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Functional & Integrative Genomics

, Volume 19, Issue 6, pp 901–918 | Cite as

Genome-wide integrated analysis of miRNA and mRNA expression profiles to identify differentially expressed miR-22-5p and miR-27b-5p in response to classical swine fever vaccine virus

  • Lalrengpuii Sailo
  • Amit KumarEmail author
  • Vaishali Sah
  • Rajni Chaudhary
  • Vikramaditya Upmanyu
  • A. K. Tiwari
  • Ajay Kumar
  • Aruna Pandey
  • Shikha Saxena
  • Akansha Singh
  • Sajad Ahmad Wani
  • Ravi Kumar GandhamEmail author
  • Anil Rai
  • B. P. Mishra
  • R. K. Singh
Original Article
  • 259 Downloads

Abstract

The present study was conducted to identify the differentially expressed miRNAs (DE miRNAs) in the peripheral blood mononuclear cells of crossbred pigs in response to CSF vaccination on 7 and 21 days of post vaccination as compared to unvaccinated control (0 dpv). Simultaneously, set of miRNA was predicted using mRNA seq data at same time point. The proportion of CD4CD8+ and CD4+CD8+ increased after vaccination, and the mean percentage inhibition was 86.89% at 21 dpv. It was observed that 22 miRNAs were commonly expressed on both the time points. Out of predicted DE miRNAs, it was found that 40 and 35 DE miRNAs were common, obtained from miRNA seq analysis and predicted using mRNA seq data on 7 dpv versus 0 dpv and 21 dpv versus 0 dpv respectively. Two DE miRNAs, ssc-miR-22-5p and ssc-miR-27b-5p, were selected based on their log2 fold change and functions of their target genes in immune process/pathway of viral infections. The validations of DE miRNAs using qRT-PCR were in concordance with miRNA seq analysis. Two set of target genes, CD40 and SWAP70 (target gene of ssc-miR-22-5p) and TLR4 and Lyn (target gene of ssc-miR-27b-5p), were validated and were in concordance with results of RNA seq analysis at a particular time point (except TLR4). The first report of genome-wide identification of differentially expressed miRNA in response to live attenuated vaccine virus of classical swine fever revealed miR-22-5p and miR-27b-5p were differentially expressed at 7 dpv and 21 dpv.

Keywords

Classical swine fever RNA seq miRNA Pig 

Abbreviations

BIOGRID

Biological General Repository for Interaction Datasets

cELISA

competitive enzyme-linked immunosorbent assay

CSF

classical swine fever

CSFV

classical swine fever virus

DEGs

differentially expressed genes

DEHC

differentially expressed highly connected

DE miRNA

differentially expressed microRNA

FACS

fluorescent-activated cell sorter

FDR

false discovery rate

FPKMs

fragments per kilobase for a million reads

GO

Gene ontology

KEGG

Kyoto Encyclopedia of Genes and Genomes

qRT-PCR

quantitative real-time polymerase chain reaction

RNA seq

RNA sequencing

RSEM

RNA seq by expectation–maximization

TPM

transcript per million

Notes

Acknowledgements

Authors are thankful to the Director, ICAR-IVRI and CABin project of IASRI for providing necessary facility for executing this research project.

Funding

The CABIN project of IASRI and SubDIC (BTISnet), ICAR-IVRI provided financial assistance.

Compliance with ethical standards

Ethics approval and consent to participate

All animal experiments were conducted under an approved protocol and oversight of Institute Animal Ethics Committee of ICAR-Indian Veterinary Research Institute as per guidelines of CPCSEA, MoEF, India.

Competing financial interests

The authors declare that they have no competing interest.

Supplementary material

10142_2019_689_MOESM1_ESM.docx (358 kb)
ESM 1 (DOCX 938 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Lalrengpuii Sailo
    • 1
  • Amit Kumar
    • 1
    Email author
  • Vaishali Sah
    • 1
  • Rajni Chaudhary
    • 1
  • Vikramaditya Upmanyu
    • 2
  • A. K. Tiwari
    • 2
  • Ajay Kumar
    • 3
  • Aruna Pandey
    • 3
  • Shikha Saxena
    • 3
  • Akansha Singh
    • 4
  • Sajad Ahmad Wani
    • 5
  • Ravi Kumar Gandham
    • 6
    Email author
  • Anil Rai
    • 7
  • B. P. Mishra
    • 8
  • R. K. Singh
    • 3
  1. 1.Animal GeneticsIndian Veterinary Research InstituteBareillyIndia
  2. 2.Standardization DivisionIndian Veterinary Research InstituteBareillyIndia
  3. 3.Animal BiochemistryIndian Veterinary Research InstituteBareillyIndia
  4. 4.Animal Genetics and BreedingIndian Veterinary Research InstituteBareillyIndia
  5. 5.Ohio State UniversityColumbusUSA
  6. 6.Animal BiotechnologyNational Institute of Animal BiotechnologyHyderabadIndia
  7. 7.Head Centre for BioinformaticsIASRINew DelhiIndia
  8. 8.BiotechnologyIndian Veterinary Research InstituteBareillyIndia

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