Chromatin Study Links Inflammation to Endothelial Remodeling in Capillary Malformations

Cutaneous capillary malformations, commonly known as port wine stains, are congenital vascular anomalies that affect between 0.3 and 0.9 percent of newborns and are marked by progressive capillary dilation and vascular remodeling in the skin. Under the microscope, these lesions show proliferation of endothelial cells and smooth muscle cells, replication of the basement membrane, disruption of the vascular barrier, and progressive vessel dilatation. The endothelial cells within these lesions also display differentiation-impaired, stem-cell-like features. Although several somatic mutations have been associated with capillary malformations, the most frequently identified is GNAQ p.R183Q, which is typically present at low variant allele fractions, averaging about 4.25 percent in skin lesions, and is distributed among multiple cell types within lesions. Experimental work has shown that endothelial force-expression of GNAQ p.R183Q promotes vascular enlargement, yet the regulatory mechanisms driving endothelial remodeling in this disease have remained incompletely defined.

A new study, published as a Brief Report on 14 September 2026 in an open access journal, takes an integrative genomics approach to this question. The researchers, led by Irving Mao and Vi Nguyen as co-first authors, with senior author Wenbin Tan, built on their previous work generating capillary malformation-specific induced pluripotent stem cells, induced endothelial cells derived from them, and vascular organoids. These models recapitulate multiple disease-relevant phenotypes despite lacking detectable GNAQ p.R183Q and other common low-variant-allele-frequency mutations after reprogramming from lesional dermal fibroblasts. To probe the pathological signaling underlying the endothelial phenotypes in these models, the team profiled bulk chromatin accessibility using ATAC-seq and gene expression using RNA-seq in capillary malformation and control induced endothelial cells, then intersected differentially accessible regions, differentially expressed genes, and candidate peak-to-gene links to build a high-confidence regulatory panel.

The chromatin accessibility analysis revealed that genome-wide peak distributions were largely comparable between capillary malformation and control induced endothelial cells, indicating preserved global chromatin organization. Most accessible regions localized to intronic and intergenic regions, with promoter-associated peaks representing a smaller fraction, and strong enrichment of accessibility around transcription start sites was observed. Differential accessibility analysis, using a false discovery rate threshold of less than 0.05 and an absolute log2 fold-change threshold greater than 0.583, identified 877 upregulated differentially accessible regions and 224 downregulated regions in the capillary malformation cells. The authors interpret this pattern as evidence that these cells retain overall chromatin organization but exhibit selective remodeling of regulatory elements, predominantly within distal genomic regions rather than promoters.

Motif analysis of these differentially accessible regions pointed to specific transcription factor programs. Regions with increased accessibility in capillary malformation cells were enriched for motifs corresponding to transcription factors of endothelial identity and remodeling, including FOX-family, NKX2.5, and FLI1 motifs, whereas regions with decreased accessibility were enriched for RUNX, RFX, and FOS motifs. Functional enrichment of genes associated with the upregulated regions highlighted TGF-beta/SMAD signaling, Wnt signaling, epithelial-to-mesenchymal transition, leukocyte aggregation and chemotaxis. In addition, the upregulated regions were enriched for negative regulation of biosynthetic, differentiation- and developmental-related processes, while histone H3 demethylation was the only significantly enriched term among the downregulated regions. Together, the authors write, these findings suggest that chromatin remodeling in capillary malformation induced endothelial cells preferentially activates inflammatory and developmental regulatory programs.

The transcriptomic side of the analysis mirrored these chromatin findings. Bulk RNA-seq identified 1142 upregulated and 1149 downregulated differentially expressed genes in the capillary malformation cells. Enrichment analyses revealed dysregulation of stem cell differentiation and chromatin remodeling, inflammatory pathways, apoptosis, cell-cell adhesion, phagocytosis, extracellular matrix disassembly, and metabolic signaling pathways. The enriched inflammatory pathways in particular included TNF/NF-kappaB signaling, interleukin 1, 2, 6, and 10 pathways, Toll-like cascades, and leukocyte and lymphocyte activation. Representative genes involved in endothelial differentiation, remodeling, adhesion, and inflammatory pathways showed coordinated expression changes across the capillary malformation and control groups. The authors conclude that these transcriptional changes indicate the cells adopt an inflammatory and differentiation-impaired state consistent with endothelial remodeling.

To nominate upstream regulators, the team inferred transcription factor activity from both data types using chromVAR for chromatin accessibility and the DoRothEA/VIPER framework for gene expression, and performed footprinting analysis with TOBIAS to estimate transcription factor binding from the ATAC-seq data. Activity inference showed concordant shifts of regulators linked to endothelial identity and inflammatory signaling, including NR2F2, GRHL2, RELA/REL, and the Notch effector RBPJ. Footprinting demonstrated altered accessibility at motif sites corresponding to RUNX, FOX, GRHL2, and NR2F2 family members. The authors say these results suggest coordinated rewiring of endothelial developmental and inflammatory transcriptional networks in the capillary malformation cells.

The integrative core of the study connected chromatin and transcriptome directly. Using gene regulatory windows of 100 kilobases on either side of transcription start sites and Pearson correlation thresholds of an absolute coefficient above 0.8 with nominal p less than 0.05, the researchers identified candidate peak-to-gene links spanning both promoter-proximal and distal regulatory elements, including canonical endothelial genes such as TEK, CDH5, FGD5, and NOTCH1. Intersecting differentially accessible region-associated genes, differentially expressed genes, and high-confidence links yielded 156 overlapping genes supported by 232 linked peaks. GREAT analysis of this integrated peak set showed enrichment of stem cell development and differentiation, inflammatory pathways including TNF/NF-kappaB signaling, Toll-like pathways, and leukocyte and lymphocyte activation and aggregation, extracellular matrix reorganization, and lipid-related metabolisms. At the level of individual loci, a capillary malformation-associated accessible element at the KLF6 locus, peak 8184, showed increased accessibility and expression, while a regulatory element at the TGFBI locus, peak 65114, showed decreased accessibility accompanied by reduced transcript abundance.

One of the most striking findings concerned loci where increased chromatin accessibility coexisted with reduced transcriptional output. Analyzing genes with increased ATAC accessibility but decreased RNA expression supported by high-confidence links, the team identified 40 genes associated with 54 candidate regulatory peaks. Nearly all of these discordant events, 53 of the 54 peaks, were associated with distal regulatory elements, with only one promoter-proximal peak identified. Functional categorization showed enrichment of transcription factors and transcriptional regulators, 32.5 percent or 13 of 40 genes, signaling transduction molecules at 22.5 percent or 9 of 40, and structural or matrix proteins at 20 percent or 8 of 40. Pathway analysis linked these distal peak-associated genes to development and morphogenesis, including heart development, embryonic morphogenesis, endodermal cell fate specification, angiogenesis involved in coronary vascular morphogenesis, and regulation of the basement membrane in the embryonic body. Representative regulators in this set included the transcription factors RARB, NANOG, SOX2, TFAP2A, GLIS3, BNC2, and ZIC4, the co-regulators IRF2BPL and NCOR2, chromatin remodeling factors including ARID5B, DRAXIN, DPF1, and DPF3, and receptors such as APLNR, TGFBR1, and TLR4, most of which the authors note have roles in endothelial differentiation and function.

In the discussion, the authors highlight TNF/NF-kappaB and Notch signaling as prominent pathways from the transcriptomic profiles, noting that these pathways can engage in bidirectional crosstalk in endothelial cells, providing a plausible route for coupling inflammatory cues and endothelial fate at the chromatin level. They stress, however, that causal roles will require direct testing through NF-kappaB and Notch perturbation followed by assessment of endothelial differentiation, barrier function, inflammatory activation, and chromatin accessibility changes. The limitations are stated explicitly: the peak-to-gene links are correlation-based and therefore candidate rather than causal relationships; bulk profiling masks potential heterogeneity within the cell populations; the limited sample size necessitates cautious interpretation; the study is descriptive and lacks validation experiments; and the observed chromatin patterns could be partially related to donor-specific epigenetic variation, reprogramming-associated remodeling, or batch-to-batch differentiation effects. The enriched histone modification terms raise the possibility that disease-associated chromatin states may be incompletely reset during reprogramming or re-established during endothelial differentiation, though the molecular basis remains unknown. The raw and processed datasets are publicly available through the Gene Expression Omnibus and Sequence Read Archive under accessions PRJNA1511292, PRJNA997591, GSE343411, and GSE240770, and the bioinformatic code is provided in the supplementary materials.

Subject of Research: Integrative chromatin accessibility and transcriptomic profiling of induced endothelial cells from capillary malformations

Article Title: Integrated chromatin accessibility and transcriptomic profiling provide insights into inflammation-associated endothelial remodeling in capillary malformations

Article References: Mao, I., Nguyen, V., Li, F., Wenceslau, C. F., & Tan, W. (2026). Integrated chromatin accessibility and transcriptomic profiling provide insights into inflammation-associated endothelial remodeling in capillary malformations. Cell Signaling, Inflammation & Disease, 1(1), Article 6. https://doi.org/10.1186/s44505-026-00007-9

Image Credits: AI Generated

DOI: 10.1186/s44505-026-00007-9

Keywords: capillary malformation, port wine stain, ATAC-seq, RNA-seq, chromatin accessibility, endothelial cells, inflammation, NF-kappaB, Notch signaling, induced pluripotent stem cells, transcription factors, vascular anomaly