It has been reported that SARS-CoV-2 infection associated ARDS is linked with the development of pulmonary fibrotic changes after recovery [22], manifesting as respiratory failure and leading to a poor prognosis and an enormous burden to public health [6]. However, the molecular mechanism and effective therapies is still ill-defined. This study was to explore the key molecular elements and probable biomarkers and to identify potential targeted drugs for pulmonary fibrosis post-COVID-19 associated ARDS.
We analyzed three datasets from GEO database and identified 116 common DEGs. These DEGs reflect the expression characteristics in pulmonary fibrosis following COVID-19 associated ARDS compared with healthy subjects. The functional analysis reveals that the common DEGs are predominantly associated with response to components of pathogens, inflammatory response, apoptosis, MAPK signaling pathway, transcription regulation, DNA binding and protein binding. In most patients, severe infection has likely led to ARDS, a major cause of early-stage edema and later-stage fibrosis in the lungs, thereby worsening the lung condition. The secondary lung injury and cytokine storm are linked to a significant increase in immune and inflammatory responses, leading to the activation and uncontrolled release of various mediators, especially TGF-β [23]. Meanwhile, SARS-CoV-2 induces apoptosis in alveolar cells, pneumocytes, bronchial cells, and T-lymphocytes, subsequently resulting in neutrophils death. Macrophages then migrate into the lungs to clear the debris by engulfing and digesting the dead cells, releasing increased amounts of TGF-β [8]. This is consistent with our observation that the functional enrichment of apoptosis and inflammatory response is evidenced in pulmonary fibrosis following COVID-19 associated ARDS. Research has shown that a variety of transcription factors are regulated by MAPK signaling, leading to the upregulation of pro-apoptotic proteins and the downregulation of anti-apoptotic proteins [24]. Therefore, we suppose that once the lung is infected with SARS-CoV-2 and progresses to ARDS, the MAPK cascade is activated, subsequently triggering downstream transcription factors. These transcription factors regulate gene expression, initiating a series of cellular responses, including apoptosis and immunoreaction, which gradually progress to pulmonary fibrosis. Our finding provides important evidence supporting the fibrogenesis mechanism and suggests that antifibrotic therapy for COVID-19 patients could be achieved by mediating MAPK and apoptosis.
Based on PPI network construction and hub genes identification, we explored potential biomarkers, mechanisms and drug targets for pulmonary fibrosis post-COVID-19 ARDS patients. Developing new drugs rapidly for emerging diseases is often unrealistic, so repurposing existing drugs can be highly beneficial. Drug repurposing seeks new indications for known drugs, thus narrowing down candidates, avoiding safety issues, and shortening development time [25]. In view of this, we predicted candidate drugs targeting hub genes to explore promising treatments for this deadly complication of pulmonary fibrosis following COVID-19 associated ARDS.
Our study found that FCER1A has the strongest interactions with other genes and is likely the most critical gene in pulmonary fibrosis following COVID-19 associated ARDS. FCER1A encodes the α-subunit of immunoglobulin E (IgE) receptor FcεRI, is known to participate in immune reactions and mediate the release of inflammatory mediators such as histamine, and is important in allergic disease especially asthma [26]. Chen et al. [27] found that the IgE concentration in serum was significantly elevated in patients of pneumoconiosis and mice exposed to silica, and FcεRI deficiency provide substantial protection against pulmonary inflammation and fibrosis induced by silica in a mouse model. Kim et al. [28] found that inhibition of sirtuin2 reduces mast cell-mediated allergic airway inflammation and fibrosis via blocking FcεRI/TGF-β signaling pathway. However, the role of FCER1A in pulmonary fibrosis following infection remains unclear. In our study, FCER1A was commonly downregulated in three datasets, thus we suppose that FcεRI might play a detrimental role in case of pulmonary fibrosis post-COVID-19 ARDS. Three FDA-approved drugs associated with FCER1A were identified: omalizumab, mizolastine and desloratadine. Binding to IgE, omalizumab is approved for treating allergic asthma in individuals sensitive to perennial allergens with elevated IgE levels [29]. Cao et al. [30] found that blocking IgE-FcεR1 signaling in mice by administrating the omalizumab suppressed cardiac hypertrophy and cardiac interstitial fibrosis significantly. Meanwhile, as antihistamine for allergic rhinitis and chronic urticaria, mizolastine and desloratadine block histamine H1 receptors of FcεR1-activated mast cells and basophils to alleviate symptoms [31]. Our study suggests that omalizumab, mizolastine, and desloratadine, interfering with IgE-FcεR1 signaling, may offer potential therapeutic benefits for managing pulmonary fibrosis post-COVID-19 ARDS patients.
GATA2 is a member of the family of zinc finger transcription factors known to regulate alveolar macrophage phagocytosis and erythropoiesis [32]. It has been reported that GATA2 deficiency is associated with pulmonary fibrosis related to pulmonary alveolar proteinosis [33, 34]. However, the effect of GATA2 expression on pulmonary fibrosis post-COVID-19 is unclear. Herein, our study revealed that the expression of GATA2 was commonly inhibited, pointing out the potential role of GATA2 in pulmonary fibrosis post-COVID-19 associated ARDS. In addition, we identified epoetin alfa associated with GATA2 as a potential remedy. Epoetin alfa stimulates erythropoiesis by activating EPO receptor and downstream pathways, while GATA2 regulates the gene expression of EPO receptor, making it more sensitive to epoetin alfa [35]. However, the effect of epoetin alfa to GATA and pulmonary fibrosis post-COVID-19 ARDS is unclear, waiting for further experimental exploration.
CLC, referring to Charcot-Leyden crystal galectin or galectin-10 (Gal-10), belongs to the galectin superfamily that share highly conserved amino acid sequences constituting the carbohydrate recognition domain. CLC is considered as a hallmark of eosinophil involvement in allergic reactions and associated immune responses [36]. Meanwhile, evidences suggest that other member, like Gal-3, of the galectin superfamily could play a crucial role in COVID-19 [37] and pulmonary fibrosis [38]. However, the effect of CLC in pulmonary fibrosis post-COVID-19 has not been explored. Our study found that CLC is downregulated commonly in three datasets, indicating it the promising diagnostic biomarker and probable role in pulmonary fibrosis following COVID-19 associated ARDS. TD139, an inhaled small-molecule inhibitor of Gal-3, was found to be safe, well tolerated, and effective in engaging its target and reducing plasma biomarkers linked to IPF progression [38]. Herein, we identified moxidectin, which is a CLC-targeted anti-parasitic agent approved for the prevention of Onchocerca volvulus caused river blindness [39], as a potential drug for pulmonary fibrosis following COVID-19 associated ARDS. The effectiveness of moxidectin needs to be further confirmed.
In addition, our study explores the transcriptional and post-transcriptional regulators of hub genes by revealing the relationships between TFs and hub genes as well as miRNAs and hub genes. Among the identified TFs, FOXL1, CREB1, YY1, GATA3, and E2F1 were reported to participate in the regulation of pulmonary fibrosis [40–44], and FOXC1 was reported to promote FGFR1 isoform switching following induction of TGF-β-mediated epithelial-to-mesenchymal transition, which is considered to contribute to pathogenesis of fibrosis [45]. Besides, CREB1 regulates SARS-CoV-2 proliferation by viral helicase nsp13 association [46], and the overexpression of GATA3 was associated with the severity and fatal outcome of COVID-19 [47]. Moreover, CREB1 participates in the regulation of acute lung injury [48]. Bioinformatics analyses suggests that hsa-miR-26b-5p [49] and hsa-miR-524-5p [50] may develop as diagnostic biomarkers and potential therapeutic targets for IPF, while hsa-miR-27a-3p [51] could be a potential regulator for patients with combined pulmonary fibrosis and emphysema. Also, downregulation of miR-1290 may be helpful in the treatment of pulmonary fibrosis and viral infections such as influenza A [52]. Our study suggests that these TFs and miRNAs might play a role in pulmonary fibrosis following COVID-19 associated ARDS, but further investigation is needed to confirm this.
Finally, we conducted a gene-disease analysis to predict the relationships between hub genes and other diseases. These findings may inspire the development of potential therapies of pulmonary fibrosis post-COVID-19 ARDS, based on insights from the onset, progression and management of these diseases. Disorders or diseases, including deficiency of combined immune cells like B and natural killer lymphoid, acute myeloid leukemia, myelodysplastic syndrome, and Emberger syndrome (primary lymphedema with myelodysplasia), have been reported to result from germline mutations in GATA2 gene and to represent various manifestations of a same condition, subsequently termed GATA2 deficiency [53, 54]. Meanwhile, GATA2 deficiency is associated with pulmonary fibrosis related to pulmonary alveolar proteinosis [33, 34] and probably pulmonary fibrosis post-COVID-19 ARDS as mentioned above. It suggests that these diseases might share the same pathogenesis, and their treatment could provide insights for the treatment of pulmonary fibrosis following COVID-19 associated ARDS. On the other hand, mutations in the telomerase lead to dyskeratosis congenita, a bone marrow failure syndrome marked by mucocutaneous abnormalities, pulmonary fibrosis, and increased susceptibility to acute myeloid leukemia and myelodysplastic syndrome [55], indicating the future directions of treatment of pulmonary fibrosis post-COVID-19 ARDS. Omenn syndrome manifests as severe combined immune deficiency characterized by enlarged lymphoid tissue, elevated IgE levels, and eosinophilia, presenting as a distinct inflammatory process. The inflammation in these patients is initiated by clonally expanded T cells, which secrete a host of cytokines that drive autoimmune as well as allergic inflammation due to inadequate regulation by other components of the immune system [56]. The gene-disease interaction in our study suggests similar molecular mechanisms in the progression of these diseases, which could inform the development of new therapeutic strategies for pulmonary fibrosis post-COVID-19 ARDS.