Novel Predictive Spatial Biomarker in Non-Small Cell Lung Carcinoma: The Diversity of Niches Unlocking Treatment Sensitivity (DONUTS)

Cottrell, T. R.; Roskes, J. S.; Fotheringham, M.; Cohen, E.; Zhang, B.; Engle, L. L.; Wang, D.; Will, E.; Sunshine, J. C.; Jimenez-Sanchez, D.; Zheng, Z.; Caushi, J. X.; Zhang, J.; D'Amiano, N.; Stein-Deutsch, J.; Uttam, S.; Pirie, K.; Vlaminck, D.; Mataj, M.; Fiorante, A.; Espinosa, N.; Popa, T.; Ogurtsova, A.; Soto-Diaz, S.; Eminizer, M.; Tabrisky, S.; Jorquera, A.; Skidmore, J.; Medvedev, D.; Chaft, J. E.; Brahmer, J. R.; Conroy, M.; Reuss, J. E.; Danilova, L.; Ji, H.; Forde, P. M.; Pardoll, D. M.; Smith, K. N.; Green, B. F.; Szalay, A. S.; Taube, J. M.

doi:10.1101/2025.08.13.665980

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bioRxiv · 10.1101/2025.08.13.665980

Novel Predictive Spatial Biomarker in Non-Small Cell Lung Carcinoma: The Diversity of Niches Unlocking Treatment Sensitivity (DONUTS)

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Abstract

Probabilistic spatial modelling techniques developed on large-scale tumor-immune Atlases ([~]35M individually mapped cells; 50,000 high power fields) were used to characterize predictive features of treatment-responsive lung cancer. We identified CD8+FoxP3+ cell density as a robust pre-treatment biomarker for outcomes across disease stages and therapy types. In parallel, single-cell RNAseq studies of CD8+FoxP3+ T-cells revealed an activated, early effector phenotype, substantiating an anti-tumor role, and contrasting with CD4+FoxP3+ T-regulatory cells. A spatial biomarker was developed using an empirical probabilistic model to define the immediate cell neighbors or niche surrounding CD8+FoxP3+ cells and proximity to the tumor-stromal boundary. The resultant Diversity of Niches Unlocking Treatment Sensitivity (DONUTS) are more prevalent than the CD8+FoxP3+ cells themselves, mitigating sampling error in small biopsies. Further, the DONUTS only require four markers, are additive to PD-L1, and associate with tertiary lymphoid structure counts. Taken together, the DONUTS represent a next-generation predictive biomarker poised for clinical implementation. HIGHLIGHTSO_LILarge-scale tumor-immune Atlases drive robust computational biomarker development C_LIO_LICD8+FoxP3+ cells are anti-tumor T-cells and predict response to therapy C_LIO_LIThe niches or spatial donuts around CD8+FoxP3+ cells boost biomarker performance C_LIO_LICD8+FoxP3+ donuts are hallmarks of a larger immune organization that includes TLS C_LI

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Cottrell, T. R., Roskes, J. S., Fotheringham, M., Cohen, E., Zhang, B., Engle, L. L., Wang, D., Will, E., Sunshine, J. C., Jimenez-Sanchez, D., Zheng, Z., Caushi, J. X., Zhang, J., D'Amiano, N., Stein-Deutsch, J., Uttam, S., Pirie, K., Vlaminck, D., Mataj, M., Fiorante, A., Espinosa, N., Popa, T., Ogurtsova, A., Soto-Diaz, S., Eminizer, M., Tabrisky, S., Jorquera, A., Skidmore, J., Medvedev, D., Chaft, J. E., Brahmer, J. R., Conroy, M., Reuss, J. E., Danilova, L., Ji, H., Forde, P. M., Pardoll, D. M., Smith, K. N., Green, B. F., Szalay, A. S., Taube, J. M.. 2025-08-15. Novel Predictive Spatial Biomarker in Non-Small Cell Lung Carcinoma: The Diversity of Niches Unlocking Treatment Sensitivity (DONUTS). https://doi.org/10.1101/2025.08.13.665980

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