Top 10 CRP-associated genes.

<p>CRP-gene expression association effect sizes (Beta) with 95% confidence intervals (CI) and p-values adjusted for 5% FDR (Adjusted p-value) are shown.</p

Pairwise modelling pipeline of whole genome sequencing (WGS), RNA sequencing (RNA-seq) and C-reactive protein (CRP) data.

<p>(A) First, we identified genes whose expression levels (denoted by E) were significantly associated with CRP. Second, we used these genes to perform a <i>cis</i>-eQTL analysis and extract SNPs (denoted by G) that act on the expression of those genes. Third, for each triplet (G, E, CRP), we used maximum likelihood to select the best supported model out of a limited number of possible models–given that G is correlated with E, E is correlated with CRP and assuming directed acyclic graphs. The dashed edge in model IV indicates that either E acts on CRP or vice versa–these two models are Markov equivalent so we cannot differentiate between them. Fourth, we ensured that the best candidate models fulfilled necessary partial correlation criteria. Fifth, we subjected the best candidates to MR analysis where the instruments were chosen from published GWAS summary statistics. Finally, we validated the findings using cell culture stimulation assays. (B) Venn diagram of available sample sizes.</p

Upregulation of <i>CD59</i> surface expression by CRP in cell culture experiments.

<p>Peripheral blood cells from two donors were treated with five increasing doses of CRP protein. For negative controls, the cells were not treated with CRP or were treated with additive NaN₃ only. The <i>CD59</i> antigen values were measured after 48 hours and are shown in mean fluorescent intensity units as the arbitrary values of flow cytometry. Black dots represent individual measurements in different replicates, red dots are the averages and whiskers represent ±1 standard errors.</p

Analytical validation of the causal CRP and <i>CD59</i> link.

<p>(A) QQ-plot of p-values from the association analysis between CRP-associated SNPs and <i>CD59</i> expression. The empirical quantiles are not in line with the theoretical quantiles of the uniform distribution (Kolmogorov-Smirnov p = 0.026) and there is some enrichment of small p-values. (B) Funnel plot of minor allele frequency corrected genetic effects on CRP against causal effect estimates between CRP and <i>CD59</i> expression for each CRP-associated SNP. (C) Scatter plot of the genetic effect on <i>CD59</i> expression against the genetic effect on CRP. Causal effect slope estimates from the TSLS solutions with the GRS_CRP instrument and with all the 16 CRP-associated SNPs as instruments (both forced through zero) are coloured in blue and green, respectively. The bias-corrected slope from the MR-Egger regression is shown in red.</p

Gene supported by the causal model with Δ_AIC ≥ 10 using the strongest <i>cis</i>-eQTL.

<p>Gene supported by the causal model with Δ_AIC ≥ 10 using the strongest <i>cis</i>-eQTL.</p

Genes supported by the colliding model with Δ_AIC ≥ 10 for at least one of the independent <i>cis</i>-eQTLs.

<p>Genes supported by the colliding model with Δ_AIC ≥ 10 for at least one of the independent <i>cis</i>-eQTLs.</p

Image_7_Cytotoxic CD8+ Temra cells show loss of chromatin accessibility at genes associated with T cell activation.jpeg

As humans age, their memory T cell compartment expands due to the lifelong exposure to antigens. This expansion is characterized by terminally differentiated CD8+ T cells (Temra), which possess NK cell-like phenotype and are associated with chronic inflammatory conditions. Temra cells are predominantly driven by the sporadic reactivation of cytomegalovirus (CMV), yet their epigenomic patterns and cellular heterogeneity remain understudied. To address this gap, we correlated their gene expression profiles with chromatin openness and conducted single-cell transcriptome analysis, comparing them to other CD8+ subsets and CMV-responses. We confirmed that Temra cells exhibit high expression of genes associated with cytotoxicity and lower expression of costimulatory and chemokine genes. The data revealed that CMV-responsive CD8+ T cells (Tcmv) were predominantly derived from a mixed population of Temra and memory cells (Tcm/em) and shared their transcriptomic profiles. Using ATAC-seq analysis, we identified 1449 differentially accessible chromatin regions between CD8+ Temra and Tcm/em cells, of which only 127 sites gained chromatin accessibility in Temra cells. We further identified 51 gene loci, including costimulatory CD27, CD28, and ICOS genes, whose chromatin accessibility correlated with their gene expression. The differential chromatin regions Tcm/em cells were enriched in motifs that bind multiple transcriptional activators, such as Jun/Fos, NFkappaB, and STAT, whereas the open regions in Temra cells mainly contained binding sites of T-box transcription factors. Our single-cell analysis of CD8+CCR7loCD45RAhi sorted Temra population showed several subsets of Temra and NKT-like cells and CMC1+ Temra populations in older individuals that were shifted towards decreased cytotoxicity. Among CD8+CCR7loCD45RAhi sorted cells, we found a decreased proportion of IL7R+ Tcm/em-like and MAIT cells in individuals with high levels of CMV antibodies (CMVhi). These results shed new light on the molecular and cellular heterogeneity of CD8+ Temra cells and their relationship to aging and CMV infection.</p

Image_9_Cytotoxic CD8+ Temra cells show loss of chromatin accessibility at genes associated with T cell activation.png

As humans age, their memory T cell compartment expands due to the lifelong exposure to antigens. This expansion is characterized by terminally differentiated CD8+ T cells (Temra), which possess NK cell-like phenotype and are associated with chronic inflammatory conditions. Temra cells are predominantly driven by the sporadic reactivation of cytomegalovirus (CMV), yet their epigenomic patterns and cellular heterogeneity remain understudied. To address this gap, we correlated their gene expression profiles with chromatin openness and conducted single-cell transcriptome analysis, comparing them to other CD8+ subsets and CMV-responses. We confirmed that Temra cells exhibit high expression of genes associated with cytotoxicity and lower expression of costimulatory and chemokine genes. The data revealed that CMV-responsive CD8+ T cells (Tcmv) were predominantly derived from a mixed population of Temra and memory cells (Tcm/em) and shared their transcriptomic profiles. Using ATAC-seq analysis, we identified 1449 differentially accessible chromatin regions between CD8+ Temra and Tcm/em cells, of which only 127 sites gained chromatin accessibility in Temra cells. We further identified 51 gene loci, including costimulatory CD27, CD28, and ICOS genes, whose chromatin accessibility correlated with their gene expression. The differential chromatin regions Tcm/em cells were enriched in motifs that bind multiple transcriptional activators, such as Jun/Fos, NFkappaB, and STAT, whereas the open regions in Temra cells mainly contained binding sites of T-box transcription factors. Our single-cell analysis of CD8+CCR7loCD45RAhi sorted Temra population showed several subsets of Temra and NKT-like cells and CMC1+ Temra populations in older individuals that were shifted towards decreased cytotoxicity. Among CD8+CCR7loCD45RAhi sorted cells, we found a decreased proportion of IL7R+ Tcm/em-like and MAIT cells in individuals with high levels of CMV antibodies (CMVhi). These results shed new light on the molecular and cellular heterogeneity of CD8+ Temra cells and their relationship to aging and CMV infection.</p

Image_5_Cytotoxic CD8+ Temra cells show loss of chromatin accessibility at genes associated with T cell activation.jpeg

As humans age, their memory T cell compartment expands due to the lifelong exposure to antigens. This expansion is characterized by terminally differentiated CD8+ T cells (Temra), which possess NK cell-like phenotype and are associated with chronic inflammatory conditions. Temra cells are predominantly driven by the sporadic reactivation of cytomegalovirus (CMV), yet their epigenomic patterns and cellular heterogeneity remain understudied. To address this gap, we correlated their gene expression profiles with chromatin openness and conducted single-cell transcriptome analysis, comparing them to other CD8+ subsets and CMV-responses. We confirmed that Temra cells exhibit high expression of genes associated with cytotoxicity and lower expression of costimulatory and chemokine genes. The data revealed that CMV-responsive CD8+ T cells (Tcmv) were predominantly derived from a mixed population of Temra and memory cells (Tcm/em) and shared their transcriptomic profiles. Using ATAC-seq analysis, we identified 1449 differentially accessible chromatin regions between CD8+ Temra and Tcm/em cells, of which only 127 sites gained chromatin accessibility in Temra cells. We further identified 51 gene loci, including costimulatory CD27, CD28, and ICOS genes, whose chromatin accessibility correlated with their gene expression. The differential chromatin regions Tcm/em cells were enriched in motifs that bind multiple transcriptional activators, such as Jun/Fos, NFkappaB, and STAT, whereas the open regions in Temra cells mainly contained binding sites of T-box transcription factors. Our single-cell analysis of CD8+CCR7loCD45RAhi sorted Temra population showed several subsets of Temra and NKT-like cells and CMC1+ Temra populations in older individuals that were shifted towards decreased cytotoxicity. Among CD8+CCR7loCD45RAhi sorted cells, we found a decreased proportion of IL7R+ Tcm/em-like and MAIT cells in individuals with high levels of CMV antibodies (CMVhi). These results shed new light on the molecular and cellular heterogeneity of CD8+ Temra cells and their relationship to aging and CMV infection.</p

DataSheet_1_Cytotoxic CD8+ Temra cells show loss of chromatin accessibility at genes associated with T cell activation.csv

As humans age, their memory T cell compartment expands due to the lifelong exposure to antigens. This expansion is characterized by terminally differentiated CD8+ T cells (Temra), which possess NK cell-like phenotype and are associated with chronic inflammatory conditions. Temra cells are predominantly driven by the sporadic reactivation of cytomegalovirus (CMV), yet their epigenomic patterns and cellular heterogeneity remain understudied. To address this gap, we correlated their gene expression profiles with chromatin openness and conducted single-cell transcriptome analysis, comparing them to other CD8+ subsets and CMV-responses. We confirmed that Temra cells exhibit high expression of genes associated with cytotoxicity and lower expression of costimulatory and chemokine genes. The data revealed that CMV-responsive CD8+ T cells (Tcmv) were predominantly derived from a mixed population of Temra and memory cells (Tcm/em) and shared their transcriptomic profiles. Using ATAC-seq analysis, we identified 1449 differentially accessible chromatin regions between CD8+ Temra and Tcm/em cells, of which only 127 sites gained chromatin accessibility in Temra cells. We further identified 51 gene loci, including costimulatory CD27, CD28, and ICOS genes, whose chromatin accessibility correlated with their gene expression. The differential chromatin regions Tcm/em cells were enriched in motifs that bind multiple transcriptional activators, such as Jun/Fos, NFkappaB, and STAT, whereas the open regions in Temra cells mainly contained binding sites of T-box transcription factors. Our single-cell analysis of CD8+CCR7loCD45RAhi sorted Temra population showed several subsets of Temra and NKT-like cells and CMC1+ Temra populations in older individuals that were shifted towards decreased cytotoxicity. Among CD8+CCR7loCD45RAhi sorted cells, we found a decreased proportion of IL7R+ Tcm/em-like and MAIT cells in individuals with high levels of CMV antibodies (CMVhi). These results shed new light on the molecular and cellular heterogeneity of CD8+ Temra cells and their relationship to aging and CMV infection.</p