Key Regulatory Elements of the TGFß-LRRC15 Axis Predict Disease Progression and Immunotherapy Resistance Across Cancer Types

Transforming growth factor-beta (TGFß) has dual roles in cancer, initially suppressing tumors but later promoting metastasis and immune evasion. Efforts to inhibit TGFß have been largely unsuccessful due to significant toxicity and indiscriminate immunosuppression. Leucine-rich repeat-containing protein 15 (LRRC15) is a TGFß-regulated antigen expressed by mesenchymal-derived cancer cells and cancer-associated fibroblasts (CAFs). In preclinical studies, ablation of TGFß-driven LRRC15+ CAFs increased tumor infiltration of CD8+ T cells. However, the underlying pathobiological mechanisms prompting TGFß's upregulation of LRRC15 expression are unclear. Using an integrated approach combining functional compound screening with single-cell RNA sequencing, we reveal key genomic features regulating TGFß's ability to increase LRRC15 expression on cancer cells. Construction of gene regulatory networks converged our analyses on four key genes—MMP2, SPARC, TGFßR2, and WNT5B—central to TGFß-induced LRRC15 pathobiology. Validation of these genes in cell models and their use in predicting immunotherapy responses highlight their potential in refining immunotherapy strategies and personalizing co-treatment options. Overall design: 3 TGFß-inducible cell lines (HUO9, RPMI7951, U118) and 3 TGFß-noninducible cell lines (CALU1, KASUMI2, SAOS2), were FACS sorted for the top 1% of LRRC15+ cells by AlexaFluor647-DUNP19 staining. LRRC15+ and LRRC15- cells for each cell line were sequenced using scRNAseq, totaling to 12 sample.