Journal: bioRxiv

Article Title: Integration of genetic and epigenetic data pinpoints autoimmune specific remodelling of enhancer landscape in CD4+ T cells

doi: 10.1101/2024.01.11.575022

Figure Lengend Snippet: A) Schematic representation of experimental procedure of CD4+ T cell isolation and H3K27ac ChIP-seq assay from patients and healthy controls; table containing sample information (F=female; M = male). B) Genomic tracks with H3K27ac signal around CD4 and CD28 genes for representative disease and control samples. C) PCA based on the top 1000 most variable acetylated peaks within each disease and corresponding control samples. D) K-means clustering of consensus peakset based on log2 fold changes in H3K27ac marks between patient and control samples in each disease. E) GO enrichment terms for each cluster in D based on closest genes using GREAT.

Article Snippet: For CRISPRi experiments, frozen healthy donor naive CD4+ T cells were obtained from AllCells.

Techniques: Cell Isolation, ChIP-sequencing

Journal: bioRxiv

Article Title: Integration of genetic and epigenetic data pinpoints autoimmune specific remodelling of enhancer landscape in CD4+ T cells

doi: 10.1101/2024.01.11.575022

Figure Lengend Snippet: A) Upset plot of shared and unique significantly differential TFs across diseases. B) Inflammation relevant differential TFs (zoomed in) shared across all ADs. C) Disease-specific differential activity of CD4+ T helper cell lineage defining TFs. D-G) Volcano plot with differential TF activity (x-axis) vs log 10 adjusted p-value (y-axis) for SLE (D), Graves’ disease (E), Psoriasis (F), and JIA (G). Selected disease specific TFs are highlighted.

Article Snippet: For CRISPRi experiments, frozen healthy donor naive CD4+ T cells were obtained from AllCells.

Techniques: Activity Assay

Journal: bioRxiv

Article Title: Integration of genetic and epigenetic data pinpoints autoimmune specific remodelling of enhancer landscape in CD4+ T cells

doi: 10.1101/2024.01.11.575022

Figure Lengend Snippet: A) Schematic of T cell eGRN inference from paired RNA- and ATAC-seq data from naive CD4+ T cells from healthy individuals. B) Schematic representation of the naive CD4+ T cell eGRN. Numbers indicate the total number of transcription factors (TFs, red), single-nucleotide polymorphisms (SNPs, yellow), enhancers (peaks, green) and genes (orange) included in the network. C) Percentage of overlapping peak-gene connections from the T cell eGRN with known eQTL-gene interactions (y-axis). Data is shown for significant and non-significant peak-gene correlation pairs (x-axis) obtained from the naive CD4+ T cell eGRN. White numbers in bars indicate the number of overlapping genes / total number of genes. D) Percentage of peak-gene interactions (x-axis) from the T cell eGRN with peaks associated to the transcription start site (TSS) of the nearest genes, or another gene (y-axis). E) Percentage of genes (x-axis) from the naive CD4+ T cell eGRN linked to enhancers, enhancers & promoters or only promoters (y-axis). F) GO enrichment of biological processes based on all genes included in the whole naive CD4+ T cell eGRN (whole eGRN) and specific communities (indicated by numbers, x-axis). Top TFs for each community (based on degree) are highlighted.

Article Snippet: For CRISPRi experiments, frozen healthy donor naive CD4+ T cells were obtained from AllCells.

Techniques:

Journal: bioRxiv

Article Title: Integration of genetic and epigenetic data pinpoints autoimmune specific remodelling of enhancer landscape in CD4+ T cells

doi: 10.1101/2024.01.11.575022

Figure Lengend Snippet: A) Overview of AD eGRNs generation method from the CD4+ T cell eGRN through overlap with disease specific molecular evidence (ME). B) Number of unique transcription factors (TFs), peaks, genes and total connections included in each disease specific eGRN. C) Upset plot showing the intersection of genes across the disease specific eGRNs. Shades in barplots indicate the proportion of genes with specific ME. D-E) Enrichment of genes from the disease specific eGRNs (x-axis) with disease associated genes (D) and known drug targets obtained from the Open Targets Platform (D). Number of genes are indicated in the bars (*= Fisher’s exact test p-value <0.05 & odds ratio > 1). F) GO term enrichment analysis of AD eGRNs (columns). Pso. = psoriasis, Gra. = Graves’ disease. G) Enrichment of community genes from (x-axis) across AD eGRNs. Only significant enrichments are shown (Fisher’s exact test p-value < 0.05 & odds ratio > 1). H) Force-directed visualisation of the AD eGRNs. Colours correspond to genes coming belonging to enriched communities.

Article Snippet: For CRISPRi experiments, frozen healthy donor naive CD4+ T cells were obtained from AllCells.

Techniques:

Journal: bioRxiv

Article Title: Integration of genetic and epigenetic data pinpoints autoimmune specific remodelling of enhancer landscape in CD4+ T cells

doi: 10.1101/2024.01.11.575022

Figure Lengend Snippet: A) Enrichment (log2 odds ratio, y-axis) of T cell specific SEs across the naive CD4+ T cell eGRN and AD specific eGRNs (x-axis) (Fishers’ exact test, * = p-value <0.05). Number of genes from the eGRNs overlapping with super enhancers are indicated. B) H3K27ac changes in autoimmune patients versus controls (y-axis) for enhancers from AD specific eGRNs. Enhancers are separated based on their overlap with T cell specific super enhancers (black = overlapping, grey = non-overlapping). Number of unique enhancers is indicated. * = p-value <0.05 (T test). C) Gene expression changes in JIA patients upon BET inhibitor treatment versus no treatment (JQ1+ vs JQ1-, y-axis) for genes connected to JIA-specific differential enhancers from JIA-eGRN (Enhancer-Gene eGRN) and enhancer-gene connected only by proximity (Enhancer-Gene proximity). Genes are stratified based on whether they are connected to T cell specific SE (black = overlapping, grey = non-overlapping) * = p-value <=0.1; ** = p-value <=0.01; NS = Non-significant (T test). D) JIA-eGRN with TF, enhancer and gene connection for JIA specific differential enhancers within SEs in JIA-eGRN

Article Snippet: For CRISPRi experiments, frozen healthy donor naive CD4+ T cells were obtained from AllCells.

Techniques: Expressing

Journal: bioRxiv

Article Title: Integration of genetic and epigenetic data pinpoints autoimmune specific remodelling of enhancer landscape in CD4+ T cells

doi: 10.1101/2024.01.11.575022

Figure Lengend Snippet: A ) Ranked list of prioritised genes relevant for AD (y-axis) based on their presence in AD specific eGRNs, and different types of molecular evidence associated with them (x-axis). B ) Genomic context of ICOS / CTLA4 / CD28 and their links to AD eGRN enhancers (top grey boxes), binding sites for differential TF (blue boxes with TFs highlighted in black), differential H3K27ac peaks in AD (pink boxes), hQTL-GWAS peaks (purple boxes) and GWAS-SNPs associated with AD (dark green stripes). C ) Change in gene expression of ICOS / CTLA4 / CD28 in stimulated versus resting CD4+ T cells (DESeq2 log2 fold change, y-axis). D ) Change in H3K27ac signal of enhancers from the AD eGRNs linked to ICOS / CTLA4 / CD28 in AD patients versus controls (DESeq2 log2 fold change, y-axis). E ) Differential TF activity in AD patients versus controls (calculated using DiffTF, y-axis) for KLF3 and SP2. F) Expression of ICOS / CTLA4 / CD28 upon CRISPRi-mediated enhancer inhibition in primary human CD4+ T cells. mRNA expression relative to one non-targeting control gRNA (scramble) is shown as mean ± SEM. G ) Genomic context of ANKRD55 / IL6ST and their links to AD eGRN enhancers. H ) Change in H3K27ac signal of enhancers from the AD eGRNs linked to ANKRD55 / IL6ST (x-axis). I ) Differential TF activity in AD patients versus controls for KLF3 and SP2. J ) Change in gene expression of ANKRD55 / IL6ST (x-axis) in stimulated versus resting CD4+ T cells. K ) Expression of IL6ST upon CRISPRi-mediated enhancer inhibition in primary human CD4+ T cells. * = p-value <0.05, ** = p-value <0.01, *** = p-value <0.001.

Article Snippet: For CRISPRi experiments, frozen healthy donor naive CD4+ T cells were obtained from AllCells.

Techniques: Binding Assay, Expressing, Activity Assay, Inhibition