bims-pimaco 2022-02-13 papers

Issue of 2022‒02‒13
six papers selected by
Lucas B. Zeiger
Beatson Institute for Cancer Research

Cell Rep. 2022 Feb 08. pii: S2211-1247(22)00067-5. [Epub ahead of print]38(6): 110351

CRAF dimerization with ARAF regulates KRAS-driven tumor growth.

KRAS, which is mutated in ∼30% of all cancers, activates the RAF-MEK-ERK signaling cascade. CRAF is required for growth of KRAS mutant lung tumors, but the requirement for CRAF kinase activity is unknown. Here, we show that subsets of KRAS mutant tumors are dependent on CRAF for growth. Kinase-dead but not dimer-defective CRAF rescues growth inhibition, suggesting that dimerization but not kinase activity is required. Quantitative proteomics demonstrates increased levels of CRAF:ARAF dimers in KRAS mutant cells, and depletion of both CRAF and ARAF rescues the CRAF-loss phenotype. Mechanistically, CRAF depletion causes sustained ERK activation and induction of cell-cycle arrest, while treatment with low-dose MEK or ERK inhibitor rescues the CRAF-loss phenotype. Our studies highlight the role of CRAF in regulating MAPK signal intensity to promote tumorigenesis downstream of mutant KRAS and suggest that disrupting CRAF dimerization or degrading CRAF may have therapeutic benefit.

Keywords: ARAF; BRAF; CRAF; ERK; KRAS; MAPK; MEK; cancer; dimerization; kinase

DOI: https://doi.org/10.1016/j.celrep.2022.110351

Cell Rep. 2022 Feb 08. pii: S2211-1247(22)00033-X. [Epub ahead of print]38(6): 110322

Identification of the nucleotide-free state as a therapeutic vulnerability for inhibition of selected oncogenic RAS mutants.

Imran Khan, Akiko Koide, Mariyam Zuberi, Gayatri Ketavarapu, Eric Denbaum, Kai Wen Teng, J Matthew Rhett, Russell Spencer-Smith, G Aaron Hobbs, Ernest Ramsay Camp, Shohei Koide, John P O'Bryan.

RAS guanosine triphosphatases (GTPases) are mutated in nearly 20% of human tumors, making them an attractive therapeutic target. Following our discovery that nucleotide-free RAS (apo RAS) regulates cell signaling, we selectively target this state as an approach to inhibit RAS function. Here, we describe the R15 monobody that exclusively binds the apo state of all three RAS isoforms in vitro, regardless of the mutation status, and captures RAS in the apo state in cells. R15 inhibits the signaling and transforming activity of a subset of RAS mutants with elevated intrinsic nucleotide exchange rates (i.e., fast exchange mutants). Intracellular expression of R15 reduces the tumor-forming capacity of cancer cell lines driven by select RAS mutants and KRAS(G12D)-mutant patient-derived xenografts (PDXs). Thus, our approach establishes an opportunity to selectively inhibit a subset of RAS mutants by targeting the apo state with drug-like molecules.

Keywords: PDX; anti-RAS biologics; apo-RAS; colon cancer; lung cancer; monobody; multiplex imaging; pancreatic cancer; protein engineering; tumorigenesis

DOI: https://doi.org/10.1016/j.celrep.2022.110322

Dis Model Mech. 2022 Feb 01. pii: dmm049280. [Epub ahead of print]15(2):

RAS-mediated tumor stress adaptation and the targeting opportunities it presents.

Alexandra Redding, Andrew E Aplin, Elda Grabocka.

Cellular stress is known to function in synergistic cooperation with oncogenic mutations during tumorigenesis to drive cancer progression. Oncogenic RAS is a strong inducer of a variety of pro-tumorigenic cellular stresses, and also enhances the ability of cells to tolerate these stresses through multiple mechanisms. Many of these oncogenic, RAS-driven, stress-adaptive mechanisms have also been implicated in tolerance and resistance to chemotherapy and to therapies that target the RAS pathway. Understanding how oncogenic RAS shapes cellular stress adaptation and how this functions in drug resistance is of vital importance for identifying new therapeutic targets and therapeutic combinations to treat RAS-driven cancers.

Keywords: Drug resistance; RAS; RAS-pathway targeting; Stress adaptation; Tumor-associated stress

DOI: https://doi.org/10.1242/dmm.049280

J Anus Rectum Colon. 2022 ;6(1): 52-57

A Trial Protocol of Precision Medicine for Patients with RAS Wild Metastatic Colorectal Cancer Using Liquid Biopsy (RAS-liquid Study): A Prospective, Multicenter Observational Study.

Akihisa Matsuda, Takeshi Yamada, Takao Takahashi, Keiji Hirata, Takeshi Nagasaka, Kei Ishimaru, Kazuhiro Sakamoto, Keiji Koda, Toshiaki Ishikawa, Hideyuki Ishida, Kenji Matsuda, Hidekazu Kuramochi, Yoichiro Yoshida, Hiromichi Sonoda, Hiroshi Yoshida.

Background: Anti-epidermal growth factor receptor (EGFR) therapy has been identified to prolong the survival of metastatic colorectal cancer (mCRC) patients without RAS mutations. However, its efficacy is not always consistent for these patients. Genomic profiles of primary tumors and metastases are not always concordant; thus, chemotherapeutic agents can alter the tumor molecular profile. This molecular heterogeneity may explain resistance to anti-EGFR therapy. Liquid biopsy using circulating tumor DNA (ctDNA) is a novel, non-invasive diagnostic tool that can accommodate this molecular heterogeneity, providing a comprehensive, real-time view of the molecular landscape. In this study, we evaluated the predictive value of genomic mutations in ctDNA for primary and acquired resistance to anti-EGFR therapy.Methods/Design: This study is a prospective, multicenter, observational study of mCRC patients with wild-type tissue RAS treated with cytotoxic agents and anti-EGFR antibodies as first-line therapy. Genomic mutations, including RAS, BRAF, PIK3CA, and EGFR in ctDNA, are assessed via Droplet Digital PCR before starting chemotherapy and every 3 months thereafter until disease progression. The target sample size is estimated to be 100. The primary endpoint is the response rate in patients without RAS mutation in their blood sample before starting chemotherapy.
Discussion: This study will clarify the predictive value of baseline RAS mutation in ctDNA for responses to anti-EGFR therapy; the frequency of emerging RAS, BRAF, PIK3CA, and EGFR mutations in ctDNA; and the association with secondary resistance to anti-EGFR therapy in first-line therapy for wild-type tissue RAS mCRC patients.

Keywords: anti-EGFR antibody; cell-free DNA; circulating tumor DNA; liquid biopsy; metastatic colorectal cancer

DOI: https://doi.org/10.23922/jarc.2021-042

Nanoscale. 2022 Feb 10.

Predicting the conformational variability of oncogenic GTP-bound G12D mutated KRas-4B proteins at zwitterionic model cell membranes.

Huixia Lu, Jordi Martí.

KRas proteins are the largest family of mutated Ras isoforms, participating in a wide variety of cancers. Due to their importance, large effort is being carried out on drug development by small-molecule inhibitors. However, understanding protein conformational variability remains a challenge in drug discovery. In the case of the Ras family, their multiple conformational states can affect the binding of potential drug inhibitors. To overcome this challenge, we propose a computational framework based on combined all-atom Molecular Dynamics and Metadynamics simulations in order to accurately access conformational variants of the target protein. We tested the methodology using a G12D mutated GTP bound oncogenic KRas-4B protein located at the interface of a DOPC/DOPS/cholesterol model anionic cell membrane. Two main orientations of KRas-4B at the anionic membrane have been determined. The corresponding torsional angles are taken as reliable reaction coordinates so that free-energy landscapes are obtained by well-tempered metadynamics simulations, revealing local and global minima of the free-energy hypersurface and unveiling reactive paths of the system between the two preferential orientations. We have observed that GTP-binding to KRas-4B has huge influence on the stabilisation of the protein and it can potentially help to open Switch I/II druggable pockets, lowering energy barriers between stable states and resulting in cumulative conformers of KRas-4B. This may highlight new opportunities for targeting the unique meta-stable states through the design of new efficient drugs.

DOI: https://doi.org/10.1039/d1nr07622a

Cell Metab. 2022 Feb 01. pii: S1550-4131(22)00022-5. [Epub ahead of print]

The hallmarks of cancer metabolism: Still emerging.

Natalya N Pavlova, Jiajun Zhu, Craig B Thompson.

Metabolism of cancer cells is geared toward biomass production and proliferation. Since the metabolic resources within the local tissue are finite, this can lead to nutrient depletion and accumulation of metabolic waste. To maintain growth in these conditions, cancer cells employ a variety of metabolic adaptations, the nature of which is collectively determined by the physiology of their cell of origin, the identity of transforming lesions, and the tissue in which cancer cells reside. Furthermore, select metabolites not only serve as substrates for energy and biomass generation, but can also regulate gene and protein expression and influence the behavior of non-transformed cells in the tumor vicinity. As they grow and metastasize, tumors can also affect and be affected by the nutrient distribution within the body. In this hallmark update, recent advances are incorporated into a conceptual framework that may help guide further research efforts in exploring cancer cell metabolism.

DOI: https://doi.org/10.1016/j.cmet.2022.01.007