Identification of Potential Key Long Non-Coding RNAs and Target Genes Associated with Pneumonia Using Long Non-Coding RNA Sequencing (lncRNA-Seq): A Preliminary Study

Abstract

BACKGROUND This study aimed to identify the potential key long non-coding RNAs (lncRNAs) and target genes associated with pneumonia using lncRNA sequencing (lncRNA-seq). MATERIAL AND METHODS A total of 9 peripheral blood samples from patients with mild pneumonia (n=3) and severe pneumonia (n=3), as well as volunteers without pneumonia (n=3), were received for lncRNA-seq. Based on the sequencing data, differentially expressed lncRNAs (DE-lncRNAs) were identified by the limma package. After the functional enrichment analysis, target genes of DE-lncRNAs were predicted, and the regulatory network was constructed. RESULTS In total, 99 DE-lncRNAs (14 upregulated and 85 downregulated ones) were identified in the mild pneumonia group and 85 (72 upregulated and 13 downregulated ones) in the severe pneumonia group, compared with the control group. Among these DE-lncRNAs, 9 lncRNAs were upregulated in both the mild and severe pneumonia groups. A set of 868 genes were predicted to be targeted by these 9 DE-lncRNAs. In the network, RP11-248E9.5 and RP11-456D7.1 targeted the majority of genes. RP11-248E9.5 regulated several genes together with CTD-2300H10.2, such as QRFP and EPS8. Both upregulated RP11-456D7.1 and RP11-96C23.9 regulated several genes, such as PDK2. RP11-456D7.1 also positively regulated CCL21. CONCLUSIONS These novel lncRNAs and their target genes may be closely associated with the progression of pneumonia.

Figure 1

The heat maps of the differentially expressed long non-coding RNAs (DE-lncRNAs). (A) The heat map of DE-lncRNAs between the mild pneumonia and control groups. (B) The heat map of DE-lncRNAs between the severe pneumonia and control groups. (C) The heat map of DE-lncRNAs between the mild and severe pneumonia groups. Each row represents a lncRNA, and each column represents a sample. Green indicates downregulated and red indicates upregulated. WLL1–3 represent the severe pneumonia samples; WLL4–6 represent the mild pneumonia samples; and WLL7–9 represent the control samples.

Figure 2

The regulatory network of the 9 long non-coding RNAs (lncRNAs) that are differentially expressed in both mild and severe pneumonia. Dark red nodes represent the lncRNAs, and purple nodes represent the target genes. Lines represent the regulatory relationships between lncRNAs and target genes.