Integrative Analysis of Checkpoint Blockade Response in Advanced Non-Small Cell Lung Cancer

Ravi, A.; Gainor, J. F.; Arniella, M. B.; Holton, M.; Freeman, S. S.; Stewart, C.; Leshchiner, I.; Kim, J.; Akiyama, Y.; Griffin, A. T.; Vokes, N. I.; Sakhi, M.; Kamesan, V.; Rizvi, H.; Ricciuti, B.; Forde, P. M.; Anagnostou, V.; Reiss, J. W.; Gibbons, D. L.; Pennell, N. A.; Velcheti, V.; Digumarthy, S. R.; Mino-Kenudson, M.; Califano, A.; Heymach, J. V.; Herbst, R. S.; Brahmer, J. R.; Schalper, K. A.; Velculescu, V. E.; Henick, B. S.; Rizvi, N.; Janne, P. A.; Awad, M. M.; Chow, A.; Greenbaum, B. D.; Luksza, M.; Shaw, A. T.; Wolchok, J.; Hacohen, N.; Getz, G.; Hellmann, M. D.

doi:10.1101/2022.03.21.485199

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bioRxiv · 10.1101/2022.03.21.485199

Integrative Analysis of Checkpoint Blockade Response in Advanced Non-Small Cell Lung Cancer

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Abstract

Anti-PD-1/PD-L1 agents have transformed the treatment landscape of advanced non-small cell lung cancer (NSCLC). While our understanding of the biology underlying immune checkpoint blockade in NSCLC is still incomplete, studies to date have established predictive roles for PD-L1 tumor expression and tumor mutational burden (TMB). To expand our understanding of the molecular features underlying response to checkpoint inhibitors in NSCLC, we describe here the first joint analysis of the Stand Up 2 Cancer - Mark Foundation (SU2C-MARK) Cohort, a resource of whole exome and/or RNA sequencing from 393 patients with NSCLC treated with anti-PD-(L)1 therapy, along with matched clinical response annotation. We identify a number of associations between molecular features and outcome, including: 1) favorable (e.g., ATM altered), and unfavorable (e.g., TERT amplified) genomic subgroups, 2) distinct immune infiltration signatures associated with wound healing (unfavorable) and immune activation (favorable), and 3) a novel de-differentiated tumor-intrinsic subtype characterized by expression of endodermal lineage genes, immune activation, and enhanced response rate. Taken together, results from this cohort extend our understanding of NSCLC-specific predictors, providing a rich set of molecular and immunologic hypotheses with which to further our understanding of the biology of checkpoint blockade in NSCLC.

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Ravi, A., Gainor, J. F., Arniella, M. B., Holton, M., Freeman, S. S., Stewart, C., Leshchiner, I., Kim, J., Akiyama, Y., Griffin, A. T., Vokes, N. I., Sakhi, M., Kamesan, V., Rizvi, H., Ricciuti, B., Forde, P. M., Anagnostou, V., Reiss, J. W., Gibbons, D. L., Pennell, N. A., Velcheti, V., Digumarthy, S. R., Mino-Kenudson, M., Califano, A., Heymach, J. V., Herbst, R. S., Brahmer, J. R., Schalper, K. A., Velculescu, V. E., Henick, B. S., Rizvi, N., Janne, P. A., Awad, M. M., Chow, A., Greenbaum, B. D., Luksza, M., Shaw, A. T., Wolchok, J., Hacohen, N., Getz, G., Hellmann, M. D.. 2022-03-23. Integrative Analysis of Checkpoint Blockade Response in Advanced Non-Small Cell Lung Cancer. https://doi.org/10.1101/2022.03.21.485199

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