In this study, we demonstrated that there were notable changes in the expression profiles of lncRNA and mRNA in PBMCs of mild and severe IAP patients.
At present, there is only little data available on lncRNAs related to influenza infection. This study was designed to increase our knowledge of this relation. The study revealed that there were 80 lncRNAs (40 upregulated and 40 downregulated) and 180 mRNAs (120 upregulated and 60 downregulated) differentially expressed in mild IAP patients compared with severe IAP patients.
Among those dysregulated lncRNAs, some of them have been reported in human diseases. For example, the lncRNA CA5BP1 have a protective role in the pathogenesis of acute myocardial infarction[12] and high levels of lncRNA SBDSP1 were associated with unfavorable prognosis of colorectal cancer [13]. However, none of these lncRNAs have been reported to be involved in influenza infection.
From the microarray profile, it was interesting to note that compared with the severe group, a significant proportion of differentially up-regulated mRNAs in mild IAP patients have been proved to play protective roles in influenza or other virus infections. For example, CD 83 has been proved to play a protective role against influenza A virus(IAV) infection by activating the innate and acquired antiviral immune response[14]. Interleukin-1 beta (IL-1β)[15] is a key component of the cytokine storm evoked by influenza infection [16] and could recruit CD4(+) T cells to the site of infection and improve survival during influenza virus infection [17]. Schlafen family member 5 (SLFN5) has been proved to play an antiviral role in herpes simplex virus 1(HSV-1) infection by binding viral DNA and suppressing viral transcription[18].
In the top ten down-regulated mRNAs, matrix metallopeptidase 8 (MMP8)[19] and S100 calcium binding protein A12 (S100A12)[20] have been proved to be biomarkers that correlate with disease severity and poor outcome in influenza and COVID-19 patients, respectively. The results of our study are consistent with the above-mentioned research, which also indirectly demonstrated that our research results are credible.
KEGG analysis identified only three significantly altered pathways between mild and severe IAP patients, including NF-κB signaling pathway, MAPK signaling pathway, and TNF signaling pathway. These pathways have been demonstrated to make great contributions to the pathogenesis of influenza infection[21]. For example, NF‐κB signaling pathway is a critical regulator that control the expression of various antiviral cytokines, such as interferon-α (IFN-α) and interferon-β (IFN-β) upon influenza virus infection [22, 23]. TNF-α expression plays essential role via regulating the CD8(+) T cell mediated immune response to influenza infection [24, 25]. MAPK family members could regulates the production of antiviral chemokines and cytokines such as TNF-α, monocyte chemotactic protein-1(MCP-1), interleukin (IL)-6 and IL -8[26, 27]. Except for the direct antiviral effect on influenza infection, both MAPK and TNF signaling pathways are involved in the process of the activation of NF-κB signaling pathway[28–30] .
As the function of the majority of lncRNAs remains unclear, the lncRNA-mRNA interaction network was used to predict the function of differentially expressed lncRNAs. A total of 16 lncRNAs and 64 mRNAs were identified as the hub genes. Five of the top 10 up-regulated lncRNAs were listed in the lncRNA-mRNA network, including XIST, NR_110028, NONHSAT137711, NR_037600, CA5BP1 and NONHSAT105043. Among those including mRNAs, DDX3X[31], IL4R[32], MAL[33], CDR2[34], and CAMK4[35] were previously reported in influenza infection. For example, the host protein DEAD box helicase 3 X-linked ,also known as DDX3X, has been proved to be an antiviral protein during influenza infection by coordinating the activation of the nucleotide-binding oligomerization domain-like receptor with a pyrin domain 3 (NLRP3) inflammasome, assembly of stress granules, and activation of type I interferon (IFN) signaling[31]. IL-4R is a key member of IL-4 signaling, which is essential for the B cell response during influenza infection. Miyauchi K and colleagues found that IL-4R-deficient B cells showed less proliferation and a marked reduction of dual-specific B cells in germinal center, which lead to the reduction of the protective antibodies [32].Although not reported in influenza infection, existing evidence showed that SLFN5[18] and RPS4Y1[36] was involved in the pathogenesis of HPV and RSV infection, respectively.
On the other hand, previous studies have demonstrated that PIK3R1[37], BIRC3[38] and PLCG1[39] are all important regulators of NF-κB signaling pathway, meanwhile BIRC3[40] and PIK3R1[41] are pivotal mediators in the regulation of TNF signaling pathway.
Taken together, we can speculate that hub lncRNAs such as NONHSAT105043 might contribute to the pathogenesis of influenza infection via interaction with hub mRNAs, such as DDX3X[31] and IL4R. It was subsequently indicated that those hub lncRNAs might play crucial roles in influenza infection via regulating NF-κB, TNF, and MAPK signaling pathway expression. Furthermore, several interactions between hub lncRNAs and mRNAs, including lncRNA NONHSAT105043-DDX3X, CA5BP1-DDX3X, and CA5BP1-IL-4R, deserve further investigation in the future studies.
Limitation
There are some limitations to the interpretation of this study. First, only a small number of patients were enrolled. Therefore, the differences we identified between mild and severe IAP patients need to be further validated by larger scale studies. Secondly, the quantitative RT-PCR Validation results were only partly consistent with the microarray data in the current study, which may be attributable to the limited patient’s number. Thirdly, the sex ratio in our study is imbalanced. Most of the rerolled patients were male, especially in the severe group.