RNA-Seq data from the milk somatic cell transcriptome of Assaf sheep in response to experimental inoculation of an Escherichia coli Lipopolysaccharide
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ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Ovis aries
SUBMITTER: Rocio Pelayo
PROVIDER: E-MTAB-13994 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:This research investigates the influence of nutritional protein restriction (NPR) during prepuberty on FE and the milk transcriptome of dairy Assaf ewes during their first lactation. Additionally, it evaluates the differences in the milk transcriptome between lactating ewes with divergent FE using the feed conversion ratio (FCR) and residual feed intake (RFI) indices and assesses milk gene expression as a predictor of FE.
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Project description:The knowledge of the genetic architecture behind feed efficiency would allow to breed more efficient animals maximizing farm profitability and reducing the environmental impact of animal production. This study analyzes high throughput gene expression data from milk samples to determine key genes and biological mechanisms associated to feed efficiency in dairy sheep.A detailed description of the sheep management practices and calculations for the feed efficiency index (FEI) are detailed in 10.3168/jds.2020-19061. For these analyses, we selected animals with divergent FEI values from a group of 40 lactating Assaf ewes. RNA-Seq was performed on milk somatic cell samples from 8 high feed efficiency sheep (H-FE), FEI = −0.29 (SD = 0.23), RFI = −0.16 (SD = 0.25), and 8 low feed efficiency sheep (L-FE), FEI = 0.81 (SD = 0.24), RFI = 0.19 (SD = 0.24)).
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Project description:Once daily milking reduces milk yield and alters mammary transcriptome resulting in a decrease in milk protein synthesis as well as an induction of the apoptotic signaling networks. A local regulation due to milk stasis in the tissue could contribute to this effect but such mechanisms have not yet been described. To challenge this hypothesis, cows were milked unilaterally, once daily on one udder half and twice daily on the other one, and variations in gene expression were studied in biopsies as well as in mammary epithelial cells (MEC) shed into milk during the lactation process (milk MEC). This study therefore also contributes to decipher if transcript variations in milk purified MEC can reflect that of the mammary tissue. We compared the mammary transcript profiles in biopsies collected from unilaterally once versus twice-daily milked udder halves, 504 transcripts were differentially expressed: 193 and 232 transcripts were up- and down-regulated, respectively. A first category of transcripts, which accumulation levels are mostly up-regulated, relates to mechanisms involved in cell renewal, such as cell cycle, cellular growth and proliferation, cell death and cellular development. A second family, mostly down-regulated, is involved in small molecule biochemistry, amino acid, lipid and carbohydrate metabolisms as well as molecular transport. A third category, mostly up-regulated, includes transcripts expressed in non-epithelial mammary cells such as adipocytes, endothelial and immune cells and cells from the connective tissue. These results are consistent with previous data showing a decrease in mammary synthesis activity and an activation of cell death during once daily milking. They further suggest that during once daily milking the local milk accumulation has a major effect on mammary remodeling. Interestingly, some transcripts belonged to a third family described as M-BM-+ molecular transports M-BM-;. The expression of the 21 mRNA was then analyzed by RT-par in MEC (Table 4). Seven transcripts (NUCB2, RNASE4, ABCG2, RNASE1, SLC34A2, Cap1, FABP3, LALBA, SCD) were significantly down-regulated in milk purified MEC. Six were also significantly down-regulated in mammary biopsies. These transcripts are mostly involved in milk synthesis. We therefore conclude that milk purified MEC cannot be used as general markers of variations occurring in the mammary tissue but that variations in some transcripts listed above can be useful indicators. In this experimental design, udder halves were unilaterally milked once daily and the contralateral udder halves twice daily. Each mammary biopsy RNA sample from one udder half was compared to the one of the contralateral udder half in 5 dye-swaps corresponding to 5 animal replications, minimizing the animal variability. One dye swap corresponded to one comparison meaning two slides.
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Project description:Mastitis is an inflammation of the mammary gland (MG), usually due to bacterial infection. Although considerable attention has been paid to this economically important disease, the early stages of the host response remain poorly defined. In particular, it is unclear how mammary epithelial cells (MEC), a first barrier against pathogens, respond to infection. Indeed, it is difficult to differentiate between the contributions of MEC and infiltrating immune cells to gene expression profiles of mammary tissue during mastitis. The current investigation examines the response of MEC at the early stage of infection using a non invasive RNA sampling method taking advantage of the presence of cytoplasmic crescents contained in milk fat globules. We have recently shown that, in goats, Milk Fat Globules (MFG) provide a unique source of RNA to study the in vivo regulation of gene expression in MEC. This non invasive RNA sampling method was used during the time course of an experimental intra mammary infection (IMI) with S. aureus. Experiments were performed using ovine microarrays (Agilent) to compare gene expression patterns before infection, at 12h, 18h and 24h post-infection (PI). Furthermore, we combined this approach with laser capture microdissection of MEC isolated from frozen slides of mammary tissue to study some specific genes at the late stage of infection (30h PI). We show that at 18h PI, before the burst of somatic cells in milk, MEC play an important role in the recruitment and activation of inflammatory cells through the IL-8 signaling pathways. Then, at the late stage of infection (30h PI), the contribution of MEC in immune response changes to produce different acute phase proteins, including SAA3, serpin A1 and PTX3. These cells also express factors that contribute directly to fighting infection, such as S100A12. In summary, we demonstrate for the first time in vivo how MEC orchestrate innate immune response during an IMI with S. aureus in the goat species. We report here new opportunities to assess the dynamics of gene expression in the mammary gland, thus providing significant advances in the understanding of MEC immune capacity.M-bM-^@M-^BFurthermore, the production of some molecules by MEC, in the early stages of IMI, could provide sensitive biomarkers for early detection and therefore, treatment of mastitis. Experiments were performed using ovine microarrays (Agilent) to compare gene expression patterns before infection, at 12h, 18h and 24h post-infection (PI). 20 sample records; mono-colour experimental design
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