bims-pimaco 2022-01-23 papers

Cancer Discov. 2022 Jan 19.

Expanding the Reach of Precision Oncology by Drugging All KRAS Mutants.

Marco H Hofmann, Daniel Gerlach, Sandra Misale, Mark Petronczki, Norbert Kraut.

KRAS is the most frequently mutated oncogene, harboring mutations in approximately one in seven cancers. Allele-specific KRASG12C inhibitors are currently changing the treatment paradigm for patients with KRAS G12C-mutated non-small cell lung cancer and colorectal cancer. The success of addressing a previously elusive KRAS allele has fueled drug discovery efforts for all KRAS mutants. Pan-KRAS drugs have the potential to address broad patient populations, including KRAS G12D-, KRAS G12V-, KRAS G13D-, KRAS G12R-, and KRAS G12A-mutant or KRAS wild-type-amplified cancers, as well as cancers with acquired resistance to KRASG12C inhibitors. Here, we review actively pursued allele-specific and pan-KRAS inhibition strategies and their potential utility. SIGNIFICANCE: Mutant-selective KRASG12C inhibitors target a fraction (approximately 13.6%) of all KRAS-driven cancers. A broad arsenal of KRAS drugs is needed to comprehensively conquer KRAS-driven cancers. Conceptually, we foresee two future classes of KRAS medicines: mutant-selective KRAS drugs targeting individual variant alleles and pan-KRAS therapeutics targeting a broad range of KRAS alterations.

DOI: https://doi.org/10.1158/2159-8290.CD-21-1331

Cancer Discov. 2022 Jan 19.

A Structure Is Worth a Thousand Words: New Insights for RAS and RAF Regulation.

Dhirendra K Simanshu, Deborah K Morrison.

The RAS GTPases are frequently mutated in human cancer, with KRAS being the predominant tumor driver. For many years, it has been known that the structure and function of RAS are integrally linked, as structural changes induced by GTP binding or mutational events determine the ability of RAS to interact with regulators and effectors. Recently, a wealth of information has emerged from structures of specific KRAS mutants and from structures of multiprotein complexes containing RAS and/or RAF, an essential effector of RAS. These structures provide key insights regarding RAS and RAF regulation as well as promising new strategies for therapeutic intervention. SIGNIFICANCE: The RAS GTPases are major drivers of tumorigenesis, and for RAS proteins to exert their full oncogenic potential, they must interact with the RAF kinases to initiate ERK cascade signaling. Although binding to RAS is typically a prerequisite for RAF to become an activated kinase, determining the molecular mechanisms by which this interaction results in RAF activation has been a challenging task. A major advance in understanding this process and RAF regulation has come from recent structural studies of various RAS and RAF multiprotein signaling complexes, revealing new avenues for drug discovery.

DOI: https://doi.org/10.1158/2159-8290.CD-21-1494

NPJ Syst Biol Appl. 2022 Jan 19. 8(1): 2

Diffusion kernel-based predictive modeling of KRAS dependency in KRAS wild type cancer cell lines.

Bastian Ulmer, Margarete Odenthal, Reinhard Buettner, Wilfried Roth, Michael Kloth.

Recent progress in clinical development of KRAS inhibitors has raised interest in predicting the tumor dependency on frequently mutated RAS-pathway oncogenes. However, even without such activating mutations, RAS proteins represent core components in signal integration of several membrane-bound kinases. This raises the question of applications of specific inhibitors independent from the mutational status. Here, we examined CRISPR/RNAi data from over 700 cancer cell lines and identified a subset of cell lines without KRAS gain-of-function mutations (KRASwt) which are dependent on KRAS expression. Combining machine learning-based modeling and whole transcriptome data with prior variable selection through protein-protein interaction network analysis by a diffusion kernel successfully predicted KRAS dependency in the KRASwt subgroup and in all investigated cancer cell lines. In contrast, modeling by RAS activating events (RAE) or previously published RAS RNA-signatures did not provide reliable results, highlighting the heterogeneous distribution of RAE in KRASwt cell lines and the importance of methodological references for expression signature modeling. Furthermore, we show that predictors of KRASwt models contain non-substitutable information signals, indicating a KRAS dependency phenotype in the KRASwt subgroup. Our data suggest that KRAS dependent cancers harboring KRAS wild type status could be targeted by directed therapeutic approaches. RNA-based machine learning models could help in identifying responsive and non-responsive tumors.

DOI: https://doi.org/10.1038/s41540-021-00211-8

J Exp Clin Cancer Res. 2022 Jan 17. 41(1): 25

Metabolic synthetic lethality by targeting NOP56 and mTOR in KRAS-mutant lung cancer.

Zhang Yang, Shun-Qing Liang, Liang Zhao, Haitang Yang, Thomas M Marti, Balazs Hegedüs, Yanyun Gao, Bin Zheng, Chun Chen, Wenxiang Wang, Patrick Dorn, Gregor J Kocher, Ralph A Schmid, Ren-Wang Peng.

BACKGROUND: Oncogenic KRAS mutations are prevalent in human cancers, but effective treatment of KRAS-mutant malignancies remains a major challenge in the clinic. Increasing evidence suggests that aberrant metabolism plays a central role in KRAS-driven oncogenic transformation. The aim of this study is to identify selective metabolic dependency induced by mutant KRAS and to exploit it for the treatment of the disease.
METHOD: We performed an integrated analysis of RNAi- and CRISPR-based functional genomic datasets (n = 5) to identify novel genes selectively required for KRAS-mutant cancer. We further screened a customized library of chemical inhibitors for candidates that are synthetic lethal with NOP56 depletion. Functional studies were carried out by genetic knockdown using siRNAs and shRNAs, knockout using CRISPR/Cas9, and/or pharmacological inhibition, followed by cell viability and apoptotic assays. Protein expression was determined by Western blot. Metabolic ROS was measured by flow cytometry-based quantification.
RESULTS: We demonstrated that nucleolar protein 5A (NOP56), a core component of small nucleolar ribonucleoprotein complexes (snoRNPs) with an essential role in ribosome biogenesis, confers a metabolic dependency by regulating ROS homeostasis in KRAS-mutant lung cancer cells and that NOP56 depletion causes synthetic lethal susceptibility to inhibition of mTOR. Mechanistically, cancer cells with reduced NOP56 are subjected to higher levels of ROS and rely on mTOR signaling to balance oxidative stress and survive. We also discovered that IRE1α-mediated unfolded protein response (UPR) regulates this process by activating mTOR through p38 MAPK. Consequently, co-targeting of NOP56 and mTOR profoundly enhances KRAS-mutant tumor cell death in vitro and in vivo.
CONCLUSIONS: Our findings reveal a previously unrecognized mechanism in which NOP56 and mTOR cooperate to play a homeostatic role in the response to oxidative stress and suggest a new rationale for the treatment of KRAS-mutant cancers.

Keywords: KRAS-mutant cancer; NOP56; ROS; Synthetic lethal vulnerability; mTOR

DOI: https://doi.org/10.1186/s13046-022-02240-5

Cancer Discov. 2022 Jan 19.

RAS at 40: Update from the RAS Initiative.

Dwight V Nissley, Frank McCormick.

The RAS Initiative was launched in 2013 to address unmet clinical needs of patients with KRAS-driven cancers. The Initiative is based at Frederick National Laboratory for Cancer Research in Frederick, MD, and involves multiple collaborations with the RAS research community in academia and industry with the shared goal of developing RAS therapies.

DOI: https://doi.org/10.1158/2159-8290.CD-21-1554

Oncogene. 2022 Jan 21.

Oncogenic potential of BEST4 in colorectal cancer via activation of PI3K/Akt signaling.

Xiao-Shun He, Wen-Long Ye, Yu-Juan Zhang, Xiao-Qin Yang, Feng Liu, Jing-Ru Wang, Xiao-Lu Ding, Yun Yang, Ruo-Nan Zhang, Yuan-Yuan Zhao, Hai-Xia Bi, Ling-Chuan Guo, Wen-Juan Gan, Hua Wu.

BEST4 is a member of the bestrophin protein family that plays a critical role in human intestinal epithelial cells. However, its role and mechanism in colorectal cancer (CRC) remain largely elusive. Here, we investigated the role and clinical significance of BEST4 in CRC. Our results demonstrate that BEST4 expression is upregulated in clinical CRC samples and its high-level expression correlates with advanced TNM (tumor, lymph nodes, distant metastasis) stage, LNM (lymph node metastasis), and poor survival. Functional studies revealed that ectopic expression of BEST4 promoted CRC cell proliferation and metastasis, whereas the depletion of BEST4 had the opposite effect both in vitro and in vivo. Mechanistically, BEST4 binds to the p85α regulatory subunit of phosphatidylinositol-3-kinase (PI3K) and promotes p110 kinase activity; this leads to activation of Akt signaling and expression of MYC and CCND1, which are critical regulators of cell proliferation and metastasis. In clinical samples, the expression of BEST4 is positively associated with the expression of phosphorylated Akt, MYC and CCND1. Pharmacological inhibition of Akt activity markedly repressed BEST4-mediated Akt signaling and proliferation and metastasis of CRC cells. Importantly, the interaction between BEST4 and p85α was also enhanced by epidermal growth factor (EGF) in CRC cells. Therapeutically, BEST4 suppression effectively sensitized CRC cells to gefitinib treatment in vivo. Taken together, our findings indicate the oncogenic potential of BEST4 in colorectal carcinogenesis and metastasis by modulating BEST4/PI3K/Akt signaling, highlighting a potential strategy for CRC therapy.

DOI: https://doi.org/10.1038/s41388-021-02160-2

J Pathol. 2022 Jan 17.

Characterization of RNF43 frameshift mutations that drive Wnt ligand- and R-spondin-dependent colon cancer.

Daisuke Yamamoto, Hiroko Oshima, Dong Wang, Haruna Takeda, Kenji Kita, Xuelian Lei, Mizuho Nakayama, Kazuhiro Murakami, Takashi Ohama, Hirofumi Takemura, Mutsumi Toyota, Hiromu Suzuki, Noriyuki Inaki, Masanobu Oshima.

Loss-of-function mutations in RNF43 induce activation of Wnt ligand-dependent Wnt/β-catenin signaling through stabilization of the Frizzled receptor, which is often found in microsatellite instability (MSI)-type colorectal cancer (CRC) that develops from sessile serrated adenomas. However, the mechanism underlying how RNF43 mutations promote tumorigenesis remains poorly understood. In this study, we established nine human CRC-derived organoids and found that three organoid lines carried RNF43 frameshift mutations associated with MSI-high and BRAFV600E mutations, suggesting that these CRCs developed through the serrated pathway. RNF43 frameshift mutant organoids required both Wnt ligands and R-spondin for proliferation, indicating that suppression of ZNRF3 and retained RNF43 function by R-spondin are required to achieve an indispensable level of Wnt activation for tumorigenesis. However, active β-catenin levels in RNF43 mutant organoids were lower than those in APC two-hit mutant CRC, suggesting a lower threshold for Wnt activation in CRC that developed through the serrated pathway. Interestingly, transplantation of RNF43 mutant organoids with intestinal myofibroblasts accelerated the β-catenin nuclear accumulation and proliferation of xenograft tumors, indicating a key role of stromal cells in the promotion of the malignant phenotype of RNF43 mutant CRC cells. Sequencing of subcloned organoid cell-expressed transcripts revealed that two organoid lines carried monoallelic RNF43 cis-mutations, with two RNF43 frameshift mutations introduced in the same allele and the wild-type RNF43 allele remaining, while the other organoid line carried two-hit biallelic RNF43 trans-mutations. These results suggest that heterozygous RNF43 frameshift mutations contribute to CRC development via the serrated pathway; however, a second-hit RNF43 mutation may be advantageous in tumorigenesis compared with a single-hit mutation through further activation of Wnt signaling. Finally, treatment with the PORCN inhibitor significantly suppressed RNF43 mutant cell-derived PDX tumor development. These results suggest a novel mechanism underlying RNF43 mutation-associated CRC development and the therapeutic potential of Wnt ligand inhibition against RNF43 mutant CRC. This article is protected by copyright. All rights reserved.

Keywords: POCRN inhibitor; RNF43; Wnt ligand; colorectal cancer; organoid; serrated pathway

DOI: https://doi.org/10.1002/path.5868