Gene · 2025
Dynamic expression and functional analysis of circRNAs during albendazole resistance of Haemonchus contortus.
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Chen Xindi, Wang Tengyu, Liu Chunxia, Gao Wa, Wu Weijie, Wang Wenlong
Аннотация
BACKGROUND: Circular RNAs (circRNAs) are increasingly recognized as important regulators of splicing, transcription and gene expression, and may contribute to drug resistance. The purpose of this study was to investigate the potential roles of circRNAs in the development of albendazole (ABZ) resistance in Haemonchus contortus (H. contortus). By analysing the numbers, species, structural characteristics and functions of circRNAs, we constructed regulatory networks to provide insight into circRNA-mediated mechanisms associated with ABZ resistance.
METHODS: In this study, ABZ-sensitive (ABZ-S) strains, ABZ-resistant (ABZ-RA) strains and ABZ-resistant treatment (ABZ-RB) strains of H. contortus were subjected to high-throughput sequencing and cDNA library construction with the Illumina HiSeqTM 4000 platform. The find_circ software was used to predict circRNAs on the basis of quality-control data, and the source genes of differentially expressed circRNAs (DEcircRNAs) were annotated through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Mireap, TargetScan, Miranda and miRTarBase (version 6.1) were applied to predict the interactions of miRNAs and mRNAs with DEcircRNAs, and OriginPro software was used to visualize the circRNA‒miRNA‒mRNA networks. Nine DEcircRNAs were randomly selected from the comparisons, and their expression was validated by quantitative real-time polymerase chain reaction (qRT‒PCR) to assess the consistency with RNA-seq data.
RESULTS: A total of 5695 circRNAs were identified across the three strain comparisons, with lengths ranging from 126 to 95,630 nt. Among them, 364, 252 and 311unique DEcircRNAs were identified in ABZ-S, ABZ-RA, ABZ-RB, respectively. These DEcircRNAs were associated with 1369 parental genes involved in 974 GO terms and 326 KEGG pathways, including 86 metabolic pathways. Complex competitive endogenous RNA (ceRNA) regulatory networks were constructed among DEcircRNAs, differentially expressed microRNAs (DEmiRNAs), and differentially expressed messenger RNAs (DEmRNAs). The ceRNA network comprised 110 DEcircRNAs, 41 DEmiRNAs and 10 DEmRNAs, of which 35 were related to metabolism and 37 to organismal systems. Validation experiments confirmed expression differences for nine DEcircRNAs.
CONCLUSIONS: The high-throughput identification of DEcircRNAs in drug-resistant strains suggests that some circRNAs may participate in the development of ABZ resistance by regulating source genes and functioning as ceRNAs. These regulatory processes may involve pathways such as ABC transporters and drug metabolism-cytochrome P450.
METHODS: In this study, ABZ-sensitive (ABZ-S) strains, ABZ-resistant (ABZ-RA) strains and ABZ-resistant treatment (ABZ-RB) strains of H. contortus were subjected to high-throughput sequencing and cDNA library construction with the Illumina HiSeqTM 4000 platform. The find_circ software was used to predict circRNAs on the basis of quality-control data, and the source genes of differentially expressed circRNAs (DEcircRNAs) were annotated through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Mireap, TargetScan, Miranda and miRTarBase (version 6.1) were applied to predict the interactions of miRNAs and mRNAs with DEcircRNAs, and OriginPro software was used to visualize the circRNA‒miRNA‒mRNA networks. Nine DEcircRNAs were randomly selected from the comparisons, and their expression was validated by quantitative real-time polymerase chain reaction (qRT‒PCR) to assess the consistency with RNA-seq data.
RESULTS: A total of 5695 circRNAs were identified across the three strain comparisons, with lengths ranging from 126 to 95,630 nt. Among them, 364, 252 and 311unique DEcircRNAs were identified in ABZ-S, ABZ-RA, ABZ-RB, respectively. These DEcircRNAs were associated with 1369 parental genes involved in 974 GO terms and 326 KEGG pathways, including 86 metabolic pathways. Complex competitive endogenous RNA (ceRNA) regulatory networks were constructed among DEcircRNAs, differentially expressed microRNAs (DEmiRNAs), and differentially expressed messenger RNAs (DEmRNAs). The ceRNA network comprised 110 DEcircRNAs, 41 DEmiRNAs and 10 DEmRNAs, of which 35 were related to metabolism and 37 to organismal systems. Validation experiments confirmed expression differences for nine DEcircRNAs.
CONCLUSIONS: The high-throughput identification of DEcircRNAs in drug-resistant strains suggests that some circRNAs may participate in the development of ABZ resistance by regulating source genes and functioning as ceRNAs. These regulatory processes may involve pathways such as ABC transporters and drug metabolism-cytochrome P450.