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Spatial transcriptomics identifies differentiation, lipid metabolism, and retinoid pathway alterations in acne vulgaris
Joseph S. Durgin, Natalia A. Veniaminova, Thomas J. Huyge, Shih-Ying Tsai, Jennifer Fox, Yuli Cai, Mrinal K. Sarkar, Lam C. Tsoi, Johann E. Gudjonsson, Sunny Y. Wong
Joseph S. Durgin, Natalia A. Veniaminova, Thomas J. Huyge, Shih-Ying Tsai, Jennifer Fox, Yuli Cai, Mrinal K. Sarkar, Lam C. Tsoi, Johann E. Gudjonsson, Sunny Y. Wong
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Research Article Dermatology Development

Spatial transcriptomics identifies differentiation, lipid metabolism, and retinoid pathway alterations in acne vulgaris

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Abstract

Acne vulgaris is a common skin condition involving complex interactions among lipid-secreting sebaceous glands, keratinocytes, immune cells, and microbiota. While retinoids are effective for treating acne, disease pathogenesis remains poorly understood. In particular, it remains unclear how different subtypes of acne, including inflammatory (pustular) and noninflammatory (comedonal) lesions, vary in gene expression, signaling, and sebaceous gland involvement. Here, we performed spatial transcriptomics on healthy, nonlesional, comedonal, and pustular acne skin using a custom panel targeting sebaceous differentiation, lipid metabolism, and retinoid signaling pathways. We also designed a specialized segmentation pipeline to improve transcript assignment in the spatially complex sebaceous gland. Our analyses identified a PPARG+ transitional basal cell state in sebocytes and revealed that comedonal skin upregulates sebogenesis genes, whereas pustular skin downregulates sebogenesis. Both lesion types exhibited increased AP-1 transcription factors and elevated FABP5, a chaperone that blunts retinoic acid receptor signaling. Finally, we demonstrated that an AP-1 inhibitor, T-5224, downregulates FABP5 in human keratinocytes and reduces pustule formation in a mouse model of high-fat diet–induced folliculitis. Altogether, these findings indicate that altered lipogenesis, retinoid signaling, and keratinocyte differentiation are key features of acne, and nominate AP-1 and FABP5 as potential therapeutic targets.

Authors

Joseph S. Durgin, Natalia A. Veniaminova, Thomas J. Huyge, Shih-Ying Tsai, Jennifer Fox, Yuli Cai, Mrinal K. Sarkar, Lam C. Tsoi, Johann E. Gudjonsson, Sunny Y. Wong

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Figure 3

Sebaceous gland spatial transcriptomics analysis.

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Sebaceous gland spatial transcriptomics analysis.
(A) Subclustering on p...
(A) Subclustering on pooled sebocytes from all specimens, revealing 3 subpopulations (Sebocyte 1–3). Sebocyte 1 (basal) highly expresses KRT5, PPARG, and TP63. Sebocyte 2 and 3 (differentiated) lose KRT5 and gain KRT79. (B) Expression of lipid and retinoid metabolism genes across Sebocyte clusters. (C) UMAP plot of all Sebocyte clusters. The inset shows the spatial coordinates of cells, labeled by cluster, in a representative healthy sample. (D) UMAP plot of Sebocyte subclusters labeled by expression of PPARG, MKI67 (Ki-67), and KRT5. (E) Sebogenesis score across different skin conditions, calculated in sebocytes based on composite lipogenic gene expression (FASN, AWAT1, AWAT2, ACACA, SREBF1). (F) Notable DEGs among all pooled sebocytes, separated by disease state. (G) Spatial distribution of normalized FASN expression in representative healthy and comedonal samples. Statistical significance was determined using a 1-way ANOVA with post hoc t test and Tukey’s correction for multiple comparisons (****P < 0.0001). Data are shown as mean ± 95% CI.

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