Exploration of Targeted Anti-tumor Therapy

Table 8. 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*
Cell line	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

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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

Declarations

Author contributions

IAV: Conceptualization, Investigation, Writing—original draft, Writing—review & editing.

Conflicts of interest

The author declares that there have no conflicts of interest.

Ethical approval

The study was an analysis of previously published data and was exempt from approval by an Ethics Committee.

Consent to participate

The study was an analysis of previously published data and informed consent was not required or obtained.

Consent to publication

Not applicable.

Availability of data and materials

The datasets analyzed for this study can be found in the Cancer Genome Atlas [http://www.cancer.gov/ccg/]; Cancer Cell Line Encyclopedia [http://www.sites.broadintitute.org/ccle/]; Genomics of Drug Sensitivity in Cancer (GDSC) project [http://www.cancerrxgene.org]; project Achilles, Drive, Marcotte DEMETER2 [http://www.depmap.org/portal/achilles]; DepMap, Public 24Q2+Score, and Chronos projects [http://www.depmap.org].

Funding

Not applicable.

Copyright

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Open Exploration maintains a neutral stance on jurisdictional claims in published institutional affiliations and maps. All opinions expressed in this article are the personal views of the author(s) and do not represent the stance of the editorial team or the publisher.

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