Examination of the xanthosine response on gene expression of mammary epithelial cells using RNA-seq technology

  • Choudhary, Shanti (School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University) ;
  • Li, Wenli (Cell Wall Biology and Utilization Research, USDA-ARS) ;
  • Bickhart, Derek (Cell Wall Biology and Utilization Research, USDA-ARS) ;
  • Verma, Ramneek (School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University) ;
  • Sethi, R.S. (School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University) ;
  • Mukhopadhyay, C.S. (School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University) ;
  • Choudhary, Ratan K. (School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University)
  • Received : 2018.02.01
  • Accepted : 2018.07.09
  • Published : 2018.07.31


Background: Xanthosine treatment has been previously reported to increase mammary stem cell population and milk production in cattle and goats. However, the underlying molecular mechanisms associated with the increase in stem cell population and milk production remain unclear. Methods: Primiparous Beetal goats were assigned to the study. Five days post-partum, one mammary gland of each goat was infused with xanthosine (TRT) twice daily ($2{\times}$) for 3 days consecutively, and the other gland served as a control (CON). Milk samples from the TRT and CON glands were collected on the 10th day after the last xanthosine infusion and the total RNA was isolated from milk fat globules (MEGs). Total RNA in MFGs was mainly derived from the milk epithelial cells (MECs) as evidenced by expression of milk synthesis genes. Significant differentially expressed genes (DEGs) were subjected to Gene Ontology (GO) terms using PANTHER and gene networks were generated using STRING db. Results: Preliminary analysis indicated that each individual goat responded to xanthosine treatment differently, with this trend being correlated with specific DEGs within the same animal's mammary gland. Several pathways are impacted by these DEGs, including cell communication, cell proliferation and anti-microbials. Conclusions: This study provides valuable insights into transcriptomic changes in milk producing epithelial cells in response to xanthosine treatment. Further characterization of DEGs identified in this study is likely to delineate the molecular mechanisms of increased milk production and stem or progenitor cell population by the xanthosine treatment.


Goat;Milk fat globule;RNA sequencing;Xanthosine;RT-qPCR


Supported by : Department of Biotechnology, Govt. of India


  1. Akers RM, Capuco AV, Keys JE. Mammary histology and alveolar cell differentiation during late gestation and early lactation in mammary tissue of beef and dairy heifers. Livest Sci. 2006;105:44-9.
  2. Zhang X, Liu N, Ma D, Liu L, Jiang L, Zhou Y, et al. Receptor for activated C kinase 1 (RACK1) promotes the progression of OSCC via the AKT/mTOR pathway. Int J Oncol. 2016;49:539-48.
  3. Choudhary S, Choudhary RK. Rapid and efficient method of total RNA isolation from milk fat for transcriptome analysis of mammary gland. Am Dairy Sci Assoc Annu Meet, J Dairy Sci. 2017;100(Suppl. 2)
  4. Chen Q, Wu Y, Zhang M, Xu W, Guo X, Yan X, et al. Milk fat globule is an alternative to mammary epithelial cells for gene expression analysis in buffalo. J Dairy Res. 2016;83:1-7.
  5. Canovas A, Rincon G, Bevilacqua C, Islas-Trejo A, Brenaut P, Hovey RC, et al. Comparison of five different RNA sources to examine the lactating bovine mammary gland transcriptome using RNA-sequencing. Sci Rep. 2014;4:5297.
  6. Brenaut P, Bangera R, Bevilacqua C, Rebours E, Cebo C, Martin P. Validation of RNA isolated from milk fat globules to profile mammary epithelial cell expression during lactation and transcriptional response to a bacterial infection. J Dairy Sci Elsevier. 2012;95:6130-44.
  7. Paten AM, Duncan EJ, Pain SJ, Peterson SW, Kenyon PR, Blair HT, et al. Functional development of the adult ovine mammary gland--insights from gene expression profiling. BMC Genomics. 2015;16:748.
  8. Shi H, Zhu J, Luo J, Cao W, Shi H, Yao D, et al. Genes regulating lipid and protein metabolism are highly expressed in mammary gland of lactating dairy goats. Funct Integr Genomics. 2015;15:309-21.
  9. Choudhary RK, Kaur H, Choudhary S, Verma R. Distribution and analysis of milk fat globule and crescent in murrah buffalo and crossbred cow. Proc Natl Acad Sci India Sect B Biol Sci. 2015;87:167-72.
  10. Menard O, Ahmad S, Rousseau F, Briard-Bion V, Gaucheron F, Lopez C. Buffalo vs. cow milk fat globules: size distribution, zeta-potential, compositions in total fatty acids and in polar lipids from the milk fat globule membrane. Food Chem. 2010;120:544-51.
  11. Maningat PD, Sen P, Rijnkels M, Sunehag AL, Hadsell DL, Bray M, et al. Gene expression in the human mammary epithelium during lactation: the milk fat globule transcriptome. Physiol Genomics. 2009;37:12-22.
  12. Lemay DG, Hovey RC, Hartono SR, Hinde K, Smilowitz JT, Ventimiglia F, et al. Sequencing the transcriptome of milk production: milk trumps mammary tissue. BMC Genomics 2013;14:872.
  13. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9:676-82.
  14. Choudhary S, Choudhary RK. Rapid and efficient method of total RNA isolation from milk fat for transcriptome analysis of mammary gland. Proc Natl Acad Sci India Sect B Biol Sci. 2017;
  15. Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat Genet. 2017;49:643-50.
  16. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
  17. Risso D, Ngai J, Speed TP, Dudoit S. Normalization of RNA-seq data using factor analysis of control genes or samples. Nat Biotechnol. 2014;32:896-902.
  18. Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. PrimerBLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics. 2012;13:134.
  19. Kapila N, Kishore A, Sodhi M, Sharma A, Kumar P, Mohanty a K, et al. Identification of appropriate reference genes for qRT-PCR analysis of heatstressed mammary epithelial cells in riverine buffaloes (Bubalus bubalis). ISRN Biotechnol. 2013;2013:1-9.
  20. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002;3:1-11.
  21. Spitsberg VL, Matitashvili E, Gorewit RC. Association and coexpression of fatty-acid-binding protein and glycoprotein CD36 in the bovine mammary gland. Eur J Biochem. 1995;230:872-8.
  22. Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, et al. PANTHER version 11: expanded annotation data from gene ontology and Reactome pathways and data analysis tool enhancements, Nucleic Acids Res 2017;45: D183-D189.
  23. Choudhary RK, Capuco AV. In vitro expansion of the mammary stem/ progenitor cell population by xanthosine treatment. BMC Cell Biol. 2012;13:14.
  24. Rambhatla L, Ram-Mohan S, Cheng JJ, Sherley JL. Immortal DNA strand cosegregation requires p53/IMPDH-dependent asymmetric self-renewal associated with adult stem cells. Cancer Res. 2005;65:3155-61.
  25. Capuco AV, Evock-Clover CM, Minuti A, Wood DL. In vivo expansion of the mammary stem/ progenitor cell population by xanthosine infusion. Exp Biol Med (Maywood). 2009;234:475-82.
  26. Rauner G, Barash I. Xanthosine administration does not affect the proportion of epithelial stem cells in bovine mammary tissue, but has a latent negative effect on cell proliferation. Exp Cell Res. 2014;328:186-96.
  27. Prpar Mihevc S, Ogorevc J, Dovc P. Lineage-specific markers of goat mammary cells in primary culture. Vitr Cell Dev Biol Anim. 2014;50:926-36.
  28. Boutinaud M, Jammes H. Potential uses of milk epithelial cells: a review. Reprod Nutr Dev. 2002;42:133-47.
  29. Anand V, Dogra N, Singh S, Kumar SN, Jena MK, Malakar D, et al. Establishment and characterization of a buffalo (Bubalus bubalis) mammary epithelial cell line. PLoS One. 2012;7:e40469.
  30. Lemay DG, Ballard OA, Hughes MA, Morrow AL, Horseman ND, NommsenRivers LA. RNA sequencing of the human milk fat layer transcriptome reveals distinct gene expression profiles at three stages of lactation. PLoS One. 2013;8:e67531.
  31. Bionaz M, Loor JJ. ACSL1, AGPAT6, FABP3, LPIN1, and SLC27A6 are the most abundant isoforms in bovine mammary tissue and their expression is affected by stage of lactation. J Nutr. 2008;138:1019-24.
  32. Mihevc SP, Dovc P. Mammary tumors in ruminants. Acta argiculturae Slov. 2013;102:83-6.
  33. Choudhary RK, Choudhary S, Pathak D, Verma R. Mucin 1 aberrently expresses n goat mammary carcinoma. 27th Annu. Meet. Indian Soc. Reprod. Fertil. 2017:0072.
  34. Choudhary RK, Choudhary RK, Choudhary S, Verma R. CD10 is a marker of goat mammary Cancer. EC Vet Sci. 2016;01:1-2.
  35. Baldassarre H, Deslauriers J, Neveu N, Bordignon V. Detection of endoplasmic reticulum stress markers and production enhancement treatments in transgenic goats expressing recombinant human butyrylcholinesterase. Transgenic Res. 2011;20:1265-72.
  36. Moh MC, Shen S. The roles of cell adhesion molecules in tumor suppression and cell migration: a new paradox. Cell Adhes Migr. 2009;3:334-6.
  37. Chiou S, Wang C, Tseng Y, Lee Y, Chen S, Chou C, et al. A novel role for ${\beta}$ 2-microglobulin : a precursor of antibacterial chemokine in respiratory epithelial cells. Sci Rep. 2016:1-12.
  38. Orsi N. The antimicrobial activity of lactoferrin: current status and perspectives. Biometals. 2004;17:189-96.
  39. Ginestier C, Hur MH, Charafe-Jauffret E, Monville F, Dutcher J, Brown M, et al. ALDH1 is a marker of normal and malignant human mammary stem cells and a predictor of poor clinical outcome. Cell Stem Cell. 2007;1:555-67.
  40. Taylor SC, Laperriere G, Germain H. Droplet Digital PCR versus qPCR for gene expression analysis with low abundant targets: from variable nonsense to publication quality data. Sci Rep. Nature Publishing Group; 2017;7:2409.
  41. Baratta M, Chal F. Adults mammary stem cell in cow ' s Milk : new perspectives and future challenge. J Vet Sci Anim Husb. 2013;1:5-6.
  42. Cregan MD, Fan Y, Appelbee A, Brown ML, Klopcic B, Koppen J, et al. Identification of nestin-positive putative mammary stem cells in human breastmilk. Cell Tissue Res. 2007;329:129-36.