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Araya MK, Chen W, Ke Y, Zhou Y, Gorfe AA, Hancock JF, Liu J. Differential Lipid Binding Specificities of RAP1A and RAP1B are Encoded by the Amino Acid Sequence of the Membrane Anchors. J Am Chem Soc 2024. [PMID: 39001846 DOI: 10.1021/jacs.4c02183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
RAP1 proteins belong to the RAS family of small GTPases that operate as molecular switches by cycling between GDP-bound inactive and GTP-bound active states. The C-terminal anchors of RAP1 proteins are known to direct membrane localization, but how these anchors organize RAP1 on the plasma membrane (PM) has not been investigated. Using high-resolution imaging, we show that RAP1A and RAP1B form spatially segregated nanoclusters on the inner leaflet of the PM, with further lateral segregation between GDP-bound and GTP-bound proteins. The C-terminal polybasic anchors of RAP1A and RAP1B differ in their amino acid sequences and exhibit different lipid binding specificities, which can be modified by single-point mutations in the respective polybasic domains (PBD). Molecular dynamics simulations reveal that single PBD mutations substantially reduce the interactions of the membrane anchors with the PM lipid phosphatidylserine. In summary, we show that aggregate lipid binding specificity encoded within the C-terminal anchor determines PM association and nanoclustering of RAP1A and RAP1B. Taken together with previous observations on RAC1 and KRAS, the study reveals that the PBD sequences of small GTPase membrane anchors can encode distinct lipid binding specificities that govern PM interactions.
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Affiliation(s)
- Mussie K Araya
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Wei Chen
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Yuepeng Ke
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas 77030, United States
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, Texas 77030, United States
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas 77030, United States
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, Texas 77030, United States
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
- Graduate School of Biological Sciences, M. D. Anderson Cancer Center and University of Texas Health Science Center, Houston, Texas 77030, United States
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
- Graduate School of Biological Sciences, M. D. Anderson Cancer Center and University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Junchen Liu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
- Graduate School of Biological Sciences, M. D. Anderson Cancer Center and University of Texas Health Science Center, Houston, Texas 77030, United States
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2
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Lee AA, Kim NH, Alvarez S, Ren H, DeGrandchamp JB, Lew LJN, Groves JT. Bimodality in Ras signaling originates from processivity of the Ras activator SOS without deterministic bistability. SCIENCE ADVANCES 2024; 10:eadi0707. [PMID: 38905351 PMCID: PMC11192083 DOI: 10.1126/sciadv.adi0707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 05/15/2024] [Indexed: 06/23/2024]
Abstract
Ras is a small GTPase that is central to important functional decisions in diverse cell types. An important aspect of Ras signaling is its ability to exhibit bimodal or switch-like activity. We describe the total reconstitution of a receptor-mediated Ras activation-deactivation reaction catalyzed by SOS and p120-RasGAP on supported lipid membrane microarrays. The results reveal a bimodal Ras activation response, which is not a result of deterministic bistability but is rather driven by the distinct processivity of the Ras activator, SOS. Furthermore, the bimodal response is controlled by the condensation state of the scaffold protein, LAT, to which SOS is recruited. Processivity-driven bimodality leads to stochastic bursts of Ras activation even under strongly deactivating conditions. This behavior contrasts deterministic bistability and may be more resistant to pharmacological inhibition.
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Affiliation(s)
- Albert A. Lee
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Neil H. Kim
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Steven Alvarez
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA
| | - He Ren
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | | | - L. J. Nugent Lew
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Jay T. Groves
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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3
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Arora N, Liang H, Yao W, Ying H, Liu J, Zhou Y. Lysophosphatidylcholine acyltransferase 1 suppresses nanoclustering and function of KRAS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596653. [PMID: 38853864 PMCID: PMC11160780 DOI: 10.1101/2024.05.30.596653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
KRAS is frequently mutated in cancer, contributing to 20% of all human cancer especially pancreatic, colorectal and lung cancer. Signaling of the constitutively active KRAS oncogenic mutants is mostly compartmentalized to proteolipid nanoclusters on the plasma membrane (PM). Signaling nanoclusters of many KRAS mutants selectively enrich phosphatidylserine (PS) lipids with unsaturated sn-2 acyl chains, but not the fully saturated PS species. Thus, remodeling PS acyl chains may suppress KRAS oncogenesis. Lysophosphatidylcholine acyltransferases (LPCATs) remodel sn-2 acyl chains of phospholipids, with LPCAT1 preferentially generating the fully saturated lipids. Here, we show that stable expression of LPCAT1 depletes major PS species with unsaturated sn-2 chains while decreasing minor phosphatidylcholine (PC) species with the corresponding acyl chains. LPCAT1 expression more effectively disrupts the nanoclustering of oncogenic GFP-KRASG12V, which is restored by acute addback of exogenous unsaturated PS. LPCAT1 expression compromises signaling and oncogenic activities of the KRAS-dependent pancreatic tumor lines. LPCAT1 expression sensitizes human pancreatic tumor MiaPaCa-2 cells to KRASG12C specific inhibitor, Sotorasib. Statistical analyses of patient data further reveal that pancreatic cancer patients with KRAS mutations express less LPCAT1. Higher LPCAT1 expression also improves survival probability of pancreatic and lung adenocarcinoma patients with KRAS mutations. Thus, PS acyl chain remodeling selectively suppresses KRAS oncogenesis.
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Affiliation(s)
- Neha Arora
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Wantong Yao
- Department of Translational Molecular Pathology, Division of Pathology-Lab Medicine Div, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Haoqiang Ying
- Department of Molecular and Cellular Oncology, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Junchen Liu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
- Program of Biochemistry and Cell Biology, Graduate School of Biological Sciences, M. D. Anderson Cancer Center and University of Texas Health Science Center, Houston, Texas, USA
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4
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Liu NF, Enomoto M, Marshall CB, Ikura M. Reconstitution and characterization of BRAF in complex with 14-3-3 and KRAS4B on nanodiscs. Protein Sci 2024; 33:e5016. [PMID: 38747381 PMCID: PMC11094772 DOI: 10.1002/pro.5016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/17/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024]
Abstract
RAF kinases are key components of the RAS-MAPK signaling pathway, which drives cell growth and is frequently overactivated in cancer. Upstream signaling activates the small GTPase RAS, which recruits RAF to the cell membrane, driving a transition of the latter from an auto-inhibited monomeric conformation to an active dimer. Despite recent progress, mechanistic details underlying RAF activation remain unclear, particularly the role of RAS and the membrane in mediating this conformational rearrangement of RAF together with 14-3-3 to permit RAF kinase domain dimerization. Here, we reconstituted an active complex of dimeric BRAF, a 14-3-3 dimer and two KRAS4B on a nanodisc bilayer and verified that its assembly is GTP-dependent. Biolayer interferometry (BLI) was used to compare the binding affinities of monomeric versus dimeric full-length BRAF:14-3-3 complexes for KRAS4B-conjugated nanodiscs (RAS-ND) and to investigate the effects of membrane lipid composition and spatial density of KRAS4B on binding. 1,2-Dioleoyl-sn-glycero-3-phospho-L-serine (DOPS) and higher KRAS4B density enhanced the interaction of BRAF:14-3-3 with RAS-ND to different degrees depending on BRAF oligomeric state. We utilized our reconstituted system to dissect the effects of KRAS4B and the membrane on the kinase activity of monomeric and dimeric BRAF:14-3-3 complexes, finding that KRAS4B or nanodiscs alone were insufficient to stimulate activity, whereas RAS-ND increased activity of both states of BRAF. The reconstituted assembly of full-length BRAF with 14-3-3 and KRAS on a cell-free, defined lipid bilayer offers a more holistic biophysical perspective to probe regulation of this multimeric signaling complex at the membrane surface.
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Affiliation(s)
- Ningdi F. Liu
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoOntarioCanada
| | - Masahiro Enomoto
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
| | | | - Mitsuhiko Ikura
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoOntarioCanada
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5
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Arora N, Mu H, Liang H, Zhao W, Zhou Y. RAS G-domains allosterically contribute to the recognition of lipid headgroups and acyl chains. J Cell Biol 2024; 223:e202307121. [PMID: 38334958 PMCID: PMC10857904 DOI: 10.1083/jcb.202307121] [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: 08/17/2023] [Revised: 12/15/2023] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
Mutant RAS are major contributors to cancer and signal primarily from nanoclusters on the plasma membrane (PM). Their C-terminal membrane anchors are main features of membrane association. However, the same RAS isoform bound to different guanine nucleotides spatially segregate. Different RAS nanoclusters all enrich a phospholipid, phosphatidylserine (PS). These findings suggest more complex membrane interactions. Our electron microscopy-spatial analysis shows that wild-types, G12V mutants, and membrane anchors of isoforms HRAS, KRAS4A, and KRAS4B prefer distinct PS species. Mechanistically, reorientation of KRAS4B G-domain exposes distinct residues, such as Arg 135 in orientation state 1 (OS1) and Arg 73/Arg 102 in OS2, to the PM and differentially facilitates the recognition of PS acyl chains. Allele-specific oncogenic mutations of KRAS4B also shift G-domain reorientation equilibrium. Indeed, KRAS4BG12V, KRAS4BG12D, KRAS4BG12C, KRAS4BG13D, and KRAS4BQ61H associate with PM lipids with headgroup and acyl chain specificities. Distribution of these KRAS4B oncogenic mutants favors different nanoscale membrane topography. Thus, RAS G-domains allosterically facilitate membrane lateral distribution.
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Affiliation(s)
- Neha Arora
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Huanwen Mu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Wenting Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, Singapore
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
- Program of Molecular and Translational Biology, Graduate School of Biological Sciences, M.D. Anderson Cancer Center and University of Texas Health Science Center, Houston, TX, USA
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6
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Erazo-Oliveras A, Muñoz-Vega M, Salinas ML, Wang X, Chapkin RS. Dysregulation of cellular membrane homeostasis as a crucial modulator of cancer risk. FEBS J 2024; 291:1299-1352. [PMID: 36282100 PMCID: PMC10126207 DOI: 10.1111/febs.16665] [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: 06/18/2022] [Revised: 09/09/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
Cellular membranes serve as an epicentre combining extracellular and cytosolic components with membranous effectors, which together support numerous fundamental cellular signalling pathways that mediate biological responses. To execute their functions, membrane proteins, lipids and carbohydrates arrange, in a highly coordinated manner, into well-defined assemblies displaying diverse biological and biophysical characteristics that modulate several signalling events. The loss of membrane homeostasis can trigger oncogenic signalling. More recently, it has been documented that select membrane active dietaries (MADs) can reshape biological membranes and subsequently decrease cancer risk. In this review, we emphasize the significance of membrane domain structure, organization and their signalling functionalities as well as how loss of membrane homeostasis can steer aberrant signalling. Moreover, we describe in detail the complexities associated with the examination of these membrane domains and their association with cancer. Finally, we summarize the current literature on MADs and their effects on cellular membranes, including various mechanisms of dietary chemoprevention/interception and the functional links between nutritional bioactives, membrane homeostasis and cancer biology.
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Affiliation(s)
- Alfredo Erazo-Oliveras
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Mónica Muñoz-Vega
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Michael L. Salinas
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Xiaoli Wang
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Robert S. Chapkin
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
- Center for Environmental Health Research; Texas A&M University; College Station, Texas, 77843; USA
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7
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Kervin TA, Overduin M. Membranes are functionalized by a proteolipid code. BMC Biol 2024; 22:46. [PMID: 38414038 PMCID: PMC10898092 DOI: 10.1186/s12915-024-01849-6] [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: 10/02/2023] [Accepted: 02/16/2024] [Indexed: 02/29/2024] Open
Abstract
Membranes are protein and lipid structures that surround cells and other biological compartments. We present a conceptual model wherein all membranes are organized into structural and functional zones. The assembly of zones such as receptor clusters, protein-coated pits, lamellipodia, cell junctions, and membrane fusion sites is explained to occur through a protein-lipid code. This challenges the theory that lipids sort proteins after forming stable membrane subregions independently of proteins.
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Affiliation(s)
- Troy A Kervin
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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8
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Garcia-Parajo MF, Mayor S. The ubiquitous nanocluster: A molecular scale organizing principle that governs cellular information flow. Curr Opin Cell Biol 2024; 86:102285. [PMID: 38056142 DOI: 10.1016/j.ceb.2023.102285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 12/08/2023]
Abstract
The language of biology at the scale of the cell is constituted of alphabets represented by biomolecules. These are stitched together in a variety of ways to create meaning. We argue that the phrases of this language are nanoscale molecular assemblies or nano-hubs for the purpose of information flow. At the cell surface information is sensed and processed via membrane receptors, often configured as multimers. These nano-assemblies serve as receiver nano-hubs, which are flexibly configured with additional nano-hubs that we term modifiers and transducers. This framework serves to process information that is transmitted for execution inside the cell. Here, we explore some examples about how nano-hubs are built and how they may contribute to cellular information flow.
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Affiliation(s)
- Maria F Garcia-Parajo
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Satyajit Mayor
- National Centre for Biological Sciences, 560065 Bangalore, India.
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9
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Li C, Quintana Perez Y, Lamaze C, Blouin CM. Lipid nanodomains and receptor signaling: From actin-based organization to membrane mechanics. Curr Opin Cell Biol 2024; 86:102308. [PMID: 38168583 DOI: 10.1016/j.ceb.2023.102308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The plasma membrane serves as the primary barrier between the cell's interior and its external surroundings, which places it at the forefront of intercellular communication, receptor signal transduction and the integration of mechanical forces from outside. Most of these signals are largely dependent on the plasma membrane heterogeneity which relies on lipid-lipid and lipid-protein interactions and the lateral nano-distribution of lipids organized by the dynamic network of cortical actin. In this review, we undertake an in-depth exploration of recent discoveries, which contribute significantly to the evolution from raft model to lipid nanodomains. Specifically, we will focus on their role in membrane receptor-mediated signaling in the context of cell membrane mechanics.
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Affiliation(s)
- Changting Li
- Institut Curie - Centre de Recherche, PSL Research University, Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Paris, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1143, Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR 3666, Paris, France
| | - Yazmina Quintana Perez
- Institut Curie - Centre de Recherche, PSL Research University, Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Paris, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1143, Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR 3666, Paris, France
| | - Christophe Lamaze
- Institut Curie - Centre de Recherche, PSL Research University, Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Paris, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1143, Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR 3666, Paris, France
| | - Cedric M Blouin
- Institut Curie - Centre de Recherche, PSL Research University, Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Paris, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1143, Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR 3666, Paris, France.
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10
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Farcas A, Janosi L. GTP-Bound N-Ras Conformational States and Substates Are Modulated by Membrane and Point Mutation. Int J Mol Sci 2024; 25:1430. [PMID: 38338709 PMCID: PMC11154311 DOI: 10.3390/ijms25031430] [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: 11/29/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024] Open
Abstract
Oncogenic Ras proteins are known to present multiple conformational states, as reported by the great variety of crystallographic structures. The GTP-bound states are grouped into two main states: the "inactive" state 1 and the "active" state 2. Recent reports on H-Ras have shown that state 2 exhibits two substates, directly related to the orientation of Tyr32: toward the GTP-bound pocket and outwards. In this paper, we show that N-Ras exhibits another substate of state 2, related to a third orientation of Tyr32, toward Ala18 and parallel to the GTP-bound pocket. We also show that this substate is highly sampled in the G12V mutation of N-Ras and barely present in its wild-type form, and that the G12V mutation prohibits the sampling of the GTPase-activating protein (GAP) binding substate, rendering this mutation oncogenic. Furthermore, using molecular dynamics simulations, we explore the importance of the membrane on N-Ras' conformational state dynamics and its strong influence on Ras protein stability. Moreover, the membrane has a significant influence on the conformational (sub)states sampling of Ras. This, in turn, is of crucial importance in the activation/deactivation cycle of Ras, due to the binding of guanine nucleotide exchange factor proteins (GEFs)/GTPase-activating proteins (GAPs).
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Affiliation(s)
| | - Lorant Janosi
- Department of Molecular and Biomolecular Physics, National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat Street, 400293 Cluj-Napoca, Romania;
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11
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Tariq M, Ikeya T, Togashi N, Fairall L, Kamei S, Mayooramurugan S, Abbott LR, Hasan A, Bueno-Alejo C, Sukegawa S, Romartinez-Alonso B, Muro Campillo MA, Hudson AJ, Ito Y, Schwabe JW, Dominguez C, Tanaka K. Structural insights into the complex of oncogenic KRas4B G12V and Rgl2, a RalA/B activator. Life Sci Alliance 2024; 7:e202302080. [PMID: 37833074 PMCID: PMC10576006 DOI: 10.26508/lsa.202302080] [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: 04/06/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
About a quarter of total human cancers carry mutations in Ras isoforms. Accumulating evidence suggests that small GTPases, RalA, and RalB, and their activators, Ral guanine nucleotide exchange factors (RalGEFs), play an essential role in oncogenic Ras-induced signalling. We studied the interaction between human KRas4B and the Ras association (RA) domain of Rgl2 (Rgl2RA), one of the RA-containing RalGEFs. We show that the G12V oncogenic KRas4B mutation changes the interaction kinetics with Rgl2RA The crystal structure of the KRas4BG12V: Rgl2RA complex shows a 2:2 heterotetramer where the switch I and switch II regions of each KRasG12V interact with both Rgl2RA molecules. This structural arrangement is highly similar to the HRasE31K:RALGDSRA crystal structure and is distinct from the well-characterised Ras:Raf complex. Interestingly, the G12V mutation was found at the dimer interface of KRas4BG12V with its partner. Our study reveals a potentially distinct mode of Ras:effector complex formation by RalGEFs and offers a possible mechanistic explanation for how the oncogenic KRas4BG12V hyperactivates the RalA/B pathway.
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Affiliation(s)
- Mishal Tariq
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Teppei Ikeya
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Naoyuki Togashi
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Louise Fairall
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Shun Kamei
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Sannojah Mayooramurugan
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Lauren R Abbott
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Anab Hasan
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Carlos Bueno-Alejo
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Sakura Sukegawa
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Beatriz Romartinez-Alonso
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Miguel Angel Muro Campillo
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Andrew J Hudson
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Department of Chemistry, University of Leicester, Leicester, UK
| | - Yutaka Ito
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - John Wr Schwabe
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Cyril Dominguez
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Kayoko Tanaka
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
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12
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Brenner RJ, Landgraf AD, Bum-Erdene K, Gonzalez-Gutierrez G, Meroueh SO. Crystal Packing Reveals a Potential Autoinhibited KRAS Dimer Interface and a Strategy for Small-Molecule Inhibition of RAS Signaling. Biochemistry 2023; 62:3206-3213. [PMID: 37938120 PMCID: PMC10904212 DOI: 10.1021/acs.biochem.3c00378] [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] [Indexed: 11/09/2023]
Abstract
KRAS GTPases harbor oncogenic mutations in more than 25% of human tumors. KRAS is considered to be largely undruggable due to the lack of a suitable small-molecule binding site. Here, we report a unique crystal structure of His-tagged KRASG12D that reveals a remarkable conformational change. The Switch I loop of one His-KRASG12D structure extends into the Switch I/II pocket of another His-KRASG12D in an adjacent unit cell to create an elaborate interface that is reminiscent of high-affinity protein-protein complexes. We explore the contributions of amino acids at this interface using alanine-scanning studies with alchemical free energy perturbation calculations based on explicit-solvent molecular dynamics simulations. Several interface amino acids were found to be hot spots as they contributed more than 1.5 kcal/mol to the protein-protein interaction. Computational analysis of the complex revealed the presence of two large binding pockets that possess physicochemical features typically found in pockets considered druggable. Small-molecule binding to these pockets may stabilize this autoinhibited structure of KRAS if it exists in cells to provide a new strategy to inhibit RAS signaling.
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Affiliation(s)
- Robert J. Brenner
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Alexander D. Landgraf
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Khuchtumur Bum-Erdene
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Samy O. Meroueh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
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13
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Jurado M, Zorzano A, Castaño O. Cooperativity and oscillations: Regulatory mechanisms of K-Ras nanoclusters. Comput Biol Med 2023; 166:107455. [PMID: 37742420 DOI: 10.1016/j.compbiomed.2023.107455] [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: 11/28/2022] [Revised: 08/07/2023] [Accepted: 09/04/2023] [Indexed: 09/26/2023]
Abstract
K-Ras nanoclusters (NCs) concentrate all required molecules belonging to the extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase (MAPK) pathway in a small area where signaling events take place, increasing efficiency and specificity of signaling. Such nanostructures are characterized by controlled sizes and lifetimes distributions, but there is a poor understanding of the mechanisms involved in their dynamics of growth/decay. Here, a minimum computational model is presented to analyze the behavior of K-Ras NCs as cooperative dynamic structures that self-regulate their growth and decay according to their size. Indeed, the proposed model reveals that the growth and the local production of a K-Ras nanocluster depend positively on its actual size, whilst its lifetime is inversely proportional to the root of its size. The cooperative binding between the structural constituents of the NC (K-Ras proteins) induces oscillations in the size distributions of K-Ras NCs allowing them to range within controlled values, regulating the growth/decay dynamics of these NCs. Thereby, the size of a K-Ras NC is proposed as a key factor to regulate cell signaling, opening a range of possibilities to develop strategies for use in chronic diseases and cancer.
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Affiliation(s)
- Manuel Jurado
- Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Antonio Zorzano
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; CIBER of Diabetes and Associated Metabolic Diseases, Barcelona, Spain; Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain.
| | - Oscar Castaño
- Electronics and Biomedical Engineering, Universitat de Barcelona (UB), Barcelona, Spain; Nanobioengineering and Biomaterials, Institute of Nanoscience and Nanotechnology of the University of Barcelona, Barcelona, Spain
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14
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Rehl KM, Selvakumar J, Pitsch RL, Hoang D, Arumugam K, Harshman SW, Gorfe AA, Cho KJ. A new ferrocene derivative blocks K-Ras localization and function by oxidative modification at His95. Life Sci Alliance 2023; 6:e202302094. [PMID: 37666666 PMCID: PMC10477449 DOI: 10.26508/lsa.202302094] [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: 04/12/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/06/2023] Open
Abstract
Ras proteins are membrane-bound GTPases that regulate essential cellular processes at the plasma membrane (PM). Constitutively active mutations of K-Ras, one of the three Ras isoforms in mammalian cells, are frequently found in human cancers. Ferrocene derivatives, which elevate cellular reactive oxygen species (ROS), have shown to block the growth of non-small cell lung cancers harboring oncogenic mutant K-Ras. Here, we tested a novel ferrocene derivative on the growth of pancreatic ductal adenocarcinoma and non-small cell lung cancer. Our compound, which elevated cellular ROS levels, inhibited the growth of K-Ras-driven cancers, and abrogated the PM binding and signaling of K-Ras in an isoform-specific manner. These effects were reversed upon antioxidant supplementation, suggesting a ROS-mediated mechanism. We further identified that K-Ras His95 residue plays an important role in this process, and it is putatively oxidized by cellular ROS. Together, our study demonstrates that the redox system directly regulates K-Ras/PM binding and signaling via oxidative modification at the His95, and proposes a role of oncogenic mutant K-Ras in the recently described antioxidant-induced growth and metastasis of K-Ras-driven cancers.
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Affiliation(s)
- Kristen M Rehl
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
| | - Jayaraman Selvakumar
- Department of Chemistry, College of Science and Mathematics, Wright State University, Dayton, OH, USA
| | - Rhonda L Pitsch
- https://ror.org/02e2egq70 Air Force Research Laboratory, Wright-Patterson AFB, OH, USA
| | - Don Hoang
- Department of Chemistry, College of Science and Mathematics, Wright State University, Dayton, OH, USA
| | - Kuppuswamy Arumugam
- Department of Chemistry, College of Science and Mathematics, Wright State University, Dayton, OH, USA
| | - Sean W Harshman
- https://ror.org/02e2egq70 Air Force Research Laboratory, Wright-Patterson AFB, OH, USA
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
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15
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Morstein J, Shrestha R, Van QN, López CA, Arora N, Tonelli M, Liang H, Chen D, Zhou Y, Hancock JF, Stephen AG, Turbyville TJ, Shokat KM. Direct Modulators of K-Ras-Membrane Interactions. ACS Chem Biol 2023; 18:2082-2093. [PMID: 37579045 PMCID: PMC10510109 DOI: 10.1021/acschembio.3c00413] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023]
Abstract
Protein-membrane interactions (PMIs) are ubiquitous in cellular signaling. Initial steps of signal transduction cascades often rely on transient and dynamic interactions with the inner plasma membrane leaflet to populate and regulate signaling hotspots. Methods to target and modulate these interactions could yield attractive tool compounds and drug candidates. Here, we demonstrate that the conjugation of a medium-chain lipid tail to the covalent K-Ras(G12C) binder MRTX849 at a solvent-exposed site enables such direct modulation of PMIs. The conjugated lipid tail interacts with the tethered membrane and changes the relative membrane orientation and conformation of K-Ras(G12C), as shown by molecular dynamics (MD) simulation-supported NMR studies. In cells, this PMI modulation restricts the lateral mobility of K-Ras(G12C) and disrupts nanoclusters. The described strategy could be broadly applicable to selectively modulate transient PMIs.
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Affiliation(s)
- Johannes Morstein
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Rebika Shrestha
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Que N. Van
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - César A. López
- Theoretical
Biology and Biophysics Group, Los Alamos
National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Neha Arora
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Marco Tonelli
- National
Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Hong Liang
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - De Chen
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Yong Zhou
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - John F. Hancock
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Andrew G. Stephen
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Thomas J. Turbyville
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Kevan M. Shokat
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
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16
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Liu J, Arora N, Zhou Y. RAS GTPases and Interleaflet Coupling in the Plasma Membrane. Cold Spring Harb Perspect Biol 2023; 15:a041414. [PMID: 37463719 PMCID: PMC10513163 DOI: 10.1101/cshperspect.a041414] [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] [Indexed: 07/20/2023]
Abstract
RAS genes are frequently mutated in cancer. The primary signaling compartment of wild-type and constitutively active oncogenic mutant RAS proteins is the inner leaflet of the plasma membrane (PM). Thus, a better understanding of the unique environment of the PM inner leaflet is important to shed further light on RAS function. Over the past few decades, an integrated approach of superresolution imaging, molecular dynamic simulations, and biophysical assays has yielded new insights into the capacity of RAS proteins to sort lipids with specific headgroups and acyl chains, to assemble signaling nanoclusters on the inner PM. RAS proteins also sense and respond to changes in components of the outer PM leaflet, including glycophosphatidylinositol-anchored proteins, sphingophospholipids, glycosphingolipids, and galectins, as well as cholesterol that translocates between the two leaflets. Such communication between the inner and outer leaflets of the PM, called interleaflet coupling, allows RAS to potentially integrate extracellular mechanical and electrostatic information with intracellular biochemical signaling events, and reciprocally allows mutant RAS-transformed tumor cells to modify tumor microenvironments. Here, we review RAS-lipid interactions and speculate on potential mechanisms that allow communication between the opposing leaflets of the PM.
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Affiliation(s)
- Junchen Liu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Neha Arora
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
- Biochemistry and Cell Biology Program, Graduate School of Biomedical Sciences, MD Anderson Cancer Center and University of Texas, Houston, Texas 77030, USA
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17
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Lee AA, Kim NH, Alvarez S, Ren H, DeGrandchamp JB, Lew LJN, Groves JT. Bimodality in Ras signaling originates from processivity of the Ras activator SOS without classic kinetic bistability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549263. [PMID: 37503094 PMCID: PMC10370109 DOI: 10.1101/2023.07.17.549263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Ras is a small GTPase that is central to important functional decisions in diverse cell types. An important aspect of Ras signaling is its ability to exhibit bimodal, or switch-like activity. We describe the total reconstitution of a receptor-mediated Ras activation-deactivation reaction catalyzed by SOS and p120-RasGAP on supported lipid membrane microarrays. The results reveal a bimodal Ras activation response, which is not a result of classic kinetic bistability, but is rather driven by the distinct processivity of the Ras activator, SOS. Furthermore, the bimodal response is controlled by the condensation state of the scaffold protein, LAT, to which SOS is recruited. Processivity-driven bimodality leads to stochastic bursts of Ras activation even under strongly deactivating conditions. This behavior contrasts classic kinetic bistability and is distinctly more resistant to pharmacological inhibition.
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18
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Caballero N, Kruse K, Giamarchi T. Phase separation on surfaces in the presence of matter exchange. Phys Rev E 2023; 108:L012801. [PMID: 37583133 DOI: 10.1103/physreve.108.l012801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/17/2023] [Indexed: 08/17/2023]
Abstract
We present a field theory to describe the composition of a surface spontaneously exchanging matter with its bulk environment. By only assuming matter conservation in the system, we show with extensive numerical simulations that, depending on the matter exchange rates, a complex patterned composition distribution emerges on the surface. For one-dimensional systems we show analytically and numerically that coarsening is arrested and as a consequence domains have a characteristic length scale. Our results show that the causes of heterogeneous lipid composition in cellular membranes may be justified in simple physical terms.
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Affiliation(s)
- Nirvana Caballero
- Department of Quantum Matter Physics, University of Geneva, 24 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland
| | - Karsten Kruse
- Department of Biochemistry, Department of Theoretical Physics, and NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Thierry Giamarchi
- Department of Quantum Matter Physics, University of Geneva, 24 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland
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19
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Simanshu DK, Philips MR, Hancock JF. Consensus on the RAS dimerization hypothesis: Strong evidence for lipid-mediated clustering but not for G-domain-mediated interactions. Mol Cell 2023; 83:1210-1215. [PMID: 36990093 PMCID: PMC10150945 DOI: 10.1016/j.molcel.2023.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/24/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
One of the open questions in RAS biology is the existence of RAS dimers and their role in RAF dimerization and activation. The idea of RAS dimers arose from the discovery that RAF kinases function as obligate dimers, which generated the hypothesis that RAF dimer formation might be nucleated by G-domain-mediated RAS dimerization. Here, we review the evidence for RAS dimerization and describe a recent discussion among RAS researchers that led to a consensus that the clustering of two or more RAS proteins is not due to the stable association of G-domains but, instead, is a consequence of RAS C-terminal membrane anchors and the membrane phospholipids with which they interact.
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Affiliation(s)
- Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Mark R Philips
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA.
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.
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20
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Babu Manoharan G, Guzmán C, Najumudeen AK, Abankwa D. Detection of Ras nanoclustering-dependent homo-FRET using fluorescence anisotropy measurements. Eur J Cell Biol 2023; 102:151314. [PMID: 37058825 DOI: 10.1016/j.ejcb.2023.151314] [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: 12/13/2022] [Revised: 03/10/2023] [Accepted: 04/10/2023] [Indexed: 04/16/2023] Open
Abstract
The small GTPase Ras is frequently mutated in cancer and a driver of tumorigenesis. The recent years have shown great progress in drug-targeting Ras and understanding how it operates on the plasma membrane. We now know that Ras is non-randomly organized into proteo-lipid complexes on the membrane, called nanoclusters. Nanoclusters contain only a few Ras proteins and are necessary for the recruitment of downstream effectors, such as Raf. If tagged with fluorescent proteins, the dense packing of Ras in nanoclusters can be analyzed by Förster/ fluorescence resonance energy transfer (FRET). Loss of FRET can therefore report on decreased nanoclustering and any process upstream of it, such as Ras lipid modifications and correct trafficking. Thus, cellular FRET screens employing Ras-derived fluorescence biosensors are potentially powerful tools to discover chemical or genetic modulators of functional Ras membrane organization. Here we implement fluorescence anisotropy-based homo-FRET measurements of Ras-derived constructs labelled with only one fluorescent protein on a confocal microscope and a fluorescence plate reader. We show that homo-FRET of both H-Ras- and K-Ras-derived constructs can sensitively report on Ras-lipidation and -trafficking inhibitors, as well as on genetic perturbations of proteins regulating membrane anchorage. By exploiting the switch I/II-binding Ras-dimerizing compound BI-2852, this assay is also suitable to report on the engagement of the K-Ras switch II pocket by small molecules such as AMG 510. Given that homo-FRET only requires one fluorescent protein tagged Ras construct, this approach has significant advantages to create Ras-nanoclustering FRET-biosensor reporter cell lines, as compared to the more common hetero-FRET approaches.
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Affiliation(s)
- Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Camilo Guzmán
- Euro-BioImaging ERIC, Statutory Seat, Turku, Finland
| | - Arafath Kaja Najumudeen
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Daniel Abankwa
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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21
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Rehl KM, Selvakumar J, Hoang D, Arumugam K, Gorfe AA, Cho KJ. A new ferrocene derivative blocks KRAS localization and function by oxidative modification at His95. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534499. [PMID: 37034642 PMCID: PMC10081197 DOI: 10.1101/2023.03.28.534499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Ras proteins are membrane-bound GTPases that regulate essential cellular processes at the plasma membrane (PM). Constitutively active mutations of K-Ras, one of the three Ras isoforms in mammalian cells, are frequently found in human cancers. Ferrocene derivatives, which elevate cellular reactive oxygen species (ROS), have shown to block the growth of non-small cell lung cancers (NSCLCs) harboring oncogenic mutant K-Ras. Here, we developed and tested a novel ferrocene derivative on the growth of human pancreatic ductal adenocarcinoma (PDAC) and NSCLC. Our compound inhibited the growth of K-Ras-dependent PDAC and NSCLC and abrogated the PM binding and signaling of K-Ras, but not other Ras isoforms. These effects were reversed upon antioxidant supplementation, suggesting a ROS-mediated mechanism. We further identified K-Ras His95 residue in the G-domain as being involved in the ferrocene-induced K-Ras PM dissociation via oxidative modification. Together, our studies demonstrate that the redox system directly regulates K-Ras PM binding and signaling via oxidative modification at the His95, and proposes a role of oncogenic mutant K-Ras in the recently described antioxidant-induced metastasis in K-Ras-driven lung cancers.
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22
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Zhou Y, Hancock JF. RAS nanoclusters are cell surface transducers that convert extracellular stimuli to intracellular signalling. FEBS Lett 2023; 597:892-908. [PMID: 36595205 PMCID: PMC10919257 DOI: 10.1002/1873-3468.14569] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 01/04/2023]
Abstract
Mutations of rat sarcoma virus (RAS) oncogenes (HRAS, KRAS and NRAS) can contribute to the development of cancers and genetic disorders (RASopathies). The spatiotemporal organization of RAS is an important property that warrants further investigation. In order to function, wild-type or oncogenic mutants of RAS must be localized to the inner leaflet of the plasma membrane (PM), which is driven by interactions between their C-terminal membrane-anchoring domains and PM lipids. The isoform-specific RAS-lipid interactions promote the formation of nanoclusters on the PM. As main sites for effector recruitment, these nanoclusters are biologically important. Since the spatial distribution of lipids is sensitive to changing environments, such as mechanical and electrical perturbations, RAS nanoclusters act as transducers to convert external stimuli to intracellular mitogenic signalling. As such, effective inhibition of RAS oncogenesis requires consideration of the complex interplay between RAS nanoclusters and various cell surface and extracellular stimuli. In this review, we discuss in detail how, by sorting specific lipids in the PM, RAS nanoclusters act as transducers to convert external stimuli into intracellular signalling.
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Affiliation(s)
- Yong Zhou
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, McGovern Medical School, TX, USA
- Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and University of Texas Health Science Center, TX, USA
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, McGovern Medical School, TX, USA
- Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and University of Texas Health Science Center, TX, USA
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23
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Glycolysis regulates KRAS plasma membrane localization and function through defined glycosphingolipids. Nat Commun 2023; 14:465. [PMID: 36709325 PMCID: PMC9884228 DOI: 10.1038/s41467-023-36128-5] [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: 07/05/2022] [Accepted: 01/17/2023] [Indexed: 01/29/2023] Open
Abstract
Oncogenic KRAS expression generates a metabolic dependency on aerobic glycolysis, known as the Warburg effect. We report an effect of increased glycolytic flux that feeds into glycosphingolipid biosynthesis and is directly linked to KRAS oncogenic function. High resolution imaging and genetic approaches show that a defined subset of outer leaflet glycosphingolipids, including GM3 and SM4, is required to maintain KRAS plasma membrane localization, with GM3 engaging in cross-bilayer coupling to maintain inner leaflet phosphatidylserine content. Thus, glycolysis is critical for KRAS plasma membrane localization and nanoscale spatial organization. Reciprocally oncogenic KRAS selectively upregulates cellular content of these same glycosphingolipids, whose depletion in turn abrogates KRAS oncogenesis in pancreatic cancer models. Our findings expand the role of the Warburg effect beyond ATP generation and biomass building to high-level regulation of KRAS function. The positive feedforward loop between oncogenic KRAS signaling and glycosphingolipid synthesis represents a vulnerability with therapeutic potential.
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24
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Sarkar S, Goswami D. Lifetime of actin-dependent protein nanoclusters. Biophys J 2023; 122:290-300. [PMID: 36518075 PMCID: PMC9892618 DOI: 10.1016/j.bpj.2022.12.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/23/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Protein nanoclusters (PNCs) are dynamic collections of a few proteins that spatially organize in nanometer-length clusters. PNCs are one of the principal forms of spatial organization of membrane proteins, and they have been shown or hypothesized to be important in various cellular processes, including cell signaling. PNCs show remarkable diversity in size, shape, and lifetime. In particular, the lifetime of PNCs can vary over a wide range of timescales. The diversity in size and shape can be explained by the interaction of the clustering proteins with the actin cytoskeleton or the lipid membrane, but very little is known about the processes that determine the lifetime of the nanoclusters. In this paper, using mathematical modeling of the cluster dynamics, we model the biophysical processes that determine the lifetime of actin-dependent PNCs. In particular, we investigated the role of actin aster fragmentation, which had been suggested to be a key determinant of the PNC lifetime, and we found that it is important only for a small class of PNCs. A simple extension of our model allowed us to investigate the kinetics of protein-ligand interaction near PNCs. We found an anomalous increase in the lifetime of ligands near PNCs, which agrees remarkably well with experimental data on RAS-RAF kinetics. In particular, analysis of the RAS-RAF data through our model provides falsifiable predictions and novel hypotheses that will not only shed light on the role of RAS-RAF kinetics in various cancers, but also will be useful in studying membrane protein clustering in general.
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Affiliation(s)
- Sumantra Sarkar
- The Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico; Theoretical Biophysics (T-6) Group, Los Alamos National Laboratory, Los Alamos, New Mexico; Department of Physics, Indian Institute of Science, Bengaluru, Karnataka 560012, India.
| | - Debanjan Goswami
- NCI RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, Maryland.
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25
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Remodeling of the Plasma Membrane by Surface-Bound Protein Monomers and Oligomers: The Critical Role of Intrinsically Disordered Regions. J Membr Biol 2022; 255:651-663. [PMID: 35930019 PMCID: PMC9718270 DOI: 10.1007/s00232-022-00256-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/07/2022] [Indexed: 12/24/2022]
Abstract
The plasma membrane (PM) of cells is a dynamic structure whose morphology and composition is in constant flux. PM morphologic changes are particularly relevant for the assembly and disassembly of signaling platforms involving surface-bound signaling proteins, as well as for many other mechanochemical processes that occur at the PM surface. Surface-bound membrane proteins (SBMP) require efficient association with the PM for their function, which is often achieved by the coordinated interactions of intrinsically disordered regions (IDRs) and globular domains with membrane lipids. This review focuses on the role of IDR-containing SBMPs in remodeling the composition and curvature of the PM. The ability of IDR-bearing SBMPs to remodel the Gaussian and mean curvature energies of the PM is intimately linked to their ability to sort subsets of phospholipids into nanoclusters. We therefore discuss how IDRs of many SBMPs encode lipid-binding specificity or facilitate cluster formation, both of which increase their membrane remodeling capacity, and how SBMP oligomers alter membrane shape by monolayer surface area expansion and molecular crowding.
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26
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DiPasquale M, Nguyen MHL, Castillo SR, Dib IJ, Kelley EG, Marquardt D. Vitamin E Does Not Disturb Polyunsaturated Fatty Acid Lipid Domains. Biochemistry 2022; 61:2366-2376. [PMID: 36227768 DOI: 10.1021/acs.biochem.2c00405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The function of vitamin E in biomembranes remains a prominent topic of discussion. As its limitations as an antioxidant persist and novel functions are discovered, our understanding of the role of vitamin E becomes increasingly enigmatic. As a group of lipophilic molecules (tocopherols and tocotrienols), vitamin E has been shown to influence the properties of its host membrane, and a wealth of research has connected vitamin E to polyunsaturated fatty acid (PUFA) lipids. Here, we use contrast-matched small-angle neutron scattering and differential scanning calorimetry to integrate these fields by examining the influence of vitamin E on lipid domain stability in PUFA-based lipid mixtures. The influence of α-tocopherol, γ-tocopherol, and α-tocopherylquinone on the lateral organization of a 1:1 lipid mixture of saturated distearoylphosphatidylcholine (DSPC) and polyunsaturated palmitoyl-linoleoylphosphatidylcholine (PLiPC) with cholesterol provides a complement to our growing understanding of the influence of tocopherol on lipid phases. Characterization of domain melting suggests a slight depression in the transition temperature and a decrease in transition cooperativity. Tocopherol concentrations that are an order of magnitude higher than anticipated physiological concentrations (2 mol percent) do not significantly perturb lipid domains; however, addition of 10 mol percent is able to destabilize domains and promote lipid mixing. In contrast to this behavior, increasing concentrations of the oxidized product of α-tocopherol (α-tocopherylquinone) induces a proportional increase in domain stabilization. We speculate how the contrasting effect of the oxidized product may supplement the antioxidant response of vitamin E.
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Affiliation(s)
- Mitchell DiPasquale
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, OntarioN9B3P4, Canada
| | - Michael H L Nguyen
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, OntarioN9B3P4, Canada
| | - Stuart R Castillo
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, OntarioN9B3P4, Canada
| | - Isabelle J Dib
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, OntarioN9B3P4, Canada
| | - Elizabeth G Kelley
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland20878, United States
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, OntarioN9B3P4, Canada.,Department of Physics, University of Windsor, Windsor, OntarioN9B3P4, Canada
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Dent P, Booth L, Poklepovic A, Hancock JF. Neratinib as a Potential Therapeutic for Mutant RAS and Osimertinib-Resistant Tumours. EUROPEAN MEDICAL JOURNAL 2022. [DOI: 10.33590/emj/10197202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Neratinib was developed as an irreversible catalytic inhibitor of ERBB2, which also acts to inhibit ERBB1 and ERBB4. Neratinib is U.S. Food and Drug Administration (FDA)-approved as a neo-adjuvant therapy for use in HER2+ breast cancer. More recently, chemical biology analyses and the authors’ own bench work have demonstrated that neratinib has additional targets, which open up the possibility of using the drug in cell types that either lack ERBB receptor family expression or who rely on survival signalling downstream of growth factor receptors. Neratinib rapidly disrupted mutant RAS nanoclustering, which was followed by mutant rat sarcoma virus proteins translocating via LC3-associated phagocytosis into the cytosol where they were degraded by macroautophagy. Neratinib catalytically inhibited the MAP4K mammalian STE20-like protein kinase 4 and also caused its degradation via macroautophagy. This resulted in ezrin dephosphorylation and the plasma membrane becoming flaccid. Neratinib disrupted the nanoclustering of RAC1, which was associated with dephosphorylation of PAK1 and Merlin, and with increased phosphorylation of the Merlin binding partners large tumour suppressor kinase 1/2, YAP, and TAZ. YAP and TAZ exited the nucleus. Neratinib retained its anti-tumour efficacy against NSCLC cells made resistant to either afatinib or to osimertinib. Collectively, these findings argue that the possibilities for the further development of neratinib as cancer therapeutic in malignancies that do not express or over-express members of the ERBB receptor family are potentially wide-ranging.
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Active emulsions in living cell membranes driven by contractile stresses and transbilayer coupling. Proc Natl Acad Sci U S A 2022; 119:e2123056119. [PMID: 35867835 PMCID: PMC9335261 DOI: 10.1073/pnas.2123056119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The spatiotemporal organization of proteins and lipids on the cell surface has direct functional consequences for signaling, sorting, and endocytosis. Earlier studies have shown that multiple types of membrane proteins, including transmembrane proteins that have cytoplasmic actin binding capacity and lipid-tethered glycosylphosphatidylinositol-anchored proteins (GPI-APs), form nanoscale clusters driven by active contractile flows generated by the actin cortex. To gain insight into the role of lipids in organizing membrane domains in living cells, we study the molecular interactions that promote the actively generated nanoclusters of GPI-APs and transmembrane proteins. This motivates a theoretical description, wherein a combination of active contractile stresses and transbilayer coupling drives the creation of active emulsions, mesoscale liquid order (lo) domains of the GPI-APs and lipids, at temperatures greater than equilibrium lipid phase segregation. To test these ideas, we use spatial imaging of molecular clustering combined with local membrane order, and we demonstrate that mesoscopic domains enriched in nanoclusters of GPI-APs are maintained by cortical actin activity and transbilayer interactions and exhibit significant lipid order, consistent with predictions of the active composite model.
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Nanoscopic Spatial Association between Ras and Phosphatidylserine on the Cell Membrane Studied with Multicolor Super Resolution Microscopy. Biomolecules 2022; 12:biom12081033. [PMID: 35892343 PMCID: PMC9332490 DOI: 10.3390/biom12081033] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 07/02/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022] Open
Abstract
Recent work suggests that Ras small GTPases interact with the anionic lipid phosphatidylserine (PS) in an isoform-specific manner, with direct implications for their biological functions. Studies on PS-Ras associations in cells, however, have relied on immuno-EM imaging of membrane sheets. To study their spatial relationships in intact cells, we have combined the use of Lact-C2-GFP, a biosensor for PS, with multicolor super resolution imaging based on DNA-PAINT. At ~20 nm spatial resolution, the resulting super resolution images clearly show the nonuniform molecular distribution of PS on the cell membrane and its co-enrichment with caveolae, as well as with unidentified membrane structures. Two-color imaging followed by spatial analysis shows that KRas-G12D and HRas-G12V both co-enrich with PS in model U2OS cells, confirming previous observations, yet exhibit clear differences in their association patterns. Whereas HRas-G12V is almost always co-enriched with PS, KRas-G12D is strongly co-enriched with PS in about half of the cells, with the other half exhibiting a more moderate association. In addition, perturbations to the actin cytoskeleton differentially impact PS association with the two Ras isoforms. These results suggest that PS-Ras association is context-dependent and demonstrate the utility of multiplexed super resolution imaging in defining the complex interplay between Ras and the membrane.
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Altered CXCR4 dynamics at the cell membrane impairs directed cell migration in WHIM syndrome patients. Proc Natl Acad Sci U S A 2022; 119:e2119483119. [PMID: 35588454 PMCID: PMC9173760 DOI: 10.1073/pnas.2119483119] [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] [Indexed: 01/14/2023] Open
Abstract
SignificanceNew imaging-based approaches are incorporating new concepts to our knowledge of biological processes. The analysis of receptor dynamics involved in cell movement using single-particle tracking demonstrates that cells require chemokine-mediated receptor clustering to sense appropriately chemoattractant gradients. Here, we report that this process does not occur in T cells expressing CXCR4R334X, a mutant form of CXCR4 linked to WHIM syndrome (warts, hypogammaglobulinemia, infections, myelokathexis). The underlaying molecular mechanism involves inappropriate actin cytoskeleton remodeling due to the inadequate β-arrestin1 activation by CXCR4R334X, which alters its lateral mobility and spatial organization. These defects, associated to CXCR4R334X expression, contribute to the retention of hematopoietic precursors in bone marrow niches and explain the severe immunological symptoms associated with WHIM syndrome.
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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: 15] [Impact Index Per Article: 7.5] [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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Martinez-Sanchez A, Baumeister W, Lučić V. Statistical spatial analysis for cryo-electron tomography. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 218:106693. [PMID: 35240361 DOI: 10.1016/j.cmpb.2022.106693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/23/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Cryo-electron tomography (cryo-ET) is uniquely suited to precisely localize macromolecular complexes in situ, that is in a close-to-native state within their cellular compartments, in three-dimensions at high resolution. Point pattern analysis (PPA) allows quantitative characterization of the spatial organization of particles. However, current implementations of PPA functions are not suitable for applications to cryo-ET data because they do not consider the real, typically irregular 3D shape of cellular compartments and molecular complexes. Here, we designed and implemented first and the second-order, uni- and bivariate PPA functions in a Python package for statistical spatial analysis of particles located in three dimensional regions of arbitrary shape, such as those encountered in cellular cryo-ET imaging (PyOrg). To validate the implemented functions, we applied them to specially designed synthetic datasets. This allowed us to find the algorithmic solutions that provide the best accuracy and computational performance, and to evaluate the precision of the implemented functions. Applications to experimental data showed that despite the higher computational demand, the use of the second-order functions is advantageous to the first-order ones, because they allow characterization of the particle organization and statistical inference over a range of distance scales, as well as the comparative analysis between experimental groups comprising multiple tomograms. Altogether, PyOrg is a versatile, precise, and efficient open-source software for reliable quantitative characterization of macromolecular organization within cellular compartments imaged in situ by cryo-ET, as well as to other 3D imaging systems where real-size particles are located within regions possessing complex geometry.
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Affiliation(s)
- Antonio Martinez-Sanchez
- Department of Computer Sciences, Faculty of Sciences - Campus Llamaquique, University of Oviedo, Oviedo 33007, Spain; Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario s/n, Oviedo 33011, Spain; Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Am Klopferespitz 18, Martinsried 82152, Germany.
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Am Klopferespitz 18, Martinsried 82152, Germany
| | - Vladan Lučić
- Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Am Klopferespitz 18, Martinsried 82152, Germany.
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Seguin L. KRAS Addiction Promotes Cancer Cell Adaptation in Harsh Microenvironment Through Macropinocytosis. Subcell Biochem 2022; 98:189-204. [PMID: 35378709 DOI: 10.1007/978-3-030-94004-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
KRAS is the most frequently mutated oncogene in cancer and despite intensive studies, attempts to develop effective therapies targeting KRAS or its downstream signaling have failed mostly due to the complexity of KRAS activation and function in cancer initiation and progression. Over the years, KRAS has been involved in several biological processes including cell survival, proliferation, and metabolism by promoting not only a favorable tumor environment but also a cell-microenvironment dialog to allow cancer cells to adapt to tumor microenvironment scarcity. One of the mechanisms involved in this adaption is KRAS-mediated macropinocytosis. Macropinocytosis is an evolutionarily conserved, large-scale, and nonselective form of endocytosis involving actin-driven cell membrane remodeling to engulf large amounts of extracellular fluids and proteins from the local environment. While macropinocytosis process has been known for decades, recent gain interest due to its regulation of KRAS-driven tumor growth in adverse microenvironments. By promoting extracellular protein and other macromolecules internalization, macropinocytosis provides a survival mechanism under nutrient scarce conditions and the potential for unrestricted tumor growth. Thus, a better understanding of macropinocytotic process is needed to develop alternative therapeutic strategies.
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Mu H, Zeng Y, Zhuang Y, Gao W, Zhou Y, Rajalingam K, Zhao W. Patterning of Oncogenic Ras Clustering in Live Cells Using Vertically Aligned Nanostructure Arrays. NANO LETTERS 2022; 22:1007-1016. [PMID: 35044178 DOI: 10.1021/acs.nanolett.1c03886] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
As a dominant oncogenic protein, Ras is well-known to segregate into clusters on the plasma membrane for activating downstream signaling. However, current technologies for direct measurements of Ras clustering are limited to sophisticated high-resolution techniques like electron microscopy and fluorescence lifetime imaging. To further promote fundamental investigations and the related drug development, we hereby introduce a nanobar-based platform which effectively guides Ras clusters into quantifiable patterns in live cells that is resolvable under conventional microscopy. Major Ras isoforms, K-Ras, H-Ras, and N-Ras, were differentiated, as well as their highly prevalent oncogenic mutants G12V and G13D. Moreover, the isoform specificity and the sensitivity of a Ras inhibitor were successfully characterized on nanobars. We envision that this nanobar-based platform will serve as an effective tool to read Ras clustering on the plasma membrane, enabling a novel avenue both to decipher Ras regulations and to facilitate anti-Ras drug development.
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Affiliation(s)
- Huanwen Mu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457, Singapore
- Ageing Research Institute for Society and Education, Nanyang Technological University, Singapore 637335, Singapore
| | - Yongpeng Zeng
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457, Singapore
| | - Yinyin Zhuang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457, Singapore
| | - Weibo Gao
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- The Photonics Institute and Centre for Disruptive Photonic Technologies, Nanyang Technological University, Singapore 637371, Singapore
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Sciences Center, Houston, Texas 77030, United States
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center and UTHealth Graduate School of Biomedical Sciences, Houston, Texas 77030, United States
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center Mainz, Johannes Gutenberg University, D 55131 Mainz, Germany
- University Cancer Center Mainz, University Medical Center Mainz, Johannes Gutenberg University, D 55131 Mainz, Germany
| | - Wenting Zhao
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457, Singapore
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Pavic K, Chippalkatti R, Abankwa D. Drug targeting opportunities en route to Ras nanoclusters. Adv Cancer Res 2022; 153:63-99. [PMID: 35101236 DOI: 10.1016/bs.acr.2021.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Disruption of the native membrane organization of Ras by the farnesyltransferase inhibitor tipifarnib in the late 1990s constituted the first indirect approach to drug target Ras. Since then, our understanding of how dynamically Ras shuttles between subcellular locations has changed significantly. Ras proteins have to arrive at the plasma membrane for efficient MAPK-signal propagation. On the plasma membrane Ras proteins are organized into isoform specific proteo-lipid assemblies called nanocluster. Recent evidence suggests that Ras nanocluster have a specific lipid composition, which supports the recruitment of effectors such as Raf. Conversely, effectors possess lipid-recognition motifs, which appear to serve as co-incidence detectors for the lipid domain of a given Ras isoform. Evidence suggests that dimeric Raf proteins then co-assemble dimeric Ras in an immobile complex, thus forming the minimal unit of an active nanocluster. Here we review established and novel trafficking chaperones and trafficking factors of Ras, along with the set of lipid and protein modulators of Ras nanoclustering. We highlight drug targeting approaches and opportunities against these determinants of functional Ras membrane organization. Finally, we reflect on implications for Ras signaling in polarized cells, such as epithelia, which are a common origin of tumorigenesis.
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Affiliation(s)
- Karolina Pavic
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rohan Chippalkatti
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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Ozdemir ES, Koester AM, Nan X. Ras Multimers on the Membrane: Many Ways for a Heart-to-Heart Conversation. Genes (Basel) 2022; 13:219. [PMID: 35205266 PMCID: PMC8872464 DOI: 10.3390/genes13020219] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
Formation of Ras multimers, including dimers and nanoclusters, has emerged as an exciting, new front of research in the 'old' field of Ras biomedicine. With significant advances made in the past few years, we are beginning to understand the structure of Ras multimers and, albeit preliminary, mechanisms that regulate their formation in vitro and in cells. Here we aim to synthesize the knowledge accrued thus far on Ras multimers, particularly the presence of multiple globular (G-) domain interfaces, and discuss how membrane nanodomain composition and structure would influence Ras multimer formation. We end with some general thoughts on the potential implications of Ras multimers in basic and translational biology.
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Affiliation(s)
- E. Sila Ozdemir
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
| | - Anna M. Koester
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
| | - Xiaolin Nan
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
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Components of the phosphatidylserine endoplasmic reticulum to plasma membrane transport mechanism as targets for KRAS inhibition in pancreatic cancer. Proc Natl Acad Sci U S A 2021; 118:2114126118. [PMID: 34903667 DOI: 10.1073/pnas.2114126118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
KRAS is mutated in 90% of human pancreatic ductal adenocarcinomas (PDACs). To function, KRAS must localize to the plasma membrane (PM) via a C-terminal membrane anchor that specifically engages phosphatidylserine (PtdSer). This anchor-binding specificity renders KRAS-PM localization and signaling capacity critically dependent on PM PtdSer content. We now show that the PtdSer lipid transport proteins, ORP5 and ORP8, which are essential for maintaining PM PtdSer levels and hence KRAS PM localization, are required for KRAS oncogenesis. Knockdown of either protein, separately or simultaneously, abrogated growth of KRAS-mutant but not KRAS-wild-type pancreatic cancer cell xenografts. ORP5 or ORP8 knockout also abrogated tumor growth in an immune-competent orthotopic pancreatic cancer mouse model. Analysis of human datasets revealed that all components of this PtdSer transport mechanism, including the PM-localized EFR3A-PI4KIIIα complex that generates phosphatidylinositol-4-phosphate (PI4P), and endoplasmic reticulum (ER)-localized SAC1 phosphatase that hydrolyzes counter transported PI4P, are significantly up-regulated in pancreatic tumors compared to normal tissue. Taken together, these results support targeting PI4KIIIα in KRAS-mutant cancers to deplete the PM-to-ER PI4P gradient, reducing PM PtdSer content. We therefore repurposed the US Food and Drug Administration-approved hepatitis C antiviral agent, simeprevir, as a PI4KIIIα inhibitor In a PDAC setting. Simeprevir potently mislocalized KRAS from the PM, reduced the clonogenic potential of pancreatic cancer cell lines in vitro, and abrogated the growth of KRAS-dependent tumors in vivo with enhanced efficacy when combined with MAPK and PI3K inhibitors. We conclude that the cellular ER-to-PM PtdSer transport mechanism is essential for KRAS PM localization and oncogenesis and is accessible to therapeutic intervention.
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Gora RJ, de Jong B, van Hage P, Rhiemus MA, van Steenis F, van Noort J, Schmidt T, Schaaf MJM. Analysis of the H-Ras mobility pattern in vivo shows cellular heterogeneity inside epidermal tissue. Dis Model Mech 2021; 15:274496. [PMID: 34927194 PMCID: PMC8891639 DOI: 10.1242/dmm.049099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 12/14/2021] [Indexed: 12/04/2022] Open
Abstract
Developments in single-molecule microscopy (SMM) have enabled imaging individual proteins in biological systems, focusing on the analysis of protein mobility patterns inside cultured cells. In the present study, SMM was applied in vivo, using the zebrafish embryo model. We studied dynamics of the membrane protein H-Ras, its membrane-anchoring domain, C10H-Ras, and mutants, using total internal reflection fluorescence microscopy. Our results consistently confirm the presence of fast- and slow-diffusing subpopulations of molecules, which confine to microdomains within the plasma membrane. The active mutant H-RasV12 exhibits higher diffusion rates and is confined to larger domains than the wild-type H-Ras and its inactive mutant H-RasN17. Subsequently, we demonstrate that the structure and composition of the plasma membrane have an imperative role in modulating H-Ras mobility patterns. Ultimately, we establish that differences between cells within the same embryo largely contribute to the overall data variability. Our findings agree with a model in which the cell architecture and the protein activation state determine protein mobility, underlining the importance of SMM imaging for studying factors influencing protein dynamics in an intact living organism. This article has an associated First Person interview with the first author of the paper. Summary: Single-molecule microscopy analysis of factors altering the in vivo dynamics of H-Ras proteins in epidermal cells in living zebrafish embryos revealed that cell architecture and protein activation state determine protein mobility.
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Affiliation(s)
- Radoslaw J Gora
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Babette de Jong
- Biological, Soft and Complex Systems, Leiden Institute of Physics, Leiden University, Bohrweg 2, 2333 CA, Leiden, the Netherlands
| | - Patrick van Hage
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Mary Ann Rhiemus
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Fjodor van Steenis
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - John van Noort
- Biological, Soft and Complex Systems, Leiden Institute of Physics, Leiden University, Bohrweg 2, 2333 CA, Leiden, the Netherlands
| | - Thomas Schmidt
- Biological, Soft and Complex Systems, Leiden Institute of Physics, Leiden University, Bohrweg 2, 2333 CA, Leiden, the Netherlands
| | - Marcel J M Schaaf
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
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Nussinov R, Tsai CJ, Jang H. Signaling in the crowded cell. Curr Opin Struct Biol 2021; 71:43-50. [PMID: 34218161 PMCID: PMC8648894 DOI: 10.1016/j.sbi.2021.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/05/2021] [Accepted: 05/26/2021] [Indexed: 12/11/2022]
Abstract
High-resolution technologies have clarified some of the principles underlying cellular actions. However, understanding how cells receive, communicate, and respond to signals is still challenging. Questions include how efficient regulation of assemblies, which execute cell actions at the nanoscales, transmits productively at micrometer scales, especially considering the crowded environment, and how the cell organization makes it happen. Here, we describe how cells can navigate long-range diffusion-controlled signaling via association/dissociation of spatially proximal entities. Dynamic clusters can span the cell, engaging in most signaling steps. Effective local concentration, allostery, scaffolding, affinities, and the chemical and mechanical properties of the macromolecules and the environment play key roles. Signaling strength and duration matter, for example, deciding if a mutation promotes cancer or developmental syndromes.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
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Targeting small GTPases and their downstream pathways with intracellular macromolecule binders to define alternative therapeutic strategies in cancer. Biochem Soc Trans 2021; 49:2021-2035. [PMID: 34623375 DOI: 10.1042/bst20201059] [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: 07/21/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022]
Abstract
The RAS superfamily of small GTPases regulates major physiological cellular processes. Mutation or deregulation of these small GTPases, their regulators and/or their effectors are associated with many diseases including cancer. Hence, targeting these classes of proteins is an important therapeutic strategy in cancer. This has been recently achieved with the approval of the first KRASG12C covalent inhibitors for the clinic. However, many other mutants and small GTPases are still considered as 'undruggable' with small molecule inhibitors because of a lack of well-defined pocket(s) at their surface. Therefore, alternative therapeutic strategies have been developed to target these proteins. In this review, we discuss the use of intracellular antibodies and derivatives - reagents that bind their antigen inside the cells - for the discovery of novel inhibitory mechanisms, targetable features and therapeutic strategies to inhibit small GTPases and their downstream pathways. These reagents are also versatile tools used to better understand the biological mechanisms regulated by small GTPases and to accelerate the drug discovery process.
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41
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Mysore VP, Zhou ZW, Ambrogio C, Li L, Kapp JN, Lu C, Wang Q, Tucker MR, Okoro JJ, Nagy-Davidescu G, Bai X, Plückthun A, Jänne PA, Westover KD, Shan Y, Shaw DE. A structural model of a Ras-Raf signalosome. Nat Struct Mol Biol 2021; 28:847-857. [PMID: 34625747 PMCID: PMC8643099 DOI: 10.1038/s41594-021-00667-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/25/2021] [Indexed: 01/29/2023]
Abstract
The protein K-Ras functions as a molecular switch in signaling pathways regulating cell growth. In the human mitogen-activated protein kinase (MAPK) pathway, which is implicated in many cancers, multiple K-Ras proteins are thought to assemble at the cell membrane with Ras effector proteins from the Raf family. Here we propose an atomistic structural model for such an assembly. Our starting point was an asymmetric guanosine triphosphate-mediated K-Ras dimer model, which we generated using unbiased molecular dynamics simulations and verified with mutagenesis experiments. Adding further K-Ras monomers in a head-to-tail fashion led to a compact helical assembly, a model we validated using electron microscopy and cell-based experiments. This assembly stabilizes K-Ras in its active state and presents composite interfaces to facilitate Raf binding. Guided by existing experimental data, we then positioned C-Raf, the downstream kinase MEK1 and accessory proteins (Galectin-3 and 14-3-3σ) on and around the helical assembly. The resulting Ras-Raf signalosome model offers an explanation for a large body of data on MAPK signaling.
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Affiliation(s)
| | - Zhi-Wei Zhou
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chiara Ambrogio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Turin, Turin, Italy
| | - Lianbo Li
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonas N Kapp
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Chunya Lu
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qi Wang
- D. E. Shaw Research, New York, NY, USA
| | | | - Jeffrey J Okoro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Xiaochen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - David E Shaw
- D. E. Shaw Research, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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42
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RAS Dimers: The Novice Couple at the RAS-ERK Pathway Ball. Genes (Basel) 2021; 12:genes12101556. [PMID: 34680951 PMCID: PMC8535645 DOI: 10.3390/genes12101556] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 02/07/2023] Open
Abstract
Signals conveyed through the RAS-ERK pathway constitute a pivotal regulatory element in cancer-related cellular processes. Recently, RAS dimerization has been proposed as a key step in the relay of RAS signals, critically contributing to RAF activation. RAS clustering at plasma membrane microdomains and endomembranes facilitates RAS dimerization in response to stimulation, promoting RAF dimerization and subsequent activation. Remarkably, inhibiting RAS dimerization forestalls tumorigenesis in cellular and animal models. Thus, the pharmacological disruption of RAS dimers has emerged as an additional target for cancer researchers in the quest for a means to curtail aberrant RAS activity.
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43
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Zhou Y, Hancock JF. Lipid Profiles of RAS Nanoclusters Regulate RAS Function. Biomolecules 2021; 11:biom11101439. [PMID: 34680072 PMCID: PMC8533076 DOI: 10.3390/biom11101439] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022] Open
Abstract
The lipid-anchored RAS (Rat sarcoma) small GTPases (guanosine triphosphate hydrolases) are highly prevalent in human cancer. Traditional strategies of targeting the enzymatic activities of RAS have been shown to be difficult. Alternatively, RAS function and pathology are mostly restricted to nanoclusters on the plasma membrane (PM). Lipids are important structural components of these signaling platforms on the PM. However, how RAS nanoclusters selectively enrich distinct lipids in the PM, how different lipids contribute to RAS signaling and oncogenesis and whether the selective lipid sorting of RAS nanoclusters can be targeted have not been well-understood. Latest advances in quantitative super-resolution imaging and molecular dynamic simulations have allowed detailed characterization RAS/lipid interactions. In this review, we discuss the latest findings on the select lipid composition (with headgroup and acyl chain specificities) within RAS nanoclusters, the specific mechanisms for the select lipid sorting of RAS nanoclusters on the PM and how perturbing lipid compositions within RAS nanoclusters impacts RAS function and pathology. We also describe different strategies of manipulating lipid composition within RAS nanoclusters on the PM.
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44
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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45
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Zhou Y, Ariotti N, Rae J, Liang H, Tillu V, Tee S, Bastiani M, Bademosi AT, Collins BM, Meunier FA, Hancock JF, Parton RG. Caveolin-1 and cavin1 act synergistically to generate a unique lipid environment in caveolae. J Cell Biol 2021; 220:211716. [PMID: 33496726 PMCID: PMC7844427 DOI: 10.1083/jcb.202005138] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 11/20/2020] [Accepted: 12/21/2020] [Indexed: 01/09/2023] Open
Abstract
Caveolae are specialized domains of the vertebrate cell surface with a well-defined morphology and crucial roles in cell migration and mechanoprotection. Unique compositions of proteins and lipids determine membrane architectures. The precise caveolar lipid profile and the roles of the major caveolar structural proteins, caveolins and cavins, in selectively sorting lipids have not been defined. Here, we used quantitative nanoscale lipid mapping together with molecular dynamic simulations to define the caveolar lipid profile. We show that caveolin-1 (CAV1) and cavin1 individually sort distinct plasma membrane lipids. Intact caveolar structures composed of both CAV1 and cavin1 further generate a unique lipid nano-environment. The caveolar lipid sorting capability includes selectivities for lipid headgroups and acyl chains. Because lipid headgroup metabolism and acyl chain remodeling are tightly regulated, this selective lipid sorting may allow caveolae to act as transit hubs to direct communications among lipid metabolism, vesicular trafficking, and signaling.
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Affiliation(s)
- Yong Zhou
- Department of Integrative Biology and Pharmacology, University of Texas Medical School, Houston, TX
| | - Nicholas Ariotti
- University of New South Wales Sydney, Mark Wainwright Analytical Center, Sydney, New South Wales, Australia.,University of New South Wales Sydney, Department of Pathology, School of Medical Sciences, Kensington, Sydney, New South Wales, Australia
| | - James Rae
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, University of Texas Medical School, Houston, TX
| | - Vikas Tillu
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Shern Tee
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Michele Bastiani
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Adekunle T Bademosi
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Brett M Collins
- University of New South Wales Sydney, Department of Pathology, School of Medical Sciences, Kensington, Sydney, New South Wales, Australia
| | - Frederic A Meunier
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Medical School, Houston, TX.,Program in Cell and Regulatory Biology, University of Texas Graduate School of Biomedical Sciences, Houston, TX
| | - Robert G Parton
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia.,The University of Queensland, Centre for Microscopy and Microanalysis, Brisbane, Queensland, Australia
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Abstract
Pancreatic cancer is an almost incurable malignancy whose incidence has increased over the past 30 years. Instead of pursuing the development of modalities utilizing 'traditional' cytotoxic chemotherapeutic agents, we have explored the possibilities of developing novel multi-kinase inhibitor drug combinations to kill this tumor type. Several approaches using the multi-kinase inhibitors sorafenib, regorafenib, and neratinib have been safely translated from the bench to the bedside, with objective anti-tumor responses. This review will discuss our prior preclinical and clinical studies and discuss future clinical opportunities in this disease.
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47
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Motta M, Sagi-Dain L, Krumbach OHF, Hahn A, Peleg A, German A, Lissewski C, Coppola S, Pantaleoni F, Kocherscheid L, Altmüller F, Schanze D, Logeswaran T, Chahrokh-Zadeh S, Munzig A, Nakhaei-Rad S, Cavé H, Ahmadian MR, Tartaglia M, Zenker M. Activating MRAS mutations cause Noonan syndrome associated with hypertrophic cardiomyopathy. Hum Mol Genet 2021; 29:1772-1783. [PMID: 31108500 DOI: 10.1093/hmg/ddz108] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 02/07/2023] Open
Abstract
The RASopathies are a group of genetic syndromes caused by upregulated RAS signaling. Noonan syndrome (NS), the most common entity among the RASopathies, is characterized mainly by short stature, cardiac anomalies and distinctive facial features. Mutations in multiple RAS-MAPK pathway-related genes have been associated with NS and related phenotypes. We describe two unrelated patients presenting with hypertrophic cardiomyopathy (HCM) and dysmorphic features suggestive of NS. One of them died in the neonatal period because of cardiac failure. Targeted sequencing revealed de novo MRAS variants, c.203C > T (p.Thr68Ile) and c.67G > C (p.Gly23Arg) as causative events. MRAS has only recently been related to NS based on the observation of two unrelated affected individuals with de novo variants involving the same codons here found mutated. Gly23 and Thr68 are highly conserved residues, and the corresponding codons are known hotspots for RASopathy-associated mutations in other RAS proteins. Functional analyses documented high level of activation of MRAS mutants due to impaired GTPase activity, which was associated with constitutive plasma membrane targeting, prolonged localization in non-raft microdomains, enhanced binding to PPP1CB and SHOC2 protein, and variably increased MAPK and PI3K-AKT activation. This report provides additional evidence that a narrow spectrum of activating mutations in MRAS represents another rare cause of NS, and that MRAS has to be counted among the RASopathy genes predisposing to HCM. Moreover, our findings further emphasize the relevance of the MRAS-SHOC2-PPP1CB axis in the control of MAPK signaling, and the contribution of both MAPK and PI3K-AKT pathways in MRAS functional upregulation.
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Affiliation(s)
- Marialetizia Motta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Lena Sagi-Dain
- The Human Genetic institute, Carmel Medical Center, Ruth and Bruce Rappaport Faculty of Medicine, Israel Institute of Technology, Haifa, Israel
| | - Oliver H F Krumbach
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
| | - Andreas Hahn
- Department of Child Neurology, University Hospital, Gießen, Germany
| | - Amir Peleg
- The Human Genetic institute, Carmel Medical Center, Ruth and Bruce Rappaport Faculty of Medicine, Israel Institute of Technology, Haifa, Israel
| | - Alina German
- Pediatric Department, Bnai-Zion Medical Center and Clalit Health Maintenance Organization, Haifa, Israel
| | | | - Simona Coppola
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | | | - Denny Schanze
- Institute of Human Genetics, University Hospital, Magdeburg, Germany
| | | | | | - Anna Munzig
- Center of Human Genetics and Laboratory Diagnostics, Martinsried, Germany
| | - Saeideh Nakhaei-Rad
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
| | - Hélène Cavé
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, 75019 Paris, France.,INSERM UMR 1131, Institut de Recherche Saint-Louis, Université de Paris, 75010 Paris, France
| | - Mohammad R Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Martin Zenker
- Institute of Human Genetics, University Hospital, Magdeburg, Germany
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48
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Inhibition of RAS: proven and potential vulnerabilities. Biochem Soc Trans 2021; 48:1831-1841. [PMID: 32869838 DOI: 10.1042/bst20190023] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023]
Abstract
RAS is a membrane localized small GTPase frequently mutated in human cancer. As such, RAS has been a focal target for developing cancer therapeutics since its discovery nearly four decades ago. However, efforts to directly target RAS have been challenging due to the apparent lack of readily discernable deep pockets for binding small molecule inhibitors leading many to consider RAS as undruggable. An important milestone in direct RAS inhibition was achieved recently with the groundbreaking discovery of covalent inhibitors that target the mutant Cys residue in KRAS(G12C). Surprisingly, these G12C-reactive compounds only target mutant RAS in the GDP-bound state thereby locking it in the inactive conformation and blocking its ability to couple with downstream effector pathways. Building on this success, several groups have developed similar compounds that selectively target KRAS(G12C), with AMG510 and MRTX849 the first to advance to clinical trials. Both have shown early promising results. Though the success with these compounds has reignited the possibility of direct pharmacological inhibition of RAS, these covalent inhibitors are limited to treating KRAS(G12C) tumors which account for <15% of all RAS mutants in human tumors. Thus, there remains an unmet need to identify more broadly efficacious RAS inhibitors. Here, we will discuss the current state of RAS(G12C) inhibitors and the potential for inhibiting additional RAS mutants through targeting RAS dimerization which has emerged as an important step in the allosteric regulation of RAS function.
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49
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Campbell SL, Philips MR. Post-translational modification of RAS proteins. Curr Opin Struct Biol 2021; 71:180-192. [PMID: 34365229 DOI: 10.1016/j.sbi.2021.06.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 06/25/2021] [Indexed: 11/26/2022]
Abstract
Mutations of RAS genes drive cancer more frequently than any other oncogene. RAS proteins integrate signals from a wide array of receptors and initiate downstream signaling through pathways that control cellular growth. RAS proteins are fundamentally binary molecular switches in which the off/on state is determined by the binding of GDP or GTP, respectively. As such, the intrinsic and regulated nucleotide-binding and hydrolytic properties of the RAS GTPase were historically believed to account for the entirety of the regulation of RAS signaling. However, it is increasingly clear that RAS proteins are also regulated by a vast array of post-translational modifications (PTMs). The current challenge is to understand what are the functional consequences of these modifications and which are physiologically relevant. Because PTMs are catalyzed by enzymes that may offer targets for drug discovery, the study of RAS PTMs has been a high priority for RAS biologists.
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Affiliation(s)
| | - Mark R Philips
- Perlmutter Cancer Center, NYU Grossman School of Medicine, USA
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50
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Dent P, Booth L, Poklepovic A, Von Hoff D, Martinez J, Zhou Y, Hancock JF. Osimertinib-resistant NSCLC cells activate ERBB2 and YAP/TAZ and are killed by neratinib. Biochem Pharmacol 2021; 190:114642. [PMID: 34077739 PMCID: PMC11082938 DOI: 10.1016/j.bcp.2021.114642] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 11/15/2022]
Abstract
We performed additional mechanistic analyses to redefine neratinib biology and determined the mechanisms by which the multi-kinase inhibitor neratinib interacted with the thymidylate synthase inhibitor pemetrexed to kill NSCLC cells expressing either mutant KRAS (G12S; Q61H; G12A; G12C) or mutant NRAS (Q61K) or mutant ERBB1 (L858R; L858R T790M; exon 19 deletion). Neratinib rapidly reduced KRASG12V and RAC1G12V nanoclustering which was followed by KRASG12V, but not RAC1G12V, being extensively mislocalized away from the plasma membrane. This correlated with reduced levels of, and reorganized membrane localization of phosphatidylserine and cholesterol. Reduced nanoclustering was not associated with inactivation of ERBB1, Merlin or Ezrin. The drug combination killed cells expressing mutant KRAS, NRAS or mutant ERBB1 proteins. Afatinib or osimertinib resistant cells were killed with a similar efficacy to non-resistant cells. Compared to osimertinib-resistant cells, sensitive cells had less ERBB2 Y1248 phosphorylation. In osimertinib resistant H1975 cells, the drug combination was less capable of inactivating AKT, mTOR, STAT3, STAT5, ERK1/2 whereas it gained the ability to inactivate ERBB3. In resistant H1650 cells, the drug combination was less capable of inactivating JAK2 and STAT5. Sensitive cells exhibited elevated basal phosphorylation of YAP and TAZ. In resistant cells, portions of YAP and TAZ were localized in the nucleus. [Neratinib + pemetrexed] increased phosphorylation of YAP and TAZ, caused their nuclear exit, and enhanced ERBB2 degradation. Thus, neratinib targets an unidentified protein whose functional inhibition directly results in RAS inactivation and tumor cell killing. Our data prove that, albeit indirectly, oncogenic RAS proteins are druggable by neratinib.
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Affiliation(s)
- Paul Dent
- Department of Biochemistry and Molecular Biology, Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Translational Genomics Research Institute (TGEN), Phoenix, AZ 85004, United States; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX 77030, United States; Inflammation & Autoimmunity Group, National Institute of Environmental Health Sciences, Triangle Park, NC 27709, United States.
| | - Laurence Booth
- Department of Biochemistry and Molecular Biology, Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Translational Genomics Research Institute (TGEN), Phoenix, AZ 85004, United States; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX 77030, United States; Inflammation & Autoimmunity Group, National Institute of Environmental Health Sciences, Triangle Park, NC 27709, United States
| | - Andrew Poklepovic
- Department of Biochemistry and Molecular Biology, Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Translational Genomics Research Institute (TGEN), Phoenix, AZ 85004, United States; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX 77030, United States; Inflammation & Autoimmunity Group, National Institute of Environmental Health Sciences, Triangle Park, NC 27709, United States
| | - Daniel Von Hoff
- Department of Biochemistry and Molecular Biology, Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Translational Genomics Research Institute (TGEN), Phoenix, AZ 85004, United States; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX 77030, United States; Inflammation & Autoimmunity Group, National Institute of Environmental Health Sciences, Triangle Park, NC 27709, United States
| | - Jennifer Martinez
- Department of Biochemistry and Molecular Biology, Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Translational Genomics Research Institute (TGEN), Phoenix, AZ 85004, United States; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX 77030, United States; Inflammation & Autoimmunity Group, National Institute of Environmental Health Sciences, Triangle Park, NC 27709, United States
| | - Yong Zhou
- Department of Biochemistry and Molecular Biology, Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Translational Genomics Research Institute (TGEN), Phoenix, AZ 85004, United States; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX 77030, United States; Inflammation & Autoimmunity Group, National Institute of Environmental Health Sciences, Triangle Park, NC 27709, United States
| | - John F Hancock
- Department of Biochemistry and Molecular Biology, Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Translational Genomics Research Institute (TGEN), Phoenix, AZ 85004, United States; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX 77030, United States; Inflammation & Autoimmunity Group, National Institute of Environmental Health Sciences, Triangle Park, NC 27709, United States
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