{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,5]],"date-time":"2026-09-05T10:06:19Z","timestamp":1788602779947,"version":"build-2803163510"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,4,2]],"date-time":"2021-04-02T00:00:00Z","timestamp":1617321600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,4,2]],"date-time":"2021-04-02T00:00:00Z","timestamp":1617321600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000200","name":"United States Agency for International Development","doi-asserted-by":"publisher","award":["AID-OAA-A-13-00080"],"award-info":[{"award-number":["AID-OAA-A-13-00080"]}],"id":[{"id":"10.13039\/100000200","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Newcastle disease (ND) has a great impact on poultry health and welfare with its most virulent (velogenic) strain. In addition, issues exacerbated by the increase in global temperatures necessitates a greater understanding of the host immune response when facing a combination of biotic and abiotic stress factors in poultry production. Previous investigations have revealed that the host immune response is tissue-specific. The goal of this study was to identify genes and\/or signaling pathways associated with immune response to NDV (Newcastle disease virus) in the trachea, an essential organ where NDV replicate after the infection, by profiling the tissue specific transcriptome response in two genetically distinct inbred chicken lines when exposed to both abiotic and biotic stressors. Fayoumis appear to be able to respond more effectively (lower viral titer, higher antibody levels, immune gene up-regulation) and earlier than Leghorns. Our results suggest NDV infection in Fayoumis appears to elicit proinflammatory processes, and pathways such as the inhibition of cell viability, cell proliferation of lymphocytes, and transactivation of RNA, more rapidly than in Leghorns. These differences in immune response converge at later timepoints which may indicate that Leghorns eventually regulate its immune response to infection. The profiling of the gene expression response in the trachea adds to our understanding of the chicken host response to NDV infection and heat stress on a whole genome level and provides potential candidate genes and signaling pathways for further investigation into the characterization of the time-specific and pathway specific responses in Fayoumis and Leghorns.<\/jats:p>","DOI":"10.1038\/s41598-021-86795-x","type":"journal-article","created":{"date-parts":[[2021,4,2]],"date-time":"2021-04-02T06:03:08Z","timestamp":1617343388000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Distinct transcriptomic response to Newcastle disease virus infection during heat stress in chicken tracheal epithelial tissue"],"prefix":"10.1038","volume":"11","author":[{"given":"Perot","family":"Saelao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ganrea","family":"Chanthavixay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vivian","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rodrigo A.","family":"Gallardo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jack C. M.","family":"Dekkers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan J.","family":"Lamont","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Terra","family":"Kelly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huaijun","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,4,2]]},"reference":[{"key":"86795_CR1","doi-asserted-by":"publisher","first-page":"1580","DOI":"10.1093\/ps\/82.10.1580","volume":"82","author":"JR Bartlett","year":"2003","unstructured":"Bartlett, J. R., Smith, M. O., Yan, Q. & Li, L. Effects of different levels of selenium on growth performance and immunocompetence of broilers under heat stress. Poult. Sci. 82, 1580\u20131588 (2003).","journal-title":"Poult. Sci."},{"issue":"9","key":"86795_CR2","doi-asserted-by":"publisher","first-page":"2808","DOI":"10.1093\/jn\/133.9.2808","volume":"133","author":"K Sahin","year":"2003","unstructured":"Sahin, K. & Kucuk, O. Zinc supplementation alleviates heat stress in laying Japanese quail. J. Nutr. 133(9), 2808\u20132811. https:\/\/doi.org\/10.1093\/jn\/133.9.2808 (2003) (PMID: 12949369).","journal-title":"J. Nutr."},{"key":"86795_CR3","unstructured":"Bjorkquist, A. et al. QTL for body composition traits during heat stress revealed in an advanced intercross line of chickens. Proceedings of the 10th World Congress of Genetics Applied to Livestock Production 3\u20135 (2014)."},{"key":"86795_CR4","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/S0165-2478(00)00246-7","volume":"74","author":"KM Anderson","year":"2000","unstructured":"Anderson, K. M. & Srivastava, P. K. Heat, heat shock, heat shock proteins and death: A central link in innate and adaptive immune responses. Immunol. Lett. 74, 35\u201339 (2000).","journal-title":"Immunol. Lett."},{"key":"86795_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0164575","volume":"11","author":"A Slawinska","year":"2016","unstructured":"Slawinska, A., Hsieh, J. C., Schmidt, C. J. & Lamont, S. J. Heat stress and lipopolysaccharide stimulation of chicken macrophage-like cell line activates expression of distinct sets of genes. PLoS ONE 11, 1\u201317 (2016).","journal-title":"PLoS ONE"},{"key":"86795_CR6","unstructured":"ICTV. International committee on taxonomy of viruses. Virus taxonomy: 2018b Release. 2019 [cited 2020 4\/5\/20]; Available from: https:\/\/talk.ictvonline.org\/ictv-reports\/ictv_online_report\/negative-sense-rna-viruses\/mononegavirales\/w\/paramyxoviridae."},{"key":"86795_CR7","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1111\/j.1751-0813.1942.tb01466.x","volume":"18","author":"HE Albiston","year":"1942","unstructured":"Albiston, H. E. & Gorrie, C. J. R. Newcastle disease in Victoria. Aust. Vet. J. 18, 75\u201379 (1942).","journal-title":"Aust. Vet. J."},{"key":"86795_CR8","doi-asserted-by":"publisher","unstructured":"Paramyxoviridae and Pneumoviridae. in Fenner\u2019s Veterinary Virology 327\u2013356 (Elsevier, 2017). https:\/\/doi.org\/10.1016\/B978-0-12-800946-8.00017-9.","DOI":"10.1016\/B978-0-12-800946-8.00017-9"},{"key":"86795_CR9","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1136\/vr.160.14.482","volume":"160","author":"E Aldous","year":"2007","unstructured":"Aldous, E. et al. Outbreak of Newcastle disease in pheasants (Phasianus colchicus) in south-east England in July 2005. Vet. Rec. 160, 482\u2013484 (2007).","journal-title":"Vet. Rec."},{"key":"86795_CR10","doi-asserted-by":"publisher","first-page":"1223","DOI":"10.1099\/00221287-146-5-1223","volume":"146","author":"GF Browning","year":"2000","unstructured":"Browning, G. F., Whithear, K. G., Gaunson, J. E. & Philip, C. J. Lymphocytic infiltration in the chicken trachea in response to Mycoplasma gallisepticum infection. Microbiology 146, 1223\u20131229 (2000).","journal-title":"Microbiology"},{"key":"86795_CR11","doi-asserted-by":"publisher","unstructured":"Deist, M. S. et al. Novel mechanisms revealed in the trachea transcriptome of resistant and susceptible chicken lines following infection with Newcastle disease virus. Clin. Vaccine Immunol. CVI.00027\u201317 (2017). https:\/\/doi.org\/10.1128\/CVI.00027-17.","DOI":"10.1128\/CVI.00027-17"},{"key":"86795_CR12","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1080\/03079450701774850","volume":"37","author":"KM Zaffuto","year":"2008","unstructured":"Zaffuto, K. M., Estevez, C. N. & Afonso, C. L. Primary chicken tracheal cell culture system for the study of infection with avian respiratory viruses. Avian Pathol. 37, 25\u201331 (2008).","journal-title":"Avian Pathol."},{"key":"86795_CR13","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1186\/1471-2164-10-512","volume":"10","author":"Y Wang","year":"2009","unstructured":"Wang, Y. et al. Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach. BMC Genomics 10, 512\u2013512 (2009).","journal-title":"BMC Genomics"},{"key":"86795_CR14","doi-asserted-by":"publisher","unstructured":"Wang, Y. et al. Physiological responses to heat stress in two genetically distinct chicken inbred lines. Poultry Sci. 1\u201311 (2018). https:\/\/doi.org\/10.3382\/ps\/pex363.","DOI":"10.3382\/ps\/pex363"},{"key":"86795_CR15","unstructured":"Lakshmanan, N., Kaiser, M. G. & Lamon, S. J. Marek\u2019s disease resistance in MHC-congenic lines from Leghorn and Fayoumi breeds. in Current research on Marek\u2019s disease. Proceedings of the 5th International Symposium vol. pp. 57\u201362 (American Association of Avian Pathologists, 1996)."},{"key":"86795_CR16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1023\/B:TROP.0000009524.47913.d4","volume":"36","author":"MK Hassan","year":"2004","unstructured":"Hassan, M. K., Afify, M. A. & Aly, M. M. Genetic resistance of Egyptian chickens to infectious bursal disease and newcastle disease. Trop. Anim. Health Prod. 36, 1\u20139 (2004).","journal-title":"Trop. Anim. Health Prod."},{"key":"86795_CR17","doi-asserted-by":"publisher","first-page":"579","DOI":"10.3390\/genes9120579","volume":"9","author":"P Saelao","year":"2018","unstructured":"Saelao, P. et al. Integrated proteomic and transcriptomic analysis of differential expression of chicken lung tissue in response to NDV infection during heat stress. Genes 9, 579 (2018).","journal-title":"Genes"},{"key":"86795_CR18","doi-asserted-by":"crossref","unstructured":"Saelao, P. et al. Novel insights into the host immune response of chicken Harderian gland tissue during Newcastle disease virus infection and heat treatment. BMC Vet. Res. 14, (2018).","DOI":"10.1186\/s12917-018-1583-0"},{"key":"86795_CR19","first-page":"10","volume":"59","author":"C Cray","year":"2009","unstructured":"Cray, C., Zaias, J. & Altman, N. H. Acute phase response in animals: A review. Comp. Med. 59, 10 (2009).","journal-title":"Comp. Med."},{"key":"86795_CR20","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1111\/j.1349-7006.2007.00720.x","volume":"99","author":"A Takaoka","year":"2008","unstructured":"Takaoka, A., Tamura, T. & Taniguchi, T. Interferon regulatory factor family of transcription factors and regulation of oncogenesis. Cancer Sci. 99, 467\u2013478 (2008).","journal-title":"Cancer Sci."},{"key":"86795_CR21","doi-asserted-by":"publisher","first-page":"6096","DOI":"10.1016\/j.vaccine.2006.05.027","volume":"24","author":"WGJ Degen","year":"2006","unstructured":"Degen, W. G. J. et al. Molecular immunophenotyping of lungs and spleens in naive and vaccinated chickens early after pulmonary avian influenza A (H9N2) virus infection. Vaccine 24, 6096\u20136109 (2006).","journal-title":"Vaccine"},{"key":"86795_CR22","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/S0165-2427(99)00008-2","volume":"68","author":"AE Gehad","year":"1999","unstructured":"Gehad, A. E., Mashaly, M. M., Siegel, H. S., Dunnington, E. A. & Siegel, P. B. Effect of genetic selection and MHC haplotypes on lymphocyte proliferation and interleukin-2 like activity in chicken lines selected for high and low antibody production against sheep red blood cells. Vet. Immunol. Immunopathol. 68, 13\u201324 (1999).","journal-title":"Vet. Immunol. Immunopathol."},{"key":"86795_CR23","doi-asserted-by":"publisher","first-page":"a001651","DOI":"10.1101\/cshperspect.a001651","volume":"1","author":"T Lawrence","year":"2009","unstructured":"Lawrence, T. The nuclear factor NF-\u03b2 pathway in inflammation. Cold Spring Harb. Perspect. Biol. 1, a001651\u2013a001651 (2009).","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"86795_CR24","doi-asserted-by":"crossref","unstructured":"Vobhenrich, C. A. J. & Di Santo, J. P. Interleukin signaling. Cell 12, PR760\u2013PR763 (2002).","DOI":"10.1016\/S0960-9822(02)01286-1"},{"key":"86795_CR25","doi-asserted-by":"publisher","first-page":"61","DOI":"10.3390\/genes10010061","volume":"10","author":"P Saelao","year":"2019","unstructured":"Saelao, P. et al. Genetics and genomic regions affecting response to newcastle disease virus infection under heat stress in layer chickens. Genes 10, 61 (2019).","journal-title":"Genes"},{"key":"86795_CR26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12864-017-4380-4","volume":"18","author":"MS Deist","year":"2017","unstructured":"Deist, M. S. et al. Resistant and susceptible chicken lines show distinctive responses to Newcastle disease virus infection in the lung transcriptome. BMC Genomics 18, 1\u201315 (2017).","journal-title":"BMC Genomics"},{"key":"86795_CR27","unstructured":"R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (2018)."},{"key":"86795_CR28","unstructured":"Andrew, S. FastQC: a quality control tool for high throughput sequence data."},{"key":"86795_CR29","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"86795_CR30","doi-asserted-by":"publisher","DOI":"10.1101\/002824","author":"S Anders","year":"2014","unstructured":"Anders, S., Pyl, P. T. & Huber, W. HTSeq: A Python framework to work with high-throughput sequencing data. https:\/\/doi.org\/10.1101\/002824 (2014).","journal-title":"HTSeq: A Python framework to work with high-throughput sequencing data."},{"key":"86795_CR31","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139\u2013140 (2010).","journal-title":"Bioinformatics"},{"key":"86795_CR32","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1093\/bioinformatics\/btt703","volume":"30","author":"A Kr\u00e4mer","year":"2014","unstructured":"Kr\u00e4mer, A., Green, J., Pollard, J. & Tugendreich, S. Causal analysis approaches in ingenuity pathway analysis. Bioinformatics 30, 523\u2013530 (2014).","journal-title":"Bioinformatics"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-021-86795-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-021-86795-x","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-021-86795-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,3]],"date-time":"2022-12-03T01:10:56Z","timestamp":1670029856000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-021-86795-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,4,2]]},"references-count":32,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2021,12]]}},"alternative-id":["86795"],"URL":"https:\/\/doi.org\/10.1038\/s41598-021-86795-x","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,4,2]]},"assertion":[{"value":"14 December 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 March 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 April 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"7450"}}