CRISPR Screening Identifies Mechanisms of Resistance to KRASG12C and SHP2 Inhibitor Combinations in Non-Small Cell Lung Cancer
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Abstract
Although KRASG12C inhibitors show clinical activity in patients with KRAS G12C mutated non–small cell lung cancer (NSCLC) and other solid tumor malignancies, response is limited by multiple mechanisms of resistance. The KRASG12C inhibitor JDQ443 shows enhanced preclinical antitumor activity combined with the SHP2 inhibitor TNO155, and the combination is currently under clinical evaluation. To identify rational combination strategies that could help overcome or prevent some types of resistance, we evaluated the duration of tumor responses to JDQ443 ± TNO155, alone or combined with the PI3Kα inhibitor alpelisib and/or the cyclin-dependent kinase 4/6 inhibitor ribociclib, in xenograft models derived from a KRASG12C-mutant NSCLC line and investigated the genetic mechanisms associated with loss of response to combined KRASG12C/SHP2 inhibition. Tumor regression by single-agent JDQ443 at clinically relevant doses lasted on average 2 weeks and was increasingly extended by the double, triple, or quadruple combinations. Growth resumption was accompanied by progressively increased KRAS G12C amplification. Functional genome-wide CRISPR screening in KRASG12C-dependent NSCLC lines with distinct mutational profiles to identify adaptive mechanisms of resistance revealed sensitizing and rescuing genetic interactions with KRASG12C/SHP2 coinhibition; FGFR1 loss was the strongest sensitizer, and PTEN loss the strongest rescuer. Consistently, the antiproliferative activity of KRASG12C/SHP2 inhibition was strongly enhanced by PI3K inhibitors. Overall, KRAS G12C amplification and alterations of the MAPK/PI3K pathway were predominant mechanisms of resistance to combined KRASG12C/SHP2 inhibitors in preclinical settings. The biological nodes identified by CRISPR screening might provide additional starting points for effective combination treatments. Significance: Identification of resistance mechanisms to KRASG12C/SHP2 coinhibition highlights the need for additional combination therapies for lung cancer beyond on-pathway combinations and offers the basis for development of more effective combination approaches. See related commentary by Johnson and Haigis, p. 4005
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KRAS G12C inhibitors activate RHOA signaling, which drives YAP nuclear localization and enhances tumor survival via YAP/TEAD activity.
“KRAS G12C inhibitors activate RHOA signaling, which drives YAP nuclear localization and enhances tumor survival via YAP/TEAD activity.”
From The Role of KRAS Mutations in Colorectal Cancer: Biological Insights, Clinical Implications, and Future Therapeutic Perspectives (2025) · cites this paper as [73]
Inhibiting TEAD synergistically enhances the efficacy of KRAS G12C inhibitors.
“inhibiting TEAD has been shown to synergistically enhance the efficacy of KRAS G12C inhibitors [73]”
From The Role of KRAS Mutations in Colorectal Cancer: Biological Insights, Clinical Implications, and Future Therapeutic Perspectives (2025) · cites this paper as [73]
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- Authors
- Prahallad, A., Weiss, A., Voshol, H., Kerr, G., Sprouffske, K., Yuan, T., Ruddy, D., Meistertzheim, M., Kazic-Legueux, M., Kottarathil, T., Piquet, M., Cao, Y., Martinuzzi-Duboc, L., Buhles, A., Adler, F., Mannino, S., Tordella, L., Sansregret, L., Maira, S.-M., Graus Porta, D., Fedele, C., & Brachmann, S. M.
- Affiliations
- Novartis (Switzerland) (CH)
- 1Novartis Institutes for BioMedical Research, Basel, Switzerland.
- 2Novartis Institutes for BioMedical Research, Cambridge, Massachusetts.
- Corresponding author
- Brachmann, Saskia M.
- ORCID
- Prahallad, Anirudh
- Weiss, Andreas
- Voshol, Hans
- Kerr, Grainne
- Sprouffske, Kathleen
- Yuan, Tina
- Ruddy, David
- Meistertzheim, Morgane
- Kazic-Legueux, Malika
- Kottarathil, Tina
- Piquet, Michelle
- Cao, Yichen
- Martinuzzi-Duboc, Laetitia
- Buhles, Alexandra
- Adler, Flavia
- Mannino, Salvatore
- Tordella, Luca
- Sansregret, Laurent
- Maira, Sauveur-Michel
- Graus Porta, Diana
- Fedele, Carmine
- Brachmann, Saskia M.
- Venue
- Cancer Research
- Published
- 2023-11-07
- Volume
- 83
- Issue
- 24
- Pages
- 4130-4141
- ISSN
- 0008-5472 (ISSN-L)
- 1538-7445
- PMC
- PMC10722132
- OpenAlex
- W4388464575
- Cited by
- 30
- References
- 59
- Citations by year
- 2026: 6 · 2025: 16 · 2024: 7 · 2023: 1
- FWCI
- 5.53
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cancer Research (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- Novartis Pharmaceuticals Corporation (n/a)
- Topics
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Lung Cancer Treatments and Mutations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Keywords
- KRAS G12C inhibitors, SHP2 inhibitors, non-small cell lung cancer, drug resistance mechanisms, TNO155, alpelisib, ribociclib, PTEN loss, PI3K/mTOR pathway, combination therapy, adaptive resistance, CRISPR screen
- MeSH terms
- Carcinoma, Non-Small-Cell Lung, Enzyme Inhibitors, Humans, Lung Neoplasms, Mutation, Pyrazoles, Proto-Oncogene Proteins p21(ras), Phosphatidylinositol 3-Kinases, Cell Line, Tumor, Protein Kinase Inhibitors, Early Detection of Cancer, Clustered Regularly Interspaced Short Palindromic Repeats
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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