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Comparative transcriptome analysis reveals early pregnancy-specific genes expressed in peripheral blood of pregnant sows.

ABSTRACT: Early and accurate diagnosis of pregnancy is important for effective management of an economical pig farm. Besides the currently available methods used in early diagnosis of sows, circulating nucleic acids in peripheral blood may contain some early pregnancy-specific molecular markers. For the first time, microarray analysis of peripheral blood from pregnant sows versus non-pregnant sows identified 127 up-regulated and 56 down-regulated genes at day 14 post-insemination. Gene Ontology annotation grouped the total differently expressed genes into 3 significantly enriched terms, cell surface receptor linked signal transduction, G-protein coupled receptor protein signaling pathway and regulation of vesicle-mediated transport. Signaling pathway analysis revealed the only one significantly changed pathway was arachidonic acid metabolism. Of the differently expressed genes, nine (including LPAR3, RXFP4, GALP, CBR1, CBR2, GPX6, USP18, LHB and NR5A1) were found to exert function related to early pregnancy processes. This study provides a clue that differentially abundant RNAs in maternal peripheral blood can help to identify the molecular markers of early pregnancy in pigs.

SUBMITTER: Shen J

PROVIDER: S-EPMC4257664 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Comparative transcriptome analysis reveals early pregnancy-specific genes expressed in peripheral blood of pregnant sows.

Shen Junye J Zhou Chuanli C Zhu Shien S Shi Wenqing W Hu Maishun M Fu Xiangwei X Wang Chuduan C Wang Yachun Y Zhang Qin Q Yu Ying Y

PloS one 20141205 12

Early and accurate diagnosis of pregnancy is important for effective management of an economical pig farm. Besides the currently available methods used in early diagnosis of sows, circulating nucleic acids in peripheral blood may contain some early pregnancy-specific molecular markers. For the first time, microarray analysis of peripheral blood from pregnant sows versus non-pregnant sows identified 127 up-regulated and 56 down-regulated genes at day 14 post-insemination. Gene Ontology annotation ...[more]

PMID: 25479131

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Project description:[Background] DNA methylation plays a crucial role in regulating cell proliferation, differentiation, gene expression, and embryonic development. However, the comprehensive changes in genome-wide DNA methylation during early pregnancy in sows remain unknown. This study aimed to investigate the DNA methylation profiles and to construct an early gene pool of sows during early gestation.[Results] In this investigation, we utilized blood samples from 20 healthy sows and applied Reduced Representation Bisulfite Sequencing (RBSS) technology to systematically examine alterations in DNA methylation in sow blood during early pregnancy. Screening and validating the Methylation differential genes by using bisulfite sequencing PCR (BSP) and Quantitative Real-time PCR (RT-qPCR). Our findings indicated a significant increase in methylation levels on day 28 of pregnancy (pre28) compared to non-pregnancy (ctrl) across various gene elements, including CGI, promoter, and genebody. A total of 64,908 differentially methylated sites (DMCs) and 12,119 differentially methylated regions (DMRs) were identified, predominantly exhibiting methylation upregulation. Randomly selected five differentially methylated genes—VBP1, UPRT (upregulated methylation), RPL10, RAB33A, and CD93 (downregulated methylation)—were validated. Between the pregnant (pre28) and non-pregnant (ctrl) groups the BSP results showed highly significant methylation differences (P<0.01) in VBP1, UPRT, RPL10, and RAB33A. DMC gene ontology (GO) analysis revealed significant enrichment in nuclear receptor activity, negative regulation of cysteine-type endopeptidase activity during apoptosis, heme binding, and hormonal activity. DMRs GO analysis highlighted significant enrichment in 1-acylglycerol-3-phosphate O-acyltransferase activity, regulation of transforming growth factor β receptor signaling pathway, mitochondrial outer membrane and myotubular cell development, and cellular calcium homeostasis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant enrichment in the MAPK signaling pathway and the PI3K-Akt signaling pathway.[Conclusion] During sow early gestation, DNA methylation is significant changes and is mainly upregulated. The observed upregulation of DNA methylation during early gestation in sows may regulate the MAPK and PI3K-Akt signaling pathways, potentially influencing embryonic development. Methylated differential genes VBP1 and RPL10 can be used as potential markers for early sow pregnancy diagnosis. These findings offer novel insights into the epigenetic changes occurring in sows during early gestation.

Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was initially identified in China and currently worldwide dispersed, resulting in the coronavirus disease 2019 (COVID-19) pandemic. Notably, COVID-19 is characterized by systemic inflammation. However, the potential mechanisms of the "cytokine storm" of COVID-19 are still limited. In this study, fourteen peripheral blood samples from COVID-19 patients (n = 10) and healthy donors (n = 4) were collected to perform the whole-transcriptome sequencing. Lung tissues of COVID-19 patients (70%) presenting with ground-glass opacity. Also, the leukocytes and lymphocytes were significantly decreased in COVID-19 compared with the control group (p < 0.05). In total, 25,482 differentially expressed messenger RNAs (DE mRNA), 23 differentially expressed microRNAs (DE miRNA), and 410 differentially expressed long noncoding RNAs (DE lncRNAs) were identified in the COVID-19 samples compared to the healthy controls. Gene Ontology (GO) analysis showed that the upregulated DE mRNAs were mainly involved in antigen processing and presentation of endogenous antigen, positive regulation of T cell mediated cytotoxicity, and positive regulation of gamma-delta T cell activation. The downregulated DE mRNAs were mainly concentrated in the glycogen biosynthetic process. We also established the protein-protein interaction (PPI) networks of up/downregulated DE mRNAs and identified 4 modules. Functional enrichment analyses indicated that these module targets were associated with positive regulation of cytokine production, cytokine-mediated signaling pathway, leukocyte differentiation, and migration. A total of 6 hub genes were selected in the PPI module networks including AKT1, TNFRSF1B, FCGR2A, CXCL8, STAT3, and TLR2. Moreover, a competing endogenous RNA network showed the interactions between lncRNAs, mRNAs, and miRNAs. Our results highlight the potential pathogenesis of excessive cytokine production such as MSTRG.119845.30/hsa-miR-20a-5p/TNFRSF1B, MSTRG.119845.30/hsa-miR-29b-2-5p/FCGR2A, and MSTRG.106112.2/hsa-miR-6501-5p/STAT3 axis, which may also play an important role in the development of ground-glass opacity in COVID-19 patients. This study gives new insights into inflammation regulatory mechanisms of coding and noncoding RNAs in COVID-19, which may provide novel diagnostic biomarkers and therapeutic avenues for COVID-19 patients.

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Comparative transcriptome analysis reveals early pregnancy-specific genes expressed in peripheral blood of pregnant sows.

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Comparative transcriptome analysis reveals early pregnancy-specific genes expressed in peripheral blood of pregnant sows.

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