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. 2018 Mar 29:8:93.
doi: 10.3389/fcimb.2018.00093. eCollection 2018.

Analysis of microRNAs Expression Profiles in Madin-Darby Bovine Kidney Cells Infected With Caprine Parainfluenza Virus Type 3

Jizong Li  1   2   3 , Li Mao  1   2 , Wenliang Li  1   2 , Fei Hao  1   2 , Chunyan Zhong  1   2   4 , Xing Zhu  4 , Xinqin Ji  4 , Leilei Yang  1   2 , Wenwen Zhang  1   2 , Maojun Liu  1   2 , Jieyuan Jiang  1   2
Affiliations

Analysis of microRNAs Expression Profiles in Madin-Darby Bovine Kidney Cells Infected With Caprine Parainfluenza Virus Type 3

Jizong Li et al. Front Cell Infect Microbiol. .

Abstract

Caprine parainfluenza virus type 3 (CPIV3) is a newly emerging pathogenic respiratory agent infecting both young and adult goats, and it was identified in eastern China in 2013. Cellular microRNAs (miRNAs) have been reported to be important modulators of the intricate virus-host interactions. In order to elucidate the role of miRNAs in madin-darby bovine kidney (MDBK) cells during CPIV3 infection. In this study, we performed high-throughput sequencing technology to analyze small RNA libraries in CPIV3-infected and mock-infected MDBK cells. The results showed that a total of 249 known and 152 novel candidate miRNAs were differentially expressed in MDBK cells after CPIV3 infection, and 22,981 and 22,572 target genes were predicted, respectively. In addition, RT-qPCR assay was used to further confirm the expression patterns of 13 of these differentially expressed miRNAs and their mRNA targets. Functional annotation analysis showed these up- and downregulated target genes were mainly involved in MAPK signaling pathway, Jak-STAT signaling pathway, Toll-like receptor signaling pathway, p53 signaling pathway, focal adhesion, NF-kappa B signaling pathway, and apoptosis, et al. To our knowledge, this is the first report of the comparative expression of miRNAs in MDBK cells after CPIV3 infection. Our finding provides information concerning miRNAs expression profile in response to CPIV3 infection, and offers clues for identifying potential candidates for antiviral therapies against CPIV3.

Keywords: caprine parainfluenza virus type 3; high-throughput sequencing; host-pathogen interactions; madin-darby bovine kidney cell line; microRNAs.

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Figures

Figure 1
Figure 1
Length distribution of the clean reads of the sequences. The x-axis indicates the length of reads. The y-axis indicates the percentage of each length in the reads.
Figure 2
Figure 2
Differential expression levels of known miRNAs (A) and novel miRNAs (B) in CPIV3-infected and mock-infected groups. The x and y axes show the differential expression levels of miRNAs of the two groups. The red points represent up-expressed miRNAs with a ratio >2, the blue points represent equally- expressed miRNAs with a ratio ≥1/2 and ≤ 2, and the green points represent down- expressed miRNAs with a ratio <1/2.
Figure 3
Figure 3
The ranged in size and base bias at the first position of miRNA identified in CPIV3-infected and mock-infected cells. (A) CPIV3-infected cells (B) mock-infected cells. The x-axis indicates miRNAs lengths from 18 to 30 nt. The y-axis indicates the percentage of the base bias of miRNAs at the first position of each length.
Figure 4
Figure 4
Validation of miRNA (A) and mRNA targets (B) expression by qRT-PCR. The fold change of expression of 12 miRNAs and their mRNA targets in CPIV3 infected vs. CPIV3 uninfected MDBK cells was calculated using the 2-ΔΔct method and represented as the n-fold change.
Figure 5
Figure 5
Relationships between miRNAs and inversely correlated immune target genes. Green indicates miRNAs; red indicates immune target genes.
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