The DOI matches its Crossref record; 38 of the 39 references it cites were found in a registry or an index.
Development of siRNA Payloads to Target KRAS -Mutant Cancer
Open accessPublished version of a preprint
Abstract
UNLABELLED: RNAi is a powerful tool for target identification and can lead to novel therapies for pharmacologically intractable targets such as KRAS. RNAi therapy must combine potent siRNA payloads with reliable in vivo delivery for efficient target inhibition. We used a functional "Sensor" assay to establish a library of potent siRNAs against RAS pathway genes and to show that they efficiently suppress their targets at low dose. This reduces off-target effects and enables combination gene knockdown. We administered Sensor siRNAs in vitro and in vivo and validated the delivery of KRAS siRNA alone and siRNA targeting the complete RAF effector node (A/B/CRAF) as promising strategies to treat KRAS-mutant colorectal cancer. We further demonstrate that improved therapeutic efficacy is achieved by formulating siRNA payloads that combine both single-gene siRNA and node-targeted siRNAs (KRAS + PIK3CA/B). The customizable nature of Sensor siRNA payloads offers a universal platform for the combination target identification and development of RNAi therapeutics. SIGNIFICANCE: To advance RNAi therapy for KRAS-mutant cancer, we developed a validated siRNA library against RAS pathway genes that enables combination gene silencing. Using an in vivo model for real-time siRNA delivery tracking, we show that siRNA-mediated inhibition of KRAS as well as RAF or PI3K combinations can impair KRAS-mutant colorectal cancer in xenograft models.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Each siRNA is then processed by the endogenous RNA-induced silencing complex prior to binding to the target RNA, in this case, KRAS, thereby inhibiting translation and promoting mRNA degradation [66,67,68].”
From KRAS: Biology, Inhibition, and Mechanisms of Inhibitor Resistance (2024) · cites this paper as [67]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Bartel (2004) · doi:10.1016/s0092-8674(04)00045-5 · Cited by 34,714
Hannon, G. J. (2002) · Nature · doi:10.1038/418244a · Cited by 3,651
Hopkins, A. L., & Groom, C. R. (2002) · Nature Reviews Drug Discovery · doi:10.1038/nrd892 · Cited by 3,305 · cited 1×
“RNAi can, in principle, be applied to reversibly silence any target gene [reviewed in (8, 9)], thereby increasing the druggable landscape from 10% to virtually 100% of the genome (10, 11).”
BackgroundEvidence of RNAi in humans from systemically administered siRNA via targeted nanoparticles
Davis, M. E., Zuckerman, J. E., Choi, C. H. J., Seligson, D. B., Tolcher, A. W., Alabi, C. A., Yen, Y., Heidel, J. D., & Ribas, A. (2010) · Nature · doi:10.1038/nature08956 · Cited by 2,541 · cited 2×
“Sensor siRNAs can be effectively delivered in vivo To test the therapeutic efficacy of Sensor siRNAs in vivo, we used previously characterized cyclodextrin-polymer nanoparticles (29, 30) to deliver Sensor siRNAs to tumors in mice.”
BackgroundMethodExpression profiling reveals off-target gene regulation by RNAi
Jackson, A. L., Bartz, S. R., Schelter, J., Kobayashi, S. V., Burchard, J., Mao, M., Li, B., Cavet, G., & Linsley, P. S. (2003) · Nature Biotechnology · doi:10.1038/nbt831 · Cited by 2,370
RAF inhibitors transactivate RAF dimers and ERK signalling in cells with wild-type BRAF
Poulikakos, P. I., Zhang, C., Bollag, G. E., Shokat, K. M., & Rosen, N. X. (2010) · Nature · doi:10.1038/nature08902 · Cited by 1,841 · cited 2×
“In comparison, the small molecule BRAF inhibitor PLX4720 did not inhibit the proliferation of KRAS-mutant cells (Figure 4B), as previously reported (2, 3, 26).”
BackgroundResultRAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth
Hatzivassiliou, G., Song, K. W., Yen, I., Brandhuber, B. J., Anderson, D. J., Alvarado, R., Ludlam, M. J. C., Stokoe, D., Gloor, S. L., Vigers, G. P. A., et al. (2010) · Nature · doi:10.1038/nature08833 · Cited by 1,649 · cited 2×
“In comparison, the small molecule BRAF inhibitor PLX4720 did not inhibit the proliferation of KRAS-mutant cells (Figure 4B), as previously reported (2, 3, 26).”
BackgroundResultKinase-Dead BRAF and Oncogenic RAS Cooperate to Drive Tumor Progression through CRAF
Heidorn, S. J., Milagre, C. S., Whittaker, S. R., Nourry, A., Niculescu‐Duvaz, I., Dhomen, N. S., Hussain, J., Reis-Filho, J. S., Springer, C. J., Pritchard, C. A., et al. (2010) · Cell · doi:10.1016/j.cell.2009.12.040 · Cited by 1,497 · cited 2×
“This finding is consistent with recent reports that CRAF plays a critical role in RAS-driven lung carcinoma and melanoma (24-26).”
ResultRas oncogenes: split personalities
Karnoub, A. E., & Weinberg, R. A. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2438 · Cited by 1,467 · cited 1×
“Many KRAS effectors, including RAF, PI3K, RAL and RAC, have RAS-independent means of activation (36), which can be circumvented through direct targeting of effector nodes in addition to KRAS.”
BackgroundAltered cell cycle arrest and gene amplification potential accompany loss of wild-type p53
Livingstone, L. R., White, A., Sprouse, J., Livanos, E., Jacks, T., & Tlsty, T. D. (1992) · Cell · doi:10.1016/0092-8674(92)90243-6 · Cited by 1,328 · cited 9×
“Trp53 -/-MEFs (21) were grown in DMEM supplemented with 10% FBS. KRAS -/-MEFs were obtained from Dr. Mariano Barbacid (CNIO).”
BackgroundMethodInfluentialCoding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs
Tay, Y., Kats, L. M., Salmena, L., Weiss, D., Tan, S. M., Ala, U., Karreth, F. A., Poliseno, L., Provero, P., Cunto, F. D., et al. (2011) · Cell · doi:10.1016/j.cell.2011.09.029 · Cited by 1,025
Davis, M. E. (2009) · Molecular Pharmaceutics · doi:10.1021/mp900015y · Cited by 979
3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets
Birmingham, A., Anderson, E. M., Reynolds, A., Ilsley-Tyree, D., Leake, D., Fedorov, Y., Baskerville, S., Maksimova, E., Robinson, K., Karpilow, J., et al. (2006) · Nature Methods · doi:10.1038/nmeth854 · Cited by 920 · cited 1×
“8 Off-target effects remain a major concern with RNAi experiments and can occur through several mechanisms, including (i) sequence-dependent cross-hybridization to unintended mRNA targets (17, 18); (ii) sequence-independent saturation of the RNAi machinery (19); and (iii) other as yet undefined mechanisms.”
BackgroundSingh, A., Greninger, P., Rhodes, D., Koopman, L., Violette, S., Bardeesy, N., & Settleman, J. (2009) · Cancer Cell · doi:10.1016/j.ccr.2009.03.022 · Cited by 841 · cited 1×
“S2B), though as previously reported, heterogeneity amongst cell lines was observed (16).”
ResultRinehart, J., Adjei, A. A., LoRusso, P. M., Waterhouse, D., Hecht, J. R., Natale, R. B., Hamid, O., Varterasian, M., Asbury, P., Kaldjian, E. P., et al. (2004) · Journal of Clinical Oncology · doi:10.1200/jco.2004.01.185 · Cited by 645
Binding of Ras to Phosphoinositide 3-Kinase p110α Is Required for Ras- Driven Tumorigenesis in Mice
Gupta, S., Ramjaun, A. R., Haiko, P., Wang, Y., Warne, P. H., Nicke, B., Nye, E. L., Stamp, G., Alitalo, K. K., & Downward, J. (2007) · Cell · doi:10.1016/j.cell.2007.03.051 · Cited by 603
Hu‐Lieskovan, S., Heidel, J. D., Bartlett, D. W., Davis, M. E., & Triche, T. J. (2005) · Cancer Research · doi:10.1158/0008-5472.can-05-0565 · Cited by 568 · cited 1×
“Preclinical studies indicate that they are safe in animals (31, 32) and, indeed, these particles have been used in human clinical trials for the treatment of solid tumors (30).”
BackgroundProbing tumor phenotypes using stable and regulated synthetic microRNA precursors
Dickins, R., Hemann, M., Zilfou, J. T., Simpson, D. R., Ibarra, I., Hannon, G., & Lowe, S. (2005) · Nature Genetics · doi:10.1038/ng1651 · Cited by 561
Self-citationKinetic analysis of the RNAi enzyme complex
Haley, B., & Zamore, P. D. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb780 · Cited by 544 · cited 1×
“As competition of RNAi triggers for incorporation and retention in RISC is concentration dependent (20) and since bulk transfected siRNAs can outcompete endogenous miRNAs for RISC loading (19), we set out to specifically investigate dose-dependent RNAi off-target effects by testing shRNAs and siRNAs in cells where the…”
BackgroundTransfection of small RNAs globally perturbs gene regulation by endogenous microRNAs
Khan, A. A., Betel, D., Miller, M. L., Sander, C., Leslie, C. S., & Marks, D. S. (2009) · Nature Biotechnology · doi:10.1038/nbt.1543 · Cited by 534
Shimizu, T., Tolcher, A. W., Papadopoulos, K. P., Beeram, M., Rasco, D. W., Smith, L. S., Gunn, S., Smetzer, L., Mays, T. A., Kaiser, B., et al. (2012) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-11-2381 · Cited by 431 · cited 1×
“Combinations of MEK and PI3K inhibitors are currently being evaluated in clinical trials, though toxicity in normal tissue could limit their therapeutic window (7).”
BackgroundHeidel, J. D., Yu, Z., Liu, J. Y.-C., Rele, S. M., Liang, Y., Zeidan, R. K., Kornbrust, D. J., & Davis, M. E. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701458104 · Cited by 390
Genetic analysis of Ras signalling pathways in cell proliferation, migration and survival
Drosten, M., Dhawahir, A., Sum, E. Y. M., Urosevic, J., Lechuga, C. G., Esteban, L. M., Castellano, E., Guerra, C., Santos, E., & Barbacid, M. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.7 · Cited by 347 · cited 1×
“To test dose-dependent off-target effects of such Sensor-derived siRNAs, we transfected siKRAS_234 and siKRAS_355, which target both human and mouse KRAS, into Kras mouse embryonic fibroblasts (23) at 0.”
An accurate and interpretable model for siRNA efficacy prediction
Vert, J., Foveau, N., Lajaunie, C., & Vandenbrouck, Y. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-520 · Cited by 338
Therapeutic Strategies for Targeting Ras Proteins
Gysin, S., Salt, M. B., Young, A. E., & McCormick, F. (2011) · Genes & Cancer · doi:10.1177/1947601911412376 · Cited by 329 · cited 1×
“Despite intense efforts, pharmacological inhibition of KRAS itself (1) and inhibition of individual effector kinases downstream of KRAS such as RAF (2, 3) and MEK (4-6) have so far been unsuccessful in treating KRAS-mutant tumors.”
BackgroundSelf-citationBlasco, R. B., Francoz, S., Santamaría, D., Cañamero, M., Dubus, P., Charron, J., Baccarini, M., & Barbacid, M. (2011) · Cancer Cell · doi:10.1016/j.ccr.2011.04.002 · Cited by 302 · cited 1×
“This finding is consistent with recent reports that CRAF plays a critical role in RAS-driven lung carcinoma and melanoma (24-26).”
ResultSmall RNA combination therapy for lung cancer
Xue, W., Dahlman, J. E., Tammela, T., Khan, O. F., Sood, S., Dave, A., Cai, W., Chirino, L. M., Yang, G. R., Bronson, R. T., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1412686111 · Cited by 247 · cited 1×
“These results are corroborated by a parallel study from Xue et al, where nanoparticlemediated delivery of KRAS siRNA and other small RNAs was shown to inhibit the growth of KRAS-mutant lung cancers (35).”
ResultHaura, E. B., Ricart, A. D., Larson, T. G., Stella, P. J., Bazhenova, L., Miller, V. A., Cohen, R. B., Eisenberg, P. D., Selaru, P., Wilner, K. D., et al. (2010) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-09-1920 · Cited by 237
Functional Identification of Optimized RNAi Triggers Using a Massively Parallel Sensor Assay
Fellmann, C., Zuber, J. A., McJunkin, K., Chang, K., Malone, C. D., Dickins, R. A., Xu, Q., Hengartner, M. O., Elledge, S. J., Hannon, G. J., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.02.008 · Cited by 222
Self-citationNanoparticle-Based Delivery of RNAi Therapeutics: Progress and Challenges
Zhou, J., Shum, K., Burnett, J., & Rossi, J. J. (2013) · Pharmaceuticals · doi:10.3390/ph6010085 · Cited by 211 · cited 1×
“While delivery is still a major challenge, more reliable lipid and polymeric nanoparticles are in development to deliver siRNA payloads to target tissues [reviewed in (12)].”
BackgroundEffects of Raf Dimerization and Its Inhibition on Normal and Disease-Associated Raf Signaling
Freeman, A. K., Ritt, D. A., & Morrison, D. K. (2013) · Molecular Cell · doi:10.1016/j.molcel.2012.12.018 · Cited by 211 · cited 1×
“Thus RAF inhibition by siRNA and small molecules may exert distinct biological effects, likely owing to the unique mechanism of RAF activation (27, 28).”
BackgroundStable RNA interference rules for silencing
Fellmann, C., & Lowe, S. W. (2013) · Nature Cell Biology · doi:10.1038/ncb2895 · Cited by 170 · cited 1×
“Additionally, off-target effects, which can be due to sequence-dependent and -independent gene deregulation [reviewed (13)], must be minimized for meaningful interpretation of phenotypic outcomes.”
BackgroundSelf-citationHainsworth, J. D., Cebotaru, C. L., Kanarev, V., Ciuleanu, T., Damyanov, D., Stella, P. J., Ganchev, H., Pover, G. M., Morris, C. D., & Tzekova, V. (2010) · Journal of Thoracic Oncology · doi:10.1097/jto.0b013e3181e8b3a3 · Cited by 162 · cited 5×
“As most major RAS effectors are indeed comprised of multi-isoform families (MEK1/2, ERK1/2, PIK3CA/B/D, RALA/B, etc.), it may be important to consider entire effector nodes as targets for drug development.”
BackgroundInfluentialRequirement for Interaction of PI3-Kinase p110α with RAS in Lung Tumor Maintenance
Castellano, E., Sheridan, C., Thin, M. Z., Nye, E., Spencer-Dene, B., Diefenbacher, M., Moore, C., Kumar, M., Murillo, M., Grönroos, E., et al. (2013) · Cancer Cell · doi:10.1016/j.ccr.2013.09.012 · Cited by 161
C-Raf Is Required for the Initiation of Lung Cancer by K-RasG12D
Karreth, F. A., Frese, K. K., DeNicola, G. M., Baccarini, M., & Tuveson, D. A. (2011) · Cancer Discovery · doi:10.1158/2159-8290.cd-10-0044 · Cited by 149
RAF Inhibitors Activate the MAPK Pathway by Relieving Inhibitory Autophosphorylation
Holderfield, M. T., Merritt, H., Chan, J., Wallroth, M., Tandeske, L., Zhai, H., Tellew, J. E., Hardy, S. F., Hekmat-Nejad, M., Stuart, D. D., et al. (2013) · Cancer Cell · doi:10.1016/j.ccr.2013.03.033 · Cited by 134
Self-citationObjective assessment of cancer genes for drug discovery
Patel, M. N., Halling‐Brown, M., Tym, J. E., Workman, P., & Al‐Lazikani, B. (2012) · Nature Reviews Drug Discovery · doi:10.1038/nrd3913 · Cited by 133 · cited 1×
“RNAi can, in principle, be applied to reversibly silence any target gene [reviewed in (8, 9)], thereby increasing the druggable landscape from 10% to virtually 100% of the genome (10, 11).”
BackgroundWeng, M., Lee, J., Wei, S., Li, Q., Shahamatdar, S., Hsu, D. J., Schetter, A. J., Swatkoski, S., Mannan, P., Garfield, S. H., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1207673110 · Cited by 69 · cited 1×
“To measure protein level, total cell lysates were subjected to immunoblotting as previously described (37).”
MethodSelf-citation
Cited by
Sorted by citations
Exosomes facilitate therapeutic targeting of oncogenic KRAS in pancreatic cancer
Kamerkar, S., LeBleu, V. S., Sugimoto, H., Yang, S., Ruivo, C. F., Melo, S. A., Lee, J. J., & Kalluri, R. (2017) · Nature · doi:10.1038/nature22341 · Cited by 2,639
RAS Proteins and Their Regulators in Human Disease
Simanshu, D. K., Nissley, D. V., & McCormick, F. (2017) · Cell · doi:10.1016/j.cell.2017.06.009 · Cited by 1,943
Self-citationRAS isoforms and mutations in cancer at a glance
Hobbs, G. A., Der, C. J., & Rossman, K. L. (2016) · Journal of Cell Science · doi:10.1242/jcs.182873 · Cited by 973
“…metabolism), (v) unbiased genetic or chemical screens for synthetic lethal interactors (Barbie et al., 2009; Kumar et al., 2012; Luo et al., 2009; Sarthy et al., 2007; Scholl et al., 2009) and (vi) RNA interference (RNAi) of KRAS expression (Pecot et al., 2014; Xue et al., 2014; Yuan et al., 2014).”
BackgroundRole of oncogenic KRAS in the diagnosis, prognosis and treatment of pancreatic cancer
Buscail, L., Bournet, B., & Cordelier, P. (2020) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0245-4 · Cited by 721
Genetics and biology of pancreatic ductal adenocarcinoma
Ying, H., Dey, P., Yao, W., Kimmelman, A. C., Draetta, G. F., Maitra, A., & DePinho, R. A. (2016) · Genes & Development · doi:10.1101/gad.275776.115 · Cited by 527
Metadata
- Authors
- Yuan, T. L., Fellmann, C., Lee, C.-S., Ritchie, C. D., Thapar, V., Lee, L. C., Hsu, D. J., Grace, D., Carver, J. O., Zuber, J., Luo, J., McCormick, F., & Lowe, S. W.
- Affiliations
- University of California, San Francisco (US)
- Cold Spring Harbor Laboratory (US)
- National Cancer Institute (US)
- Memorial Sloan Kettering Cancer Center (US)
- Research Institute of Molecular Pathology (AT)
- Corresponding author
- Luo, Ji
- McCormick, Frank
- Lowe, Scott W.
- ORCID
- Venue
- Cancer Discovery
- Published
- 2014-09-30
- Volume
- 4
- Issue
- 10
- Pages
- 1182-1197
- ISSN
- 2159-8274 (ISSN-L)
- 2159-8290
- PMC
- PMC4184972
- OpenAlex
- W2098360608
- Cited by
- 113
- References
- 39
- Citations by year
- 2026: 4 · 2025: 9 · 2024: 8 · 2023: 7 · 2022: 12 · 2021: 8 · 2020: 10 · 2019: 12 · 2018: 9 · 2017: 12 · 2016: 12 · 2015: 9 · 2014: 1
- FWCI
- 4.65
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Cancer Discovery (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health
- U.S. Public Health Service (1ZIABC011437)
- National Cancer Institute (ZIABC011437, U01CA168409, U01CA168370, T32CA108462, P01CA013106, P30CA008748)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Keywords
- siRNA, KRAS mutation, RNAi therapeutics, siRNA delivery, siRNA library, Ras signaling, Raf-1, PIK3CA, PIK3CB, colorectal cancer, off-target effects, xenograft models
- MeSH terms
- Animals, Disease Models, Animal, Humans, Mutation, Neoplasms, Genes, ras, Reproducibility of Results, Signal Transduction, Gene Library, Cluster Analysis, Drug Delivery Systems, Gene Transfer Techniques, Phosphatidylinositol 3-Kinases, Gene Expression Profiling, Xenograft Model Antitumor Assays, RNA Interference, RNA, Small Interfering, Cell Line, Tumor, Tumor Burden, Mice, Nanoparticles, Gene Knockdown Techniques
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 ›
Are you an author, or do you see a problem with this page? Request a review
