Open Access
Research (Published online: 01-09-2018)
1. An innovative approach to predict immune-associated genes mutually targeted by cow and human milk microRNAs expression profiles
Kaj Chokeshaiusaha, Thanida Sananmuang, Denis Puthier and Catherine Nguyen
Veterinary World, 11(9): 1203-1209

Kaj Chokeshaiusaha: Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chonburi, Thailand.
Thanida Sananmuang: Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chonburi, Thailand.
Denis Puthier: Aix-Marseille Universite, INSERM UMR 1090, TAGC, Marseille, France.
Catherine Nguyen: Aix-Marseille Universite, INSERM UMR 1090, TAGC, Marseille, France.

doi: 10.14202/vetworld.2018.1203-1209

Share this article on [Facebook] [LinkedIn]

Article history: Received: 31-05-2018, Accepted: 16-07-2018, Published online: 01-09-2018

Corresponding author: Kaj Chokeshaiusaha


Citation: Chokeshaiusaha K, Sananmuang T, Puthier D, Nguyen C (2018) An innovative approach to predict immune-associated genes mutually targeted by cow and human milk microRNAs (miRNAs) expression profiles, Veterinary World, 11(9): 1203-1209.

Aim: Milk is rich in miRNAs - the endogenous small non-coding RNA responsible for gene post-transcriptional silencing. Milk miRNAs were previously evidenced to affect consumer's immune response. While most studies relied on a few well-characterized milk miRNAs to relate their immunoregulatory roles on target genes among mammals, this study introduced a procedure to predict the target genes based on overall milk miRNA expression profiles - the miRNome data of cow and human.

Materials and Methods: Cow and human milk miRNome expression datasets of cow and human milk lipids at 2, 4, and 6 months of lactation periods were preprocessed and predicted for their target genes using TargetScanHuman. Enrichment analysis was performed using target genes to extract the immune-associated gene ontology (GO) terms shared between the two species. The genes within these terms with more than 50 different miRNAs of each species targeting were selected and reviewed for their immunological functions.

Results: A total of 146 and 129 miRNAs were identified in cow and human milk with several miRNAs reproduced from other previous reports. Enrichment analysis revealed nine immune-related GO terms shared between cow and human (adjusted p≤0.01). There were 14 genes related to these terms with more than 50 miRNA genes of each species targeting them. These genes were evidenced for their major roles in lymphocyte stimulation and differentiation.

Conclusion: A novel procedure to determine mutual immune-associated genes targeted by milk miRNAs was demonstrated using cow and human milk miRNome data. As far as we know, this was the 1st time that milk miRNA target genes had been identified based on such cross-species approach. Hopefully, the introduced strategy should hereby facilitate a variety of cross-species miRNA studies in the future.

Keywords: immune-associated target gene, microRNAs, milk, miRNome.


1. Li, R., Dudemaine, P.L., Zhao, X., Lei, C. and Ibeagha-Awemu, E.M. (2016) Comparative analysis of the miRNome of bovine milk fat, whey and cells. PLoS One, 11(4): e0154129. [Crossref]

2. Alsaweed, M., Lai, C.T., Hartmann, P.E., Geddes, D.T. and Kakulas, F. (2016) Human milk cells and lipids conserve numerous known and novel miRNAs, some of which are differentially expressed during lactation. PLoS One, 11(4): e0152610. [Crossref]

3. Chen, T., Xi, Q.Y., Ye, R.S., Cheng, X., Qi, Q.E. and Wang, S.B.I. (2014) Exploration of microRNAs in porcine milk exosomes. BMC Genomics, 15(1): e1471-2164-15-100. [Crossref]

4. Izumi, H., Kosaka, N., Shimizu, T., Sekine, K., Ochiya, T. and Takase M. (2014) Time-dependent expression profiles of microRNAs and mRNAs in rat milk whey. PLoS One, 9(2): e88843. [Crossref]

5. Modepalli, V., Kumar, A., Hinds, L.A., Sharp, J.A., Nicholas, K.R. and Lefevre, C. (2014) Differential temporal expression of milk miRNA during the lactation cycle of the marsupial tammar wallaby (Macropus eugenii). BMC Genomics, 15(1): e1471-2164-15-1012. [Crossref]

6. Kosaka, N., Izumi, H., Sekine, K. and Ochiya, T. (2010) MicroRNA as a new immune-regulatory agent in breast milk. Silence, 1(1): 7. [Crossref] [PubMed] [PMC]

7. Winter, J., Jung, S., Keller, S., Gregory, R.I. and Diederichs, S. (2009) Many roads to maturity: MicroRNA biogenesis pathways and their regulation. Nat. Cell Biol., 11(3): 228-234. [Crossref] [PubMed]

8. Izumi, H., Tsuda, M., Sato, Y., Kosaka, N., Ochiya, T. and Iwamoto, H.I.W. (2015) Bovine milk exosomes contain microRNA and mRNA and are taken up by human macrophages. J. Dairy Sci., 98(5): 2920-2933. [Crossref] [PubMed]

9. Baier, S.R., Nguyen, C., Xie, F., Wood, J.R. and Zempleni, J. (2014) 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., 144(10): 1495-1500. [Crossref] [PubMed] [PMC]

10. Sun, Q., Chen, X., Yu, J., Zen, K., Zhang, C.Y. and Li, L. (2013) Immune modulatory function of abundant immune-related microRNAs in microvesicles from bovine colostrum. Protein Cell, 4(3): 197-210. [Crossref] [PubMed] [PMC]

11. Admyre, C., Johansson, S.M., Qazi, K.R., Filen, J.J., Lahesmaa, R. and Norman, M.I.W. (2007) Exosomes with immune modulatory features are present in human breast milk. J. Immunol., 179(3): 1969-1978. [Crossref]

12. Li, Q.J., Chau, J., Ebert, P.J.R., Sylvester, G., Min, H. and Liu, G.I.W. (2007) miR-181a is an intrinsic modulator of T cell sensitivity and selection. Cell, 129(1): 147-161. [Crossref] [PubMed]

13. Gaidatzis, D., Nimwegen, E., van Hausser, J. and Zavolan, M. (2007) Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics, 8: 69. [Crossref] [PubMed] [PMC]

14. Friedman, R.C., Farh, K.K.H., Burge, C.B. and Bartel, D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19(1): 92-105. [Crossref] [PubMed] [PMC]

15. Chokeshaiusaha, K., Thanawongnuwech, R., Puthier, D. and Nguyen, C. (2016) Inspection of C-type lectin superfamily expression profile in chicken and mouse dendritic cells. Thai. J. Vet. Med., 46(3): 443-453.

16. Martin, M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J., 17(1): 10. [Crossref]

17. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J. and Homer, N.I.W. (2009) The sequence alignment/map format and SAM tools. Bioinformatics, 25(16): 2078-2079. [Crossref] [PubMed] [PMC]

18. Ramirez, F., Dundar, F., Diehl, S., Gruning, B.A. and Manke, T. (2014) Deep tools: A flexible platform for exploring deep-sequencing data. Nucleic Acids Res., 42(W1): W187-W191. [Crossref] [PubMed] [PMC]

19. Love, M.I., Anders, S. and Huber, W. (2014) Differential analysis of count data-the DESeq2 package. Genome Biol., 15: 550.

20. Yu, G., Wang, L.G, Han, Y. and He, Q.Y. (2012) Cluster profiler: An R package for comparing biological themes among gene clusters. Omi A J. Integr. Biol., 16(5): 284-287. [Crossref] [PubMed] [PMC]

21. Gu, Z., Eils, R. and Schlesner, M. (2016) Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics, 32(18): 2847-2849. [Crossref] [PubMed]

22. Csardi, G. and Nepusz, T. (2006) The igraph software package for complex network research. Int. J. Complex Syst., 1695: 1-9.

23. Wang, X.P., Luoreng, Z.M., Zan, L.S, Li, F. and Li, N. (2017) Bovine miR-146a regulates inflammatory cytokines of bovine mammary epithelial cells via targeting the TRAF6 gene. J. Dairy Sci., 100(9): 7648-7658. [Crossref] [PubMed]

24. Sonda, N., Simonato, F., Peranzoni, E., Cali, B., Bortoluzzi, S. and Bisognin, A.I.W. (2013) MiR-142-3p prevents macrophage differentiation during cancer-induced myelopoiesis. Immunity, 38(6): 1236-1249. [Crossref] [PubMed]

25. Wu, H., Jiang, K., Ma, X., Yin, N., Zhao, G. and Qiu, C.I.W. (2018) IFN-t mediated control of bovine major histocompatibility complex class I expression and function via the regulation of bta-miR-148b/152 in bovine endometrial epithelial cells. Front Immunol., 9: 167. [Crossref]

26. Zhu, J., Yao, K., Guo, J., Shi, H., Ma, L. and Wang, Q.I.W. (2017) miR-181a and miR-150 regulate dendritic cell immune inflammatory responses and cardiomyocyte apoptosis via targeting JAK1-STAT1/c-Fos pathway. J. Cell Mol. Med., 21(11): 2884-2895. [Crossref] [PubMed] [PMC]

27. Lee, H.M., Kim, T.S. and Jo, E.K. (2016) MiR-146 and miR-125 in the regulation of innate immunity and inflammation. BMB Rep., 49(6): 311-318. [Crossref] [PMC]

28. Sathe, A., Ayyar, K. and Reddy, K.V.R. (2014) MicroRNA let-7 in the spotlight: Role in innate immunity. Inflamm. Cell Signal, 1: 66-75.

29. Chen, X.M., Splinter, P.L., O'Hara, S.P. and La Russo, N.F. (2007) A cellular micro-RNA, let-7i, regulates toll-like receptor 4 expression and contributes to cholangiocyte immune responses against Cryptosporidium parvum infection. J. Biol. Chem., 282(39): 28929-28938. [Crossref] [PubMed] [PMC]

30. Witkos, T.M., Koscianska, E. and Krzyzosiak, W.J. (2011) Practical aspects of microRNA target prediction. Curr. Mol. Med., 11(2): 93-109. [Crossref] [PMC]

31. Raghunandan, R., Frissora, F.W. and Muthusamy, N. (2013) Modulation of Ets-1 expression in B lymphocytes is dependent on the antigen receptor-mediated activation signals and cell cycle status. Scand. J. Immunol., 77(2): 75-83. [Crossref] [PubMed]

32. Garrett-Sinha, L.A. (2013) Review of Ets1 structure, function, and roles in immunity. Cell Mol. Life Sci., 70(18): 3375-3390. [Crossref] [PubMed] [PMC]

33. Klaewsongkram, J., Yang, Y., Golech, S., Katz, J., Kaestner, K.H. and Weng, N.P. (2007) Kruppel-like factor 4 regulates B cell number and activation-induced B cell proliferation. J. Immunol., 179(7): 4679-4684. [Crossref]

34. Hart, G.T., Hogquist, K.A. and Jameson, S.C. (2012) Kruppel-like factors in lymphocyte biology. J. Immunol., 188(2): 521-526. [Crossref] [PubMed] [PMC]

35. Wen, A.Y., Sakamoto, K.M. and Miller, L.S. (2010) The role of the transcription factor CREB in immune function. J. Immunol., 185(11): 6413-6419. [Crossref] [PubMed] [PMC]

36. Preston, G.C., Sinclair, L.V., Kaskar, A., Hukelmann, J.L., Navarro, M.N. and Ferrero, I.I.W. (2015) Single cell tuning of Myc expression by antigen receptor signal strength and interleukin-2 in T lymphocytes. EMBO J., 34(15): 2008-2024. [Crossref] [PubMed] [PMC]

37. Donnell, K.A.O., Yu, D., Zeller, K.I., Kim, J., Racke, F. and Dang, C.V.I. (2006) Activation of transferrin receptor 1 by c-Myc enhances cellular proliferation and tumorigenesis activation of transferrin receptor 1 by c-Myc enhances cellular proliferation and tumorigenesis. Mol. Cell Biol., 26(6): 2373-2386. [Crossref] [PubMed] [PMC]

38. Sweeney, T.E., Suliman, H.B., Hollingsworth, J.W. and Piantadosi, C.A. (2010) Differential regulation of the PGC family of genes in a mouse model of Staphylococcus aureus sepsis. PLoS One, 5(7): e11606. [Crossref]

39. Gnanaprakasam, J.N.R. and Wang, R. (2017) MYC in regulating immunity: Metabolism and beyond. Genes (Basel), 8(3): 88. [Crossref]

40. Kumar, V. and Gabrilovich, D.I. (2014) Hypoxia-inducible factors in regulation of immune responses in tumour microenvironment. Immunology, 143(4): 512-519. [Crossref] [PubMed] [PMC]

41. Xia, Y. and Schneyer, A.L. (2009) The biology of activin: Recent advances in structure, regulation and function. J. Endocrinol., 202(1): 1-12. [Crossref]

42. Okkenhaug, K. (2013) Signaling by the phosphoinositide 3-kinase family in immune cells. Annu. Rev. Immunol., 31(1): 675-704. [Crossref] [PubMed] [PMC]

43. Renault, T.T. and Chipuk, J.E. (2013) Getting away with murder: How does the BCL-2 family of proteins kill with immunity? Ann. N. Y. Acad. Sci., 1285(1): 59-79. [Crossref] [PubMed] [PMC]

44. Broome, H.E, Dargan, C.M., Krajewski, S. and Reed, J.C. (1995) Expression of Bcl-2, Bcl-x, and Bax after T cell activation and IL-2 withdrawal. J. Immunol. (Baltimore, Md 1950), 155(5): 2311-2317.

45. Noti, J.D. (1977) Sp3 mediates transcriptional activation of the leukocyte integrin genes CD11C and CD11B and cooperates with c-Jun to activate CD11C. J. Biol. Chem., 272(38): 24038-24045. [Crossref]

46. Grekova, M.C., Salerno, K., Mikkilineni, R. and Richert, J.R. (2002) Sp3 expression in immune cells: A quantitative study. Lab Investig., 82(9): 1131-1138. [Crossref]

47. Cao, Z., Wara, A.K., Icli, B., Sun, X., Packard, R.R.S. and Esen, F.I.W. (2009) Kruppel-like factor KLF10 targets transforming growth factor-beta1 to regulate CD4(+)CD25(-) T cells and T regulatory cells. J. Biol. Chem., 284(37): 24914-24924. [Crossref] [PubMed] [PMC]

48. Papadakis, K.A., Krempski, J., Reiter, J., Svingen, P., Xiong, Y. and Sarmento, O.F.I. (2015) Kruppel-like factor KLF10 regulates transforming growth factor receptor II expression and TGF-β signaling in CD8+ T lymphocytes. Am. J. Physiol. Cell. Physiol., 308(5): C362-C371. [Crossref]