Cellular Heterogeneity in Erectile Dysfunction: An In-silico Analysis Revealing PER1, BHLHE40, NFIL3, and KLF10 as Circadian Rhythm Genes

Jun 17, 2026Current medicinal chemistry

Cell Differences in Erectile Dysfunction Linked to Daily Rhythm Genes PER1, BHLHE40, NFIL3, and KLF10

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Abstract

Single-cell analysis of human corpus cavernosum tissues shows reduced fibroblasts and expanded pericytes in organic erectile dysfunction (ED).

Core circadian genes (PER1, BHLHE40, NFIL3, KLF10) exhibited distinct expression patterns in different cell types.
Endothelial cells demonstrated a monotonic decline in circadian gene activity, while fibroblasts showed an early-peak decay.
Altered cellular interactions were observed, including TGF-β/ECM-mediated fibroblast-vascular crosstalk and increased endothelial-immune adhesion.
NFIL3 was identified as having a druggable pocket, with in silico docking indicating stable binding of potential clinical compounds.
Circadian rhythm dysregulation is suggested to be a significant contributor to organic ED.

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INTRODUCTION: Despite advances in understanding the vascular basis of erectile dysfunction (ED), the cellular heterogeneity and gene regulatory dynamics underlying organic ED remain unclear. In this study, we characterize the cell type-specific expression and roles of circadian rhythm genes (CRGs) in the human corpus cavernosum affected by organic ED.

METHODS: We performed an integrative single-cell analysis of human corpus cavernosum tissues (GSE206528) from healthy controls and patients with organic ED. Cell identities were annotated using Seurat, followed by pseudotemporal trajectory inference with Monocle 2, intercellular communication profiling via CellChat, and quantification of circadian rhythm gene activity using AUCell. Candidate therapeutics targeting dysregulated circadian genes were prioritized through Enrichr-based drug enrichment analysis and evaluated by AutoDock 4-mediated molecular docking.

RESULTS: Single-cell RNA-seq analysis of the corpus cavernosum in organic ED revealed reduced fibroblasts and expanded pericytes. The identified core circadian genes (PER1, BHLHE40, NFIL3, KLF10) displayed stage-specific pseudotime dynamics: monotonic decline in endothelial cells versus early-peak decay in fibroblasts, and correlated with pathological crosstalk, including TGF-β/ECM-mediated fibroblast-vascular interactions and enhanced endothelial-immune adhesion. NFIL3 harbored a conserved druggable pocket, and in silico docking confirmed stable binding of repurposable clinical compounds, highlighting circadian targets for therapy.

DISCUSSION: This study utilized single-cell RNA sequencing to elucidate the cellular and molecular landscape of the corpus cavernosum in patients with organic ED. The findings revealed significant alterations in cellular composition, circadian gene regulation, and intercellular communication networks.

CONCLUSION: Our research characterized circadian rhythm dysregulation as an active, cell type-specific contributor to organic ED and identified NFIL3 as a promising druggable target for chronotherapeutic intervention.

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Cellular Heterogeneity in Erectile Dysfunction: An In-silico Analysis Revealing PER1, BHLHE40, NFIL3, and KLF10 as Circadian Rhythm Genes

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