Rewiring of gene expression in PWBC at artificial insemination is predictive of pregnancy outcome in cattle (Bos taurus)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA609112 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11194200.fastq.gz | Fastqsanger.gz | |||
| SRR11194201.fastq.gz | Fastqsanger.gz | |||
| SRR11194202.fastq.gz | Fastqsanger.gz | |||
| SRR11194203.fastq.gz | Fastqsanger.gz | |||
| SRR11194204.fastq.gz | Fastqsanger.gz |
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Project description:Infertility is a disease that affects humans and cattle in similar ways. The resemblance includes complex genetic architecture, multiple etiology, low heritability of fertility related traits in females, and the frequency in the female population. Here, we used cattle as a biomedical model to test the hypothesis that gene expression profiles of protein-coding genes expressed in peripheral white blood cells (PWBCs), and circulating micro RNAs in plasma, are associated with female fertility, measured by pregnancy outcome. We drew blood samples from 17 female calves on the day of artificial insemination and analyzed transcript abundance for 10496 genes in PWBCs and 290 circulating micro RNAs. The females were later classified as pregnant to artificial insemination, pregnant to natural breeding or not pregnant. We identified 1860 genes producing significant differential coexpression (eFDR<0.002) based on pregnancy outcome. Additionally, 237 micro RNAs and 2274 genes in PWBCs presented differential coexpression based on pregnancy outcome. Furthermore, using a machine learning prediction algorithm we detected a subset of genes whose abundance could be used for blind categorization of pregnancy outcome. Our results provide strong evidence that bloodborne transcript abundance is highly associated with fertility in females.
2020-02-28 | GSE146041 | GEO
Project description:The objective of this research was to identify a set of genes whose transcript abundance is predictive of a cow’s ability to become pregnant following artificial insemination (AI). Endometrial epithelial cells from the uterine body were collected for RNA sequencing using the cytobrush method from 193 first-service Holstein cows at estrus prior to AI (day 0). A group of 253 first-service cows not used for cytobrush collection were controls. There was no effect of cytobrush collection on pregnancy outcomes at day 30 or 70, or on pregnancy loss between day 30 and 70. There were 2 upregulated and 214 downregulated genes (FDR < 0.05, absolute fold change > 2-fold) for cows pregnant at day 30 versus those that were not pregnant. Functional terms overrepresented in the downregulated genes included those related to immune and inflammatory responses. Machine learning for fertility biomarkers with the R package BORUTA resulted in identification of 57 biomarkers that predicted pregnancy outcome at day 30 with an average accuracy of 77%. Thus, machine learning can identify predictive biomarkers of pregnancy in endometrium with high accuracy. Moreover, sampling of endometrial epithelium using the cytobrush can help understand functional characteristics of the endometrium at AI without compromising cow fertility.
2024-04-10 | GSE248266 | GEO
Project description:Machine learning analysis to identify endometrial transcriptomic biomarkers predictive of pregnancy success following artificial insemination in dairy cows
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Project description:Sequencing of commercial boar semen use in artificial insemination
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Project description:The aims of this study were to 1) identify the earliest transcriptional response of the bovine endometrium to the presence of the conceptus (using RNAseq), 2) investigate if these genes are regulated by interferon tau (IFNT) in vivo, and 3) determine if they are predictive of the pregnancy status of postpartum dairy cows. RNAseq identified 459 differentially expressed genes (DEGs) between pregnant and cyclic endometria on day 16. Quantitative real-time PCR analysis of selected genes revealed PARP12, ZNFX1, HERC6, IFI16, RNF213, and DDX58 expression increased in pregnant compared with cyclic endo- metria on day 16 and were directly upregulated by intrauterine infusion of IFNT in vivo for 2 h (P < 0.05). On day 13 following estrous endometrial expression of nine genes increased [ARHGAP1, MGC127874, LIMS2, TBC1D1, FBXL7, C25H16orf71, LOC507810, ZSWIM4, and one novel gene (ENSBTAT00000050193)] and seven genes decreased (SERBP1, SRGAP2, AL7A1, TBK1, F2RL2, MGC128929, and WBSCR17; P < 0.05) in pregnant compared with cyclic heifers. Of these DEGs, significant differences in expression between pregnant and cyclic endometria were maintained on day 16 for F2RL2, LIMS2, LOC507810, MGC127874, TBC1D1, WBSCR17, and ZSWIM4 (P < 0.05) both their expression was not directly regulated by IFNT in vivo. Analysis of the expression of selected interferon-stimulated genes in blood samples from postpartum dairy cows revealed a significant increase (P < 0.05) in expression of ZXFX1, PARP12, SAMD9, and HERC6 on day 18 following artificial insemination in cows subsequently confirmed pregnant compared with cyclic controls. In conclusion, RNAseq identified a number of novel pregnancy-associated genes in the endometrium of cattle during early pregnancy that are not regulated by IFNT in vivo. In addition, a number of genes that are directly regulated by short term exposure to IFNT in vivo are differentially expressed on day 18 following estrus detection in the blood of postpartum dairy cows depending on their pregnancy status. mRNA profiles of pregnant vs not pregnant cross-bred beef heifers at days 13 and 16 (n=5 per group)
2014-04-01 | E-GEOD-56392 | biostudies-arrayexpress
Project description:Early pregnancy diagnosis is key to maximise productivity of dairy herds. We previously showed that an increase in the levels of miR-26 could be detected as soon as day 8 of pregnancy in heifers. The aims of this study were to determine whether 1) plasma miR-26 levels would be distinctly elevated, retrospectively, early after artificial insemination in lactating cows with successful compared to failed pregnancies, 2) the early increase in miRNA levels in cows with successful pregnancy could be accounted for by changes in miRNA expression in white blood cells (WBCs), presumably induced by the effects of embryo-derived interferon tau (IFNt), and 3) plasma miRNA levels may provide a reliable early predictor of pregnancy that could be used at a herd level. Blood samples were taken from a total of 34 dairy cows (lactation number 1 to 4) before (D0) and 9 and 18 days after artificial insemination at oestrus, followed by confirmation of pregnancy status by ultrasound on D32. In addition, WBCs collected from non-pregnant cows (n = 4) were stimulated in vitro with recombinant ovine IFNt (0-100 pg/ml). Levels of miRNAs and ISG15, a known IFNt-induced gene, were quantified by qPCR. Relative to D0, a larger increase in plasma miR-26a (P = 0.04) occurred on D9 in cows later confirmed to be pregnant (n = 12) than in cows with a failed pregnancy (n = 22). Expression of miR-26a in WBCs was not affected (P>0.1) by pregnancy status or IFNt stimulation in vitro, in contrast to ISG15 expression which increased markedly (P<0.0001) both in WBC samples collected on D18 from animals later confirmed to be pregnant, and in WBCs after stimulation with IFNt in vitro. Finally, ROC analyses revealed that miR-26a on D9 or D18 could predict pregnancy outcome with much lower accuracy than WBC ISG15 on D18 (Likelihood ratio, 2.3 vs 15.4). In summary, a modest increase in plasma miR-26a levels occurs during early pregnancy in mature dairy cows which may not accounted for by changes in miRNA levels in WBCs or the effects of IFNt. Moreover, compared to ISG15, changes in miR-26a levels may not provide an accurate test for early diagnosis of pregnancy in cows.
| S-EPMC10420342 | biostudies-literature
Project description:The aims of this study were to 1) identify the earliest transcriptional response of the bovine endometrium to the presence of the conceptus (using RNAseq), 2) investigate if these genes are regulated by interferon tau (IFNT) in vivo, and 3) determine if they are predictive of the pregnancy status of postpartum dairy cows. RNAseq identified 459 differentially expressed genes (DEGs) between pregnant and cyclic endometria on day 16. Quantitative real-time PCR analysis of selected genes revealed PARP12, ZNFX1, HERC6, IFI16, RNF213, and DDX58 expression increased in pregnant compared with cyclic endo- metria on day 16 and were directly upregulated by intrauterine infusion of IFNT in vivo for 2 h (P < 0.05). On day 13 following estrous endometrial expression of nine genes increased [ARHGAP1, MGC127874, LIMS2, TBC1D1, FBXL7, C25H16orf71, LOC507810, ZSWIM4, and one novel gene (ENSBTAT00000050193)] and seven genes decreased (SERBP1, SRGAP2, AL7A1, TBK1, F2RL2, MGC128929, and WBSCR17; P < 0.05) in pregnant compared with cyclic heifers. Of these DEGs, significant differences in expression between pregnant and cyclic endometria were maintained on day 16 for F2RL2, LIMS2, LOC507810, MGC127874, TBC1D1, WBSCR17, and ZSWIM4 (P < 0.05) both their expression was not directly regulated by IFNT in vivo. Analysis of the expression of selected interferon-stimulated genes in blood samples from postpartum dairy cows revealed a significant increase (P < 0.05) in expression of ZXFX1, PARP12, SAMD9, and HERC6 on day 18 following artificial insemination in cows subsequently confirmed pregnant compared with cyclic controls. In conclusion, RNAseq identified a number of novel pregnancy-associated genes in the endometrium of cattle during early pregnancy that are not regulated by IFNT in vivo. In addition, a number of genes that are directly regulated by short term exposure to IFNT in vivo are differentially expressed on day 18 following estrus detection in the blood of postpartum dairy cows depending on their pregnancy status.
2014-04-01 | GSE56392 | GEO
Project description:Sperm cells are characterized by a unique epigenome, and an incorrect establishment of DNA methylation patterns during the differentiation of male germ cells into spermatozoa has been associated with male infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bovine sperm is still scarce. The purpose of this study is to compare the methylomes of sperm and somatic cell types in cattle using the RRBS technology.
2018-05-03 | GSE102169 | GEO
Project description:Sperm cells are characterized by a unique epigenome, and an incorrect establishment of DNA methylation patterns during the differentiation of male germ cells into spermatozoa has been associated with male infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bovine sperm is still scarce. The purpose of this study is to compare the methylomes of sperm and somatic cell types in cattle using the MeDIP-chip technology (methylated DNA immunoprecipitation followed by microarray hybridation).
2018-05-03 | GSE102960 | GEO
Project description:Background: In food production animals, especially cattle, the diagnosis of gestation is an important issue because the timing of gestation has direct effects on the running of farms. Various methods have been used to detect gestation, but none of them are ideal because of problems with the timing of detection, or the accuracy, simplicity, or cost of the method, etc. A new method for detecting gestation, which involves assessing interferon-tau-related gene expression in peripheral blood leucocytes (PBL), was recently proposed. PBL fractionation methods were used to examine whether the expression profiles of various PBL populations could be used as reliable diagnostic markers of bovine gestation. Methods: PBL were collected on days 0 (just before artificial insemination), 7, 14, 17, 21, and 28 of gestation. The gene expression levels of the PBL were assessed with microarray analysis and/or quantitative real-time reverse transcription (q)-PCR. PBL fractions were collected with flow cytometry or density gradient cell separation using Histopaque 1083 or Ficoll-Conray solution. The expression levels of four interferon-tau-related genes, interferon-stimulated protein 15 kDa (ISG15), myxovirus-resistance (Mx) 1 and 2, and 2'-5'-oligoadenylate synthetase (OAS1), were then analysed in each fraction until day 28 of gestation using qPCR. Results: Miroarray analysis detected 72 and 28 genes significantly higher in whole PBL on days 14 and 21 of gestation compare to those on day 0, respectively. They involved interferon-tau responded genes. The expression levels of these genes increased with the progression of gestation. In the flow cytometry experiment, on day 14 all of the genes displayed significantly higher expression levels in the granulocyte fraction than the other fractions, and their expression levels gradually decreased until day 28 of gestation. Strong correlations were observed between the expression levels of the four genes in the granulocyte fractions obtained with flow cytometry and density gradient separation. Conclusions: The expression profile of the four abovementioned genes could be a useful diagnostic biomarker of bovine gestation. Assessing the expression levels of ISG15, Mx1, Mx2 and OAS1 in a granulocyte fraction obtained with density gradient separation is a practical way of detecting gestation in cows within three weeks of insemination. Gene expression profiles were analyzed in the peripheral blood leucocytes at days 0 (n=5), 14 (n=3) and 21 (n=5) after artificial insemination in cow.
2013-01-31 | E-GEOD-42894 | biostudies-arrayexpress