Transcriptome of pig whole blood microRNAs provides insight into immune system development
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE140780 | GEO | 2021/12/01
REPOSITORIES: GEO
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Project description:Transcriptome of pig whole blood microRNAs provides insight into immune system development
| PRJNA590937 | ENA
Project description:Germ-free mice feature a profoundly underdeveloped immune system. Despite recent studies that emphasize the role of specific bacteria-derived metabolites in immune cell development and differentiation, it remains unclear how the lack of microbiota leads to immune deficiencies. Here, we performed droplet-based single-cell RNA sequencing to analyze the bone marrow and peripheral blood of both germ-free and specific pathogen-free mice, identifying 25 distinct cell types. Our findings suggest that neutrophil apoptosis in germ-free mice may be associated with the absence of niacin dehydrogenase, which is derived primarily from Pseudomonas. In addition, germ-free mice exhibited elevated excretion of 5’-methylthioadenosine, increased ERK activation induced by reactive oxygen species, and cessation of the bone marrow stromal antigen 2 signaling pathway in germ-free mice. The responses of monocytes and CD8+ T cells to interferon β and interferon γ were reduced in germ-free mice, which explains their increased susceptibility to viruses. Together, we identified a regulatory mechanism that connects immunodeficiency with the absence of microbiota in germ-free mice and validated these findings using multiple techniques.
2025-04-25 | GSE295200 | GEO
Project description:Background: As an “immune-privileged organ”, the rate of spontaneous and operational tolerance was higher after liver transplantation (LT) compared with other solid organs. However, modern immunosuppression regimens still have multiple complications, which require a deeper understanding of the real mechanism of inducing immune tolerance. Methods: Homogenic and allogeneic rat LT models were established, and recipient tissue was collected on postoperative day 7. The degree of LT rejection was evaluated by liver pathological changes and liver function. Differentially expressed genes (DEGs) were detected by transcriptome sequencing and identified by RT-PCR. The functional properties of DEGs were characterized by the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome pathway analyses. The cells infiltrating the graft and recipient spleen and peripheral blood were evaluated by immunofluorescence assays and flow cytometry. Result: A total of 1465 DEGs were screened, including 1177 up-regulated genes and 288 down-regulated genes. GO enrichment and KEGG pathway analysis indicated that DEGs were involved in several immunobiological processes, including immune system process, immune response, regulation of immune response, T cell activation, cytokine-cytokine receptor interaction, allograft rejection, Th1,Th2 and Th17 cell differentiation. Reactome results showed that PD-1 signaling was also enriched. Further research confirmed that the expression of multiple immune cell markers increased, and most marker of T cell exhaustion changed significantly. Flow cytometry results showed that the proportion of Treg decreased in the allogeneic group, while CD4+PD-1+ T and CD8+PD-1+ T cells increased. Conclusion: This study, to our knowledge, was the first to reveal the impact of liver transplantation rejection on the liver at the omics level. Our results revealed that the progression of LT rejection involves multiple immune cells, activation of various immune pathways and special changes of immune checkpoints, which provides potential reference for potential risk assessment and pathogenesis. However, further clinical validation is also needed.
2022-12-09 | GSE210164 | GEO
Project description:Background: Turner syndrome, a common sex chromosome aneuploidy, has characteristics and malformations associated with the phenotype. Fetal amniotic fluid is a complex biological material that could contribute to the understanding Turner syndrome pathogenesis. Global gene expression analysis of Turner syndrome fetal amniotic fluid supernatant was utilized to identify organ systems and specific genes that may play a role in the pathophysiologic changes that are seen in individuals with Turner syndrome. Methods: Global gene expression analysis was performed utilizing cell-free RNA from five midtrimester fetuses with Turner syndrome matched with five euploid female fetuses. Total RNA was extracted, amplified, hybridized onto GeneChipM-BM-. Human Genome U133 Plus 2.0 arrays. Network and pathway analysis of differentially expressed genes were completed. Chromosomal distribution of gene expression differences, differential expression by pathway and organ system (a M-bM-^@M-^\Turner syndrome core transcriptomeM-bM-^@M-^]), and candidate genes that could play a pathological role were identified. Results: There were 470 differentially expressed genes identified in the Turner syndrome transcriptome. The differentially expressed genes were distributed randomly across different chromosomes. Among genes on the X chromosome, XIST was down-regulated, and SHOX not differentially expressed. The most highly represented organ systems were hematologic/immune and neurologic. Increased representation of differentially expressed genes in the hematologic/immune system distinguishes the Turner syndrome transcriptome from the euploid, trisomy 18 and trisomy 21 transcriptomes previously studied in our laboratory. Manual curation of the differentially expressed gene list identified genes including NFATC3, IGFBP5, and LDLR that warrant further study. 2nd trimester amniotic fluid mRNA expression was compared between 5 Turners and 5 euploid fetuses.
2014-06-13 | E-GEOD-58435 | biostudies-arrayexpress
Project description:Nonunion describes bone fractures that fail to heal, resulting in the fracture callus failing to fully ossify or, in atrophic cases, not forming altogether. Fracture healing is regulated, in part, by the balance of pro-inflammatory and anti-inflammatory processes occurring within the bone marrow and surface cell populations. We sought to further understand the role of osteoimmunology (i.e., study of the close relationship between the immune system and bone) by examining immune cell gene expression via single-cell RNA sequencing of intramedullary canal tissue obtained from human patients with femoral nonunions. Intramedullary canal tissue samples obtained by reaming were collected at the time of surgical repair for femur fracture nonunion (n=5) or from native bone controls when harvesting autologous bone graft (n=4). Cells within the samples were isolated and analyzed using the Chromium single cell system (10x Genomics, Inc) and Illumina sequencers. Twenty-three distinct cell clusters were identified, with higher cell proportions in the nonunion samples for monocytes and CD14+ dendritic cells (DC), and lower proportions of T cells, myelocytes, and promyelocytes in nonunion samples. Gene expression differences were identified in each of the cell clusters from cell types associated with osteoimmunology, including CD14+DC, monocytes, T cells, promyelocytes, and myelocytes. These results provide human derived gene profiles that can further our understanding of pathways that may be a cause or a consequence of nonunion, providing the clinical rationale to focus on specific components of osteoimmunology. Statement of Clinical Significance. The novel single-cell approach may lead to clinically relevant diagnostic biomarkers during earlier stages of nonunion development and/or investigation into therapeutic options.
2022-11-15 | GSE217792 | GEO
Project description:To investigate the differences between disease types, RNA was isolated from healthy, SjS and SLE blood samples. We then performed gene expression profiling analysis using data obtained from RNA-seq.
2023-03-01 | GSE222408 | GEO
Project description:It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks postzygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment. Comparing the genome sequences and chromatin contact maps of the Visayan warty pig (Sus cebifrons) and domestic pig (Sus scrofa), we characterized the dynamics of chromosomal structure evolution during Sus speciation, revealing the similar chromosome conformation as the potential biological mechanism of frequent postdivergence hybridization among Suidae. We further investigated the different signatures of adaptive selection and domestication in Visayan warty pig and domestic pig with specific emphasize on the evolution of olfactory and gustatory genes, elucidating higher olfactory diversity in Visayan warty pig and positive and relaxed evolution of bitter and fat taste receptors, respectively, in domestic pig. Our comprehensive evolutionary and comparative genome analyses provide insight into the dynamics of genomes and how these change over relative short evolutionary times, as well as how these genomic differences encode for differences in the phenotypes.
| S-EPMC9178973 | biostudies-literature
Project description:Blood is the pipeline of the immune system. Assessing changes in transcript abundance in blood on a genome-wide scale affords a comprehensive view of the status of the immune system during development. However, little is known about the changes of gene expression in blood across multiple developmental stages in pigs. In this study, we performed transcriptomic analysis of messenger RNA (mRNA) and long noncoding RNA (lncRNA) expressed in whole-blood tissue from pigs of natal, suckling, weaning, sexual maturity and adult stages. A total of 5,946 lncRNA and 12,354 mRNA transcripts were identified to be substantially expressed. Short time-series expression miner (STEM) and functional enrichment analysis showed that genes with the greatest variation of expression levels between suckling period (0, 7 and 28 days) and the late stage of development (180 days and 2 years) might function in transcription, immune function, and apoptotic process. Functional prediction indicated the expression correlation and functional relatedness between mRNAs and lncRNAs. Additionally, a number of T cell-related genes were continuously up-regulated during lactation, suggesting this phase is significant for the establishment of piglet adaptive immunity. Notably, the TCONS_00192752 and TCONS-00086451 lncRNA might promote blood immune development by up-regulating the tumor necrosis factor receptor-associated factor 3 (TRAF3) and nuclear factor of activated T-cells cytoplasmic 2 (NFATC2) expression, respectively. Our research provides the first catalog of the developing pig whole-blood, and will accelerate clinical researches of immune system development with pig models.
2019-12-17 | GSE123923 | GEO
Project description:Single-cell RNA-seq provides insight into the underdeveloped immune system of germ-free mice
| PRJNA1253696 | ENA
Project description:The aims were to explore whether saliva composition could reflect the physiopathological changes occurring in canine pyometra and to identify potential biomarkers of the disease using a high-throughput quantitative proteomic analysis. Saliva samples from six healthy (H) and six bitches with pyometra (P) were analysed using Tandem Mass Tags (TMT) - based approach.
2020-04-27 | PXD018692 | Pride