Single-cell spatial profiling identifies a mucosal-like epithelial signature in hidradenitis suppurativa tunnels

Hidradenitis Suppurativa (HS) is a chronic, relapsing inflammatory skin disease affecting 1-4% of the population. In advanced HS, tunnels (dermal sinus tracts) often form, perpetuating chronic inflammation. Early immunohistochemistry studies found atypical keratin staining in tunnel epithelium, suggesting keratinocyte dysregulation influenced by ongoing inflammation. To date, the gene-expression features of HS tunnels have not been directly characterized relative to lesional (L-epi) or non-lesional epidermis (NL-epi), leaving their molecular profile largely undefined. We performed spatio-temporal-enhanced-resolution-omics-sequencing (STEREOseq), which provides spatial transcriptomes at single-cell resolution, on lesional and non-lesional skin specimens from the same patient with advanced HS (Hurley stage III).

Tissue samples were sent to MGI, and STEREOseq was performed in their facility under standard manufacturer-recommended procedures. Pre-frozen OCT tissues were transversely sectioned at 10 micrometer thickness (Leica CM1950 cyrostat). Tissue sections were adhered to the Stereo-seq chip surface and incubated at 37 C for 5 minutes. Then, tissues were fixed in methanol and incubated at -20 C for 30 minutes and then dried. Nuclear staining and imaging were performed with ssDNA Qubit dye and fluorescent microscopy (FITC channel). Immediately adjacent tissue sections were collected for histological examination with hematoxylin and eosin. The tissue on the chip was permeabilized, incubated at 37 C, and then washed. Released RNA from permeabilized tissues was captured by the DNB and reverse transcribed overnight at 42 C. After in situ reverse transcription, tissue patches were washed and digested with tissue removal buffer at 55 C for 10 minutes. cDNA-containing chips were then subjected to cDNA release treatment and collection. The resulting cDNAs were amplified and purified using SPRI-bead purification for DNB generation.