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Mozzarelli AM, Simanshu DK, Castel P. Functional and structural insights into RAS effector proteins. Mol Cell 2024; 84:2807-2821. [PMID: 39025071 PMCID: PMC11316660 DOI: 10.1016/j.molcel.2024.06.027] [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: 03/08/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/20/2024]
Abstract
RAS proteins are conserved guanosine triphosphate (GTP) hydrolases (GTPases) that act as molecular binary switches and play vital roles in numerous cellular processes. Upon GTP binding, RAS GTPases adopt an active conformation and interact with specific proteins termed RAS effectors that contain a conserved ubiquitin-like domain, thereby facilitating downstream signaling. Over 50 effector proteins have been identified in the human proteome, and many have been studied as potential mediators of RAS-dependent signaling pathways. Biochemical and structural analyses have provided mechanistic insights into these effectors, and studies using model organisms have complemented our understanding of their role in physiology and disease. Yet, many critical aspects regarding the dynamics and biological function of RAS-effector complexes remain to be elucidated. In this review, we discuss the mechanisms and functions of known RAS effector proteins, provide structural perspectives on RAS-effector interactions, evaluate their significance in RAS-mediated signaling, and explore their potential as therapeutic targets.
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Affiliation(s)
- Alessandro M Mozzarelli
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Laura and Isaac Perlmutter NYU Cancer Center, NYU Langone Health, New York, NY, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Pau Castel
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Laura and Isaac Perlmutter NYU Cancer Center, NYU Langone Health, New York, NY, USA.
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2
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Jeon H, Tkacik E, Eck MJ. Signaling from RAS to RAF: The Molecules and Their Mechanisms. Annu Rev Biochem 2024; 93:289-316. [PMID: 38316136 DOI: 10.1146/annurev-biochem-052521-040754] [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] [Indexed: 02/07/2024]
Abstract
RAF family protein kinases are a key node in the RAS/RAF/MAP kinase pathway, the signaling cascade that controls cellular proliferation, differentiation, and survival in response to engagement of growth factor receptors on the cell surface. Over the past few years, structural and biochemical studies have provided new understanding of RAF autoregulation, RAF activation by RAS and the SHOC2 phosphatase complex, and RAF engagement with HSP90-CDC37 chaperone complexes. These studies have important implications for pharmacologic targeting of the pathway. They reveal RAF in distinct regulatory states and show that the functional RAF switch is an integrated complex of RAF with its substrate (MEK) and a 14-3-3 dimer. Here we review these advances, placing them in the context of decades of investigation of RAF regulation. We explore the insights they provide into aberrant activation of the pathway in cancer and RASopathies (developmental syndromes caused by germline mutations in components of the pathway).
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Affiliation(s)
- Hyesung Jeon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA;
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Emre Tkacik
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA;
- Systems, Synthetic, and Quantitative Biology PhD Program, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA;
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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3
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Spencer-Smith R. The RAF cysteine-rich domain: Structure, function, and role in disease. Adv Cancer Res 2024; 164:69-91. [PMID: 39306370 DOI: 10.1016/bs.acr.2024.04.009] [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] [Indexed: 09/25/2024]
Abstract
RAF kinases, consisting of ARAF, BRAF and CRAF, are direct effectors of RAS GTPases and critical for signal transduction through the RAS-MAPK pathway. Driver mutations in BRAF are commonplace in human cancer, while germline mutations in BRAF and CRAF cause RASopathy development syndromes. However, there remains a lack of effective drugs that target RAF function, which is partially due to the complexity of the RAF activation cycle. Therefore, greater understanding of RAF regulation is required to identify new approaches that target its function in disease. A key piece of this puzzle is the RAF zinc finger, often referred to as the cysteine-rich domain (CRD). The CRD is a lipid and protein binding domain which plays complex and opposing roles in the RAF activation cycle. Firstly, it supports the RAS-RAF interaction during RAF activation by binding to phosphatidylserine (PS) in the plasma membrane and by making direct RAS contacts. Conversely, under quiescent conditions the CRD also plays a critical role in maintaining RAF in a closed, autoinhibited state. However, the interplay between these activities and their relative importance for RAF activation were not well understood. Recent structural and biochemical studies have contributed greatly to our understanding of these roles and identified functional differences between BRAF CRD and that of CRAF. This chapter provides an in-depth review of the CRDs roles in RAF regulation and how they may inform novel approaches to target RAF function.
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Affiliation(s)
- Russell Spencer-Smith
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina.
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4
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Bullones-Bolaños A, Martín-Muñoz P, Vallejo-Grijalba C, Bernal-Bayard J, Ramos-Morales F. Specificities and redundancies in the NEL family of bacterial E3 ubiquitin ligases of Salmonella enterica serovar Typhimurium. Front Immunol 2024; 15:1328707. [PMID: 38361917 PMCID: PMC10867120 DOI: 10.3389/fimmu.2024.1328707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
Salmonella enterica serovar Typhimurium expresses two type III secretion systems, T3SS1 and T3SS2, which are encoded in Salmonella pathogenicity island 1 (SPI1) and SPI2, respectively. These are essential virulent factors that secrete more than 40 effectors that are translocated into host animal cells. This study focuses on three of these effectors, SlrP, SspH1, and SspH2, which are members of the NEL family of E3 ubiquitin ligases. We compared their expression, regulation, and translocation patterns, their role in cell invasion and intracellular proliferation, their ability to interact and ubiquitinate specific host partners, and their effect on cytokine secretion. We found that transcription of the three genes encoding these effectors depends on the virulence regulator PhoP. Although the three effectors have the potential to be secreted through T3SS1 and T3SS2, the secretion of SspH1 and SspH2 is largely restricted to T3SS2 due to their expression pattern. We detected a role for these effectors in proliferation inside fibroblasts that is masked by redundancy. The generation of chimeric proteins allowed us to demonstrate that the N-terminal part of these proteins, containing the leucine-rich repeat motifs, confers specificity towards ubiquitination targets. Furthermore, the polyubiquitination patterns generated were different for each effector, with Lys48 linkages being predominant for SspH1 and SspH2. Finally, our experiments support an anti-inflammatory role for SspH1 and SspH2.
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Affiliation(s)
| | | | | | - Joaquín Bernal-Bayard
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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5
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Riaud M, Maxwell J, Soria-Bretones I, Dankner M, Li M, Rose AAN. The role of CRAF in cancer progression: from molecular mechanisms to precision therapies. Nat Rev Cancer 2024; 24:105-122. [PMID: 38195917 DOI: 10.1038/s41568-023-00650-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
Abstract
The RAF family of kinases includes key activators of the pro-tumourigenic mitogen-activated protein kinase pathway. Hyperactivation of RAF proteins, particularly BRAF and CRAF, drives tumour progression and drug resistance in many types of cancer. Although BRAF is the most studied RAF protein, partially owing to its high mutation incidence in melanoma, the role of CRAF in tumourigenesis and drug resistance is becoming increasingly clinically relevant. Here, we summarize the main known regulatory mechanisms and gene alterations that contribute to CRAF activity, highlighting the different oncogenic roles of CRAF, and categorize RAF1 (CRAF) mutations according to the effect on kinase activity. Additionally, we emphasize the effect that CRAF alterations may have on drug resistance and how precision therapies could effectively target CRAF-dependent tumours. Here, we discuss preclinical and clinical findings that may lead to improved treatments for all types of oncogenic RAF1 alterations in cancer.
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Affiliation(s)
- Melody Riaud
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Jennifer Maxwell
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Isabel Soria-Bretones
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Matthew Dankner
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Meredith Li
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - April A N Rose
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada.
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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6
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Trebino TE, Markusic B, Nan H, Banerjee S, Wang Z. Unveiling the domain-specific and RAS isoform-specific details of BRAF kinase regulation. eLife 2023; 12:RP88836. [PMID: 38150000 PMCID: PMC10752582 DOI: 10.7554/elife.88836] [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: 12/28/2023] Open
Abstract
BRAF is a key member in the MAPK signaling pathway essential for cell growth, proliferation, and differentiation. Mutant BRAF is often the underlying cause of various types of cancer and mutant RAS, the upstream regulator of BRAF, is a driver of up to one-third of all cancers. BRAF interacts with RAS and undergoes a conformational change from an inactive, autoinhibited monomer to an active dimer, which propagates downstream signaling. Because of BRAF's complex regulation mechanism, the exact order and magnitude of its activation steps have yet to be confirmed experimentally. By studying the inter- and intramolecular interactions of BRAF, we unveil the domain-specific and isoform-specific details of BRAF regulation through pulldown assays, open surface plasmon resonance (OpenSPR), and hydrogen-deuterium exchange mass spectrometry (HDX-MS). We demonstrate that the BRAF specific region (BSR) and cysteine rich domain (CRD) play a crucial role in regulating the activation of BRAF in a RAS isoform-specific manner. Moreover, we quantified the binding affinities between BRAF N-terminal and kinase domains (KD) to reveal their individual roles in autoinhibition. Our findings also indicate that oncogenic BRAF-KDD594G mutant has a lower affinity for the N-terminal domains, implicating that pathogenic BRAF acts through decreased propensity for autoinhibition. Collectively, our study provides valuable insight into the activation mechanism of BRAF kinase to guide the development of new therapeutic strategies for cancer treatment.
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Affiliation(s)
| | - Borna Markusic
- Rowan UniversityGlassboroUnited States
- Max Planck Institute of BiophysicsFrankfurt am MainGermany
| | - Haihan Nan
- Rowan UniversityGlassboroUnited States
- School of Laboratory Medicine and Life Science, Wenzhou Medical UniversityWenzhouChina
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Altas B, Tuffy LP, Patrizi A, Dimova K, Soykan T, Brandenburg C, Romanowski AJ, Whitten JR, Robertson CD, Khim SN, Crutcher GW, Ambrozkiewicz MC, Yagensky O, Krueger-Burg D, Hammer M, Hsiao HH, Laskowski PR, Dyck L, Puche AC, Sassoè-Pognetto M, Chua JJE, Urlaub H, Jahn O, Brose N, Poulopoulos A. Region-Specific Phosphorylation Determines Neuroligin-3 Localization to Excitatory Versus Inhibitory Synapses. Biol Psychiatry 2023:S0006-3223(23)01799-7. [PMID: 38154503 PMCID: PMC11209832 DOI: 10.1016/j.biopsych.2023.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND Neuroligin-3 is a postsynaptic adhesion molecule involved in synapse development and function. It is implicated in rare, monogenic forms of autism, and its shedding is critical to the tumor microenvironment of gliomas. While other members of the neuroligin family exhibit synapse-type specificity in localization and function through distinct interactions with postsynaptic scaffold proteins, the specificity of neuroligin-3 synaptic localization remains largely unknown. METHODS We investigated the synaptic localization of neuroligin-3 across regions in mouse and human brain samples after validating antibody specificity in knockout animals. We raised a phospho-specific neuroligin antibody and used phosphoproteomics, cell-based assays, and in utero CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/Cas9) knockout and gene replacement to identify mechanisms that regulate neuroligin-3 localization to distinct synapse types. RESULTS Neuroligin-3 exhibits region-dependent synapse specificity, largely localizing to excitatory synapses in cortical regions and inhibitory synapses in subcortical regions of the brain in both mice and humans. We identified specific phosphorylation of cortical neuroligin-3 at a key binding site for recruitment to inhibitory synapses, while subcortical neuroligin-3 remained unphosphorylated. In vitro, phosphomimetic mutation of that site disrupted neuroligin-3 association with the inhibitory postsynaptic scaffolding protein gephyrin. In vivo, phosphomimetic mutants of neuroligin-3 localized to excitatory postsynapses, while phospho-null mutants localized to inhibitory postsynapses. CONCLUSIONS These data reveal an unexpected region-specific pattern of neuroligin-3 synapse specificity, as well as a phosphorylation-dependent mechanism that regulates its recruitment to either excitatory or inhibitory synapses. These findings add to our understanding of how neuroligin-3 is involved in conditions that may affect the balance of excitation and inhibition.
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Affiliation(s)
- Bekir Altas
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Liam P Tuffy
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Annarita Patrizi
- Department of Neuroscience Rita Levi Montalcini, University of Turin, Turin, Italy
| | - Kalina Dimova
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Neuroproteomics Group, Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Tolga Soykan
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Cheryl Brandenburg
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Andrea J Romanowski
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Julia R Whitten
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Colin D Robertson
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Saovleak N Khim
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Garrett W Crutcher
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Mateusz C Ambrozkiewicz
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Oleksandr Yagensky
- Research Group Protein Trafficking in Synaptic Development and Function, Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Dilja Krueger-Burg
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Matthieu Hammer
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - He-Hsuan Hsiao
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Pawel R Laskowski
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Lydia Dyck
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Adam C Puche
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland
| | | | - John J E Chua
- Research Group Protein Trafficking in Synaptic Development and Function, Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Olaf Jahn
- Neuroproteomics Group, Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Translational Neuroproteomics Group, Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Alexandros Poulopoulos
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland; Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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8
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Chakraborty J, Chakraborty S, Chakraborty S, Narayan MN. Entanglement of MAPK pathways with gene expression and its omnipresence in the etiology for cancer and neurodegenerative disorders. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194988. [PMID: 37739217 DOI: 10.1016/j.bbagrm.2023.194988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Mitogen Activated Protein Kinase (MAPK) is one of the most well characterized cellular signaling pathways that controls fundamental cellular processes including proliferation, differentiation, and apoptosis. These cellular functions are consequences of transcription of regulatory genes that are influenced and regulated by the MAP-Kinase signaling cascade. MAP kinase components such as Receptor Tyrosine Kinases (RTKs) sense external cues or ligands and transmit these signals via multiple protein complexes such as RAS-RAF, MEK, and ERKs and eventually modulate the transcription factors inside the nucleus to induce transcription and other regulatory functions. Aberrant activation, dysregulation of this signaling pathway, and genetic alterations in any of these components results in the developmental disorders, cancer, and neurodegenerative disorders. Over the years, the MAPK pathway has been a prime pharmacological target, to treat complex human disorders that are genetically linked such as cancer, Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. The current review re-visits the mechanism of MAPK pathways in gene expression regulation. Further, a current update on the progress of the mechanistic understanding of MAPK components is discussed from a disease perspective.
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Affiliation(s)
- Joydeep Chakraborty
- Institute for Advancing Health through Agriculture, Texas A&M Agrilife, College Station, TX, USA
| | - Sayan Chakraborty
- Department of Anesthesiology, Weill Cornell School of Medicine, New York, USA
| | - Sohag Chakraborty
- Human Oncology & Pathogenesis Program (HOPP), Memorial Sloan Kettering Cancer Center, New York, USA
| | - Mahesh N Narayan
- Department of Chemistry and Biochemistry, University of Texas, El Paso, TX, USA.
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9
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Kohorn BD, Yang N, Weinstock M, Asper G, Ball I, Rajiv D. Golgi ELMO1 binds QUA1, QUA2, GAUT9, and ELMO4 and is required for pectin accumulation in Arabidopsis. PLoS One 2023; 18:e0293961. [PMID: 37939087 PMCID: PMC10631678 DOI: 10.1371/journal.pone.0293961] [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: 09/01/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023] Open
Abstract
Pectin and its modification influence the plasticity and strength of the plant cell wall controlling cell adhesion, size, shape, and pathogen resistance. The Golgi membrane anchored QUA1, QUA2, and GAUT9 Golgi enzymes synthesize and esterify pectin, which is then secreted and selectively de-esterified to potentiate structure influencing crosslinks in the cell wall. Mutations in members of the family of non-enzymatic ELMO Golgi membrane proteins lead to a reduction of pectin levels, cell adhesion, and hypocotyl tensile strength. Results from immunoprecipitation of Golgi protein complexes reveal that ELMO1-GFP is associated with pectin biosynthesis and modifying enzymes QUA1, QUA2, and GAUT9. In a yeast two and three hybrid assay, ELMO1 can bind directly to QUA1, GAUT9 or ELMO4, but QUA1, QUA2 or GAUT9 do not bind to each other. A yeast 3 hybrid assay provides evidence that ELMO1 can mediate the binding of QUA1 and QUA2. Taken together, these results indicate that the 20 kDa ELMO1 serves to facilitate some aspect of pectin synthesis and modification that leads to sufficient accumulation to allow cell adhesion, and we speculate that ELMOs help to scaffold key enzymes in this process.
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Affiliation(s)
- Bruce D. Kohorn
- Department of Biology, Bowdoin College, Brunswick, ME, United States of America
| | - Nuoya Yang
- Department of Biology, Bowdoin College, Brunswick, ME, United States of America
| | - Margaret Weinstock
- Department of Biology, Bowdoin College, Brunswick, ME, United States of America
| | - Garrison Asper
- Department of Biology, Bowdoin College, Brunswick, ME, United States of America
| | - Isabel Ball
- Department of Biology, Bowdoin College, Brunswick, ME, United States of America
| | - Devaki Rajiv
- Department of Biology, Bowdoin College, Brunswick, ME, United States of America
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10
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Trebino T, Markusic B, Nan H, Banerjee S, Wang Z. Unveiling the Domain-Specific and RAS Isoform-Specific Details of BRAF Regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538112. [PMID: 37163002 PMCID: PMC10168249 DOI: 10.1101/2023.04.24.538112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
BRAF is a key member in the MAPK signaling pathway essential for cell growth, proliferation, and differentiation. Dysregulation or mutation of BRAF is often the underlying cause of various types of cancer. RAS, a small GTPase protein that acts upstream of BRAF, has been identified as a driver of up to one-third of all cancers. When BRAF interacts with RAS via the RAS binding domain (RBD) and membrane recruitment, BRAF undergoes a conformational change from an inactive, autoinhibited monomer to an active dimer and subsequently phosphorylates MEK to propagate the signal. Despite the central role of BRAF in cellular signaling, the exact order and magnitude of its activation steps has yet to be confirmed experimentally. By studying the inter- and intramolecular interactions of BRAF, we unveil the domain-specific and isoform-specific details of BRAF regulation. We employed pulldown assays, open surface plasmon resonance (OpenSPR), and hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate the roles of the regulatory regions in BRAF activation and autoinhibition. Our results demonstrate that the BRAF specific region (BSR) and cysteine rich domain (CRD) play a crucial role in regulating the activity of BRAF. Moreover, we quantified the autoinhibitory binding affinities between the N-terminal domains and the kinase domain (KD) of BRAF and revealed the individual roles of the BRAF regulatory domains. Additionally, our findings provide evidence that the BSR negatively regulates BRAF activation in a RAS isoform-specific manner. Our findings also indicate that oncogenic BRAF-KDD594G mutant has a lower affinity for the regulatory domains, implicating that pathogenic BRAF acts through decreased propensity for autoinhibition. Collectively, our study provides valuable insights into the activation mechanism of BRAF kinase and may help to guide the development of new therapeutic strategies for cancer treatment.
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Affiliation(s)
- Tarah Trebino
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
| | - Borna Markusic
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
- Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Haihan Nan
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Shrhea Banerjee
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
| | - Zhihong Wang
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
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11
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Rapone R, Del Maestro L, Bouyioukos C, Albini S, Cruz-Tapias P, Joliot V, Cosson B, Ait-Si-Ali S. The cytoplasmic fraction of the histone lysine methyltransferase Setdb1 is essential for embryonic stem cells. iScience 2023; 26:107386. [PMID: 37559904 PMCID: PMC10407132 DOI: 10.1016/j.isci.2023.107386] [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: 06/15/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023] Open
Abstract
The major lysine methyltransferase (KMT) Setdb1 is essential for self-renewal and viability of mouse embryonic stem cells (mESCs). Setdb1 was primarily known to methylate the lysine 9 of histone 3 (H3K9) in the nucleus, where it regulates chromatin functions. However, Setdb1 is also massively localized in the cytoplasm, including in mESCs, where its role remains elusive. Here, we show that the cytoplasmic Setdb1 (cSetdb1) is essential for the survival of mESCs. Yeast two-hybrid analysis revealed that cSetdb1 interacts with several regulators of mRNA stability and protein translation machinery, such as the ESCs-specific E3 ubiquitin ligase and mRNA silencer Trim71/Lin41. We found that cSetdb1 is required for the integrity of Trim71 complex(es) involved in mRNA metabolism and translation. cSetdb1 modulates the abundance of mRNAs and the rate of newly synthesized proteins. Altogether, our data uncovered the cytoplasmic post-transcriptional regulation of gene expression mediated by a key epigenetic regulator.
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Affiliation(s)
- Roberta Rapone
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Laurence Del Maestro
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Costas Bouyioukos
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Sonia Albini
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Paola Cruz-Tapias
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Véronique Joliot
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Bertrand Cosson
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Slimane Ait-Si-Ali
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
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12
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Park E, Rawson S, Schmoker A, Kim BW, Oh S, Song K, Jeon H, Eck MJ. Cryo-EM structure of a RAS/RAF recruitment complex. Nat Commun 2023; 14:4580. [PMID: 37516774 PMCID: PMC10387098 DOI: 10.1038/s41467-023-40299-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 07/19/2023] [Indexed: 07/31/2023] Open
Abstract
RAF-family kinases are activated by recruitment to the plasma membrane by GTP-bound RAS, whereupon they initiate signaling through the MAP kinase cascade. Prior structural studies of KRAS with RAF have focused on the isolated RAS-binding and cysteine-rich domains of RAF (RBD and CRD, respectively), which interact directly with RAS. Here we describe cryo-EM structures of a KRAS bound to intact BRAF in an autoinhibited state with MEK1 and a 14-3-3 dimer. Analysis of this KRAS/BRAF/MEK1/14-3-3 complex reveals KRAS bound to the RAS-binding domain of BRAF, captured in two orientations. Core autoinhibitory interactions in the complex are unperturbed by binding of KRAS and in vitro activation studies confirm that KRAS binding is insufficient to activate BRAF, absent membrane recruitment. These structures illustrate the separability of binding and activation of BRAF by RAS and suggest stabilization of this pre-activation intermediate as an alternative therapeutic strategy to blocking binding of KRAS.
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Affiliation(s)
- Eunyoung Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Pfizer R&D Center, 3200 Walnut St, Boulder, CO, 80301, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Anna Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Byeong-Won Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Chungbuk, 28160, Republic of Korea
| | - Sehee Oh
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA, 01605, USA
| | - Hyesung Jeon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
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13
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Daniel JA, Elizarova S, Shaib AH, Chouaib AA, Magnussen HM, Wang J, Brose N, Rhee J, Tirard M. An intellectual-disability-associated mutation of the transcriptional regulator NACC1 impairs glutamatergic neurotransmission. Front Mol Neurosci 2023; 16:1115880. [PMID: 37533751 PMCID: PMC10393139 DOI: 10.3389/fnmol.2023.1115880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 06/14/2023] [Indexed: 08/04/2023] Open
Abstract
Advances in genome sequencing technologies have favored the identification of rare de novo mutations linked to neurological disorders in humans. Recently, a de novo autosomal dominant mutation in NACC1 was identified (NM_052876.3: c.892C > T, NP_443108.1; p.Arg298Trp), associated with severe neurological symptoms including intellectual disability, microcephaly, and epilepsy. As NACC1 had never before been associated with neurological diseases, we investigated how this mutation might lead to altered brain function. We examined neurotransmission in autaptic glutamatergic mouse neurons expressing the murine homolog of the human mutant NACC1, i.e., Nacc1-R284W. We observed that expression of Nacc1-R284W impaired glutamatergic neurotransmission in a cell-autonomous manner, likely through a dominant negative mechanism. Furthermore, by screening for Nacc1 interaction targets in the brain, we identified SynGAP1, GluK2A, and several SUMO E3 ligases as novel Nacc1 interaction partners. At a biochemical level, Nacc1-R284W exhibited reduced binding to SynGAP1 and GluK2A, and also showed greatly increased SUMOylation. Ablating the SUMOylation of Nacc1-R284W partially restored its interaction with SynGAP1 but did not restore binding to GluK2A. Overall, these data indicate a role for Nacc1 in regulating glutamatergic neurotransmission, which is substantially impaired by the expression of a disease-associated Nacc1 mutant. This study provides the first functional insights into potential deficits in neuronal function in patients expressing the de novo mutant NACC1 protein.
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Affiliation(s)
- James A. Daniel
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sofia Elizarova
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Ali H. Shaib
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Abed A. Chouaib
- Department of Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), Saarland University, Homburg, Germany
| | - Helge M. Magnussen
- MRC Protein Phosphorylation and Ubiquitination Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia University Irving Medical Center, New York, NY, United States
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - JeongSeop Rhee
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Marilyn Tirard
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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14
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Li Y, Liang ZY, Wang HL. N6-methyl-2'-deoxyadenosine promotes self-renewal of BFU-E progenitor in erythropoiesis. iScience 2023; 26:106924. [PMID: 37283807 PMCID: PMC10239700 DOI: 10.1016/j.isci.2023.106924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/08/2023] [Accepted: 05/15/2023] [Indexed: 06/08/2023] Open
Abstract
Red blood cells supply the oxygen required for all human cells and are in demand for emerging blood-loss therapy. Here we identified N6-methyl-2'-deoxyadenosine (6mdA) as an agonist that promotes the hyperproliferation of burst-forming unit erythroid (BFU-E) progenitor cells. In addition, 6mdA represses the apoptosis of erythroid progenitor cells (EPCs). Combined use of with SCF and EPO enabled cultures of isolated BFU-E to be expanded up to 5,000-fold. Transcriptome analysis showed that 6mdA upregulates the expression of the EPC-associated factors c-Kit, Myb, and Gata2 and downregulates that of the erythroid maturation-related transcription factors Gata1, Spi1, and Klf1. Mechanistic studies suggested that 6mdA enhances and prolongs the activation of erythropoiesis-associated master gene c-Kit and its downstream signaling, leading to expansion and accumulation of EPCs. Collectively, we demonstrate that 6mdA can efficiently stimulate the EPC hyperproliferation and provide a new regenerative medicine recipe to improve ex vivo generation of red blood cells.
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Affiliation(s)
- Yao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Yu Liang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hai-Lin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Environment and Health, Jianghan University, Wuhan, Hubei 430056, China
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15
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Structural basis of the oncogenic KRAS mutant and GJ101 complex. Biochem Biophys Res Commun 2023; 641:27-33. [PMID: 36516586 DOI: 10.1016/j.bbrc.2022.12.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022]
Abstract
KRAS mutations occur in a quarter of all human cancers. When activated in its GTP-bound form, RAS stimulates diverse cellular systems, such as cell division, differentiation, growth, and apoptosis through the activations of various signaling pathways, which include mitogen-activated protein kinase (MAPK), phosphoinositide 3 kinases (PI3K), and RAL-GEFs pathways. We found that GJ101 (65LYDVA69) binds directly to the KRAS mutant (G12V) and showed tumor-suppressive activity. In addition, the GJ101 peptide inhibited KRAS mutant as determined by a [α-32P] guanosine triphosphate (GTP) binding assay and suppressed pancreatic cell line in a cell proliferation assay. Herein, the complex structure of KRAS and GJ101 was clarified by X-ray crystallography. Isothermal titration calorimetry showed that GJ101 binds highly with KRAS mutant and the complex structure of KRAS G12V.GJ101 complex presented that the residue of Q61 directly interacted with L65 of GJ101. Overall, the results suggest GJ101 be considered a developmental starting point for KRAS G12V inhibitor.
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16
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Kolch W, Berta D, Rosta E. Dynamic regulation of RAS and RAS signaling. Biochem J 2023; 480:1-23. [PMID: 36607281 PMCID: PMC9988006 DOI: 10.1042/bcj20220234] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023]
Abstract
RAS proteins regulate most aspects of cellular physiology. They are mutated in 30% of human cancers and 4% of developmental disorders termed Rasopathies. They cycle between active GTP-bound and inactive GDP-bound states. When active, they can interact with a wide range of effectors that control fundamental biochemical and biological processes. Emerging evidence suggests that RAS proteins are not simple on/off switches but sophisticated information processing devices that compute cell fate decisions by integrating external and internal cues. A critical component of this compute function is the dynamic regulation of RAS activation and downstream signaling that allows RAS to produce a rich and nuanced spectrum of biological outputs. We discuss recent findings how the dynamics of RAS and its downstream signaling is regulated. Starting from the structural and biochemical properties of wild-type and mutant RAS proteins and their activation cycle, we examine higher molecular assemblies, effector interactions and downstream signaling outputs, all under the aspect of dynamic regulation. We also consider how computational and mathematical modeling approaches contribute to analyze and understand the pleiotropic functions of RAS in health and disease.
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Affiliation(s)
- Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dénes Berta
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, U.K
| | - Edina Rosta
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, U.K
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17
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SNRPD2 Is a Novel Substrate for the Ubiquitin Ligase Activity of the Salmonella Type III Secretion Effector SlrP. BIOLOGY 2022; 11:biology11101517. [PMID: 36290420 PMCID: PMC9598574 DOI: 10.3390/biology11101517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022]
Abstract
Simple Summary Salmonella is a genus of bacterial pathogens that can cause several diseases in humans and other animals. These bacteria can inject proteins known as effectors into animal cells through a secretion system. One of these effectors, SlrP, promotes the covalent addition of ubiquitin, a small eukaryotic protein, to specific host proteins, leading to an alteration of their stability or function. Here, we have performed a genetic screen to find new human targets of SlrP. In this way, we have identified SNRPD2, a core component of the spliceosome, the ribonucleoprotein complex that removes introns from eukaryotic pre-mRNA. SNRPD2 physically interacts with SlrP and is also a substrate of its ubiquitination activity. Lysines at positions 85 and 92 in SNRPD2 are among the residues that were ubiquitinated in the presence of SlrP. The identification of new host targets of Salmonella effectors contributes to a better understanding of the biological processes that are highjacked by these pathogens during infection, and can help in the design of future therapeutic strategies. Abstract SlrP is a protein with E3 ubiquitin ligase activity that is translocated by Salmonella enterica serovar Typhimurium into eukaryotic host cells through a type III secretion system. A yeast two-hybrid screen was performed to find new human partners for this protein. Among the interacting proteins identified by this screen was SNRPD2, a core component of the spliceosome. In vitro ubiquitination assays demonstrated that SNRPD2 is a substrate for the catalytic activity of SlrP, but not for other members of the NEL family of E3 ubiquitin ligases, SspH1 and SspH2. The lysine residues modified by this activity were identified by mass spectrometry. The identification of a new ubiquitination target for SlrP is a relevant contribution to the understanding of the role of this Salmonella effector.
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18
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19
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Swiatnicki M, Engel L, Shrestha R, Alves J, Goueli SA, Zegzouti H. Profiling oncogenic KRAS mutant drugs with a cell-based Lumit p-ERK immunoassay. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:249-257. [PMID: 35288294 DOI: 10.1016/j.slasd.2022.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
KRAS is one of the most heavily mutated oncogenes in cancer and targeting mutant KRAS with drugs has proven difficult. However, recent FDA approval of the KRAS G12C selective inhibitor sotorasib (AMG-510), has breathed new life into the drive to develop mutant KRAS inhibitors. In an effort to study RAS inhibitors in cells and identify new compounds that inhibit Ras signaling, western blotting and ELISA assays are commonly used. These traditional immunoassays are tedious, require multiple washing steps, and are not easily adaptable to a high throughput screening (HTS) format. To overcome these limitations, we applied Lumit immunoassay technology to analyze RAS signaling pathway activation and inhibition through the detection of phosphorylated ERK. The assay we developed was used to rank order potencies of allele specific inhibitors within cell lines harboring various activating KRAS mutations. An inhibition profile was obtained indicating various potencies and selectivity of the inhibitors, including MRTX-1133, which was shown to be highly potent against KRAS G12D signaling. MRTX-1133 had approximately 40 and 400 times less inhibitory potency against G12C and G12V mutant KRAS, respectively, while no inhibition of WT KRAS was observed. The potency of PROTAC compound LC-2 targeting selective degradation of KRAS G12C was also tested using the Lumit pERK immunoassay, and a maximal decrease in RAS signaling was achieved. Lumit immunoassays provide a rapid, homogeneous platform for detecting signaling pathway activation and inhibition. Our results demonstrate that this bioluminescent technology can streamline the analysis of signaling pathways of interest, such as RAS-dependent pathways, and be used to identify much needed inhibitors. The results further imply that similar assay designs could be applied to other signaling pathway nodes.
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Affiliation(s)
| | - Laurie Engel
- Promega Corporation, R&D Department, Madison, WI, USA
| | - Riva Shrestha
- Promega Corporation, R&D Department, Madison, WI, USA
| | - Juliano Alves
- Promega Corporation, R&D Department, Madison, WI, USA
| | - Said A Goueli
- Promega Corporation, R&D Department, Madison, WI, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI. USA
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20
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Zhao J, Luo Z. Discovery of Raf Family Is a Milestone in Deciphering the Ras-Mediated Intracellular Signaling Pathway. Int J Mol Sci 2022; 23:ijms23095158. [PMID: 35563547 PMCID: PMC9101324 DOI: 10.3390/ijms23095158] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/27/2023] Open
Abstract
The Ras-Raf-MEK-ERK signaling pathway, the first well-established MAPK pathway, plays essential roles in cell proliferation, survival, differentiation and development. It is activated in over 40% of human cancers owing to mutations of Ras, membrane receptor tyrosine kinases and other oncogenes. The Raf family consists of three isoforms, A-Raf, B-Raf and C-Raf. Since the first discovery of a truncated mutant of C-Raf as a transforming oncogene carried by a murine retrovirus, forty years of extensive studies have provided a wealth of information on the mechanisms underlying the activation, regulation and biological functions of the Raf family. However, the mechanisms by which activation of A-Raf and C-Raf is accomplished are still not completely understood. In contrast, B-Raf can be easily activated by binding of Ras-GTP, followed by cis-autophosphorylation of the activation loop, which accounts for the fact that this isoform is frequently mutated in many cancers, especially melanoma. The identification of oncogenic B-Raf mutations has led to accelerated drug development that targets Raf signaling in cancer. However, the effort has not proved as effective as anticipated, inasmuch as the mechanism of Raf activation involves multiple steps, factors and phosphorylation of different sites, as well as complex interactions between Raf isoforms. In this review, we will focus on the physiological complexity of the regulation of Raf kinases and their connection to the ERK phosphorylation cascade and then discuss the role of Raf in tumorigenesis and the clinical application of Raf inhibitors in the treatment of cancer.
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Affiliation(s)
- Jingtong Zhao
- Queen Mary School, Nanchang University, Nanchang 330031, China;
| | - Zhijun Luo
- Queen Mary School, Nanchang University, Nanchang 330031, China;
- Provincial Key Laboratory of Tumor Pathogens and Molecular Pathology, Nanchang University, Nanchang 330031, China
- NCU-QMUL Joint Research Institute of Precision Medical Science, Nanchang 330031, China
- Correspondence:
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21
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Mullen PJ, Christofk HR. The Metabolic Relationship Between Viral Infection and Cancer. ANNUAL REVIEW OF CANCER BIOLOGY 2022. [DOI: 10.1146/annurev-cancerbio-070120-090423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Viruses are fundamental tools in cancer research. They were used to discover the first oncogenes in the 1970s, and they are now being modified for use as antitumor therapeutics. Key to both of these oncogenic and oncolytic properties is the ability of viruses to rewire host cell metabolism. In this review, we describe how viral oncogenes alter metabolism to increase the synthesis of macromolecules necessary for both viral replication and tumor growth. We then describe how understanding the specific metabolic requirements of virus-infected cells can help guide strategies to improve the efficacy of oncolytic viruses, and we highlight immunometabolism and tumor microenvironment research that could also increase the therapeutic benefits of oncolytic viruses. We also describe how studies describing the therapeutic effects of dietary nutrient restriction in cancer can suggest new avenues for research into antiviral therapeutics.
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Affiliation(s)
- Peter J. Mullen
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Heather R. Christofk
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center and Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, California, USA
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22
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Simanshu DK, Morrison DK. A Structure is Worth a Thousand Words: New Insights for RAS and RAF Regulation. Cancer Discov 2022; 12:899-912. [PMID: 35046094 PMCID: PMC8983508 DOI: 10.1158/2159-8290.cd-21-1494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022]
Abstract
The RAS GTPases are frequently mutated in human cancer, with KRAS being the predominant tumor driver. For many years, it has been known that the structure and function of RAS are integrally linked, as structural changes induced by GTP binding or mutational events determine the ability of RAS to interact with regulators and effectors. Recently, a wealth of information has emerged from structures of specific KRAS mutants and from structures of multiprotein complexes containing RAS and/or RAF, an essential effector of RAS. These structures provide key insights regarding RAS and RAF regulation as well as promising new strategies for therapeutic intervention. SIGNIFICANCE The RAS GTPases are major drivers of tumorigenesis, and for RAS proteins to exert their full oncogenic potential, they must interact with the RAF kinases to initiate ERK cascade signaling. Although binding to RAS is typically a prerequisite for RAF to become an activated kinase, determining the molecular mechanisms by which this interaction results in RAF activation has been a challenging task. A major advance in understanding this process and RAF regulation has come from recent structural studies of various RAS and RAF multiprotein signaling complexes, revealing new avenues for drug discovery.
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Affiliation(s)
- Dhirendra K. Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Deborah K. Morrison
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
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23
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Désage AL, Léonce C, Swalduz A, Ortiz-Cuaran S. Targeting KRAS Mutant in Non-Small Cell Lung Cancer: Novel Insights Into Therapeutic Strategies. Front Oncol 2022; 12:796832. [PMID: 35251972 PMCID: PMC8889932 DOI: 10.3389/fonc.2022.796832] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 01/07/2022] [Indexed: 12/17/2022] Open
Abstract
Although KRAS-activating mutations represent the most common oncogenic driver in non-small cell lung cancer (NSCLC), various attempts to inhibit KRAS failed in the past decade. KRAS mutations are associated with a poor prognosis and a poor response to standard therapeutic regimen. The recent development of new therapeutic agents (i.e., adagrasib, sotorasib) that target specifically KRAS G12C in its GDP-bound state has evidenced an unprecedented success in the treatment of this subgroup of patients. Despite providing pre-clinical and clinical efficacy, several mechanisms of acquired resistance to KRAS G12C inhibitors have been reported. In this setting, combined therapeutic strategies including inhibition of either SHP2, SOS1 or downstream effectors of KRAS G12C seem particularly interesting to overcome acquired resistance. In this review, we will discuss the novel therapeutic strategies targeting KRAS G12C and promising approaches of combined therapy to overcome acquired resistance to KRAS G12C inhibitors.
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Affiliation(s)
- Anne-Laure Désage
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France.,Department of Pulmonology and Thoracic Oncology, North Hospital, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Camille Léonce
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
| | - Aurélie Swalduz
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France.,Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Sandra Ortiz-Cuaran
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
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24
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Abstract
In this review, I provide a brief history of the discovery of RAS and the GAPs and GEFs that regulate its activity from a personal perspective. Much of this history has been driven by technological breakthroughs that occurred concurrently, such as molecular cloning, cDNA expression to analyze RAS proteins and their structures, and application of PCR to detect mutations. I discuss the RAS superfamily and RAS proteins as therapeutic targets, including recent advances in developing RAS inhibitors. I also describe the role of the RAS Initiative at Frederick National Laboratory for Cancer Research in advancing development of RAS inhibitors and providing new insights into signaling complexes and interaction of RAS proteins with the plasma membrane.
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Affiliation(s)
- Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States; Frederick National Laboratory for Cancer Research, Frederick, MD, United States.
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25
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Structural insights into the BRAF monomer-to-dimer transition mediated by RAS binding. Nat Commun 2022; 13:486. [PMID: 35078985 PMCID: PMC8789793 DOI: 10.1038/s41467-022-28084-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/07/2022] [Indexed: 12/20/2022] Open
Abstract
RAF kinases are essential effectors of RAS, but how RAS binding initiates the conformational changes needed for autoinhibited RAF monomers to form active dimers has remained unclear. Here, we present cryo-electron microscopy structures of full-length BRAF complexes derived from mammalian cells: autoinhibited, monomeric BRAF:14-3-32:MEK and BRAF:14-3-32 complexes, and an inhibitor-bound, dimeric BRAF2:14-3-32 complex, at 3.7, 4.1, and 3.9 Å resolution, respectively. In both autoinhibited, monomeric structures, the RAS binding domain (RBD) of BRAF is resolved, revealing that the RBD forms an extensive contact interface with the 14-3-3 protomer bound to the BRAF C-terminal site and that key basic residues required for RBD-RAS binding are exposed. Moreover, through structure-guided mutational studies, our findings indicate that RAS-RAF binding is a dynamic process and that RBD residues at the center of the RBD:14-3-3 interface have a dual function, first contributing to RAF autoinhibition and then to the full spectrum of RAS-RBD interactions. RAF kinases are essential for RAS protein signalling but how RAS binding regulates dimerization and activation of RAF has remained unclear. Here, the authors report cryoEM structures that provide mechanistic insights into the RAS-mediated monomer-to-dimer transition of full-length BRAF.
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26
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Riedesser JE, Ebert MP, Betge J. Precision medicine for metastatic colorectal cancer in clinical practice. Ther Adv Med Oncol 2022; 14:17588359211072703. [PMID: 35237350 PMCID: PMC8882813 DOI: 10.1177/17588359211072703] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022] Open
Abstract
Globally, metastatic colorectal cancer is one of the leading causes for cancer-related death. Treatment limited to conventional chemotherapeutics extended life for only a few months. However, advances in surgical approaches and medical treatment regimens have greatly increased survival, even leading to long-term remission in selected patients. Advances in multiomics analysis of tumors have built a foundation for molecular-targeted therapies. Furthermore, immunotherapies are on the edge of revolutionizing oncological practice. This review summarizes recent advances in the growing toolbox of personalized treatment for patients with metastatic colorectal cancer. We provide an overview of current multimodal therapy and explain novel immunotherapy and targeted therapy approaches in detail. We emphasize clinically relevant therapies, such as inhibitors of MAPK signaling, and give recommendations for clinical practice. Finally, we describe the potential predictive impact of molecular subtypes and provide an outlook on novel concepts, such as functional precision medicine.
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Affiliation(s)
- Julian E. Riedesser
- Junior Clinical Cooperation Unit Translational
Gastrointestinal Oncology and Preclinical Models, German Cancer Research
Center (DKFZ), Heidelberg, Germany
| | - Matthias P. Ebert
- Department of Medicine II, University Medical
Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim,
GermanyMannheim Cancer Center, University Medical Center Mannheim, Medical
Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Johannes Betge
- Junior Clinical Cooperation Unit Translational
Gastrointestinal Oncology and Preclinical Models, German Cancer Research
Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg 69120, GermanyDKFZ-Hector
Cancer Institute at University Medical Center Mannheim, Mannheim,
Germany.Department of Medicine II, University Medical Center Mannheim,
Medical Faculty Mannheim, Heidelberg University, Mannheim, GermanyMannheim
Cancer Center, University Medical Center Mannheim, Medical Faculty Mannheim,
Heidelberg University, Mannheim, Germany
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Khan PS, Rajesh P, Rajendra P, Chaskar MG, Rohidas A, Jaiprakash S. Recent advances in B-RAF inhibitors as anticancer agents. Bioorg Chem 2022; 120:105597. [PMID: 35033817 DOI: 10.1016/j.bioorg.2022.105597] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/23/2021] [Accepted: 01/01/2022] [Indexed: 12/24/2022]
Abstract
The significance of B-RAF in the promotion of cell proliferation and motility was explored by the researchers in the past. However, in 2002, several researchers found that mutation in B-RAF leads to cancer. Extensive research on B-RAF mutations suggested B-RAF V600E mutation as a critical predictive, prognostic and diagnostic biomarker in numerous cancers such as melanoma, thyroid, and colorectal cancers. Based on the significance of B-RAF kinase and associated mutation, the present review will give a brief overview about structure and functions of B-RAF enzyme, its role in different types of cancer, available drugs in the market for B-RAF inhibition, chemical classification and SAR studies of reported investigational B-RAF inhibitors in patented and non-patented literature during last decade. The SAR provided for all the reported inhibitors will help researchers to gain knowledge about the possible structural features required for selective B-RAF inhibition. This insightful analysis of B-RAF will certainly help researchers to develop novel anticancer agents in the future.
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Affiliation(s)
- Pathan Shahebaaz Khan
- Y. B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Rauza Baugh, Aurangabad, MS 431001, India
| | - Patil Rajesh
- Sinhgad Technical Education Society's, Smt. Kashibai Navale College of Pharmacy, Kondhwa (Bk), Pune, India
| | - Patil Rajendra
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, M.S., India
| | - Manohar G Chaskar
- Prof Ramkrishna More College, Akurdi, Pune 411044, Maharashtra, India
| | - Arote Rohidas
- Department of Molecular Genetics, School of Dentistry, Seoul National University, Seoul. Republic of Korea
| | - Sangshetti Jaiprakash
- Y. B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Rauza Baugh, Aurangabad, MS 431001, India.
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28
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Conformation-locking antibodies for the discovery and characterization of KRAS inhibitors. Nat Biotechnol 2022; 40:769-778. [PMID: 34992247 DOI: 10.1038/s41587-021-01126-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/07/2021] [Indexed: 11/08/2022]
Abstract
Small molecules that stabilize inactive protein conformations are an underutilized strategy for drugging dynamic or otherwise intractable proteins. To facilitate the discovery and characterization of such inhibitors, we created a screening platform to identify conformation-locking antibodies for molecular probes (CLAMPs) that distinguish and induce rare protein conformational states. Applying the approach to KRAS, we discovered CLAMPs that recognize the open conformation of KRASG12C stabilized by covalent inhibitors. One CLAMP enables the visualization of KRASG12C covalent modification in vivo and can be used to investigate response heterogeneity to KRASG12C inhibitors in patient tumors. A second CLAMP enhances the affinity of weak ligands binding to the KRASG12C switch II region (SWII) by stabilizing a specific conformation of KRASG12C, thereby enabling the discovery of such ligands that could serve as leads for the development of drugs in a high-throughput screen. We show that combining the complementary properties of antibodies and small molecules facilitates the study and drugging of dynamic proteins.
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29
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KRAS-G12C covalent inhibitors: A game changer in the scene of cancer therapies. Crit Rev Oncol Hematol 2021; 168:103524. [PMID: 34800654 DOI: 10.1016/j.critrevonc.2021.103524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/05/2021] [Accepted: 11/02/2021] [Indexed: 12/14/2022] Open
Abstract
RAS is the most frequently mutated oncogene in human cancer. Scientists attempted for decades to target this protein or its pathways, however, all the attempts failed and RAS was labeled as "undruggable". With KRAS-G12C covalent inhibitors entering clinical trials, the myth of this "undruggable" RAS is fading away. In 2021, the Food and Drug Administration (FDA) approved the use of Sotorasib (Lumakras) for the treatment of adult patients with KRAS-G12C mutated locally advanced or metastatic NSCLC, following at least one prior systemic therapy. However, and as every other drug, KRAS-G12C inhibitors are facing intrinsic and acquired resistances. In order to overcome these resistances, researchers are now working on combination strategies. Furthermore, studies are currently ongoing to better elucidate the status of KRAS-G12C as a predictive and prognostic tool and to strengthen its role in the field of personalized medicine.
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30
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Crunden JL, Diezmann S. Hsp90 interaction networks in fungi-tools and techniques. FEMS Yeast Res 2021; 21:6413543. [PMID: 34718512 PMCID: PMC8599792 DOI: 10.1093/femsyr/foab054] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/26/2021] [Indexed: 01/01/2023] Open
Abstract
Heat-shock protein 90 (Hsp90) is a central regulator of cellular proteostasis. It stabilizes numerous proteins that are involved in fundamental processes of life, including cell growth, cell-cycle progression and the environmental response. In addition to stabilizing proteins, Hsp90 governs gene expression and controls the release of cryptic genetic variation. Given its central role in evolution and development, it is important to identify proteins and genes that interact with Hsp90. This requires sophisticated genetic and biochemical tools, including extensive mutant collections, suitable epitope tags, proteomics approaches and Hsp90-specific pharmacological inhibitors for chemogenomic screens. These usually only exist in model organisms, such as the yeast Saccharomyces cerevisiae. Yet, the importance of other fungal species, such as Candida albicans and Cryptococcus neoformans, as serious human pathogens accelerated the development of genetic tools to study their virulence and stress response pathways. These tools can also be exploited to map Hsp90 interaction networks. Here, we review tools and techniques for Hsp90 network mapping available in different fungi and provide a summary of existing mapping efforts. Mapping Hsp90 networks in fungal species spanning >500 million years of evolution provides a unique vantage point, allowing tracking of the evolutionary history of eukaryotic Hsp90 networks.
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Affiliation(s)
- Julia L Crunden
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Stephanie Diezmann
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
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31
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Kim J, Jeon YJ, Lim SC, Ryu J, Lee JH, Chang IY, You HJ. Akt-mediated Ephexin1-Ras interaction promotes oncogenic Ras signaling and colorectal and lung cancer cell proliferation. Cell Death Dis 2021; 12:1013. [PMID: 34711817 PMCID: PMC8553951 DOI: 10.1038/s41419-021-04332-0] [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: 08/20/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 02/07/2023]
Abstract
ABSTRCT Ephexin1 was reported to be highly upregulated by oncogenic Ras, but the functional consequences of this remain poorly understood. Here, we show that Ephexin1 is highly expressed in colorectal cancer (CRC) and lung cancer (LC) patient tissues. Knockdown of Ephexin1 markedly inhibited the cell growth of CRC and LC cells with oncogenic Ras mutations. Ephexin1 contributes to the positive regulation of Ras-mediated downstream target genes and promotes Ras-induced skin tumorigenesis. Mechanically, Akt phosphorylates Ephexin1 at Ser16 and Ser18 (pSer16/18) and pSer16/18 Ephexin1 then interacts with oncogenic K-Ras to promote downstream MAPK signaling, facilitating tumorigenesis. Furthermore, pSer16/18 Ephexin1 is associated with both an increased tumor grade and metastatic cases of CRC and LC, and those that highly express pSer16/18 exhibit poor overall survival rates. These data indicate that Ephexin1 plays a critical role in the Ras-mediated CRC and LC and pSer16/18 Ephexin1 might be an effective therapeutic target for CRC and LC.
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Affiliation(s)
- Jeeho Kim
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of medicine, 375 Seosuk-Dong, Gwangju, 501-759, South Korea
- Department of Pharmacology, Chosun University School of medicine, 375 Seosuk-Dong, Gwangju, 501-759, South Korea
| | - Young Jin Jeon
- Department of Pharmacology, Chosun University School of medicine, 375 Seosuk-Dong, Gwangju, 501-759, South Korea
| | - Sung-Chul Lim
- Department of Pathology, Chosun University School of medicine, 375 Seosuk-Dong, Gwangju, 501-759, South Korea
| | - Joohyun Ryu
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN, 55912, USA
| | - Jung-Hee Lee
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of medicine, 375 Seosuk-Dong, Gwangju, 501-759, South Korea
- Department of Cellular and Molecular Medicine, Chosun University School of medicine, 375 Seosuk-Dong, Gwangju, 501-759, South Korea
| | - In-Youb Chang
- Department of Anatomy, Chosun University School of medicine, 375 Seosuk-Dong, Gwangju, 501-759, South Korea.
| | - Ho Jin You
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of medicine, 375 Seosuk-Dong, Gwangju, 501-759, South Korea.
- Department of Pharmacology, Chosun University School of medicine, 375 Seosuk-Dong, Gwangju, 501-759, South Korea.
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32
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Akt-mediated Ephexin1-Ras interaction promotes oncogenic Ras signaling and colorectal and lung cancer cell proliferation. Cell Death Dis 2021. [PMID: 34711817 DOI: 10.1038/s41419-021-04332-0.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
ABSTRCT Ephexin1 was reported to be highly upregulated by oncogenic Ras, but the functional consequences of this remain poorly understood. Here, we show that Ephexin1 is highly expressed in colorectal cancer (CRC) and lung cancer (LC) patient tissues. Knockdown of Ephexin1 markedly inhibited the cell growth of CRC and LC cells with oncogenic Ras mutations. Ephexin1 contributes to the positive regulation of Ras-mediated downstream target genes and promotes Ras-induced skin tumorigenesis. Mechanically, Akt phosphorylates Ephexin1 at Ser16 and Ser18 (pSer16/18) and pSer16/18 Ephexin1 then interacts with oncogenic K-Ras to promote downstream MAPK signaling, facilitating tumorigenesis. Furthermore, pSer16/18 Ephexin1 is associated with both an increased tumor grade and metastatic cases of CRC and LC, and those that highly express pSer16/18 exhibit poor overall survival rates. These data indicate that Ephexin1 plays a critical role in the Ras-mediated CRC and LC and pSer16/18 Ephexin1 might be an effective therapeutic target for CRC and LC.
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33
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Poitras TM, Munchrath E, Zochodne DW. Neurobiological Opportunities in Diabetic Polyneuropathy. Neurotherapeutics 2021; 18:2303-2323. [PMID: 34935118 PMCID: PMC8804062 DOI: 10.1007/s13311-021-01138-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 12/29/2022] Open
Abstract
This review highlights a selection of potential translational directions for the treatment of diabetic polyneuropathy (DPN) currently irreversible and without approved interventions beyond pain management. The list does not include all diabetic targets that have been generated over several decades of research but focuses on newer work. The emphasis is firstly on approaches that support the viability and growth of peripheral neurons and their ability to withstand a barrage of diabetic alterations. We include a section describing Schwann cell targets and finally how mitochondrial damage has been a common element in discussing neuropathic damage. Most of the molecules and pathways described here have not yet reached clinical trials, but many trials have been negative to date. Nonetheless, these failures clear the pathway for new thoughts over reversing DPN.
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Affiliation(s)
- Trevor M Poitras
- Peripheral Nerve Research Laboratory, Division of Neurology, Department of Medicine and the Neuroscience and Mental Health Institute, University of Alberta, 7-132A Clinical Sciences Building, 11350-83 Ave, Edmonton, AB, T6G 2G3, Canada
| | - Easton Munchrath
- Peripheral Nerve Research Laboratory, Division of Neurology, Department of Medicine and the Neuroscience and Mental Health Institute, University of Alberta, 7-132A Clinical Sciences Building, 11350-83 Ave, Edmonton, AB, T6G 2G3, Canada
| | - Douglas W Zochodne
- Peripheral Nerve Research Laboratory, Division of Neurology, Department of Medicine and the Neuroscience and Mental Health Institute, University of Alberta, 7-132A Clinical Sciences Building, 11350-83 Ave, Edmonton, AB, T6G 2G3, Canada.
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34
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Cook FA, Cook SJ. Inhibition of RAF dimers: it takes two to tango. Biochem Soc Trans 2021; 49:237-251. [PMID: 33367512 PMCID: PMC7924995 DOI: 10.1042/bst20200485] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023]
Abstract
The RAS-regulated RAF-MEK1/2-ERK1/2 pathway promotes cell proliferation and survival and RAS and BRAF proteins are commonly mutated in cancer. This has fuelled the development of small molecule kinase inhibitors including ATP-competitive RAF inhibitors. Type I and type I½ ATP-competitive RAF inhibitors are effective in BRAFV600E/K-mutant cancer cells. However, in RAS-mutant cells these compounds instead promote RAS-dependent dimerisation and paradoxical activation of wild-type RAF proteins. RAF dimerisation is mediated by two key regions within each RAF protein; the RKTR motif of the αC-helix and the NtA-region of the dimer partner. Dimer formation requires the adoption of a closed, active kinase conformation which can be induced by RAS-dependent activation of RAF or by the binding of type I and I½ RAF inhibitors. Binding of type I or I½ RAF inhibitors to one dimer partner reduces the binding affinity of the other, thereby leaving a single dimer partner uninhibited and able to activate MEK. To overcome this paradox two classes of drug are currently under development; type II pan-RAF inhibitors that induce RAF dimer formation but bind both dimer partners thus allowing effective inhibition of both wild-type RAF dimer partners and monomeric active class I mutant RAF, and the recently developed "paradox breakers" which interrupt BRAF dimerisation through disruption of the αC-helix. Here we review the regulation of RAF proteins, including RAF dimers, and the progress towards effective targeting of the wild-type RAF proteins.
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Affiliation(s)
- Frazer A. Cook
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Simon J. Cook
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K
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35
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Hashemi S, Hosseini SM, Ghalyanchilangeroudi A, Sheikhi N. Transcriptome based analysis of apoptosis genes in chickens co-infected with avian infectious bronchitis virus and pathogenic Escherichia coli. IRANIAN JOURNAL OF MICROBIOLOGY 2021; 13:17-22. [PMID: 33889358 PMCID: PMC8043830 DOI: 10.18502/ijm.v13i1.5487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND OBJECTIVES Infection with Infectious bronchitis virus (IBV) and avian pathogenic Escherichia coli (APEC) is an important respiratory infection worldwide. Apoptosis is a physiological process of cell death that occurs as part of normal development and responds to a variety of physiological and pathophysiological stimuli. The identification of molecular mechanisms of action or inaction of key apoptotic proteins is important. This study aimed to investigate apoptotic related genes in the trachea tissue of infected (IBV variant 2, and APEC serotype O78: K80) SPF chickens group compared to the control group. MATERIALS AND METHODS Forty SPF chickens was divided into 2 groups. Differential transcriptional profile in the infected SPF chickens trachea tissue was compared to those of control group in the early stage of infection by Illumina RNA-seq technique paired-end and strand-specific sequencing. Differentially expressed genes (DEGs) of transcriptome profiling of the trachea from the infected group were identified. Gene ontology category, KEGG pathway, and STRING analysis were analyzed to identify relationships among differentially expressed genes. RESULTS Twenty-eight apoptotic genes were identified. They consisted of six pathways related to cell death: the extrinsic pathway, intrinsic pathway, endoplasmic reticulum stress pathway, MAPK signaling pathway, and cell death by NFkB and activates mTOR pathway and some regulator and apoptosis inhibitors. CONCLUSION All of the apoptotic genes in our study were up-regulated. Among these genes, the more fold change value was for TRADD and BCL2A1 genes, and the less fold change value was for MAP3K14, NFKB1, PIK3CB, and ITPR2 genes.
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Affiliation(s)
- Shabnam Hashemi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Seyed Masoud Hosseini
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Arash Ghalyanchilangeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Nariman Sheikhi
- Department of Clinical Sciences, College of Veterinary, Tehran Sciences and Research Branch, Islamic Azad University, Tehran, Iran
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36
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Castel P, Holtz-Morris A, Kwon Y, Suter BP, McCormick F. DoMY-Seq: A yeast two-hybrid-based technique for precision mapping of protein-protein interaction motifs. J Biol Chem 2021; 296:100023. [PMID: 33410398 PMCID: PMC7949039 DOI: 10.1074/jbc.ra120.014284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/23/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022] Open
Abstract
Interactions between proteins are fundamental for every biological process and especially important in cell signaling pathways. Biochemical techniques that evaluate these protein-protein interactions (PPIs), such as in vitro pull downs and coimmunoprecipitations, have become popular in most laboratories and are essential to identify and validate novel protein binding partners. Most PPIs occur through small domains or motifs, which are challenging and laborious to map by using standard biochemical approaches because they generally require the cloning of several truncation mutants. Moreover, these classical methodologies provide limited resolution of the interacting interface. Here, we describe the development of an alternative technique to overcome these limitations termed "Protein Domain mapping using Yeast 2 Hybrid-Next Generation Sequencing" (DoMY-Seq), which leverages both yeast two-hybrid and next-generation sequencing techniques. In brief, our approach involves creating a library of fragments derived from an open reading frame of interest and enriching for the interacting fragments using a yeast two-hybrid reporter system. Next-generation sequencing is then subsequently employed to read and map the sequence of the interacting fragment, yielding a high-resolution plot of the binding interface. We optimized DoMY-Seq by taking advantage of the well-described and high-affinity interaction between KRAS and CRAF, and we provide high-resolution domain mapping on this and other protein-interacting pairs, including CRAF-MEK1, RIT1-RGL3, and p53-MDM2. Thus, DoMY-Seq provides an unbiased alternative method to rapidly identify the domains involved in PPIs by advancing the use of yeast two-hybrid technology.
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Affiliation(s)
- Pau Castel
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA.
| | | | | | | | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
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37
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Ash1 and Tup1 dependent repression of the Saccharomyces cerevisiae HO promoter requires activator-dependent nucleosome eviction. PLoS Genet 2020; 16:e1009133. [PMID: 33382702 PMCID: PMC7806131 DOI: 10.1371/journal.pgen.1009133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/13/2021] [Accepted: 11/25/2020] [Indexed: 11/30/2022] Open
Abstract
Transcriptional regulation of the Saccharomyces cerevisiae HO gene is highly complex, requiring a balance of multiple activating and repressing factors to ensure that only a few transcripts are produced in mother cells within a narrow window of the cell cycle. Here, we show that the Ash1 repressor associates with two DNA sequences that are usually concealed within nucleosomes in the HO promoter and recruits the Tup1 corepressor and the Rpd3 histone deacetylase, both of which are required for full repression in daughters. Genome-wide ChIP identified greater than 200 additional sites of co-localization of these factors, primarily within large, intergenic regions from which they could regulate adjacent genes. Most Ash1 binding sites are in nucleosome depleted regions (NDRs), while a small number overlap nucleosomes, similar to HO. We demonstrate that Ash1 binding to the HO promoter does not occur in the absence of the Swi5 transcription factor, which recruits coactivators that evict nucleosomes, including the nucleosomes obscuring the Ash1 binding sites. In the absence of Swi5, artificial nucleosome depletion allowed Ash1 to bind, demonstrating that nucleosomes are inhibitory to Ash1 binding. The location of binding sites within nucleosomes may therefore be a mechanism for limiting repressive activity to periods of nucleosome eviction that are otherwise associated with activation of the promoter. Our results illustrate that activation and repression can be intricately connected, and events set in motion by an activator may also ensure the appropriate level of repression and reset the promoter for the next activation cycle. Nucleosomes inhibit both gene expression and DNA-binding by regulatory factors. Here we examine the role of nucleosomes in regulating the binding of repressive transcription factors to the complex promoter for the yeast HO gene. Ash1 is a sequence-specific DNA-binding protein, and we show that it recruits the Tup1 global repressive factor to the HO promoter. Using a method to determine where Ash1 and Tup1 are bound to DNA throughout the genome, we discovered that Tup1 is also present at most places where Ash1 binds. The majority of these sites are in “Nucleosome Depleted Regions,” or NDRs, where the absence of chromatin makes factor binding easier. We discovered that the HO promoter is an exception, in that the two places where Ash1 binds overlap nucleosomes. Activation of the HO promoter is a complex, multi-step process, and we demonstrated that chromatin factors transiently evict these nucleosomes from the HO promoter during the cell cycle, allowing Ash1 to bind and recruit Tup1. Thus, activators must evict nucleosomes from the promoter to allow the repressive machinery to bind.
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38
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Abstract
RAS proteins control a number of essential cellular processes as molecular switches in the human body. Presumably due to their important signalling role, RAS proteins are among the most frequently mutated oncogenes in human cancers. Hence, numerous efforts were done to develop appropriate therapies for RAS-mutant cancers in the last three decades. This review aimed to collect all of the reported small molecules that affect RAS signalling. These molecules can be divided in four main branches. First, we address approaches blocking RAS membrane association. Second, we focus on the stabilization efforts of non-productive RAS complexes. Third, we examine the approach to block RAS downstream signalling through disturbance of RAS-effector complex formation. Finally, we discuss direct inhibition; particularly the most recently reported covalent inhibitors, which are already advanced to human clinical trials.
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Affiliation(s)
- Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, Budapest, H-1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, Budapest, H-1117, Hungary.
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39
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Pisapia P, Pepe F, Iaccarino A, Sgariglia R, Nacchio M, Russo G, Gragnano G, Malapelle U, Troncone G. BRAF: A Two-Faced Janus. Cells 2020; 9:E2549. [PMID: 33260892 PMCID: PMC7760616 DOI: 10.3390/cells9122549] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/18/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022] Open
Abstract
Gain-of-function of V-Raf Murine Sarcoma Viral Oncogene Homolog B (BRAF) is one of the most frequent oncogenic mutations in numerous cancers, including thyroid papillary carcinoma, melanoma, colon, and lung carcinomas, and to a lesser extent, ovarian and glioblastoma multiforme. This mutation aberrantly activates the mitogen-activated protein (MAP) kinase extracellular signal-regulated kinase (MEK)/extracellular signal-regulated kinase (ERK) signaling pathway, thereby eliciting metastatic processes. The relevance of BRAF mutations stems from its prognostic value and, equally important, from its relevant therapeutic utility as an actionable target for personalized treatment. Here, we discuss the double facets of BRAF. In particular, we argue the need to implement diagnostic molecular algorithms that are able to detect this biomarker in order to streamline and refine diagnostic and therapeutic decisions.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (P.P.); (F.P.); (A.I.); (R.S.); (M.N.); (G.R.); (G.G.); (U.M.)
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40
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Luo L, Chen Y, Chen X, Zheng Y, Zhou V, Yu M, Burns R, Zhu W, Fu G, Felix JC, Hartley C, Damnernsawad A, Zhang J, Wen R, Drobyski WR, Gao C, Wang D. Kras-Deficient T Cells Attenuate Graft-versus-Host Disease but Retain Graft-versus-Leukemia Activity. THE JOURNAL OF IMMUNOLOGY 2020; 205:3480-3490. [PMID: 33158956 DOI: 10.4049/jimmunol.2000006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 10/08/2020] [Indexed: 12/24/2022]
Abstract
Acute graft-versus-host disease (aGVHD) is one major serious complication that is induced by alloreactive donor T cells recognizing host Ags and limits the success of allogeneic hematopoietic stem cell transplantation. In the current studies, we identified a critical role of Kras in regulating alloreactive T cell function during aGVHD. Kras deletion in donor T cells dramatically reduced aGVHD mortality and severity in an MHC-mismatched allogeneic hematopoietic stem cell transplantation mouse model but largely maintained the antitumor capacity. Kras-deficient CD4 and CD8 T cells exhibited impaired TCR-induced activation of the ERK pathway. Kras deficiency altered TCR-induced gene expression profiles, including the reduced expression of various inflammatory cytokines and chemokines. Moreover, Kras deficiency inhibited IL-6-mediated Th17 cell differentiation and impaired IL-6-induced ERK activation and gene expression in CD4 T cells. These findings support Kras as a novel and effective therapeutic target for aGVHD.
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Affiliation(s)
- Lan Luo
- Blood Research Institute, Versiti, Milwaukee, WI 53226.,Department of Hematology, Chinese People's Liberation Army General Hospital, Beijing 100853, China
| | - Yuhong Chen
- Blood Research Institute, Versiti, Milwaukee, WI 53226
| | - Xiao Chen
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Yongwei Zheng
- Blood Research Institute, Versiti, Milwaukee, WI 53226
| | - Vivian Zhou
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Mei Yu
- Blood Research Institute, Versiti, Milwaukee, WI 53226
| | - Robert Burns
- Blood Research Institute, Versiti, Milwaukee, WI 53226
| | - Wen Zhu
- Blood Research Institute, Versiti, Milwaukee, WI 53226.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Guoping Fu
- Blood Research Institute, Versiti, Milwaukee, WI 53226
| | - Juan C Felix
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226; and
| | - Christopher Hartley
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226; and
| | - Alisa Damnernsawad
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706
| | - Jing Zhang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706
| | - Renren Wen
- Blood Research Institute, Versiti, Milwaukee, WI 53226
| | | | - Chunji Gao
- Department of Hematology, Chinese People's Liberation Army General Hospital, Beijing 100853, China
| | - Demin Wang
- Blood Research Institute, Versiti, Milwaukee, WI 53226; .,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226
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Abstract
The Ras oncogene is notoriously difficult to target with specific therapeutics. Consequently, there is interest to better understand the Ras signaling pathways to identify potential targetable effectors. Recently, the mechanistic target of rapamycin complex 2 (mTORC2) was identified as an evolutionarily conserved Ras effector. mTORC2 regulates essential cellular processes, including metabolism, survival, growth, proliferation and migration. Moreover, increasing evidence implicate mTORC2 in oncogenesis. Little is known about the regulation of mTORC2 activity, but proposed mechanisms include a role for phosphatidylinositol (3,4,5)-trisphosphate - which is produced by class I phosphatidylinositol 3-kinases (PI3Ks), well-characterized Ras effectors. Therefore, the relationship between Ras, PI3K and mTORC2, in both normal physiology and cancer is unclear; moreover, seemingly conflicting observations have been reported. Here, we review the evidence on potential links between Ras, PI3K and mTORC2. Interestingly, data suggest that Ras and PI3K are both direct regulators of mTORC2 but that they act on distinct pools of mTORC2: Ras activates mTORC2 at the plasma membrane, whereas PI3K activates mTORC2 at intracellular compartments. Consequently, we propose a model to explain how Ras and PI3K can differentially regulate mTORC2, and highlight the diversity in the mechanisms of mTORC2 regulation, which appear to be determined by the stimulus, cell type, and the molecularly and spatially distinct mTORC2 pools.
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42
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Malapelle U, Rossi G, Pisapia P, Barberis M, Buttitta F, Castiglione F, Cecere FL, Grimaldi AM, Iaccarino A, Marchetti A, Massi D, Medicina D, Mele F, Minari R, Orlando E, Pagni F, Palmieri G, Righi L, Russo A, Tommasi S, Vermi W, Troncone G. BRAF as a positive predictive biomarker: Focus on lung cancer and melanoma patients. Crit Rev Oncol Hematol 2020; 156:103118. [PMID: 33038627 DOI: 10.1016/j.critrevonc.2020.103118] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023] Open
Abstract
In the era of personalized medicine, BRAF mutational assessment is mandatory in advanced-stage melanoma and non-small cell lung cancer (NSCLC) patients. The identification of actionable mutations is crucial for the adequate management of these patients. To date various drugs have been implemented in clinical practice. Similarly, various methods may be adopted for the identification of BRAF mutations. Here, we briefly review the current literature on BRAF in melanoma and NSCLC, focusing attention in particular on the different methods and drugs adopted in these patients. In addition, an overview of the real-world practice in different Italian laboratories with high expertise in molecular predictive pathology testing is provided.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giulio Rossi
- Pathology Unit, Azienda USL Romagna, St. Maria delle Croci Hospital, Ravenna, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Massimo Barberis
- Unit of Histopathology and Molecular Diagnostics, European Institute of Oncology IRCCS, Milano, Italy
| | - Fiamma Buttitta
- Center for Advanced Studies and Technology (CAST) - Department of Medical, Oral and Biotechnological Sciences, University of Chieti, Italy
| | - Francesca Castiglione
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy
| | | | - Antonio Maria Grimaldi
- Unit of Melanoma, Cancer Immunotherapy and Development Therapeutics, Istituto Nazionale Tumori IRCCS Fondazione Pascale, Napoli, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonio Marchetti
- Center for Advanced Studies and Technology (CAST) - Department of Medical, Oral and Biotechnological Sciences, University of Chieti, Italy
| | - Daniela Massi
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Daniela Medicina
- Section of Pathology, Asst Spedali Civili di Brescia, Brescia, Italy
| | - Fabio Mele
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Roberta Minari
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Elisabetta Orlando
- Department of Health Promotion, Mother and Child care, Internal Medicine and Medical Specialties (ProMISE), Unit of Anatomic Pathology, University of Palermo, Palermo, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, University Milan Bicocca, Milan, Italy
| | - Giuseppe Palmieri
- Unit of Cancer Genetics, Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Luisella Righi
- Department of Oncology, San Luigi Hospital, University of Turin, Turin, Italy
| | | | - Stefania Tommasi
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - William Vermi
- Section of Pathology, Asst Spedali Civili di Brescia, Brescia, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy.
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Freire MÁ. Viral silencing suppressors and cellular proteins partner with plant RRP6-like exoribonucleases. Virus Genes 2020; 56:621-631. [PMID: 32519287 DOI: 10.1007/s11262-020-01775-z] [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: 02/20/2020] [Accepted: 06/02/2020] [Indexed: 10/24/2022]
Abstract
RNA silencing and RNA decay are functionally interlaced, regulate gene expression and play a pivotal role in antiviral responses. As a counter-defensive strategy, many plant and mammalian viruses encode suppressors which interfere with both mechanisms. However, the protein interactions that connect these pathways remain elusive. Previous work reported that RNA silencing suppressors from different potyviruses, together with translation initiation factors EIF(iso)4E, interacted with the C-terminal region of the tobacco exoribonuclease RRP6-like 2, a component of the RNA decay exosome complex. Here, we investigate whether other viral silencing suppressors and cellular proteins might also bind RRP6-like exoribonucleases. A candidate search approach based on yeast two-hybrid protein interaction assays showed that three other unrelated viral suppressors, two from plant viruses and one from a mammalian virus, bound the C-terminus of the tobacco RRP6-like 2, the full-length of the Arabidopsis RRP6L1 protein and its C-terminal region. In addition, RRP6-like proteins were found to interact with members of the cellular double-stranded RNA-binding protein (DRB) family involved in RNA silencing. The C-terminal regions of RRP6L proteins are engaged in homotypic and heterotypic interactions and were predicted to be disordered. Collectively, these results suggest a protein interaction network that connects components of RNA decay and RNA silencing that is targeted by viral silencing suppressors.
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Affiliation(s)
- Miguel Ángel Freire
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, Universidad Nacional de Córdoba (UNC), Av. Vélez Sarsfield 299, CC 495, 5000, Córdoba, Argentina.
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Increased expression of hras induces early, but not full, senescence in the immortal fish cell line, EPC. Gene 2020; 765:145116. [PMID: 32896589 DOI: 10.1016/j.gene.2020.145116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 01/24/2023]
Abstract
In contrast to most mammals including human, fish cell lines have long been known to be immortal, with little sign of cellular senescence, despite the absence of transformation. Recently, our laboratory reported that DNA demethylation with 5-aza-2'-deoxycytidine (5-Aza-dC) induces telomere-independent cellular senescence and senescence-associated secretory phenotype (SASP) in an immortal fish cell line, EPC (Epithelioma papulosum cyprini). However, it is not known how fish derived cultured cells are usually resistant to aging in vitro. In this study, we focused on Ras, which carries out the main role of Ras-induced senescence (RIS), and investigated the role of Ras in the regulation of senescence in EPC cells. Our results show that 5-Aza-dC induced the expression of the ras (hras, kras, nras) gene in EPC cells. EPC cells overexpressing HRas or its constitutively active form (HRasV12) showed p53-dependent senescence-like growth arrest and senescence-associated β-galactosidase (SA-β-gal) activity with a large and/or flat morphology characteristic of cell senescence. On the other hand, the SASP was not induced. These results imply that the increased expression of HRas contributes to early senescence in EPC cells, but it alone may not be sufficient for the full senescence, even if HRas is aberrantly activated. Thus, the limited mechanism of RIS may play a role in the senescence-resistance of fish cell lines.
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45
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Cabanillas ME, Dadu R, Iyer P, Wanland KB, Busaidy NL, Ying A, Gule-Monroe M, Wang JR, Zafereo M, Hofmann MC. Acquired Secondary RAS Mutation in BRAF V600E-Mutated Thyroid Cancer Patients Treated with BRAF Inhibitors. Thyroid 2020; 30:1288-1296. [PMID: 32216548 PMCID: PMC7869871 DOI: 10.1089/thy.2019.0514] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background: The BRAFV600E mutation is the most common driver mutation in papillary thyroid cancer (PTC) and anaplastic thyroid cancer (ATC). This mutation is considered actionable and, for BRAFV600E-mutated ATC, a BRAF inhibitor (dabrafenib) in combination with an MEK inhibitor (trametinib) is FDA approved. BRAF inhibitors have also shown efficacy in BRAFV600E-mutated PTC. However, as with all targeted therapies, resistance to these drugs eventually develops. It is essential that we understand the mechanisms of resistance to the BRAF inhibitors in thyroid cancer to develop future strategies to effectively treat these patients and improve survival. Patients: Herein, we describe four patients with thyroid cancer treated with selective BRAF inhibitors, who developed a RAS mutation in addition to the BRAFV600E mutation at progression. Results: Patients 1 and 3 acquired a KRASG12V mutation in the progressive tumor, patient 2 acquired a NRASQ61K mutation in a progressive lymph node, and patient 4 acquired NRASG13D mutation on liquid biopsy performed at the time of radiographic disease progression. Conclusion: Similar to the melanoma experience, the emergence of RAS mutations appears to act as a mechanism of resistance to BRAF inhibitors in thyroid cancers.
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Affiliation(s)
- Maria E. Cabanillas
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Address correspondence to: Maria E. Cabanillas, MD, Department of Endocrine Neoplasia and Hormonal Disorders, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Ramona Dadu
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Pryianka Iyer
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kacey B. Wanland
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Naifa L. Busaidy
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anita Ying
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Maria Gule-Monroe
- Department of Diagnostic Radiology, and The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jennifer R. Wang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark Zafereo
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marie-Claude Hofmann
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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46
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Araujo-Garrido JL, Baisón-Olmo F, Bernal-Bayard J, Romero F, Ramos-Morales F. Tubulin Folding Cofactor TBCB is a Target of the Salmonella Effector Protein SseK1. Int J Mol Sci 2020; 21:ijms21093193. [PMID: 32366039 PMCID: PMC7246435 DOI: 10.3390/ijms21093193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/11/2022] Open
Abstract
Salmonella enterica serovar Typhimurium is a human and animal pathogen that uses type III secretion system effectors to manipulate the host cell and fulfill infection. SseK1 is a Salmonella effector with glycosyltransferase activity. We carried out a yeast two-hybrid screen and have identified tubulin-binding cofactor B (TBCB) as a new binding partner for this effector. SseK1 catalyzed the addition of N-acetylglucosamine to arginine on TBCB, and its expression promoted the stabilization of the microtubule cytoskeleton of HEK293T cells. The conserved Asp-x-Asp (DxD) motif that is essential for the activity of SseK1 was required for the binding and modification of TBCB and for the effect on the cytoskeleton. Our study has identified a novel target for SseK1 and suggests that this effector may have a role in the manipulation of the host cell microtubule network to provide a safe niche for this pathogen.
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Affiliation(s)
- Juan Luis Araujo-Garrido
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (J.L.A.-G.); (F.B.-O.); (J.B.-B.)
| | - Fernando Baisón-Olmo
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (J.L.A.-G.); (F.B.-O.); (J.B.-B.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 1058, Chile
| | - Joaquín Bernal-Bayard
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (J.L.A.-G.); (F.B.-O.); (J.B.-B.)
| | - Francisco Romero
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain;
| | - Francisco Ramos-Morales
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (J.L.A.-G.); (F.B.-O.); (J.B.-B.)
- Correspondence:
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47
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Hartmann C, Schwietzer YA, Kummer D, Kirschnick N, Hoppe E, Thüring EM, Glaesner-Ebnet M, Brinkmann F, Gerke V, Reuter S, Nakayama M, Ebnet K. The mitochondrial outer membrane protein SYNJ2BP interacts with the cell adhesion molecule TMIGD1 and can recruit it to mitochondria. BMC Mol Cell Biol 2020; 21:30. [PMID: 32303178 PMCID: PMC7164261 DOI: 10.1186/s12860-020-00274-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/06/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Transmembrane and immunoglobulin domain-containing protein 1 (TMIGD1) is a recently identified cell adhesion molecule which is predominantly expressed by epithelial cells of the intestine and the kidney. Its expression is downregulated in both colon and renal cancer suggesting a tumor suppressive activity. The function of TMIGD1 at the cellular level is largely unclear. Published work suggests a protective role of TMIGD1 during oxidative stress in kidney epithelial cells, but the underlying molecular mechanisms are unknown. RESULTS In this study, we address the subcellular localization of TMIGD1 in renal epithelial cells and identify a cytoplasmic scaffold protein as interaction partner of TMIGD1. We find that TMIGD1 localizes to different compartments in renal epithelial cells and that this localization is regulated by cell confluency. Whereas it localizes to mitochondria in subconfluent cells it is localized at cell-cell contacts in confluent cells. We find that cell-cell contact localization is regulated by N-glycosylation and that both the extracellular and the cytoplasmic domain contribute to this localization. We identify Synaptojanin 2-binding protein (SYNJ2BP), a PDZ domain-containing cytoplasmic protein, which localizes to both mitochondria and the plasma membrane, as interaction partner of TMIGD1. The interaction of TMIGD1 and SYNJ2BP is mediated by the PDZ domain of SYNJ2BP and the C-terminal PDZ domain-binding motif of TMIGD1. We also find that SYNJ2BP can actively recruit TMIGD1 to mitochondria providing a potential mechanism for the localization of TMIGD1 at mitochondria. CONCLUSIONS This study describes TMIGD1 as an adhesion receptor that can localize to both mitochondria and cell-cell junctions in renal epithelial cells. It identifies SYNJ2BP as an interaction partner of TMIGD1 providing a potential mechanism underlying the localization of TMIGD1 at mitochondria. The study thus lays the basis for a better understanding of the molecular function of TMIGD1 during oxidative stress regulation.
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Affiliation(s)
- Christian Hartmann
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Ysabel Alessa Schwietzer
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Daniel Kummer
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Interdisciplinary Clinical Research Center (IZKF), University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Nils Kirschnick
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Esther Hoppe
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Eva-Maria Thüring
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Mark Glaesner-Ebnet
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Frauke Brinkmann
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Volker Gerke
- Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Stefan Reuter
- Department of Medicine D, Division of General Internal Medicine, Nephrology and Rheumatology, University Hospital of Münster, 48149, Münster, Germany
| | - Masanori Nakayama
- Laboratory for Cell Polarity and Organogenesis, Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Klaus Ebnet
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany. .,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany. .,Interdisciplinary Clinical Research Center (IZKF), University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany. .,Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, 48419, Münster, Germany.
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48
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Chen S, Li F, Xu D, Hou K, Fang W, Li Y. The Function of RAS Mutation in Cancer and Advances in its Drug Research. Curr Pharm Des 2020; 25:1105-1114. [PMID: 31057104 DOI: 10.2174/1381612825666190506122228] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/18/2019] [Indexed: 12/12/2022]
Abstract
RAS (H-ras, K-ras, and N-ras), as the second largest mutated gene driver in various human cancers, has long been a vital research target for cancer. Its function is to transform the extracellular environment into a cascade of intracellular signal transduction. RAS mutant protein regulates tumor cell proliferation, apoptosis, metabolism and angiogenesis through downstream MAPK, PI3K and other signaling pathways. In KRAS or other RAS-driven cancers, current treatments include direct inhibitors and upstream/downstream signaling pathway inhibitors. However, the research on these inhibitors has been largely restricted due to their escape inhibition and off-target toxicity. In this paper, we started with the role of normal and mutant RAS genes in cancer, elucidated the relevant RAS regulating pathways, and highlighted the important research advancements in RAS inhibitor research. We concluded that for the crosstalk between RAS pathways, the effect of single regulation may be limited, and the multi-target drug combined compensation mechanism is becoming a research hotspot.
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Affiliation(s)
- Shijie Chen
- State Key Laboratory of Natural Medicines, Department of Physiology, China Phar maceutical University, Nanjing 210009, China
| | - Fengyang Li
- State Key Laboratory of Natural Medicines, Department of Physiology, China Phar maceutical University, Nanjing 210009, China
| | - Dan Xu
- State Key Laboratory of Natural Medicines, Department of Physiology, China Phar maceutical University, Nanjing 210009, China
| | - Kai Hou
- State Key Laboratory of Natural Medicines, Department of Physiology, China Phar maceutical University, Nanjing 210009, China
| | - Weirong Fang
- State Key Laboratory of Natural Medicines, Department of Physiology, China Phar maceutical University, Nanjing 210009, China
| | - Yunman Li
- State Key Laboratory of Natural Medicines, Department of Physiology, China Phar maceutical University, Nanjing 210009, China
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49
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Khan I, Rhett JM, O'Bryan JP. Therapeutic targeting of RAS: New hope for drugging the "undruggable". BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2020; 1867:118570. [PMID: 31678118 PMCID: PMC6937383 DOI: 10.1016/j.bbamcr.2019.118570] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/01/2019] [Accepted: 10/14/2019] [Indexed: 12/18/2022]
Abstract
RAS is the most frequently mutated oncogene in cancer and a critical driver of oncogenesis. Therapeutic targeting of RAS has been a goal of cancer research for more than 30 years due to its essential role in tumor formation and maintenance. Yet the quest to inhibit this challenging foe has been elusive. Although once considered "undruggable", the struggle to directly inhibit RAS has seen recent success with the development of pharmacological agents that specifically target the KRAS(G12C) mutant protein, which include the first direct RAS inhibitor to gain entry to clinical trials. However, the limited applicability of these inhibitors to G12C-mutant tumors demands further efforts to identify more broadly efficacious RAS inhibitors. Understanding allosteric influences on RAS may open new avenues to inhibit RAS. Here, we provide a brief overview of RAS biology and biochemistry, discuss the allosteric regulation of RAS, and summarize the various approaches to develop RAS inhibitors.
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Affiliation(s)
- Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, United States of America; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, United States of America
| | - J Matthew Rhett
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, United States of America; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, United States of America
| | - John P O'Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, United States of America; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, United States of America.
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50
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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: 306] [Impact Index Per Article: 76.5] [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.
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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
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