ScRNA-seq of day 32 p.i. GC B cells induced by experimental Plasmodium infection following the inducible deletion of IL-21 from CD4 T cells on day 16-18
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PROVIDER: PRJNA1065457 | ENA |
REPOSITORIES: ENA
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Project description:IL-21 is critical for initiating humoral immune responses, but whether sustained IL-21 production by T follicular helper cells regulates the quality or output of memory B cells and plasma cells during an established germinal center response is unknown. Here, we applied scRNA and approaches to determine the heterogeneity of germinal center B cells from Plasmodium infected mice with or without truncated IL-21 expression.
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Project description:This study compared the gene expression of extraembryonic membranes (EEM) from in vitro produced (IVP) and in vivo (AI) derived embryos. Samples of EEM from AI and IVP pregnancies were collected on days 18 and 32. A piece of the conceptus (day 18) or chorioallantois (day 32) were used for DNA and RNA isolation and subsequent determination of the sex by amplification of a Y-linked region of the DNA. The male and female ratios were analyzed by Chi-square of SAS. A subset of three female and three male EEM samples from each group (AI and IVP, days 18 and 32) were used for transcriptome analysis. Differentially expressed genes (DEGs) between groups, sex, and days were determined using edgeR-robust. A false discovery rate (FDR) <0.05 was used for statistical significance, and Toppgene platform was used for biological processes analysis. Sex ratio was similar on day 18 for AI and IVP groups. On day 32, the IVP group had a greater number of females than males (75 vs 25%, P=0.004). On day 18 female embryos, out of 71 DEGs identified, 50 were upregulated in IVP, and 21 in AI. The trophectoderm marker, TKDP2, was upregulated in the AI group, whereas IGF2, which is involved in placenta development, and APOA2, APOB, and APOE, which are important for lipid metabolism, were upregulated in the IVP group. Male embryos on day 18 had 22 DEGs, being 15 upregulated in AI and 7 in IVP. Female embryos on day 32 had 74 DEGs, with 21 upregulated in AI and 53 in IVP embryos. Some of the genes with increased expression in the IVP group were PTGIS, APOB, and APOH, which are related to lipid synthesis and metabolism. Male embryos on day 32 presented 899 DEGs, 564 upregulated in AI and 335 in IVP. Embryos from IVP had increased expression of genes related to embryo development, morphogenesis, neurogenesis, and developmental growth. In addition, male IVP embryos had decreased expression of genes related to lipid and carbohydrate metabolism. Interestingly, PLAC8B, BRB, pregnancy-associated glycoproteins (PAG) 7, 9, 10, and 19, were also downregulated in IVP male EEM. When comparing IVP males and females, there were 6753 DEGs, with 3091 being upregulated in females, and 3662 in male conceptuses on day 18. Some of the genes upregulated in females were related to placental function such as TKDP4, PLAC8A and PAGs 6, 8, 10, 12, 17, 18 and 19. On males, IFNT-related genes were upregulated (IFNT, IFNT2 IFNT3 and IFN-T). On day d32, there were 6772 DEGs, with 3252 genes with increased expression in female, and 3520 in male placentas. Among the genes increased in female placentas are genes involved in placentation: PAGs 17, 19, 9 and PLAC8B. On the other hand, PAG1 was detected as highly expressed in male placentas. In conclusion, IVP-derived male embryos were more susceptible to alterations in gene expression and these effects extend to the peri-implantation period including genes associated with placental development and markers of placental function.
2023-12-15 | GSE192417 | GEO
Project description:Paraburkholderia sp. 32 strain:32 Genome sequencing
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Project description:The oscillation status of the circadian clock during late gestation is not clear. To gain a better understanding on the oscillation state of the clock and possible influences by maternal cues, we performed transcriptome analyses on the fetal liver tissue during late gestation. Fetal liver transcriptome data were analyzed and compared to adult mouse data in the public database: GSE11923 and GSE13093 (only samples GSM327130 to GSM327141). Re-analyzed (gc-RMA) data from GSE11923 and GSE13093 linked below as supplementary files. Fetal mouse liver tissues were collected at four hours intervals across embryonic day 18 and day 19. Groups 1 and 2.
2011-09-30 | E-GEOD-28622 | biostudies-arrayexpress
Project description:Xylella fastidiosa 32 strain:32 Genome sequencing and assembly
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Project description:Glucocorticoids (GCs) are commonly used to treat patients suffering from lymphoid malignancies i.e. leukemia and multiple myeloma. Although GCs are known to be strong inducers of apoptosis in lymphoid cells, the molecular determinants of GC therapy resistance are poorly understood. Although GC treatment triggers important changes in gene expression, few studies have addressed the regulatory role of small regulatory microRNAs (miRNAs) in GC therapy response. Only recently, aberrant microRNA expression has been linked to the development of haematological malignancies and microRNAs have become master regulators of drug resistance. We identified GC inducible mRNA and microRNA transcription profiles in GC sensitive MM1S as compared to GC resistant MM1R cells. Transcriptome analysis revealed that GCs regulate multiple genes involved in cell cycle control, cell organization and cell death in MM1S, which remain unaffected in MM1R cells. Correspondingly, GCs selectively trigger cell death in MM1S but not in MM1R. Out of 32 microRNAs responsive to GC in MM1S cells but not in MM1R cells, mir-150 was identified as the most persistent GC responsive microRNA. Furthermore, Ingenuity Pathways Analysis (IPA) revealed that ectopic transfection of a synthetic mir-150 mimics GC therapy response in MM1S cells, associated with selective changes in mRNA levels of typical GR transactivated and transrepressed target genes. Although mir-150 largely mirrors GC responsive changes in gene expression of the transcription factor Myb, GR chaperone FKBP5, cell cycle modulator proteins (IL23A, SKP2, CDKN1A), chemokine signaling proteins (CXCR4, CX3CR1, CCL3) and mTOR/UPR stress related proteins (DDIT4, TXNIP), we also observed mir-150 selective effects on transcription factors (NR3C2 (MR), Myb, Fos, Jun, C/EBP-beta, IRF4, NFE2L1, ATF3, ATF4,), chaperone molecules HSPA8, HSP90AB1), the sodium channel SCNN1G and UPR stress proteins (TRIB3, DDIT3). Remarkably, mir-150 overexpression was not able to overcome GC therapy resistance, since we could not detect GC like effects of mir-150 in GR (NR3C1) deficient MM1R cells. Altogether GC-inducible mir-150 adds a novel complex layer of regulation for fine tuning GC specific therapeutic responses in multiple myeloma.
2014-12-01 | GSE59805 | GEO
Project description:Several different immune-activated cell types with particular cytokine patterns are identified such as keratinocytes, T helper cells, cytotoxic T cells, dendritic cells, macrophages, fibroblasts, and endothelial cells. The expression of well-known pathogenic factors such as TNF-α, IL-8 (CXCL8), L-23 and IL-17 is confirmed in different inflammatory cells. Furthermore, IL-14 (TXLNA; alpha-taxilin), IL-18 and IL-32 are identified as less well-known, and putative new pathogenic factors. Prominent expression of IL-18 is found in keratinocytes, macrophages and Langerhans cells, prominent IL-32 is found in T helper and regulatory T cells, IL-14 is mainly expressed by keratinocytes, fibroblasts and macrophages. Validation of gene expression is performed by ISH of human skin samples. In a murine model of psoriasis, IL-14 and IL-18 are significantly higher expressed in psoriasis-like skin lesions than in normal skin. In an analysis of serum samples from psoriasis patients, IL-18 shows higher expression in psoriasis patients compared to controls, and serum levels in psoriasis responded to treatment with IL-17 inhibitors.
2023-08-14 | GSE221648 | GEO