Sequencing the transcriptome of milk production: Milk trumps mammary tissue

Danielle G. Lemay, Russell C. Hovey, Stella R. Hartono, Katie Hinde, Jennifer T. Smilowitz, Frank Ventimiglia, Kimberli A. Schmidt, Joyce W.S. Lee, Alma Islas-Trejo, Pedro I. Silva, Ian Korf, Juan F. Medrano, Peter A. Barry, J. B. German

Research output: Contribution to journalArticlepeer-review

42 Scopus citations


Background: Studies of normal human mammary gland development and function have mostly relied on cell culture, limited surgical specimens, and rodent models. Although RNA extracted from human milk has been used to assay the mammary transcriptome non-invasively, this assay has not been adequately validated in primates. Thus, the objectives of the current study were to assess the suitability of lactating rhesus macaques as a model for lactating humans and to determine whether RNA extracted from milk fractions is representative of RNA extracted from mammary tissue for the purpose of studying the transcriptome of milk-producing cells.Results: We confirmed that macaque milk contains cytoplasmic crescents and that ample high-quality RNA can be obtained for sequencing. Using RNA sequencing, RNA extracted from macaque milk fat and milk cell fractions more accurately represented RNA from mammary epithelial cells (cells that produce milk) than did RNA from whole mammary tissue. Mammary epithelium-specific transcripts were more abundant in macaque milk fat, whereas adipose or stroma-specific transcripts were more abundant in mammary tissue. Functional analyses confirmed the validity of milk as a source of RNA from milk-producing mammary epithelial cells.Conclusions: RNA extracted from the milk fat during lactation accurately portrayed the RNA profile of milk-producing mammary epithelial cells in a non-human primate. However, this sample type clearly requires protocols that minimize RNA degradation. Overall, we validated the use of RNA extracted from human and macaque milk and provided evidence to support the use of lactating macaques as a model for human lactation.

Original languageEnglish (US)
Article number872
JournalBMC Genomics
Issue number1
StatePublished - Dec 12 2013
Externally publishedYes


  • Bioinformatics
  • Human
  • Mammary gland
  • Milk
  • Milk RNA
  • Milk processing
  • RNA-Seq
  • Rhesus macaque
  • Transcriptome
  • Transcriptomics

ASJC Scopus subject areas

  • Biotechnology
  • Genetics


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