CRATER tumor niches facilitate CD8+ T cell engagement and correspond with immunotherapy success
Aya Ludin, Georgia L. Stirtz, Asaf Tal, Ajit J. Nirmal, Kathleen L. Pfaff, Michael P. Manos, N. Besson, Nebiyat Eskndir, Billie Porter, Stephanie M. Jones, Hannah Mae Faulkner, Qiyu Gong, Sophia Liu, Irving Barrera, Lijian Wu, Cecília Pessoa Rodrigues, Aditi Sahu, Elizabeth R. Jerison, Joao V. Alessi, Biagio Ricciuti, Douglas S. Richardson, Jodi D. Weiss, Hadley M. Moreau, Meredith E. Stanhope, Alexander B. Afeyan, James E. Sefton, W Mccall, Emily Formato, Song Yang, Yi Zhou, David P. Hoytema van Konijnenburg, Hannah L. Cole, Miguel Córdova, Liang Deng, Milind Rajadhyaksha, Stephen R. Quake, Mark M. Awad, Fei Chen, Kai W. Wucherpfennig, Peter K. Sorger, F. Stephen Hodi, Scott J. Rodig, Gëorge F. Murphy, Leonard I. Zon
Abstract
T cell-mediated tumor killing underlies immunotherapy success. Here, we used long-term in vivo imaging and high-resolution spatial transcriptomics of zebrafish endogenous melanoma, as well as multiplex imaging of human melanoma, to identify domains facilitating the immune response during immunotherapy. We identified cancer regions of antigen presentation and T cell engagement and retention (CRATERs) as pockets at the stroma-melanocyte boundaries of zebrafish and human melanoma. CRATERs are rich in antigen-recognition molecules, harboring the highest density of CD8 + T cells in tumors. In zebrafish, CD8 + T cells formed prolonged interactions with melanoma cells within CRATERs, characteristic of antigen recognition. Following immunostimulatory treatment, CRATERs expanded, becoming the major sites of activated CD8 + T cell accumulation and tumor killing. In humans, elevation in CRATER density in biopsies following immune checkpoint blockade (ICB) therapy correlated with a clinical response to therapy. CRATERs are structures that show active tumor killing and may be useful as a diagnostic indicator for immunotherapy success.