some changes persist related to tolerance, autoimmunity, and response to viral rechallenge.

HLA-DQB1

In our data, aspartic acid (D) at position 57 in HLA-DQB1 was associated with greater disease severity and higher viral load following SARS-CoV-2 infection. In contrast, the absence of aspartic acid at position 57 was associated with lower abundance of CD8 T cells expressing severity-associated TCR genes. Moreover, the HLA-DQB1 locus has also been associated with PASC73 and with failure to seroconvert after COVID-19 vaccination74. Class II HLA proteins, such as HLA-DQB1, present antigens to CD4 T-helper cells, which in turn modulates cytotoxic CD8 T cell development via DC cross- priming75,76. In COVID-19, delayed generation of circulating CD4 T follicular helper cells (cTfh) has been associated with increased disease severity36. Therefore, our data suggest that COVID-19 severity is associated with antigen presentation by HLA-DQB1 to CD4 T helper cells, which influences development of anti-viral CD8 T cells and antibodies.

 

[Hutan]

The alpha-variant wave of the COVID-19 pandemic provided a unique opportunity to study, at single-cell resolution, how near-universal exposure to the same pathogen can lead to either effective or dysfunctional immune responses in humans.

Reading that prompted a rather off-topic thought that exposure to a pathogen can probably sometimes lead to severe Covid-19 and sometimes not, and sometimes lead to ME/CFS and sometimes not. There is no consistent response either to the pathogen nor with the person, nor even with the combination of pathogen + person. That is, any hypothesis for ME/CFS needs to explain why a person seemingly can have Covid-19 one time and not get ME/CFS, but can be exposed another time and get ME/CFS.

As far as I know, there hasn't been much study of people who got ME/CFS after their second or later Covid-19 infection. Perhaps looking for the factors that might tip someone towards ME/CFS in those people might be useful.