CRISPR screens identify a novel combination treatment targeting BCL-XL and WNT signaling for KRAS/BRAF-mutated colorectal cancers

• Published in: Oncogene 2021-05, Vol.40 (18), p.3287-3302
• Main Authors: Jung, Hae Rim, Oh, Yumi, Na, Deukchae, Min, Seoyeon, Kang, Jinjoo, Jang, Dongjun, Shin, Seungjae, Kim, Jiwon, Lee, Sang Eun, Jeong, Eui Man, An, Joon Yong, Sung, Chang Ohk, Lee, Won-Suk, Lee, Charles, Cho, Sung-Yup
• Format: Article
• Language: English
• Subjects: 13/2; 13/31; 13/51; 13/89; 38/39; 38/47; 38/77; 42/109; 45/15; 631/67/1059/602; 631/67/1504/1885; 64/60; Apoptosis; Bcl-2 protein; Bcl-x protein; Cell activation; Cell Biology; Cell death; Chemotherapy; Colorectal cancer; Colorectal carcinoma; CRISPR; Epidermal growth factor receptors; Gene silencing; Genomes; Human Genetics; Internal Medicine; K-Ras protein; Mcl-1 protein; Medicine; Medicine & Public Health; Metastases; Mutation; Oncology; Patients; Therapeutic targets; Wnt protein; Xenografts; β-Catenin
• ISSN: 0950-9232; 1476-5594; 1476-5594
• DOI: 10.1038/s41388-021-01777-7

Metastatic or recurrent colorectal cancer (CRC) patients require systemic chemotherapy, but the therapeutic options of targeted agents remain limited. CRC patients with KRAS or BRAF gene mutations exhibit a worse prognosis and are resistant to anti-EGFR treatment. Previous studies have shown that the expression of anti-apoptotic protein BCL-X L is increased in CRC patients with KRAS / BRAF mutations, suggesting BCL-X L as a therapeutic target for this subgroup. Here, we performed genome-wide CRISPR/Cas9 screens of cell lines with KRAS mutations to investigate the factors required for sensitivity to BCL-X L inhibitor ABT-263 using single-guide RNAs (sgRNAs) that induce loss-of-function mutations. In the presence of ABT-263, sgRNAs targeting negative regulators of WNT signaling (resulting in WNT activation) were enriched, whereas sgRNAs targeting positive regulators of WNT signaling (resulting in WNT inhibition) were depleted in ABT-263-resistant cells. The activation of WNT signaling was highly associated with an increased expression ratio of anti- to pro-apoptotic BCL-2 family genes in CRC samples. Genetic and pharmacologic inhibition of WNT signaling using β-catenin short hairpin RNA or TNIK inhibitor NCB-0846, respectively, augmented ABT-263-induced cell death in KRAS / BRAF -mutated cells. Inhibition of WNT signaling resulted in transcriptional repression of the anti-apoptotic BCL-2 family member, MCL1 , via the functional inhibition of the β-catenin-containing complex at the MCL1 promoter. In addition, the combination of ABT-263 and NCB-0846 exhibited synergistic effects in in vivo patient-derived xenograft (PDX) models with KRAS mutations. Our data provide a novel targeted combination treatment strategy for the CRC patient subgroup with KRAS or BRAF mutations.