Single-cell chromatin maps of thymic carcinoma reveal a conserved malignant state and its immunosuppressive dependencies

Thymic carcinoma is a rare and aggressive malignancy with limited therapeutic options. Although recent single-cell transcriptomic studies have begun to resolve its cellular composition, its regulatory landscape remains poorly characterized. We present a single-cell chromatin accessibility resource comprising 26,661 high-quality nuclei from three tumors and two adjacent normal tissues, with annotated malignant and immune populations, cell-type-resolved peaks, and gene activity estimates. To illustrate its utility, exploratory analyses identified a recurrent tumor cluster, T3, in all three tumors examined, with shared accessibility at therapeutically relevant loci, including KIT , FGFR3 , and SYK , and an inferred regulatory program involving ELF2 , BCLAF1 , PBX3 , IKZF1 , NFKB1 , TFDP2 , and POU2AF1 , alongside exhaustion-associated CD8⁺ T-cell and M2-like macrophage chromatin programs. Given the cohort size, these observations are descriptive and hypothesis-generating. This resource provides a foundation for future functional and translational studies of thymic carcinoma.