Chromatin accessibility is an early marker of severe COVID-19 disease (2023)

Coronavirus disease 2019 (COVID-19) can produce a variety of clinical manifestations, ranging from asymptomatic illness to fatal outcome. Therefore, there is great interest in the development of biomarkers that can distinguish severe from mild progression of the disease.

Scientific Reports magazine plans to publish a new studyresearch station*A preprint server explores the potential use of chromatin remodeling to predict the clinical course of COVID-19 severity.

Study:Differences in chromatin accessibility in peripheral blood mononuclear cells underlie the severity of COVID-19 disease prior to seroconversion.Credit: Rost9/Shutterstock.com

This news article is a commentary on the preliminary scientific report, which had not been peer-reviewed at the time of publication. Since its initial publication, the scientific report has been peer-reviewed and accepted for publication in a scientific journal. The Sources section at the end of this article provides links to the preliminary and peer-reviewed reports.show source code

introduce

Evidence is accumulating that an exaggerated inflammatory immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays an important role in the clinical severity of COVID-19. To this end, the level of chromatin accessibility and gene expression in peripheral blood mononuclear cells (PBMCs), which comprise multiple immune cell subtypes, are markers of responses to SARS-CoV-2 at the molecular level.

Mild disease appears to be associated with deficient expression of type I and type III interferons (IFNs), whereas severe disease is often characterized by higher levels of pro-inflammatory factors such as interleukin-6 (IL-6) and factor alpha tumor necrosis (TNF). ).-α). α) and more monocytes and associated chemokines and cytokines in peripheral blood.

To study this, regulatory chromatin presents transcription factor motifs that become more accessible as the inflammatory response begins. Thus, these motifs can serve as reliable biomarkers of these changes.

To analyze epigenetic changes over time, features of the mature immune response can be used to refer to when the host was in the host's immune response. For example, the appearance of anti-SARS-CoV-2 antibodies marked the development of adaptive immunity, a departure from the innate immune response.

This switch to adaptive immunity usually occurs within two weeks of symptom onset and is accompanied by clinical improvement, unless the patient shows signs of disease progression. The current study investigates the possibility that transcription factor motifs may be biomarkers of early changes indicative of positive or potentially harmful immune responses in COVID-19.

research result

In the current study, the investigators used single-cell, massive assays, including assay for transposase-accessible chromatin (ATAC-seq) sequencing and ribonucleic acid sequencing (RNA-seq) of chromatin-accessible regions. These tests were performed on patient samples before and after seroconversion to assess changes within PBMCs over time.

The study cohort was selected from the Molecular Epidemiology of Suspected Infections Study (MESSI), a community-based prospective research cohort. Divided into four groups, including pre-pandemic healthy controls, close contacts of SARS-CoV-2-infected patients who tested negative for viral and serological tests, outpatients with mild SARS-CoV-2 infection who nevertheless tested positive, as well as moderately and severely ill patients. He tested positive for COVID-19.

Interestingly, across all reported symptoms, symptom severity was highly similar in close contacts who remained seronegative for two months or more after exposure. However, the situation in mild cases/close contacts is significantly different than in moderate cases. In fact, people with moderate illness more frequently reported loss of smell and taste, headaches, malaise, and fatigue, compared with reports of mild cough and runny nose from COVID-19 in close contacts.

CD14+ monocytes undergo extensive chromatin remodeling with severity-specific epigenetic biomarkers prior to seroconversion.(A)scRNA-seq UMAP of all CD14+ monocytes collected from individuals with mild and moderate IgG-. UMAP stained according to disease severity (left) and number of clusters (right).(of the)A heatmap representation of regulatory activity was calculated for each pool of scRNA-seq using SCENIC. The activity of the top 10 regulators (right) is plotted for each group of cells for UMAP (bottom). Black boxes indicate interest groups.(C)scATAC-seq UMAP of all CD14+ monocytes collected from subjects with mild and moderate IgG. UMAP stained according to disease severity (left) and number of clusters (right).(Four)Heatmap of transcription factor motif enrichment (right) for identified regulators plotted for each scATAC-seq pool (bottom).(cinco)Correlogram of clusters linked by regulatory activity between scRNA-seq (columns) and scATAC-seq (rows). Black boxes indicate interest groups.(F)Functional accumulation analysis of downregulated (KLF6, FOS, POU2F2, HMGB1) or upregulated (mild: IRF7, IRF1, STAT1; moderate: CEBPB, KLF3) regulators in scRNA-seq groups 2, 4 and 7 (panel E ).

Transcription pattern in PBMC

Transcript profiles in PBMCs differed in terms of gene expression levels between cases and healthy controls, but not between cases with mild or moderate symptoms. Thirty genes were differentially expressed in seronegative cases with mild or moderate symptoms, while 43 genes were differentially expressed in seropositive cases with mild or moderate symptoms.

The IL-8 precursor CXCL8 was expressed at higher levels in the control group. When the scientists examined 455 differential access regions (DARs) in mild and moderate cases that had not yet developed antibodies, they found 73 regions that showed differential accessibility depending on disease severity and epigenetic responses.

Further analysis revealed that mild seronegative cases had higher levels of transcription factors and signaling pathways associated with viral infections compared to moderate seronegative cases. Both mild and moderate cases showed epigenetic changes that triggered chromatin remodeling without the expected transcriptional activity occurring. That is, the transcription factor motifs are readily accessible even when gene expression remains low.

Several genes have been found to be upregulated, most of which regulate inflammation. All types of PBMC showed increased accessibility to chromatin regulatory domains (DORCs), suggesting that they are preparing for activation. Most of the cells with the highest accumulation of PBMC during the seronegative phase were CD14+ monocytes.

CD14+ monocytes undergo chromatin remodeling by DORC, which is regulated by superenhancers. The regions involved in CD14+ monocytes from mildly symptomatic patients were compared to the regulatory region of CCAAT enhancer binding protein with respect to IFN regulator 7 (IRF7), IRF1, and signal transducer and activator of transcription 1 (STAT1, transcription factor beta (CEBPB) and, in moderate cases, the regulatory region of Kruppel-like factor 3 (KLF3) is enriched.

In the seropositive cases, another 375 regions showed differential accessibility to chromatin. Of these, the mild cases had more accessible chromatin and therefore showed dysregulation of myeloid development.

Functional enrichment analysis revealed that most of the differentially expressed transcription factors are related to the adaptive immune response, specifically the transition from innate to adaptive immunity. The analysis shows that B andT cellsThe receptors are activated.

Influence

The current results suggest that certain subpopulations of PBMC undergo massive chromatin remodeling early in SARS-CoV-2 infection, corresponding to mild and moderate symptoms before antibody formation. Even before actual transcription occurs, transcription factor activity levels and chromatin accessibility at this early stage can differentiate cases based on disease severity. This occurs mainly in CD14+ monocytes.

The results shed light on previous research on chromatin accessibility in critically ill and convalescent COVID-19 cases. The increased accessibility of the KLF and CREB transcription factor motifs in mild to moderate cases suggests a role for epigenetic activation in monocyte maturation. This has already been shown to occur early in SARS-CoV-2 infection, and this study shows that its level of activation varies depending on the severity of the disease.

Mild disease is associated with rapid viral control characterized by activation of antiviral signaling pathways such as those mediated by IRF1 and IRF7. In contrast, in the most severe disease, a dysregulated immune response begins with ineffective viral control and reduced antiviral responses, both consistent with moderate disease.

Although CD14+ monocytes have been more actively involved in chromatin remodeling and early epigenetic regulation over time, these motifs have been found to be no more accessible after seroconversion during seronegative periods. At this point, the antibody-producing cells were more active, suggesting adaptive immunity in recovering COVID-19 patients.

„These changes precede in time the transcriptional expression of signaling pathways associated with adaptive immunity...and suggest that detection of key components of chromatin remodeling early in the disease could hold promise for a new COVID-19 diagnostic tools class.".

This news article is a commentary on the preliminary scientific report, which had not been peer-reviewed at the time of publication. Since its initial publication, the scientific report has been peer-reviewed and accepted for publication in a scientific journal. The Sources section at the end of this article provides links to the preliminary and peer-reviewed reports.show source code