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Ma X, Liu A, Liu R, Zhang L, Zheng Z, Li Y, Tian S. Identification and functional analysis of differentially expressed proteins in high and low freezing tolerance sheep sperm. Theriogenology 2023; 211:212-223. [PMID: 37659252 DOI: 10.1016/j.theriogenology.2023.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 05/15/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
The purpose of this study was to identify proteins associated with differences in the freezing tolerance of sheep sperm and to analyze their functions. Qualified fresh semen from four breeds of rams, the Australian White, white-head Dorper, Black-head Dorper, and Hu sheep breeds, were selected for cryopreservation. The sperm freezing tolerance was investigated by evaluation of the overall vitality, progressive vitality, and rapidly advance vitality of the sperm. A differential model of sperm freezing tolerance was constructed for sheep breeds showing significant differences. Differentially expressed proteins associated with sperm freezing tolerance were identified using iTRAQ and the protein functions were analyzed. It was found that sperm freezing tolerance was best in Hu sheep and worst in white-head Dorper sheep. These two breeds were used for the construction of a model based on differences in freezing tolerance and the identification of sperm proteins expressed differentially before freezing and after thawing. A total of 128 differentially expressed proteins (88 up-regulated and 40 down-regulated) were identified before freezing and after thawing in Hu sheep sperm (fresh/frozen Hu sheep sperm referred to as HL vs. HF), while 219 differentially expressed proteins (106 up-regulated and 113 down-regulated) were identified in white-head Dorper sheep (fresh/frozen white-head Dorper sheep sperm referred to as WL vs. WF). A comparison of these differentially expressed proteins showed that 57 proteins overlapped between the two breeds while 71 were only expressed in Hu sheep and 162 were only expressed in white-head Dorper sheep. Functional annotation and enrichment analyses of differentially expressed proteins down-regulated in Hu sheep involved in phosphorylation of phosphatidylinositol phosphate kinases, regulation of GTPase activity and glycolysis/gluconeogenesis signaling pathway. Up-regulated proteins of Hu sheep participated in oxidoreductase activity and oxidative phosphorylation process of sperm freezing. Furthermore, down-regulated in white-head Dorper sheep involved in the metabolic regulation of carbohydrate and nuclear sugar metabolism. Up-regulated proteins of white-head Dorper sheep involved in the ferroptosis and oxidative phosphorylation pathways. Collectively, These proteins were found to participate mainly in oxidative phosphorylation as well as phosphorylation and metabolic processes in the mitochondria to affect the freezing tolerance of sheep sperm.
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Affiliation(s)
- Xiaofei Ma
- College of Animal Science and Technology, Hebei Agricultural University, Hebei, Baoding, China
| | - Aiju Liu
- Department of Agricultural and Animal Husbandry Engineering, Cangzhou Technical College, Hebei, Cangzhou, China
| | - Ruoyan Liu
- College of Animal Science and Technology, Hebei Agricultural University, Hebei, Baoding, China
| | - Limeng Zhang
- Laboratory of Molecular Biology, Zhengzhou Normal University, Henan, Zhengzhou, China
| | - Zhong Zheng
- College of Animal Science and Technology, Hebei Agricultural University, Hebei, Baoding, China
| | - Yuexin Li
- College of Animal Science and Technology, Hebei Agricultural University, Hebei, Baoding, China
| | - Shujun Tian
- College of Animal Science and Technology, Hebei Agricultural University, Hebei, Baoding, China.
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2
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Martin-Vega A, Cobb MH. Navigating the ERK1/2 MAPK Cascade. Biomolecules 2023; 13:1555. [PMID: 37892237 PMCID: PMC10605237 DOI: 10.3390/biom13101555] [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: 09/30/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
The RAS-ERK pathway is a fundamental signaling cascade crucial for many biological processes including proliferation, cell cycle control, growth, and survival; common across all cell types. Notably, ERK1/2 are implicated in specific processes in a context-dependent manner as in stem cells and pancreatic β-cells. Alterations in the different components of this cascade result in dysregulation of the effector kinases ERK1/2 which communicate with hundreds of substrates. Aberrant activation of the pathway contributes to a range of disorders, including cancer. This review provides an overview of the structure, activation, regulation, and mutational frequency of the different tiers of the cascade; with a particular focus on ERK1/2. We highlight the importance of scaffold proteins that contribute to kinase localization and coordinate interaction dynamics of the kinases with substrates, activators, and inhibitors. Additionally, we explore innovative therapeutic approaches emphasizing promising avenues in this field.
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Affiliation(s)
- Ana Martin-Vega
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
| | - Melanie H. Cobb
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA
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3
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Song F, Dai Q, Grimm MO, Steinbach D. The Antithetic Roles of IQGAP2 and IQGAP3 in Cancers. Cancers (Basel) 2023; 15:cancers15041115. [PMID: 36831467 PMCID: PMC9953781 DOI: 10.3390/cancers15041115] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
The scaffold protein family of IQ motif-containing GTPase-activating proteins (IQGAP1, 2, and 3) share a high degree of homology and comprise six functional domains. IQGAPs bind and regulate the cytoskeleton, interact with MAP kinases and calmodulin, and have GTPase-related activity, as well as a RasGAP domain. Thus, IQGAPs regulate multiple cellular processes and pathways, affecting cell division, growth, cell-cell interactions, migration, and invasion. In the past decade, significant evidence on the function of IQGAPs in signal transduction during carcinogenesis has emerged. Compared with IQGAP1, IQGAP2 and IQGAP3 were less analyzed. In this review, we summarize the different signaling pathways affected by IQGAP2 and IQGAP3, and the antithetic roles of IQGAP2 and IQGAP3 in different types of cancer. IQGAP2 expression is reduced and plays a tumor suppressor role in most solid cancer types, while IQGAP3 is overexpressed and acts as an oncogene. In lymphoma, for example, IQGAPs have partially opposite functions. There is considerable evidence that IQGAPs regulate a multitude of pathways to modulate cancer processes and chemoresistance, but some questions, such as how they trigger this signaling, through which domains, and why they play opposite roles on the same pathways, are still unanswered.
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Affiliation(s)
- Fei Song
- Department of Urology, Jena University Hospital, 07740 Jena, Germany
| | - Qingqing Dai
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, 07740 Jena, Germany
| | - Marc-Oliver Grimm
- Department of Urology, Jena University Hospital, 07740 Jena, Germany
| | - Daniel Steinbach
- Department of Urology, Jena University Hospital, 07740 Jena, Germany
- Correspondence:
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4
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Huang T, Tian Q, He Z, Xiao H, Yuan C, Lin Z, Yuan J, Yao M. Transcriptome analysis of PBMCs isolated from piglets treated with a miR-124 sponge construct identified miR124/IQGAP2/Rho GTPase as a target pathway support Salmonella Typhimurium infection. Mol Genet Genomics 2023; 298:213-227. [PMID: 36380106 DOI: 10.1007/s00438-022-01976-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022]
Abstract
miR-124 is a significantly up-regulated miRNA in peripheral blood collected from piglets infected with Salmonella Typhimurium, suggesting that it may play an important role in Salmonella pathogenesis. This study focused on the transcriptomic analysis of peripheral blood mononuclear cells (PBMCs) isolated from miR-124 sponge and Salmonella Typhimurium-treated piglets, and trying to investigate the function of miR-124 in Salmonella infection. The transcriptome profiling analysis revealed that 2778 genes in miR-124 sponge + Salmonella Typhimurium treatment versus control, 2271 genes in Salmonella Typhimurium treatment versus control, and 1301 genes in miR-124 sponge + Salmonella Typhimurium versus Salmonella Typhimurium treatment, were differentially expressed, respectively (FDR < 0.05 and fold change > 2.0). Pathway analysis indicated that the MAPK signaling pathway, Ribosome pathway, and T-cell receptor signaling pathway were the most significantly enriched pathway in differentially expressed genes between miR-124 sponge + Salmonella Typhimurium and Salmonella Typhimurium along treatment (FDR < 0.05). Reporter assays and electrophoretic mobility shift assays showed that miR-124 is a crucial regulatory factor that targets IQ motif containing GTPase-activating protein 2 (IQGAP2). Cell culture experiment indicated that miR-124 attenuated the Salmonella Typhimurium-mediated activation of CDC42 and RAC1 (P < 0.05). Cultured PBMCs treated with miR-124 and IQGAP2-siRNA had higher intracellular Salmonella count than control samples, particularly 12 h post-infection (P < 0.05). Immunofluorescence analysis revealed that miR-124 treatment reduced the percentage of LAMP-1-positive phagosomes. The miR-124 could be an important regulator for IQGAP2/Rho GTPase pathway in Salmonella Typhimurium-infected PBMCs, and this pathway could be a target for Salmonella that support its infection in PBMCs in piglets.
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Affiliation(s)
- Tinghua Huang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Qi Tian
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Zhen He
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Hong Xiao
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Chen Yuan
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Zezhao Lin
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jing Yuan
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Min Yao
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China.
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DiRusso CJ, Dashtiahangar M, Gilmore TD. Scaffold proteins as dynamic integrators of biological processes. J Biol Chem 2022; 298:102628. [PMID: 36273588 PMCID: PMC9672449 DOI: 10.1016/j.jbc.2022.102628] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/15/2022] Open
Abstract
Scaffold proteins act as molecular hubs for the docking of multiple proteins to organize efficient functional units for signaling cascades. Over 300 human proteins have been characterized as scaffolds, acting in a variety of signaling pathways. While the term scaffold implies a static, supportive platform, it is now clear that scaffolds are not simply inert docking stations but can undergo conformational changes that affect their dependent signaling pathways. In this review, we catalog scaffold proteins that have been shown to undergo actionable conformational changes, with a focus on the role that conformational change plays in the activity of the classic yeast scaffold STE5, as well as three human scaffold proteins (KSR, NEMO, SHANK3) that are integral to well-known signaling pathways (RAS, NF-κB, postsynaptic density). We also discuss scaffold protein conformational changes vis-à-vis liquid-liquid phase separation. Changes in scaffold structure have also been implicated in human disease, and we discuss how aberrant conformational changes may be involved in disease-related dysregulation of scaffold and signaling functions. Finally, we discuss how understanding these conformational dynamics will provide insight into the flexibility of signaling cascades and may enhance our ability to treat scaffold-associated diseases.
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6
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Sayedyahossein S, Smith J, Barnaeva E, Li Z, Choe J, Ronzetti M, Dextras C, Hu X, Marugan J, Southall N, Baljinnyam B, Thines L, Tran AD, Ferrer M, Sacks DB. Discovery of small molecule inhibitors that effectively disrupt IQGAP1-Cdc42 interaction in breast cancer cells. Sci Rep 2022; 12:17372. [PMID: 36253497 PMCID: PMC9576799 DOI: 10.1038/s41598-022-21342-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/26/2022] [Indexed: 01/10/2023] Open
Abstract
The small GTPase Cdc42 is an integral component of the cytoskeleton, and its dysregulation leads to pathophysiological conditions, such as cancer. Binding of Cdc42 to the scaffold protein IQGAP1 stabilizes Cdc42 in its active form. The interaction between Cdc42 and IQGAP1 enhances migration and invasion of cancer cells. Disrupting this association could impair neoplastic progression and metastasis; however, no effective means to achieve this has been described. Here, we screened 78,500 compounds using a homogeneous time resolved fluorescence-based assay to identify small molecules that disrupt the binding of Cdc42 to IQGAP1. From the combined results of the validation assay and counter-screens, we selected 44 potent compounds for cell-based experiments. Immunoprecipitation and cell viability analysis rendered four lead compounds, namely NCGC00131308, NCGC00098561, MLS000332963 and NCGC00138812, three of which inhibited proliferation and migration of breast carcinoma cells. Microscale thermophoresis revealed that two compounds bind directly to Cdc42. One compound reduced the amount of active Cdc42 in cells and effectively impaired filopodia formation. Docking analysis provided plausible models of the compounds binding to the hydrophobic pocket adjacent to the GTP binding site of Cdc42. In conclusion, we identified small molecules that inhibit binding between Cdc42 and IQGAP1, which could potentially yield chemotherapeutic agents.
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Affiliation(s)
- Samar Sayedyahossein
- grid.94365.3d0000 0001 2297 5165Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892 USA ,grid.39381.300000 0004 1936 8884Present Address: Department of Physiology and Pharmacology, University of Western Ontario, London, ON Canada
| | - Jessica Smith
- grid.94365.3d0000 0001 2297 5165Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Present Address: Center for Scientific Review, National Institutes of Health, Bethesda, MD USA
| | - Elena Barnaeva
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Zhigang Li
- grid.94365.3d0000 0001 2297 5165Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jun Choe
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Michael Ronzetti
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Christopher Dextras
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Xin Hu
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Juan Marugan
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Noel Southall
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Bolormaa Baljinnyam
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - Louise Thines
- grid.94365.3d0000 0001 2297 5165Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Andy D. Tran
- grid.48336.3a0000 0004 1936 8075Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, NCI, National Institutes of Health, Rockville, MD USA
| | - Marc Ferrer
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD USA
| | - David B. Sacks
- grid.94365.3d0000 0001 2297 5165Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892 USA
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7
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CDC42-IQGAP Interactions Scrutinized: New Insights into the Binding Properties of the GAP-Related Domain. Int J Mol Sci 2022; 23:ijms23168842. [PMID: 36012107 PMCID: PMC9408373 DOI: 10.3390/ijms23168842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 11/17/2022] Open
Abstract
The IQ motif-containing GTPase-activating protein (IQGAP) family composes of three highly-related and evolutionarily conserved paralogs (IQGAP1, IQGAP2 and IQGAP3), which fine tune as scaffolding proteins numerous fundamental cellular processes. IQGAP1 is described as an effector of CDC42, although its effector function yet re-mains unclear. Biophysical, biochemical and molecular dynamic simulation studies have proposed that IQGAP RASGAP-related domains (GRDs) bind to the switch regions and the insert helix of CDC42 in a GTP-dependent manner. Our kinetic and equilibrium studies have shown that IQGAP1 GRD binds, in contrast to its C-terminal 794 amino acids (called C794), CDC42 in a nucleotide-independent manner indicating a binding outside the switch regions. To resolve this discrepancy and move beyond the one-sided view of GRD, we carried out affinity measurements and a systematic mutational analysis of the interfacing residues between GRD and CDC42 based on the crystal structure of the IQGAP2 GRD-CDC42Q61L GTP complex. We determined a 100-fold lower affinity of the GRD1 of IQGAP1 and of GRD2 of IQGAP2 for CDC42 mGppNHp in comparison to C794/C795 proteins. Moreover, partial and major mutation of CDC42 switch regions substantially affected C794/C795 binding but only a little GRD1 and remarkably not at all the GRD2 binding. However, we clearly showed that GRD2 contributes to the overall affinity of C795 by using a 11 amino acid mutated GRD variant. Furthermore, the GRD1 binding to the CDC42 was abolished using specific point mutations within the insert helix of CDC42 clearly supporting the notion that CDC42 binding site(s) of IQGAP GRD lies outside the switch regions among others in the insert helix. Collectively, this study provides further evidence for a mechanistic framework model that is based on a multi-step binding process, in which IQGAP GRD might act as a ‘scaffolding domain’ by binding CDC42 irrespective of its nucleotide-bound forms, followed by other IQGAP domains downstream of GRD that act as an effector domain and is in charge for a GTP-dependent interaction with CDC42.
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8
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Dai Q, Ain Q, Rooney M, Song F, Zipprich A. Role of IQ Motif-Containing GTPase-Activating Proteins in Hepatocellular Carcinoma. Front Oncol 2022; 12:920652. [PMID: 35785216 PMCID: PMC9243542 DOI: 10.3389/fonc.2022.920652] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/10/2022] [Indexed: 11/21/2022] Open
Abstract
IQ motif-containing GTPase-activating proteins (IQGAPs) are a class of scaffolding proteins, including IQGAP1, IQGAP2, and IQGAP3, which govern multiple cellular activities by facilitating cytoskeletal remodeling and cellular signal transduction. The role of IQGAPs in cancer initiation and progression has received increasing attention in recent years, especially in hepatocellular carcinoma (HCC), where the aberrant expression of IQGAPs is closely related to patient prognosis. IQGAP1 and 3 are upregulated and are considered oncogenes in HCC, while IQGAP2 is downregulated and functions as a tumor suppressor. This review details the three IQGAP isoforms and their respective structures. The expression and role of each protein in different liver diseases and mainly in HCC, as well as the underlying mechanisms, are also presented. This review also provides a reference for further studies on IQGAPs in HCC.
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Affiliation(s)
- Qingqing Dai
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
- Else Kröner Graduate School for Medical Students “Jena School for Ageing Medicine (JSAM)”, Jena University Hospital, Jena, Germany
| | - Quratul Ain
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
| | - Michael Rooney
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
| | - Fei Song
- Department of Urology, Jena University Hospital, Jena, Germany
| | - Alexander Zipprich
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
- *Correspondence: Alexander Zipprich,
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9
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Jahid S, Ortega JA, Vuong LM, Acquistapace IM, Hachey SJ, Flesher JL, La Serra MA, Brindani N, La Sala G, Manigrasso J, Arencibia JM, Bertozzi SM, Summa M, Bertorelli R, Armirotti A, Jin R, Liu Z, Chen CF, Edwards R, Hughes CCW, De Vivo M, Ganesan AK. Structure-based design of CDC42 effector interaction inhibitors for the treatment of cancer. Cell Rep 2022; 39:110641. [PMID: 35385746 PMCID: PMC9127750 DOI: 10.1016/j.celrep.2022.110641] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/01/2022] [Accepted: 03/16/2022] [Indexed: 01/21/2023] Open
Abstract
CDC42 family GTPases (RHOJ, RHOQ, CDC42) are upregulated but rarely mutated in cancer and control both the ability of tumor cells to invade surrounding tissues and the ability of endothelial cells to vascularize tumors. Here, we use computer-aided drug design to discover a chemical entity (ARN22089) that has broad activity against a panel of cancer cell lines, inhibits S6 phosphorylation and MAPK activation, activates pro-inflammatory and apoptotic signaling, and blocks tumor growth and angiogenesis in 3D vascularized microtumor models (VMT) in vitro. Additionally, ARN22089 has a favorable pharmacokinetic profile and can inhibit the growth of BRAF mutant mouse melanomas and patient-derived xenografts in vivo. ARN22089 selectively blocks CDC42 effector interactions without affecting the binding between closely related GTPases and their downstream effectors. Taken together, we identify a class of therapeutic agents that influence tumor growth by modulating CDC42 signaling in both the tumor cell and its microenvironment.
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Affiliation(s)
- Sohail Jahid
- Department of Dermatology, University of California, Irvine, CA 92697, USA
| | - Jose A Ortega
- Laboratory of Molecular Modeling and Drug Design, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Linh M Vuong
- Department of Dermatology, University of California, Irvine, CA 92697, USA
| | - Isabella Maria Acquistapace
- Laboratory of Molecular Modeling and Drug Design, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Stephanie J Hachey
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - Jessica L Flesher
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Maria Antonietta La Serra
- Laboratory of Molecular Modeling and Drug Design, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Nicoletta Brindani
- Laboratory of Molecular Modeling and Drug Design, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Giuseppina La Sala
- Laboratory of Molecular Modeling and Drug Design, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Jacopo Manigrasso
- Laboratory of Molecular Modeling and Drug Design, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Jose M Arencibia
- Laboratory of Molecular Modeling and Drug Design, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Sine Mandrup Bertozzi
- Analytical Chemistry and Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Maria Summa
- Analytical Chemistry and Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Rosalia Bertorelli
- Analytical Chemistry and Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Andrea Armirotti
- Analytical Chemistry and Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Rongsheng Jin
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - Zheng Liu
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - Chi-Fen Chen
- Department of Dermatology, University of California, Irvine, CA 92697, USA
| | - Robert Edwards
- Department of Pathology and Lab Medicine, University of California, Irvine, CA 92697, USA
| | - Christopher C W Hughes
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Design, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.
| | - Anand K Ganesan
- Department of Dermatology, University of California, Irvine, CA 92697, USA; Department of Biological Chemistry, University of California, Irvine, CA 92697, USA.
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10
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Mosaddeghzadeh N, Nouri K, Krumbach OHF, Amin E, Dvorsky R, Ahmadian MR. Selectivity Determinants of RHO GTPase Binding to IQGAPs. Int J Mol Sci 2021; 22:12596. [PMID: 34830479 PMCID: PMC8625570 DOI: 10.3390/ijms222212596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/13/2022] Open
Abstract
IQ motif-containing GTPase-activating proteins (IQGAPs) modulate a wide range of cellular processes by acting as scaffolds and driving protein components into distinct signaling networks. Their functional states have been proposed to be controlled by members of the RHO family of GTPases, among other regulators. In this study, we show that IQGAP1 and IQGAP2 can associate with CDC42 and RAC1-like proteins but not with RIF, RHOD, or RHO-like proteins, including RHOA. This seems to be based on the distribution of charged surface residues, which varies significantly among RHO GTPases despite their high sequence homology. Although effector proteins bind first to the highly flexible switch regions of RHO GTPases, additional contacts outside are required for effector activation. Sequence alignment and structural, mutational, and competitive biochemical analyses revealed that RHO GTPases possess paralog-specific residues outside the two highly conserved switch regions that essentially determine the selectivity of RHO GTPase binding to IQGAPs. Amino acid substitution of these specific residues in RHOA to the corresponding residues in RAC1 resulted in RHOA association with IQGAP1. Thus, electrostatics most likely plays a decisive role in these interactions.
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Affiliation(s)
- Niloufar Mosaddeghzadeh
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.M.); (K.N.); (O.H.F.K.); (E.A.); (R.D.)
| | - Kazem Nouri
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.M.); (K.N.); (O.H.F.K.); (E.A.); (R.D.)
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Oliver H. F. Krumbach
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.M.); (K.N.); (O.H.F.K.); (E.A.); (R.D.)
| | - Ehsan Amin
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.M.); (K.N.); (O.H.F.K.); (E.A.); (R.D.)
- Medical Faculty, Institute of Neural and Sensory Physiology, University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Radovan Dvorsky
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.M.); (K.N.); (O.H.F.K.); (E.A.); (R.D.)
| | - Mohammad R. Ahmadian
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.M.); (K.N.); (O.H.F.K.); (E.A.); (R.D.)
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11
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Hoeprich GJ, Sinclair AN, Shekhar S, Goode BL. Single-molecule imaging of IQGAP1 regulating actin filament dynamics. Mol Biol Cell 2021; 33:ar2. [PMID: 34731043 PMCID: PMC8886817 DOI: 10.1091/mbc.e21-04-0211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
IQGAP is a conserved family of actin-binding proteins with essential roles in cell motility, cytokinesis, and cell adhesion, yet there remains a limited understanding of how IQGAP proteins directly influence actin filament dynamics. To close this gap, we used single-molecule and single-filament total internal reflection fluorescence microscopy to observe IQGAP regulating actin dynamics in real time. To our knowledge, this is the first study to do so. Our results demonstrate that full-length human IQGAP1 forms dimers that stably bind to actin filament sides and transiently cap barbed ends. These interactions organize filaments into thin bundles, suppress barbed end growth, and inhibit filament disassembly. Surprisingly, each activity depends on distinct combinations of IQGAP1 domains and/or dimerization, suggesting that different mechanisms underlie each functional effect on actin. These observations have important implications for how IQGAP functions as an actin regulator in vivo and how it may be regulated in different biological settings.
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Affiliation(s)
- Gregory J Hoeprich
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Amy N Sinclair
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Shashank Shekhar
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02453, USA.,Present address: Departments of Physics and Cell Biology, Emory University, Atlanta, GA 30322
| | - Bruce L Goode
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02453, USA
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12
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Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses. Nat Genet 2021; 53:1260-1269. [PMID: 34226706 PMCID: PMC8349845 DOI: 10.1038/s41588-021-00892-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 05/28/2021] [Indexed: 02/06/2023]
Abstract
Exome association studies to date have generally been underpowered to systematically evaluate the phenotypic impact of very rare coding variants. We leveraged extensive haplotype sharing between 49,960 exome-sequenced UK Biobank participants and the remainder of the cohort (total N~500K) to impute exome-wide variants with accuracy (R2>0.5) down to minor allele frequency (MAF) ~0.00005. Association and fine-mapping analyses of 54 quantitative traits identified 1,189 significant associations (P<5 x 10−8) involving 675 distinct rare protein-altering variants (MAF<0.01) that passed stringent filters for likely causality. Across all traits, 49% of associations (578/1,189) occurred in genes with two or more hits; follow-up analyses of these genes identified allelic series containing up to 45 distinct likely-causal variants. Our results demonstrate the utility of within-cohort imputation in population-scale GWAS cohorts, provide a catalog of likely-causal, large-effect coding variant associations, and foreshadow the insights that will be revealed as genetic biobank studies continue to grow.
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13
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Molecular subversion of Cdc42 signalling in cancer. Biochem Soc Trans 2021; 49:1425-1442. [PMID: 34196668 PMCID: PMC8412110 DOI: 10.1042/bst20200557] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 12/21/2022]
Abstract
Cdc42 is a member of the Rho family of small GTPases and a master regulator of the actin cytoskeleton, controlling cell motility, polarity and cell cycle progression. This small G protein and its regulators have been the subject of many years of fruitful investigation and the advent of functional genomics and proteomics has opened up new avenues of exploration including how it functions at specific locations in the cell. This has coincided with the introduction of new structural techniques with the ability to study small GTPases in the context of the membrane. The role of Cdc42 in cancer is well established but the molecular details of its action are still being uncovered. Here we review alterations found to Cdc42 itself and to key components of the signal transduction pathways it controls in cancer. Given the challenges encountered with targeting small G proteins directly therapeutically, it is arguably the regulators of Cdc42 and the effector signalling pathways downstream of the small G protein which will be the most tractable targets for therapeutic intervention. These will require interrogation in order to fully understand the global signalling contribution of Cdc42, unlock the potential for mapping new signalling axes and ultimately produce inhibitors of Cdc42 driven signalling.
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14
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Özsoy Ş, Vujovic F, Simonian M, Valova V, Hunter N, Farahani RM. Cannibalized erythroblasts accelerate developmental neurogenesis by regulating mitochondrial dynamics. Cell Rep 2021; 35:108942. [PMID: 33826895 DOI: 10.1016/j.celrep.2021.108942] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/18/2020] [Accepted: 03/12/2021] [Indexed: 11/29/2022] Open
Abstract
Metabolic support was long considered to be the only developmental function of hematopoiesis, a view that is gradually changing. Here, we disclose a mechanism triggered during neurulation that programs brain development by donation of sacrificial yolk sac erythroblasts to neuroepithelial cells. At embryonic day (E) 8.5, neuroepithelial cells transiently integrate with the endothelium of yolk sac blood vessels and cannibalize intravascular erythroblasts as transient heme-rich endosymbionts. This cannibalistic behavior instructs precocious neuronal differentiation of neuroepithelial cells in the proximity of blood vessels. By experiments in vitro, we show that access to erythroblastic heme accelerates the pace of neurogenesis by induction of a truncated neurogenic differentiation program from a poised state. Mechanistically, the poised state is invoked by activation of the mitochondrial electron transport chain that leads to amplified production of reactive oxygen species in addition to omnipresent guanosine triphosphate (GTP) with consequential upregulation of pro-differentiation β-catenin.
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Affiliation(s)
- Şükran Özsoy
- IDR/Westmead Institute for Medical Research, Westmead, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Filip Vujovic
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Mary Simonian
- IDR/Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Valentina Valova
- Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Ramin M Farahani
- IDR/Westmead Institute for Medical Research, Westmead, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
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15
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Peng X, Wang T, Gao H, Yue X, Bian W, Mei J, Zhang Y. The interplay between IQGAP1 and small GTPases in cancer metastasis. Biomed Pharmacother 2021; 135:111243. [PMID: 33434854 DOI: 10.1016/j.biopha.2021.111243] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/27/2020] [Accepted: 12/31/2020] [Indexed: 01/07/2023] Open
Abstract
The metastatic spread of tumor cells to distant anatomical locations is a critical cause for disease progression and leads to more than 90 % of cancer-related deaths. IQ motif-containing GTPase-activating protein 1 (IQGAP1), a prominent regulator in the cancer metastasis process, is a scaffold protein that interacts with components of the cytoskeleton. As a critical node within the small GTPase network, IQGAP1 acts as a binding partner of several small GTPases, which in turn function as molecular switches to control most cellular processes, including cell migration and invasion. Given the significant interaction between IQGAP1 and small GTPases in cancer metastasis, we briefly elucidate the role of IQGAP1 in regulating cancer metastasis and the varied interactions existing between IQGAP1 and small GTPases. In addition, the potential regulators for IQGAP1 activity and its interaction with small GTPases are also incorporated in this review. Overall, we comprehensively summarize the role of IQGAP1 in cancer tumorigenicity and metastasis, which may be a potential anti-tumor target to restrain cancer progression.
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Affiliation(s)
- Xiafeng Peng
- Department of Gynecology and Obstetrics, Wuxi Maternal and Child Health Hospital, the Affiliated Hospital to Nanjing Medical University, Wuxi, 214023, China; First Clinical Medicine College, Nanjing Medical University, Nanjing, 211166, China.
| | - Tiejun Wang
- Department of Gynecology and Obstetrics, Wuxi Maternal and Child Health Hospital, the Affiliated Hospital to Nanjing Medical University, Wuxi, 214023, China.
| | - Han Gao
- School of Medicine, Jiangnan University, Wuxi, 214122, China.
| | - Xin Yue
- First Clinical Medicine College, Nanjing Medical University, Nanjing, 211166, China.
| | - Weiqi Bian
- First Clinical Medicine College, Nanjing Medical University, Nanjing, 211166, China.
| | - Jie Mei
- Department of Gynecology and Obstetrics, Wuxi Maternal and Child Health Hospital, the Affiliated Hospital to Nanjing Medical University, Wuxi, 214023, China; Wuxi Clinical Medical College, Nanjing Medical University, Wuxi, 214023, China.
| | - Yan Zhang
- Department of Gynecology and Obstetrics, Wuxi Maternal and Child Health Hospital, the Affiliated Hospital to Nanjing Medical University, Wuxi, 214023, China.
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16
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Haspel N, Jang H, Nussinov R. Active and Inactive Cdc42 Differ in Their Insert Region Conformational Dynamics. Biophys J 2021; 120:306-318. [PMID: 33347888 PMCID: PMC7840443 DOI: 10.1016/j.bpj.2020.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 12/26/2022] Open
Abstract
Cell division control protein 42 homolog (Cdc42) protein, a Ras superfamily GTPase, regulates cellular activities, including cancer progression. Using all-atom molecular dynamics (MD) simulations and essential dynamic analysis, we investigated the structure and dynamics of the catalytic domains of GDP-bound (inactive) and GTP-bound (active) Cdc42 in solution. We discovered substantial differences in the dynamics of the inactive and active forms, particularly in the "insert region" (residues 122-135), which plays a role in Cdc42 activation and binding to effectors. The insert region has larger conformational flexibility in the GDP-bound Cdc42 than in the GTP-bound Cdc42. The G2 loop and switch I at the effector lobe of the catalytic domain exhibit large conformational changes in both the GDP- and the GTP-bound systems, but in the GTP-bound Cdc42, the switch I interactions with GTP are retained. Oncogenic mutations were identified in the Ras superfamily. In Cdc42, the G12V and Q61L mutations decrease the GTPase activity. We simulated these mutations in both GDP- and GTP-bound Cdc42. Although the overall structural organization is quite similar between the wild type and the mutants, there are small differences in the conformational dynamics, especially in the two switch regions. Taken together, the G12V and Q61L mutations may play a role similar to their K-Ras counterparts in nucleotide binding and activation. The conformational differences, which are mainly in the insert region and, to a lesser extent, in the switch regions flanking the nucleotide binding site, can shed light on binding and activation. We propose that the differences are due to a network of hydrogen bonds that gets disrupted when Cdc42 is bound to GDP, a disruption that does not exist in other Rho GTPases. The differences in the dynamics between the two Cdc42 states suggest that the inactive conformation has reduced ability to bind to effectors.
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Affiliation(s)
- Nurit Haspel
- Department of Computer Science, University of Massachusetts Boston, Boston, Massachusetts
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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17
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Construction of a Novel Multigene Panel Potently Predicting Poor Prognosis in Patients with Clear Cell Renal Cell Carcinoma. Cancers (Basel) 2020; 12:cancers12113471. [PMID: 33266355 PMCID: PMC7700485 DOI: 10.3390/cancers12113471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/02/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Clear cell renal cell carcinoma (ccRCC) is the predominant cause of kidney cancer death attributed to its prevalence (70%) and its nature being the most aggressive form of kidney cancer. Most ccRCC deaths are resulted from metastasis. It is essential to know which ccRCCs are at risk of metastasis and the development to lethal disease; however, our capacity for such analysis remains poor. To improve this diagnostic capacity, we have examined a comprehensive ccRCC dataset containing 512 patients and have produced a 9-gene signature. This signature is novel; all its 9 components genes are unknown to be related to ccRCC. Importantly, all 9 individual genes possess significant ability in diagnosis of ccRCC metastasis and fatality; the combination of these genes or this signature predicts deadly ccRCCs at an impressive efficiency. This research will open new avenues in ccRCC research and will have a major impact in reducing ccRCC-associated deaths. Abstract We observed associations of IQGAP1 downregulation with poor overall survival (OS) in clear cell renal cell carcinoma (ccRCC). Differentially expressed genes (DEGs, n = 611) were derived from ccRCCs with (n = 111) and without IQGAP1 (n = 397) reduction using the TCGA PanCancer Atlas ccRCC dataset. These DEGs exhibit downregulations of immune response and upregulations of DNA damage repair pathways. Through randomization of the TCGA dataset into a training and testing subpopulation, a 9-gene panel (SigIQGAP1NW) was derived; it predicts poor OS in training, testing, and the full population at a hazard ratio (HR) 2.718, p < 2 × 10−16, p = 1.08 × 10−5, and p < 2 × 10−16, respectively. SigIQGAP1NW independently associates with poor OS (HR 1.80, p = 2.85 × 10−6) after adjusting for a set of clinical features, and it discriminates ccRCC mortality at time-dependent AUC values of 70% at 13.8 months, 69%/31M, 69%/49M, and 75.3%/71M. All nine component genes of SigIQGAP1NW are novel to ccRCC. The inclusion of RECQL4 (a DNA helicase) in SigIQGAP1NW agrees with IQGAP1 DEGs enhancing DNA repair. THSD7A affects kidney function; its presence in SigIQGAP1NW is consistent with our observed THSD7A downregulation in ccRCC (n = 523) compared to non-tumor kidney tissues (n = 100). Collectively, we report a novel multigene panel that robustly predicts poor OS in ccRCC.
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18
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Zheng CW, Zeng RJ, Xu LY, Li EM. Rho GTPases: Promising candidates for overcoming chemotherapeutic resistance. Cancer Lett 2020; 475:65-78. [PMID: 31981606 DOI: 10.1016/j.canlet.2020.01.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/17/2020] [Accepted: 01/17/2020] [Indexed: 02/06/2023]
Abstract
Despite therapeutic advances, resistance to chemotherapy remains a major challenge to patients with malignancies. Rho GTPases are essential for the development and progression of various diseases including cancer, and a vast number of studies have linked Rho GTPases to chemoresistance. Therefore, understanding the underlying mechanisms can expound the effects of Rho GTPases towards chemotherapeutic agents, and targeting Rho GTPases is a promising strategy to downregulate the chemo-protective pathways and overcome chemoresistance. Importantly, exceptions in certain biological conditions and interactions among the members of Rho GTPases should be noted. In this review, we focus on the role of Rho GTPases, particularly Rac1, in regulating chemoresistance and provide an overview of their related mechanisms and available inhibitors, which may offer novel options for future targeted cancer therapy.
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Affiliation(s)
- Chun-Wen Zheng
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China; The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
| | - Rui-Jie Zeng
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China; The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
| | - Li-Yan Xu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China; Institute of Oncologic Pathology, Shantou University Medical College, Shantou, 515041, China.
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China; The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China.
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19
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Gorisse L, Li Z, Wagner CD, Worthylake DK, Zappacosta F, Hedman AC, Annan RS, Sacks DB. Ubiquitination of the scaffold protein IQGAP1 diminishes its interaction with and activation of the Rho GTPase CDC42. J Biol Chem 2020; 295:4822-4835. [PMID: 32094223 DOI: 10.1074/jbc.ra119.011491] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/19/2020] [Indexed: 12/12/2022] Open
Abstract
IQ motif-containing GTPase-activating protein 1 (IQGAP1) is a scaffold protein that interacts with numerous binding partners and thereby regulates fundamental biological processes. The functions of IQGAP1 are modulated by several mechanisms, including protein binding, self-association, subcellular localization, and phosphorylation. Proteome-wide screens have indicated that IQGAP1 is ubiquitinated, but the possible effects of this post-translational modification on its function are unknown. Here we characterized and evaluated the function of IQGAP1 ubiquitination. Using MS-based analysis in HEK293 cells, we identified six lysine residues (Lys-556, -1155, -1230, -1465, -1475, and -1528) as ubiquitination sites in IQGAP1. To elucidate the biological consequences of IQGAP1 ubiquitination, we converted each of these lysines to arginine and found that replacing two of these residues, Lys-1155 and Lys-1230, in the GAP-related domain of IQGAP1 (termed IQGAP1 GRD-2K) reduces its ubiquitination. Moreover, IQGAP1 GRD-2K bound a significantly greater proportion of the two Rho GTPases cell division cycle 42 (CDC42) and Rac family small GTPase 1 (RAC1) than did WT IQGAP1. Consistent with this observation, reconstitution of IQGAP1-null cells with IQGAP1 GRD-2K significantly increased the amount of active CDC42 and enhanced cell migration significantly more than WT IQGAP1. Our results reveal that ubiquitination of the CDC42 regulator IQGAP1 alters its ability to bind to and activate this GTPase, leading to physiological effects. Collectively, these findings expand our view of the role of ubiquitination in cell signaling and provide additional insight into CDC42 regulation.
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Affiliation(s)
- Laëtitia Gorisse
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland 20892
| | - Zhigang Li
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland 20892
| | - Craig D Wagner
- Discovery Analytical, GlaxoSmithKline, Collegeville, Pennsylvania 19426
| | - David K Worthylake
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences, New Orleans, Louisiana 70112
| | | | - Andrew C Hedman
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland 20892
| | - Roland S Annan
- Discovery Analytical, GlaxoSmithKline, Collegeville, Pennsylvania 19426
| | - David B Sacks
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland 20892
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20
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Trenton NJ, McLaughlin RT, Bellamkonda SK, Tsao DS, Rodzinski A, Mace EM, Orange JS, Schweikhard V, Diehl MR. Membrane and Actin Tethering Transitions Help IQGAP1 Coordinate GTPase and Lipid Messenger Signaling. Biophys J 2020; 118:586-599. [PMID: 31952801 PMCID: PMC7002982 DOI: 10.1016/j.bpj.2019.12.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/22/2019] [Accepted: 12/09/2019] [Indexed: 12/30/2022] Open
Abstract
The coordination of lipid messenger signaling with cytoskeletal regulation is central to many organelle-specific regulatory processes. This coupling often depends on the function of multidomain scaffolds that orchestrate transient interactions among multiple signaling intermediates and regulatory proteins on organelles. The number of possible scaffold interaction partners and the ability for these interactions to occur at different timescales makes investigations of scaffold functions challenging. This work employs live cell imaging to probe how the multidomain scaffold IQ motif containing GTPase activating protein 1 (IQGAP1) coordinates the activities of proteins affecting local actin polymerization, membrane processing, and phosphoinositide signaling. Using endosomes that are confined by a local actin network as a model system, we demonstrate that IQGAP1 can transition between different actin and endosomal membrane tethered states. Fast scaffold binding/disassociation transitions are shown to be driven by interactions between C-terminal scaffold domains and Rho GTPases at the membrane. Fluctuations in these binding modes are linked to negative regulation of actin polymerization. Although this control governs core elements of IQGAP1 dynamics, actin binding by the N-terminal calponin homology domain of the scaffold is shown to help the scaffold track the temporal development of endosome membrane markers, implying actin associations bolster membrane and actin coordination. Importantly, these effects are not easily distilled purely through standard (static) co-localization analyses or traditional pathway perturbations methods and were resolved by performing dynamic correlation and multiple regression analyses of IQGAP1 scaffold mutants. Using these capabilities with pharmacological inhibition, we provide evidence that membrane tethering is dependent on the activities of the lipid kinase phosphoinositide 3-kinase in addition to the Rho GTPases Rac1 and Cdc42. Overall, these methods and results point to a scaffold tethering mechanism that allows IQGAP1 to help control the amplitude of phosphoinositide lipid messenger signaling by coordinating signaling intermediate activities with the development and disassembly of local actin cytoskeletal networks.
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Affiliation(s)
| | - R Tyler McLaughlin
- Department of Bioengineering, Rice University, Houston, Texas; Graduate Program in Systems, Synthetic and Physical Biology, Rice University, Houston, Texas
| | | | - David S Tsao
- Department of Bioengineering, Rice University, Houston, Texas
| | | | - Emily M Mace
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
| | - Jordan S Orange
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
| | | | - Michael R Diehl
- Department of Bioengineering, Rice University, Houston, Texas; Graduate Program in Systems, Synthetic and Physical Biology, Rice University, Houston, Texas; Department of Chemistry, Rice University, Houston, Texas.
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21
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Rezaei-Lotfi S, Farahani RM. Coupled cycling and regulation of metazoan morphogenesis. Cell Div 2020; 15:1. [PMID: 32002022 PMCID: PMC6986050 DOI: 10.1186/s13008-020-0059-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/16/2020] [Indexed: 01/01/2023] Open
Abstract
Metazoan animals are characterized by restricted phenotypic heterogeneity (i.e. morphological disparity) of organisms within various species, a feature that contrasts sharply with intra-species morphological diversity observed in the plant kingdom. Robust emergence of morphogenic blueprint in metazoan animals reflects restricted autonomy of individual cells in adoption of fate outcomes such as differentiation. Fates of individual cells are linked to and influenced by fates of neighboring cells at the population level. Such coupling is a common property of all self-organising systems and propels emergence of order from simple interactions between individual cells without supervision by external directing forces. As a consequence of coupling, expected functional relationship between the constituent cells of an organ system is robustly established concurrent with multiple rounds of cell division during morphogenesis. Notably, the molecular regulation of multicellular coupling during morphogenic self-organisation remains largely unexplored. Here, we review the existing literature on multicellular self-organisation with particular emphasis on recent discovery that β-catenin is the key coupling factor that programs emergence of multi-cellular self-organisation by regulating synchronised cycling of individual cells.
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Affiliation(s)
| | - Ramin M Farahani
- IDR/Westmead Institute for Medical Research, Westmead, Australia.,2Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006 Australia
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22
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Zhang M, Li Z, Jang H, Hedman AC, Sacks DB, Nussinov R. Ca 2+-Dependent Switch of Calmodulin Interaction Mode with Tandem IQ Motifs in the Scaffolding Protein IQGAP1. Biochemistry 2019; 58:4903-4911. [PMID: 31724397 PMCID: PMC8195445 DOI: 10.1021/acs.biochem.9b00854] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
IQ domain GTPase-activating scaffolding protein 1 (IQGAP1) mediates cytoskeleton, cell migration, proliferation, and apoptosis events. Calmodulin (CaM) modulates IQGAP1 functions by binding to its four tandem IQ motifs. Exactly how CaM binds the IQ motifs and which functions of IQGAP1 CaM regulates and how are fundamental mechanistic questions. We combine experimental pull-down assays, mutational data, and molecular dynamics simulations to understand the IQ-CaM complexes with and without Ca2+ at the atomic level. Apo-CaM favors the IQ3 and IQ4 motifs but not the IQ1 and IQ2 motifs that lack two hydrophobic residues for interactions with apo-CaM's hydrophobic pocket. Ca2+-CaM binds all four IQ motifs, with both N- and C-lobes tightly wrapped around each motif. Ca2+ promotes IQ-CaM interactions and increases the amount of IQGAP1-loaded CaM for IQGAP1-mediated signaling. Collectively, we describe IQ-CaM binding in atomistic detail and feature the emergence of Ca2+ as a key modulator of the CaM-IQGAP1 interactions.
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Affiliation(s)
- Mingzhen Zhang
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 20892, United States
| | - Zhigang Li
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Hyunbum Jang
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Andrew C. Hedman
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - David B. Sacks
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ruth Nussinov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 20892, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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23
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Rezaei-Lotfi S, Hunter N, Farahani RM. Coupled cycling programs multicellular self-organization of neural progenitors. Cell Cycle 2019; 18:2040-2054. [PMID: 31286803 PMCID: PMC6681778 DOI: 10.1080/15384101.2019.1638692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 02/06/2023] Open
Abstract
Self-organization is central to the morphogenesis of multicellular organisms. However, the molecular platform that coordinates the robust emergence of complex morphological patterns from local interactions between cells remains unresolved. Here we demonstrate that neural self- organization is driven by coupled cycling of progenitor cells. In a coupled cycling mode, intercellular contacts relay extrinsic cues to override the intrinsic cycling rhythm of an individual cell and synchronize the population. The stringency of coupling and hence the synchronicity of the population is programmed by recruitment of a key coupler, β-catenin, into junctional complexes. As such, multicellular self-organization is driven by the same basic mathematical principle that governs synchronized behavior of macro-scale biological systems as diverse as the synchronized chirping of crickets, flashing of fireflies and schooling of fish; that is synchronization by coupling. It is proposed that coupled cycling foreshadows a fundamental adaptive change that facilitated evolution and diversification of multicellular life forms.
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Affiliation(s)
- Saba Rezaei-Lotfi
- IDR/Westmead Institute for Medical Research, Sydney, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research, Sydney, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Ramin M Farahani
- IDR/Westmead Institute for Medical Research, Sydney, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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24
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Scheffzek K, Shivalingaiah G. Ras-Specific GTPase-Activating Proteins-Structures, Mechanisms, and Interactions. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a031500. [PMID: 30104198 DOI: 10.1101/cshperspect.a031500] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ras-specific GTPase-activating proteins (RasGAPs) down-regulate the biological activity of Ras proteins by accelerating their intrinsic rate of GTP hydrolysis, basically by a transition state stabilizing mechanism. Oncogenic Ras is commonly not sensitive to RasGAPs caused by interference of mutants with the electronic or steric requirements of the transition state, resulting in up-regulation of activated Ras in respective cells. RasGAPs are modular proteins containing a helical catalytic RasGAP module surrounded by smaller domains that are frequently involved in the subcellular localization or contributing to regulatory features of their host proteins. In this review, we summarize current knowledge about RasGAP structure, mechanism, regulation, and dual-substrate specificity and discuss in some detail neurofibromin, one of the most important negative Ras regulators in cellular growth control and neuronal function.
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Affiliation(s)
- Klaus Scheffzek
- Division of Biological Chemistry (Biocenter), Medical University of Innsbruck, A-6020 Innsbruck, Austria
| | - Giridhar Shivalingaiah
- Division of Biological Chemistry (Biocenter), Medical University of Innsbruck, A-6020 Innsbruck, Austria
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25
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Xie Y, Zheng L, Tao L. Downregulation of IQGAP2 Correlates with Prostate Cancer Recurrence and Metastasis. Transl Oncol 2018; 12:236-244. [PMID: 30428404 PMCID: PMC6232700 DOI: 10.1016/j.tranon.2018.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 01/01/2023] Open
Abstract
IQGAP2 was recently reported as a tumor suppressor of prostate cancer (PC). Nonetheless, its clinical implications remain unknown. To address this issue, we extracted data related to IQGAP2 mRNA expression and genomic alterations from multiple large datasets within the Oncomine and cBioPortal databases and performed in silico analyses to determine a potential association of IQGAP2 mRNA expression and its genomic alterations with PC progression. In 4 cohorts consisting of 118 normal prostate tissues and 277 PCs, IQGAP2 mRNA expression was significantly elevated particularly in low-grade (primary Gleason score ≤3) PCs; these changes separate PC from normal tissues with area under curve values of 0.7-0.8. Significant reductions in IQGAP2 mRNA levels and gene copy number occurred in more than 70 metastases compared to at least 230 local PCs. This duo-alteration in IQGAP2 expression supports IQGAP2 elevation suppressing and its downregulation facilitating PC progression. Deletion and missense mutations were detected in 23 of 492 primary PCs; these alterations significantly associate with PC recurrence (HR=2.71; 95% CI: 1.35-5.44; P=.005) after adjusting for known risk factors and correlate with reductions in disease-free survival (DFS, P=.002). IQGAP2 (5q13.3) genomic alterations were observed in SPOP-marked PCs and co-occurred with deletion in the RN7SK (16p12.2), SNORA50A (16q21), and SNORA50C (17q23.3) genes; the co-occurrence associated with reductions in DFS (P=4.14e-4). In two independent PC populations, MSKCC (n=130) and TCGA provisional (n=490), reductions in IQGAP2 mRNA expression were significantly associated with DFS. Collectively, this investigation reveals an association of IQGAP2 with PC progression.
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Affiliation(s)
- Yanyun Xie
- Division of Nephrology, Xiangya Hospital, Central South University, Hunan, Changsha, China.
| | - Linfeng Zheng
- Division of Nephrology, Xiangya Hospital, Central South University, Hunan, Changsha, China
| | - Lijian Tao
- Division of Nephrology, Xiangya Hospital, Central South University, Hunan, Changsha, China
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26
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Ozdemir ES, Jang H, Gursoy A, Keskin O, Li Z, Sacks DB, Nussinov R. Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2. J Biol Chem 2018; 293:3685-3699. [PMID: 29358323 PMCID: PMC5846150 DOI: 10.1074/jbc.ra117.001596] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/12/2018] [Indexed: 12/22/2022] Open
Abstract
IQ motif-containing GTPase-activating proteins (IQGAPs) are scaffolding proteins playing central roles in cell-cell adhesion, polarity, and motility. The Rho GTPases Cdc42 and Rac1, in their GTP-bound active forms, interact with all three human IQGAPs. The IQGAP-Cdc42 interaction promotes metastasis by enhancing actin polymerization. However, despite their high sequence identity, Cdc42 and Rac1 differ in their interactions with IQGAP. Two Cdc42 molecules can bind to the Ex-domain and the RasGAP site of the GTPase-activating protein (GAP)-related domain (GRD) of IQGAP and promote IQGAP dimerization. Only one Rac1 molecule might bind to the RasGAP site of GRD and may not facilitate the dimerization, and the exact mechanism of Cdc42 and Rac1 binding to IQGAP is unclear. Using all-atom molecular dynamics simulations, site-directed mutagenesis, and Western blotting, we unraveled the detailed mechanisms of Cdc42 and Rac1 interactions with IQGAP2. We observed that Cdc42 binding to the Ex-domain of GRD of IQGAP2 (GRD2) releases the Ex-domain at the C-terminal region of GRD2, facilitating IQGAP2 dimerization. Cdc42 binding to the Ex-domain promoted allosteric changes in the RasGAP site, providing a binding site for the second Cdc42 in the RasGAP site. Of note, the Cdc42 "insert loop" was important for the interaction of the first Cdc42 with the Ex-domain. By contrast, differences in Rac1 insert-loop sequence and structure precluded its interaction with the Ex-domain. Rac1 could bind only to the RasGAP site of apo-GRD2 and could not facilitate IQGAP2 dimerization. Our detailed mechanistic insights help decipher how Cdc42 can stimulate actin polymerization in metastasis.
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Affiliation(s)
- E Sila Ozdemir
- From the Departments of Chemical and Biological Engineering and
| | - Hyunbum Jang
- the Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, NCI-Frederick, Frederick, Maryland 21702
| | - Attila Gursoy
- Computer Engineering, Koc University, Istanbul 34450, Turkey,
| | - Ozlem Keskin
- From the Departments of Chemical and Biological Engineering and
| | - Zhigang Li
- the Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland 20892, and
| | - David B Sacks
- the Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Ruth Nussinov
- the Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, NCI-Frederick, Frederick, Maryland 21702,
- the Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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27
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Abstract
How do Ras isoforms attain oncogenic specificity at the membrane? Oncogenic KRas, HRas, and NRas (K-Ras, H-Ras, and N-Ras) differentially populate distinct cancers. How they selectively activate effectors and why is KRas4B the most prevalent are highly significant questions. Here, we consider determinants that may bias isoform-specific effector activation and signaling at the membrane. We merge functional data with a conformational view to provide mechanistic insight. Cell-specific expression levels, pathway cross-talk, and distinct interactions are the key, but conformational trends can modulate selectivity. There are two major pathways in oncogenic Ras-driven proliferation: MAPK (Raf/MEK/ERK) and PI3Kα/Akt/mTOR. All membrane-anchored, proximally located, oncogenic Ras isoforms can promote Raf dimerization and fully activate MAPK signaling. So why the differential statistics of oncogenic isoforms in distinct cancers and what makes KRas so highly oncogenic? Many cell-specific factors may be at play, including higher KRAS mRNA levels. As a key factor, we suggest that because only KRas4B binds calmodulin, only KRas can fully activate PI3Kα/Akt signaling. We propose that full activation of both MAPK and PI3Kα/Akt proliferative pathways by oncogenic KRas4B-but not by HRas or NRas-may help explain why the KRas4B isoform is especially highly populated in certain cancers. We further discuss pharmacologic implications. Cancer Res; 78(3); 593-602. ©2017 AACR.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland. .,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
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28
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Nussinov R, Tsai CJ, Jang H. Oncogenic Ras Isoforms Signaling Specificity at the Membrane. Cancer Res 2018; 78:593-602. [PMID: 29273632 PMCID: PMC5811325 DOI: 10.1158/0008-5472.can-17-2727] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/13/2017] [Accepted: 11/10/2017] [Indexed: 01/21/2023]
Abstract
How do Ras isoforms attain oncogenic specificity at the membrane? Oncogenic KRas, HRas, and NRas (K-Ras, H-Ras, and N-Ras) differentially populate distinct cancers. How they selectively activate effectors and why is KRas4B the most prevalent are highly significant questions. Here, we consider determinants that may bias isoform-specific effector activation and signaling at the membrane. We merge functional data with a conformational view to provide mechanistic insight. Cell-specific expression levels, pathway cross-talk, and distinct interactions are the key, but conformational trends can modulate selectivity. There are two major pathways in oncogenic Ras-driven proliferation: MAPK (Raf/MEK/ERK) and PI3Kα/Akt/mTOR. All membrane-anchored, proximally located, oncogenic Ras isoforms can promote Raf dimerization and fully activate MAPK signaling. So why the differential statistics of oncogenic isoforms in distinct cancers and what makes KRas so highly oncogenic? Many cell-specific factors may be at play, including higher KRAS mRNA levels. As a key factor, we suggest that because only KRas4B binds calmodulin, only KRas can fully activate PI3Kα/Akt signaling. We propose that full activation of both MAPK and PI3Kα/Akt proliferative pathways by oncogenic KRas4B-but not by HRas or NRas-may help explain why the KRas4B isoform is especially highly populated in certain cancers. We further discuss pharmacologic implications. Cancer Res; 78(3); 593-602. ©2017 AACR.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
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29
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Abstract
The specific and rapid formation of protein complexes, involving IQGAP family proteins, is essential for diverse cellular processes, such as adhesion, polarization, and directional migration. Although CDC42 and RAC1, prominent members of the RHO GTPase family, have been implicated in binding to and activating IQGAP1, the exact nature of this protein-protein recognition process has remained obscure. Here, we propose a mechanistic framework model that is based on a multiple-step binding process, which is a prerequisite for the dynamic functions of IQGAP1 as a scaffolding protein and a critical mechanism in temporal regulation and integration of cellular pathways.
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Affiliation(s)
- Kazem Nouri
- Institute of Biochemistry and Molecular Biology II, Medical faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - David J Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton, BN2 4GJ, United Kingdom
| | - Mohammad R Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical faculty of the Heinrich-Heine University, Düsseldorf, Germany
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30
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Samson EB, Tsao DS, Zimak J, McLaughlin RT, Trenton NJ, Mace EM, Orange JS, Schweikhard V, Diehl MR. The coordinating role of IQGAP1 in the regulation of local, endosome-specific actin networks. Biol Open 2017; 6:785-799. [PMID: 28455356 PMCID: PMC5483015 DOI: 10.1242/bio.022624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 04/12/2017] [Indexed: 12/27/2022] Open
Abstract
IQGAP1 is a large, multi-domain scaffold that helps orchestrate cell signaling and cytoskeletal mechanics by controlling interactions among a spectrum of receptors, signaling intermediates, and cytoskeletal proteins. While this coordination is known to impact cell morphology, motility, cell adhesion, and vesicular traffic, among other functions, the spatiotemporal properties and regulatory mechanisms of IQGAP1 have not been fully resolved. Herein, we describe a series of super-resolution and live-cell imaging analyses that identified a role for IQGAP1 in the regulation of an actin cytoskeletal shell surrounding a novel membranous compartment that localizes selectively to the basal cortex of polarized epithelial cells (MCF-10A). We also show that IQGAP1 appears to both stabilize the actin coating and constrain its growth. Loss of compartmental IQGAP1 initiates a disassembly mechanism involving rapid and unconstrained actin polymerization around the compartment and dispersal of its vesicle contents. Together, these findings suggest IQGAP1 achieves this control by harnessing both stabilizing and antagonistic interactions with actin. They also demonstrate the utility of these compartments for image-based investigations of the spatial and temporal dynamics of IQGAP1 within endosome-specific actin networks.
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Affiliation(s)
- Edward B Samson
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - David S Tsao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Jan Zimak
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - R Tyler McLaughlin
- Graduate Program in Systems, Synthetic and Physical Biology, Rice University, Houston, TX 77030, USA
| | | | - Emily M Mace
- Center for Human Immunobiology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA
| | - Jordan S Orange
- Center for Human Immunobiology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA
| | | | - Michael R Diehl
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
- Department of Chemistry, Rice University, Houston, TX 77030, USA
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31
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Liu J, Kurella VB, LeCour L, Vanagunas T, Worthylake DK. The IQGAP1 N-Terminus Forms Dimers, and the Dimer Interface Is Required for Binding F-Actin and Calcium-Bound Calmodulin. Biochemistry 2016; 55:6433-6444. [PMID: 27798963 DOI: 10.1021/acs.biochem.6b00745] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
IQGAP1 is a multidomain scaffold protein involved in many cellular processes. We have determined the crystal structure of an N-terminal fragment spanning residues 1-191 (CHDF hereafter) that contains the entire calponin homology domain. The structure of the CHDF is very similar to those of other type 3 calponin homology domains like those from calponin, Vav, and the yeast IQGAP1 ortholog Rng2. However, in the crystal, two CHDF molecules form a "head-to-head" or parallel dimer through mostly hydrophobic interactions. Binding experiments indicate that the CHDF binds to both F-actin and Ca2+/calmodulin, but binding is mutually exclusive. On the basis of the structure, two dimer interface substitutions were introduced. While CHDFL157D disrupts the dimer in gel filtration experiments, oxidized CHDFK161C stabilizes the dimer. These results imply that the CHDF forms the same dimer in solution that is seen in the crystal structure. The disulfide-stabilized dimer displays a reduced level of F-actin binding in sedimentation assays and shows no binding to Ca2+/calmodulin in isothermal titration calorimetry (ITC) experiments, indicating that interface residues are utilized for both binding events. The Calmodulin Target Database predicts that residues 93KK94 are important for CaM binding, and indeed, the 93EE94 double mutation displays a reduced level of binding to Ca2+/calmodulin in ITC experiments. Our results indicate that the CHDF dimer interface is used for both F-actin and Ca2+/calmodulin binding, and the 93KK94 pair, near the interface, is also used for Ca2+/calmodulin binding. These results are also consistent with full-length IQGAP1 forming a parallel homodimer.
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Affiliation(s)
- Jing Liu
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center-New Orleans , 1901 Perdido Street, New Orleans, Louisiana 70112, United States
| | - Vinodh B Kurella
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center-New Orleans , 1901 Perdido Street, New Orleans, Louisiana 70112, United States
| | - Louis LeCour
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center-New Orleans , 1901 Perdido Street, New Orleans, Louisiana 70112, United States
| | - Tomas Vanagunas
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center-New Orleans , 1901 Perdido Street, New Orleans, Louisiana 70112, United States
| | - David K Worthylake
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center-New Orleans , 1901 Perdido Street, New Orleans, Louisiana 70112, United States
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32
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Nouri K, Fansa EK, Amin E, Dvorsky R, Gremer L, Willbold D, Schmitt L, Timson DJ, Ahmadian MR. IQGAP1 Interaction with RHO Family Proteins Revisited: KINETIC AND EQUILIBRIUM EVIDENCE FOR MULTIPLE DISTINCT BINDING SITES. J Biol Chem 2016; 291:26364-26376. [PMID: 27815503 PMCID: PMC5159498 DOI: 10.1074/jbc.m116.752121] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/27/2016] [Indexed: 11/16/2022] Open
Abstract
IQ motif-containing GTPase activating protein 1 (IQGAP1) plays a central role in the physical assembly of relevant signaling networks that are responsible for various cellular processes, including cell adhesion, polarity, and transmigration. The RHO family proteins CDC42 and RAC1 have been shown to mainly interact with the GAP-related domain (GRD) of IQGAP1. However, the role of its RASGAP C-terminal (RGCT) and C-terminal domains in the interactions with RHO proteins has remained obscure. Here, we demonstrate that IQGAP1 interactions with RHO proteins underlie a multiple-step binding mechanism: (i) a high affinity, GTP-dependent binding of RGCT to the switch regions of CDC42 or RAC1 and (ii) a very low affinity binding of GRD and a C terminus adjacent to the switch regions. These data were confirmed by phosphomimetic mutation of serine 1443 to glutamate within RGCT, which led to a significant reduction of IQGAP1 affinity for CDC42 and RAC1, clearly disclosing the critical role of RGCT for these interactions. Unlike CDC42, an extremely low affinity was determined for the RAC1-GRD interaction, suggesting that the molecular nature of IQGAP1 interaction with CDC42 partially differs from that of RAC1. Our study provides new insights into the interaction characteristics of IQGAP1 with RHO family proteins and highlights the complementary importance of kinetic and equilibrium analyses. We propose that the ability of IQGAP1 to interact with RHO proteins is based on a multiple-step binding process, which is a prerequisite for the dynamic functions of IQGAP1 as a scaffolding protein and a critical mechanism in temporal regulation and integration of IQGAP1-mediated cellular responses.
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Affiliation(s)
- Kazem Nouri
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Eyad K Fansa
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Ehsan Amin
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Radovan Dvorsky
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Lothar Gremer
- the Institute of Physical Biology, Heinrich-Heine University, 40225 Düsseldorf, Germany.,Forschungszentrum Jülich, ICS-6, 52428 Jülich, Germany
| | - Dieter Willbold
- the Institute of Physical Biology, Heinrich-Heine University, 40225 Düsseldorf, Germany.,Forschungszentrum Jülich, ICS-6, 52428 Jülich, Germany
| | - Lutz Schmitt
- the Institute of Biochemistry, Heinrich-Heine University, 40225 Düsseldorf, Germany, and
| | - David J Timson
- the School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, United Kingdom
| | - Mohammad R Ahmadian
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, 40225 Düsseldorf, Germany,
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