Abstract
Bovine milk is rich in exosomes, which contain abundant miRNAs and play important roles in the regulation of neonatal growth and development of adaptive immunity. Here, we analyzed miRNA expression profiles of bovine milk exosomes from three healthy and three mastitic cows, and then six miRNA libraries were constructed. Interestingly, we detected no scRNAs and few snRNAs in milk exosomes; this result indicated a potential preference for RNA packaging in milk exosomes. A total of 492 known and 980 novel exosomal miRNAs were detected, and the 10 most expressed miRNAs in the six samples accounted for 80–90% of total miRNA-associated reads. Expression analyses identified 18 miRNAs with significantly different expression between healthy and infected animals; the predicted target genes of differentially expressed miRNAs were significantly enriched in immune system process, response to stimulus, growth, etc. Moreover, target genes were significantly enriched in several Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including inflammatory, immune, and cancer pathways. Our survey provided comprehensive information about milk exosomes and exosomal miRNAs involved in mastitis. Moreover, the differentially expressed miRNAs, especially miR-223 and miR-142-5p, could be considered as potential candidates for mastitis.
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Admyre C, Johansson SM, Qazi KR, Filen JJ, Lahesmaa R, Norman M, Neve EPA, Scheynius A, Gabrielsson S (2007) Exosomes with immune modulatory features are present in human breast milk. J Immunol 179(3):1969–1978. https://doi.org/10.4049/jimmunol.179.3.1969
Aline F, Bout D, Amigorena S, Roingeard P, Dimier-Poisson I (2004) Toxoplasma gondii antigen-pulsed-dendritic cell-derived exosomes induce a protective immune response against T. gondii infection. Infect Immun 72(7):4127–4137. https://doi.org/10.1128/IAI.72.7.4127-4137.2004
Andre F, Schartz NEC, Movassagh M, Flament C, Pautier P, Morice P, Pomel C, Lhomme C, Escudier B, le Chevalier T, Tursz T, Amigorena S, Raposo G, Angevin E, Zitvogel L (2002) Malignant effusions and immunogenic tumour-derived exosomes. Lancet 360(9329):295–305. https://doi.org/10.1016/S0140-6736(02)09552-1
Bannerman DD, Paape MJ, Lee J-W, Zhao X, Hope JC, Rainard P (2004) Escherichia coli and Staphylococcus aureus elicit differential innate immune responses following intramammary infection. Clin Diagn Lab Immunol 11(3):463–472. https://doi.org/10.1128/CDLI.11.3.463-472.2004
Chen C-Z, Li L, Lodish HF, Bartel DP (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science (80- ) 303:83–86. https://doi.org/10.1126/science.1091903
Chen X, Gao C, Li H, Huang L, Sun Q, Dong Y, Tian C, Gao S, Dong H, Guan D, Hu X, Zhao S, Li L, Zhu L, Yan Q, Zhang J, Zen K, Zhang CY (2010) Identification and characterization of microRNAs in raw milk during different periods of lactation, commercial fluid, and powdered milk products. Cell Res 20(10):1128–1137. https://doi.org/10.1038/cr.2010.80
Chivet M, Javalet C, Hemming F, Pernet-Gallay K, Laulagnier K, Fraboulet S, Sadoul R (2013) Exosomes as a novel way of interneuronal communication. Biochem Soc Trans 41(1):241–244. https://doi.org/10.1042/BST20120266
De Schepper S, De Ketelaere A, Bannerman DD, Paape MJ, Peelman L, Burvenich C (2008) The toll-like receptor-4 (TLR-4) pathway and its possible role in the pathogenesis of Escherichia coli mastitis in dairy cattle. Vet Res 39(1):1–23. https://doi.org/10.1051/vetres:2007044
DeGraves FJ, Fetrow J (1993) Economics of mastitis and mastitis control. Vet Clin North Am Food Anim Pract 9(3):421–434. https://doi.org/10.1016/S0749-0720(15)30611-3
Dilda F, Gioia G, Pisani L, Restelli L, Lecchi C, Albonico F, Bronzo V, Mortarino M, Ceciliani F (2012) Escherichia coli lipopolysaccharides and Staphylococcus aureus enterotoxin B differentially modulate inflammatory microRNAs in bovine monocytes. Vet J 192(3):514–516. https://doi.org/10.1016/j.tvjl.2011.08.018
Elsarraj HS, YH KV, Carletti M, Salah SM, Raimo M, Taverna D, Prochasson P, Bharadwaj U, Tweardy DJ, Christenson LK, Behbod F (2013) A novel role of microRNA146b in promoting mammary alveolar progenitor cell maintenance. J Cell Sci 126(11):2446–2458. https://doi.org/10.1242/jcs.119214
Fazi F, Rosa A, Fatica A, Gelmetti V, De Marchis ML, Nervi C, Bozzoni I (2005) A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPα regulates human granulopoiesis. Cell 123(5):819–831. https://doi.org/10.1016/j.cell.2005.09.023
Février B, Raposo G (2004) Exosomes: endosomal-derived vesicles shipping extracellular messages. Curr Opin Cell Biol 16(4):415–421. https://doi.org/10.1016/j.ceb.2004.06.003
Fu X, Shen Y, Wang W, Li X (2017) MiR-30a-5p ameliorates spinal cord injury-induced inflammatory responses and oxidative stress by targeting Neurod 1 through MAPK/ERK signaling. Clin Exp Pharmacol Physiol 45(1):68–74. https://doi.org/10.1111/1440-1681.12856
Gatti J-L, Métayer S, Belghazi M, Dacheux F, Dacheux J-L (2005) Identification, proteomic profiling, and origin of ram epididymal fluid exosome-like vesicles 1. Biol Reprod 72(6):1452–1465. https://doi.org/10.1095/biolreprod.104.036426
Gu Y, Li M, Wang T, Liang Y, Zhong Z, Wang X, Zhou Q, Chen L, Lang Q, He Z, Chen X, Gong J, Gao X, Li X, Lv X (2012) Lactation-related microRNA expression profiles of porcine breast milk exosomes. PLoS One 7(8):e43691. https://doi.org/10.1371/journal.pone.0043691
Guduricfuchs J et al (2012) Deep sequencing reveals predominant expression of miR-21 amongst the small non-coding RNAs in retinal microvascular endothelial cells. J Cell Biochem 113(6):2098–2111. https://doi.org/10.1002/jcb.24084
Hessvik NP, Phuyal S, Brech A, Sandvig K, Llorente A (2012) Profiling of microRNAs in exosomes released from PC-3 prostate cancer cells. Biochim Biophys Acta 1819(11-12):1154–1163. https://doi.org/10.1016/j.bbagrm.2012.08.016
Janas T, Janas MM, Sapoń K, Janas T (2015) Mechanisms of RNA loading into exosomes. FEBS Lett 589(13):1391–1398. https://doi.org/10.1016/j.febslet.2015.04.036
Jiang K et al (2017) MicroRNA-1468-5p inhibits glioma cell proliferation and induces cell cycle arrest by targeting RRM1. Am J Cancer Res 7:784
Jin W, Ibeagha-Awemu EM, Liang G, Beaudoin F, Zhao X (2014) Transcriptome microRNA profiling of bovine mammary epithelial cells challenged with Escherichia coli or Staphylococcus aureus bacteria reveals pathogen directed microRNA expression profiles. BMC Genomics 15(1):181. https://doi.org/10.1186/1471-2164-15-181
Kirsty J et al (2013) Escherichia coli- and Staphylococcus aureus-induced mastitis differentially modulate transcriptional responses in neighbouring uninfected bovine mammary gland quarters. BMC Genomics 14(1):36. https://doi.org/10.1186/1471-2164-14-36
Kolhe R, Hunter M, Liu S, Jadeja RN, Pundkar C, Mondal AK, Mendhe B, Drewry M, Rojiani MV, Liu Y, Isales CM, Guldberg RE, Hamrick MW, Fulzele S (2017) Gender-specific differential expression of exosomal miRNA in synovial fluid of patients with osteoarthritis. Sci Rep 7(1):2029. https://doi.org/10.1038/s41598-017-01905-y
Kowal J, Arras G, Colombo M, Jouve M, Morath JP, Primdal-Bengtson B, Dingli F, Loew D, Tkach M, Théry C (2016) Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes. Proc Natl Acad Sci 113(8):E968–E977. https://doi.org/10.1073/pnas.1521230113
Kumar D, Gupta D, Shankar S, Srivastava RK (2015) Biomolecular characterization of exosomes released from cancer stem cells: possible implications for biomarker and treatment of cancer. Oncotarget 6(5):3280–3291. https://doi.org/10.18632/oncotarget.2462
Lawless N, Foroushani AB, McCabe MS, O’Farrelly C, Lynn DJ (2013) Next generation sequencing reveals the expression of a unique miRNA profile in response to a gram-positive bacterial infection. PLoS One 8(3):e57543. https://doi.org/10.1371/journal.pone.0057543
Levänen B, Bhakta NR, Torregrosa Paredes P, Barbeau R, Hiltbrunner S, Pollack JL, Sköld CM, Svartengren M, Grunewald J, Gabrielsson S, Eklund A, Larsson BM, Woodruff PG, Erle DJ, Wheelock ÅM (2013) Altered microRNA profiles in bronchoalveolar lavage fluid exosomes in asthmatic patients. J Allergy Clin Immunol 131(3):894–903.e8. https://doi.org/10.1016/j.jaci.2012.11.039
Li R, Zhang CL, Liao XX, Chen D, Wang WQ, Zhu YH, Geng XH, Ji DJ, Mao YJ, Gong YC, Yang ZP (2015) Transcriptome microRNA profiling of bovine mammary glands infected with Staphylococcus aureus. Int J Mol Sci 16(3):4997–5013. https://doi.org/10.3390/ijms16034997
Liao J, Liu R, Yin L, Pu Y (2014) Expression profiling of exosomal miRNAs derived from human esophageal cancer cells by Solexa high-throughput sequencing. Int J Mol Sci 15(9):15530–15551. https://doi.org/10.3390/ijms150915530
Lv L-L, Cao YH, Ni HF, Xu M, Liu D, Liu H, Chen PS, Liu BC (2013) MicroRNA-29c in urinary exosome/microvesicle as a biomarker of renal fibrosis. Am J Physiol Renal Physiol 305(8):F1220–F1227. https://doi.org/10.1152/ajprenal.00148.2013
Michael A, Bajracharya S, Yuen P, Zhou H, Star R, Illei G, Alevizos I (2010) Exosomes from human saliva as a source of microRNA biomarkers. Oral Dis 16(1):34–38. https://doi.org/10.1111/j.1601-0825.2009.01604.x
Mittelbrunn M, Gutiérrez-Vázquez C, Villarroya-Beltri C, González S, Sánchez-Cabo F, González MÁ, Bernad A, Sánchez-Madrid F (2011) Unidirectional transfer of microRNA-loaded exosomes from T cells to antigen-presenting cells. Nat Commun 2:282. https://doi.org/10.1038/ncomms1285
Munagala R, Aqil F, Jeyabalan J, Gupta RC (2016) Bovine milk-derived exosomes for drug delivery. Cancer Lett 371(1):48–61. https://doi.org/10.1016/j.canlet.2015.10.020
Naeem A, Zhong K, Moisá S, Drackley J, Moyes K, Loor J (2012) Bioinformatics analysis of microRNA and putative target genes in bovine mammary tissue infected with Streptococcus uberis. J Dairy Sci 95(11):6397–6408. https://doi.org/10.3168/jds.2011-5173
Pêche H, Heslan M, Usal C, Amigorena S, Cuturi MC (2003) Presentation of donor major histocompatibility complex antigens by bone marrow dendritic cell-derived exosomes modulates allograft rejection1. Transplantation 76(10):1503–1510. https://doi.org/10.1097/01.TP.0000092494.75313.38
Pisitkun T, Shen RF, Knepper MA (2004) Identification and proteomic profiling of exosomes in human urine. Proc Natl Acad Sci U S A 101(36):13368–13373. https://doi.org/10.1073/pnas.0403453101
Porstner M, Winkelmann R, Daum P, Schmid J, Pracht K, Côrte-Real J, Schreiber S, Haftmann C, Brandl A, Mashreghi MF, Gelse K, Hauke M, Wirries I, Zwick M, Roth E, Radbruch A, Wittmann J, Jäck HM (2015) miR-148a promotes plasma cell differentiation and targets the germinal center transcription factors Mitf and Bach2. Eur J Immunol 45(4):1206–1215. https://doi.org/10.1002/eji.201444637
Raposo G, Nijman HW, Stoorvogel W, Liejendekker R, Harding CV, Melief CJ, Geuze HJ (1996) B lymphocytes secrete antigen-presenting vesicles. J Exp Med 183(3):1161–1172. https://doi.org/10.1084/jem.183.3.1161
Rossol M, Heine H, Meusch U, Quandt D, Klein C, Sweet MJ, Hauschildt S (2011) LPS-induced cytokine production in human monocytes and macrophages. Crit Rev Immunol 31(5):379–446. https://doi.org/10.1615/CritRevImmunol.v31.i5.20
Saunderson SC, Dunn AC, Crocker PR, McLellan AD (2014) CD169 mediates the capture of exosomes in spleen and lymph node. Blood 123(2):208–216. https://doi.org/10.1182/blood-2013-03-489732
Skog J, Würdinger T, van Rijn S, Meijer DH, Gainche L, Sena-Esteves M, Curry WT Jr, Carter BS, Krichevsky AM, Breakefield XO (2008) Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers. Nat Cell Biol 10(12):1470–1476. https://doi.org/10.1038/ncb1800
Sun W, Shen W, Yang S, Hu F, Li H, Zhu T-H (2010) miR-223 and miR-142 attenuate hematopoietic cell proliferation, and miR-223 positively regulates miR-142 through LMO2 isoforms and CEBP-β. Cell Res 20(10):1158–1169. https://doi.org/10.1038/cr.2010.134
Sun J, Aswath K, Schroeder SG, Lippolis JD, Reinhardt TA, Sonstegard TS (2015) MicroRNA expression profiles of bovine milk exosomes in response to Staphylococcus aureus infection. BMC Genomics 16(1):806. https://doi.org/10.1186/s12864-015-2044-9
Taganov KD, Boldin MP, Chang KJ, Baltimore D (2006) NF-κB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses. Proc Natl Acad Sci U S A 103(33):12481–12486. https://doi.org/10.1073/pnas.0605298103
Teng GG, Wang WH, Dai Y, Wang SJ, Chu YX, Li J (2013) Let-7b is involved in the inflammation and immune responses associated with Helicobacter pylori infection by targeting Toll-like receptor 4. PLoS One 8(2):e56709. https://doi.org/10.1371/journal.pone.0056709
Thomou T, Mori MA, Dreyfuss JM, Konishi M, Sakaguchi M, Wolfrum C, Rao TN, Winnay JN, Garcia-Martin R, Grinspoon SK, Gorden P, Kahn CR (2017) Adipose-derived circulating miRNAs regulate gene expression in other tissues. Nature 542(7642):450–455. https://doi.org/10.1038/nature21365
Torregrosa Paredes P, Gutzeit C, Johansson S, Admyre C, Stenius F, Alm J, Scheynius A, Gabrielsson S (2014) Differences in exosome populations in human breast milk in relation to allergic sensitization and lifestyle. Allergy 69(4):463–471. https://doi.org/10.1111/all.12357
Valadi H, Ekström K, Bossios A, Sjöstrand M, Lee JJ, Lötvall JO (2007) Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol 9(6):654–659. https://doi.org/10.1038/ncb1596
Wahlgren J, Karlson TDL, Brisslert M, Sani FV, Telemo E, Sunnerhagen P, Valadi H (2012) Plasma exosomes can deliver exogenous short interfering RNA to monocytes and lymphocytes. Nucleic Acids Res 40(17):e130. https://doi.org/10.1093/nar/gks463
Wang H, Hou L, Li A, Duan Y, Gao H, Song X (2014) Expression of serum exosomal microRNA-21 in human hepatocellular carcinoma. Biomed Res Int 2014:1–5. https://doi.org/10.1155/2014/864894
Wang X, Ma P, Liu J, Zhang Q, Zhang Y, Ding X, Jiang L, Wang Y, Zhang Y, Sun D, Zhang S, Su G, 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 Genet 16(1):1–9. https://doi.org/10.1186/s12863-015-0263-3
Wang XP, Zhuo ML, Zan LS, Raza SHA, Li F, Li N, Liu S (2016) Expression patterns of miR-146a and miR-146b in mastitis infected dairy cattle. Mol Cell Probes 30(5):342–344. https://doi.org/10.1016/j.mcp.2016.08.004
Wang W, Gao J, Wang F (2017) MiR-663a/MiR-423-5p are involved in the pathogenesis of lupus nephritis via modulating the activation of NF-κB by targeting TNIP2. Am J Transl Res 9(8):3796–3803
Wieckowski E, Whiteside TL (2006) Human tumor-derived vs dendritic cell-derived exosomes have distinct biologic roles and molecular profiles. Immunol Res 36(1-3):247–254. https://doi.org/10.1385/IR:36:1:247
Zadoks RN, Middleton JR, McDougall S, Katholm J, Schukken YH (2011) Molecular epidemiology of mastitis pathogens of dairy cattle and comparative relevance to humans. J Mammary Gland Biol Neoplasia 16(4):357–372. https://doi.org/10.1007/s10911-011-9236-y
Zhou Q, Li M, Wang X, Li Q, Wang T, Zhu Q, Zhou X, Wang X, Gao X, Li X (2012) Immune-related microRNAs are abundant in breast milk exosomes. Int J Biol Sci 8(1):118–123. https://doi.org/10.7150/ijbs.8.118
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This research was supported by the Science and Technology Support Program in Sichuan (No. 2014NZ0032-A).
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SJL and MCC contributed to concept design. HBH and WDX performed the animal experiments. MCC, BWL, and YS performed the RNA and protein isolation and western blot. MCC, HBH, and XBJ performed data analysis. MCC, SYC, and JW prepared the manuscript. All authors read and approved the final manuscript.
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All experiments were carried out according to the Regulations for the Administration of Affairs Concerning Experimental Animals published by the Ministry of Science and Technology, China in 2004 and approved by the Institutional Animal Care and Use Committee of Sichuan Agricultural University, China.
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The authors declare that they have no conflict of interest.
Electronic supplementary material
Fig S1.
Distribution and classification of small RNA reads in the HH and HM. (PPT 442 kb)
Fig S2.
Comparison of the results of miRNA-sequencing and qRT-PCR. (PPT 159 kb)
Table S1.
The SCC of six Holstein cows. (XLSX 9 kb)
Table S2.
Primer sequences for qRT-PCR. (XLSX 10 kb)
Table S3.
The length and expression of miRNAs. (XLSX 10 kb)
Table S4.
The read counts and miRNA family analysis of novel miRNAs (XLSX 69 kb)
Table S5.
The expression of differentially expressed miRNAs. (XLSX 12 kb)
Table S6.
KEGG pathways of the target genes. (XLSX 10 kb)
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Cai, M., He, H., Jia, X. et al. Genome-wide microRNA profiling of bovine milk-derived exosomes infected with Staphylococcus aureus. Cell Stress and Chaperones 23, 663–672 (2018). https://doi.org/10.1007/s12192-018-0876-3
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DOI: https://doi.org/10.1007/s12192-018-0876-3