High-throughput analysis of CircRNA in cows with naturally infected Staphylococcus aureus mammary gland

References

• El-Ashker M, Gwida M, Monecke S, et al. Antimicrobial resistance pattern and virulence profile of S. aureus isolated from household cattleand buffalo with mastitis in Egypt. Vet Microbiol. 2020;240:108535.
   PubMed Web of Science ®Google Scholar
• Monistero V1, Barberio A2, Biscarini F, et al. Different distribution of antimicrobial resistance genes and virulence profiles of Staphylococcus aureus strains isolated from clinical mastitis in six countries. J Dairy Sci. 2020;103(4):3431–3446.
   PubMed Web of Science ®Google Scholar
• Cai J, Li J, Zhou Y, et al. Staphylococcus aureus facilitates its survival in bovine macrophages by blocking autophagic flux. J Cell Mol Med. 2020;24(6):3460–3468.
   PubMed Web of Science ®Google Scholar
• Botaro BG, Cortinhas CS, Dibbern AG, et al. Staphylococcus aureus intramammary infection affects milk yield and SCC of dairy cows. Trop Anim Health Prod. 2015;47(1):61–66.
   PubMed Web of Science ®Google Scholar
• Gomes F, Henriques M. Control of bovine mastitis: old and recent therapeutic approaches. Curr Microbiol. 2016;72(4):377–382.
   PubMed Web of Science ®Google Scholar
• Hogeveen H, Huijps K, Lam T. Economic aspects of mastitis: new developments. N Z Vet J. 2011;59(1):16–23.
   PubMed Web of Science ®Google Scholar
• Johler S, Tichaczek-Dischinger PS, Rau J, et al. Outbreak of Staphylococcal food poisoning due to SEA-producing Staphylococcus aureus. Foodborne Pathog Dis. 2013;10(9):777–781.
   PubMed Web of Science ®Google Scholar
• Li C, Li L, Chen K, et al. UFL1 alleviates lipopolysaccharide-induced cell damage and inflammation via regulation of the TLR4/NF-κB pathway in bovine mammary epithelial cells. Oxid Med Cell Long. 2019;2019:1–17.
   Web of Science ®Google Scholar
• Li B, Xi P, Wang Z, et al. PI3K/Akt/mTOR signaling pathway participates in Streptococcus uberis-induced inflammation in mammary epithelial cells in concert with the classical TLRs/NF-ĸB pathway. Vet Microbiol. 2018;227:103–111.
   PubMed Web of Science ®Google Scholar
• Zhang X, Wang Y, Xiao C, et al. Resveratrol inhibits LPS-induced mice mastitis through attenuating the MAPK and NF-κB signaling pathway. Microb Pathog. 2017;107:462–467.
   PubMed Web of Science ®Google Scholar
• Cocquerelle C, Mascrez B, Hétuin D, Bailleul B. Mis-splicing yields circular RNA molecules. Faseb J. 1993;7(1):155–160.
   PubMed Web of Science ®Google Scholar
• Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495(7441):333–338.
   PubMed Web of Science ®Google Scholar
• Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. Cell-type specific features of circular RNA expression. PLoS Genet. 2013;9(9):e1003777.
   PubMed Web of Science ®Google Scholar
• Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One. 2012;7(2):e30733.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Zhang XO, Chen T, et al. Circular intronic long noncoding RNAs. Mol Cell. 2013;51(6):792–806.
   PubMed Web of Science ®Google Scholar
• Ebert MS, Neilson JR, Sharp PA. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods. 2007;4(9):721–726.
   PubMed Web of Science ®Google Scholar
• Guo JU, Agarwal V, Guo H, Bartel DP. Expanded identification and characterization of mammalian circular RNAs. Genome Biol. 2014;15(7):409.
   PubMed Web of Science ®Google Scholar
• Hansen TB, Jensen TI, Clausen BH, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495(7441):384–388.
   PubMed Web of Science ®Google Scholar
• Nair AA, Niu N, Tang X, et al. Circular RNAs and their associations with breast cancer subtypes. Oncotarget. 2016;7(49):80967–80979.
   PubMedGoogle Scholar
• Yang R, Xing L, Zheng X, et al. The circRNA circAGFG1 acts as a sponge of miR-195-5p to promote triple-negative breast cancer progression through regulating CCNE1 expression. Mol Cancer. 2019;18(1):4.
   PubMed Web of Science ®Google Scholar
• Zhang HD, Jiang LH, Sun DW, et al. CircRNA: a novel type of biomarker for cancer. Breast Cancer. 2018;25(1):1–7.
   PubMed Web of Science ®Google Scholar
• Li P, Chen S, Chen H, et al. Using circular RNA as a novel type of biomarker in the screening of gastric cancer. Clin Chim Acta. 2015;444:132–136.
   PubMed Web of Science ®Google Scholar
• Dong Y, Xie M, Jiang Y, et al. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol. 2013;31(2):135–141.
   PubMed Web of Science ®Google Scholar
• Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7(3):562–578.
   PubMed Web of Science ®Google Scholar
• Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016;11(9):1650–1667.
   PubMed Web of Science ®Google Scholar
• Zhang X-O, Dong R, Zhang Y, et al. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016;26(9):1277–1287.
   PubMed Web of Science ®Google Scholar
• Frazee AC, Pertea G, Jaffe AE, et al. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat Biotechnol. 2015;33(3):243–246.
   PubMed Web of Science ®Google Scholar
• Robinson MD, Mccarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–140.
   PubMed Web of Science ®Google Scholar
• Xie C, Mao X, Huang J, et al. Kobas 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 2011;39(Web Server issue):W316–W322.
   PubMedGoogle Scholar
• Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017;45(D1):D353–D361.
   PubMed Web of Science ®Google Scholar
• Agarwal V, Subtelny AO, Thiru P, Ulitsky I, Bartel DP. Predicting microRNA targeting efficacy in Drosophila. Genome Biol. 2018;19(1):152.
   PubMedGoogle Scholar
• Saito R, Smoot ME, Ono K, et al. Atravel guide to Cytoscape plugins. Nat Methods. 2012;9(11):1069–1076.
   PubMed Web of Science ®Google Scholar
• Li J, Li Q, Chen L, Gao Y, Li J. Expression profile of circular RNAs in infantile hemangioma detected by RNA-Seq. Medicine (Baltimore). 2018;97(21):e10882.
   PubMed Web of Science ®Google Scholar
• Livak KJ, Schmittgen TD. Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2− ΔΔCT Method. Methods. 2001;25(4):402–408.
   PubMed Web of Science ®Google Scholar
• Cote-Gravel J, Malouin F. Symposium review: features of Staphylococcus aureus mastitis pathogenesis that guide vaccine development strategies. J Dairy Sci. 2018;102(5):4727–4740.
   PubMed Web of Science ®Google Scholar
• Detilleux J, Kastelic JP, Barkema HW. Mediation analysis to estimate direct and indirect milk losses due to clinical mastitis in dairy cattle. Prev Vet Med. 2015;118(4):449–456.
   PubMed Web of Science ®Google Scholar
• Halasa T, Huijps K, Osteras O, Hogeveen H. Economic effects of bovine mastitis and mastitis management: a review. Vet Q. 2007;29(1):18–31.
   PubMed Web of Science ®Google Scholar
• Sadeghi-Sefidmazgi A, Moradi-Shahrbabak M, Nejati-Javaremi A, Miraei-Ashtiani SR, Amer PR. Estimation of economic values and financial losses associated with clinical mastitis and somatic cell score in Holstein dairy cattle. Animal. 2011;5(1):33–42.
   PubMed Web of Science ®Google Scholar
• Seegers H, Fourichon C, Beaudeau F. Production effects related to mastitis and mastitis economics in dairy cattle herds. Vet Res. 2003;34(5):475–491.
   PubMed Web of Science ®Google Scholar
• Ma S, Niu M, Hao Z, Liu M, Tong C, Zhao X. Selective packaged circular RNAs in milk extracellular vesicles during Staphylococcus aureus infection may have potential against bacterial infection. RNA Biol. 2021;18(5):818–831.
   PubMed Web of Science ®Google Scholar
• Sang Y, Chen B, Song X, et al. circRNA_0025202 Regulates Tamoxifen Sensitivity and Tumor Progression via Regulating the miR-182-5p/FOXO3a Axis in Breast Cancer. Mol Ther. 2019;27(9):1638–1652.
   PubMed Web of Science ®Google Scholar
• Zeng K, He B, Yang BB, et al. The pro-metastasis effect of circANKS1B in breast cancer. Mol Cancer. 2018;17(1):160.
   PubMed Web of Science ®Google Scholar
• Zheng X, Huang M, Xing L, et al. The circRNA circSEPT9 mediated by E2F1 and EIF4A3 facilitates the carcinogenesis and development of triple-negative breast cancer. Mol Cancer. 2020;19(1):73.
   PubMed Web of Science ®Google Scholar
• Sharifi S, Pakdel A, Ebrahimi M, Reecy JM, Fazeli Farsani S, Ebrahimie E. Integration of machine learning and meta-analysis identifies the transcriptomic bio-signature of mastitis disease in cattle. PLoS One. 2018;13(2):e0191227.
   PubMed Web of Science ®Google Scholar
• Fu Y, Jiang H, Liu JB, et al. Genome-wide analysis of circular RNAs in bovine cumulus cells treated with BMP15 and GDF9. Sci Rep. 2018;8(1):7944.
   PubMedGoogle Scholar
• Stelwagen K, Singh K. The role of tight junctions in mammary gland function. J Mammary Gland Biol Neoplasia. 2014;19(1):131–138.
   PubMed Web of Science ®Google Scholar
• Alhopuro P, Karhu A, Winqvist R, Waltering K, Visakorpi T, Aaltonen LA. Somatic mutation analysis of MYH11 in breast and prostate cancer. BMC Cancer. 2008;8:263.
   PubMed Web of Science ®Google Scholar
• Ai D, Yao J, Yang F, et al. TRPS1: a highly sensitive and specific marker for breast carcinoma, especially for triple-negative breast cancer. Mod Pathol. 2021;34(4):710–719.
   PubMed Web of Science ®Google Scholar
• Lin C, Xu X. YAP1-TEAD1-Glut1 axis dictates the oncogenic phenotypes of breast cancer cells by modulating glycolysis. Biomed Pharmacother. 2017;95:789–794.
   PubMed Web of Science ®Google Scholar
• Nolan J, Dunne SS, Mustafa W, Sivananthan L, Kiely PA, Dunne CP. Proposed hypothesis and rationale for association between mastitis and breast cancer. Med Hypotheses. 2020;144:110057.
   PubMed Web of Science ®Google Scholar
• Dai H, Wei G, Wang Y, Ma N, Chang G, Shen X. Sodium butyrate promotes lipopolysaccharide-induced innate immune responses by enhancing mitogen-activated protein kinase activation and histone acetylation in bovine mammary epithelial cells. J Dairy Sci. 2020;103(12):11636–11652.
   PubMed Web of Science ®Google Scholar
• LUoreng ZM, Yang J, Wang XP, Wei DW, Zan LS. Expression Profiling of microRNA From Peripheral Blood of Dairy Cows in Response to Staphylococcus aureus-Infected Mastitis. Front Vet Sci. 2021;8:691196.
   PubMed Web of Science ®Google Scholar
• Oztürk LK, Emekli-Alturfan E, Kaşikci E, Demir G, Yarat A. Salivary total sialic acid levels increase in breast cancer patients: a preliminary study. Med Chem. 2011;7(5):443–447.
   PubMed Web of Science ®Google Scholar
• Huang M, Zhong Z, Lv M, et al. Comprehensive analysis of diferentially expressed profles of lncRNAs and circRNAs with associated co-expression and ceRNA networks in bladder carcinoma. Oncotarget. 2016;7(30):47186–47200.
   PubMedGoogle Scholar
• Prajapati KS, Shuaib M, Kushwaha PP, Singh AK, Kumar S. Identification of cancer stemness related miRNA(s) using integrated bioinformatics analysis and in vitro validation. 3 Biotech. 2021;11(10):446.
   PubMedGoogle Scholar
• Revathidevi S, Manikandan M, Rao AK, et al. Analysis of APOBEC3A/3B germline deletion polymorphism in breast, cervical and oral cancers from South India and its impact on miRNA regulation. Tumour Biol. 2016;37(9):11983–11990.
   PubMedGoogle Scholar
• Tanman Ü, Yangın S, Cansaran-Duman D. Determination of dysregulated miRNA expression levels by qRT-PCR after the application of Usnic acid to breast cancer. Anticancer Agents Med Chem. 2020;20(5):548–558.
   PubMed Web of Science ®Google Scholar
• Wang XX, Ye FG, Zhang J, et al. Serum miR-4530 sensitizes breast cancer to neoadjuvant chemotherapy by suppressing RUNX2. Cancer Manag Res. 2018;10:4393–4400.
   PubMed Web of Science ®Google Scholar