Disrupted regulatory networks, epigenetic profiling, and inborn genetic predisposition of COVID19 associated multisystem inflammatory syndrome in children

Coronavirus disease COVID-19 is caused by infection with SARS-CoV-2. Although children typically present with mild symptoms or are asymptomatic, a subset of children can develop a postinfectious SARS-CoV-2-related multisystem inflammatory syndrome in children (MIS-C). MIS-C is a life-threatening, hyperinflammatory syndrome that resembles Kawasaki disease (KD) and toxic shock syndrome in younger children, and cytokine storm syndrome or macrophage activation syndrome in older children. MIS-C usually occurs 2-6 weeks after the initial SARS-CoV-2 infection, and its diagnosis requires the exclusion of a wide range of other disorders. Due to its rarity, limited data are available on the course of the disease, dynamics of clinical and laboratory parameters, and very limited information on prognosis and outcome. Moreover, the pathophysiology of MIS-C is not fully understood. This is the first study aiming to comprehensively enlighten the transcriptomic and epigenetic signature at the time of MIS-C onset. We will investigate the paired gene expression and chromatin accessibility profiles at the time of MIS-C onset as well as a genome wide methylation signature. The purpose of this project is to improve the understanding of underlying regulatory networks that are disrupted during MIS-C onset and epigenetic changes to support clinical impressions for particular dynamics of clinical and laboratory features and purpose possible directions which could guide the prescription of more targeted treatment. Secondly, we aim to identify inborn genetic variants associated with MIS-C susceptibility, and correspondingly propose better ways to establish an early diagnosis, and potentially prevent this condition. We hypothesize that regulatory networks and epigenetic patterns that are involved in innate as well as adaptive immune systems are disrupted during MIS-C onset and secondly, inborn genetic variations of regions coding or regulating for those disrupted regulatory networks are associated with MIS-C susceptibility. For this project blood samples from 88 MIS-C patients diagnosed at the University Children’s Hospital, University Medical Center Ljubljana are already collected during the MIS-C onset, before treatment, and at 6 months in remission. To comprehensively investigate the molecular mechanisms underlying MIS-C pathogenesis and to identify potential biomarkers and therapeutic targets, we propose a six-part multi-omic research project: WP 1: Clinical characteristics and biobanking; WP2: We will utilize Single Cell Multiome ATAC + Gene Expression sequencing to detect specific blood cell types and regulatory networks that are disrupted in MIS-C onset. We will also evaluate the scRNA-seq signature with bulk RNA-seq of selected cell types on an independent patient cohort to ensure the robustness of our findings. WP3: We will employ advanced bioinformatic analysis on data generated in WP2 to evaluate the differential expression of non-coding elements and determine if they play a role in MIS-C pathogenesis; WP4: We will use the resulting transcriptomic sequences from WP2 to detect possible disease-causing variants associated with MIS-C susceptibility; WP5: With Oxford Nanopore Technology long-read sequencing technology we will determine whole genome differentially methylated regions; WP6: Integration of all data into advanced machine learning models in order to guide the construction of proposed guidelines for the prescription of more targeted treatment. The project will result in transcriptomic, epigenomic and genetic signatures associated with MIS-C flare that could be further evaluated in larger multicentre international studies. Moreover, a better understanding of the disrupted regulatory networks that are driving inflammation in MIS-C, could lead to new insights into diseases with similar clinical presentations as KD. The data generated by this project have the potential to contribute to numerous impactful publications on the pathophysiology of MIS-C.