نوع مقاله : مقاله پژوهشی
نویسندگان
1 دانشجوی دکتری، گروه علوم دامی، دانشکده کشاورزی، دانشگاه فردوسی مشهد
2 استاد ، گروه علوم دامی، دانشکده کشاورزی، دانشگاه فردوسی مشهد
3 استادیار ، گروه علوم دامی، دانشکده کشاورزی، دانشگاه فردوسی مشهد
چکیده
کلیدواژه‌ها
عنوان مقاله [English]
نویسندگان [English]
Background and objectives: Mastitis is an inflammatory disease in dairy cows that occurs in response to infectious factors. This inflammatory disease have a high negative economic impact on dairy industry. In recent decades, somatic cell score has been used as an indirect method to control mastitis. Resistance to infection disease may be defined as the ability of an animal to have an immune response to prevent the spread of pathogens after infection. Previous studies showed that animals differ in their genetic ability for immune competence. Genetic resistance to mastitis involves interconnected biological mechanisms that result from differences in the response to mastitis that activate and regulate different levels of the immune response. A better understanding of the immune system and the metabolic pathways involved in responding to various pathogens may be used as a complementary approach to control of the disease. Several studies have been evaluated genetic mechanisms affecting somatic cells score in dairy cows. Many candidate genes affecting somatic cells score has been introduced. But the complex relationships between genes and pathways that affect them have not been fully identified yet. The main purpose of this study is to integrate the results of recent genome-wide association studies on somatic cells score using meta-analysis to obtain a set of important genes and pathways.
Materials and methods: In this study, a search for the genome-wide association studies dataset in Google Scholar was performed using the keywords Dairy cows, Genome wide association studies, and Somatic cells score. Gene sets were available in different populations of dairy cow breeds (Holstein and Friesian breeds and red cows) in 11 independent studies from 2011 to 2019. 218 candidate genes for somatic cells score were found from genome-wide association studies. The number of common genes in dairy cows was examined using Venn diagram. Then, all available genes were combined and evaluated using meta-analysis. The ClueGO v2.5.4 plugin were used to conduct gene ontology analysis and KEGG pathways. The CluePedia v1.5.4 plugin in Cytoscape v3.7.2 were used to visualize genes and protein-protein interactions.
Results: The results showed that U6, DCK, and NPFFR2 genes as the key candidate genes have an important role in combating infection and pathogens in the development of mastitis. Some biological processes, cellular components, molecular functions, and related pathways were identified. The most important biological process, cellular components and molecular function pathways were mesenchymal cell development (P=3.92e-04), apical plasma membrane (P=2.83e-03), and solute: cation symporter activity (P=3.71e-04), respectively.
Conclusion: Generally, the results of this study showed that meta-analysis based on a large number of original data revealed the most important candidate genes involved in the fight against mastitis pathways, this information provides a solid foundation for the development of new treatments for mastitis. Therefore, identification of important genes and gene ontology term enrichment (with high power and accuracy) can play an effective role in genomic evaluation and design of breeding programs aimed at controlling mastitis in dairy cows.
کلیدواژه‌ها [English]
Abdel-Shafy, H., Bortfeldt, R.H., Tetens, J. and Brockmann, G.A. 2014. Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle. Genetics Selection Evolution. 46:1–10.
2.Abuelo, A., Hernández, J., Benedito, J.L. and Castillo, C. 2015. The importance of the oxidative status of dairy cattle in the periparturient period: Revisiting antioxidant supplementation. Journal of Animal Physiology and Animal Nutrition. 99:1003–1016.
3.Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Walter, P. 2002a. Innate immunity. In Molecular Biology of the Cell. 4th edition. Garland Science.
4.Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Walter, P. 2002b. Transport from the Trans Golgi Network to the cell exterior: Exocytosis. In Molecular Biology of the Cell. 4th edition. Garland Science.
5.Almeida, R.A., Luther, D.A., Park, H.M. and Oliver, S.P. 2006. Identification, isolation, and partial characterization of a novel Streptococcus uberis adhesion molecule (SUAM). Veterinary Microbiology. 115:183-191.
6.Almeida, R.A. and Oliver, S.P. 1993. Antiphagocytic effect of the capsule of Streptococcus uberis. Journal of Veterinary Medicine, Series B. 40:707-714.
7.Ayoub, I.A., Bendel, R.B. and Yang, T.J. 1996. Increase in the proportion of CD4+ T lymphocytes and the levels of transforming growth factor-β in the milk of mastitic cows. Immunology and Infectious Diseases. 6:145-150.
8.Bakhtiarizadeh, M.R., Mirzaei, S., Norouzi, M., Sheybani, N. and Vafaei Sadi, M.S. 2020. Identification of gene modules and hub genes involved in mastitis development using a systems biology approach. Frontiers in Genetics. 11:1–16.
9.Barber, M.R. and Yang, T.J. 1998. Chemotactic activities in nonmastitic and mastitic mammary secretions: Presence of interleukin-8 in mastitic but not nonmastitic secretions. Clinical and Diagnostic Laboratory Immunology. 5:82-86.
10.Barman, S., Adhikary, L., Chakrabarti, A.K., Bernas, C., Kawaoka, Y. and Nayak, D.P. 2004. Role of transmembrane domain and cytoplasmic tail amino acid sequences of influenza a virus veuraminidase in Raft association and virus budding. Journal of Virology. 78:5258-5269.
11.Bindea, G., Galon, J. and Mlecnik, B. 2013. CluePedia Cytoscape plugin: Pathway insights using integrated experimental and in silico data. Bioinformatics. 29:661–663.
13.Bloch, D.B., Nakajima, A., Gulick, T., Chiche, J.D., Orth, D., de la Monte, S.M. and Bloch, K.D. 2000. Sp110 localizes to the PML-Sp100 nuclear body and may function as a nuclear hormone receptor transcriptional coactivator. Molecular and Cellular Biology. 20:6138-6146.
14.Brøndum, R.F., Su, G., Lund, M.S., Bowman, P.J., Goddard, M.E. and Hayes, B.J. 2012. Genome position specific priors for genomic prediction. BMC Genomics. 13:1-11.
15.Cahuascanco, B., Bahamonde, J., Huaman, O., Jervis, M., Cortez, J., Palomino, J., Escobar, A., Retamal, P., Torres, C.G. and Peralta, O.A. 2019. Bovine fetal mesenchymal stem cells exert antiproliferative effect against mastitis causing pathogen Staphylococcus aureus. Veterinary Research. 50:1-10.
16.Cai, Z., Guldbrandtsen, B., Lund, M.S. and Sahana, G. 2018. Prioritizing candidate genes post-GWAS using multiple sources of data for mastitis resistance in dairy cattle. BMC Genomics. 19:1-11.
17.Carneiro, L.C., Cronin, J.G. and Sheldon, I.M. 2016. Mechanisms linking bacterial infections of the bovine endometrium to disease and infertility. Reproductive Biology. 16:1-7.
18.Chang, S.T., Tchitchek, N., Ghosh, D., Benecke, A. and Katze, M.G. 2011. A chemokine gene expression signature derived from meta-analysis predicts the pathogenicity of viral respiratory infections. BMC Systems Biology. 5:1-11.
19.Chopra, A., Ali, S.A., Bathla, S., Rawat, P., Vohra, V., Kumar, S. and Mohanty, A.K. 2020. High-resolution mass spectrometer–based ultra-deep profile of milk whey proteome in Indian Zebu (Sahiwal) cattle. Frontiers in Nutrition. 7.
20.Cole, J.B., Wiggans, G.R., Ma, L., Sonstegard, T.S., Lawlor, T.J., Crooker, B.A., Van Tassell, C.P., Yang, J., Wang, S., Matukumalli, L.K. and Da, Y. 2011. Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows. BMC Genomics. 12:1–17.
21.Dego, O.K., Van Dijk, J.E. and Nederbragt, H. 2002. Factors involved in the early pathogenesis of bovine Staphylococcus aureus mastitis with emphasis on bacterial adhesion and invasion. A review. Veterinary Quarterly. 24:181-198.
22.Durán, A.M., Román, P.S.I., Ruiz, L.F.J., González, P.E., Vásquez, P.C.G., Bagnato, A. and Strillacci, M.G. 2017. Genome-wide association study for milk somatic cell score in holstein cattle using copy number variation as markers. Journal of Animal Breeding and Genetics. 134:49–59.
23.Gerros, T.C., Semrad, S.D., Proctor, R.A. and LaBorde, A. 1993. Effect of dose and method of administration of endotoxin on cell mediator release in neonatal calves. American Journal of Veterinary Research. 54:2121-2127.
24.Gruver, A.L., Hudson, L.L. and Sempowski, G.D. 2007. Immunosenescence of ageing. Journal of Pathology. 211:144-156.
25.Guma, M., Ronacher, L., Liu-Bryan, R., Takai, S., Karin, M. and Corr, M. 2009. Caspase 1-independent activation of interleukin-1β in neutrophil-predominant inflammation. Arthritis and Rheumatism: Official Journal of the American College of Rheumatology. 60:3642-3650.
26.Han, B., Wang, L., Wei, M., Rajani, C., Yang, H., Xie, G. and Jia, W. 2020. Fructose fuels tumor growth through the polyol pathway and GLUT 8 transporter. bioRxiv.
27.Haron, A.W., Abdullah, F.F.J., Tijjani, A., Abba, Y., Adamu, L., Mohammed, K., Amir, A.M.M., Sadiq, M.A. and Lila, M.A.M. 2014. The use of Na+ and K+ ion concentrations as potential diagnostic indicators of subclinical mastitis in dairy cows. Veterinary World. 7.
28.Heringstad, B., Klemetsdal, G. and Ruane, J. 2000. Selection for mastitis resistance in dairy cattle: A review with focus on the situation in the Nordic countries. Livestock Production Science. 64:95-106.
29.Hibbitt, K.G. and Benians, M. 1971. Some effects in vivo of the teat canal and effects in vitro of cationic proteins on Staphylococci. Microbiology. 68:123-128.
30.Hou, P., Zhao, G., He, C., Wang, H. and He, H. 2018. Biopanning of polypeptides binding to bovine ephemeral fever virus G1 protein from phage display peptide library. BMC Veterinary Research. 14:1-9.
31.Hsu, K.S. and Kao, H.Y. 2018. PML: Regulation and multifaceted function beyond tumor suppression. Journal of Cell and Bioscience. 8:1-21.
32.Hur, J.H., Lee, S.H., Kim, A.Y. and Koh, Y.H. 2018. Regulation of synaptic architecture and synaptic vesicle pools by nervous wreck at drosophila type 1b glutamatergic synapses. Journal of Experimental and Molecular Medicine. 50:462.
33.Ibeagha-Awemu, E.M., Peters, S.O., Akwanji, K.A., Imumorin, I.G. and Zhao, X. 2016. High density genome wide genotyping-by-sequencing and association identifies common and low frequency SNPs, and novel candidate genes influencing cow milk traits. Scientific Reports. 6:1–18.
34.Imtiyaz, H.Z. and Simon, M.C. 2010. Hypoxia-inducible factors as essential regulators of inflammation. Diverse Effects of Hypoxia on Tumor Progression. 105-120.
35.Jiang, J., Ma, L., Prakapenka, D., VanRaden, P.M., Cole, J.B. and Da, Y. 2019. A large-scale genome-wide association study in U.S. Holstein cattle. Journal of Frontiers in Genetics. 10:412.
36.Jinquan, T., Deleuran, B., Gesser, B., Maare, H., Deleuran, M., Larsen, C.G. and Thestrup-Pedersen, K. 1995. Regulation of human T lymphocyte chemotaxis in vitro by T cell-derived cytokines IL-2, IFN-γ, IL-4, IL-10, and IL-13. Journal of Immunology. 154:742-3752.
37.Jóźwik, A., Krzyzewski, J., Strzałkowska, N., Poławska, E., Bagnicka, E., Wierzbicka, A., Niemczuk, K., Lipińska, P. and Horbańczuk, J.O. 2012. Relations between the oxidative status, mastitis, milk quality and disorders of reproductive functions in dairy cows - A review. Journal of Animal Science Papers and Reports. 30:297-307.
38.Kasama, T., Strieter, R.M., Lukacs, N.W., Burdick, M.D. and Kunkel, S.L. 1994. Regulation of neutrophil-derived chemokine expression by IL-10. Journal of Immunology. 152:3559-3569.
39.Keen, P.M., Waterman, A.E. and Bourne, F.J. 1988. Oxygen concentration in milk of healthy and mastitic cows and implications of low oxygen tension for the killing of Staphylococcus aureus by bovine neutrophils. Journal of Dairy Science. 55:513-519.
40.Khatkar, M.S., Thomson, P.C., Tammen, I. and Raadsma, H.W. 2004. Quantitative trait loci mapping in dairy cattle: Review and meta-analysis. Genetics Selection Evolution. 36:163-190.
41.Lee, Y.S., Hwang, S.G., Kim, J.K., Park, T.H., Kim, Y.R., Myeong, H.S., Choi, J.D., Kwon, K., Jang, C.S., Ro, Y.T., Noh, Y.H. and Kim, S.Y. 2016. Identification of novel therapeutic target genes in acquired lapatinib-resistant breast cancer by integrative meta-analysis. Tumor Biology. 37:2285-2297.
42.Li, H., Li, T., Guo, Y., Li, Y., Zhang, Y., Teng, N., Zhang, F. and Yang, G. 2018. Molecular characterization and expression patterns of a non-mammalian toll-like receptor gene (TLR21) in larvae ontogeny of common carp (Cyprinus carpio L.) and upon immune stimulation. BMC Veterinary Research. 14:1-9.
43.Lingwood, D. and Simons, K. 2010. Lipid rafts as a membrane-organizing principle. Science. 327:46-50.
44.Marete, A., Sahana, G., Fritz, S., Lefebvre, R., Barbat, A., Lund, M.S., Guldbrandtsen, B. and Boichard, D. 2018. Genome-wide association study for milking speed in French Holstein cows. Journal of Dairy Science. 101:6205–6219.
45.Meredith, B.K., Berry, D.P., Kearney, F., Finlay, E.K., Fahey, A.G., Bradley, D.G. and Lynn, D.J. 2013. A genome-wide association study for somatic cell score using the Illumina high-density bovine beadchip identifies several novel QTL potentially related to mastitis susceptibility. Frontiers in Genetics. 4:1–10.
46.Meredith, B.K., Kearney, F.J., Finlay, E.K., Bradley, D.G., Fahey, A.G., Berry, D.P. and Lynn, D.J. 2012. Genome-wide associations for milk production and somatic cell score in Holstein-Friesian cattle in Ireland. BMC Genetics. 13:1-11.
47.Milanino, R., Cassini, A., Conforti, A., Franco, L., Marrella, M., Moretti, U. and Velo, G.P. 1986. Copper and zinc status during acute inflammation: studies on blood, liver and kidneys metal levels in normal and inflamed rats. Journal of Agents and Actions. 19:215-223.
48.Moretti, R., Soglia, D., Chessa, S., Sartore, S., Finocchiaro, R., Rasero, R. and Sacchi, P. 2021. Identification of SNPs associated with somatic cell score in candidate genes in italian holstein friesian bulls. Animals. 11:336.
49.Nichols, B. 2003. Caveosomes and endocytosis of lipid rafts. Journal of Cell Science. 116:4707-4714.
50.Ohtsuka, H., Terasawa, S., Watanabe, C., Kohiruimaki, M., Mukai, M., Ando, T., Petrovski, K.R. and Morris, S. 2010. Effect of parity on lymphocytes in peripheral blood and colostrum of healthy holstein dairy cows. Canadian Journal of Veterinary Research. 74:130-135.
51.Oliver, S.P., Almeida, R.A. and Calvinho, L.F. 1998. Virulence factors of Streptococcus uberis isolated from cows with mastitis. Journal of Veterinary Medicine. 45:461-471.
52.Paape, M.J., Bannerman, D.D., Zhao, X. and Lee, J.W. 2003. The bovine neutrophil: Structure and function in blood and milk. Veterinary Research. 34:597-627.
53.Patel, D., Almeida, R.A., Dunlap, J.R. and Oliver, S.P. 2009. Bovine lactoferrin serves as a molecular bridge for internalization of Streptococcus uberis into bovine mammary epithelial cells. Journal of Veterinary Microbiology. 137:297-301.
54.Payankaulam, S., Raicu, A.M. and Arnosti, D.N. 2019. Transcriptional regulation of INSR, the insulin receptor gene. Genes. 10:984.
55.Pennings, J.L.A., Kimman, T.G. and Janssen, R. 2008. Identification of a common gene expression response in different lung inflammatory diseases in rodents and macaques. PLoS ONE. 3:2596.
56.Picker, L.J. 1994. Control of lymphocyte homing. Current Opinion in Immunology. 6:394–406.
57.Ramasamy, A., Mondry, A., Holmes, C.C. and Altman, D.G. 2008. Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Medicine. 5: e184.
58.Rung, J. and Brazma, A. 2013. Reuse of public genome-wide gene expression data. Nature Reviews Genetics. 14:89-99.
59.Sahana, G., Guldbrandtsen, B., Thomsen, B., Holm, L.E., Panitz, F., Brøndum, R.F., Bendixen, C. and Lund, M.S. 2014. Genome-wide association study using high-density single nucleotide polymorphism arrays and whole-genome sequences for clinical mastitis traits in dairy cattle. Journal of Dairy Science. 97:7258–7275.
60.Sarif, A. and Muhammad, G. 2008. Somatic cell count as an indicator of udder health status under modern dairy production: A review. Pakistan Veterinary Journal. 28:194–200.
61.Schukken, Y.H., Günther, J., Fitzpatrick, J., Fontaine, M.C., Goetze, L., Holst, O., Leigh, J., Petzl, W., Schuberth, H.J., Sipka, A. and Smith, D.G.E. 2011. Host-response patterns of intramammary infections in dairy cows. Veterinary immunology and immunopathology. 144:270-289.
62.Shah, M., Patel, K., Fried, V.A. and Sehgal, P.B. 2002. Interactions of STAT3 with caveolin-1 and heat shock protein 90 in plasma membrane raft and cytosolic complexes: Preservation of cytokine signaling during fever. Journal of Biological Chemistry. 277: 45662-45669.
63.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.
64.Sharifi, S., Pakdel, A. and Ebrahimi, E. 2017. Meta-analysis of transcriptomic data of mammary gland infected by Escherichia coli Bacteria in dairy cows. Iranian Journal of Animal Science. 48:343-352.
65.Shennan, D.B. 1998. Mammary gland membrane transport systems. Journal of Mammary Gland Biology and Neoplasia. 3:247–258.
66.Shennan, D.B. and Peaker, M. 2000. Transport of milk constituents by the mammary gland. Physiological Reviews. 80:925–951.65.
67.Shirasuna, K. and Iwata, H. 2017. Effect of aging on the female reproductive function. Journal of Contraception and Reproductive Medicine. 2:1-8.
68.Smaragdov, M.G. 2006. Genetic mapping of loci responsible for milk production traits in dairy cattle. Russian Journal of Genetics. 42:1-15.
69.Smith, D.A. 2019. The sliding-filament theory of muscle contraction. Springer International Publishing.
70.Song, M.J., Kim, K.H., Yoon, J.M. and Kim, J.B. 2006. Activation of Toll-like receptor 4 is associated with insulin resistance in adipocytes. Biochemical and Biophysical Research Communications. 346:739-745.
71.Strillacci, M.G., Frigo, E., Schiavini, F., Samoré, A.B., Canavesi, F., Vevey, M., Cozzi, M.C., Soller, M., Lipkin, E. and Bagnato, A. 2014. Genome-wide association study for somatic cell score in Valdostana Red Pied cattle breed using pooled DNA. BMC Genetics. 15:1-10.
72.Triantafilou, M., Morath, S., Mackie, A., Hartung, T. and Triantafilou, K. 2004. Lateral diffusion of Toll-like receptors reveals that they are transiently confined within lipid rafts on the plasma membrane. Journal of Cell Science. 117:4007-4014.
73.Turrigiano, G.G. 2008. The self-tuning neuron: synaptic scaling of excitatory synapses. Cell. 135:422-435.
74.Van den Heuvel-Eibrink, M.M., Wiemer, E.A.C., Kuijpers, M., Pieters, R. and Sonneveld, P. 2001. Absence of mutations in the deoxycytidine kinase (dCK) gene in patients with relapsed and/or refractory acute myeloid leukemia (AML). Leukemia. 15:855–856.
75.Vaught, D., Chen, J. and Brantley-Sieders, D.M. 2009. Regulation of mammary gland branching morphogenesis by EphA2 receptor tyrosine kinase. Journal of Molecular Biology of the Cell. 20:2572-2581.
76.Wang, D., Meng, Q., Huo, L., Yang, M., Wang, L., Chen, X., Wang, J., Li, Z., Ye, X., Liu, N., Li, Q., Dai, Z., Ouyang, H., Li, N., Zhou, J., Chen, L. and Liu, L. 2015. Overexpression of Hdac6 enhances resistance to virus infection in embryonic stem cells and in mice. Journal of Protein and Cell. 6:152-156.
77.Wang, M., Moisá, S., Khan, M.J., Wang, J., Bu, D. and Loor, J.J. 2012. MicroRNA expression patterns in the bovine mammary gland are affected by stage of lactation. Journal of Dairy Science. 95:6529-6535.
78.Wang, X., Ma, P., Liu, J., Zhang, Q., Zhang, Yuan, Ding, X., Jiang, L., Wang, Y., Zhang, Yi, Sun, D., Zhang, S., Su, G. and Yu, Y. 2015. Genome-wide association study in Chinese Holstein cows reveal two candidate genes for somatic cell score as an indicator for mastitis susceptibility. BMC Genetics. 16:1–9.
80.Wu, X., Lund, M.S., Sahana, G., Guldbrandtsen, B., Sun, D., Zhang, Q. and Su, G. 2015. Association analysis for udder health based on SNP-panel and sequence data in Danish Holsteins. Journal of Genetics Selection Evolution. 47:1-14.
81.Xu, W., Huang, H., Yu, L. and Cao, L. 2015. Meta-analysis of gene expression profiles indicates genes in spliceosome pathway are up-regulated in hepatocellular carcinoma (HCC). Journal of Medical Oncology. 32:96.
82.Yue, S.J., Zhao, Y.Q., Gu, X.R., Yin, B., Jiang, Y.L., Wang, Z.H. and Shi, K.R. 2017. A genome-wide association study suggests new candidate genes for milk production traits in Chinese Holstein cattle. Journal of Animal Genetics. 48: 677–681.
83.Zarrin, M., Ahmadpour, A. and Bruckmaier, R.M. 2019. Interaction effect of insulin infusion and induced mastitis by lipopolysaccharide on glucose metabolism and glucagon hormone secretion in dairy cows. Animal Production Research. 8.
84.Zhang, L., Wu, Z.Q., Wang, Y.J., Wang, M. and Yang, W.C. 2020. MiR-143 regulates milk fat synthesis by targeting smad3 in bovine mammary epithelial cells. Animals. 10:1453.
85.Zhao, G., Wang, H., Hou, P., He, C. and He, H. 2018. Rapid visual detection of Mycobacterium avium subsp. paratuberculosis by recombinase polymerase amplification combined with a lateral flow dipstick. Journal of Veterinary Science. 19:242.
)