Gene knocks out with CRISPR in colorectal cancer cell lines with or without APC and other WNT/β-catenin pathway mutations
| Cell line | APC | RNF43 | CTNNB1 | TCF7L2 | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene effect | Z-score | Rank | Gene effect | Z-score | Rank | Gene effect | Z-score | Rank | Gene effect | Z-score | Rank | |
| Quadruple mutated | ||||||||||||
| HCT-15 | –0.27 | 0.23 | 10,419 | –0.07 | –0.7 | 3,831 | –1.36 | –3.08 | 122 | 0.09 | 0.75 | 13,906 |
| KM12 | –0.21 | 0.45 | 12,777 | 0.19 | 1.67 | 17,604 | –1.42 | –3.22 | 15 | –0.25 | –0.65 | 3,705 |
| LoVo | –0.44 | –0.42 | 5,884 | –0.12 | –1.11 | 2,469 | –1.16 | –2.54 | 189 | –0.47 | –1.55 | 1,284 |
| LS411N | –0.13 | 0.76 | 12,095 | 0.03 | 0.25 | 9,534 | –2.51 | –6.15 | 19 | –0.6 | –2.09 | 1,222 |
| SNU-C4 | –0.61 | –1.06 | 2,218 | 0.13 | 1.13 | 15,995 | –1.72 | –4.04 | 11 | –1 | –3.69 | 21 |
| SNU-C5 | –0.35 | –0.08 | 7,663 | –0.04 | –0.42 | 5,354 | –0.32 | –0.27 | 6,313 | –0.22 | –0.55 | 4,629 |
| APC only mutated | ||||||||||||
| C75 | –0.13 | 0.75 | 12,681 | 0.21 | 1.9 | 16,539 | –1.2 | –2.64 | 477 | –0.92 | –3.37 | 155 |
| C80 | 0.13 | 1.82 | 16,873 | –0.006 | –0.09 | 8,039 | –1.12 | –2.42 | 456 | –0.71 | –2.5 | 401 |
| C84 | –0.76 | –1.66 | 1,204 | 0.06 | 0.53 | 11,781 | –2.11 | –5.09 | 4 | –0.79 | –2.84 | 174 |
| COLO 201 | –0.28 | 0.18 | 10,692 | 0.06 | 0.56 | 14,017 | –1.9 | –4.52 | 14 | –0.91 | –3.32 | 37 |
| DiFi | –0.05 | 1.06 | 13,404 | 0.1 | 0.9 | 12,728 | –1.08 | –2.31 | 924 | –0.6 | –2.09 | 1,219 |
| HCC2998 | –0.35 | –0.07 | 7,755 | –0.02 | –0.26 | 6,743 | –1.58 | –3.65 | 195 | –0.69 | –2.44 | 746 |
| MDST8 | –0.39 | –0.24 | 6,913 | 0.06 | 0.51 | 12,398 | –0.89 | –1.82 | 777 | –0.05 | 0.13 | 9,717 |
| SW1116 | –0.43 | –0.37 | 4,910 | 0.03 | 0.32 | 12,360 | –0.35 | –0.36 | 4,978 | –0.74 | –2.62 | 73 |
| Triple mutated | ||||||||||||
| HCC-56 | 0.05 | 1.51 | 16,795 | 0.1 | 0.88 | 14,525 | –0.53 | –0.84 | 3,428 | –0.71 | –2.52 | 182 |
| HCT 116 | –0.12 | 0.81 | 13,695 | 0.05 | 0.41 | 11,203 | –0.61 | –1.07 | 2,413 | –0.52 | –1.75 | 953 |
| LS1034 | 0.28 | 2.38 | 17,489 | 0.23 | 2.03 | 17,082 | –1.71 | –4.01 | 43 | –1.03 | –3.78 | 63 |
| NCI-H716 | –0.34 | –0.05 | 7,958 | 0.04 | 0.41 | 10,878 | 0.01 | 0.61 | 12,069 | 0.09 | 0.72 | 12,712 |
| RKO | 0.01 | 1.36 | 17,773 | 0.07 | 0.66 | 15,835 | –0.06 | 0.4 | 13,860 | –0.02 | 0.23 | 12,188 |
| Quadruple wild type | ||||||||||||
| C10 | –0.72 | –1.51 | 1,919 | –0.01 | –0.14 | 7,219 | –0.05 | 0.44 | 10,809 | –0.08 | 0.01 | 8,181 |
| C99 | –0.25 | 0.3 | 10,691 | 0.02 | 0.15 | 9,788 | –1.09 | –2.35 | 563 | –0.52 | –1.75 | 1,355 |
| LS513 | –0.18 | 0.57 | 12,725 | –0.09 | –0.85 | 3,479 | –1 | –2.11 | 496 | –0.77 | –2.75 | 176 |
Data are from the DepMap, Public 24Q2+Score, and Chronos projects. The Z-score was computed as the gene effect minus the mean across cell line models divided by the standard deviation (SD). Not all cell lines of the original cohorts had data available in the CRISPR arrays. APC: adenomatous polyposis coli