RNA sequencing reveals CircRNA expression profiles in chicken embryo fibroblasts infected with velogenic Newcastle disease virus

Libin Chen; Jiayu Ruan; Yiyi Chen; Wenxuan Deng; Jinyu Lai; Lei Fan; Juncheng Cai; Chan Ding; Qiuyan Lin; Bin Xiang; Tao Ren

doi:10.3389/fvets.2023.1167444

RNA sequencing reveals CircRNA expression profiles in chicken embryo fibroblasts infected with velogenic Newcastle disease virus

Front Vet Sci. 2023 Mar 29:10:1167444. doi: 10.3389/fvets.2023.1167444. eCollection 2023.

Authors

Libin Chen^{1

2

3

4}, Jiayu Ruan^{1

2

3

4}, Yiyi Chen^{1

2

3

4}, Wenxuan Deng^{1

2

3

4}, Jinyu Lai^{1

2

3

4}, Lei Fan^{1

2

3

4}, Juncheng Cai^{1

2

3

4}, Chan Ding⁵, Qiuyan Lin^{1

2

3

4}, Bin Xiang⁶, Tao Ren^{1

2

3

4}

Affiliations

¹ College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
² Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China.
³ National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China.
⁴ Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.
⁵ Shanghai Veterinary Research Institute (SHVRI), Chinese Academy of Agricultural Sciences (CAAS), Shanghai, China.
⁶ College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan, China.

Abstract

Introduction: Newcastle disease virus (NDV) is an important avian pathogen prevalent worldwide; it has an extensive host range and seriously harms the poultry industry. Velogenic NDV strains exhibit high pathogenicity and mortality in chickens. Circular RNAs (circRNAs) are among the most abundant and conserved eukaryotic transcripts. They are part of the innate immunity and antiviral response. However, the relationship between circRNAs and NDV infection is unclear.

Methods: In this study, we used circRNA transcriptome sequencing to analyze the differences in circRNA expression profiles post velogenic NDV infection in chicken embryo fibroblasts (CEFs). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to reveal significant enrichment of differentially expressed (DE) circRNAs. The circRNA- miRNA-mRNA interaction networks were further predicted. Moreover, circ-EZH2 was selected to determine its effect on NDV infection in CEFs.

Results: NDV infection altered circRNA expression profiles in CEFs, and 86 significantly DE circRNAs were identified. GO and KEGG enrichment analyses revealed significant enrichment of DE circRNAs for metabolism-related pathways, such as lysine degradation, glutaminergic synapse, and alanine, aspartic-acid, and glutamic-acid metabolism. The circRNA- miRNA-mRNA interaction networks further demonstrated that CEFs might combat NDV infection by regulating metabolism through circRNA-targeted mRNAs and miRNAs. Furthermore, we verified that circ-EZH2 overexpression and knockdown inhibited and promoted NDV replication, respectively, indicating that circRNAs are involved in NDV replication.

Conclusions: These results demonstrate that CEFs exert antiviral responses by forming circRNAs, offering new insights into the mechanisms underlying NDV-host interactions.

Keywords: Newcastle disease virus; RNA sequencing; chicken embryo fibroblasts; circular RNA; infection.

Grants and funding

This research was supported by the National Key Research and Development Program of China (2022YFD1801004), Guangdong Provincial Special Fund for Modern Agriculture Industry Technology Innovation Teams (No. 2023KJ119), and the National Natural Science Foundation of China (No. 31902251).