Available at: https://digitalcommons.calpoly.edu/theses/2519
Date of Award
MS in Agriculture - Animal Science
The mammary gland is an organ common to all mammals; it is of value for neonatal nourishment, human nutrition through dairy consumption, and is a source of pathology in humans through the development of breast cancer. While transcriptomic analyses have been applied to cultured mammary epithelial cells (MEC) and to whole gland samples, few have studied purified MEC isolated directly from the gland in vivo. To identify the differentially expressed genes influencing MEC development during pregnancy and the differences between the nulliparous and primiparous quiescent states, primary MEC were isolated from virgin, pregnant, and primiparous quiescent sibling mice. Computational analysis was attempted using two differing platforms for the analysis of RNA sequencing data, the commercially-available CLC Genomics Workbench and the recently-launched, publicly-available Green Line Analysis. In the virgin-to-pregnant and virgin-to-post-lactational quiescent developmental comparisons, 31.02% and 26.97% of differentially detected genes, respectively, were dually detected by both platforms (p-value<0.05), with the remaining genes being detected in one platform but not the other. Expression was likewise compared for the dually differentially expressed genes detected with high (>500 RPKM), medium (10-500 RPKM), and low (0.02-9.99 RPKM) expression between the two developmental comparisons. In the virgin-to-pregnant and virgin-to-post-lactational quiescent developmental comparisons, 30.00% and 1.04% of differentially detected genes with high expression, respectively, were dually detected by both platforms (p-value<0.05); 30.51% and 7.60% of differentially detected genes with medium expression, respectively, were dually detected by both platforms (p-value<0.05); and 26.68% and 11.33% of differentially detected genes with high expression, respectively, were dually detected by both platforms (p-value<0.05). Although a small portion of differentially detected genes were dually detected between the two platforms, functional analysis for biological meaning revealed similar depictions of the underlying biological themes. The developmental comparison between the virgin and pregnant states suggests through enhanced mitochondrial processes, amino acid availability, cellular communication, and immune responses the lactational capacity is being established during the first half of pregnancy, when MEC are devoted to growth and proliferation and formation of the alveolus is not yet occurring. The developmental comparison between the virgin and primiparous quiescent states indicates an overall decrease in oncogenic pathways yet increase in ribosomal integrity may be associated with the parity-induced protection against breast cancer. Last, parallel analysis of the transcriptome and proteome from the same sample source allowed for the comparison of two differing means of analyzing the molecular phenotype and showed regulation of mRNA abundance may not necessarily reflect the expression pattern of the corresponding protein. A mathematical phenomenon was noted in the percent of dually detected transcripts relative to proteins, suggesting perhaps twenty percent of MEC genes are actively expressed at a given time.