[1] Steinkraus BR, Toegel M, Fulga TA. Tiny giants of gene regulation: experimental strategies for microRNA functional studies. Wiley Interdiscip. Rev.: Dev. Biol. 2016:5;311–62.
[2] Weber JA, Baxter DH, Zhang S, Huang DY, Huang KH, Lee MJ, Galas DJ, Wang K. The microRNA spectrum in 12 body fluids. Clin. Chem. 2010:56;1733–41.
[3] Alsaweed M, Hartmann PE, Geddes DT, Kakulas F. MicroRNAs in Breastmilk and the Lactating Breast: Potential Immunoprotectors and Developmental Regulators for the Infant and the Mother. Int. J. Environ. Res. Public Health 2015;12:13981–4020.
[4] Alsaweed M, Lai CT, Hartmann PE, Geddes DT, Kakulas F. Human milk miRNAs primarily originate from the mammary gland resulting in unique miRNA profiles of fractionated milk. Sci. Rep. 2016;6:20680–92.
[5] Keller S, Sanderson MP, Stoeck A, Altevogt P. Exosomes: from biogenesis and secretion to biological function. Immunol. Lett. 2006:107;102–8.
[6] Van der Pol E, Böing AN, Harrison P, Sturk A, Nieuwland R. Classification, functions, and clinical relevance of extracellular vesicles. Pharmacol. Rev. 2012:64;676–705.
[7] Hata T, Murakami K, Nakatani H, Yamamoto Y, Matsuda T, Aoki N. Isolation of bovine milk-derived microvesicles carrying mRNAs and microRNAs. Biochem. Biophys. Res Commun. 2010:396;528–33.
[8] Baddela VS, Nayan V, Rani P, Onteru SK, Singh D. Physicochemical Biomolecular Insights into Buffalo Milk-Derived Nanovesicles. Appl. Biochem. Biotechnol. 2016:178;544–57.
[9] Na RS, E GX, Sun W, Sun XW, Qiu XY, Chen LP, Huang YF. Expressional analysis of immune-related miRNAs in breast milk. Genet. Mol. Res. 2015:14;11371–6.
[10] Chen T, Xi QY, Ye RS, Cheng X, Qi QE, Wang SB, Shu G, Wang LN, Zhu XT, Jiang QY, Zhang YL. Exploration of microRNAs in porcine milk exosomes. BMC Genomics 2014:15;100.
[11] Modepalli V, Kumar A, Hinds LA, Sharp JA, Nicholas KR, Lefevre C. Differential temporal expression of milk miRNA during the lactation cycle of the marsupial tammar wallaby (Macropus eugenii). BMC Genomics 2014:15;1012.
[12] Admyre C, Johansson SM, Qazi KR, Filén JJ, Lahesmaa R, Norman M, Neve EP, Scheynius A, Gabrielsson S. Exosomes with immune modulatory features are present in human breast milk. J. Immunol. 2007;179:1969–1978.
[13] Kosaka, N., Izumi, H., Sekine, K., Ochiya, T., 2010. microRNA as a new immune-regulatory agent in breast milk. Silence 1, 7.
[14] Zhou Q, Li M, Wang X, Li Q, Wang T, Zhu Q, Zhou X, Wang X, Gao X, Li X. Immune-related microRNAs are abundant in breast milk exosomes. Int. J. Biol. Sci. 2012:8;118–123.
[15] Mulcahy LA, Pink RC, Carter DR. Routes and mechanisms of extracellular vesicle uptake. J. Extracell. Vesicles 2014:3;24641.
[16] Wolf T, Baier SR, Zempleni J. The Intestinal Transport of Bovine Milk Exosomes Is Mediated by Endocytosis in Human Colon Carcinoma Caco–2 Cells and Rat Small Intestinal IEC–6 Cells. J. Nutr. 2015:145;2201–6.
[17] Manca S, Upadhyaya B, Mutai E, Desaulniers AT, Cederberg RA, White BR, Zempleni J. Milk exosomes are bioavailable and distinct microRNA cargos have unique tissue distribution patterns. Sci. Rep. 2018:8;11321.
[18] Chen T, Xie MY, Sun JJ, Ye RS, Cheng X, Sun RP, Wei LM, Li M, Lin DL, Jiang QY, Xi QY, Zhang YL. Porcine milk-derived exosomes promote proliferation of intestinal epithelial cells. Sci. Rep. 2016:20;33862.
[19] Arntz OJ, Pieters BC, Oliveira MC, Broeren MG, Bennink MB, De Vries M, Van Lent PL, Koenders MI, Van den Berg WB, Van der Kraan PM, Van de Loo FA. Oral administration of bovine milk derived extracellular vesicles attenuates arthritis in two mouse models. Mol. Nutr. Food Res. 2015:59;1701–12.
[20] Pan JH, Zhou H, Zhao XX, Ding H, Li W, Qin L, Pan YL. Role of exosomes and exosomal microRNAs in hepatocellular carcinoma: potential in diagnosis and antitumour treatments (Review). Int. J. Mol. Med. 2018:41;1809–16.
[21] Ni Q, Stevic I, Pan C, Müller V, Oliviera-Ferrer L, Pantel K, Schwarzenbach H. Different signatures of miR–16, miR–30b and miR–93 in exosomes from breast cancer and DCIS patients. Sci. Rep. 2018:28;12974.
[22] Yang TT, Liu CG, Gao SC, Zhang Y, Wang PC. The serum exosome derived microRNA–135a, –193b, and –384 were potential Alzheimer’s disease biomarkers. Biomed. Environ. Sci. 2018:31;87–96.
[23] Jin W, Ibeagha-Awemu EM, Liang G, Beaudoin F, Zhao X, Guan LL. Transcriptome microRNA profiling of bovine mammary epithelial cells challenged with Escherichia coli or Staphylococcus aureus bacteria reveals pathogen directed microRNA expression profiles. BMC Genomics 2014:15;181.
[24] Li R, Zhang CL, Liao XX, Chen D, Wang WQ, Zhu YH, Geng XH, Ji DJ, Mao YJ, Gong YC, Yang ZP. Transcriptome microRNA profiling of bovine mammary glands infected with Staphylococcus aureus. Int. J. Mol. Sci. 2015:16;4997–5013.
[25] Sun J, Aswath K, Schroeder SG, Lippolis JD, Reinhardt TA, Sonstegard TS. MicroRNA expression profiles of bovine milk exosomes in response to Staphylococcus aureus infection. BMC Genomics 2015:16;806.
[26] Cai M, He H, Jia X, Chen S, Wang J, Shi Y, Liu B, Xiao W, Lai S. Genome-wide microRNA profiling of bovine milk-derived exosomes infected with Staphylococcus aureus. Cell Stress Chaperones 2018:23;663–72.
[27] Michaelsen KF. Cow’s milk in the prevention and treatment of stunting and wasting. Food Nutr. Bull. 2013:34;249–51.
[28] Melnik BC, Schmitz G. Exosomes of pasteurized milk: potential pathogens of Western diseases. J. Transl. Med. 2019:17;3.
[29] Golan-Gerstl R, Elbaum SY, Moshayoff V, Schecter D, Leshkowitz D, Reif S. Characterization and biological function of milk-derived miRNAs. Mol. Nutr. Food Res. 2017:61;10.
[30] Benmoussa A, Lee CH, Laffont B, Savard P, Laugier J, Boilard E, Gilbert C, Fliss I, Provost P. Commercial dairy cow milk microRNAs resist digestion under simulated gastrointestinal tract conditions. J. Nutr. 2016:146;2206–15.
[31] Kusuma RJ, Manca S, Friemel T, Sukreet S, Nguyen C, Zempleni J. Human vascular endothelial cells transport foreign exosomes from cow’s milk by endocytosis. Am. J. Physiol. Cell Physiol. 2016:310;C800–7.
[32] Baier SR, Nguyen C, Xie F, Wood JR, Zempleni J. MicroRNAs are absorbed in biologically meaningful amounts from nutritionally relevant doses of cow milk and affect gene expression in peripheral blood mononuclear cells, HEK–293 kidney cell cultures, and mouse livers. J. Nutr. 2014:144;1495–500.
[33] Zhang T, Hu J, Wang X, Zhao X, Li Z, Niu J, Steer CJ, Zheng G, Song G. MicroRNA–378 promotes hepatic inflammation and fibrosis via modulation of the NF-κB-TNFα pathway. J. Hepatol. 2019:70;87–96.
[34] Lee DY, Deng Z, Wang CH, Yang BB. MicroRNA–378 promotes cell survival, tumor growth, and angiogenesis by targeting SuFu and Fus–1 expression. Proc. Natl. Acad. Sci. U.S. A. 2007:104;20350–5.
[35] Chang H, Wang Y, Liu H, Nan X, Wong S, Peng S, Gu Y, Zhao H, Feng H. Mutant Runx2 regulates amelogenesis and osteogenesis through a miR–185–5p-Dlx2 axis. Cell Death Dis. 2017:8;3221.
[36] Zhang D, Lee H, Cao Y, Dela Cruz CS, Jin Y. miR–185 mediates lung epithelial cell death after oxidative stress. Am. J. Physiol. Lung Cell. Mol. Physiol. 2016:310;L700–10.
[37] Chang S, Fang K, Zhang K, Wang J. Network-based analysis of Schizophrenia genome-wide association data to detect the joint functional association signals. PLoS One 2015:10;e0133404.
[38] Keramati AR, Fathzadeh M, Go GW, Singh R, Choi M, Faramarzi S, Mane S, Kasaei M, Sarajzadeh-Fard K, Hwa J, Kidd KK, Babaee Bigi MA, Malekzadeh R, Hosseinian A, Babaei M, Lifton RP, Mani A. A form of the metabolic syndrome associated with mutations in DYRK1B. N. Engl. J. Med. 2014:370;1909–19.
[39] Neuner SM, Garfinkel BP, Wilmott LA, Ignatowska-Jankowska BM, Citri A, Orly J, Lu L, Overall RW, Mulligan MK, Kempermann G, Williams RW, O’Connell KM, Kaczorowski CC. Systems genetics identifies Hp1bp3 as a novel modulator of cognitive aging. Neurobiol. Aging 2016:46;58–67.
[40] Neuner SM, Ding S, Kaczorowski CC. Knockdown of heterochromatin protein 1 binding protein 3 recapitulates phenotypic, cellular, and molecular features of aging. Aging Cell 2019:18(1);e12886. doi: 10.1111/acel.12886.
[41] Collins EC, Appert A, Ariza-McNaughton L, Pannell R, Yamada Y, Rabbitts TH. Mouse Af9 is a controller of embryo patterning, like Mll, whose human homologue fuses with Af9 after chromosomal translocation in leukemia. Mol. Cell. Biol. 2002:22;7313–24.
[42] Pramparo T, Grosso S, Messa J, Zatterale A, Bonaglia MC, Chessa L, Balestri P, Rocchi M, Zuffardi O, Giorda R. Loss-of-function mutation of the AF9/MLLT3 gene in a girl with neuromotor development delay, cerebellar ataxia, and epilepsy. Hum. Genet. 2005:118;76–81.
[43] Bartels CF, Bükülmez H, Padayatti P, Rhee DK, Van Ravenswaaij-Arts C, Pauli RM, Mundlos S, Chitayat D, Shih LY, Al-Gazali LI, Kant S, Cole T, Morton J, Cormier-Daire V, Faivre L, Lees M, Kirk J, Mortier GR, Leroy J, Zabel B, Kim CA, Crow Y, Braverman NE, Van den Akker F, Warman ML. Mutations in the transmembrane natriuretic peptide receptor NPR-B impair skeletal growth and cause acromesomelic dysplasia, type Maroteaux. Am. J. Hum. Genet. 2004:75;27–34.
[44] Stojkovic T, Vissing J, Petit F, Piraud M, Orngreen MC, Andersen G, Claeys KG, Wary C, Hogrel JY, Laforêt P. Muscle glycogenosis due to phosphoglucomutase 1 deficiency. N. Engl. J. Med. 2009:361;425–7.
[45] Tegtmeyer LC, Rust S, Van Scherpenzeel M, Ng BG, Losfeld ME, Timal S, Raymond K, He P, Ichikawa M, Veltman J, Huijben K, Shin YS, Sharma V, Adamowicz M, Lammens M, Reunert J, Witten A, Schrapers E, Matthijs G, Jaeken J, Rymen D, Stojkovic T, Laforêt P, Petit F, Aumaître O, Czarnowska E, Piraud M, Podskarbi T, Stanley CA, Matalon R, Burda P, Seyyedi S, Debus V, Socha P, Sykut-Cegielska J, Van Spronsen F, De Meirleir L, Vajro P, DeClue T, Ficicioglu C, Wada Y, Wevers RA, Vanderschaeghe D, Callewaert N, Fingerhut R, Van Schaftingen E, Freeze HH, Morava E, Lefeber DJ, Marquardt T. Multiple phenotypes in phosphoglucomutase 1 deficiency. N. Engl. J. Med. 2014:370;533–42.
[46] Pérez B, Medrano C, Ecay MJ, Ruiz-Sala P, Martínez-Pardo M, Ugarte M, Pérez-Cerdá C. A novel congenital disorder of glycosylation type without central nervous system involvement caused by mutations in the phosphoglucomutase 1 gene. J. Inherit. Metab. Dis. 2013:36;535–42.
[47] Willeit P, Skroblin P, Moschen AR, Yin X, Kaudewitz D, Zampetaki A, Barwari T, Whitehead M, Ramírez CM, Goedeke L, Rotllan N, Bonora E, Hughes AD, Santer P, Fernández-Hernando C, Tilg H, Willeit J, Kiechl S, Mayr M. Circulating MicroRNA–122 Is Associated With the Risk of New-Onset Metabolic Syndrome and Type 2 Diabetes. Diabetes 2017:66;347–57.
[48] Brest P, Lapaquette P, Souidi M, Lebrigand K, Cesaro A, Vouret-Craviari V, Mari B, Barbry P, Mosnier JF, Hébuternel X, Harel-Bellan A, Mograbi B, Darfeuille-Michaud A, Hofman P. A synonymous variant in irgm alters a binding site for mir–196 and causes deregulation of irgm-dependent xenophagy in Crohn’s disease. Nat. Genet. 2011:43,242–5.
[49] Li L, Zhou L, Wang L, Xue H, Zhao X. Characterization of methicillin-resistant and -susceptible staphylococcal isolates from bovine milk in northwestern china. PLoS One 2015:10;e0116699.
[50] Munagala R, Aqil F, Jeyabalan J, Gupta RC. Bovine milk-derived exosomes for drug delivery. Cancer Lett. 2016:371(1);48–61.
[51] Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011:17;10.
[52] Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic. Acids Res. 2014:42;D68–73.
[53] Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. 2012:40;37–52.
[54] Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014:15;550.
[55] BenjaminiY, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B 1995:57,289–300.
[56] Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol. 2013:5;R1.
[57] Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009:4;44–57.