Journal: Nature Communications

Article Title: The sex-biased chromatin modifier SMC1A promotes autoimmunity by shaping inflammatory pathways in patients with SLE

doi: 10.1038/s41467-025-65309-7

Figure Lengend Snippet: A SMC1A levels (DESeq2 normalized counts) in blood RNA-sequencing from male and female SLE and healthy individuals (n = 15/group). Log2-fold change for the male versus female comparison, with corresponding p-values, were generated using DESeq2 without adjustment for multiple comparisons. B TaqMan Assays was performed to assay differential SMC1A mRNA levels in blood monocytes from clusters of healthy (n = 10 males, 8 females) and SLE individuals (n = 18 males, 21 females). Mixed model analysis accounted for nested data structure and inter-individual variability, introducing sex (male versus female), state (SLE versus healthy) and the sex × state interaction as within-cluster covariates. Least Squares Means method was used for post-hoc sex comparisons without multiple-testing adjustment. C Western immunoblotting for SMC1A and GAPDH in blood monocytes from SLE patients (n = 4 male/female pairs). The lower lane provides a summary of the SMC1A levels were normalized by GAPDH. Mixed model analysis was performed as above. D SMC1A expression levels (normalized) in the blood from male (n = 27) and female (n = 25) patients with ankylosing spondylitis (AS). The GEO dataset GSE73754 was analyzed using shinyGEO (ILMN_1652006 probe). P-value was produced from unpaired Student’s t test. E RT-qPCR (SYBR Green) was performed to assay SMC1A mRNA levels in blood monocytes from AS patients (n = 16 male/female pairs) and healthy individuals (n = 9 male/female pairs). Mixed model analysis was performed as in ( B ). F SMC1A levels (normalized) in blood RNA-sequencing from 46,XX females (n = 15), males with Klinefelter syndrome (47,XXY) (n = 35) and 46,XY males (n = 15). Dataset GSE42331 was analyzed and expression levels were normalized with the Bioinformatics Array Research Tool. ANOVA was performed with post-hoc Tukey’s test. G Experimental setup to generate SLE-like monocytes. Healthy CD14 + monocytes were pre-treated with IFNα and TNF for 18 h, followed by LPS for 1–4 h. Created in BioRender. H SMC1A mRNA (RT-qPCR) in blood monocytes from healthy individuals (n = 13 male/female pairs), either untreated (basal state) or stimulated as described in ( G ) (SLE-like). Mixed model analysis was performed as described in ( B ). In all panels, dots represent different individuals, and bar plots show the mean ± standard error (SE) expression. All p-values are two-tailed.

Article Snippet: The SMC1A primers and probe (Hs00196849_m1) and GAPDH primers and probe (Hs02786624_g1) were part of TaqMan gene expression assays from Applied Biosystems.

Techniques: RNA Sequencing, Comparison, Generated, Western Blot, Expressing, Produced, Quantitative RT-PCR, SYBR Green Assay, Two Tailed Test

Journal: Nature Communications

Article Title: The sex-biased chromatin modifier SMC1A promotes autoimmunity by shaping inflammatory pathways in patients with SLE

doi: 10.1038/s41467-025-65309-7

Figure Lengend Snippet: A CD14 + monocytes purified from healthy individuals were transfected with siRNA against SMC1A for 4 h, then pre-treated with recombinant IFNα and TNF for 18 h, followed by a 3-h LPS challenge. Created in BioRender. B RT-qPCR was used to measure SMC1A mRNA levels in SMC1A -silenced ( SMC1A si) or control-silenced (ctrl si; scramble) CD14 + monocytes from healthy individuals (n = 3), which were either untreated (basal state) or stimulated (SLE-like state). Quantification was performed using the 2 –ΔΔCT method (ΔCt = SMC1A Ct minus 18S Ct). Each dot represents a different donor, and bar plots show the mean ± standard error (SE) expression. ANOVA was performed followed by post-hoc Tukey’s test. C Volcano plot of DEGs from RNA sequencing analysis of SMC1A -silenced ( SMC1A si) compared to control-silenced (ctrl si; scramble) CD14 + monocytes in the basal state (triplicates, p-value < 0.05). Log2 fold change (log2FC) along with the corresponding p-values were generated using DESeq2. The y-axis represents the –log10(p-values), while the x-axis shows the log2FC in expression levels of genes in SMC1A -silenced versus control-silenced CD14 + monocytes. D Volcano plot of DEGs from RNA sequencing analysis of SMC1A -silenced ( SMC1A si) compared to control-silenced (ctrl si; scramble) CD14 + monocytes in the SLE-like state (triplicates, p < 0.05). The y-axis represents the –log10(p-values), while the x-axis shows the log2FC in expression levels of genes in SMC1A -silenced versus control-silenced CD14 + monocytes (generated using DESeq2). E Scatter plot of gene expression changes (Log2FC; SMC1A -silenced versus control-silenced cells) in CD14 + monocytes under basal (y-axis) and SLE-like (x-axis) conditions. Analysis was performed in the combined list of 860 DEGs shown in ( C , D ). Green dots represent DEGs specific to basal-state monocytes, blue to SLE-like monocytes, and yellow to both. F Enrichment analysis for over-represented Gene Ontology (GO) terms in DEGs upon SMC1A silencing in basal and SLE-like monocytes. All p-values are two-tailed.

Article Snippet: The SMC1A primers and probe (Hs00196849_m1) and GAPDH primers and probe (Hs02786624_g1) were part of TaqMan gene expression assays from Applied Biosystems.

Techniques: Purification, Transfection, Recombinant, Quantitative RT-PCR, Control, Expressing, RNA Sequencing, Generated, Gene Expression, Two Tailed Test

Journal: Nature Communications

Article Title: The sex-biased chromatin modifier SMC1A promotes autoimmunity by shaping inflammatory pathways in patients with SLE

doi: 10.1038/s41467-025-65309-7

Figure Lengend Snippet: A Comparison of lupus-responsive genes (significantly altered in SLE-like vs. basal CD14⁺ monocytes; triplicates, |log 2 FC| ≥ 1, adjusted p < 0.05) with DEGs from RNA-sequencing of CD14⁺ monocytes from SLE patients (n = 10, unselected for sex) versus healthy controls (n = 9, unselected for sex) using the same thresholds (|log 2 FC| ≥ 1, adjusted p < 0.05). The y-axis shows log 2 FC in SLE-like versus basal monocytes, and the x-axis shows log 2 FC in SLE versus healthy monocytes. Each dot represents a gene. Genes commonly downregulated fall in the lower-left quadrant, while commonly upregulated genes fall in the upper-right quadrant. Fisher’s exact test revealed significant overlap between transcriptionally activated lupus-responsive genes and SLE-specific DEGs (p = 2.0e-148). B Functional enrichment analysis (Gene Ontology terms) of lupus-responsive genes. The left panel shows enriched pathways among DEGs in SLE versus healthy CD14⁺ monocytes; the right panel shows enriched pathways among lupus-responsive genes (SLE-like versus basal monocytes). C Dot plot showing log 2 FC changes in lupus-responsive genes that were also differentially expressed upon SMC1A silencing versus control silencing in CD14⁺ monocytes (Fig. ). Results are presented separately for genes up- or down-regulated in SMC1A -silenced versus control-silenced cells under basal (left two panels) or SLE-like (right two panels) conditions. Horizontal lines indicate median log 2 FC values. One-way ANOVA was performed, followed by post-hoc comparisons using the Least Squares Means method. All p-values are two-tailed.

Article Snippet: The SMC1A primers and probe (Hs00196849_m1) and GAPDH primers and probe (Hs02786624_g1) were part of TaqMan gene expression assays from Applied Biosystems.

Techniques: Comparison, RNA Sequencing, Functional Assay, Control, Two Tailed Test

Journal: Nature Communications

Article Title: The sex-biased chromatin modifier SMC1A promotes autoimmunity by shaping inflammatory pathways in patients with SLE

doi: 10.1038/s41467-025-65309-7

Figure Lengend Snippet: A Volcano plot of differential genomic binding events (|log2FC| > 1, p < 0.001 generated using DESeq2) from SMC1A ChIP-sequencing analysis in SLE-like (n = 3) versus basal (n = 2) male CD14 + monocytes. Blue dots represent regions with reduced SMC1A binding (n = 1131) and red dots with increased SMC1A binding (n = 6839). B Stacked bar graph showing the genomic distribution of reduced (upper lane) and increased (lower lane) SMC1A binding events in SLE-like versus basal monocytes from the ChIP-seq analysis shown in ( A ). C Proportion of genes associated with promoter and enhancer genomic regions that demonstrate reduced (down-bound) or increased (up-bound) SMC1A binding during transition from basal to SLE-like monocytes. D Volcano plot illustrating H3K27ac signal changes (|log2FC| > 1, p < 0.001 generated using DESeq2) from ChIP-sequencing analysis in SLE-like (n = 4) versus basal (n = 3) CD14 + monocytes. Blue dots represent regions with reduced (n = 274), and red dots with increased (n = 502) H3K27ac signal. E Area-proportional euler diagram displaying the intersection of genes associated with differential—increased (designated with up-arrow) or reduced (designated with down-arrow)—SMC1A binding and H3K27ac signal. The majority (295 out of 440, 67%) of genes with increased H3K27ac signal showed enriched SMC1A binding. F Functional enrichment analysis (Gene Ontology terms) of genes associated with both increased SMC1A binding and increased H3K27ac signal in SLE-like compared to basal monocytes. All p-values are two-tailed.

Article Snippet: The SMC1A primers and probe (Hs00196849_m1) and GAPDH primers and probe (Hs02786624_g1) were part of TaqMan gene expression assays from Applied Biosystems.

Techniques: Binding Assay, Generated, ChIP-sequencing, Functional Assay, Two Tailed Test

Journal: Nature Communications

Article Title: The sex-biased chromatin modifier SMC1A promotes autoimmunity by shaping inflammatory pathways in patients with SLE

doi: 10.1038/s41467-025-65309-7

Figure Lengend Snippet: A Schematic representation of the integration analysis of ATAC-sequencing (GEO dataset GSE100383 ; n = 3 lupus-like monocytes), SMC1A (Fig. ) and H3K27ac (Fig. ) ChIP-sequencing data in SLE-like and unstimulated (basal state) CD14 + monocytes. Chromatin activity states combined with SMC1A binding enrichment at specific genome regions were used to define the putative regulatory role of SMC1A in the context of lupus. Created in BioRender. B Genome-wide map of ATAC-seq, H3K27ac ChIP-seq and SMC1A ChIP-seq peaks in monocytes cultured under SLE-like and basal conditions. Differentially SMC1A-bound regions were intersected with Ensembl Transcription Start Sites (TSS) and FANTOM5 enhancer elements (enhancer TSSs [eTSSs]), each extended by 500 base pairs, upstream and downstream. Only promoters from transcribed genes were kept in the dataset. Enhancers were linked to their putative target genes using the GeneHancer database. To define actively transcribed regulatory elements, H3K27ac and ATAC-seq peaks under lupus-like condition were intersected (using bedtools ) with the promoters and enhancers as described above.

Article Snippet: The SMC1A primers and probe (Hs00196849_m1) and GAPDH primers and probe (Hs02786624_g1) were part of TaqMan gene expression assays from Applied Biosystems.

Techniques: Sequencing, ChIP-sequencing, Activity Assay, Binding Assay, Genome Wide, Cell Culture

Journal: Nature Communications

Article Title: The sex-biased chromatin modifier SMC1A promotes autoimmunity by shaping inflammatory pathways in patients with SLE

doi: 10.1038/s41467-025-65309-7

Figure Lengend Snippet: A Bar-dot plot of expression changes (log2FC) in transcriptionally upregulated, lupus-responsive genes based on chromatin activity and SMC1A binding enrichment at their cognate enhancer regions in SLE-like versus unstimulated monocytes. Each dot represents a different gene. +/– signs indicate active/inactive chromatin, respectively and arrows indicate increased/reduced binding of SMC1A. Wilcoxon signed-ranked test was performed with multiple testing correction. Increased binding of SMC1A on active enhancers is associated with significantly higher induction of the associated genes (red- versus brown-colored bars, p = 1.9e-5). B Bar-dot plot of log2FC in transcriptionally upregulated, lupus-responsive genes based on chromatin activity and SMC1A binding enrichment at their cognate promoter regions in SLE-like versus unstimulated monocytes. Each dot represents a different gene. Wilcoxon signed-ranked test was performed with multiple testing correction. Increased binding of SMC1A on active promoters is associated with significantly higher induction of the associated genes (red- versus brown-colored bars, p = 8.3e-06). C Bar-dot plot of gene expression changes (log2FC) in transcriptionally upregulated, lupus-responsive genes based on enriched SMC1A binding at cognate active promoters (left bar), active enhancers (middle bar), or both (right bar). Each dot represents a different gene. In ( A – C ), the box represents the interquartile range of log2FC values, with the vertical line indicating the median across each category of epigenome features. Whiskers extend to 1.5× the interquartile range, and points outside the whiskers represent outliers. Wilcoxon signed-ranked test was performed with multiple testing correction. D Effect of SMC1A gene silencing on log2FC of lupus-responsive genes, according to presence of active chromatin and enriched SMC1A binding at the cognate regulatory elements in SLE-like monocytes. +/– signs indicate active/inactive chromatin, respectively; E enhancer, P promoter. Filled circles represent means and error bars the 95% confidence interval. In each group of genes on the x-axis, one-samples t-test was performed to define statistically significant deviation from zero (** p < 0.01; *** p < 0.001). E Functional enrichment analysis (Gene Ontology) of Group B (n = 301) and C (n = 24) genes ( D ). F Functional enrichment analysis (Gene Ontology) of Group A genes (n = 530; Fig. 6D). All p-values are two-tailed.

Article Snippet: The SMC1A primers and probe (Hs00196849_m1) and GAPDH primers and probe (Hs02786624_g1) were part of TaqMan gene expression assays from Applied Biosystems.

Techniques: Expressing, Activity Assay, Binding Assay, Gene Expression, Functional Assay, Two Tailed Test

Journal: Nature Communications

Article Title: The sex-biased chromatin modifier SMC1A promotes autoimmunity by shaping inflammatory pathways in patients with SLE

doi: 10.1038/s41467-025-65309-7

Figure Lengend Snippet: A Volcano plot of DEGs belonging to Groups B and C (Fig. ) in SLE-like versus basal-state CD14⁺ monocytes. A subset of 277 genes met the criteria for SMC1A target genes, defined as showing significant transcriptional upregulation (log 2 FC ≥ 1, adjusted p < 0.05), active enhancer activity, and enriched SMC1A binding at the cognate enhancer. B Functional enrichment analysis (Gene Ontology terms) of the 277 SMC1A target genes. C Genome browser tracks showing SMC1A and H3K27ac ChIP-seq peaks in basal and SLE-like monocytes, together with ATAC-seq peaks in SLE-like monocytes, at the IL6 (left) and GBP5 (right) loci.

Article Snippet: The SMC1A primers and probe (Hs00196849_m1) and GAPDH primers and probe (Hs02786624_g1) were part of TaqMan gene expression assays from Applied Biosystems.

Techniques: Activity Assay, Binding Assay, Functional Assay, ChIP-sequencing

Journal: Nature Communications

Article Title: The sex-biased chromatin modifier SMC1A promotes autoimmunity by shaping inflammatory pathways in patients with SLE

doi: 10.1038/s41467-025-65309-7

Figure Lengend Snippet: A Volcano plot of DEGs from QuantSeq 3′ mRNA sequencing performed in blood monocytes from female (n = 8) compared to male (n = 10) SLE patients (|log2-FC| > 1, p < 0.05 generated using DESeq2). Blue dots represent genes overexpressed in males (n = 149), and red dots represent those overexpressed in females (n = 596) with SLE. B Functional enrichment analysis (Gene Ontology) of DEGs with female overexpression in SLE monocytes. C Functional enrichment analysis (Gene Ontology) of DEGs with male overexpression in SLE monocytes. D Detection of cytokines by LEGENDplex immunoassays at supernatants of cultured (4 h) SLE patient-derived monocytes (n = 9 pairs of males and females). Each dot represents an individual, the bar plots show the mean ± standard error (SE). Mixed model analysis was performed accounting for nested data structure and inter-individual variability, and introducing sex (male versus female) as within-cluster predictor. E Heatmap displaying z-score-transformed expression levels of 277 SMC1A-regulated genes in male and female SLE monocytes (same individuals as in ( A ); n = 8 females and n = 10 males). Each row represents a gene, and each column represents an individual. A total of 62 SMC1A target-genes (22.4%) were overexpressed in females, while only 2 (0.7%) were overexpressed in males with SLE (Fig. 8A-B). ( F ) Scatter plot showing the aggregated expression levels (after z-transformation) of all 277 SMC1A-regulated genes in female and male SLE monocytes (same individuals as in ( E ); n = 8 females and n = 10 males). Each dot represents a different individual and the bars indicate the minimum and maximum values. Mixed model analysis was performed as in ( D ). G Scatter plot showing the correlation between gene expression changes (Log2FC) in female versus male SLE monocytes (y-axis) and gene expression changes (Log2FC) in SMC1A si versus control si lupus-like monocytes (x-axis). Each circle represents a different protein-coding gene: red-colored are SMC1A target-genes whereas blue-colored are genes with active promoters and enhancers but without enriched SMC1A binding in SLE-like monocytes. Linear regression revealed negative associations which were stronger in SMC1A target-genes ( β -coefficient ± SE = −1.861 ± 0.338, p = 8.1e-08) compared to non-SMC1A-target-genes ( β ± SE = −0.673 ± 0.120, p = 3.1e-08) (p < 0.001 for the difference between the two slopes). All p-values are two-tailed.

Article Snippet: The SMC1A primers and probe (Hs00196849_m1) and GAPDH primers and probe (Hs02786624_g1) were part of TaqMan gene expression assays from Applied Biosystems.

Techniques: Sequencing, Generated, Functional Assay, Over Expression, Cell Culture, Derivative Assay, Transformation Assay, Expressing, Gene Expression, Control, Binding Assay, Two Tailed Test

Journal: Nature Communications

Article Title: The sex-biased chromatin modifier SMC1A promotes autoimmunity by shaping inflammatory pathways in patients with SLE

doi: 10.1038/s41467-025-65309-7

Figure Lengend Snippet: RT-qPCR was performed to quantify IL6 ( A ) and IL1A ( B ) mRNA in CD14 + monocytes (n = 6 pairs of male and female donors) cultured under unstimulated (basal state) and SLE-like conditions. Quantification was performed using the 2 –ΔΔCT method. Each dot represents a different donor, and bar plots show the mean ± standard error (SE). Mixed model analysis was performed accounting for nested data structure and inter-individual variability, and introducing sex (male versus female), monocyte condition (SLE-like versus basal) and the interaction of sex × monocyte condition as within-cluster predictors. The Least Squares Means (LSM) method was used for post-hoc comparisons between selected groups. RT-qPCR was performed to quantify IL6 ( C ), IL1A ( D ) and SMC1A mRNA levels in monocytes (n = 4 pairs of male and female donors) cultured under unstimulated (basal state) and SLE-like conditions. Mixed model analysis was performed with IL6 ( C ) or IL1A ( D ) as the dependent variable, using sex, monocyte condition, SMC1A expression levels and their interaction with monocyte condition as within-cluster predictors. The corresponding beta ( β ) coefficients and p-values are shown. E ChIP-PCR for chromatin-normalized SMC1A enrichment (relative to gene desert region) at enhancer regions of IL6 (left panel) and IL1A (middle panel) and promoter region of IL6 (right panel) in lupus-like monocytes (n = 4 pairs of male and female donors). Each dot represents a different donor, and bar plots show the mean ± SE enrichment. Mixed model analysis was performed accounting for nested data structure and inter-individual variability, and introducing sex as within-cluster predictor. F RT-qPCR was performed to measure IL6 and IL1A mRNA in SMC1A -silenced ( SMC1A si) compared to control-silenced (ctrl si; scramble) monocytes cultured under lupus conditions (n = 4 replicates). Quantification was performed using the 2 –ΔΔCT method. Each dot represents a different donor, and bar plots show the mean ± SE. Paired t -test was performed. G ELISA was performed to quantify secretion of IL-6 by SMC1A -silenced ( SMC1A si) compared to control-silenced (ctrl si; scramble) monocytes cultured (4 h) under lupus conditions (n = 9 replicates). Each dot represents a different donor, and bar plots show the mean ± SE. Paired t -test was performed. All p-values are two-tailed.

Article Snippet: The SMC1A primers and probe (Hs00196849_m1) and GAPDH primers and probe (Hs02786624_g1) were part of TaqMan gene expression assays from Applied Biosystems.

Techniques: Quantitative RT-PCR, Cell Culture, Expressing, Control, Enzyme-linked Immunosorbent Assay, Two Tailed Test

Journal: Nature Communications

Article Title: The sex-biased chromatin modifier SMC1A promotes autoimmunity by shaping inflammatory pathways in patients with SLE

doi: 10.1038/s41467-025-65309-7

Figure Lengend Snippet: SMC1A , a cohesin complex subunit escaping X-chromosome inactivation, shows enhanced female-biased expression in monocytes from SLE patients as well as in those cultured under lupus-inducing conditions. Under lupus-inducing conditions, SMC1A is redistributed to the active regulatory elements of immune-related genes in monocytes, leading to increased transcriptional levels. Increased SMC1A binding at the enhancers of inflammatory genes, such as IL6 and IL1A , in female than male monocytes during lupus may lead to higher expression levels in the former group. Importantly, SMC1A-regulated genes are upregulated in female monocytes from SLE patients, correlating with a more inflammatory molecular and cytokine fingerprint, as compared to male counterparts. Created in BioRender.

Article Snippet: The SMC1A primers and probe (Hs00196849_m1) and GAPDH primers and probe (Hs02786624_g1) were part of TaqMan gene expression assays from Applied Biosystems.

Techniques: Expressing, Cell Culture, Binding Assay