Journal: bioRxiv

Article Title: SURVIVIN IN SYNERGY WITH BAF/SWI COMPLEX BINDS BIVALENT CHROMATIN REGIONS AND ACTIVATES DNA DAMAGE RESPONSE IN CD4+ T CELLS

doi: 10.1101/2024.03.05.583464

Figure Lengend Snippet: (A) Cartoon of analysis strategy. BvCR within genomic regulatory elements ( cis -RE, grey boxes) connected to genes, filtered on the protein-coding genes expressed in CD4 + cells, by RNA-seq. Transcription difference in CD4 + cells treated with IFNg or IFNg+YM155 compared to sham cultures was calculated by DESeq2. Differentially expressed genes (DEG) were defined by a nominal p-value<0.05. (B) Radar plot of Spearman’s rho correlations between H3K4me3 and H3K27me3 tag deposition change in all and survivin-positive BvCR and transcription change in CD4 + cells treated with IFNg or IFNg+YM155. Arrows indicate direction of transcription change. (C) Bubble plot of enrichment in biological processes among CD4 + expressed genes connected to all and survivin-positive BvCR. Bubble size indicates protein number in the process. Color intensity shows false discovery range (FDR). (D) Nodes of the DDR network are colored by dominant H3 mark in BvCR connected to genes within nodes (top map) and by transcription change after IFNγ or YM155 treatment (bottom map). Size of bubble corresponds to percentage of BvCR-connected genes within each node. DDR, DNA damage response. MMR, mismatch repair. RFC, replicator factor C. SSB, single strand break. DSB, double-strand break. HR, homologous recombination. MRN, MRE11-RAD50-NBS1. (E) Confocal image of THP1 nucleus showing presence of survivin (red), nucleus (blue) and BRG1 or H3K4me3 (green). (F) Heatmap of normalized tag deposition of H3 marks, by ChIP-seq, in BvCR connected to DEG treated with IFNγ+YM155. Shaded squares indicate survivin-positive BvCR. Genes connected to multiple BvCR are marked in bold. (G) Heatmap of RNA-seq transcription difference in genes annotated to DNA repair and stress response categories. Transcription difference was calculated by DESeq2 statistics, p-values * < 0.05, ** < 0.01, *** <0.001.

Article Snippet: RNA from the CD4 + cell cultures was prepared using the Norgen Total RNA kit (17200 Norgen Biotek, Ontario, Canada).

Techniques: RNA Sequencing Assay, Homologous Recombination, ChIP-sequencing

Journal: bioRxiv

Article Title: SURVIVIN IN SYNERGY WITH BAF/SWI COMPLEX BINDS BIVALENT CHROMATIN REGIONS AND ACTIVATES DNA DAMAGE RESPONSE IN CD4+ T CELLS

doi: 10.1101/2024.03.05.583464

Figure Lengend Snippet: (A) Dot correlation plot of normalized mean expression of BRG1, BIRC5 and IFNG genes in CD4 + cells of patients with rheumatoid arthritis. Spearman’s rho values are indicated. (B) Venn diagram of differentially expressed genes (DEG) in BRG1 hi CD4 + cells connected to BvCR and in IFNγ-treated CD4 + cells. Heatmap of Spearman’s rho correlation values of genes connected to BvCR in BRG1 hi and BRG1 lo cells identified by weighted correlation network analysis (WGCNA). (C) Heatmap of expression difference in T cell specific markers identified by RNA-seq in BRG1 hi CD4 + cells and in CD4 + cells before and after treatment with abatacept (ABAT, n=14), tocilizumab (TOCI, n=6) and methotrexate (MTX, n=28) and in CD4 + cells of JAKi-treated (n=23) and untreated (n=9) RA patients. Expression difference in CD4 + cells before and after treatment (for ABAT, TOCI and MTX) and in JAKi treated and untreated patients was calculated by DESeq2. Nominal p-values are indicated. * < 0.05, ** < 0.01, *** <0.001. (D) Venn diagram of DEG changed with treatment in the DNA damage response (DDR) network. DDR network map of DEG changed with treatment. Node size indicates the percentage of BRG1 hi DEG. Node color indicates the percentage of DEG in the node. (E) Heatmap of expression difference in BAF/SWI complex proteins in BRG1 hi CD4 + cells and in CD4 + cells after treatment, by RNA-seq. Expression difference was calculated by DESeq2. Nominal p-values are indicated. * < 0.05, ** < 0.01, *** <0.001. (F) Heatmap of expression difference in DDR network genes in BRG1 hi CD4 + cells and in CD4 + cells after treatment.

Article Snippet: RNA from the CD4 + cell cultures was prepared using the Norgen Total RNA kit (17200 Norgen Biotek, Ontario, Canada).

Techniques: Expressing, RNA Sequencing Assay

Journal: Current Research in Immunology

Article Title: Gamma-tocotrienol modifies methylation of HOXA10, IRF4 and RORα genes in CD4 + T-lymphocytes: Evidence from a syngeneic mouse model of breast cancer ☆

doi: 10.1016/j.crimmu.2021.10.001

Figure Lengend Snippet: Comparing percentage of DNA methylation in CD4 + T-lymphocytes from ( A ) control (no tumour) or ( B ) tumour-induced mice fed with (A) vehicle (soy oil) or (B) γT3 (γT3 in soy oil). Genomic DNA was extracted from CD4 + T-lymphocytes (QIAGEN DNeasy Blood and Tissue mini kit) isolated from peripheral blood at autopsy. The DNA was analysed for modification in the DNA methylation of the 22 genes that were annotated in the commercial DNA methylation array (EpiTech Methyl II signature PCR for murine T-helper differentiation array plate, SABioscience, USA). Data is represented as mean percentage of methylation ± standard deviation (SD) and is representative of at least three independent mice. (*P < 0.05 versus vehicle, tumour).

Article Snippet: Genomic DNA was extracted from the isolated CD4 + T-lymphocytes using the QIAGEN DNeasy Blood and Tissue mini kit as recommended by the manufacturer's protocol (QIAGEN, USA).

Techniques: DNA Methylation Assay, Control, Isolation, Modification, Methylation, Standard Deviation

Journal: Current Research in Immunology

Article Title: Gamma-tocotrienol modifies methylation of HOXA10, IRF4 and RORα genes in CD4 + T-lymphocytes: Evidence from a syngeneic mouse model of breast cancer ☆

doi: 10.1016/j.crimmu.2021.10.001

Figure Lengend Snippet: Comparing percentage of DNA methylation in CD4 + T-lymphocytes from tumour-induced mice fed with (A) vehicle (soy oil) or (B) γT3 (γT3 in soy oil). Genomic DNA was extracted from CD4 + T-lymphocytes (QIAGEN DNeasy Blood and Tissue mini kit) isolated from peripheral blood at autopsy. The DNA was analysed for modification in the DNA methylation of the 22 genes that were annotated in the commercial DNA methylation array (EpiTech Methyl II signature PCR for murine T-helper differentiation array plate, SABioscience, USA). Data is represented as mean percentage of methylation ± standard deviation (SD) and is representative of at least three independent mice. (*P < 0.05 versus vehicle, tumour).

Article Snippet: Genomic DNA was extracted from the isolated CD4 + T-lymphocytes using the QIAGEN DNeasy Blood and Tissue mini kit as recommended by the manufacturer's protocol (QIAGEN, USA).

Techniques: DNA Methylation Assay, Isolation, Modification, Methylation, Standard Deviation