Exploration of genetic basis of differential immune response to CSF vaccination in desi (indigenous) piglets using RNA-Seq approach

VAISHALI SAH; AMIT KUMAR; RAVI KUMAR; SHALU KUMARI PATHAK; SAJAD AHMAD WANI; AMIT RANJAN SAHU; VIKRAMADITYA UPMANYU; NIHAR RANJAN SAHOO; BHARAT BHUSHAN

doi:10.56093/ijans.v87i11.75820

Authors

VAISHALI SAH ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122 India
AMIT KUMAR ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122 India
RAVI KUMAR ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122 India
SHALU KUMARI PATHAK ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122 India
SAJAD AHMAD WANI ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122 India
AMIT RANJAN SAHU ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122 India
VIKRAMADITYA UPMANYU ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122 India
NIHAR RANJAN SAHOO ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122 India
BHARAT BHUSHAN ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122 India

https://doi.org/10.56093/ijans.v87i11.75820

Keywords:

CSFV, Humoral immune response, PBMCs, Pig, RNA Seq

Abstract

In the present study, the transcriptome profiling of peripheral blood mononuclear cells (PBMCs) of indigenous piglets against classical swine fever (CSF) vaccination was performed for elucidating the genetic basis of their differential humoral immunity. Piglets were vaccinated with lapinised strain of CSF virus (CSFV) followed by measurement of humoral immune response using c-ELISA at 28th day post vaccination (28dpv). The RNA sequencing data was analysed using established pipeline to determine set of differentially expressed genes (DEGs) in high responder as compared to low responder piglet. The differentially expressed important immune molecules were involved in regulating important pathways including antigen processing and presentation, T cell receptor signalling, B cell development, activation and signaling genes. The genes with differential expression also included TLR 3, 6, 7, 8, 9, and antiviral molecules such as MX, and ISG (Interferon stimulated genes) family members. The proteinprotein interaction of the immune genes was extracted for network representation. Most of the immune genes involved showed upregulation except the genes for antigen processing and presentation and T cell receptor signaling that were downregulated in the high responder. The immunologically important genes namely IFIT1, IFIT5, TAPBP, and TLR7 were validated using qRT-PCT and were observed to be in concordance with the RNA Seq results.

Downloads

Download data is not yet available.

References

1. Anders S and Huber W. 2010. Differential expression analysis for sequence count data. Genome Biology 11: R106. DOI: https://doi.org/10.1186/gb-2010-11-10-r106

2. Cao Z, Guo K, Zheng M, Ning P, Li H, Kang K, Lin Zhi, Zhang C, Liang W and Zhang Y. 2015. A comparison of the impact of Shimen and C strains of classical swine fever virus on Toll- like receptor expression. Journal of General Virology 96: 1732–45. DOI: https://doi.org/10.1099/vir.0.000129

3. Chen Z, Rijnbrand R, Jangra R K, Devaraj S G, Qu L, Ma Y, Lemon S M and Li K. 2007. Ubiquitination and proteasomal degradation of interferon regulatory factor-3 induced by Npro from a cytopathic bovine viral diarrhea virus. Virology 366: 277–92. DOI: https://doi.org/10.1016/j.virol.2007.04.023

4. Cinar M U, Islam M A, Pröll M, Kocamis H, Tholen E, Tesfaye D, Looft C, Schellander K and Uddin M J. 2013. Evaluation of suitable reference genes for gene expression studies in porcine PBMCs in response to LPS and LTA. BMC Research Notes 6(1): 56. DOI: https://doi.org/10.1186/1756-0500-6-56

5. Davies G, Genini S, Bishop S C and Guiffra E. 2009. An assessment of opportunities to dissect host genetic variation in resistance to infectious diseases in livestock. Animal 03: 415–36. DOI: https://doi.org/10.1017/S1751731108003522

6. Dev A, Iyer S, Razani B and Cheng G. 2011. NF-κB and innate immunity. Current Topics in Microbiology and Immunology 349: 115–43. DOI: https://doi.org/10.1007/82_2010_102

7. Fenstrel V and Sen G C. 2011. The ISG56/IFIT1 gene family. Journal of Interferon and Cytokine Research 31: 71–78. DOI: https://doi.org/10.1089/jir.2010.0101

8. Graham S P, Everett H E, Johns H L, Haines F J, La Rocca S A, Khatri M, Wright I K, Drew T and Crooke H R. 2010. Characterization of virus-specific peripheral blood cell cytokine responses following vaccination or infection with classical swine fever viruses. Veterinary Microbiology 142: 34–40. DOI: https://doi.org/10.1016/j.vetmic.2009.09.040

9. Graham S P, Everett H E, Haines F J, Johns H L, Sosan O A, Salguero F J, Clifford D J, Steinbach F, Drew T W and Crooke H R. 2012. Challenge of pigs with classical swine fever viruses after C-strain vaccination reveals remarkably rapid protection and insights into early immunity. PLoS One 7(1): e29310. DOI: https://doi.org/10.1371/journal.pone.0029310

10. He D N, Zhang X M, Liu K, Pang R, Zhao J, Zhou B and Chen P Y. 2014. In vitro inhibition of the replication of classical swine fever virus by porcine Mx1 protein. Antiviral Research 104: 128–35. DOI: https://doi.org/10.1016/j.antiviral.2014.01.020

11. Hilton L, Moganeradj K, Zhang G, Chen Y H, Randall R E, Mc Cauley J W and Goodbourn S. 2006. The N Pro product of bovine viral diarrhoea virus inhibits DNA binding by interferon regulatory factor 3 and targets it for proteasomal degradation and induces its proteasomal degradation. Journal of Virology 81: 3087–96. DOI: https://doi.org/10.1128/JVI.01145-06

12. Jackson J T, Nasa C, Shi W, Huntington N D, Bogue C W, Alexander W S and McCormack M P. 2015. A crucial role for the homeodomain transcription factor Hhex in lymphopoiesis. Blood 125: 803–14. DOI: https://doi.org/10.1182/blood-2014-06-579813

13. Jiang D, Guo H, Xu C, Chang J, Gu B, Wang L, Block T M and Guo J T. 2008. Identification of three interferon-inducible cellular enzymes that inhibit the replication of hepatitis C virus. Journal of Virology 82(4): 1665–78. DOI: https://doi.org/10.1128/JVI.02113-07

14. Jiang D, Weidner J M, Qing M, Pan X B, Guo H, Xu C, Zhang X, Birk A, Chang J, Shi P Y and Block T M. 2010. Identification of five interferon-induced cellular proteins that inhibit west nile virus and dengue virus infections. Journal of Virology 84: 8332–41. DOI: https://doi.org/10.1128/JVI.02199-09

15. Kawai T and Akira S. 2006. TLR Signalling. Cell Death and Differentiation 13: 816–25. DOI: https://doi.org/10.1038/sj.cdd.4401850

16. Leng N, Dawson J A, Thomson J A, Ruotti V, Rissman A I, Smits B M G, Haag J D, Gould M N, Stewart R M and Kendziorski C. 2013. EBSeq: an empirical Bayes hierarchical model for inference in RNA-Seq experiments. Bioinformatics 29(8): 1035–43. DOI: https://doi.org/10.1093/bioinformatics/btt087

17. Lewis C R G, Torremorell M, Galina-Pantoja L and Bishop S C. 2009. Genetic parameters for performance traits in commercial sows estimated before and after an outbreak of porcine reproductive and respiratory syndrome. Journal of Animal Science 87(3): 876–84. DOI: https://doi.org/10.2527/jas.2008-0892

18. Maddaly R, Pai G, Balaji S, Sivaramakrishnan P, Srinivasan L, Sunder S S and Paul S F. 2010. Receptors and signaling mechanisms for B lymphocyte activation, proliferation and differentiation–insights from both in vivo and in vitro approaches. FEBS Letters 584: 4883–94. DOI: https://doi.org/10.1016/j.febslet.2010.08.022

19. Medzhitov R and Janeway C. 2000. The toll receptor family and microbial recognition. Trends in Microbiology 8(10): 452–56. Mitchell P S, Emerman M and Malik H S. 2013. An evolutionary perspective on the broad antiviral specificity of MxA. Current Opinion in Microbiology 16: 493–99. DOI: https://doi.org/10.1016/j.mib.2013.04.005

20. Oliveros J C. 2007. http://bioinfogp.cnb.csic.es/tools/venny/ Palm M, Garigliany M M, Cornet F and Desmecht D. 2010.

21. Interferon-induced Sus scrofa Mx1 blocks endocytic traffic of incoming influenza A virus particles. Veterinary Research 41(3): 29. DOI: https://doi.org/10.1051/vetres/2010001

22. Pathak S K, Sah V, Sailo L, Chaudhary R, Singh A, Kumar R and Kumar A. 2017a. Expression profiling of immune genes in Classical Swine Fever vaccinated indigenous and crossbred piglets. Indian Journal of Animal Sciences 87(10): 1184–89.

23. Pathak S K, Kumar A, Bhuwana G, Sah V, Upmanyu V, Tiwari A K, Sahoo A P, Sahoo A R, Wani S A, Panigrahi M, Sahoo N R and Kumar R. 2017a. RNA Seq analysis for transcriptome profiling in response to classical swine fever vaccination in indigenous and crossbred pigs. Functional and Integrative Genomics 17: 607–20. DOI: https://doi.org/10.1007/s10142-017-0558-8

24. Payne D, Drinkwater S, Baretto R, Duddridge M and Browning M J. 2009. Expression of chemokine receptors CXCR4, CXCR5 and CCR7 on B and T lymphocytes from patients with primary antibody deficiency. Clinical Experimental Immunology 156(2): 254–62. DOI: https://doi.org/10.1111/j.1365-2249.2009.03889.x

25. Pichlmair A, Lassnig C, Eberle C A, Górna M W, Baumann C L, Burkard T R, Bürckstümmer T, Stefanovic A, Krieger S, Bennett K L and Rülicke T. 2011. IFIT1 is an antiviral protein that recognizes 5 [prime]-triphosphate RNA. Nature Immunology 12(7):624–30. DOI: https://doi.org/10.1038/ni.2048

26. Pulendran B and Ahmad R. 2006. Translating innate immunity into immunological memory: implications for vaccine development. Cell 124: 849–63. DOI: https://doi.org/10.1016/j.cell.2006.02.019

27. Reimand J, Arak T and Vilo J. 2011. g:Profiler—a web server for functional interpretation of gene lists. Nucleic Acids Research 39: 307–15. DOI: https://doi.org/10.1093/nar/gkr378

28. Robinson M D and Oshlack A. 2010. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology 11: R25. DOI: https://doi.org/10.1186/gb-2010-11-3-r25

29. Seago J, Hilton L, Reid E, Doceul V, Jeyatheesan J, Moganeradj K, McCauley J, Charleston B and Goodbourn S. 2007. The Npro product of classical swine fever virus and bovine viral diarrhoea virus uses a conserved mechanism to target interferon regulatory factor-3. Journal of General Virology 88: 3002–06. DOI: https://doi.org/10.1099/vir.0.82934-0

30. Seo J Y, Yaneva R, Hinson E R and Cresswell P. 2011. Human cytomegalovirus directly induces the antiviral protein viperin to enhance infectivity. Science 332(6033): 1093–97. DOI: https://doi.org/10.1126/science.1202007

31. Shannon P, Markiel A, Ozier O, Baliga N S, Wang J T, Ramage D, Amin N, Schwikowski B and Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13: 2498–2504. DOI: https://doi.org/10.1101/gr.1239303

32. Singh A, Kumar A, Sahoo N R, Upmanyu V, Kumar B, Bhushan B and Sharma D. 2016. Association of humoral response to classical swine fever vaccination with single nucleotide polymorphisms of swine leukocyte antigens. Journal of Applied Animal Research 44(1): 99–103. DOI: https://doi.org/10.1080/09712119.2015.1013965

33. Stark C, Breitkreutz B, Reguly T, Boucher L, Breitkreutz A and Tyers M. 2006. BIOGRID: a general repository for interaction datasets. Nucleic Acid Research 34: 535–39. DOI: https://doi.org/10.1093/nar/gkj109

34. Summerfield, Artur and Nicolas Ruggli. 2015. Immune responses against classical swine fever virus: between ignorance and lunacy. Frontiers in Veterinary Science 2:10. DOI: https://doi.org/10.3389/fvets.2015.00010

35. Suradhat S, Damrongwatanapokin S and Thanawongnuwech R. 2007. Factors critical for successful vaccination against classical swine fever in endemic areas. Veterinary Microbiology 119(1): 1–9. DOI: https://doi.org/10.1016/j.vetmic.2006.10.003

36. Suthram S, Shlomi T, Ruppin E, Sharan R and Ideker T. 2006. A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics 7:1. DOI: https://doi.org/10.1186/1471-2105-7-360

37. Wang X, Hinson E R and Cresswell P. 2007. The interferon- inducible protein viperin inhibits influenza virus release by perturbing lipid rafts. Cell Host and Microbe 2(2): 96–105. DOI: https://doi.org/10.1016/j.chom.2007.06.009

38. Woyach J A, Johnson A J and Byrd J C. 2012. The B-cell receptor signaling pathway as a therapeutic target in CLL. Blood 120: 1175–84. DOI: https://doi.org/10.1182/blood-2012-02-362624

39. Zhang X M, He D N, Zhou B, Pang R, Liu K, Zhao J and Chen P Y. 2013. In vitro inhibition of vesicular stomatitis virus replication by purified porcine Mx1 protein fused to HIV-1 Tat protein transduction domain (PTD). Antiviral Research 99: 149–57. DOI: https://doi.org/10.1016/j.antiviral.2013.05.009

40. Zhang Y, Burke C W, Ryman K D and Klimstra W B. 2007. Identification and characterization of interferon-induced proteins that inhibit alphavirus replication. Journal of Virology 81(20): 11246–55. DOI: https://doi.org/10.1128/JVI.01282-07