传染性胃肠炎病毒感染PK-15细胞环状RNA表达谱分析

doi:10.16431/j.cnki.1671-7236.2024.10.026

Abstract

Abstract: 【Objective】 This study was aimed to analyze the effects of Transmissible gastroenteritis virus (TGEV) infection on circular RNA (circRNA) expression in porcine kidney epithelial cells (PK-15) and the potential regulatory functions of differentially expressed circRNA. 【Method】 Illumina HiSeq 4000 sequencing platform was used to sequence circRNA transcriptome of PK-15 cells (control) and TGEV-infected PK-15 cells，then screened differentially expressed circRNA. GO function and KEGG pathway enrichment analysis of differentially expressed circRNAs-derived genes were performed. TGEV infection-associated circRNA-miRNA-mRNA regulatory network was predicted. Moreover，12 differentially expressed circRNAs were randomly selected to verify their expression by Real-time quantitative PCR. 【Result】 Sequencing results revealed 1 029 novel circRNAs. Compared with PK-15 cells，a total of 128 significantly differentially expressed circRNAs were identified in TGEV-infected PK-15 cells，of which 70 circRNAs were upregulated and 58 circRNAs were downregulated. GO functional analysis showed that the genes originating from differentially expressed circRNAs in TGEV-infected PK-15 cells were mainly enriched in biological processes such as cellular macromolecular metabolic processes and cellular metabolism，cellular components such as intracellular fractions and intracellular membrane-bound organelles，and molecular functions such as organic ring compound binding and nucleic acid binding. KEGG pathway enrichment results showed that the differentially expressed circRNAs source genes in TGEV-infected PK-15 cells were mainly enriched in actin cytoskeleton regulation，influenza A，hepatitis C，cAMP signaling pathway，mTOR signaling pathway，etc. The circRNA-miRNA-mRNA regulatory network revealed that there was a large and complex circRNA regulatory network in TGEV-infected PK-15 cells，and a variety of circRNAs regulated innate immunity and transmembrane ion transport by targeting genes IFNAR1，IFNAR2 and NHE3 via miRNAs，thereby affecting TGEV infection and symptoms. Real-time quantitative PCR showed that the expression of 12 differentially expressed circRNAs were consistent with the basal trend of RNA-Seq results. 【Conclusion】 TGEV altered circRNA expression in PK-15 cells. Differentially expressed circRNA-derived genes were widely involved in cellular macromolecular metabolism，viral infection and cAMP signaling pathways. Multiple target genes IFNAR1，IFNAR2 and NHE3 associated with innate immunity and TGEV pathogenesis were regulated by circRNA. The results revealed the potential function of circRNA in TGEV-host interactions.

Key words: circular RNA (circRNA); Transmissible gastroenteritis virus (TGEV); PK-15 cells; transcriptome

CLC Number:

S852.65⁺9.6

YANG Xiwang, DU Yunsha, LIU Rui, MEI Caiqiu, LI Wenting, LIU Xiao. circRNA Expression Profiling Analysis of Transmissible Gastroenteritis Virus-infected PK-15 Cells[J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(10): 4450-4464.

References

[1] XIA L，YANG Y，WANG J，et al. Impact of TGEV infection on the pig small intestine[J]. Virology Journal，2018，15(1):102.
[2] LIU Q，WANG H Y. Porcine enteric coronaviruses: An updated overview of the pathogenesis，prevalence，and diagnosis[J]. Veterinary Research Communications，2021，45(2-3):75-86.
[3] CHEN Y，ZHANG Y，WANG X，et al. Transmissible gastroenteritis virus: An update review and perspective[J]. Viruses，2023，15(2):359.
[4] VLASOVA A N，DIAZ A，DAMTIE D，et al. Novel Canine coronavirus isolated from a hospitalized patient with pneumonia in east malaysia[J]. Clinical Infectious Diseases，2022，74(3):446-454.
[5] DING X，YANG L，GENG X，et al. circRNAs as potential biomarkers for the clinicopathology and prognosis of glioma patients: A Meta-analysis[J]. BMC Cancer，2020，20(1):1005.
[6] YANG L，WILUSZ J E，CHEN L L. Biogenesis and regulatory roles of circular RNAs[J]. Annual Review of Cell and Developmental Biology，2022，38:263-289.
[7] ZHOU W Y，CAI Z R，LIU J，et al. circular RNA: Metabolism，functions and interactions with proteins[J]. Molecular Cancer，2020，19(1):172.
[8] LIAO Y，GUO S，LIU G，et al. Host non-coding RNA regulates Influenza A virus replication[J]. Viruses，2021，14(1): 51.
[9] TAGAWA T，OH D，DREMEL S，et al. A virus-induced circular RNA maintains latent infection of Kaposi’s sarcoma herpesvirus[J]. Proceedings of the National Academy of Sciences of the United States of America，2023，120(6):e2212864120.
[10] DU N，LI K，WANG Y，et al. circRNA circBACH1 facilitates Hepatitis B virus replication and hepatoma development by regulating the miR-200a-3p/MAP3K2 axis[J]. Histology and Histopathology，2022，37(9):863-877.
[11] GAO Y，ZHANG J，ZHAO F. Circular RNA identification based on multiple seed matching[J]. Briefings in Bioinformatics，2018，19(5):803-810.
[12] LANGMEAD B，TRAPNELL C，POP M，et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome[J]. Genome Biology，2009，10(3):R25.
[13] ZHOU L，CHEN J，LI Z，et al. Integrated profiling of microRNAs and mRNAs: microRNAs located on xq27.3 associate with clear cell renal cell carcinoma[J]. PLoS One，2010，5(12):e15224.
[14] LOVE M I，HUBER W，ANDERS S. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2[J]. Genome Biology，2014，15(12):550.
[15] SHEMESH M，LOCHTE S，PIEHLER J，et al. IFNAR1 and IFNAR2 play distinct roles in initiating type Ⅰ interferon-induced JAK-STAT signaling and activating STATs[J]. Science Signaling，2021，14(710):eabe4627.
[16] YAUGEL-NOVOA M，BOURLET T，LONGET S，et al. Association of IFNAR1 and IFNAR2 with COVID-19 severity[J]. The Lancet. Microbe，2023，4(7):e487.
[17] SADLER A J，WILLIAMS B R. Interferon-inducible antiviral effectors[J]. Nature Reviews Immunology，2008，8(7):559-568.
[18] SCHNEIDER W M，CHEVILLOTTE M D，RICE C M. Interferon-stimulated genes: A complex web of host defenses[J]. Annual Review of Immunology，2014，32:513-545.
[19] PLATANIAS L C. Mechanisms of type-Ⅰ- and type-Ⅱ-interferon-mediated signalling[J]. Nature Reviews. Immunology，2005，5(5):375-386.
[20] IVASHKIV L B，DONLIN L T. Regulation of type Ⅰ interferon responses[J]. Nature Reviews Immunology，2014，14(1):36-49.
[21] CRUZ J L，BECARES M，SOLA I，et al. Alphacoronavirus protein 7 modulates host innate immune response[J]. Journal of Virology，2013，87(17):9754-9767.
[22] SHEN Z，YANG Y，YANG S，et al. Structural and biological basis of Alphacoronavirus NSP1 associated with host proliferation and immune evasion[J]. Viruses，2020，12(8):812.
[23] KIELA P R，GHISHAN F K. Physiology of intestinal absorption and secretion[J]. Best Practice & Research. Clinical Gastroenterology，2016，30(2):145-159.
[24] ANDEREGG M A，GYIMESI G，HO T M，et al. The less well-known little brothers: The SLC9B/NHA sodium proton exchanger subfamily-structure，function，regulation and potential drug-target approaches[J]. Frontiers in Physiology，2022，13:898508.
[25] HONEGGER K J，CAPUANO P，WINTER C，et al. Regulation of sodium-proton exchanger isoform 3(NHE3) by PKA and exchange protein directly activated by cAMP (EPAC)[J]. Proceedings of the National Academy of Sciences of the United States of America，2006，103(3):803-808.
[26] NIU Z，XU S，ZHANG Y，et al. Transmissible gastroenteritis virus nucleocapsid protein interacts with Na(⁺)/H(⁺) exchanger 3 to reduce Na(⁺)/H(⁺) exchanger activity and promote piglet diarrhea[J]. Journal of Virology，2022，96(22):e0147322.
[27] YANG Y，YU Q，SONG H，et al. Decreased NHE3 activity and trafficking in TGEV-infected IPEC-J2 cells via the SGLT1-mediated P38 MAPK/Akt2 pathway[J]. Virus Research，2020，280:197901.
[28] ZHANG C，CUI H，HUANG C，et al. Interactions of circRNAs with methylation: An important aspect of circRNA biogenesis and function (review)[J]. Molecular Medicine Reports，2022，25(5):169.
[29] XUE M，WANG W，HE H，et al. Different mechanisms are utilized by Coronavirus Transmissible gastroenteritis virus to regulate interferon lambda 1 and interferon lambda 3 production[J]. Journal of Virology，2022，96(24):e0138822.
[30] ZHOU Y，XU C，GU S，et al. Integrated metabolomic and transcriptomic analyses reveal deoxycholic acid promotes Transmissible gastroenteritis virus infection by inhibiting phosphorylation of NF-κB and STAT3[J]. BMC Genomics，2024，25(1):239.
[31] ZHANG S，CAO Y，XU C，et al. Integrated metabolomics and transcriptomics analyses reveal metabolic responses to TGEV infection in porcine intestinal epithelial cells[J]. The Journal of General Virology，2023，104(12):001942.
[32] WU J，SHI X，WU L，et al. Genome-wide DNA methylome and transcriptome analysis of porcine testicular cells infected with Transmissible gastroenteritis virus[J]. Frontiers in Veterinary Science，2021，8:779323.
[33] JANISSEN R，WOODMAN A，SHENGJULER D，et al. Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses[J]. Molecular Cell，2021，81(21):4467-4480.e4467.
[34] RAWAL G，YIM-IM W，ALJETS E，et al. Porcine respiratory coronavirus (PRCV): Isolation and characterization of a variant PRCV from USA pigs[J]. Pathogens，2023，12(9):1097.
[35] BRITTON P，GARWES D J，PAGE K，et al. Molecular aspects of the relationship of Transmissible gastroenteritis virus (TGEV) with Porcine respiratory coronavirus (PRCV)[J]. Advances in Experimental Medicine and Biology，1990，276:441-446.
[36] BONIOTTI M B，PAPETTI A，LAVAZZA A，et al. Porcine epidemic diarrhea virus and discovery of a recombinant Swine enteric coronavirus，Italy[J]. Emerging Infectious Diseases，2016，22(1):83-87.
[37] DE NOVA P J G，CORTEY M. A retrospective study of Porcine epidemic diarrhoea virus (PEDV) reveals the presence of Swine enteric coronavirus (SeCoV) since 1993 and the recent introduction of a recombinant PEDV-SeCoV in Spain[J]. Transboundary and Emerging Diseases，2020，67(6):2911-2922.
[38] BELSHAM G J，RASMUSSEN T B，NORMANN P，et al. Characterization of a novel chimeric Swine enteric coronavirus from diseased pigs in central Eastern Europe in 2016[J]. Transboundary and Emerging Diseases，2016，63(6):595-601.
[39] AKIMKIN V，BEER M，BLOME S，et al. New chimeric Porcine coronavirus in swine feces，Germany，2012[J]. Emerging Infectious Diseases，2016，22(7):1314-1315.
[40] GUO R，FAN B，CHANG X，et al. Characterization and evaluation of the pathogenicity of a natural recombinant Transmissible gastroenteritis virus in China[J]. Virology，2020，545:24-32.
[41] ZHANG X，ZHU Y，ZHU X，et al. Identification of a natural recombinant Transmissible gastroenteritis virus between Purdue and Miller clusters in China[J]. Emerging Microbes & Infections，2017，6(8):e74.
[42] DECARO N，MARI V，CAMPOLO M，et al. Recombinant canine coronaviruses related to Transmissible gastroenteritis virus of swine are circulating in dogs[J]. Journal of Virology，2009，83(3):1532-1537.
[43] VLASOVA A N，DIAZ A，DAMTIE D，et al. Novel Canine coronavirus isolated from a hospitalized patient with pneumonia in East Malaysia[J]. Clinical Infectious Diseases，2022，74(3):446-454.
[44] GONG Y，TANG N，LIU P，et al. Newcastle disease virus degrades SIRT3via PINK1-PRKN-dependent mitophagy to reprogram energy metabolism in infected cells[J]. Autophagy，2022，18(7):1503-1521.
[45] WANG R，ZHU Y，REN C，et al. Influenza A virus protein PB1-F2 impairs innate immunity by inducing mitophagy[J]. Autophagy，2021，17(2):496-511.
[46] CHEN H，SUN H，YOU F，et al. Activation of STAT6 by STING is critical for antiviral innate immunity[J]. Cell，2011，147(2):436-446.

circRNA Expression Profiling Analysis of Transmissible Gastroenteritis Virus-infected PK-15 Cells

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