Study suggests that epigenetic memory in innate immune cells could be the key to explaining long COVID

By Dr. Liji Thomas, MDReviewed by Aimee MolineuxFeb 15 2022

A fascinating, new study may provide a partial explanation for the long-term immunologic phenomena associated with coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Introduction

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

During acute COVID-19, there are flu-like symptoms, along with respiratory features which may eventually progress to involve multiple other organs. With severe disease, prolonged fever, high levels of inflammatory signaling molecules, complement activation and tissue damage occur. This is mediated by delayed adaptive responses with high innate immune cell activity.

In survivors, symptoms are often reported to persist after the initial infection, but vary widely from person to person. These include post-acute sequelae of COVID-19 (PASC) as well as COVID-19-associated multisystem inflammatory syndrome in adults (MIS-A) and children (MIS-C). The underlying basis of these post-COVID-19 syndromes is unknown, but it could be due to persistent immune changes, that could also cause alterations in the individual’s response to other pathogens or vaccines.

One intriguing possibility is the induction of long-term epigenetic changes in the innate immune cells and their progenitors, which cause alterations of baseline and responsive innate immunity, both progenitor and mature cells. These changes maintain an immunologic memory of the encounter with an infectious or pro-inflammatory agent and are cumulatively termed trained innate immunity.

Epigenetic changes of this sort involve alterations in chromatin that cause adaptive changes in the type of cell response and the breadth of such responses. The cells that undergo such alterations may be long-lived innate immune cells, epithelial stem cells or hematopoietic progenitors, or the differentiated cells resulting from these precursors.

Mouse studies have shown that hematopoietic stem and progenitor cells (HSPC) are also involved in such durable epigenetic reprogramming. The result is that their progeny cells carry the memory of the inflammation-inducing agent and therefore show a different phenotype, also calledcentral trained immunity.

HSPCs are long-lived precursors of many immune cells, with self-renewing properties. This makes them unique in their capacity to harbor the epigenetic memory of inflammation and the reprogrammed DNA that leads to the expression of a different blood cell profile and different cell phenotypes in the mature innate immune cells. As a result, the researchers in this study sought to investigate whether this was happening with respect to HSPCs exposed to COVID-19-associated inflammation.

Findings

The current study, available on the bioRxiv* preprint server, covered the period from 2-12 months after the onset of a COVID-19 infection, either mild or severe. Single-cell studies of monocytes and their HSPC progenitors were carried out, using a novel process to enrich rare circulating HSPCs. Called Peripheral Blood Mononuclear Cell analysis with Progenitor Input Enrichment (PBMC-PIE), it provides superior access to HSPCs without requiring the painful and potentially complicated procedure of bone marrow aspiration.

In combination with PBMC-PIE, they used single-nuclei combined RNA-sequencing (RNA-seq) and assay for transposase-accessible chromatin (snRNA/ATAC-seq), to achieve high-resolution maps of the chromatin-accessible cells among many different HSPCs and PBMCs, and their transcriptomic profile.

Using PBMC-PIE, they isolated and annotated approximately 30,000 HSPCs, showing that the rare circulating HSPCs do reflect the variety of HSPCs found in bone marrow. The shift in the frequency and populations was most conspicuous for hematopoietic stem cells and multipotent progenitors (HSC/MPP). This appeared to be a broad activation response to inflammation, in order to renew the supply of white blood cells and respond effectively to the stimulus, and agreed with the active inflammatory response seen in early convalescence following severe COVID-19.

The neutrophil progenitors were also raised, in response to high plasma cytokines and acute-phase proteins, but this was seen even in late convalescence, perhaps because of the epigenetic reprogramming of the HSPCs. This was supported by the finding of differentially expressed genes (DEGs) in both mild and severe convalescent COVID-19 patients. They also found two major anti-inflammatory genes were downregulated in HSPCs and their progeny, which could potentially trigger hyperinflammatory responses.

Domains of Regulatory Chromatin (DORC) were also examined, and almost a thousand were identified. The most prominent of these included those linked to monocyte differentiation factor CEBPA, found in CD14+ monocytes than in HSC/MPP. The DORC study component revealed its ability to mirror the direction of differentiation of different lineages and the linked marker genes.

Further, they found that the ratio of chromatin binding by the two factors IRF/AP-1 result in either antiviral or pro-inflammatory responses after infection. The negative regulation of AP-1 and the persistence of IRF are apparently the drivers of the epigenetic memory response in this infection.

The results showed persistent epigenetic and transcriptional changes in HSPCs and monocytes after severe COVID-19. These changes result in an altered innate immune response, including inflammation and the differentiation of neutrophils and various monocyte phenotypes.

After a severe bout of COVID-19, the researchers found that monocytes demonstrated a reprogramming in both the HSPC progenitors and their monocyte progeny, lasting for months, with active antiviral programs driven by interferon regulatory factor/signal transducer and activator of transcription (IRF/STAT) pathways.

The changes in plasma cytokines, complement, and vascular response factors persisted for months, but eventually subsided by 4-12 months. This indicates a complete resolution of the active inflammation, while cellular composition and phenotypic changes continued to persist. This indicates the presence of epigenetic mechanisms.

Implications

The use of PBMC-PIE paired with combined snRNA/ATAC analysis allowed the HSPCs to be studied in detail along with the progeny cells. This covered chromatin alterations, gene expression, and differentiation trajectories. The combined results suggest that COVID-19, especially when severe, causes epigenetic changes in HSPCs that can last up to 12 months.

This technique also showed that bone marrow white cell production in severe COVID-19 underwent persistent alterations, favoring monocyte and neutrophil precursor HSPC production even at 4-12 months. While mild COVID-19 activates antiviral programs, severe COVID-19 induces inflammation, both persisting into convalescence but eventually resolving.

Within progenitor cells, inflammatory signaling leads to epigenetic memory that persists in self-renewing stem cells, and also is transmitted into differentiated progeny cell phenotypes. This could mean that central trained immunity is established after influenza and other viral infections.

The associated inflammatory response triggered by the activation of cytokines, chemokines, complement, and other vascular risk factors, along with tissue-migratory and persistently activated monocytes may explain PASC, especially the ongoing inflammatory changes and fibrosis of the lung and upper respiratory mucosa. In addition, altered and increased patterns of neutrophil production induced by epigenetic changes also favor inflammation.

Many other cell types also undergo epigenetic changes that may persist, manifesting in altered cell frequency, differentiation trajectories and phenotypes, while also retaining epigenetic antiviral inflammatory memory that affects future responses to infection or inflammatory agents.

This highlights the potential for acute viral infection to drive a durable program of HSPC origin that is conveyed through to progeny monocytes to mediate a heightened anti-viral response program, with potential implications for heterologous protection and resilience to seasonal infections.”

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.