Screening and Verification of Differentially Expressed Long Non-coding RNAs in the Peripheral Blood of Patients With asthma

Bioinformatics analysis of ceRNA network of autophagy-related genes in pediatric asthma

The molecular underpinnings of pediatric asthma present avenues for targeted therapies. A deeper exploration into the significance of differentially expressed autophagy-related genes (DE-ARGs) and their interactions with the long noncoding RNA (lncRNA)-microRNA (miRNA)-mRNA network may offer insights into the pathogenesis of pediatric asthma. DE-ARGs were retrieved from the Gene Expression Omnibus and the Human Autophagy Database. These DE-ARGs were subjected to comprehensive analyses, including Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, Gene Set Enrichment Analysis, and protein-protein interaction networks. The identified DE-ARGs were further verified for core gene expression. The miRDB and ENCORI databases were used for inverse miRNA predictions. Furthermore, miRNA-lncRNA interactions were predicted using LncBase and ENCORI platforms. Following the exclusion of lncRNAs exclusively localized in the nucleus and extracellular space, a competitive endogenous RNA (ceRNA) network was established and subsequently subjected to detailed analysis. The mRNA expression patterns in the ceRNA network were validated using quantitative real-time PCR. In total, 31 DE-ARGs were obtained, of which 29 were up-regulated and 2 were down-regulated. Notably, the autophagy, regulation of apoptotic signaling pathways, interferon-α/β signaling, interferon γ signaling, autophagy-animal, and apoptosis pathways were predominantly enriched in pediatric asthma. Five hub genes (VEGFA, CFLAR, RELA, FAS, and ATF6) were further analyzed using the Gene Expression Omnibus dataset to verify their expression patterns and diagnostic efficacy. Four hub genes (VEGFA, CFLAR, RELA, and FAS) were obtained. Finally, a ceRNA network of 4 mRNAs (VEGFA, CFLAR, RELA, and FAS), 3 miRNAs (hsa-miR-320b, hsa-miR-22-3p, and hsa-miR-625-5p), and 35 lncRNAs was constructed by integrating data from literature review and analyzing the predicted miRNAs and lncRNAs. Moreover, the quantitative real-time PCR data revealed a pronounced upregulation of Fas cell surface death receptor. The identification of 4 DE-ARGs, especially Fas cell surface death receptor, has shed light on their potential pivotal role in the pathogenesis of pediatric asthma. The established ceRNA network provides novel insights into the autophagy mechanism in asthma and suggests promising avenues for the development of potential therapeutic strategies.

Bioinformatic analysis and preliminary validation of potential therapeutic targets for COVID-19 infection in asthma patients

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 causes coronavirus disease 19 (COVID-19). The number of confirmed cases of COVID-19 is also rapidly increasing worldwide, posing a significant challenge to human safety. Asthma is a risk factor for COVID-19, but the underlying molecular mechanisms of the asthma-COVID-19 interaction remain unclear.

METHODS

We used transcriptome analysis to discover molecular biomarkers common to asthma and COVID-19. Gene Expression Omnibus database RNA-seq datasets (GSE195599 and GSE196822) were used to identify differentially expressed genes (DEGs) in asthma and COVID-19 patients. After intersecting the differentially expressed mRNAs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to identify the common pathogenic molecular mechanism. Bioinformatic methods were used to construct protein-protein interaction (PPI) networks and identify key genes from the networks. An online database was used to predict interactions between transcription factors and key genes. The differentially expressed long noncoding RNAs (lncRNAs) in the GSE195599 and GSE196822 datasets were intersected to construct a competing endogenous RNA (ceRNA) regulatory network. Interaction networks were constructed for key genes with RNA-binding proteins (RBPs) and oxidative stress-related proteins. The diagnostic efficacy of key genes in COVID-19 was verified with the GSE171110 dataset. The differential expression of key genes in asthma was verified with the GSE69683 dataset. An asthma cell model was established with interleukins (IL-4, IL-13 and IL-17A) and transfected with siRNA-CXCR1. The role of CXCR1 in asthma development was preliminarily confirmed.

RESULTS

By intersecting the differentially expressed genes for COVID-19 and asthma, 393 common DEGs were obtained. GO and KEGG enrichment analyses of the DEGs showed that they mainly affected inflammation-, cytokine- and immune-related functions and inflammation-related signaling pathways. By analyzing the PPI network, we obtained 10 key genes: TLR4, TLR2, MMP9, EGF, HCK, FCGR2A, SELP, NFKBIA, CXCR1, and SELL. By intersecting the differentially expressed lncRNAs for COVID-19 and asthma, 13 common differentially expressed lncRNAs were obtained. LncRNAs that regulated microRNAs (miRNAs) were mainly concentrated in intercellular signal transduction, apoptosis, immunity and other related functional pathways. The ceRNA network suggested that there were a variety of regulatory miRNAs and lncRNAs upstream of the key genes. The key genes could also bind a variety of RBPs and oxidative stress-related genes. The key genes also had good diagnostic value in the verification set. In the validation set, the expression of key genes was statistically significant in both the COVID-19 group and the asthma group compared with the healthy control group. CXCR1 expression was upregulated in asthma cell models, and interference with CXCR1 expression significantly reduced cell viability.

CONCLUSIONS

Key genes may become diagnostic and predictive biomarkers of outcomes in COVID-19 and asthma. Video Abstract.

Functional transcriptome analyses of Drosophila suzukii midgut reveal mating-dependent reproductive plasticity in females

BACKGROUND

Insect females undergo a huge transition in energy homeostasis after mating to compensate for nutrient investment during reproduction. To manage with this shift in metabolism, mated females experience extensive morphological, behavioral and physiological changes, including increased food intake and altered digestive processes. However, the mechanisms by which the digestive system responds to mating in females remain barely characterized. Here we performed transcriptomic analysis of the main digestive organ, the midgut, to investigate how gene expression varies with female mating status in Drosophila suzukii, a destructive and invasive soft fruit pest.

RESULTS

We sequenced 15,275 unique genes with an average length of 1,467 bp. In total, 652 differentially expressed genes (DEGs) were detected between virgin and mated D. suzukii female midgut libraries. The DEGs were functionally annotated utilizing the GO and KEGG pathway annotation methods. Our results showed that the major GO terms associated with the DEGs from the virgin versus mated female midgut were largely appointed to the metabolic process, response to stimulus and immune system process. We obtained a mass of protein and lipid metabolism genes which were up-regulated and carbohydrate metabolism and immune-related genes which were down-regulated at different time points after mating in female midgut by qRT-PCR. These changes in metabolism and immunity may help supply the female with the nutrients and energy required to sustain egg production.

CONCLUSION

Our study characterizes the transcriptional mechanisms driven by mating in the D. suzukii female midgut. Identification and characterization of the DEGs between virgin and mated females midgut will not only be crucial to better understand molecular research related to intestine plasticity during reproduction, but may also provide abundant target genes for the development of effective and ecofriendly pest control strategies against this economically important species.

Transcriptome analysis of sex-biased gene expression in the spotted-wing Drosophila, Drosophila suzukii (Matsumura)

Sexual dimorphism occurs widely throughout insects and has profound influences on evolutionary path. Sex-biased genes are considered to account for most of phenotypic differences between sexes. In order to explore the sex-biased genes potentially associated with sexual dimorphism and sexual development in Drosophila suzukii, a major devastating and invasive crop pest, we conducted whole-organism transcriptome profiling and sex-biased gene expression analysis on adults of both sexes. We identified transcripts of genes involved in several sex-specific physiological and functional processes, including transcripts involved in sex determination, reproduction, olfaction, and innate immune signals. A total of 11,360 differentially expressed genes were identified in the comparison, and 1,957 differentially expressed genes were female-biased and 4,231 differentially expressed genes were male-biased. The pathway predominantly enriched for differentially expressed genes was related to spliceosome, which might reflect the differences in the alternative splicing mechanism between males and females. Twenty-two sex determination and 16 sex-related reproduction genes were identified, and expression pattern analysis revealed that the majority of genes were differentially expressed between sexes. Additionally, the differences in sex-specific olfactory and immune processes were analyzed and the sex-biased expression of these genes may play important roles in pheromone and odor detection, and immune response. As a valuable dataset, our sex-specific transcriptomic data can significantly contribute to the fundamental elucidation of the molecular mechanisms of sexual dimorphism in fruit flies, and may provide candidate genes potentially useful for the development of genetic sexing strains, an important tool for sterile insect technique applications against this economically important species.