Identification of key genes fluctuated induced by avian leukemia virus (ALV-J) infection in chicken cells

  • Guohong Chen
  • Zhiteng Li
  • Shuai Su
  • Guobin ChangEmail author
  • Lingling Qiu
  • Pengfei Zhu
  • Yang Zhang
  • Qi Xu


Avian leukemia subgroup J (ALV-J) is one of the most detrimental neoplastic diseases in poultry production. However, the differences between somatic cells and immune cells post-infection remain poorly understood. The aim of our study was to detect the different responses in chicken to infection with ALV-J in different cell lines. In this study, we detected transcriptome expression changes during infection with ALV-J in chicken embryo fibroblast (CEF) and HD11 cell lines. RNA-Seq was used to determine the expression levels of mRNA transcripts from the two cell types after infection with ALV-J at 1, 4, and 7 dpi, and gene ontology analyses were used to cluster differentially expressed genes into pathways. Quantitative real-time PCR confirmed the expression of 336 and 269 differentially expressed genes in CEF and HD11 lines, respectively, involved in innate immunity (OASL, CCL4), adaptive immunity (LYZ, CD72), apoptosis and autophagy (WISP2, COMP), inflammation (JSC, IL8), and tumorgenesis (PCNA, GPX3). The notable signal transduction pathways included the PPARs signaling pathway and ECM-receptor interactions in CEF, and the Toll-like receptor, NOD-like receptor, and RIG-I-like receptor signaling pathways in HD11. To our knowledge, this is the first study to use high-throughput sequencing methods to investigate viral infection in different cell types. The results of the present study form a foundation for developing potential biological markers for viral infection.




Funding Information

This study was supported financially by the National Natural Science Foundation of China (31301966) and Science & Technology Pillar Program of Jiangsu (BE2013392).

Supplementary material

11626_2017_198_MOESM1_ESM.pdf (119 kb)
Fig. S1 (PDF 118 kb)
11626_2017_198_MOESM2_ESM.pdf (137 kb)
Fig. S2 (PDF 136 kb)
11626_2017_198_MOESM3_ESM.pdf (205 kb)
Fig. S3 (PDF 204 kb)
11626_2017_198_MOESM4_ESM.pdf (187 kb)
Fig. S4 (PDF 186 kb)
11626_2017_198_MOESM5_ESM.pdf (264 kb)
Table S1 (PDF 263 kb)
11626_2017_198_MOESM6_ESM.pdf (272 kb)
Table S2 (PDF 272 kb)
11626_2017_198_MOESM7_ESM.pdf (206 kb)
Table S3 (PDF 206 kb)
11626_2017_198_MOESM8_ESM.xlsx (20 kb)
Table S4 (XLSX 20 kb)


  1. Banerjee S, Dhar G, Haque I, Kambhampati S, Mehta S, Sengupta K et al (2008) CCN5/WISP-2 expression in breast adenocarcinoma is associated with less frequent progression of the disease and suppresses the invasive phenotypes of tumor cells. Cancer Res 68(18):7606–7612PubMedCrossRefGoogle Scholar
  2. Bergers G, Song S (2005) The role of pericytes in blood-vessel formation and maintenance. Neuro-Oncology 7(4):452PubMedPubMedCentralCrossRefGoogle Scholar
  3. Beug H, von Kirchbach A, Döderlein G, Conscience J-F, Graf T (1979) Chicken hematopoietic cells transformed by seven strains of defective avian leukemia viruses display three distinct phenotypes of differentiation. Cell 18(2):375–390PubMedCrossRefGoogle Scholar
  4. Borodina T, Adjaye J, Sultan M (2011) A strand-specific library preparation protocol for RNA sequencing. In: Daniel Jameson MV, Hans VW (eds) Methods in enzymology. Volume 500. Academic, Waltham, pp 79–98Google Scholar
  5. Bosinger SE, Hosiawa KA, Cameron MJ, Persad D, Ran L, Xu L et al (2004) Gene expression profiling of host response in models of acute HIV infection. J Immunol 173(11):6858–6863PubMedCrossRefGoogle Scholar
  6. Brogden KA (2005) Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? Nat Rev Microbiol 3:238–250PubMedCrossRefGoogle Scholar
  7. Brune K, Leffell MS, Spitznagel JK (1972) Microbicidal activity of peroxidaseless chicken heterophile leukocytes. Infect Immun 5(3):283–287PubMedPubMedCentralGoogle Scholar
  8. Brunet A, Datta SR, Greenberg ME (2001) Transcription-dependent and -independent control of neuronal survival by the PI3K-Akt signaling pathway. Curr Opin Neurobiol 11(3):297–305PubMedCrossRefGoogle Scholar
  9. Burnside J, Ouyang M, Anderson A, Bernberg E (2008) Deep sequencing of chicken microRNAs. BMC Genomics 9:185PubMedPubMedCentralCrossRefGoogle Scholar
  10. Bystry RS, Aluvihare V, Welch KA, Kallikourdis M, Betz AG (2001) B cells and professional APCs recruit regulatory T cells via CCL4. Nat Immunol 2(12):1126–1132PubMedCrossRefGoogle Scholar
  11. Carmeliet P, Jain RK (2000) Angiogenesis in cancer and other diseases. Nature 407(6801):249–257PubMedCrossRefGoogle Scholar
  12. Cui Z, Sun S, Zhang Z, Meng S (2009) Simultaneous endemic infections with subgroup J avian leukosis virus and reticuloendotheliosis virus in commercial and local breeds of chickens. Avian Pathol 38:443–448PubMedCrossRefGoogle Scholar
  13. Daynes RA, Jones DC (2002) Emerging roles of PPARs in inflammation and immunity. Nat Rev Immunol 2:748–759PubMedCrossRefGoogle Scholar
  14. Diebold S (2010) Innate recognition of viruses. Immunol Lett 128:17–20PubMedCrossRefGoogle Scholar
  15. El-kott AF, El-baz MA, Mokhtar AA (2006) Proliferating cell nuclear antigen (PCNA) overexpression and microvessel density predict survival in the urinary bladder carcinoma. Int Urol Nephrol 38:237–242PubMedCrossRefGoogle Scholar
  16. Fadly AM, Smith EJ (1999) Isolation and some characteristics of a subgroup J-like avian leukosis virus associated with myeloid leukosis in meat-type chickens in the United States. Avian Dis:391–400Google Scholar
  17. Feng S-Z, Cao W-S, Liao M (2011) The PI3K/Akt pathway is involved in early infection of some exogenous avian leukosis viruses. J Gen Virol 92(Pt 7):1688–1697PubMedCrossRefGoogle Scholar
  18. Ferrara N, Kerbel RS (2005) Angiogenesis as a therapeutic target. Nature 438(7070):967–974PubMedCrossRefGoogle Scholar
  19. Folkman J (1995) Angiogenesis in cancer, vascular, rheumatoid and other disease. Nat Med 1(1):27–30PubMedCrossRefGoogle Scholar
  20. Fritz JH, Ferrero RL, Philpott DJ, Girardin SE (2006) Nod-like proteins in immunity, inflammation and disease. Nat Immunol 7(12):1250–1257PubMedCrossRefGoogle Scholar
  21. Hang B, Sang J, Qin A, Qian K, Shao H, Mei M et al (2014) Transcription analysis of the response of chicken bursa of Fabricius to avian leukosis virus subgroup J strain JS09GY3. Virus Res 188:8–14PubMedCrossRefGoogle Scholar
  22. Hansson GK, Libby P, Schönbeck U, Yan ZQ (2002) Innate and adaptive immunity in the pathogenesis of atherosclerosis. Circ Res 91:281–291PubMedCrossRefGoogle Scholar
  23. Hattori K, Uchida K, Akaza H, Koiso K (1995) Proliferating cell nuclear antigen cyclin in human transitional cell carcinoma. Br J Urol 75:162–166PubMedCrossRefGoogle Scholar
  24. Heide V (1998) Update on subgroup J of avian leukosis. World Poult 14:2Google Scholar
  25. Hussain AI, Johnson JA, da Silva FM, Heneine W (2003) Identification and characterization of avian retroviruses in chicken embryo-derived yellow fever vaccines: investigation of transmission to vaccine recipients. J Virol 77(2):1105–1111PubMedPubMedCentralCrossRefGoogle Scholar
  26. Kano A, Haruyama T, Akaike T, Watanabe Y (1999) IRF-1 is an essential mediator in IFN-γ-induced cell cycle arrest and apoptosis of primary cultured hepatocytes. Biochem Biophys Res Commun 257:672–677PubMedCrossRefGoogle Scholar
  27. Lai Y, Gallo RL (2009) AMPed up immunity: how antimicrobial peptides have multiple roles in immune defense. Trends Immunol 30:131–141PubMedPubMedCentralCrossRefGoogle Scholar
  28. Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN (2010) RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26(4):493–500PubMedCrossRefGoogle Scholar
  29. Li H, Ji J, Xie Q, Shang H, Zhang H, Xin X et al (2012) Aberrant expression of liver microRNA in chickens infected with subgroup J avian leukosis virus. Virus Res 169(1):268–271PubMedCrossRefGoogle Scholar
  30. Li H, Wang T, Xu C, Wang D, Ren J, Li Y et al (2015) Transcriptome profile of liver at different physiological stages reveals potential mode for lipid metabolism in laying hens. BMC Genomics 16(1):763PubMedPubMedCentralCrossRefGoogle Scholar
  31. Liu H, Cao W, Li Y, Feng M, Wu X, Yu K et al (2013) Subgroup J avian leukosis virus infection inhibits autophagy in DF-1 cells. Virol J 10:196PubMedPubMedCentralCrossRefGoogle Scholar
  32. Liu H, Ong S-E, Badu-Nkansah K, Schindler J, White FM, Hynes RO (2011) CUB-domain-containing protein 1 (CDCP1) activates Src to promote melanoma metastasis. Proc Natl Acad Sci 108(4):1379–1384Google Scholar
  33. Liu H-C, Niikura M, Fulton J, Cheng H (2004) Identification of chicken lymphocyte antigen 6 complex, locus E (LY6E, alias SCA2) as a putative Marek’s disease resistance gene via a virus-host protein interaction screen. Cytogenet Genome Res 102(1–4):304–308Google Scholar
  34. Loo YM, Gale M (2011) Immune signaling by RIG-I-like receptors. Immunity 34:680–692PubMedPubMedCentralCrossRefGoogle Scholar
  35. Medzhitov R, Janeway CA (1997) Innate immunity: the virtues of a nonclonal system of recognition. Cell 91:295–298PubMedCrossRefGoogle Scholar
  36. Metzker ML (2010) Sequencing technologies [mdash] the next generation. Nat Rev Genet 11(1):31–46PubMedCrossRefGoogle Scholar
  37. Moon RT, Bowerman B, Boutros M, Perrimon N (2002) The promise and perils of Wnt signaling through β-catenin. Science 296(5573):1644–1646PubMedCrossRefGoogle Scholar
  38. Moresco EMY, LaVine D, Beutler B (2011) Toll-like receptors. Curr Biol 21(13):R488–RR93PubMedCrossRefGoogle Scholar
  39. Patan S (2004) Vasculogenesis and angiogenesis. Angiogenesis in brain tumors. Springer, New York, pp 3–32CrossRefGoogle Scholar
  40. Payne LN (1998) HPRS 103: a retro virus strikes back. The emergence of subgroup J avian leukosis virus. Avian Pathol 27(S1):S36–S45CrossRefGoogle Scholar
  41. Payne LN, Nair V (2012) The long view: 40 years of avian leukosis research. Avian Pathol 41(1):11–19PubMedCrossRefGoogle Scholar
  42. Qin L, Gao Y, Ni W, Sun M, Wang Y, Yin C et al (2013) Development and application of real-time PCR for detection of subgroup J avian leukosis virus. J Clin Microbiol 51(1):149–154PubMedPubMedCentralCrossRefGoogle Scholar
  43. Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB (2005) Gene regulation at the single-cell level. Science 307(5717):1962–1965PubMedCrossRefGoogle Scholar
  44. Roukos DH (2010) Next-generation, genome sequencing-based biomarkers: concerns and challenges for medical practice. Biomark Med 4(4):583–586PubMedCrossRefGoogle Scholar
  45. Rubin H, Fanshier L, Cornelius A, Hughes WF (1962) Tolerance and immunity in chickens after congenital and contact infection with an avian leukosis virus. Virology 17(1):143–156PubMedCrossRefGoogle Scholar
  46. Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative CT method. Nat Protoc 3(6):1101–1108PubMedCrossRefGoogle Scholar
  47. Schwarting R, Castello R (1992) Human Lyb-2 homolog CD72 is a marker for progenitor B-cell leukemias. Am J Hematol 41:151–158PubMedCrossRefGoogle Scholar
  48. Sugiarto H, Yu PL (2004) Avian antimicrobial peptides: the defense role of β-defensins. Biochem Biophys Res Commun 323:721–727PubMedCrossRefGoogle Scholar
  49. The Gene Ontology Consortium (2004) The gene ontology (GO) database and informatics resource. Nucleic Acids Res 32(suppl 1):D258–D261CrossRefGoogle Scholar
  50. Thomas PD, Mi H, Lewis S (2007) Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol 11(1):4–11PubMedCrossRefGoogle Scholar
  51. Tisoncik JR, Korth MJ, Simmons CP, Farrar J, Martin TR, Katze MG (2012) Into the eye of the cytokine storm. Microbiol Mol Biol Rev 76(1):16–32PubMedPubMedCentralCrossRefGoogle Scholar
  52. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (Oxford, England) 25(9):1105–1111CrossRefGoogle Scholar

Copyright information

© The Society for In Vitro Biology 2017

Authors and Affiliations

  • Guohong Chen
    • 1
  • Zhiteng Li
    • 1
  • Shuai Su
    • 2
  • Guobin Chang
    • 1
    Email author
  • Lingling Qiu
    • 1
  • Pengfei Zhu
    • 1
  • Yang Zhang
    • 1
  • Qi Xu
    • 1
  1. 1.College of Animal Science and TechnologyYangzhou UniversityYangzhouPeople’s Republic of China
  2. 2.College of Animal Science and Veterinary MedicineShandong Agricultural UniversityTaianPeople’s Republic of China

Personalised recommendations