Transcriptome based analysis of apoptosis genes in chickens co-infected with avian infectious bronchitis virus and pathogenic Escherichia coli
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Abstract
Background and Objectives: Infection with Infectious bronchitis virus (IBV) and avian pathogenic Escherichia coli (APEC) is an important respiratory infection worldwide. Apoptosis is a physiological process of cell death that occurs as part of normal development and responds to a variety of physiological and pathophysiological stimuli. The identification of molecular mechanisms of action or inaction of key apoptotic proteins is important. This study aimed to investigate apoptotic related genes in the trachea tissue of infected (IBV variant 2, and APEC serotype O78: K80) SPF chickens group compared to the control group.
Materials and Methods: Forty SPF chickens was divided into 2 groups. Differential transcriptional profile in the infected SPF chickens trachea tissue was compared to those of control group in the early stage of infection by Illumina RNA-seq technique paired-end and strand-specific sequencing. Differentially expressed genes (DEGs) of transcriptome profiling of the trachea from the infected group were identified. Gene ontology category, KEGG pathway, and STRING analysis were analyzed to identify relationships among differentially expressed genes.
Results: Twenty-eight apoptotic genes were identified. They consisted of six pathways related to cell death: the extrinsic pathway, intrinsic pathway, endoplasmic reticulum stress pathway, MAPK signaling pathway, and cell death by NFkB and activates mTOR pathway and some regulator and apoptosis inhibitors.
Conclusion: All of the apoptotic genes in our study were up-regulated. Among these genes, the more fold change value was for TRADD and BCL2A1 genes, and the less fold change value was for MAP3K14, NFKB1, PIK3CB, and ITPR2 genes.
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5. Danial NN, Korsmeyer SJ. Cell death: critical control points. Cell 2004; 116: 205-219.
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7. Zhang Y, Zhong X, Chen Y, Liu S, Wu G, Liu Y. Association between CASP-8 gene polymorphisms and cancer risk in some Asian population based on a HuGE review and meta-analysis. Genet Mol Res 2013; 12: 6466-6476.
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9. Concetti J, Wilson CL. NFKB1 and cancer: friend or foe? Cells 2018; 7: 133.
10. Zhang W, Liu HT. MAPK signal pathways in the regulation of cell proliferation in mammalian cells. Cell Res 2002; 12: 9-18.
11. Ashkenazi A, Dixit VM. Apoptosis control by death and decoy receptors. Curr Opin Cell Biol 1999; 11: 255-260.
12. Thorburn A. Death receptor-induced cell killing. Cell Signal 2004; 16: 139-144.
13. Engelman JA, Luo J, Cantley LC. The evolution of phosphatidylinositol 3-kinases as regulators of growth and metabolism. Nat Rev Genet 2006; 7: 606-619.
14. Dondelinger Y, Aguileta M, Goossens V, Dubuisson C, Grootjans S, Dejardin E, et al. RIPK3 contributes to TNFR1-mediated RIPK1 kinase-dependent apoptosis in conditions of cIAP1/2 depletion or TAK1 kinase inhibition. Cell Death Differ 2013; 20: 1381-1392.
15. Everett H, McFadden G. Apoptosis: an innate immune response to virus infection. Trends Microbiol 1999; 7: 160-165.
16. Bender L, Morgan M, Thomas L, Liu Z, Thorburn A. The adaptor protein TRADD activates distinct mechanisms of apoptosis from the nucleus and the cytoplasm. Cell Death Differ 2005; 12: 473-481.
17. Dromard M, Bompard G, Glondu-Lassis M, Puech C, Chalbos D, Freiss G. The putative tumor suppressor gene PTPN13/PTPL1 induces apoptosis through insulin receptor substrate-1 dephosphorylation. Cancer Res 2007; 67: 6806-6813.
18. Peng LY, Cui ZQ, Wu ZM, Fu BD, Yi PF, Shen HQ. RNA-seq profiles of chicken type II pneumocyte in response to Escherichia coli infection. PLoS One 2019; 14(6):e0217438.
19. Sun H, Liu P, Nolan LK, Lamont SJ. Avian pathogenic Escherichia coli (APEC) infection alters bone marrow transcriptome in chickens. BMC Genomics 2015; 16: 690.
20. Wei MC, Zong WX, Cheng EHY, Lindsten T, Panoutsakopoulou V, Ross AJ, et al. Proapoptotic BAX and BAK: a requisite gateway to mitochondrial dysfunction and death. Science 2001; 292: 727-730.
21. Wei MC, Lindsten T, Mootha VK, Weiler S, Gross A, Ashiya M, et al. tBID, a membrane-targeted death ligand, oligomerizes BAK to release cytochrome c. Genes Dev 2000; 14: 2060-2071.
22. Srinivasula SM, Ahmad M, Fernandes-Alnemri T, Alnemri ES. Autoactivation of procaspase-9 by Apaf-1-mediated oligomerization. Mol Cell 1998; 1: 949-957.
23. Billen LP, Shamas-Din A, Andrews Dw. Bid: a Bax-like BH3 protein. Oncogene 2008; 27 Suppl 1:S93-104.
24. Smith GC, d’adda di Fagagna F, Lakin ND, Jackson SP. Cleavage and inactivation of ATM during apoptosis. Mol Cell Biol 1999; 19: 6076-6084.
25. Cong F, Liu X, Han Z, Shao Y, Kong X, Liu S. Transcriptome analysis of chicken kidney tissues following coronavirus avian infectious bronchitis virus infection. BMC Genomics 2013; 14: 743.
26. Zhong Y, Tan YW, Liu DX. Recent progress in studies of arterivirus-and coronavirus-host interactions.
Viruses 2012; 4: 980-1010.
27. Guabiraba R, Schouler C. Avian colibacillosis: still many black holes. FEMS Microbiol Lett 2015; 362:fnv118.
28. Igney FH, Krammer PH. Death and anti-death: tumour resistance to apoptosis. Nat Rev Cancer 2002; 2: 277-288.
29. Silke J, Meier P. Inhibitor of apoptosis (IAP) proteins–modulators of cell death and inflammation. Cold Spring Harb Perspect Biol 2013; 5(2):a008730.
30. Gonzalvez F, Lawrence D, Yang B, Yee S, Pitti R, Marsters S, et al. TRAF2 Sets a threshold for extrinsic apoptosis by tagging caspase-8 with a ubiquitin shutoff timer. Mol Cell 2012; 48: 888-899.
31. Liaudet-Coopman E, Beaujouin M, Derocq D, Garcia M, Glondu-Lassis M, Laurent-Matha V, et al. Cathepsin D: newly discovered functions of a long-standing aspartic protease in cancer and apoptosis. Cancer Lett 2006; 237: 167-179.
32. Khaket TP, Singh MP, Khan I, Bhardwaj M, Kang SC. Targeting of cathepsin C induces autophagic dysregulation that directs ER stress mediated cellular cytotoxicity in colorectal cancer cells. Cell Signal 2018; 46: 92-102.
33. Kouroku Y, Fujita E, Tanida I, Ueno T, Isoai A, Kumagai H, et al. ER stress (PERK/eIF2α phosphorylation) mediates the polyglutamine-induced LC3 conversion, an essential step for autophagy formation. Cell Death Differ 2007; 14: 230-239.
34. Ogata M, Hino Si, Saito A, Morikawa K, Kondo S, Kanemoto S, et al. Autophagy is activated for cell survival after endoplasmic reticulum stress. Mol Cell Biol 2006; 26: 9220-9231.
35. Fung TS, Liao Y, Liu DX. The endoplasmic reticulum stress sensor IRE1α protects cells from apoptosis induced by the coronavirus infectious bronchitis virus. J Virol 2014; 88: 12752–12764.
36. Khan AA, Soloski MJ, Sharp AH, Schilling G, Sabatini DM, Li SH, et al. Lymphocyte apoptosis: mediation by increased type 3 inositol 1, 4, 5-trisphosphate receptor. Science 1996; 273: 503-507.
37. Wiel C, Lallet-Daher H, Gitenay D, Gras B, Le Calvé B, Augert A, et al. Endoplasmic reticulum calcium release through ITPR2 channels leads to mitochondrial calcium accumulation and senescence. Nat Commun 2014; 5: 3792.
38. Hoesel B, Schmid JA. The complexity of NF-κB signaling in inflammation and cancer. Mol Cancer 2013; 12: 86.
39. Lawrence T. The nuclear factor NF-κB pathway in inflammation. Cold Spring Harb Perspect Biol 2009; 1: a001651.
40. Chang L, Karin M. Mammalian MAP kinase signalling cascades. Nature 2001; 410: 37-40.
41. Davis RJ (2000). Signal transduction by the JNK group of MAP kinases. Inflammatory Processes: pp 13-21.
42. Dent P, Haser W, Haystead T, Vincent LA, Roberts TM, Sturgill TW. Activation of mitogen-activated protein kinase kinase by v-Raf in NIH 3T3 cells and in vitro. Science 1992; 257: 1404-1407.
43. Vojtek AB, Hollenberg SM, Cooper JA. Mammalian Ras interacts directly with the serine/threonine kinase Raf. Cell 1993; 74: 205-214.
44. He W, Wang Q, Xu J, Xu X, Padilla MT, Ren G, et al. Attenuation of TNFSF10/TRAIL-induced apoptosis by an autophagic survival pathway involving TRAF2-and RIPK1/RIP1-mediated MAPK8/JNK activation. Autophagy 2012; 8: 1811-1821.
45. Ito Y, Hart JR, Ueno L, Vogt PK. Oncogenic activity of the regulatory subunit p85β of phosphatidylinositol 3-kinase (PI3K). PNAS 2014; 111: 16826-16829.
46. Waite K, Eickholt BJ (2010). The neurodevelopmental implications of PI3K signaling. In Phosphoinositide 3-kinase in Health and Disease. Springer pp. 245-265.
2. Shakeri R, Kheirollahi A, Davoodi J. Apaf-1: Regulation and function in cell death. Biochimie 2017; 135: 111-125.
3. Yorulmaz H (2015). Apoptosis and Infections. INTECH EUROPE.
4. Gong Y, Yang J, Cai J, Liu Q, Zhang Jm, Zhang Z. Effect of Gpx3 gene silencing by siRNA on apoptosis and autophagy in chicken cardiomyocytes. J Cell Physiol 2019; 234: 7828-7838.
5. Danial NN, Korsmeyer SJ. Cell death: critical control points. Cell 2004; 116: 205-219.
6. Galluzzi L, Vitale I, Abrams J, Alnemri E, Baehrecke E, Blagosklonny M, et al. Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012. Cell Death Differ 2012; 19: 107-120.
7. Zhang Y, Zhong X, Chen Y, Liu S, Wu G, Liu Y. Association between CASP-8 gene polymorphisms and cancer risk in some Asian population based on a HuGE review and meta-analysis. Genet Mol Res 2013; 12: 6466-6476.
8. Deiss LP, Galinka H, Berissi H, Cohen O, Kimchi A. Cathepsin D protease mediates programmed cell death induced by interferon-gamma, Fas/APO-1 and TNF-alpha. EMBO J 1996; 15: 3861-3870.
9. Concetti J, Wilson CL. NFKB1 and cancer: friend or foe? Cells 2018; 7: 133.
10. Zhang W, Liu HT. MAPK signal pathways in the regulation of cell proliferation in mammalian cells. Cell Res 2002; 12: 9-18.
11. Ashkenazi A, Dixit VM. Apoptosis control by death and decoy receptors. Curr Opin Cell Biol 1999; 11: 255-260.
12. Thorburn A. Death receptor-induced cell killing. Cell Signal 2004; 16: 139-144.
13. Engelman JA, Luo J, Cantley LC. The evolution of phosphatidylinositol 3-kinases as regulators of growth and metabolism. Nat Rev Genet 2006; 7: 606-619.
14. Dondelinger Y, Aguileta M, Goossens V, Dubuisson C, Grootjans S, Dejardin E, et al. RIPK3 contributes to TNFR1-mediated RIPK1 kinase-dependent apoptosis in conditions of cIAP1/2 depletion or TAK1 kinase inhibition. Cell Death Differ 2013; 20: 1381-1392.
15. Everett H, McFadden G. Apoptosis: an innate immune response to virus infection. Trends Microbiol 1999; 7: 160-165.
16. Bender L, Morgan M, Thomas L, Liu Z, Thorburn A. The adaptor protein TRADD activates distinct mechanisms of apoptosis from the nucleus and the cytoplasm. Cell Death Differ 2005; 12: 473-481.
17. Dromard M, Bompard G, Glondu-Lassis M, Puech C, Chalbos D, Freiss G. The putative tumor suppressor gene PTPN13/PTPL1 induces apoptosis through insulin receptor substrate-1 dephosphorylation. Cancer Res 2007; 67: 6806-6813.
18. Peng LY, Cui ZQ, Wu ZM, Fu BD, Yi PF, Shen HQ. RNA-seq profiles of chicken type II pneumocyte in response to Escherichia coli infection. PLoS One 2019; 14(6):e0217438.
19. Sun H, Liu P, Nolan LK, Lamont SJ. Avian pathogenic Escherichia coli (APEC) infection alters bone marrow transcriptome in chickens. BMC Genomics 2015; 16: 690.
20. Wei MC, Zong WX, Cheng EHY, Lindsten T, Panoutsakopoulou V, Ross AJ, et al. Proapoptotic BAX and BAK: a requisite gateway to mitochondrial dysfunction and death. Science 2001; 292: 727-730.
21. Wei MC, Lindsten T, Mootha VK, Weiler S, Gross A, Ashiya M, et al. tBID, a membrane-targeted death ligand, oligomerizes BAK to release cytochrome c. Genes Dev 2000; 14: 2060-2071.
22. Srinivasula SM, Ahmad M, Fernandes-Alnemri T, Alnemri ES. Autoactivation of procaspase-9 by Apaf-1-mediated oligomerization. Mol Cell 1998; 1: 949-957.
23. Billen LP, Shamas-Din A, Andrews Dw. Bid: a Bax-like BH3 protein. Oncogene 2008; 27 Suppl 1:S93-104.
24. Smith GC, d’adda di Fagagna F, Lakin ND, Jackson SP. Cleavage and inactivation of ATM during apoptosis. Mol Cell Biol 1999; 19: 6076-6084.
25. Cong F, Liu X, Han Z, Shao Y, Kong X, Liu S. Transcriptome analysis of chicken kidney tissues following coronavirus avian infectious bronchitis virus infection. BMC Genomics 2013; 14: 743.
26. Zhong Y, Tan YW, Liu DX. Recent progress in studies of arterivirus-and coronavirus-host interactions.
Viruses 2012; 4: 980-1010.
27. Guabiraba R, Schouler C. Avian colibacillosis: still many black holes. FEMS Microbiol Lett 2015; 362:fnv118.
28. Igney FH, Krammer PH. Death and anti-death: tumour resistance to apoptosis. Nat Rev Cancer 2002; 2: 277-288.
29. Silke J, Meier P. Inhibitor of apoptosis (IAP) proteins–modulators of cell death and inflammation. Cold Spring Harb Perspect Biol 2013; 5(2):a008730.
30. Gonzalvez F, Lawrence D, Yang B, Yee S, Pitti R, Marsters S, et al. TRAF2 Sets a threshold for extrinsic apoptosis by tagging caspase-8 with a ubiquitin shutoff timer. Mol Cell 2012; 48: 888-899.
31. Liaudet-Coopman E, Beaujouin M, Derocq D, Garcia M, Glondu-Lassis M, Laurent-Matha V, et al. Cathepsin D: newly discovered functions of a long-standing aspartic protease in cancer and apoptosis. Cancer Lett 2006; 237: 167-179.
32. Khaket TP, Singh MP, Khan I, Bhardwaj M, Kang SC. Targeting of cathepsin C induces autophagic dysregulation that directs ER stress mediated cellular cytotoxicity in colorectal cancer cells. Cell Signal 2018; 46: 92-102.
33. Kouroku Y, Fujita E, Tanida I, Ueno T, Isoai A, Kumagai H, et al. ER stress (PERK/eIF2α phosphorylation) mediates the polyglutamine-induced LC3 conversion, an essential step for autophagy formation. Cell Death Differ 2007; 14: 230-239.
34. Ogata M, Hino Si, Saito A, Morikawa K, Kondo S, Kanemoto S, et al. Autophagy is activated for cell survival after endoplasmic reticulum stress. Mol Cell Biol 2006; 26: 9220-9231.
35. Fung TS, Liao Y, Liu DX. The endoplasmic reticulum stress sensor IRE1α protects cells from apoptosis induced by the coronavirus infectious bronchitis virus. J Virol 2014; 88: 12752–12764.
36. Khan AA, Soloski MJ, Sharp AH, Schilling G, Sabatini DM, Li SH, et al. Lymphocyte apoptosis: mediation by increased type 3 inositol 1, 4, 5-trisphosphate receptor. Science 1996; 273: 503-507.
37. Wiel C, Lallet-Daher H, Gitenay D, Gras B, Le Calvé B, Augert A, et al. Endoplasmic reticulum calcium release through ITPR2 channels leads to mitochondrial calcium accumulation and senescence. Nat Commun 2014; 5: 3792.
38. Hoesel B, Schmid JA. The complexity of NF-κB signaling in inflammation and cancer. Mol Cancer 2013; 12: 86.
39. Lawrence T. The nuclear factor NF-κB pathway in inflammation. Cold Spring Harb Perspect Biol 2009; 1: a001651.
40. Chang L, Karin M. Mammalian MAP kinase signalling cascades. Nature 2001; 410: 37-40.
41. Davis RJ (2000). Signal transduction by the JNK group of MAP kinases. Inflammatory Processes: pp 13-21.
42. Dent P, Haser W, Haystead T, Vincent LA, Roberts TM, Sturgill TW. Activation of mitogen-activated protein kinase kinase by v-Raf in NIH 3T3 cells and in vitro. Science 1992; 257: 1404-1407.
43. Vojtek AB, Hollenberg SM, Cooper JA. Mammalian Ras interacts directly with the serine/threonine kinase Raf. Cell 1993; 74: 205-214.
44. He W, Wang Q, Xu J, Xu X, Padilla MT, Ren G, et al. Attenuation of TNFSF10/TRAIL-induced apoptosis by an autophagic survival pathway involving TRAF2-and RIPK1/RIP1-mediated MAPK8/JNK activation. Autophagy 2012; 8: 1811-1821.
45. Ito Y, Hart JR, Ueno L, Vogt PK. Oncogenic activity of the regulatory subunit p85β of phosphatidylinositol 3-kinase (PI3K). PNAS 2014; 111: 16826-16829.
46. Waite K, Eickholt BJ (2010). The neurodevelopmental implications of PI3K signaling. In Phosphoinositide 3-kinase in Health and Disease. Springer pp. 245-265.
| Files | ||
| Issue | Vol 13 No 1 (2021) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v13i1.5487 | |
| Keywords | ||
| Chickens; Infectious bronchitis virus; Escherichia coli; Apoptosis; Ribonucleic acid sequencing | ||
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This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
How to Cite
1.
Hashemi S, Hosseini SM, Ghalyanchilangeroudi A, Sheikhi N. Transcriptome based analysis of apoptosis genes in chickens co-infected with avian infectious bronchitis virus and pathogenic Escherichia coli. Iran J Microbiol. 2021;13(1):17-22.
