Case 1. Which cell line is the most sensitive to the loss of CDK4 ?

Assume you want to study CDK4, when conducting CDK4 gene functional studies, appropriate cell line selection is methodologically critical. CDK4 demonstrates cell line-specific essentiality, meaning randomly selected models may not exhibit survival dependency on this gene. Using the DepMap 23Q2 dataset in the Essentiality Analysis module, which contains the most comprehensive collection of cell lines, we evaluated CDK4 dependency across various tissues and cell lines. Based on median dependency scores, tissues including bone, eye, testis, vulva, and breast displayed the most negative scores, reflecting heightened genetic essentiality (Figure 1A). Among all cell lines analyzed, MDA-MB-453, ES2, SNU1, VCAP, and SNU-1544 displayed the most significant negative dependency scores. Notably, the triple-negative breast cancer (TNBC) cell line MDA-MB-453 exhibited the strongest CDK4 dependence, with the highest negative score among all breast tissue-derived models (Figure 1B). Together, these findings suggest that MDA-MB-453 is the most CDK4-knockdown-sensitive breast cancer cell line model.

Case 2. Can we find potential therapeutic targets and drug candidates for KRAS-mutation cancers?

KRAS is a notorious cancer driver gene that is frequently mutated in many cancers, but KRAS protein has a very smooth surface, which makes it difficult to inhibit by a drug. In such a case, we can think of “target hop” strategy that targets other more druggable proteins instead of trying to inhibit KRAS directly. In line with this hypothesis, we screened candidate targets according to the dependency-based target prioritization pipeline.

Using Essentiality2Target’s pancancer analysis, we identified RAF1, CFLAR, and DOCK5 as potential therapeutic targets for KRAS-mutant tumors across datasets (ALL, DPP, DTI) (Figure 2A). We selected RAF1 as a representative candidate target for further investigation. Previous studies has also shown that KRAS mutations (including G12C and G12D) lead to constitutive activation of the KRAS protein, resulting in persistent activation of downstream RAF1 and subsequent tumor initiation and progression. Targeting RAF1 inhibition therefore represents a potential therapeutic strategy for KRAS-mutant tumors.

If users aim to identify which cancer type with KRAS mutation exhibits greater sensitivity to this therapeutic target, users can navigate to the Tissue section. Tissue section revealed myeloid malignancies show greatest sensitivity to RAF1 inhibition (Figure 2B). Subsequent drug screening through Essentiality2Drug identified.

The Essentiality2Drug is divided into two sections: DPP and DTI. DPP analysis identified the top 15 candidate compounds for RAF1 downregulation. Screening of FDA-approved drugs similarly revealed 15 top candidates for RAF1 downregulation (Figure 2C). Literature review confirmed the efficacy of auranofin, doxorubicin, dinaciclib, and mocetinostat against KRAS-mutant tumors. For example, Auranofin suppresses KRAS-mutant lung adenocarcinoma growth primarily through ECT2 targeting, while doxorubicin acts by disrupting cancer cell DNA repair mechanisms.

Similarly, in the DTI analysis, we identified potential RAF1-targeting inhibitors. For users interested in FDA-approved compounds, the tool can extract and present this information (Figure 2D). Published studies demonstrate the efficacy of LXH254, LY-3009120, belvarafenib, and sorafenib against KRAS-mutant tumors. LXH254 inhibits KRAS-mutant tumors through dual targeting of BRAF/CRAF dimers and BRAF monomers. Belvarafenib exerts its anti-tumor effects on KRAS-mutant cells by blocking the RAF-MEK-ERK signaling pathway. Sorafenib suppresses KRAS-mutant tumor progression through RAF1 inhibition.

Case 3. Can we find the potential therapeutic targets and drug candidates for CCNE1-amplification cancers?

CCNE1 amplification (19q12) is common in ovarian, uterine, and gastroesophageal cancers, driving cyclin E overexpression, genome instability, and therapy resistance. CCNE1-amplified tumors lack effective therapies, highlighting the need for targeted treatments.

Although cyclin E is undruggable, the GEMap enables systematic discovery of therapeutic targets for CCNE1-amplified tumors, offering a promising strategy for these cancers. Following the same analytical approach applied to KRAS, due to its consistent high ranking, CDK2 was prioritized for further study (Figure 3A). Tissue section revealed uterine cancer as the most sensitive to CDK2 inhibition, indicating strong tissue-selective dependence (Figure 3B).

Using the Essentiality2Drug module, we identified potential CDK2-targeting drugs. In the DPP analysis, we identified the top 15 candidate compounds for CDK2 downregulation. Similarly, FDA-approved drug screening identified 15 leading candidates (Figure 3C). Noticeably, many compounds exhibit anti-tumor activity, such as, PF-562271, Ceritinib and NVP-AUY922.

Similarly, the DTI analysis identified potential CDK2-targeting inhibitors (Figure 3D). Previous studies indicate that dinaciclib exerts anti-tumor effects in CCNE1-amplified tumors through CDK2 inhibition. Dinaciclib, a cyclin-dependent kinase (CDK) inhibitor, suppresses CDK2 activity, disrupting the CCNE1-CDK2 complex and inducing cell cycle arrest, thereby suppressing tumor cell proliferation. Other CDK inhibitors—including seliciclib, milciclib, zotiraciclib, alvocidib, AT-7519, and R547—may also suppress CCNE1-amplified tumors.