EpiTIL: methylation tumor infiltrating lymphocyte (TIL) predictor associates with survival in primary melanoma

Background Melanomas are immunogenic with significant variation of tumor infiltrating lymphocytes (TIL). Primary melanomas are routinely scored by pathologists, for TIL grade, as brisk, nonbrisk, and absent, but TIL grade is not utilized in staging. While brisk TIL grade predicts improved melanoma-specific survival, nonbrisk TIL grade often lacks prognostic significance. A high proportion of primary melanomas from stage II and III patients are scored as nonbrisk TIL grade. Our goal is to quantitatively predict T cell estimates in primary melanoma from DNA methylation data using immunofluorescence CD3 + staining as ground truth. Results Primary cutaneous melanomas (n = 80), analyzed for multiplex-immunofluorescence (CD3, CD8, S100) and whole-genome DNA methylation, underwent elastic net modeling of the proportion of CD3 + T lymphocytes to build a quantitative prediction model for TILs in primary melanoma called EpiTIL. Melanoma-specific survival (MSS) Kaplan–Meier curves significantly differed by primary melanoma EpiTIL tertiles ( p = 0.001). Patients with intermediate or highest tertile EpiTIL scores had higher median probability of MSS than those with lowest tertile scores. EpiTIL added significant prognostic value for MSS beyond age, sex, and stage, analyzed using proportional hazard regression modelling ( p = 0.012). EpiTIL survival prediction was validated in two multi-omic studies, TCGA (n = 352) and InterMEL (n = 399). Among TCGA melanomas, the survival curves significantly differed by EpiTIL tertile scores ( p = 0.009) and EpiTIL scores added prognostic value to clinical factors ( p < 0.002). In the InterMEL case–control study of stage II/III melanoma, patients with 5-year MSS without recurrence (controls) had a significantly higher mean EpiTIL scores than those who died of melanoma within 5 years (cases) ( p = 1.5e − 11). Using logistic regression, EpiTIL scores significantly predicted 5-year MSS without recurrence, even after adjusting for age, sex, stage and TIL grade, with OR = 4.7 ( p = 2.38e-06) comparing the highest to lowest EpiTIL tertiles. Extending the EpiTIL prediction to the Newell metastatic melanoma cohort, we found immune checkpoint inhibitor responders had a significantly higher mean EpiTIL score than non-responders ( p = 0.047). Conclusion EpiTIL is a DNA methylation-based predictor of T cell proportion that demonstrates potential prognostic value in primary melanoma, particularly for stages II and III. Furthermore, higher EpiTIL scores derived from primary melanomas were positively associated with improved therapeutic responses to immune checkpoint inhibitors in metastatic disease, highlighting its potential to identify patients most likely to benefit from immunotherapy.