Pan-cancer analysis in the real-world setting uncovers immunogenomic drivers of acquired resistance...

Immune checkpoint blockade (ICB) has revolutionized cancer therapy, yet resistance-both primary and acquired-remains a significant obstacle, affecting the majority of patients.

Here, we leverage a large-scale, real-world clinicogenomic dataset to systematically explore the molecular underpinnings of ICB resistance in the post-progression setting. We analyze over 5,000 pan-cancer patients with clinical and pre-/post-treatment genomic and transcriptomic data and systematically compare the clinical and molecular features of acquired versus primary ICB resistance.

Post-ICB progression, acquired resistance showed extended survival compared to primary resistance across all cancer types. This clinical phenotype was paralleled by a universally immune-inflamed, albeit dysfunctional, tumor microenvironment (TME) at the onset of acquired resistance, with sustained or ICB-induced inflammatory and interferon responses. We confirm previously described mechanisms of acquired resistance, including B2M loss-of-function (LoF) in non-small cell lung cancer (NSCLC), and identify novel potential mediators, including LoF of TGFBR2 in NSCLC, CYLD in head and neck cancer, and RUNX1 in triple-negative breast cancer. Further supporting their involvement in resistance, these acquired ICB alterations associated with immune-escaped TMEs, characterized by active immunomodulatory oncogenic signaling, hyperproliferation and invasiveness, or altered tumor metabolism.

These findings emphasize the heterogeneity of molecular drivers of acquired resistance to ICB within and across cancers, and highlight the potential for personalized therapeutic interventions post-progression to improve patient outcomes.