Increased expression of bone/cartilage-associated genes and core transcription factors in keloids by RNA sequencing

Fibroblasts in keloids undergo cell identity transition with altered transcriptional characteristics. However, the core transcription factors driving this cellular reprogramming remain largely unknown. Here, we report the results of transcriptional profiling from 48 keloid and 24 control dermal tissues. We identified 1187 upregulated differentially expressed genes (foldchange > 2, false discovery rate < 0.05) in keloids, which were mainly enriched in extracellular matrix organization and bone/cartilage development, with significantly increased expression of bone/cartilage-associated collagens (COL5A1, COL10A1, and COL11A1) and glycoproteins (ACAN, COMP, and SPARC). Deconvolution analysis also revealed significantly increased composition of osteoblasts in keloid dermis. A total of 92 upregulated transcription factors were screened out from differentially expressed genes and mainly enriched in transcription process and skeleton development. Additional sequencing of six keloid individuals with multiple regions and intersection further narrow the list with 10 transcription factors. Finally, AEBP1, CREB3L1, RUNX2, and ZNF469 have been identified as candidate core regulators in promoting the gaining of bone/cartilage-like characteristics in keloids. RNA-sequencing of full-skin keloids consolidated the existence of these four transcription factors. Immunohistochemistry was employed to verify the expression of AEBP1, CREB3L1, RUNX2, and ZNF469 in keloid fibroblasts. In conclusion, we bioinformatically discovered the increased expression of bone/cartilage-associated genes and candidate core transcription factors in keloids. Our findings promise to provide molecular clues to develop novel therapeutic modalities against skin fibrosis.