Transcriptional profiling of DNA damage tolerant (DDT) lymphomas after treatment either with Albendazole, Ethidium bromide or DMSO as a control
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PROVIDER: PRJNA686078 | ENA |
REPOSITORIES: ENA
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Project description:We studied the role of Albendazole in inducing loss of heterozygosity. Here, we generated RNA-seq data from DDT lymphomas after 12 hours of treatment either with Albendazole (400nM), Ethidium bromode (400 nM) or DMSO as a control.
2021-02-05 | GSE163419 | GEO
Project description:The endocrine disrupting chemical o,p'-DDT can affect reproductive organs, tissues and cells in several species. Treatment of human endometrial endothelial cells (HEEC) with 50 µM o,p'-DDT decreased the cell proliferation compared to the control. Microarray analyses revealed that o,p'-DDT affected biological processes such as the cell cycle, cell division, defence response and lipid and steroid metabolism, in cellular components such as the plasma membrane and chromosomes, with molecular functions involved in signalling, receptor and cytokine activity, confirming the results of the proliferation assay. The present study supports our previous findings of decreased proliferation and increased cell death in response to o,p'-DDT, and may offer important clues in the deduction of the mechanisms of action of o,p'-DDT. Keywords: Exposure analysis
2007-10-10 | GSE9252 | GEO
Project description:The endocrine disrupting chemical o,p'-DDT can affect reproductive organs, tissues and cells in several species. Treatment of human endometrial endothelial cells (HEEC) with 50 µM o,p'-DDT decreased the cell proliferation compared to the control. Microarray analyses revealed that o,p'-DDT affected biological processes such as the cell cycle, cell division, defence response and lipid and steroid metabolism, in cellular components such as the plasma membrane and chromosomes, with molecular functions involved in signalling, receptor and cytokine activity, confirming the results of the proliferation assay. The present study supports our previous findings of decreased proliferation and increased cell death in response to o,p'-DDT, and may offer important clues in the deduction of the mechanisms of action of o,p'-DDT. Keywords: Exposure analysis Two-condition experiments, o,p'-DDT-exposed vs. control HEEC, and individual control vs control pool. Biological replicates: 5 HEEC cultures, independently grown, exposed and harvested. One replicate per array. Dye-swaps for exposed and reference samples between replicates. variable = Exposure: o,p'-DDT-treated: Indiv1 s1 op-DDT Cy3, Indiv2 s19 op-DDT Cy3, Indiv3 s37 op-DDT Cy3, Indiv4 s55 op-DDT Cy5, Indiv5 s73 op-DDT Cy5 variable = Exposure: control: Indiv1 s2 control Cy5, Indiv2 s20 control Cy5, Indiv3 s38 control Cy5, Indiv4 s56 control Cy3, Indiv5 s74 control Cy3 variable = Exposure: individual control: Indiv1 s17 control Cy3, Indiv2 s35 control Cy5, Indiv3 s53 control Cy3, Indiv4 s71 control Cy5, Indiv5 s89 control Cy3 variable = Exposure: control pool: Pooled control s18/36/54/72/90 Cy5, Pooled control s18/36/54/72/90 Cy3, Pooled control s18/36/54/72/90 Cy5, Pooled control s18/36/54/72/90 Cy3, Pooled control s18/36/54/72/90 Cy5 repeat = Biological replicate: Indiv1 s1 op-DDT Cy3, Indiv1 s2 control Cy5, Indiv1 s17 control Cy3, sample 18 in Pooled control repeat = Biological replicate: Indiv2 s19 op-DDT Cy3, Indiv2 s20 control Cy5, Indiv2 s35 control Cy5, sample 36 in Pooled control repeat = Biological replicate: Indiv3 s37 op-DDT Cy3, Indiv3 s38 control Cy5, Indiv3 s53 control Cy3, sample 54 in Pooled control repeat = Biological replicate: Indiv4 s55 op-DDT Cy5, Indiv4 s56 control Cy3, Indiv4 s71 control Cy5, sample 72 in Pooled control repeat = Biological replicate: Indiv5 s73 op-DDT Cy5, Indiv5 s74 control Cy3, Indiv5 s89 control Cy3, sample 90 in Pooled control
2007-10-10 | E-GEOD-9252 | biostudies-arrayexpress
Project description:Transcriptional profiling of three Anopeheles arabiensis strains: (i) DDT resistant mosquitoes from the city of Bobo Dioulasso (ii) mosquitoes from Bobo Dioulasso not exposed to DDT (iii) a laboratory DDT-susceptible strain.
2012-07-30 | E-MTAB-1224 | biostudies-arrayexpress
Project description:Gestating F0 generational female rats were transiently exposed to DDT during fetal gonadal sex determination and the incidence of adult onset pathologies was assessed in the subsequent F1, F2, and F3 generations. In addition, sperm differential DNA methylation regions (DMRs) that were associated with specific pathologies in the F3 generation males were investigated. No pathology was observed in the F1 generation DDT lineage males or females compared with F1 generation controls (vehicle exposure). There was an increase of testis disease and early onset puberty in the F2 generation DDT lineage males. The F3 generation DDT males had significant increases in testis disease, prostate disease, and late onset puberty. The F3 generation DDT females had significant increases in ovarian and kidney disease. Both the F3 generation males and females had significant increases in the frequency of obesity and multiple disease. The F3 generation sperm was collected to examine DMRs for the ancestrally exposed DDT male population. Unique sets of DMRs were associated with late onset puberty, kidney disease, and multiple disease pathologies.
2018-07-31 | GSE114032 | GEO
Project description:In previous studies, the pesticide DDT was shown to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs), also called epimutations, which can mediate this epigenetic inheritance. In the current study, the developmental origins of the transgenerational DMRs during gametogenesis have been investigated. Male control and DDT lineage F3 generation rats were used to isolate embryonic day 16 (E16) prospermatogonia, postnatal day 10 (P10) spermatogonia, adult pachytene spermatocytes, round spermatids, caput epididymal spermatozoa, and caudal sperm. The DMRs between the control versus DDT lineage samples were determined at each developmental stage. The top 100 statistically significant DMRs at each stage were compared and the developmental origins of the caudal epididymal sperm DMRs were assessed.
2019-01-19 | GSE121585 | GEO
Project description:Deep-sequencing analysis of mRNA expression differences between imidacloprid and DDT resistant mutant line and iso31 (w1118) susceptible line have been obtained. A total of 357 transcripts were found to be differently expressed, with 150 upregulated and 207 downregulated genes in the resistant line.
2012-06-28 | GSE28560 | GEO
Project description:Immunoglobulin gene rearrangement and somatic hypermutation have the potential to create neoantigens in non-Hodgkin B cell lymphoma. However, the presentation of these putative immunoglobulin neoantigens by B cell lymphomas has not been proven. We used MHC immunoprecipitation followed by liquid chromatography and tandem mass spectrometry (LC-MS/MS) to define antigens presented by follicular lymphomas (FL), chronic lymphocytic leukemias (CLL), diffuse large B cell lymphoma (DLBCL) and mantle cell lymphomas (MCL). We found presentation of the clonal immunoglobulin molecule, including neoantigens by both class I and class II MHC, though more commonly in class II MHC. To determine whether B cell activation could promote presentation of immunoglobulin neoantigens, we used a toll-like receptor 9 (TLR9) agonists to upregulate expression of MHC-II. This resulted in enhanced class II MHC presentation of the immunoglobulin variable region including neoantigens. These findings demonstrate that immunoglobulin neoantigens are presented across most subtypes of B cell lymphomas. Activation of lymphoma cells to upregulate antigen presentation boosts presentation of immunoglobulin neoantigens and represents a strategy for augmenting lymphoma immunotherapies.
2019-01-07 | PXD010808 | Pride
Project description:Environmental factors have been shown to induce the epigenetic transgenerational inheritance of disease through the germline. This study was designed to investigate DDT induced concurrent alterations of a number of different epigenetic processes including DNA methylation and histone retention in sperm. Gestating female rats were exposed transiently to DDT during fetal gonadal development and then F1, F2 and F3 generation sperm were analyzed.
2018-04-27 | GSE109775 | GEO
Project description:Ataxia-telangiectasia mutated (ATM) kinase plays a central role in maintaining genomic integrity. In both humans and mice, ATM deficiency is associated with an increased incidence of lymphoid cancers that are primarily T cell in origin. We demonstrate here that when T cells are removed as targets for lymphomagenesis and as mediators of immune surveillance, ATM-deficient mice exclusively develop early onset IgM+ B cell lymphomas that by histology and gene expression profiling resemble the activated B cell-like (ABC) subset of human diffuse large B cell lymphomas (DLBCL). These ATM-deficient B cell tumors show considerable chromosomal instability and a recurrent genomic amplification of a 4.48 Mb region on chromosome 18 that contains Malt1 and is orthologous to a region similarly amplified in human ABC-DLBCL. Further, the amplification of Malt1 in these lymphomas correlates with their dependence on NF-kB, MALT1, and BCR signaling for survival, paralleling human ABC-DLBCL. This study reveals that ATM protects against development of B cell lymphomas that model human ABC-DLBCL and identifies a role for T cells in preventing the emergence of these tumors. We performed gene expression profiling on nine ATMKO.CD3epsilonKO lymphoma cell lines (n=12, 3 technical repeats). We analyzed gene expression of anti-IgM stimulated primary B cells from both ATMKO.CD3epsilonKO (n=7, 5 technical repeats) and ATMWT.CD3epsilonKO mice (n=2), and GC B cells isolated from SRBC-immunized ATMWT mice (n=3, 1 biological repeat and 2 technical repeats). We analyzed gene expression following treatment of two ATMKO.CD3epsilonKO lymphoma cell lines with the BTK inhibitor, PCI-32765, at time points (1, 3, 6, and 24 hours) as compared to time points with vehicle (DMSO) (n=8).
2015-12-09 | E-GEOD-68505 | biostudies-arrayexpress