Fig. 5: COVID-19 related SLFN5 gene is regulated via chromatin accessibility in lymphocytes. | Nature Communications

Fig. 5: COVID-19 related SLFN5 gene is regulated via chromatin accessibility in lymphocytes.

From: Unveiling genetic signatures of immune response in immune-related diseases through single-cell eQTL analysis across diverse conditions

Fig. 5: COVID-19 related SLFN5 gene is regulated via chromatin accessibility in lymphocytes.

a eQTL effects of SLFN5-rs11080327. Panels display response eQTL per stimulation: BCG-vaccination, LPS pre-BCG-vaccination, 3-month post-BCG-vaccination. Colors represent genotypes. The X-axis shows conditions. The Y-axis is SLFN5 expression. Error bars are mean values +/− SD (95%-CI) and mean expression are connected by line (n = 152 samples). Whiskers of boxplots expand to minima and maxima, boxes indicate 25th / 75th percentiles, and centers represent medians. b Regulation potentials of SLFN5-rs11080327. Track-plot includes chromosome, genome-coordination, eQTL p-values in CD4 + T cells (LMM adjusting age and sex) and COVID-19 GWAS p-values (logistic regression), OCRs (PBMC), gene-enhancer interactions (UCSC genome browser), and gene (ENSEMBL). Red dots (tracks 3, 4) denote rs11080327. Red bars (track 5) denote OCRs overlapping rs11080327. c SLFN5 expression per COVID-19 condition (CD4 + T). Dot colors and sizes indicate average expression and cells (percentage) expressing SLFN5, respectively. Violin plots show SLFN5 normalized-expression (x-axis) per cell type (adjusted-p-value = 3.71e-08, log2-FC = 0.22, LR-test, adjusted-p-value < 0.0001: ‘****’). dSLFN5-rs11080327 eQTL in COVID-19. Dot colors and sizes show average expression and cells (percentage) expressing SLFN5 per condition per genotype. Violin plots show SLFN5 normalized expression (x-axis). Convalescent, adjusted-p-value GA/AA = 2.26e-04, log2-FC GA/AA = −0.20; adjusted-p-value GG/AA = 7.91e-10, log2-FC GG/AA = − 0.24; adjusted-p-value GG/GA = 0.28, log2-FC GG/GA = -0.04. Hospitalized: adjusted-p-value GA/AA = 0.20, log2-FC GA/AA = − 0.06; adjusted-p-value GG/AA = 6.36e-05, log2-FC GG/AA = −0.06; adjusted-p-value GG/GA = 1.08e-04, log2-FC GG/GA = 0.01. LR-test (adjusted-p-value > 0.05: ‘·’, < 0.001: ‘***’, <0.0001: ‘****’). e OCRs at rs11080327 (COVID-19). The top two tracks display OCRs (CD4 + T). “Peaks” shows OCRs correlated to SLFN5 expression in “Peak2GeneLinks”. The color of connection suggests Pearson’s rho correlation. f Allelic open chromatin at eVariant in COVID-19 (CD4 + T). Green and purple denote read counts covering G/A alleles. Light blue shows gross read counts. g Allelic TF binding affinities (rs11080327). The left panel shows allelic TF-binding affinities. The right panel displays allelic TF brokenness. Colors denote significance (adjusted-p-value < 0.05). X-axis are log2-FC of binding affinity and motif-break-score (alternative to reference). h Potential regulations of SLFN5 expression upon stimulation (infection) involving allelic open chromatin (Created in BioRender. Zhan, Q. (2025) https://BioRender.com/c28r787).

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