Overlap of pro-inflammatory genes and signaling pathways between COVID-19 and MIS-C

In a recently published study medRxiv* Pre-print server, researchers in the United States characterized differential host immune responses in Acute Coronavirus Disease 2019 (COVID-19) and Pediatric Multisystem Inflammatory Syndrome (MIS-C) to guide future development of novel biomarkers for both inform diseases.

Study: Nucleic Acid Biomarkers of Immune Response and Cell and Tissue Damage in Children With COVID-19 and MIS-C. ​​​​​​​Image credit: NIAID


To date, COVID-19 and MIS-C, both caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have claimed more child lives than pediatric influenza mortality. These two diseases manifest highly inflammatory states and have distinct signatures of cell injury and cell death, with greater heterogeneity and multiple organ involvement observed in MIS-C.

In addition, these two diseases show different levels of expression for some genes including interferon-stimulated gene 15 (ISG15), sialoadhesin (SIGLEC1), and T cell receptor beta variable 11-2 (TRBV11-2). Previous studies have also shown a specific downregulation of T cell-mediated signaling pathways in MIS-C. In addition, MIS-C has clinical features that overlap with other inflammatory syndromes such as Kawasaki disease (KD), making its diagnosis difficult.

A better understanding of MIS-C pathogenesis is crucial to improve clinical diagnosis and inform targeted interventions when new variants of SARS-CoV-2 emerge. Previous analyzes of MIS-C and COVID-19 have relied on single-cell or bulk ribonucleic acid sequencing (RNA-Seq) of whole blood cells, which generally use proteomic and cytokine-based assays, have fewer markers, and lack standardized reference data.

Plasma cell-free RNA (cfRNA) and plasma cell-free DNA (cfDNA) signals are derived from cell death of circulating cells and peripheral tissues; whereas the cellular whole blood RNA (wbRNA) signal originates mainly from circulating leukocytes. In dying cells, cfDNA allows accurate quantification of cell numbers, while cfRNA allows characterization of gene expression and signaling pathways. Overall, wbRNA, cfRNA, and cfDNA-based approaches complement each other to provide a complete picture of the dynamic interplay between host and pathogen, or between cell activation, proliferation, and death.

About the study

In the present study, researchers collected blood and plasma samples from children at three children’s hospitals in the United States (US). They stratified all samples by diagnosis, time of collection, and disease severity. They used plasma samples for cfRNA and cfDNA profiling using next-generation sequencing (NGS).

Study Design and Patient Characteristics (A) Overview of sample collection and processing.  (B) Distribution of samples across analytes.  (C) Distribution of disease severity for each sample group.

Study Design and Patient Characteristics (A) Overview of sample collection and processing. (B) Distribution of samples across analytes. (C) Distribution of disease severity for each sample group.

Likewise, they performed RNA-seq on wbRNA and compared wbRNA and cfRNA profiles of 96 paired samples in MIS-C and COVID-19. Finally, they implemented BayesPrism and the transcriptome atlas of human Tabula Sapiens single cells as a reference to quantify the cell types of origin (CTO) of cfRNA. The study cohort included 211 children diagnosed with COVID-19 or MIS-C and 26 controls.

study results

Researchers identified signatures associated with cell injury and cell death that differentiated MIS-C and COVID-19 and the involvement of previously unreported cell types in MIS-C using plasma cfRNA profiles. Plasma cfDNA profiling revealed multiple organ involvement in MIS-C compared to COVID-19 and controls. On the other hand, wbRNA analysis revealed a significant overlap in pro-inflammatory signaling pathways between MIS-C and COVID-19. In addition, it demonstrated pro-inflammatory pathways specific to each disease state. Together, these results provided new insights into the differential pathogenesis of MIS-C and COVID-19 to support the development of the least invasive diagnostic tests for both acute COVID-19 and MIS-C.

The cfRNA data also revealed an enrichment of neuronal genes associated with synaptogenesis and cfRNA loading by Schwann cells, suggesting that the peripheral nervous system damage may occur in MIS-C. Future studies should elucidate the mechanisms of neurological involvement in acute MIS-C and its correlation with long-term neurodevelopment.

Furthermore, the observed increase in cfRNA from endothelial cells and pyroptosis cfRNA signatures could explain the overlapping clinical presentations between MIS-C and KD in acutely ill children. Researchers also observed an increase in cell death and a high level of heterogeneity in tissues of origin (TOO) of cfDNA in MIS-C compared to COVID-19 and controls, consistent with the systemic inflammation observed in MIS-C.


The current large, multi-hospital study of 416 blood samples from 237 patients reported a longitudinal analysis of COVID-19 and MIS-C by deep sequencing of three nucleic acids, cfRNA, wbRNA and cfDNA. Longitudinal sampling of these cell-associated and cell-free nucleic acids at acute, post-acute, 1-month, and 3 time points post-hospitalization provided a complete overview of immune responses and tissue damage associated with MIS-C and COVID-19.

In wbRNA profiling, researchers observed opposing dynamics of disintegrin and thrombospondin-motif metalloproteinase (ADAMTS2) in MIS-C and COVID-19. While elevated ADAMTS2 levels in MIS-C returned to baseline one month after hospitalization, the same did not occur in COVID-19 patients. Similarly, levels of the killer cell lectin-like receptor subfamily B member 1 (KLRB1) recovered in MIS-C one month after hospitalization but not in COVID-19. Despite the initial severity, most clinical MIS-C symptoms resolved within a few weeks, and biomarkers of inflammation and injury returned to normal. With cfRNA profiling, most biomarker measurements, such as B. CTO values, persist after one month, but returned to baseline after three months of hospitalization.

Overall, the study results demonstrated the utility of cfRNA and cfDNA as complementary nucleic acid biomarkers vis-a-vis conventional diagnostic methods based on wbRNA, cytokines and proteomics in the diagnosis of complex disease states such as MIS-C.

*Important NOTE

medRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore should not be relied upon as conclusive, guide clinical practice/health behavior, or be treated as established information.

Magazine reference:

  • Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C, Conor J Loy, Alicia Sotomayor-Gonzalez, Venice Servellita, Jenny Nguyen, Joan Lenz, Sanchita Bhattacharya, Meagen E Williams, Alexandre P Cheng, Andrew Bliss, Prachi Saldhi, Noah Brazer, Jessica Streithorst, William Suslovic, Charlotte Hsieh, Burak Bahar, Nathan Wood, Abiodun Foresythe, Amelia Gliwa, Kushmita Bhakta, Maria A. Perez, Laila Hussaini, Evan J Anderson, Ann Chahroudi , Meghan Delaney, Atul J Butte, Roberta DeBiasi, Christina A Rostad, Iwijn De Vlaminck, Charles Y Chiu, medRxiv pre-print 2022, DOI: https://doi.org/10.1101/2022.06.21.22276250, https://www.medrxiv.org/content/10.1101/2022.06.21.22276250v1

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