Community assessment of methods to deconvolve cellular composition from bulk gene expression
Brian S. White, Aurélien de Reyniès, Aaron M. Newman, Joshua J. Waterfall, Andrew Lamb, Florent Petitprez, Yating Lin, Rongshan Yu, Martin E. Guerrero-Gimenez, Sergii Domanskyi, Gianni Monaco, Verena Chung, Jineta Banerjee, Daniel S. Derrick, Alberto Valdeolivas, Haojun Li, Xu Xiao, Shun Wang, Frank Zheng, Wenxian Yang, Carlos Catania, Benjamin Lang, Thomas Bertus, Carlo Piermarocchi, Francesca Pia Caruso, Michele Ceccarelli, Thomas Yu, Xindi Guo, Julie Bletz, John A. Coller, Holden T. Maecker, Caroline Duault, Vida Shokoohi, Shailja Patel, Joanna E. Liliental, Stockard Simon, Aurélien de Reyniès, Aashi Jain, Shreya Mishra, Vibhor Kumar, Jiajie Peng, Lu Han, Gonzalo H. Otazu, Austin Meadows, Patrick Danaher, Maria K. Jaakkola, Laura L. Elo, Julien Racle, David Gfeller, Dani Livne, Sol Efroni, Tom Snir, Oliver Cast, Martin L. Miller, Dominique‐Laurent Couturier, Wennan Chang, Sha Cao, Chi Zhang, Dominik J. Otto, Kristin Reiche, Christoph Kämpf, Michael Rade, Carolin Schimmelpfennig, Markus Kreuz, Alexander Scholz, Julio Sáez-Rodríguez, Laura M. Heiser, Justin Guinney, Andrew J. Gentles
Abstract
We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression of tumor samples, through a community-wide DREAM Challenge. We assess six published and 22 community-contributed methods using in vitro and in silico transcriptional profiles of admixed cancer and healthy immune cells. Several published methods predict most cell types well, though they either were not trained to evaluate all functional CD8+ T cell states or do so with low accuracy. Several community-contributed methods address this gap, including a deep learning-based approach, whose strong performance establishes the applicability of this paradigm to deconvolution. Despite being developed largely using immune cells from healthy tissues, deconvolution methods predict levels of tumor-derived immune cells well. Our admixed and purified transcriptional profiles will be a valuable resource for developing deconvolution methods, including in response to common challenges we observe across methods, such as sensitive identification of functional CD4+ T cell states.