Pancancer Fine‐Mapping of Mutational Intolerance Identifies CHEK1 as an Immunosuppressive Driver in Lung Adenocarcinoma

ABSTRACT Mutation‐intolerant genes (MIGs), which are constrained in tumors yet variable in normal tissues, are critical for cancer survival. Herein, we developed miDriver, a computational framework using pancancer‐normal mutation contrasts to identify 1,020 MIGs across 8,096 tumors of 13 cancer types. Strikingly, MIGs are highly associated with synthetic lethality, cell‐cycle progression, and clinical outcome. CRISPR screening reveals MIGs, especially CHEK1, as cancer‐specific vulnerabilities, whose suppression impairs tumor proliferation and migration. Single‐cell transcriptomics reveals a CHEK1‐high subpopulation exhibiting stem‐like and immune‐suppressed features, linking tumor‐intrinsic fitness to microenvironment remodeling. Multiplexed immunofluorescence revealed that CHEK1 and MIF are co‐expressed in tumor cells, and CHEK1‐high tumor cells exhibit closer spatial proximity to M2‐like macrophages. Mechanistically, CHEK1 promotes p53 phosphorylation to upregulate MIF expression and secretion, thereby driving M2‐like macrophage polarization via the MIF–CD74 axis. In vivo, targeting the CHEK1–MIF axis (particularly CHEK1) broadly reverses immunosuppression. Clinically, higher tumor CHEK1 levels are associated with poorer response to anti‐PD‐1 therapy. Exemplified by CHEK1, these findings establish MIGs as dual therapeutic targets capable of simultaneously disrupting tumor‐intrinsic fitness and remodeling the immunosuppressive niche. This work proposes a novel paradigm for selectively targeting MIGs to eliminate aggressive tumor subclones while minimizing toxicity to normal cells.