1
|
Yu A, Banerjee S, Malasani S, Towolawi B, Liu Z, Wang Z. Targeting the Protein-Protein Interaction Between the CDC37 Co-Chaperone and Client Kinases by an Allosteric RAF Dimer Breaker. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.17.637148. [PMID: 40027753 PMCID: PMC11870500 DOI: 10.1101/2025.02.17.637148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Braftide, originally designed as a potent allosteric RAF kinase dimer disruptor, was intended to inhibit RAF dimerization by targeting the conserved RAF dimer interface. Intriguingly, Braftide has also been observed to trigger proteasome-mediated protein degradation with an unclear mechanism of action. This study elucidates the mechanism underlying Braftide's dual functionality and assesses its potential as a chemical probe to target kinase-chaperone interaction. CDC37, a selectivity co-chaperone in the HSP90 chaperone machinery, plays a crucial role in facilitating the recognition of client kinase. The RAF dimer interface overlaps with the CDC37-kinase client recognition motif, known as the αC helix-β4 loop. Using co-immunoprecipitation and NanoBiT assays, we confirmed Braftide's ability to selectively disrupt the CDC37-client kinase interaction while sparing HSP90. Through deuterium exchange mass spectrometry, molecular dynamic simulations, and in vitro crosslinking analyses, we mapped Braftide's binding region within the BRAF kinase domain, as well as the CDC37 region implicated in the association of CDC37-client kinase complex. Consequently, this disruption destabilizes RAF kinase clients, resulting in proteasomal degradation, reduced cellular proliferation, and increased apoptosis in cancer cell lines. Furthermore, Braftide exhibits synergy with HSP90 inhibitors, jointly destabilizing both the CDC37-RAF complex and HSP90. Our work demonstrates the feasibility of disrupting the CDC37-client kinase interaction as an innovative therapeutic strategy and identifies the αC helix-β4 loop as a novel allosteric site with significant potential for the development of next-generation therapeutics.
Collapse
|
2
|
Hossain MA. A comprehensive review of targeting RAF kinase in cancer. Eur J Pharmacol 2025; 986:177142. [PMID: 39577552 DOI: 10.1016/j.ejphar.2024.177142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Revised: 11/11/2024] [Accepted: 11/17/2024] [Indexed: 11/24/2024]
Abstract
RAF kinases, particularly the BRAF isoform, play a crucial role in the MAPK/ERK signaling pathway, regulating key cellular processes such as proliferation, differentiation, and survival. Dysregulation of this pathway often caused by mutations in the BRAF gene or alterations in upstream regulators like Ras and receptor tyrosine kinases contributes significantly to cancer development. Mutations, such as BRAF-V600E, are present in a variety of malignancies, with the highest prevalence in melanoma. Targeted therapies against RAF kinases have achieved substantial success, especially in BRAF-V600E-mutant melanomas, where inhibitors like vemurafenib and dabrafenib have demonstrated remarkable efficacy, leading to improved patient outcomes. These inhibitors have also shown clinical benefits in cancers such as thyroid and colorectal carcinoma, although to a lesser extent. Despite these successes, therapeutic resistance remains a major hurdle. Resistance mechanisms, including RAF dimerization, feedback reactivation of the MAPK pathway, and paradoxical activation of ERK signaling, often lead to diminished efficacy over time, resulting in disease progression or even secondary malignancies. In response, current research is focusing on novel therapeutic strategies, including combination therapies that target multiple components of the pathway simultaneously, such as MEK inhibitors used in tandem with RAF inhibitors. Additionally, next-generation RAF inhibitors are being developed to address resistance and enhance therapeutic specificity. This review discusses the clinical advancements in RAF-targeted therapies, with a focus on ongoing efforts to overcome therapeutic resistance and enhance outcomes for cancer patients. It also underscores the persistent challenges in effectively targeting RAF kinase in oncology.
Collapse
Affiliation(s)
- Md Arafat Hossain
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh.
| |
Collapse
|
3
|
Simon JJ, Fowler DM, Maly DJ. Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq. Nat Methods 2024; 21:2094-2106. [PMID: 39433876 PMCID: PMC11785348 DOI: 10.1038/s41592-024-02456-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 09/10/2024] [Indexed: 10/23/2024]
Abstract
Here we describe labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq), an assay for massively parallel profiling of pooled protein variants in human cells. By leveraging the intracellular self-assembly of an RNA-binding domain (RBD) with a stable, variant-encoding RNA barcode, LABEL-seq facilitates the direct measurement of protein properties and functions using simple affinity enrichments of RBD protein fusions, followed by high-throughput sequencing of co-enriched barcodes. Measurement of ~20,000 variant effects for ~1,600 BRaf variants revealed that variation at positions frequently mutated in cancer minimally impacted intracellular abundance but could dramatically alter activity, protein-protein interactions and druggability. Integrative analysis identified networks of positions with similar biochemical roles and enabled modeling of variant effects on cell proliferation and small molecule-promoted degradation. Thus, LABEL-seq enables direct measurement of multiple biochemical properties in a native cellular context, providing insights into protein function, disease mechanisms and druggability.
Collapse
Affiliation(s)
- Jessica J Simon
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| |
Collapse
|
4
|
Özgü E, Kaplan BG, Sivakumar S, Sokol ES, Aydın E, Tokat ÜM, Adibi A, Karakoç EG, Hu J, Kurzrock R, Demiray M. Therapeutic vulnerabilities and pan-cancer landscape of BRAF class III mutations in epithelial solid tumors. BJC REPORTS 2024; 2:77. [PMID: 39516363 PMCID: PMC11524077 DOI: 10.1038/s44276-024-00086-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/12/2024] [Accepted: 07/27/2024] [Indexed: 11/16/2024]
Abstract
BACKGROUND Kinase-impaired class III BRAF mutations have recently received attention as a possible prognostic factor and therapeutic target. Class III BRAF variants differ from class I and class II mutations in terms of mechanism of pathway activation and therapeutic vulnerabilities. Genomic landscape analyses of tumors in large real-world cohorts represent a great opportunity to further characterize tumor-related molecular events and treatment vulnerabilities, however, such data is not yet available for tumors with BRAF class III mutations. METHODS We investigated the pan-cancer genomic landscape of BRAF class III mutations in 376,302 patients. Patients had comprehensive genomic profiling either by FoundationOne® or FoundationOne®CDx from formalin-fixed, paraffin embedded tissue biopsies. 2 patient cases that harbored BRAF class III mutations who demonstrated dramatic response to anti-EGFR treatment were presented. RESULTS BRAF class III mutations are likely to co-occur with RAF1, NRAS and HRAS alterations, while concomitant KRAS alterations were rare. Moreover, we found that alterations that predict resistance to anti-EGFR agents were significantly less common in tumors harboring BRAF class III mutations, which is of great importance as anti-EGFR therapies are a potential targeted treatment option in these tumors. DISCUSSION Our findings suggest a heterogenous interplay of oncogenic alterations in BRAF class III mutated tumors and have important implications for the molecular mechanisms of carcinogenesis while revealing potential therapeutic vulnerabilities. HIGHLIGHTS Tumors harboring BRAF class III (BRAF vIII) mutations comprise a novel subset with distinct genomic heterogeneity. BRAF vIII mutations may sensitize tumors to anti-EGFR treatments. BRAF vIII alterations show significantly less co-occurrence with alterations that predict resistance to anti-EGFR agents. Rare tumors with limited therapy options should be screened for BRAF vIII mutations as they may benefit from anti-EGFR agents.
Collapse
Affiliation(s)
- Eylül Özgü
- Medicana International Atasehir Hospital, Demiray Precision Oncology Center, Istanbul, Turkey
| | | | | | | | - Esranur Aydın
- Medicana International Atasehir Hospital, Demiray Precision Oncology Center, Istanbul, Turkey
| | - Ünal Metin Tokat
- Medicana International Atasehir Hospital, Demiray Precision Oncology Center, Istanbul, Turkey
| | - Ashkan Adibi
- Medicana International Atasehir Hospital, Demiray Precision Oncology Center, Istanbul, Turkey
| | - Ebru Gül Karakoç
- Medicana International Atasehir Hospital, Demiray Precision Oncology Center, Istanbul, Turkey
| | - Jiancheng Hu
- National Cancer Center Singapore, Division of Cellular and Molecular Research, Singapore, Singapore
- Cancer and Stem Cell Program, Duke-NUS National Cancer Centre, 8 College Road, 169857, Singapore, Singapore
| | - Razelle Kurzrock
- Medical College of Wisconsin, Milwaukee, WI, USA
- WIN Consortium, Paris, France
| | - Mutlu Demiray
- Medicana International Atasehir Hospital, Demiray Precision Oncology Center, Istanbul, Turkey.
| |
Collapse
|
5
|
Sigaud R, Brummer T, Kocher D, Milde T, Selt F. MOST wanted: navigating the MAPK-OIS-SASP-tumor microenvironment axis in primary pediatric low-grade glioma and preclinical models. Childs Nerv Syst 2024; 40:3209-3221. [PMID: 38789691 PMCID: PMC11511703 DOI: 10.1007/s00381-024-06463-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Understanding the molecular and cellular mechanisms driving pediatric low-grade glioma (pLGG)-the most prevalent brain tumor in children-is essential for the identification and evaluation of novel effective treatments. This review explores the intricate relationship between the mitogen-activated protein kinase (MAPK) pathway, oncogene-induced senescence (OIS), the senescence-associated secretory phenotype (SASP), and the tumor microenvironment (TME), integrating these elements into a unified framework termed the MAPK/OIS/SASP/TME (MOST) axis. This integrated approach seeks to deepen our understanding of pLGG and improve therapeutic interventions by examining the MOST axis' critical influence on tumor biology and response to treatment. In this review, we assess the axis' capacity to integrate various biological processes, highlighting new targets for pLGG treatment, and the need for characterized in vitro and in vivo preclinical models recapitulating pLGG's complexity to test targets. The review underscores the need for a comprehensive strategy in pLGG research, positioning the MOST axis as a pivotal approach in understanding pLGG. This comprehensive framework will open promising avenues for patient care and guide future research towards inventive treatment options.
Collapse
Affiliation(s)
- Romain Sigaud
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.
| | - Tilman Brummer
- Institute, of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Biological Signaling Studies BIOSS, University of Freiburg and German Consortium for Translational Cancer Research (DKTK), Freiburg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniela Kocher
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.
| |
Collapse
|
6
|
Christen D, Lauinger M, Brunner M, Dengjel J, Brummer T. The mTOR pathway controls phosphorylation of BRAF at T401. Cell Commun Signal 2024; 22:428. [PMID: 39223665 PMCID: PMC11370054 DOI: 10.1186/s12964-024-01808-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 08/24/2024] [Indexed: 09/04/2024] Open
Abstract
BRAF serves as a gatekeeper of the RAS/RAF/MEK/ERK pathway, which plays a crucial role in homeostasis. Since aberrant signalling of this axis contributes to cancer and other diseases, it is tightly regulated by crosstalk with the PI3K/AKT/mTOR pathway and ERK mediated feedback loops. For example, ERK limits BRAF signalling through phosphorylation of multiple residues. One of these, T401, is widely considered as an ERK substrate following acute pathway activation by growth factors. Here, we demonstrate that prominent T401 phosphorylation (pT401) of endogenous BRAF is already observed in the absence of acute stimulation in various cell lines of murine and human origin. Importantly, the BRAF/RAF1 inhibitor naporafenib, the MEK inhibitor trametinib and the ERK inhibitor ulixertinib failed to reduce pT401 levels in these settings, supporting an alternative ERK-independent pathway to T401 phosphorylation. In contrast, the mTOR inhibitor torin1 and the dual-specific PI3K/mTOR inhibitor dactolisib significantly suppressed pT401 levels in all investigated cell types, in both a time and concentration dependent manner. Conversely, genetic mTOR pathway activation by oncogenic RHEB (Q64L) and mTOR (S2215Y and R2505P) mutants substantially increased pT401, an effect that was reverted by dactolisib and torin1 but not by trametinib. We also show that shRNAmir mediated depletion of the mTORC1 complex subunit Raptor significantly enhanced the suppression of T401 phosphorylation by a low torin1 dose, while knockdown of the mTORC2 complex subunit Rictor was less effective. Using mass spectrometry, we provide further evidence that torin1 suppresses the phosphorylation of T401, S405 and S409 but not of other important regulatory phosphorylation sites such as S446, S729 and S750. In summary, our data identify the mTOR axis and its inhibitors of (pre)clinical relevance as novel modulators of BRAF phosphorylation at T401.
Collapse
Affiliation(s)
- Daniel Christen
- Institute of Molecular Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Freiburg and, Heidelberg, 69120, Germany
| | - Manuel Lauinger
- Institute of Molecular Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Melanie Brunner
- Department of Biology, University of Fribourg, Chemin du Museé 10, 1700, Fribourg, Switzerland
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Chemin du Museé 10, 1700, Fribourg, Switzerland
| | - Tilman Brummer
- Institute of Molecular Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany.
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Freiburg and, Heidelberg, 69120, Germany.
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, University of Freiburg, 79106, Freiburg, Germany.
- Center for Biological Signalling Studies BIOSS, University of Freiburg, 79104, Freiburg, Germany.
| |
Collapse
|
7
|
Sun Y, Zhou R, Hu J, Feng S, Hu Q. Reversible control of kinase signaling through chemical-induced dephosphorylation. Commun Biol 2024; 7:1073. [PMID: 39217250 PMCID: PMC11366001 DOI: 10.1038/s42003-024-06771-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
The coordination between kinases and phosphatases is crucial for regulating the phosphorylation levels of essential signaling molecules. Methods enabling precise control of kinase activities are valuable for understanding the kinase functions and for developing targeted therapies. Here, we use the abscisic acid (ABA)-induced proximity system to reversibly control kinase signaling by recruiting phosphatases. Using this method, we found that the oncogenic tyrosine kinase BCR::ABL1 can be inhibited by recruiting various cytoplasmic phosphatases. We also discovered that the oncogenic serine/threonine kinase BRAF(V600E), which has been reported to bypass phosphorylation regulation, can be positively regulated by protein phosphatase 1 (PP1) and negatively regulated by PP5. Additionally, we observed that the dual-specificity kinase MEK1 can be inhibited by recruiting PP5. This suggests that bifunctional molecules capable of recruiting PP5 to MEK or RAF kinases could be promising anticancer drug candidates. Thus, the ABA-induced dephosphorylation method enables rapid screening of phosphatases to precisely control kinase signaling.
Collapse
Affiliation(s)
- Ying Sun
- Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Rihong Zhou
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Jin Hu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Shan Feng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Qi Hu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
| |
Collapse
|
8
|
Huber M, Brummer T. Enzyme Is the Name-Adapter Is the Game. Cells 2024; 13:1249. [PMID: 39120280 PMCID: PMC11311582 DOI: 10.3390/cells13151249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024] Open
Abstract
Signaling proteins in eukaryotes usually comprise a catalytic domain coupled to one or several interaction domains, such as SH2 and SH3 domains. An additional class of proteins critically involved in cellular communication are adapter or scaffold proteins, which fulfill their purely non-enzymatic functions by organizing protein-protein interactions. Intriguingly, certain signaling enzymes, e.g., kinases and phosphatases, have been demonstrated to promote particular cellular functions by means of their interaction domains only. In this review, we will refer to such a function as "the adapter function of an enzyme". Though many stories can be told, we will concentrate on several proteins executing critical adapter functions in cells of the immune system, such as Bruton´s tyrosine kinase (BTK), phosphatidylinositol 3-kinase (PI3K), and SH2-containing inositol phosphatase 1 (SHIP1), as well as in cancer cells, such as proteins of the rat sarcoma/extracellular signal-regulated kinase (RAS/ERK) mitogen-activated protein kinase (MAPK) pathway. We will also discuss how these adaptor functions of enzymes determine or even undermine the efficacy of targeted therapy compounds, such as ATP-competitive kinase inhibitors. Thereby, we are highlighting the need to develop pharmacological approaches, such as proteolysis-targeting chimeras (PROTACs), that eliminate the entire protein, and thus both enzymatic and adapter functions of the signaling protein. We also review how genetic knock-out and knock-in approaches can be leveraged to identify adaptor functions of signaling proteins.
Collapse
Affiliation(s)
- Michael Huber
- Institute of Biochemistry and Molecular Immunology, Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research, IMMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Center for Biological Signalling Studies BIOSS, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
9
|
Dorighi KM, Zhu A, Fortin JP, Hung-Hao Lo J, Sudhamsu J, Wendorff TJ, Durinck S, Callow M, Foster SA, Haley B. Accelerated drug-resistant variant discovery with an enhanced, scalable mutagenic base editor platform. Cell Rep 2024; 43:114313. [PMID: 38838224 DOI: 10.1016/j.celrep.2024.114313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/19/2024] [Accepted: 05/17/2024] [Indexed: 06/07/2024] Open
Abstract
Personalized cancer therapeutics bring directed treatment options to patients based on their tumor's genetic signature. Unfortunately, tumor genomes are remarkably adaptable, and acquired resistance through gene mutation frequently occurs. Identifying mutations that promote resistance within drug-treated patient populations can be cost, resource, and time intensive. Accordingly, base editing, enabled by Cas9-deaminase domain fusions, has emerged as a promising approach for rapid, large-scale gene variant screening in situ. Here, we adapt and optimize a conditional activation-induced cytidine deaminase (AID)-dead Cas9 (dCas9) system, which demonstrates greater heterogeneity of edits with an expanded footprint compared to the most commonly utilized cytosine base editor, BE4. In combination with a custom single guide RNA (sgRNA) library, we identify individual and compound variants in epidermal growth factor receptor (EGFR) and v-raf murine sarcoma viral oncogene homolog B1 (BRAF) that confer resistance to established EGFR inhibitors. This system and analytical pipeline provide a simple, highly scalable platform for cis or trans drug-modifying variant discovery and for uncovering valuable insights into protein structure-function relationships.
Collapse
Affiliation(s)
- Kristel M Dorighi
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA 94080, USA.
| | - Anqi Zhu
- Department of OMNI Bioinformatics, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Jean-Philippe Fortin
- Department of Data Science and Statistical Computing, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Jerry Hung-Hao Lo
- Department of Oncology Bioinformatics, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Jawahar Sudhamsu
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Timothy J Wendorff
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Steffen Durinck
- Department of Oncology Bioinformatics, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Marinella Callow
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Scott A Foster
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA 94080, USA.
| |
Collapse
|
10
|
Scardaci R, Berlinska E, Scaparone P, Vietti Michelina S, Garbo E, Novello S, Santamaria D, Ambrogio C. Novel RAF-directed approaches to overcome current clinical limits and block the RAS/RAF node. Mol Oncol 2024; 18:1355-1377. [PMID: 38362705 PMCID: PMC11161739 DOI: 10.1002/1878-0261.13605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/30/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Mutations in the RAS-RAF-MEK-ERK pathway are frequent alterations in cancer and RASopathies, and while RAS oncogene activation alone affects 19% of all patients and accounts for approximately 3.4 million new cases every year, less frequent alterations in the cascade's downstream effectors are also involved in cancer etiology. RAS proteins initiate the signaling cascade by promoting the dimerization of RAF kinases, which can act as oncoproteins as well: BRAFV600E is the most common oncogenic driver, mutated in the 8% of all malignancies. Research in this field led to the development of drugs that target the BRAFV600-like mutations (Class I), which are now utilized in clinics, but cause paradoxical activation of the pathway and resistance development. Furthermore, they are ineffective against non-BRAFV600E malignancies that dimerize and could be either RTK/RAS independent or dependent (Class II and III, respectively), which are still lacking an effective treatment. This review discusses the recent advances in anti-RAF therapies, including paradox breakers, dimer-inhibitors, immunotherapies, and other novel approaches, critically evaluating their efficacy in overcoming the therapeutic limitations, and their putative role in blocking the RAS pathway.
Collapse
Affiliation(s)
- Rossella Scardaci
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Ewa Berlinska
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Pietro Scaparone
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Sandra Vietti Michelina
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Edoardo Garbo
- Department of OncologyUniversity of Torino, San Luigi HospitalOrbassanoItaly
| | - Silvia Novello
- Department of OncologyUniversity of Torino, San Luigi HospitalOrbassanoItaly
| | - David Santamaria
- Centro de Investigación del CáncerCSIC‐Universidad de SalamancaSpain
| | - Chiara Ambrogio
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| |
Collapse
|
11
|
Rasmussen DM, Semonis MM, Greene JT, Muretta JM, Thompson AR, Toledo Ramos S, Thomas DD, Pomerantz WCK, Freedman TS, Levinson NM. Allosteric coupling asymmetry mediates paradoxical activation of BRAF by type II inhibitors. eLife 2024; 13:RP95481. [PMID: 38742856 PMCID: PMC11093583 DOI: 10.7554/elife.95481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
The type II class of RAF inhibitors currently in clinical trials paradoxically activate BRAF at subsaturating concentrations. Activation is mediated by induction of BRAF dimers, but why activation rather than inhibition occurs remains unclear. Using biophysical methods tracking BRAF dimerization and conformation, we built an allosteric model of inhibitor-induced dimerization that resolves the allosteric contributions of inhibitor binding to the two active sites of the dimer, revealing key differences between type I and type II RAF inhibitors. For type II inhibitors the allosteric coupling between inhibitor binding and BRAF dimerization is distributed asymmetrically across the two dimer binding sites, with binding to the first site dominating the allostery. This asymmetry results in efficient and selective induction of dimers with one inhibited and one catalytically active subunit. Our allosteric models quantitatively account for paradoxical activation data measured for 11 RAF inhibitors. Unlike type II inhibitors, type I inhibitors lack allosteric asymmetry and do not activate BRAF homodimers. Finally, NMR data reveal that BRAF homodimers are dynamically asymmetric with only one of the subunits locked in the active αC-in state. This provides a structural mechanism for how binding of only a single αC-in inhibitor molecule can induce potent BRAF dimerization and activation.
Collapse
Affiliation(s)
- Damien M Rasmussen
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Manny M Semonis
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
| | - Joseph T Greene
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
| | - Joseph M Muretta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Andrew R Thompson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | | | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | | | - Tanya S Freedman
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
- Center for Immunology, University of MinnesotaMinneapolisUnited States
- Masonic Cancer Center, University of MinnesotaMinneapolisUnited States
| | - Nicholas M Levinson
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
- Masonic Cancer Center, University of MinnesotaMinneapolisUnited States
| |
Collapse
|
12
|
Yin H, Tang Q, Xia H, Bi F. Targeting RAF dimers in RAS mutant tumors: From biology to clinic. Acta Pharm Sin B 2024; 14:1895-1923. [PMID: 38799634 PMCID: PMC11120325 DOI: 10.1016/j.apsb.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/02/2024] [Accepted: 02/20/2024] [Indexed: 05/29/2024] Open
Abstract
RAS mutations occur in approximately 30% of tumors worldwide and have a poor prognosis due to limited therapies. Covalent targeting of KRAS G12C has achieved significant success in recent years, but there is still a lack of efficient therapeutic approaches for tumors with non-G12C KRAS mutations. A highly promising approach is to target the MAPK pathway downstream of RAS, with a particular focus on RAF kinases. First-generation RAF inhibitors have been authorized to treat BRAF mutant tumors for over a decade. However, their use in RAS-mutated tumors is not recommended due to the paradoxical ERK activation mainly caused by RAF dimerization. To address the issue of RAF dimerization, type II RAF inhibitors have emerged as leading candidates. Recent clinical studies have shown the initial effectiveness of these agents against RAS mutant tumors. Promisingly, type II RAF inhibitors in combination with MEK or ERK inhibitors have demonstrated impressive efficacy in RAS mutant tumors. This review aims to clarify the importance of RAF dimerization in cellular signaling and resistance to treatment in tumors with RAS mutations, as well as recent progress in therapeutic approaches to address the problem of RAF dimerization in RAS mutant tumors.
Collapse
Affiliation(s)
- Huanhuan Yin
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qiulin Tang
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hongwei Xia
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Feng Bi
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| |
Collapse
|
13
|
Rasmussen DM, Semonis MM, Greene JT, Muretta JM, Thompson AR, Ramos ST, Thomas DD, Pomerantz WC, Freedman TS, Levinson NM. Allosteric coupling asymmetry mediates paradoxical activation of BRAF by type II inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.536450. [PMID: 37131649 PMCID: PMC10153139 DOI: 10.1101/2023.04.18.536450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The type II class of RAF inhibitors currently in clinical trials paradoxically activate BRAF at subsaturating concentrations. Activation is mediated by induction of BRAF dimers, but why activation rather than inhibition occurs remains unclear. Using biophysical methods tracking BRAF dimerization and conformation we built an allosteric model of inhibitor-induced dimerization that resolves the allosteric contributions of inhibitor binding to the two active sites of the dimer, revealing key differences between type I and type II RAF inhibitors. For type II inhibitors the allosteric coupling between inhibitor binding and BRAF dimerization is distributed asymmetrically across the two dimer binding sites, with binding to the first site dominating the allostery. This asymmetry results in efficient and selective induction of dimers with one inhibited and one catalytically active subunit. Our allosteric models quantitatively account for paradoxical activation data measured for 11 RAF inhibitors. Unlike type II inhibitors, type I inhibitors lack allosteric asymmetry and do not activate BRAF homodimers. Finally, NMR data reveal that BRAF homodimers are dynamically asymmetric with only one of the subunits locked in the active αC-in state. This provides a structural mechanism for how binding of only a single αC-in inhibitor molecule can induce potent BRAF dimerization and activation.
Collapse
Affiliation(s)
- Damien M. Rasmussen
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455
| | - Manny M. Semonis
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
| | - Joseph T. Greene
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
| | - Joseph M. Muretta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455
| | - Andrew R. Thompson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455
| | | | - David D. Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455
| | | | - Tanya S. Freedman
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
- Center for Immunology, University of Minnesota, Minneapolis, MN, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455
| | - Nicholas M. Levinson
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455
| |
Collapse
|
14
|
Yu A, Nguyen DH, Nguyen TJ, Wang Z. A novel phosphorylation site involved in dissociating RAF kinase from the scaffolding protein 14-3-3 and disrupting RAF dimerization. J Biol Chem 2023; 299:105188. [PMID: 37625591 PMCID: PMC10520314 DOI: 10.1016/j.jbc.2023.105188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Rapidly accelerated fibrosarcoma (ARAF, BRAF, CRAF) kinase is central to the MAPK pathway (RAS-RAF-MEK-ERK). Inactive RAF kinase is believed to be monomeric, autoinhibited, and cytosolic, while activated RAF is recruited to the membrane via RAS-GTP, leading to the relief of autoinhibition, phosphorylation of key regulatory sites, and dimerization of RAF protomers. Although it is well known that active and inactive BRAF have differential phosphorylation sites that play a crucial role in regulating BRAF, key details are still missing. In this study, we report the characterization of a novel phosphorylation site, BRAFS732 (equivalent in CRAFS624), located in proximity to the C-terminus binding motif for the 14-3-3 scaffolding protein. At the C terminus, 14-3-3 binds to BRAFpS729 (CRAFpS621) and enhances RAF dimerization. We conducted mutational analysis of BRAFS732A/E and CRAFS624A/E and revealed that the phosphomimetic S→E mutant decreases 14-3-3 association and RAF dimerization. In normal cell signaling, dimerized RAF phosphorylates MEK1/2, which is observed in the phospho-deficient S→A mutant. Our results suggest that phosphorylation and dephosphorylation of this site fine-tune the association of 14-3-3 and RAF dimerization, ultimately impacting MEK phosphorylation. We further characterized the BRAF homodimer and BRAF:CRAF heterodimer and identified a correlation between phosphorylation of this site with drug sensitivity. Our work reveals a novel negative regulatory role for phosphorylation of BRAFS732 and CRAFS624 in decreasing 14-3-3 association, dimerization, and MEK phosphorylation. These findings provide insight into the regulation of the MAPK pathway and may have implications for cancers driven by mutations in the pathway.
Collapse
Affiliation(s)
- Alison Yu
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Duc Huy Nguyen
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Thomas Joseph Nguyen
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Zhihong Wang
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA.
| |
Collapse
|
15
|
Lauinger M, Christen D, Klar RF, Roubaty C, Heilig CE, Stumpe M, Knox JJ, Radulovich N, Tamblyn L, Xie IY, Horak P, Forschner A, Bitzer M, Wittel UA, Boerries M, Ball CR, Heining C, Glimm H, Fröhlich M, Hübschmann D, Gallinger S, Fritsch R, Fröhling S, O’Kane GM, Dengjel J, Brummer T. BRAF Δβ3-αC in-frame deletion mutants differ in their dimerization propensity, HSP90 dependence, and druggability. SCIENCE ADVANCES 2023; 9:eade7486. [PMID: 37656784 PMCID: PMC11804575 DOI: 10.1126/sciadv.ade7486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
In-frame BRAF exon 12 deletions are increasingly identified in various tumor types. The resultant BRAFΔβ3-αC oncoproteins usually lack five amino acids in the β3-αC helix linker and sometimes contain de novo insertions. The dimerization status of BRAFΔβ3-αC oncoproteins, their precise pathomechanism, and their direct druggability by RAF inhibitors (RAFi) has been under debate. Here, we functionally characterize BRAFΔLNVTAP>F and two novel mutants, BRAFdelinsFS and BRAFΔLNVT>F, and compare them with other BRAFΔβ3-αC oncoproteins. We show that BRAFΔβ3-αC oncoproteins not only form stable homodimers and large multiprotein complexes but also require dimerization. Nevertheless, details matter as aromatic amino acids at the deletion junction of some BRAFΔβ3-αC oncoproteins, e.g., BRAFΔLNVTAP>F, increase their stability and dimerization propensity while conferring resistance to monomer-favoring RAFi such as dabrafenib or HSP 90/CDC37 inhibition. In contrast, dimer-favoring inhibitors such as naporafenib inhibit all BRAFΔβ3-αC mutants in cell lines and patient-derived organoids, suggesting that tumors driven by such oncoproteins are vulnerable to these compounds.
Collapse
Affiliation(s)
- Manuel Lauinger
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Daniel Christen
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rhena F. U. Klar
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Freeze-O Organoid Bank, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Internal Medicine I (Hematology, Oncology, and Stem Cell Transplantation), University Hospital of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carole Roubaty
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Christoph E. Heilig
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Stumpe
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Jennifer J. Knox
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laura Tamblyn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Irene Y. Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Peter Horak
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrea Forschner
- Department of Dermatology, University Hospital of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University, Tübingen, Germany
| | - Michael Bitzer
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University, Tübingen, Germany
- Center for Personalized Medicine Tübingen, Eberhard Karls University, Tübingen, Germany
- Department of Internal Medicine I, Eberhard-Karls University, Tübingen, Germany
| | - Uwe A. Wittel
- Department of General and Visceral Surgery, University of Freiburg Medical Center, Faculty of Medicine, 79106 Freiburg, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Claudia R. Ball
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden–Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Technische Universität Dresden, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Christoph Heining
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden–Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Hanno Glimm
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden–Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Fröhlich
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hübschmann
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ralph Fritsch
- Department of Internal Medicine I (Hematology, Oncology, and Stem Cell Transplantation), University Hospital of Freiburg, Freiburg, Germany
- Department of Medical Oncology and Haematology, University Hospital of Zurich, Zurich, Switzerland
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Grainne M. O’Kane
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Tilman Brummer
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Freeze-O Organoid Bank, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Center for Biological Signalling Studies BIOSS, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
16
|
Imoto H, Rauch N, Neve AJ, Khorsand F, Kreileder M, Alexopoulos LG, Rauch J, Okada M, Kholodenko BN, Rukhlenko OS. A Combination of Conformation-Specific RAF Inhibitors Overcome Drug Resistance Brought about by RAF Overexpression. Biomolecules 2023; 13:1212. [PMID: 37627277 PMCID: PMC10452107 DOI: 10.3390/biom13081212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Cancer cells often adapt to targeted therapies, yet the molecular mechanisms underlying adaptive resistance remain only partially understood. Here, we explore a mechanism of RAS/RAF/MEK/ERK (MAPK) pathway reactivation through the upregulation of RAF isoform (RAFs) abundance. Using computational modeling and in vitro experiments, we show that the upregulation of RAFs changes the concentration range of paradoxical pathway activation upon treatment with conformation-specific RAF inhibitors. Additionally, our data indicate that the signaling output upon loss or downregulation of one RAF isoform can be compensated by overexpression of other RAF isoforms. We furthermore demonstrate that, while single RAF inhibitors cannot efficiently inhibit ERK reactivation caused by RAF overexpression, a combination of two structurally distinct RAF inhibitors synergizes to robustly suppress pathway reactivation.
Collapse
Affiliation(s)
- Hiroaki Imoto
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Nora Rauch
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Ashish J. Neve
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Fahimeh Khorsand
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Martina Kreileder
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Leonidas G. Alexopoulos
- Protavio Ltd., Demokritos Science Park, 153 43 Athens, Greece
- Department of Mechanical Engineering, National Technical University of Athens, 106 82 Athens, Greece
| | - Jens Rauch
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- School of Biomolecular and Biomedical Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Mariko Okada
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Osaka 565-0871, Japan
| | - Boris N. Kholodenko
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Oleksii S. Rukhlenko
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| |
Collapse
|
17
|
Chessel A, De Crozé N, Molina MD, Taberner L, Dru P, Martin L, Lepage T. RAS-independent ERK activation by constitutively active KSR3 in non-chordate metazoa. Nat Commun 2023; 14:3970. [PMID: 37407549 DOI: 10.1038/s41467-023-39606-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 06/21/2023] [Indexed: 07/07/2023] Open
Abstract
During early development of the sea urchin embryo, activation of ERK signalling in mesodermal precursors is not triggered by extracellular RTK ligands but by a cell-autonomous, RAS-independent mechanism that was not understood. We discovered that in these cells, ERK signalling is activated through the transcriptional activation of a gene encoding a protein related to Kinase Suppressor of Ras, that we named KSR3. KSR3 belongs to a family of catalytically inactive allosteric activators of RAF. Phylogenetic analysis revealed that genes encoding kinase defective KSR3 proteins are present in most non-chordate metazoa but have been lost in flies and nematodes. We show that the structure of KSR3 factors resembles that of several oncogenic human RAF mutants and that KSR3 from echinoderms, cnidarians and hemichordates activate ERK signalling independently of RAS when overexpressed in cultured cells. Finally, we used the sequence of KSR3 factors to identify activating mutations of human B-RAF. These findings reveal key functions for this family of factors as activators of RAF in RAS-independent ERK signalling in invertebrates. They have implications on the evolution of the ERK signalling pathway and suggest a mechanism for its co-option in the course of evolution.
Collapse
Affiliation(s)
- Aline Chessel
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France
| | - Noémie De Crozé
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France
| | - Maria Dolores Molina
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - Laura Taberner
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France
| | - Philippe Dru
- CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Luc Martin
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France
| | - Thierry Lepage
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France.
| |
Collapse
|
18
|
Rohrer L, Spohr C, Beha C, Griffin R, Braun S, Halbach S, Brummer T. Analysis of RAS and drug induced homo- and heterodimerization of RAF and KSR1 proteins in living cells using split Nanoluc luciferase. Cell Commun Signal 2023; 21:136. [PMID: 37316874 DOI: 10.1186/s12964-023-01146-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
The dimerization of RAF kinases represents a key event in their activation cycle and in RAS/ERK pathway activation. Genetic, biochemical and structural approaches provided key insights into this process defining RAF signaling output and the clinical efficacy of RAF inhibitors (RAFi). However, methods reporting the dynamics of RAF dimerization in living cells and in real time are still in their infancy. Recently, split luciferase systems have been developed for the detection of protein-protein-interactions (PPIs), incl. proof-of-concept studies demonstrating the heterodimerization of the BRAF and RAF1 isoforms. Due to their small size, the Nanoluc luciferase moieties LgBiT and SmBiT, which reconstitute a light emitting holoenzyme upon fusion partner promoted interaction, appear as well-suited to study RAF dimerization. Here, we provide an extensive analysis of the suitability of the Nanoluc system to study the homo- and heterodimerization of BRAF, RAF1 and the related KSR1 pseudokinase. We show that KRASG12V promotes the homo- and heterodimerization of BRAF, while considerable KSR1 homo- and KSR1/BRAF heterodimerization already occurs in the absence of this active GTPase and requires a salt bridge between the CC-SAM domain of KSR1 and the BRAF-specific region. We demonstrate that loss-of-function mutations impairing key steps of the RAF activation cycle can be used as calibrators to gauge the dynamics of heterodimerization. This approach identified the RAS-binding domains and the C-terminal 14-3-3 binding motifs as particularly critical for the reconstitution of RAF mediated LgBiT/SmBiT reconstitution, while the dimer interface was less important for dimerization but essential for downstream signaling. We show for the first time that BRAFV600E, the most common BRAF oncoprotein whose dimerization status is controversially portrayed in the literature, forms homodimers in living cells more efficiently than its wildtype counterpart. Of note, Nanoluc activity reconstituted by BRAFV600E homodimers is highly sensitive to the paradox-breaking RAFi PLX8394, indicating a dynamic and specific PPI. We report the effects of eleven ERK pathway inhibitors on RAF dimerization, incl. third-generation compounds that are less-defined in terms of their dimer promoting abilities. We identify Naporafenib as a potent and long-lasting dimerizer and show that the split Nanoluc approach discriminates between type I, I1/2 and II RAFi. Video Abstract.
Collapse
Affiliation(s)
- Lino Rohrer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Corinna Spohr
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Carina Beha
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Ricarda Griffin
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sandra Braun
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany.
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany.
- Center for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, 79104, Germany.
| |
Collapse
|
19
|
Pan-cancer clinical impact of latent drivers from double mutations. Commun Biol 2023; 6:202. [PMID: 36808143 PMCID: PMC9941481 DOI: 10.1038/s42003-023-04519-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 01/23/2023] [Indexed: 02/22/2023] Open
Abstract
Here, we discover potential 'latent driver' mutations in cancer genomes. Latent drivers have low frequencies and minor observable translational potential. As such, to date they have escaped identification. Their discovery is important, since when paired in cis, latent driver mutations can drive cancer. Our comprehensive statistical analysis of the pan-cancer mutation profiles of ~60,000 tumor sequences from the TCGA and AACR-GENIE cohorts identifies significantly co-occurring potential latent drivers. We observe 155 same gene double mutations of which 140 individual components are cataloged as latent drivers. Evaluation of cell lines and patient-derived xenograft response data to drug treatment indicate that in certain genes double mutations may have a prominent role in increasing oncogenic activity, hence obtaining a better drug response, as in PIK3CA. Taken together, our comprehensive analyses indicate that same-gene double mutations are exceedingly rare phenomena but are a signature for some cancer types, e.g., breast, and lung cancers. The relative rarity of doublets can be explained by the likelihood of strong signals resulting in oncogene-induced senescence, and by doublets consisting of non-identical single residue components populating the background mutational load, thus not identified.
Collapse
|
20
|
Computational analysis of natural product B-Raf inhibitors. J Mol Graph Model 2023; 118:108340. [PMID: 36208592 DOI: 10.1016/j.jmgm.2022.108340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/20/2022]
Abstract
B-Raf protein is a serine-threonine kinase and an important signal transduction molecule of the MAPK signaling pathway that mediates signals from RAS to MEK, ultimately promoting various essential cellular functions. The B-Raf kinase domain is divided into two subdomains: a small N-terminal lobe and a large C-terminal lobe, with a deep catalytic cleft between them. The N-terminal lobe contains a phosphate-binding loop (P-loop) and nucleotide-binding pocket, while the C-terminal lobe binds the protein substrates and contains the catalytic loop. The ligand pharmacophore was generated by using 17 different natural products and the receptor pharmacophore was generated by using protein structures. The reported natural product B-Raf inhibitors were analyzed according to the pharmacophore analysis (HipHop fit), virtual screening tools by Lipinski's rule of five. Thirteen out of seventeen molecules share the best ligand based pharmacophoric model (HipHop_5). The best receptor based pharmacophoric model came as AADHR. The compounds were docked against the B-Raf receptors (PDB ID: 3OG7, 4XV2, 5C9C). The compound DHSilB with cDOCKER interaction energy of -62.7 kcal/mol, -83.3 kcal/mol, -73.6 kcal/mol as well as the compound DHSilA with cDOCKER interaction energy of -63.9 kcal/mol, -63.2 kcal/mol, -74.7 kcal/mol showed satisfactory interaction with the respective receptors. Finally, the MD simulation was run for 100 ns for the top docked compounds DHSilA and DHSilB with the B-Raf proteins (PDB ID: 3OG7, 4XV2 and 5C9C). After the MD simulation run for 100 ns, the ligand 2,3-dehydrosilybin A (DHSilA) was found to be more stable in terms of the trajectories of RMSD, RMSF, Rg and H-bonds.
Collapse
|
21
|
Gunderwala A, Cope N, Wang Z. Mechanism and inhibition of BRAF kinase. Curr Opin Chem Biol 2022; 71:102205. [PMID: 36067564 PMCID: PMC10396080 DOI: 10.1016/j.cbpa.2022.102205] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 01/27/2023]
Abstract
The role of BRAF in tumor initiation has been established, however, the precise mechanism of autoinhibition has only been illustrated recently by several structural studies. These structures uncovered the basis by which the regulatory domains engage in regulating the activity of BRAF kinase domain, which lead to a more complete picture of the regulation cycle of RAF kinases. Small molecule BRAF inhibitors developed specifically to target BRAFV600E have proven effective at inhibiting the most dominant BRAF mutant in melanomas, but are less potent against other BRAF mutants in RAS-driven diseases due to paradoxical activation of the MAPK pathway. A variety of new generation inhibitors that do not show paradoxical activation have been developed. Alternatively, efforts have begun to develop inhibitors targeting the dimer interface of BRAF. A deeper understanding of BRAF regulation together with more diverse BRAF inhibitors will be beneficial for drug development in RAF or RASdriven cancers.
Collapse
Affiliation(s)
- Amber Gunderwala
- Department of Chemistry & Biochemistry, College of Science and Mathematics, Rowan University, Glassboro, NJ, USA
| | - Nicholas Cope
- Department of Chemistry & Biochemistry, College of Science and Mathematics, Rowan University, Glassboro, NJ, USA
| | - Zhihong Wang
- Department of Chemistry & Biochemistry, College of Science and Mathematics, Rowan University, Glassboro, NJ, USA.
| |
Collapse
|
22
|
Advances towards Understanding the Mechanism of Action of the Hsp90 Complex. Biomolecules 2022; 12:biom12050600. [PMID: 35625528 PMCID: PMC9138868 DOI: 10.3390/biom12050600] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 12/24/2022] Open
Abstract
Hsp90 (Heat Shock Protein 90) is an ATP (Adenosine triphosphate) molecular chaperone responsible for the activation and maturation of client proteins. The mechanism by which Hsp90 achieves such activation, involving structurally diverse client proteins, has remained enigmatic. However, recent advances using structural techniques, together with advances in biochemical studies, have not only defined the chaperone cycle but have shed light on its mechanism of action. Hsp90 hydrolysis of ATP by each protomer may not be simultaneous and may be dependent on the specific client protein and co-chaperone complex involved. Surprisingly, Hsp90 appears to remodel client proteins, acting as a means by which the structure of the client protein is modified to allow its subsequent refolding to an active state, in the case of kinases, or by making the client protein competent for hormone binding, as in the case of the GR (glucocorticoid receptor). This review looks at selected examples of client proteins, such as CDK4 (cyclin-dependent kinase 4) and GR, which are activated according to the so-called ‘remodelling hypothesis’ for their activation. A detailed description of these activation mechanisms is paramount to understanding how Hsp90-associated diseases develop.
Collapse
|
23
|
Rajkumar S, Berry D, Heney KA, Strong C, Ramsay L, Lajoie M, Alkallas R, Nguyen TT, Thomson C, Ahanfeshar-Adams M, Dankner M, Petrella T, Rose AAN, Siegel PM, Watson IR. Melanomas with concurrent BRAF non-p.V600 and NF1 loss-of-function mutations are targetable by BRAF/MEK inhibitor combination therapy. Cell Rep 2022; 39:110634. [PMID: 35385748 DOI: 10.1016/j.celrep.2022.110634] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 12/15/2021] [Accepted: 03/16/2022] [Indexed: 02/08/2023] Open
Abstract
Although combination BRAF/MEK inhibition has produced significant survival benefits for BRAF p.V600 mutant melanomas, targeted therapies approved for BRAF non-p.V600 mutant melanomas remain limited. Through the analysis of 772 cutaneous melanoma exomes, we reveal that BRAF non-p.V600 mutations co-occurs more frequently with NF1 loss, but not with oncogenic NRAS mutations, than expected by chance. We present cell signaling data, which demonstrate that BRAF non-p.V600 mutants can signal as monomers and dimers within an NF1 loss context. Concordantly, BRAF inhibitors that inhibit both monomeric and dimeric BRAF synergize with MEK inhibition to significantly reduce cell viability in vitro and tumor growth in vivo in BRAF non-p.V600 mutant melanomas with co-occurring NF1 loss-of-function mutations. Our data suggest that patients harboring BRAF non-p.V600 mutant melanomas may benefit from current FDA-approved BRAF/MEK inhibitor combination therapy currently reserved for BRAF p.V600 mutant patients.
Collapse
Affiliation(s)
- Shivshankari Rajkumar
- Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Diana Berry
- Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Kayla A Heney
- Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Colton Strong
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - LeeAnn Ramsay
- Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada
| | - Mathieu Lajoie
- Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada
| | - Rached Alkallas
- Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada; Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Tan-Trieu Nguyen
- Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada
| | - Cameron Thomson
- University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | | | - Matthew Dankner
- Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada; Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Teresa Petrella
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - April A N Rose
- Department of Oncology, McGill University, Montréal, QC H4A 3T2, Canada; Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Peter M Siegel
- Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada; Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Ian R Watson
- Goodman Cancer Institute, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada; Research Institute of the McGill University Health Centre, Montréal, QC H3H 2R9, Canada.
| |
Collapse
|
24
|
Nussinov R, Zhang M, Maloney R, Tsai C, Yavuz BR, Tuncbag N, Jang H. Mechanism of activation and the rewired network: New drug design concepts. Med Res Rev 2022; 42:770-799. [PMID: 34693559 PMCID: PMC8837674 DOI: 10.1002/med.21863] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Precision oncology benefits from effective early phase drug discovery decisions. Recently, drugging inactive protein conformations has shown impressive successes, raising the cardinal questions of which targets can profit and what are the principles of the active/inactive protein pharmacology. Cancer driver mutations have been established to mimic the protein activation mechanism. We suggest that the decision whether to target an inactive (or active) conformation should largely rest on the protein mechanism of activation. We next discuss the recent identification of double (multiple) same-allele driver mutations and their impact on cell proliferation and suggest that like single driver mutations, double drivers also mimic the mechanism of activation. We further suggest that the structural perturbations of double (multiple) in cis mutations may reveal new surfaces/pockets for drug design. Finally, we underscore the preeminent role of the cellular network which is deregulated in cancer. Our structure-based review and outlook updates the traditional Mechanism of Action, informs decisions, and calls attention to the intrinsic activation mechanism of the target protein and the rewired tumor-specific network, ushering innovative considerations in precision medicine.
Collapse
Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of MedicineTel Aviv UniversityTel AvivIsrael
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
| | - Chung‐Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
| | - Bengi Ruken Yavuz
- Department of Health Informatics, Graduate School of InformaticsMiddle East Technical UniversityAnkaraTurkey
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of InformaticsMiddle East Technical UniversityAnkaraTurkey
- Department of Chemical and Biological Engineering, College of EngineeringKoc UniversityIstanbulTurkey
- Koc University Research Center for Translational Medicine, School of MedicineKoc UniversityIstanbulTurkey
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
| |
Collapse
|
25
|
Novel potential oncogenic and druggable mutations of FGFRs recur in the kinase domain across cancer types. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166313. [PMID: 34826586 DOI: 10.1016/j.bbadis.2021.166313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022]
Abstract
Fibroblast growth factor receptors (FGFRs) are recurrently altered by single nucleotide variants (SNVs) in many human cancers. The prevalence of SNVs in FGFRs depends on the cancer type. In some tumors, such as the urothelial carcinoma, mutations of FGFRs occur at very high frequency (up to 60%). Many characterized mutations occur in the extracellular or transmembrane domains, while fewer known mutations are found in the kinase domain. In this study, we performed a bioinformatics analysis to identify novel putative cancer driver or therapeutically actionable mutations of the kinase domain of FGFRs. To pinpoint those mutations that may be clinically relevant, we exploited the recurrence of alterations on analogous amino acid residues within the kinase domain (PK_Tyr_Ser-Thr) of different kinases as a predictor of functional impact. By exploiting MutationAligner and LowMACA bioinformatics resources, we highlighted novel uncharacterized mutations of FGFRs which recur in other protein kinases. By revealing unanticipated correspondence with known variants, we were able to infer their functional effects, as alterations clustering on similar residues in analogous proteins have a high probability to elicit similar effects. As FGFRs represent an important class of oncogenes and drug targets, our study opens the way for further studies to validate their driver and/or actionable nature and, in the long term, for a more efficacious application of precision oncology.
Collapse
|
26
|
Corrales E, Levit-Zerdoun E, Metzger P, Kowar S, Ku M, Brummer T, Boerries M. Dynamic transcriptome analysis reveals signatures of paradoxical effect of vemurafenib on human dermal fibroblasts. Cell Commun Signal 2021; 19:123. [PMID: 34930313 PMCID: PMC8686565 DOI: 10.1186/s12964-021-00801-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 11/09/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Vemurafenib (PLX4032) is one of the most frequently used treatments for late-stage melanoma patients with the BRAFV600E mutation; however, acquired resistance to the drug poses as a major challenge. It remains to be determined whether off-target effects of vemurafenib on normal stroma components could reshape the tumor microenvironment in a way that contributes to cancer progression and drug resistance. METHODS By using temporally-resolved RNA- and ATAC-seq, we studied the early molecular changes induced by vemurafenib in human dermal fibroblast (HDF), a main stromal component in melanoma and other tumors with high prevalence of BRAFV600 mutations. RESULTS Transcriptomics analyses revealed a stepwise up-regulation of proliferation signatures, together with a down-regulation of autophagy and proteolytic processes. The gene expression changes in HDF strongly correlated in an inverse way with those in BRAFV600E mutant malignant melanoma (MaMel) cell lines, consistent with the observation of a paradoxical effect of vemurafenib, leading to hyperphosphorylation of MEK1/2 and ERK1/2. The transcriptional changes in HDF were not strongly determined by alterations in chromatin accessibility; rather, an already permissive chromatin landscape seemed to facilitate the early accessibility to MAPK/ERK-regulated transcription factor binding sites. Combinatorial treatment with the MEK inhibitor trametinib did not preclude the paradoxical activation of MAPK/ERK signaling in HDF. When administered together, vemurafenib partially compensated for the reduction of cell viability and proliferation induced by trametinib. These paradoxical changes were restrained by using the third generation BRAF inhibitor PLX8394, a so-called paradox breaker compound. However, the advantageous effects on HDF during combination therapies were also lost. CONCLUSIONS Vemurafenib induces paradoxical changes in HDF, enabled by a permissive chromatin landscape. These changes might provide an advantage during combination therapies, by compensating for the toxicity induced in stromal cells by less specific MAPK/ERK inhibitors. Our results highlight the relevance of evaluating the effects of the drugs on non-transformed stromal components, carefully considering the implications of their administration either as mono- or combination therapies. Video Abstract.
Collapse
Affiliation(s)
- Eyleen Corrales
- Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Ella Levit-Zerdoun
- Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Patrick Metzger
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
| | - Silke Kowar
- Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
| | - Manching Ku
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Mathildenstr. 1, 79106 Freiburg, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - Melanie Boerries
- Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| |
Collapse
|
27
|
Maloney RC, Zhang M, Jang H, Nussinov R. The mechanism of activation of monomeric B-Raf V600E. Comput Struct Biotechnol J 2021; 19:3349-3363. [PMID: 34188782 PMCID: PMC8215184 DOI: 10.1016/j.csbj.2021.06.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Oncogenic mutations in the serine/threonine kinase B-Raf, particularly the V600E mutation, are frequent in cancer, making it a major drug target. Although much is known about B-Raf's active and inactive states, questions remain about the mechanism by which the protein changes between these two states. Here, we utilize molecular dynamics to investigate both wild-type and V600E B-Raf to gain mechanistic insights into the impact of the Val to Glu mutation. The results show that the wild-type and mutant follow similar activation pathways involving an extension of the activation loop and an inward motion of the αC-helix. The V600E mutation, however, destabilizes the inactive state by disrupting hydrophobic interactions present in the wild-type structure while the active state is stabilized through the formation of a salt bridge between Glu600 and Lys507. Additionally, when the activation loop is extended, the αC-helix is able to move between an inward and outward orientation as long as the DFG motif adopts a specific orientation. In that orientation Phe595 rotates away from the αC-helix, allowing the formation of a salt bridge between Lys483 and Glu501. These mechanistic insights have implications for the development of new Raf inhibitors.
Collapse
Affiliation(s)
- Ryan C. Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Corresponding author at: Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA.
| |
Collapse
|
28
|
Vido MJ, Rock J, Aplin AE. Role of serine 365 in BRAF V600E sensitivity to RAF inhibition. Pigment Cell Melanoma Res 2020; 34:696-702. [PMID: 33000894 DOI: 10.1111/pcmr.12932] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/31/2020] [Accepted: 09/18/2020] [Indexed: 01/04/2023]
Abstract
The serine-threonine kinase, BRAF, is an upstream regulator of the MEK-ERK1/2 pathway and is commonly mutated in cancer. 14-3-3 proteins bind to two sites in BRAF, N-terminal S365, and C-terminal S729. 14-3-3 binding modulates the activity and dimerization of both wild-type and non-V600 mutant forms of BRAF. In BRAF V600E mutants, the C-terminal S729 site affects dimerization of truncated splice variants. The N-terminal, S365, is removed in BRAF V600E splice variants but its importance in full-length BRAF V600 mutants remains uncertain. We tested the role of S365 in dimerization and RAF inhibitor resistance in full-length BRAF V600E. Mutating BRAF S365 site to an alanine (S365A) reduced 14-3-3 association and increased BRAF V600E homodimerization. BRAF V600E S365A displayed reduced sensitivity to RAF inhibitor at the level of MEK-ERK1/2 signaling, cell growth, and cell viability. These data suggest that alteration or removal of the S365 14-3-3 binding site may contribute to RAF inhibitor resistance.
Collapse
Affiliation(s)
- Michael J Vido
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Jefferson College of Life Sciences, Thomas Jefferson University, Philadelphia, PA, USA
| | - Justin Rock
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Jefferson College of Life Sciences, Thomas Jefferson University, Philadelphia, PA, USA
| | - Andrew E Aplin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| |
Collapse
|
29
|
Owsley J, Stein MK, Porter J, In GK, Salem M, O'Day S, Elliott A, Poorman K, Gibney G, VanderWalde A. Prevalence of class I-III BRAF mutations among 114,662 cancer patients in a large genomic database. Exp Biol Med (Maywood) 2020; 246:31-39. [PMID: 33019809 DOI: 10.1177/1535370220959657] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
IMPACT STATEMENT These data represent the largest aggregation of BRAF mutations within a single clinical database to our knowledge. The relative proportions of both BRAF V600 mutations and non-V600 mutations are informative in all cancers and by malignancy, and can serve as a definitive gold-standard for BRAF mutation cancer incidence by malignancy. The rate of BRAF mutation in human cancer in a real-world large database is lower than previously reported likely representing testing more broadly across tumor types. The relative percentages of Class II and Class III BRAF mutations are higher than previously reported, representing almost 35% of BRAF mutations in cancer. These findings provide support for the development of effective treatments for non-V600 BRAF mutations in cancer.
Collapse
Affiliation(s)
- Jeff Owsley
- Division of Hematology/Oncology, University of Tennessee Health Science Center, Germantown, TN 38138, USA
| | - Matthew K Stein
- Division of Hematology/Oncology, University of Tennessee Health Science Center, Germantown, TN 38138, USA
| | | | - Gino K In
- Division of Hematology/Oncology, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Steven O'Day
- John Wayne Cancer Institute, Santa Monica, CA 90404, USA
| | | | | | - Geoffrey Gibney
- Division of Hematology/Oncology, Georgetown University, Washington, DC 20007, USA
| | - Ari VanderWalde
- Division of Hematology/Oncology, University of Tennessee Health Science Center, Germantown, TN 38138, USA.,West Cancer Center, Germantown, TN 38138, USA
| |
Collapse
|
30
|
Botton T, Talevich E, Mishra VK, Zhang T, Shain AH, Berquet C, Gagnon A, Judson RL, Ballotti R, Ribas A, Herlyn M, Rocchi S, Brown KM, Hayward NK, Yeh I, Bastian BC. Genetic Heterogeneity of BRAF Fusion Kinases in Melanoma Affects Drug Responses. Cell Rep 2020; 29:573-588.e7. [PMID: 31618628 DOI: 10.1016/j.celrep.2019.09.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 07/26/2019] [Accepted: 09/04/2019] [Indexed: 12/15/2022] Open
Abstract
BRAF fusions are detected in numerous neoplasms, but their clinical management remains unresolved. We identified six melanoma lines harboring BRAF fusions representative of the clinical cases reported in the literature. Their unexpected heterogeneous responses to RAF and MEK inhibitors could be categorized upon specific features of the fusion kinases. Higher expression level correlated with resistance, and fusion partners containing a dimerization domain promoted paradoxical activation of the mitogen-activated protein kinase (MAPK) pathway and hyperproliferation in response to first- and second-generation RAF inhibitors. By contrast, next-generation αC-IN/DFG-OUT RAF inhibitors blunted paradoxical activation across all lines and had their therapeutic efficacy further increased in vitro and in vivo by combination with MEK inhibitors, opening perspectives in the clinical management of tumors harboring BRAF fusions.
Collapse
Affiliation(s)
- Thomas Botton
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA.
| | - Eric Talevich
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Vivek Kumar Mishra
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MA 20892, USA
| | - A Hunter Shain
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Céline Berquet
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Alexander Gagnon
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Robert L Judson
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Robert Ballotti
- U1065, Institut National de la Santé et de la Recherche Médicale, Centre Méditerranéen de Médecine Moléculaire, Université Côte d'Azur, 06200 Nice, France
| | - Antoni Ribas
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Stéphane Rocchi
- U1065, Institut National de la Santé et de la Recherche Médicale, Centre Méditerranéen de Médecine Moléculaire, Université Côte d'Azur, 06200 Nice, France
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MA 20892, USA
| | - Nicholas K Hayward
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Iwei Yeh
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Boris C Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA.
| |
Collapse
|
31
|
Usta D, Sigaud R, Buhl JL, Selt F, Marquardt V, Pauck D, Jansen J, Pusch S, Ecker J, Hielscher T, Vollmer J, Sommerkamp AC, Rubner T, Hargrave D, van Tilburg CM, Pfister SM, Jones DTW, Remke M, Brummer T, Witt O, Milde T. A Cell-Based MAPK Reporter Assay Reveals Synergistic MAPK Pathway Activity Suppression by MAPK Inhibitor Combination in BRAF-Driven Pediatric Low-Grade Glioma Cells. Mol Cancer Ther 2020; 19:1736-1750. [PMID: 32451331 DOI: 10.1158/1535-7163.mct-19-1021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 04/11/2020] [Accepted: 05/15/2020] [Indexed: 11/16/2022]
Abstract
Pilocytic astrocytomas as well as other pediatric low-grade gliomas (pLGG) exhibit genetic events leading to aberrant activation of the MAPK pathway. The most common alterations are KIAA1549:BRAF fusions and BRAFV600E and NF1 mutations. Novel drugs targeting the MAPK pathway (MAPKi) are prime candidates for the treatment of these single-pathway diseases. We aimed to develop an assay suitable for preclinical testing of MAPKi in pLGGs with the goal to identify novel MAPK pathway-suppressing synergistic drug combinations. A reporter plasmid (pDIPZ) with a MAPK-responsive ELK-1-binding element driving the expression of destabilized firefly luciferase was generated and packaged using a lentiviral vector system. Pediatric glioma cell lines with a BRAF fusion (DKFZ-BT66) and a BRAFV600E mutation (BT-40) background, respectively, were stably transfected. Modulation of the MAPK pathway activity by MAPKi was measured using the luciferase reporter and validated by detection of phosphorylated protein levels. A screening of a MAPKi library was performed, and synergy of selected combinations was calculated. Screening of a MAPKi library revealed MEK inhibitors as the class inhibiting the pathway with the lowest IC50s, followed by ERK and next-generation RAF inhibitors. Combination treatments with different MAPKi classes showed synergistic effects in BRAF fusion as well as BRAFV600E mutation backgrounds. Here, we report a novel reporter assay for medium- to high-throughput preclinical drug testing in pLGG cell lines. The assay confirmed MEK, ERK, and next-generation RAF inhibitors as potential treatment approaches for KIAA1549:BRAF and BRAFV600E-mutated pLGGs. In addition, the assay revealed that combination treatments synergistically suppressed MAPK pathway activity.
Collapse
Affiliation(s)
- Diren Usta
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.,KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Romain Sigaud
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Juliane L Buhl
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.,KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Viktoria Marquardt
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Germany, and Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Pauck
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Germany, and Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jennifer Jansen
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany, Centre for Biological Signalling Studies BIOSS, University of Freiburg, Comprehensive Cancer Center Freiburg (CCCF) and German Consortium for Translational Cancer Research (DKTK), Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Pusch
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Jonas Ecker
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.,KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Johanna Vollmer
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Alexander C Sommerkamp
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Rubner
- Flow Cytometry Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Darren Hargrave
- Neurooncology and Experimental Therapeutics, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Cornelis M van Tilburg
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.,KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc Remke
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Germany, and Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany, Centre for Biological Signalling Studies BIOSS, University of Freiburg, Comprehensive Cancer Center Freiburg (CCCF) and German Consortium for Translational Cancer Research (DKTK), Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.,KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany. .,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.,KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
32
|
Brummer T, McInnes C. RAF kinase dimerization: implications for drug discovery and clinical outcomes. Oncogene 2020; 39:4155-4169. [PMID: 32269299 DOI: 10.1038/s41388-020-1263-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 12/19/2022]
Abstract
The RAF kinases activated by RAS GTPases regulate cell growth and division by signal transduction through the ERK cascade and mutations leading to constitutive activity are key drivers of human tumors, as are upstream activators including RAS and receptor tyrosine kinases. The development of first-generation RAF inhibitors, including vemurafenib (VEM) and dabrafenib led to initial excitement due to high response rates and profound regression of malignant melanomas carrying BRAFV600E mutations. The excitement about these unprecedented response rates, however, was tempered by tumor unresponsiveness through both intrinsic and acquired drug-resistance mechanisms. In recent years much insight into the complexity of the RAS-RAF axis has been obtained and inactivation and signal transduction mechanisms indicate that RAF dimerization is a critical step in multiple cellular contexts and plays a key role in resistance. Both homo- and hetero-dimerization of BRAF and CRAF can modulate therapeutic response and disease progression in patients treated with ATP-competitive inhibitors and are therefore highly clinically significant. Ten years after the definition of the RAF dimer interface (DIF) by crystallography, this review focuses on the implications of RAF kinase dimerization in signal transduction and for drug development, both from a classical ATP-competitive standpoint and from the perspective of new therapeutic strategies including inhibiting dimer formation. A structural perspective of the DIF, how dimerization impacts inhibitor activation and the structure-based design of next-generation RAF kinase inhibitors with unique mechanisms of action is presented. We also discuss potential fields of application for DIF inhibitors, ranging from non-V600E oncoproteins and BRAF fusions to tumors driven by aberrant receptor tyrosine kinase or RAS signaling.
Collapse
Affiliation(s)
- Tilman Brummer
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Strasse 17, 79104, Freiburg im Breisgau, Germany.,German Cancer Consortium DKTK Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Centre Freiburg, University of Freiburg, Freiburg im Breisgau, Germany
| | - Campbell McInnes
- Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA.
| |
Collapse
|
33
|
Degirmenci U, Wang M, Hu J. Targeting Aberrant RAS/RAF/MEK/ERK Signaling for Cancer Therapy. Cells 2020; 9:E198. [PMID: 31941155 PMCID: PMC7017232 DOI: 10.3390/cells9010198] [Citation(s) in RCA: 366] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/29/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
The RAS/RAF/MEK/ERK (MAPK) signaling cascade is essential for cell inter- and intra-cellular communication, which regulates fundamental cell functions such as growth, survival, and differentiation. The MAPK pathway also integrates signals from complex intracellular networks in performing cellular functions. Despite the initial discovery of the core elements of the MAPK pathways nearly four decades ago, additional findings continue to make a thorough understanding of the molecular mechanisms involved in the regulation of this pathway challenging. Considerable effort has been focused on the regulation of RAF, especially after the discovery of drug resistance and paradoxical activation upon inhibitor binding to the kinase. RAF activity is regulated by phosphorylation and conformation-dependent regulation, including auto-inhibition and dimerization. In this review, we summarize the recent major findings in the study of the RAS/RAF/MEK/ERK signaling cascade, particularly with respect to the impact on clinical cancer therapy.
Collapse
Affiliation(s)
- Ufuk Degirmenci
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Mei Wang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jiancheng Hu
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| |
Collapse
|
34
|
BRAF Splice Variant Resistance to RAF Inhibitor Requires Enhanced MEK Association. Cell Rep 2019; 25:1501-1510.e3. [PMID: 30404005 DOI: 10.1016/j.celrep.2018.10.049] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 09/11/2018] [Accepted: 10/11/2018] [Indexed: 12/19/2022] Open
Abstract
Expression of aberrantly spliced BRAF V600E isoforms (BRAF V600E ΔEx) mediates resistance in 13%-30% of melanoma patients progressing on RAF inhibitors. BRAF V600E ΔEx confers resistance, in part, through enhanced dimerization. Here, we uncoupled BRAF V600E ΔEx dimerization from maintenance of MEK-ERK1/2 signaling. Furthermore, we show BRAF V600E ΔEx association with its substrate, MEK, is enhanced and required for RAF inhibitor resistance. RAF inhibitor treatment increased phosphorylation at serine 729 (S729) in BRAF V600E ΔEx. Mutation of S729 to a non-phosphorylatable residue reduced BRAF V600E ΔEx-MEK interaction, reduced dimerization or oligomerization, and increased RAF inhibitor sensitivity. Conversely, mutation of the BRAF dimerization domain elicited partial effects on MEK association and RAF inhibitor sensitivity. Our data implicate BRAF S729 in resistance to RAF inhibitor and underscore the importance of substrate association with BRAF V600E ΔEx. These findings may provide opportunities to target resistance driven by aberrantly spliced forms of BRAF V600E.
Collapse
|
35
|
Cope N, Novak B, Candelora C, Wong K, Cavallo M, Gunderwala A, Liu Z, Li Y, Wang Z. Biochemical Characterization of Full-Length Oncogenic BRAF V600E together with Molecular Dynamics Simulations Provide Insight into the Activation and Inhibition Mechanisms of RAF Kinases. Chembiochem 2019; 20:2850-2861. [PMID: 31152574 DOI: 10.1002/cbic.201900266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Indexed: 12/12/2022]
Abstract
The most prevalent BRAF mutation, V600E, occurs frequently in melanoma and other cancers. Although extensive progress has been made toward understanding the biology of RAF kinases, little in vitro characterization of full-length BRAFV600E is available. Herein, we show the successful purification of active, full-length BRAFV600E from mammalian cells for in vitro experiments. Our biochemical characterization of intact BRAFV600E together with molecular dynamics (MD) simulations of the BRAF kinase domain and cell-based assays demonstrate that BRAFV600E has several unique features that contribute to its tumorigenesis. Firstly, steady-state kinetic analyses reveal that purified BRAFV600E is more active than fully activated wild-type BRAF; this is consistent with the notion that elevated signaling output is necessary for transformation. Secondly, BRAFV600E has a higher potential to form oligomers, despite the fact that the V600E substitution confers constitutive kinase activation independent of an intact side-to-side dimer interface. Thirdly, BRAFV600E bypasses inhibitory P-loop phosphorylation to enforce the necessary elevated signaling output for tumorigenesis. Together, these results provide new insight into the biochemical properties of BRAFV600E , complementing the understanding of BRAF regulation under normal and disease conditions.
Collapse
Affiliation(s)
- Nicholas Cope
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Borna Novak
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Christine Candelora
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Kenneth Wong
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Maria Cavallo
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Amber Gunderwala
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Zhiwei Liu
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Yana Li
- Eukaryotic Tissue Culture Facility, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Zhihong Wang
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| |
Collapse
|
36
|
Khaliq M, Fallahi-Sichani M. Epigenetic Mechanisms of Escape from BRAF Oncogene Dependency. Cancers (Basel) 2019; 11:cancers11101480. [PMID: 31581557 PMCID: PMC6826668 DOI: 10.3390/cancers11101480] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/28/2019] [Accepted: 09/29/2019] [Indexed: 12/14/2022] Open
Abstract
About eight percent of all human tumors (including 50% of melanomas) carry gain-of-function mutations in the BRAF oncogene. Mutated BRAF and subsequent hyperactivation of the MAPK signaling pathway has motivated the use of MAPK-targeted therapies for these tumors. Despite great promise, however, MAPK-targeted therapies in BRAF-mutant tumors are limited by the emergence of drug resistance. Mechanisms of resistance include genetic, non-genetic and epigenetic alterations. Epigenetic plasticity, often modulated by histone-modifying enzymes and gene regulation, can influence a tumor cell's BRAF dependency and therefore, response to therapy. In this review, focusing primarily on class 1 BRAF-mutant cells, we will highlight recent work on the contribution of epigenetic mechanisms to inter- and intratumor cell heterogeneity in MAPK-targeted therapy response.
Collapse
Affiliation(s)
- Mehwish Khaliq
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
- Program in Cancer Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Mohammad Fallahi-Sichani
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
- Program in Cancer Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| |
Collapse
|
37
|
Weinberg F, Griffin R, Fröhlich M, Heining C, Braun S, Spohr C, Iconomou M, Hollek V, Röring M, Horak P, Kreutzfeldt S, Warsow G, Hutter B, Uhrig S, Neumann O, Reuss D, Heiland DH, von Kalle C, Weichert W, Stenzinger A, Brors B, Glimm H, Fröhling S, Brummer T. Identification and characterization of a BRAF fusion oncoprotein with retained autoinhibitory domains. Oncogene 2019; 39:814-832. [PMID: 31558800 DOI: 10.1038/s41388-019-1021-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/14/2022]
Abstract
Fusion proteins involving the BRAF serine/threonine kinase occur in many cancers. The oncogenic potential of BRAF fusions has been attributed to the loss of critical N-terminal domains that mediate BRAF autoinhibition. We used whole-exome and RNA sequencing in a patient with glioblastoma multiforme to identify a rearrangement between TTYH3, encoding a membrane-resident, calcium-activated chloride channel, and BRAF intron 1, resulting in a TTYH3-BRAF fusion protein that retained all features essential for BRAF autoinhibition. Accordingly, the BRAF moiety of the fusion protein alone, which represents full-length BRAF without the amino acids encoded by exon 1 (BRAFΔE1), did not induce MEK/ERK phosphorylation or transformation. Likewise, neither the TTYH3 moiety of the fusion protein nor full-length TTYH3 provoked ERK pathway activity or transformation. In contrast, TTYH3-BRAF displayed increased MEK phosphorylation potential and transforming activity, which were caused by TTYH3-mediated tethering of near-full-length BRAF to the (endo)membrane system. Consistent with this mechanism, a synthetic approach, in which BRAFΔE1 was tethered to the membrane by fusing it to the cytoplasmic tail of CD8 also induced transformation. Furthermore, we demonstrate that TTYH3-BRAF signals largely independent of a functional RAS binding domain, but requires an intact BRAF dimer interface and activation loop phosphorylation sites. Cells expressing TTYH3-BRAF exhibited increased MEK/ERK signaling, which was blocked by clinically achievable concentrations of sorafenib, trametinib, and the paradox breaker PLX8394. These data provide the first example of a fully autoinhibited BRAF protein whose oncogenic potential is dictated by a distinct fusion partner and not by a structural change in BRAF itself.
Collapse
Affiliation(s)
- Florian Weinberg
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Centre for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, Germany
| | - Ricarda Griffin
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martina Fröhlich
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Christoph Heining
- Department of Translational Medical Oncology, NCT Dresden, Dresden, and DKFZ, Heidelberg, Germany.,University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany
| | - Sandra Braun
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Centre for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, Germany
| | - Corinna Spohr
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Mary Iconomou
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Viola Hollek
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Röring
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Horak
- Department of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany.,DKTK, Heidelberg, Germany
| | - Simon Kreutzfeldt
- Department of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany.,DKTK, Heidelberg, Germany
| | - Gregor Warsow
- Omics IT and Data Management Core Facility, DKFZ, Heidelberg, Germany.,Division of Theoretical Bioinformatics, DKFZ, Heidelberg, Germany
| | - Barbara Hutter
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Sebastian Uhrig
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Olaf Neumann
- DKTK, Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Reuss
- DKTK, Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Dieter Henrik Heiland
- Department of Neurosurgery, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Translational NeuroOncology Research Group, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christof von Kalle
- Department of Translational Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University Munich, Munich, Germany.,DKTK, Munich, Germany
| | - Albrecht Stenzinger
- DKTK, Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany.,DKTK, Heidelberg, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, NCT Dresden, Dresden, and DKFZ, Heidelberg, Germany.,University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany
| | - Stefan Fröhling
- Department of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany. .,DKTK, Heidelberg, Germany.
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Centre for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, Germany. .,Comprehensive Cancer Centre Freiburg, University of Freiburg, Freiburg, Germany. .,DKTK Partner Site Freiburg and DKFZ, Heidelberg, Germany.
| |
Collapse
|
38
|
Röck R, Mayrhofer JE, Torres-Quesada O, Enzler F, Raffeiner A, Raffeiner P, Feichtner A, Huber RG, Koide S, Taylor SS, Troppmair J, Stefan E. BRAF inhibitors promote intermediate BRAF(V600E) conformations and binary interactions with activated RAS. SCIENCE ADVANCES 2019; 5:eaav8463. [PMID: 31453322 PMCID: PMC6693913 DOI: 10.1126/sciadv.aav8463] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 07/09/2019] [Indexed: 05/05/2023]
Abstract
Oncogenic BRAF mutations initiate tumor formation by unleashing the autoinhibited kinase conformation and promoting RAS-decoupled proliferative RAF-MEK-ERK signaling. We have engineered luciferase-based biosensors to systematically track full-length BRAF conformations and interactions affected by tumorigenic kinase mutations and GTP loading of RAS. Binding of structurally diverse αC-helix-OUT BRAF inhibitors (BRAFi) showed differences in specificity and efficacy by shifting patient mutation-containing BRAF reporters from the definitive opened to more closed conformations. Unexpectedly, BRAFi engagement with the catalytic pocket of V600E-mutated BRAF stabilized an intermediate and inactive kinase conformation that enhanced binary RAS:RAF interactions, also independently of RAF dimerization in melanoma cells. We present evidence that the interference with RAS interactions and nanoclustering antagonizes the sequential formation of drug-induced RAS:RAF tetramers. This suggests a previously unappreciated allosteric effect of anticancer drug-driven intramolecular communication between the kinase and RAS-binding domains of mutated BRAF, which may further promote paradoxical kinase activation and drug resistance mechanisms.
Collapse
Affiliation(s)
- Ruth Röck
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Johanna E. Mayrhofer
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Omar Torres-Quesada
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Florian Enzler
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Andrea Raffeiner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Philipp Raffeiner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Andreas Feichtner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Roland G. Huber
- Bioinformatics Institute (BII), Agency for Science Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Shohei Koide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine and Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Susan S. Taylor
- Department of Pharmacology, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of California, San Diego, San Diego, CA 92093, USA
| | - Jakob Troppmair
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Innsbruck Medical University, Innrain 66, 6020 Innsbruck, Austria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| |
Collapse
|
39
|
Sukswai N, Khoury JD. Immunohistochemistry Innovations for Diagnosis and Tissue-Based Biomarker Detection. Curr Hematol Malig Rep 2019; 14:368-375. [DOI: 10.1007/s11899-019-00533-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
40
|
Gunderwala AY, Nimbvikar AA, Cope NJ, Li Z, Wang Z. Development of Allosteric BRAF Peptide Inhibitors Targeting the Dimer Interface of BRAF. ACS Chem Biol 2019; 14:1471-1480. [PMID: 31243962 DOI: 10.1021/acschembio.9b00191] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BRAF is the most frequently mutated kinase in human cancers and is one of the major effectors of oncogenic RAS, making BRAF a target of considerable interest for anticancer drug development. Wild-type BRAF and a variety of oncogenic BRAF mutants are dependent on dimerization of the kinase domain, which also emerges as a culprit of drug resistance and side effects of current BRAF therapies. Thus, allosteric BRAF inhibitors capable of disrupting BRAF dimers could abrogate hyperactivated MAPK (mitogen-activated protein kinase) signaling driven by oncogenic BRAF or RAS and overcome the major limitations of current BRAF inhibitors. To establish this, we applied an in silico approach to design a series of peptide inhibitors targeting the dimer interface of BRAF. One resulting inhibitor was found to potently inhibit the kinase activity of BRAF homo- and heterodimers, including oncogenic BRAFG469A mutant. Moreover, this inhibitor synergizes with FDA-approved, ATP-competitive BRAF inhibitors against dimeric BRAF, suggesting that allosteric BRAF inhibitors have great potential to extend the application of current BRAF therapies. Additionally, targeting the dimer interface of BRAF kinase leads to protein degradation of both RAF and MEK, uncovering a novel scaffolding function of RAF in protecting large MAPK complexes from protein degradation. In conclusion, we have developed a potent lead peptide inhibitor for targeting the dimer interface of BRAF in cancer cells. The dual function of this peptide inhibitor validates the strategy for developing allosteric BRAF inhibitors that specifically dissociate RAF dimers and destabilize the MAPK signaling complex.
Collapse
Affiliation(s)
- Amber Y. Gunderwala
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Anushri A. Nimbvikar
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Nicholas J. Cope
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Zhijun Li
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Zhihong Wang
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
41
|
CRAF mutations in lung cancer can be oncogenic and predict sensitivity to combined type II RAF and MEK inhibition. Oncogene 2019; 38:5933-5941. [PMID: 31285551 PMCID: PMC6756226 DOI: 10.1038/s41388-019-0866-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 04/04/2019] [Accepted: 04/28/2019] [Indexed: 12/19/2022]
Abstract
Two out of 41 non-small cell lung cancer patients enrolled in a clinical study were found with a somatic CRAF mutation in their tumor, namely CRAFP261A and CRAFP207S. To our knowledge, both mutations are novel in lung cancer and CRAFP261A has not been previously reported in cancer. Expression of CRAFP261A in HEK293T cells and BEAS-2B lung epithelial cells led to increased ERK pathway activation in a dimer-dependent manner, accompanied with loss of CRAF phosphorylation at the negative regulatory S259 residue. Moreover, stable expression of CRAFP261A in mouse embryonic fibroblasts and BEAS-2B cells led to anchorage-independent growth. Consistent with a previous report, we could not observe a gain-of-function with CRAFP207S. Type II but not type I RAF inhibitors suppressed the CRAFP261A-induced ERK pathway activity in BEAS-2B cells, and combinatorial treatment with type II RAF inhibitors and a MEK inhibitor led to a stronger ERK pathway inhibition and growth arrest. Our findings suggest that the acquisition of a CRAFP261A mutation can provide oncogenic properties to cells, and that such cells are sensitive to combined MEK and type II RAF inhibitors. CRAF mutations should be diagnostically and therapeutically explored in lung and perhaps other cancers.
Collapse
|
42
|
Olea-Flores M, Zuñiga-Eulogio MD, Mendoza-Catalán MA, Rodríguez-Ruiz HA, Castañeda-Saucedo E, Ortuño-Pineda C, Padilla-Benavides T, Navarro-Tito N. Extracellular-Signal Regulated Kinase: A Central Molecule Driving Epithelial-Mesenchymal Transition in Cancer. Int J Mol Sci 2019; 20:E2885. [PMID: 31200510 PMCID: PMC6627365 DOI: 10.3390/ijms20122885] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 12/18/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a reversible cellular process, characterized by changes in gene expression and activation of proteins, favoring the trans-differentiation of the epithelial phenotype to a mesenchymal phenotype. This process increases cell migration and invasion of tumor cells, progression of the cell cycle, and resistance to apoptosis and chemotherapy, all of which support tumor progression. One of the signaling pathways involved in tumor progression is the MAPK pathway. Within this family, the ERK subfamily of proteins is known for its contributions to EMT. The ERK subfamily is divided into typical (ERK 1/2/5), and atypical (ERK 3/4/7/8) members. These kinases are overexpressed and hyperactive in various types of cancer. They regulate diverse cellular processes such as proliferation, migration, metastasis, resistance to chemotherapy, and EMT. In this context, in vitro and in vivo assays, as well as studies in human patients, have shown that ERK favors the expression, function, and subcellular relocalization of various proteins that regulate EMT, thus promoting tumor progression. In this review, we discuss the mechanistic roles of the ERK subfamily members in EMT and tumor progression in diverse biological systems.
Collapse
Affiliation(s)
- Monserrat Olea-Flores
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Miriam Daniela Zuñiga-Eulogio
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Miguel Angel Mendoza-Catalán
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Hugo Alberto Rodríguez-Ruiz
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Eduardo Castañeda-Saucedo
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Carlos Ortuño-Pineda
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Teresita Padilla-Benavides
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
| | - Napoleón Navarro-Tito
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| |
Collapse
|
43
|
Dorard C, Cseh B, Ehrenreiter K, Wimmer R, Varga A, Hirschmugl T, Maier B, Kramer K, Fürlinger S, Doma E, Baccarini M. RAF dimers control vascular permeability and cytoskeletal rearrangements at endothelial cell-cell junctions. FEBS J 2019; 286:2277-2294. [PMID: 30828992 PMCID: PMC6617973 DOI: 10.1111/febs.14802] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/17/2019] [Accepted: 03/01/2019] [Indexed: 01/07/2023]
Abstract
The endothelium functions as a semipermeable barrier regulating fluid homeostasis, nutrient, and gas supply to the tissue. Endothelial permeability is increased in several pathological conditions including inflammation and tumors; despite its clinical relevance, however, there are no specific therapies preventing vascular leakage. Here, we show that endothelial cell-restricted ablation of BRAF, a kinase frequently activated in cancer, prevents vascular leaking as well metastatic spread. BRAF regulates endothelial permeability by promoting the cytoskeletal rearrangements necessary for the remodeling of VE-Cadherin-containing endothelial cell-cell junctions and the formation of intercellular gaps. BRAF kinase activity and the ability to form complexes with RAS/RAP1 and dimers with its paralog RAF1 are required for proper permeability control, achieved mechanistically by modulating the interaction between RAF1 and the RHO effector ROKα. Thus, RAF dimerization impinges on RHO pathways to regulate cytoskeletal rearrangements, junctional plasticity, and endothelial permeability. The data advocate the development of RAF dimerization inhibitors, which would combine tumor cell autonomous effect with stabilization of the vasculature and antimetastatic spread.
Collapse
Affiliation(s)
| | - Botond Cseh
- Max F. Perutz LaboratoriesUniversity of ViennaAustria
- Present address:
Winnovation Consulting GmbHViennaAustria
| | | | - Reiner Wimmer
- Max F. Perutz LaboratoriesUniversity of ViennaAustria
- Present address:
Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Andrea Varga
- Max F. Perutz LaboratoriesUniversity of ViennaAustria
- Present address:
Department of Biophysics and Radiation BiologySemmelweis UniversityTűzoltó u. 37‐47BudapestH‐1094Hungary
| | - Tatjana Hirschmugl
- Max F. Perutz LaboratoriesUniversity of ViennaAustria
- Present address:
Ludwig Boltzmann Institute for Lung Vascular ResearchGrazAustria
| | - Barbara Maier
- Max F. Perutz LaboratoriesUniversity of ViennaAustria
- Present address:
Mount Sinai School of MedicineNew YorkNYUSA
| | - Karina Kramer
- Max F. Perutz LaboratoriesUniversity of ViennaAustria
- Present address:
Department for Health Sciences, Medicine and ResearchCenter for Regenerative MedicineDanube University KremsKremsAustria
| | - Sabine Fürlinger
- Max F. Perutz LaboratoriesUniversity of ViennaAustria
- Present address:
Boehringer Ingelheim Pharma GmbH & Co. KGBiberach a.d. RissGermany
| | - Eszter Doma
- Max F. Perutz LaboratoriesUniversity of ViennaAustria
- Present address:
Institute of Pharmacology and ToxicologyUniversity of Veterinary MedicineViennaAustria
| | | |
Collapse
|
44
|
Beneker CM, Rovoli M, Kontopidis G, Röring M, Galda S, Braun S, Brummer T, McInnes C. Design and Synthesis of Type-IV Inhibitors of BRAF Kinase That Block Dimerization and Overcome Paradoxical MEK/ERK Activation. J Med Chem 2019; 62:3886-3897. [PMID: 30977659 DOI: 10.1021/acs.jmedchem.8b01288] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Despite the clinical success of BRAF inhibitors like vemurafenib in treating metastatic melanoma, resistance has emerged through "paradoxical MEK/ERK signaling" where transactivation of one protomer occurs as a result of drug inhibition of the other partner in the activated dimer. The importance of the dimerization interface in the signaling potential of wild-type BRAF in cells expressing oncogenic Ras has recently been demonstrated and proposed as a site of therapeutic intervention in targeting cancers resistant to adenosine triphosphate competitive drugs. The proof of concept for a structure-guided approach targeting the dimerization interface is described through the design and synthesis of macrocyclic peptides that bind with high affinity to BRAF and that block paradoxical signaling in malignant melanoma cells occurring through this drug target. The lead compounds identified are type-IV kinase inhibitors and represent an ideal framework for conversion into next-generation BRAF inhibitors through macrocyclic drug discovery.
Collapse
Affiliation(s)
- Chad M Beneker
- Drug Discovery and Biomedical Sciences , College of Pharmacy , Columbia , South Carolina 29208 , United States
| | - Magdalini Rovoli
- Laboratory of Biochemistry, Department of Veterinary Medicine , University of Thessaly , Karditsa 43131 , Greece
| | - George Kontopidis
- Laboratory of Biochemistry, Department of Veterinary Medicine , University of Thessaly , Karditsa 43131 , Greece
| | - Michael Röring
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine , University of Freiburg , Freiburg 79085 , Germany
| | - Simeon Galda
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine , University of Freiburg , Freiburg 79085 , Germany
| | - Sandra Braun
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine , University of Freiburg , Freiburg 79085 , Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine , University of Freiburg , Freiburg 79085 , Germany.,Centre for Biological Signalling Studies, BIOSS , University of Freiburg , Schänzlestrasse 18 , Freiburg 79104 , Germany.,German Consortium for Translational Cancer Research DKTK, Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg 69120 , Germany
| | - Campbell McInnes
- Drug Discovery and Biomedical Sciences , College of Pharmacy , Columbia , South Carolina 29208 , United States
| |
Collapse
|
45
|
Surve SV, Myers PJ, Clayton SA, Watkins SC, Lazzara MJ, Sorkin A. Localization dynamics of endogenous fluorescently labeled RAF1 in EGF-stimulated cells. Mol Biol Cell 2019; 30:506-523. [PMID: 30586319 PMCID: PMC6594441 DOI: 10.1091/mbc.e18-08-0512] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Activation of the epidermal growth factor (EGF) receptor (EGFR) at the cell surface initiates signaling through the RAS-RAF-MAPK/ERK1/2 pathway and receptor endocytosis. Whether this signaling continues from endosomes remains unclear, because RAS is predominantly located on the plasma membrane, and the localization of endogenous RAF kinases, downstream effectors of RAS, is not defined. To examine RAF localization, we labeled endogenous RAF1 with mVenus using gene editing. From 10 to 15% of RAF1-mVenus (<2000 molecules/cell), which was initially entirely cytosolic, transiently translocated to the plasma membrane after EGF stimulation. Following an early burst of translocation, the membrane-associated RAF1-mVenus was undetectable by microscopy or subcellular fractionation, and this pool was estimated to be <200 molecules per cell. In contrast, persistent EGF-dependent translocation of RAF1-mVenus to the plasma membrane was driven by the RAF inhibitor sorafenib, which increases the affinity of Ras-GTP:RAF1 interactions. RAF1-mVenus was not found in EGFR-containing endosomes under any conditions. Computational modeling of RAF1 dynamics revealed that RAF1 membrane abundance is controlled most prominently by association and dissociation rates from RAS-GTP and by RAS-GTP concentration. The model further suggested that the relatively protracted activation of the RAF-MEK1/2-ERK1/2 module, in comparison with RAF1 membrane localization, may involve multiple rounds of cytosolic RAF1 rebinding to active RAS at the membrane.
Collapse
Affiliation(s)
- Sachin V Surve
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Paul J Myers
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22904
| | - Samantha A Clayton
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Matthew J Lazzara
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22904.,Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904
| | - Alexander Sorkin
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| |
Collapse
|
46
|
B-Raf deficiency impairs tumor initiation and progression in a murine breast cancer model. Oncogene 2019; 38:1324-1339. [DOI: 10.1038/s41388-018-0663-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 11/22/2018] [Accepted: 12/11/2018] [Indexed: 02/07/2023]
|
47
|
Yuan J, Ng WH, Tian Z, Yap J, Baccarini M, Chen Z, Hu J. Activating mutations in MEK1 enhance homodimerization and promote tumorigenesis. Sci Signal 2018; 11:eaar6795. [PMID: 30377225 DOI: 10.1126/scisignal.aar6795] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
RAS-RAF-MEK-ERK signaling has a well-defined role in cancer biology. Although aberrant pathway activation occurs mostly upstream of the kinase MEK, mutations in MEK are prevalent in some cancer subsets. Here, we found that cancer-related, activating mutations in MEK can be classified into two groups: those that relieve inhibitory interactions with the helix A region and those that are in-frame deletions of the β3-αC loop, which enhance MEK1 homodimerization. The former, helix A-associated mutants, are inhibited by traditional MEK inhibitors. However, we found that the increased homodimerization associated with the loop-deletion mutants promoted intradimer cross-phosphorylation of the activation loop and conferred differential resistance to MEK inhibitors both in vitro and in vivo. MEK1 dimerization was required both for its activation by the kinase RAF and for its catalytic activity toward the kinase ERK. Our findings not only identify a previously unknown group of MEK mutants and provide insight into some key steps in RAF-MEK-ERK activation but also have implications for the design of therapies targeting RAS-ERK signaling in cancers.
Collapse
Affiliation(s)
- Jimin Yuan
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, 169610 Singapore, Singapore
| | - Wan Hwa Ng
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, 169610 Singapore, Singapore
| | - Zizi Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiajun Yap
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, 169610 Singapore, Singapore
| | - Manuela Baccarini
- Max F. Perutz Laboratories, University of Vienna, Doktor-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Zhongzhou Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiancheng Hu
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, 169610 Singapore, Singapore.
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857 Singapore, Singapore
| |
Collapse
|
48
|
Yuan J, Ng WH, Lam PYP, Wang Y, Xia H, Yap J, Guan SP, Lee ASG, Wang M, Baccarini M, Hu J. The dimer-dependent catalytic activity of RAF family kinases is revealed through characterizing their oncogenic mutants. Oncogene 2018; 37:5719-5734. [PMID: 29930381 PMCID: PMC6202329 DOI: 10.1038/s41388-018-0365-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 12/19/2022]
Abstract
Although extensively studied for three decades, the molecular mechanisms that regulate the RAF/MEK/ERK kinase cascade remain ambiguous. Recent studies identified the dimerization of RAF as a key event in the activation of this cascade. Here, we show that in-frame deletions in the β3-αC loop activate ARAF as well as BRAF and other oncogenic kinases by enforcing homodimerization. By characterizing these RAF mutants, we find that ARAF has less allosteric and catalytic activity than the other two RAF isoforms, which arises from its non-canonical APE motif. Further, these RAF mutants exhibit a strong oncogenic potential, and a differential inhibitor resistance that correlates with their dimer affinity. Using these unique mutants, we demonstrate that active RAFs, including the BRAF(V600E) mutant, phosphorylate MEK in a dimer-dependent manner. This study characterizes a special category of oncogenic kinase mutations, and elucidates the molecular basis that underlies the differential ability of RAF isoforms to stimulate MEK-ERK pathway. Further, this study reveals a unique catalytic feature of RAF family kinases that can be exploited to control their activities for cancer therapies.
Collapse
Affiliation(s)
- Jimin Yuan
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Wan Hwa Ng
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Paula Y P Lam
- Division of Cellular and Molecular Research, Singapore, Singapore
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore
| | - Yu Wang
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Hongping Xia
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Jiajun Yap
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Shou Ping Guan
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Ann S G Lee
- Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
- Office of Clinical & Academic Faculty Affairs, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Department of Physiology, National University of Singapore, 2 Medical Drive, 117597, Singapore, Singapore
| | - Mei Wang
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore
| | - Manuela Baccarini
- Max F. Perutz Laboratories, University of Vienna, Doktor-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Jiancheng Hu
- Division of Cellular and Molecular Research, Singapore, Singapore.
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore.
| |
Collapse
|
49
|
Sheikine Y, Pavlick D, Klempner SJ, Trabucco SE, Chung JH, Rosenzweig M, Wang K, Velcheti V, Frampton GM, Peled N, Murray M, Chae YK, Albacker LA, Gay L, Husain H, Suh JH, Millis SZ, Reddy VP, Elvin JA, Hartmaier RJ, Dowlati A, Stephens P, Ross JS, Bivona TG, Miller VA, Ganesan S, Schrock AB, Ou SHI, Ali SM. BRAF in Lung Cancers: Analysis of Patient Cases Reveals Recurrent BRAF Mutations, Fusions, Kinase Duplications, and Concurrent Alterations. JCO Precis Oncol 2018; 2:1700172. [PMID: 32913992 DOI: 10.1200/po.17.00172] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Purpose Dabrafenib and trametinib are approved for the management of advanced non-small-cell lung cancers (NSCLCs) that harbor BRAF V600E mutations. Small series and pan-cancer analyses have identified non-V600 alterations as therapeutic targets. We sought to examine a large genomic data set to comprehensively characterize non-V600 BRAF alterations in lung cancer. Patients and Methods A total of 23,396 patients with lung cancer provided data to assay with comprehensive genomic profiling. Data were reviewed for predicted pathogenic BRAF base substitutions, short insertions and deletions, copy number changes, and rearrangements. Results Adenocarcinomas represented 65% of the occurrences; NSCLC not otherwise specified (NOS), 15%; squamous cell carcinoma, 12%; and small-cell lung carcinoma, 5%. BRAF was altered in 4.5% (1,048 of 23,396) of all tumors; 37.4% (n = 397) were BRAF V600E, 38% were BRAF non-V600E activating mutations, and 18% were BRAF inactivating. Rearrangements were observed at a frequency of 4.3% and consisted of N-terminal deletions (NTDs; 0.75%), kinase domain duplications (KDDs; 0.75%), and BRAF fusions (2.8%). The fusions involved three recurrent fusion partners: ARMC10, DOCK4, and TRIM24. BRAF V600E was associated with co-occurrence of SETD2 alterations, but other BRAF alterations were not and were instead associated with CDKN2A, TP53, and STK11 alterations (P < .05). Potential mechanisms of acquired resistance to BRAF V600E inhibition are demonstrated. Conclusion This series characterized the frequent occurrence (4.4%) of BRAF alterations in lung cancers. Recurrent BRAF alterations in NSCLC adenocarcinoma are comparable to the frequency of other NSCLC oncogenic drivers, such as ALK, and exceed that of ROS1 or RET. This work supports a broad profiling approach in lung cancers and suggests that non-V600E BRAF alterations represent a subgroup of lung cancers in which targeted therapy should be considered.
Collapse
Affiliation(s)
- Yuri Sheikine
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Dean Pavlick
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Samuel J Klempner
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Sally E Trabucco
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Jon H Chung
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Mark Rosenzweig
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Kai Wang
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Vamsidhar Velcheti
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Garrett M Frampton
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Nir Peled
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Molly Murray
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Young Kwang Chae
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Lee A Albacker
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Laurie Gay
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Hatim Husain
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - James H Suh
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Sherri Z Millis
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Venkataprasanth P Reddy
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Julia A Elvin
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Ryan J Hartmaier
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Afshin Dowlati
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Phil Stephens
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Jeffrey S Ross
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Trever G Bivona
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Vincent A Miller
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Shridar Ganesan
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Alexa B Schrock
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Sai-Hong Ignatius Ou
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| | - Siraj M Ali
- , Vancouver General Hospital, Vancouver, British Columbia, Canada; , , , , , , , , , , , , , , , , , , and , Foundation Medicine, Cambridge, MA; , The Angeles Clinic and Research Institute and Cedars-Sinai Medical Center, Los Angeles; , University of California San Diego, San Diego; , University of California, San Francisco, San Francisco; and , University of California, Irvine, Medical Center, Irvine, CA; , Cleveland Clinic; and , University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH; , Soroka Medical Center and Ben-Gurion University, Beer-Sheve, Israel; , Northwestern University Feinberg School of Medicine Northwestern Medical Center, Chicago, IL; and , Cancer Institute of New Jersey, New Brunswick, NJ
| |
Collapse
|
50
|
Schorch B, Heni H, Zahaf NI, Brummer T, Mione M, Schmidt G, Papatheodorou P, Aktories K. Targeting oncogenic Ras by the Clostridium perfringens toxin TpeL. Oncotarget 2018; 9:16489-16500. [PMID: 29662661 PMCID: PMC5893256 DOI: 10.18632/oncotarget.24740] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 03/02/2018] [Indexed: 12/18/2022] Open
Abstract
Clostridium perfringens toxin TpeL belongs to the family of large clostridial glycosylating toxins. The toxin causes N-acetylglucosaminylation of Ras proteins at threonine35 thereby inactivating the small GTPases. Here, we show that all main types of oncogenic Ras proteins (H-Ras, K-Ras and N-Ras) are modified by the toxin in vitro and in vivo. Toxin-catalyzed modification of Ras was accompanied by inhibition of the MAP kinase pathway. Importantly, TpeL inhibited the paradoxical activation of the MAP kinase pathway induced by the BRAF inhibitor Vemurafenib in the human melanoma cell line SBCL2. The toxin also blocked Ras signaling in a zebrafish embryo model expressing oncogenic H-RasG12V, resulting in a reduction of melanocyte number. By using the binding and translocation component of anthrax toxin (protective antigen), the glucosyltransferase domain of TpeL was effectively introduced into target cells that were not sensitive to native TpeL toxin. To reach a higher specificity towards cancer cells, a chimeric TpeL toxin was engineered that possessed the knob region of adenovirus serotype 35 fiber, which interacts with CD46 of target cells frequently overexpressed in cancer cells. The chimeric TpeL fusion toxin efficiently inhibited Ras and MAP kinases in human pancreatic cancer Capan-2 cells, which were insensitive to the wild-type toxin. The data reveal that TpeL and TpeL-related immunotoxins provide a new toolset as Ras-inactivating agents.
Collapse
Affiliation(s)
- Björn Schorch
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Hannah Heni
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Nour-Imene Zahaf
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Tilman Brummer
- Institut für Molekulare Medizin und Zellforschung, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Partner Site Freiburg, Germany, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Marina Mione
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggestein-Leopoldshafen, Germany.,Present Address: Center for Integrative Biology, University of Trento, Trento, Italy
| | - Gudula Schmidt
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Panagiotis Papatheodorou
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.,Present Address: Institute of Pharmaceutical Biotechnology, University of Ulm, Ulm, Germany.,Present Address: Institute of Pharmacology and Toxicology, University of Ulm Medical Center, Ulm, Germany
| | - Klaus Aktories
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.,Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| |
Collapse
|