Deciphering the omicron variant: integrated omics analysis reveals critical biomarkers and pathophysiological pathways

In November 2021, amidst the ongoing global pandemic of the novel coronavirus (SARS-CoV-2), South African scientists identified a new variant of concern (VOC), Omicron, which was promptly classified as such by the World Health Organization (WHO) on November 26, 2021 [1]. Despite increasing vaccination rates, Omicron and its subvariants continue to spread rapidly worldwide [2]. Compared to the early wild-type virus, Omicron exhibits a higher transmissibility and immune evasion capability, posing a significant public health challenge [3]. Studies have shown that both Omicron and the Delta variant can evade host immune responses through single-point mutations on the spike protein [4], with Omicron having a stronger binding affinity to receptors, thus enhancing its potential for immune evasion [5]. Although Omicron may be less pathogenic, it still poses a lethal threat to immunocompromised individuals or patients undergoing immunosuppressive therapy. The pathogenesis of Omicron is increasingly evidenced to be closely associated with cytokine storms [6], systemic inflammatory responses [6], and platelet count abnormalities [7]. The mechanisms related to platelet counts remain inadequately explained in the context of SARS-CoV-2 infection.

Platelets (PLT), key cellular components in maintaining vascular integrity and initiating hemostasis, are produced by megakaryocytes in the bone marrow and circulate in the blood as cell fragments [8]. They play a crucial role in the development, progression, and ultimate outcome of many diseases, intimately associated with platelet-mediated hemostasis and thrombosis, which may trigger adverse inflammatory responses [9]. Platelets can release serotonin and participate in immune responses by promoting T-cell activation, thus modulating immune reactions [10]. Their inherent adhesiveness allows them to interact with a variety of cells from both the innate and adaptive immune systems [11]. Studies, including that by Sevilya et al., have shown a direct link between platelet activation and SARS-CoV-2 infection [12], and it has been suggested that the expression of the angiotensin-converting enzyme 2 (ACE2) receptor and the transmembrane serine protease transmembrane serine protease 2 (TMPRSS2) on platelets and megakaryocytes play a role in mediating viral infection [13, 14]. Moreover, the functional heterogeneity of platelet aggregation is thought to play a role in the pathogenesis of Omicron infection, contributing to the regulation of immune function within the hematological ecosystem [15].

While current research on COVID-19 pathogenesis and the coagulation/hemostasis pathways are ongoing, most studies still focus on the perspective of biomarkers [16, 17], and there are few studies on Omicron patients. This study aims to delve into the molecular interactions among key differential proteins of the Omicron variant, to identify potential targets for intervention, and to further analyze the metabolomic characteristics in the peripheral blood of Omicron patients. The urgency of this research stems from the necessity to understand the intricate interplay between the virus's pathogenesis and the host's immune response. Given the global impact of Omicron, elucidating these mechanisms is not only of scientific interest but is imperative for the development of targeted therapies and for informing public health strategies.

Amid the current global health crisis, the rapid transmission of the Omicron variant has had profound impacts on economies and public health systems worldwide. Omicron, with its enhanced ability to evade the immune system, has shown significant transmissibility compared to previous SARS-CoV-2 strains [21]. Although our understanding of the host response dynamics to this new variant is limited, identifying biomarkers that can predict disease progression or assist in diagnosis is vital to meet the challenges posed by Omicron. Our study integrates clinical diagnostics with multi-omics analyses to compare biomarkers between individuals infected with Omicron and healthy subjects, identifying eight differentially expressed hub proteins—THBS1, ACTN1, ACTC1, POTEF, ACTB, TPM4, VCL, and ICAM1.

Significant mutations in the spike protein of Omicron enhance its ability to evade immune responses [22], which may be associated with severe clinical outcomes such as cerebral embolism, deep vein thrombosis, and respiratory failure [23]. These findings resonate with studies positioning antithrombin as a broad-spectrum inhibitor of coronavirus infection, suggesting that the coagulation pathway may be a key element in the course of Omicron infection [24]. However, the specific relationship between Omicron and the coagulation pathway has not yet been elucidated. Therefore, the relationship between the coagulation pathway and Omicron warrants deeper investigation. This study's analysis of coagulation markers, including Activated Partial Thromboplastin Time (APTT), Fibrinogen (FIB), and D-Dimer, in patients infected with the Omicron variant reveals significant alterations when compared to healthy individuals. These changes underscore a pronounced association with hemostasis, coagulation, and blood clotting pathways, mirroring the conclusions drawn in earlier research [25]. Further substantiating these findings, our GO and KEGG pathway analyses on eight central hub proteins identified a pronounced enrichment in biological pathways directly tied to hemostasis, coagulation, and blood clotting. This enrichment not only corroborates the observed changes in coagulation markers but also suggests that Omicron infection might precipitate distinct alterations in the biological processes integral to these pathways.

The interplay between inflammation and coagulation is well recognized, with inflammation able to trigger coagulation mechanisms, and vice versa [26]. In the context of COVID-19, the activation of coagulation and hemostasis pathways is considered to be mediated by the inflammatory system's tissue factors [27]. Even though Omicron exhibits biological characteristics different from previous variants, severe infections may still induce platelet activation and partial desensitization, thereby affecting the coagulation pathway [28], and the coagulation pathway plays a significant role in regulating pulmonary fibrosis, hemostatic disorders, and surfactant damage [29]. VCL, a protein located at the cytoplasmic face of cellular matrix and intercellular adhesions, is involved in linking integrins to the F-actin cytoskeleton and can act as a mechanical sensor transmitting forces to maintain cellular shape, serving as a dynamic regulator of cell adhesion [30, 31]. The high expression of VCL can enhance cellular adhesiveness, and its regulatory role in adhesion is crucial for biological processes such as leukocyte transmigration through epithelial or endothelial layers, thereby mediating the migration of leukocytes in the inflammatory response of COVID-19 [32]. ACTB protein, also known as β-actin, plays a vital role in various cellular processes such as cell division, migration, invasion, vesicle transport, and cellular structural regulation[33]. ACTB can modulate endothelial nitric oxide synthase activity, altering NO production and thus causing endothelial dysfunction, activating coagulation pathways and inflammatory responses [34]. THBS1 is a matrix glycoprotein released by activated platelets, involved in angiogenesis, inflammatory responses, platelet aggregation, cell apoptosis, and fibrosis [35]. A decline in THBS1 expression is associated with oxidative stress damage [36], and THBS1 is involved in the fibrin clot response to injury [37]. Furthermore, silencing of THBS1 can inhibit the activation of the NLRP3 inflammasome, reducing the levels of inflammatory cytokines, thereby reducing pneumonia caused by cytokine storms [38]. POTEF, as a member of the POTE ankyrin domain family, can regulate TLR signaling which is critical in innate immunity and is expressed in immune cells playing a significant role during cell invasion [39], and it can inhibit apoptosis and promote cell growth [40]. However, the role of POTEF in pneumonia caused by Omicron is not clear, and our findings suggest that POTEF is involved in tissue coagulation processes, participating in disease inflammation and cell regulatory responses.

ACTN1 is a cytoskeletal actin-binding protein [41] that, in addition to mediating sarcomere function, performs important non-muscle functions, such as the regulation of cytokinesis, cell adhesion, and migration [42]. Our study found that high expression of ACTN1 is associated with cell adhesion and is a significant factor in the development and progression of Omicron. ACTC1 is a cardiac-related protein expressed in regenerating muscle fibers in diseased mature skeletal muscle [43], and our study shows that in the Omicron group, ACTC1 expression is elevated through the actin filament organization pathway. TPM4 is a key actin-binding protein [44], and studies have shown that TPM4 expression is strongly increased in the later stages of megakaryocyte formation and that TPM4 has a functional role in thrombus formation in mammals [45, 46]. This is consistent with our findings, which indicate that TPM4 can act as a promoter in pathways such as focal adhesion, mediating the occurrence, development, and outcome of the disease. Studies suggest that focal adhesion is associated with mechanisms of cell migration [47], which can regulate mechanotransduction, cell migration, cell cycle progression, proliferation differentiation, growth, and repair [48], and our study finds focal adhesion to be related to the pathological process of the disease. Additionally, ICAM-1 is a cell surface glycoprotein and adhesion receptor that, besides being expressed on vascular endothelial cells, also functions on epithelial and immune cells, affecting inflammatory stimulation [49]. Studies indicate that ICAM-1 is associated with leukocyte-endothelial cell interactions and solute permeability changes [50]. Our study suggests that ICAM-1 has a significant association with the inflammatory exudation and endothelial barrier establishment caused by Omicron.

In addition, the tryptophan pathway can be affected by systemic inflammatory signaling factors, promoting immune suppression and evasion of immune surveillance in inflammation [51], thereby helping to suppress inflammation caused by Omicron. L-tryptophan is an essential amino acid that produces a variety of signal molecules through complex metabolic pathways [52, 53]. Studies also suggest that the L-tryptophan pathway can achieve immune suppression by depleting tryptophan, depriving proliferating T cells of essential amino acids [52, 53]. Indole-3-acetate (I3A), a metabolite depleted in the context of the microbiome and high-fat diets, has been proven to reduce the production of pro-inflammatory cytokines and inhibit cell migration towards chemokines, achieving the effect of alleviating inflammation [54]. These is consistent with our findings.

This study highlights the therapeutic potential of targeting eight differentially expressed proteins in treating Omicron infection, with Domperidone and Cytochalasin D being particularly noteworthy. Domperidone's antiviral properties, as demonstrated by stimulating prolactin secretion, suggest a dual role in enhancing both innate and adaptive immune responses [55], aligning with our findings and highlighting the necessity for further research on its clinical application parameters. Similarly, Cytochalasin D's inhibition of actin polymerization and its capacity to reverse PLT-induced suppression of cell apoptosis present a novel therapeutic pathway worth exploring [56].

The study acknowledges several limitations, such as the complexity of interpreting metabolomic data, which necessitates advanced bioinformatics and further biological validation. While eight potential biomarkers were identified, their clinical significance requires validation in a more diverse population. The absence of direct mechanistic evidence, focusing instead on associations, calls for further research to clarify how these changes affect disease progression. Despite these challenges, the study offers a comprehensive view of Omicron's pathophysiology, contributing valuable insights into coagulation and inflammation and underscoring the need for continued research to develop targeted clinical and public health strategies.

In conclusion, our study highlights the significant impact of the Omicron variant on clinical and molecular levels. The identified hub proteins, enriched in coagulation and inflammatory pathways, underscore the intricate interplay between the inflammatory response and coagulation system in the context of Omicron infection. The biomarkers discovered offer a valuable resource for potential diagnostic and prognostic applications. While Omicron's unique biological characteristics necessitate further investigation, our findings contribute to the understanding of the pathophysiological mechanisms behind its clinical manifestations. However, the limitations of our study, include a call for further research with larger cohorts to validate these biomarkers and unravel the mechanisms of Omicron-induced pathology. Our work lays the groundwork for future studies aimed at developing targeted interventions to mitigate the effects of this challenging variant.