Targeting WEE1 in ARID1A/TP53 Concurrent Mutant Colorectal Cancer by Exploiting RLoop Accumulation and DNA Repair Deficiencies

ARID1A, a SWI/SNF complex component, is frequently mutated in colorectal cancer (CRC). CRC with ARID1A/TP53 concurrent mutations shows marked sensitivity to WEE1 inhibition. ARID1A loss induces R‐loop‐mediated replication stress, impairs ATF3 transcription, and amplifies WEE1i‐induced DNA damage, suggesting a promising therapeutic vulnerability. Abstract ARID1A, a component of the SWI/SNF tumor suppressor complex, is frequently mutated in colorectal cancers (CRC). Here, it is found that CRC with ARID1A/TP53 concurrent mutations is highly sensitive to WEE1 inhibitors. ARID1A deficiency promoted the accumulation of R‐loops, leading to replication stress. This stress, combined with the loss of G1/S and G2/M checkpoint controls due to P53 and WEE1 dysfunction, resulted in substantial DNA damage. Through chromatin accessibility sequencing, it is further revealed that ARID1A loss impaired ATF3 transcription, thereby exacerbating WEE1‐inhibitor‐induced DNA damage and cell death. This preclinical evidence is supported by a phase 1b/2 trial of WEE1‐inhibitor‐based therapy in metastatic CRC patients (NCT06363552), where one patient harboring ARID1A/TP53 concurrent mutations achieved liver lesion regression. Moreover, though CRISPR knockout screening, it is found that concurrent AKT blockade significantly augmented the antitumor effects of the WEE1 inhibitor. In conclusion, WEE1 inhibition offers a promising therapeutic strategy for ARID1A/TP53 concurrent mutant CRC. ARID1A, a SWI/SNF complex component, is frequently mutated in colorectal cancer (CRC). CRC with ARID1A/TP53 concurrent mutations shows marked sensitivity to WEE1 inhibition. ARID1A loss induces R-loop-mediated replication stress, impairs ATF3 transcription, and amplifies WEE1i-induced DNA damage, suggesting a promising therapeutic vulnerability. Abstract ARID1A, a component of the SWI/SNF tumor suppressor complex, is frequently mutated in colorectal cancers (CRC). Here, it is found that CRC with ARID1A/TP53 concurrent mutations is highly sensitive to WEE1 inhibitors. ARID1A deficiency promoted the accumulation of R-loops, leading to replication stress. This stress, combined with the loss of G1/S and G2/M checkpoint controls due to P53 and WEE1 dysfunction, resulted in substantial DNA damage. Through chromatin accessibility sequencing, it is further revealed that ARID1A loss impaired ATF3 transcription, thereby exacerbating WEE1-inhibitor-induced DNA damage and cell death. This preclinical evidence is supported by a phase 1b/2 trial of WEE1-inhibitor-based therapy in metastatic CRC patients (NCT06363552), where one patient harboring ARID1A/TP53 concurrent mutations achieved liver lesion regression. Moreover, though CRISPR knockout screening, it is found that concurrent AKT blockade significantly augmented the antitumor effects of the WEE1 inhibitor. In conclusion, WEE1 inhibition offers a promising therapeutic strategy for ARID1A/TP53 concurrent mutant CRC. Advanced Science, EarlyView.