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Tang N, Luo X, Ding Z, Shi Y, Cao X, Wu S. Single-Cell Multi-Dimensional data analysis reveals the role of ARL4C in driving rheumatoid arthritis progression and Macrophage polarization dynamics. Int Immunopharmacol 2024; 141:112987. [PMID: 39182267 DOI: 10.1016/j.intimp.2024.112987] [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: 05/19/2024] [Revised: 08/03/2024] [Accepted: 08/18/2024] [Indexed: 08/27/2024]
Abstract
Rheumatoid arthritis (RA) is an enduring autoimmune inflammatory condition distinguished by continual joint inflammation, hyperplasia of the synovium, erosion of bone, and deterioration of cartilage.Fibroblast-like synoviocytes (FLSs) exhibiting "tumor-like" traits are central to this mechanism.ADP-ribosylation factor-like 4c (ARL4C) functions as a Ras-like small GTP-binding protein, significantly impacting tumor migration, invasion, and proliferation.However, it remains uncertain if ARL4C participates in the stimulation of RA FLSs exhibiting "tumor-like" features, thereby fostering the advancement of RA. In our investigation, we unveiled, for the inaugural instance, via the amalgamated scrutiny of single-cell RNA sequencing (scRNA-seq) and Bulk RNA sequencing (Bulk-seq) datasets, that activated fibroblast-like synoviocytes (FLSs) showcase high expression of ARL4C, and the ARL4C protein expression in FLSs derived from RA patients significantly surpasses that observed in individuals with osteoarthritis (OA) and traumatic injury (trauma).Silencing of the ARL4C gene markedly impeded the proliferation of RA FLSs by hindered the transition of cells from the G0/G1 phase to the S phase, and intensified cell apoptosis and diminished the migratory and invasive capabilities. Co-culture of ARL4C gene-silenced RA FLSs with monocytes/macrophages significantly inhibited the polarization of monocytes/macrophages toward M1 and the repolarization of M2 to M1.Furthermore, intra-articular injection of shARL4C significantly alleviated synovial inflammation and cartilage erosion in collagen-induced arthritis (CIA) rats. In conclusion, our discoveries propose that ARL4C assumes a central role in the synovial inflammation, cartilage degradation, and bone erosion associated with RA by triggering the PI3K/AKT and MAPK signaling pathways within RA FLSs.ARL4C holds promise as a prospective target for the development of pharmaceutical agents targeting FLSs, with the aim of addressing RA.
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Affiliation(s)
- Ning Tang
- Department of Orthopaedics, Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Xin Luo
- Department of Orthopaedics, Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Zhiyu Ding
- Department of Orthopaedics, Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Yanbin Shi
- Department of Orthopaedics, Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Xu Cao
- Department of Orthopaedics, Third Xiangya Hospital, Central South University, Changsha, 410013, China.
| | - Song Wu
- Department of Orthopaedics, Third Xiangya Hospital, Central South University, Changsha, 410013, China.
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Parise A, Cresca S, Magistrato A. Molecular dynamics simulations for the structure-based drug design: targeting small-GTPases proteins. Expert Opin Drug Discov 2024; 19:1259-1279. [PMID: 39105536 DOI: 10.1080/17460441.2024.2387856] [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: 04/18/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024]
Abstract
INTRODUCTION Molecular Dynamics (MD) simulations can support mechanism-based drug design. Indeed, MD simulations by capturing biomolecule motions at finite temperatures can reveal hidden binding sites, accurately predict drug-binding poses, and estimate the thermodynamics and kinetics, crucial information for drug discovery campaigns. Small-Guanosine Triphosphate Phosphohydrolases (GTPases) regulate a cascade of signaling events, that affect most cellular processes. Their deregulation is linked to several diseases, making them appealing drug targets. The broad roles of small-GTPases in cellular processes and the recent approval of a covalent KRas inhibitor as an anticancer agent renewed the interest in targeting small-GTPase with small molecules. AREA COVERED This review emphasizes the role of MD simulations in elucidating small-GTPase mechanisms, assessing the impact of cancer-related variants, and discovering novel inhibitors. EXPERT OPINION The application of MD simulations to small-GTPases exemplifies the role of MD simulations in the structure-based drug design process for challenging biomolecular targets. Furthermore, AI and machine learning-enhanced MD simulations, coupled with the upcoming power of quantum computing, are promising instruments to target elusive small-GTPases mutations and splice variants. This powerful synergy will aid in developing innovative therapeutic strategies associated to small-GTPases deregulation, which could potentially be used for personalized therapies and in a tissue-agnostic manner to treat tumors with mutations in small-GTPases.
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Affiliation(s)
- Angela Parise
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
| | - Sofia Cresca
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
| | - Alessandra Magistrato
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
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3
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Wee Y, Wang J, Wilson EC, Rich CP, Rogers A, Tong Z, DeGroot E, Gopal YNV, Davies MA, Ekiz HA, Tay JKH, Stubben C, Boucher KM, Oviedo JM, Fairfax KC, Williams MA, Holmen SL, Wolff RK, Grossmann AH. Tumour-intrinsic endomembrane trafficking by ARF6 shapes an immunosuppressive microenvironment that drives melanomagenesis and response to checkpoint blockade therapy. Nat Commun 2024; 15:6613. [PMID: 39098861 PMCID: PMC11298541 DOI: 10.1038/s41467-024-50881-1] [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: 01/04/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024] Open
Abstract
Tumour-host immune interactions lead to complex changes in the tumour microenvironment (TME), impacting progression, metastasis and response to therapy. While it is clear that cancer cells can have the capacity to alter immune landscapes, our understanding of this process is incomplete. Herein we show that endocytic trafficking at the plasma membrane, mediated by the small GTPase ARF6, enables melanoma cells to impose an immunosuppressive TME that accelerates tumour development. This ARF6-dependent TME is vulnerable to immune checkpoint blockade therapy (ICB) but in murine melanoma, loss of Arf6 causes resistance to ICB. Likewise, downregulation of ARF6 in patient tumours correlates with inferior overall survival after ICB. Mechanistically, these phenotypes are at least partially explained by ARF6-dependent recycling, which controls plasma membrane density of the interferon-gamma receptor. Collectively, our findings reveal the importance of endomembrane trafficking in outfitting tumour cells with the ability to shape their immune microenvironment and respond to immunotherapy.
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Affiliation(s)
- Yinshen Wee
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- School of Dentistry, Taipei Medical University, Taipei, Taiwan
| | - Junhua Wang
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- Department of Oncologic Sciences, University of Utah, Salt Lake City, UT, USA
| | - Emily C Wilson
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Coulson P Rich
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Aaron Rogers
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Zongzhong Tong
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Evelyn DeGroot
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Y N Vashisht Gopal
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gulbahce, Urla, Izmir, Turkey
| | - Joshua K H Tay
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Chris Stubben
- Bioinformatics Shared Resource, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Kenneth M Boucher
- Cancer Biostatistics Shared Resource, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Juan M Oviedo
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Keke C Fairfax
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Matthew A Williams
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Sheri L Holmen
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- Department of Oncologic Sciences, University of Utah, Salt Lake City, UT, USA
- Department of Surgery, University of Utah, Salt Lake City, UT, USA
| | - Roger K Wolff
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Allie H Grossmann
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.
- Huntsman Cancer Institute, Salt Lake City, UT, USA.
- Department of Oncologic Sciences, University of Utah, Salt Lake City, UT, USA.
- Providence Cancer Institute of Oregon, Earle A. Chiles Research Institute, Portland, OR, USA.
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Pocognoni CA, Nawara T, Bhatt JM, Lee E, Jian X, Randazzo P, Sztul E. The lipid flippase ATP8A1 regulates the recruitment of ARF effectors to the trans-Golgi Network. Arch Biochem Biophys 2024; 758:110049. [PMID: 38879142 PMCID: PMC11264237 DOI: 10.1016/j.abb.2024.110049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/18/2024] [Accepted: 06/05/2024] [Indexed: 06/30/2024]
Abstract
Formation of transport vesicles requires the coordinate activity of the coating machinery that selects cargo into the nascent vesicle and the membrane bending machinery that imparts curvature to the forming bud. Vesicle coating at the trans-Golgi Network (TGN) involves AP1, GGA2 and clathrin, which are recruited to membranes by activated ARF GTPases. The ARF activation at the TGN is mediated by the BIG1 and BIG2 guanine nucleotide exchange factors (GEFs). Membrane deformation at the TGN has been shown to be mediated by lipid flippases, including ATP8A1, that moves phospholipids from the inner to the outer leaflet of the TGN membrane. We probed a possible coupling between the coating and deformation machineries by testing for an interaction between BIG1, BIG2 and ATP8A1, and by assessing whether such an interaction may influence coating efficiency. Herein, we document that BIG1 and BIG2 co-localize with ATP8A1 in both, static and highly mobile TGN elements, and that BIG1 and BIG2 bind ATP8A1. We show that the interaction involves the catalytic Sec7 domain of the GEFs and the cytosolic C-terminal tail of ATP8A1. Moreover, we report that the expression of ATP8A1, but not ATP8A1 lacking the GEF-binding cytosolic tail, increases the generation of activated ARFs at the TGN and increases the selective recruitment of AP1, GGA2 and clathrin to TGN membranes. This occurs without increasing BIG1 or BIG2 levels at the TGN, suggesting that the binding of the ATP8A1 flippase tail to the Sec7 domain of BIG1/BIG2 increases their catalytic activity. Our results support a model in which a flippase component of the deformation machinery impacts the activity of the GEF component of the coating machinery.
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Affiliation(s)
- Cristian A Pocognoni
- Instituto de Histología y Embriología de Mendoza (IHEM), Universidad Nacional de Cuyo, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mendoza 5500, Argentina.
| | - Tomasz Nawara
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Boulevard, MCLM 731, Birmingham, AL, 35233-2008, USA
| | - Jay M Bhatt
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Boulevard, MCLM 731, Birmingham, AL, 35233-2008, USA
| | - Eunjoo Lee
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Boulevard, MCLM 731, Birmingham, AL, 35233-2008, USA
| | - Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, NHLBI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Paul Randazzo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, NHLBI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Boulevard, MCLM 731, Birmingham, AL, 35233-2008, USA
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Mohr I, Mirzaiebadizi A, Sanyal SK, Chuenban P, Ahmadian MR, Ivanov R, Bauer P. Characterization of the small Arabidopsis thaliana GTPase and ADP-ribosylation factor-like 2 protein TITAN 5. J Cell Sci 2024; 137:jcs262315. [PMID: 39056156 PMCID: PMC11361645 DOI: 10.1242/jcs.262315] [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: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 07/28/2024] Open
Abstract
Small GTPases switch between GDP- and GTP-bound states during cell signaling. The ADP-ribosylation factor (ARF) family of small GTPases is involved in vesicle trafficking. Although evolutionarily well conserved, little is known about ARF and ARF-like GTPases in plants. We characterized biochemical properties and cellular localization of the essential small ARF-like GTPase TITAN 5 (TTN5; also known as HALLIMASCH, ARL2 and ARLC1) from Arabidopsis thaliana, and two TTN5 proteins with point mutants in conserved residues, TTN5T30N and TTN5Q70L, that were expected to be unable to perform nucleotide exchange and GTP hydrolysis, respectively. TTN5 exhibited very rapid intrinsic nucleotide exchange and remarkably low GTP hydrolysis activity, functioning as a non-classical small GTPase being likely present in a GTP-loaded active form. We analyzed signals from YFP-TTN5 and HA3-TTN5 by in situ immunolocalization in Arabidopsis seedlings and through use of a transient expression system. Colocalization with endomembrane markers and pharmacological treatments suggests that TTN5 can be present at the plasma membrane and that it dynamically associates with membranes of vesicles, Golgi stacks and multivesicular bodies. Although TTN5Q70L mirrored wild-type TTN5 behavior, the TTN5T30N mutant differed in some aspects. Hence, the unusual rapid nucleotide exchange activity of TTN5 is linked with its membrane dynamics, and TTN5 likely has a role in vesicle transport within the endomembrane system.
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Affiliation(s)
- Inga Mohr
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Amin Mirzaiebadizi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Sibaji K. Sanyal
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Pichaporn Chuenban
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
- Center for Plant Genome Engineering, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Mohammad R. Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Rumen Ivanov
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Heinrich Heine University, 40225 Düsseldorf, Germany
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6
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Bannoura SF, Khan HY, Uddin MH, Mohammad RM, Pasche BC, Azmi AS. Targeting guanine nucleotide exchange factors for novel cancer drug discovery. Expert Opin Drug Discov 2024; 19:949-959. [PMID: 38884380 PMCID: PMC11380440 DOI: 10.1080/17460441.2024.2368242] [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: 02/28/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
INTRODUCTION Guanine nucleotide exchange factors (GEFs) regulate the activation of small GTPases (G proteins) of the Ras superfamily proteins controlling cellular functions. Ras superfamily proteins act as 'molecular switches' that are turned 'ON' by guanine exchange. There are five major groups of Ras family GTPases: Ras, Ran, Rho, Rab and Arf, with a variety of different GEFs regulating their GTP loading. GEFs have been implicated in various diseases including cancer. This makes GEFs attractive targets to modulate signaling networks controlled by small GTPases. AREAS COVERED In this review, the roles and mechanisms of GEFs in malignancy are outlined. The mechanism of guanine exchange activity by GEFs on a small GTPase is illustrated. Then, some examples of GEFs that are significant in cancer are presented with a discussion on recent progress in therapeutic targeting efforts using a variety of approaches. EXPERT OPINION Recently, GEFs have emerged as potential therapeutic targets for novel cancer drug development. Targeting small GTPases is challenging; thus, targeting their activation by GEFs is a promising strategy. Most GEF-targeted drugs are still in preclinical development. A deeper biological understanding of the underlying mechanisms of GEF activity and utilizing advanced technology are necessary to enhance drug discovery for GEFs in cancer.
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Affiliation(s)
- Sahar F Bannoura
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Husain Yar Khan
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Md Hafiz Uddin
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ramzi M Mohammad
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Boris C Pasche
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Asfar S Azmi
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
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7
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Lee J, Miyagishima SY, Bhattacharya D, Yoon HS. From dusk till dawn: cell cycle progression in the red seaweed Gracilariopsis chorda (Rhodophyta). iScience 2024; 27:110190. [PMID: 38984202 PMCID: PMC11231608 DOI: 10.1016/j.isci.2024.110190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/29/2024] [Accepted: 06/03/2024] [Indexed: 07/11/2024] Open
Abstract
The conserved eukaryotic functions of cell cycle genes have primarily been studied using animal/plant models and unicellular algae. Cell cycle progression and its regulatory components in red (Rhodophyta) seaweeds are poorly understood. We analyzed diurnal gene expression data to investigate the cell cycle in the red seaweed Gracilariopsis chorda. We identified cell cycle progression and transitions in G. chorda which are induced by interactions of key regulators such as E2F/DP, RBR, cyclin-dependent kinases, and cyclins from dusk to dawn. However, several typical CDK inhibitor proteins are absent in red seaweeds. Interestingly, the G1-S transition in G. chorda is controlled by delayed transcription of GINS subunit 3. We propose that the delayed S phase entry in this seaweed may have evolved to minimize DNA damage (e.g., due to UV radiation) during replication. Our results provide important insights into cell cycle-associated physiology and its molecular mechanisms in red seaweeds.
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Affiliation(s)
- JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, Korea
| | - Shin-ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
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VanWinkle PE, Wynn B, Lee E, Nawara TJ, Thomas H, Parant JM, Alvarez C, Serra R, Sztul E. Lack of Nuclear Localization of the Creb3l1 Transcription Factor Causes Defects in Caudal Fin Bifurcation in Zebrafish Danio rerio. Cells Tissues Organs 2024:1-19. [PMID: 38964305 DOI: 10.1159/000540103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
INTRODUCTION The formation of normal bone and bone healing requires the cAMP-responsive element binding protein 3-like-1 (Creb3l1) transmembrane transcription factor, as deletion of the murine CREB3L1 results in osteopenic animals with limited capacity to repair bone after a fracture. Creb3l1 undergoes regulated intramembrane proteolysis (RIP) to release the N-terminal transcription activating (TA) fragment that enters the nucleus and regulates the expression of target genes. METHODS To expand our understanding of Creb3l1's role in skeletal development and skeletal patterning, we aimed to generate animals expressing only the TA fragment of Creb3l1 lacking the transmembrane domain and thereby not regulated through RIP. However, the CRISPR/Cas9-mediated genome editing in zebrafish Danio rerio caused a frameshift mutation that added 56 random amino acids at the C-terminus of the TA fragment (TA+), making it unable to enter the nucleus. Thus, TA+ does not regulate transcription, and the creb3l1TA+/TA+ fish do not mediate creb3l1-dependent transcription. RESULTS We document that the creb3l1TA+/TA+ fish exhibit defects in the patterning of caudal fin lepidotrichia, with significantly distalized points of proximal bifurcation and decreased secondary bifurcations. Moreover, using the caudal fin amputation model, we show that creb3l1TA+/TA+ fish have decreased regeneration and that their regenerates replicate the distalization and bifurcation defects observed in intact fins of creb3l1TA+/TA+ animals. These defects correlate with altered expression of the shha and ptch2 components of the Sonic Hedgehog signaling pathway in creb3l1TA+/TA+ regenerates. CONCLUSION Together, our results uncover a previously unknown intersection between Creb3l1 and the Sonic Hedgehog pathway and document a novel role of Creb3l1 in tissue patterning.
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Affiliation(s)
- Peyton E VanWinkle
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Bridge Wynn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Eunjoo Lee
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Tomasz J Nawara
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Holly Thomas
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - John M Parant
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Cecilia Alvarez
- CIBICI-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Rosa Serra
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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9
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Song R, Watanabe H, Tjen K, Westbury BC, Makita T, Tao G, Sucov HM. A natural loss-of-function deletion of the cytohesin 1 (Cyth1) gene in BALB/cByJ mice does not impact cardiomyocyte polyploidy. Sci Rep 2024; 14:13333. [PMID: 38858421 PMCID: PMC11164939 DOI: 10.1038/s41598-024-63667-8] [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: 02/22/2024] [Accepted: 05/30/2024] [Indexed: 06/12/2024] Open
Abstract
Mammalian cardiomyocytes (CMs) mostly become polyploid shortly after birth. Because this feature may relate to several aspects of heart biology, including regeneration after injury, the mechanisms that cause polyploidy are of interest. BALB/cJ and BALB/cByJ mice are highly related sister strains that diverge substantially in CM ploidy. We identified a large deletion in the Cyth1 gene that arose uniquely in BALB/cByJ mice that creates a null allele. The deletion also results in ectopic transcription of the downstream gene Dnah17, although this transcript is unlikely to encode a protein. By evaluating the natural null allele from BALB/cByJ and an engineered knockout allele in the C57BL/6J background, we determined that absence of Cyth1 does not by itself influence CM ploidy. The ready availability of BALB/cByJ mice may be helpful to other investigations of Cyth1 in other biological processes.
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Affiliation(s)
- Ruolan Song
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, USA
| | - Hirofumi Watanabe
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, USA
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Kelsey Tjen
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, USA
| | - Baylee C Westbury
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, USA
| | - Takako Makita
- Department of Pediatrics, Medical University of South Carolina, Charleston, USA
| | - Ge Tao
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, USA
| | - Henry M Sucov
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, USA.
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10
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Natsume M, Niwa M, Ichikawa S, Okamoto T, Tsutsui H, Usukura D, Murata T, Abe R, Shimonaka M, Nishida T, Shiina I, Obata Y. Brefeldin A and M-COPA block the export of RTKs from the endoplasmic reticulum via simultaneous inactivation of ARF1, ARF4, and ARF5. J Biol Chem 2024; 300:107327. [PMID: 38679330 PMCID: PMC11127164 DOI: 10.1016/j.jbc.2024.107327] [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: 10/17/2023] [Revised: 03/20/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024] Open
Abstract
Normal receptor tyrosine kinases (RTKs) need to reach the plasma membrane (PM) for ligand-induced activation, whereas its cancer-causing mutants can be activated before reaching the PM in organelles, such as the Golgi/trans-Golgi network (TGN). Inhibitors of protein export from the endoplasmic reticulum (ER), such as brefeldin A (BFA) and 2-methylcoprophilinamide (M-COPA), can suppress the activation of mutant RTKs in cancer cells, suggesting that RTK mutants cannot initiate signaling in the ER. BFA and M-COPA block the function of ADP-ribosylation factors (ARFs) that play a crucial role in ER-Golgi protein trafficking. However, among ARF family proteins, the specific ARFs inhibited by BFA or M-COPA, that is, the ARFs involved in RTKs transport from the ER, remain unclear. In this study, we showed that M-COPA blocked the export of not only KIT but also PDGFRA/EGFR/MET RTKs from the ER. ER-retained RTKs could not fully transduce anti-apoptotic signals, thereby leading to cancer cell apoptosis. Moreover, a single knockdown of ARF1, ARF3, ARF4, ARF5, or ARF6 could not block ER export of RTKs, indicating that BFA/M-COPA treatment cannot be mimicked by the knockdown of only one ARF member. Interestingly, simultaneous transfection of ARF1, ARF4, and ARF5 siRNAs mirrored the effect of BFA/M-COPA treatment. Consistent with these results, in vitro pulldown assays showed that BFA/M-COPA blocked the function of ARF1, ARF4, and ARF5. Taken together, these results suggest that BFA/M-COPA targets at least ARF1, ARF4, and ARF5; in other words, RTKs require the simultaneous activation of ARF1, ARF4, and ARF5 for their ER export.
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Affiliation(s)
- Miyuki Natsume
- Laboratory of Intracellular Traffic & Oncology, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan; Faculty of Science, Department of Applied Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Mariko Niwa
- Laboratory of Intracellular Traffic & Oncology, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan; Faculty of Science, Department of Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Sho Ichikawa
- Laboratory of Intracellular Traffic & Oncology, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan; Faculty of Science, Department of Applied Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Takuma Okamoto
- Laboratory of Intracellular Traffic & Oncology, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan; Faculty of Science, Department of Applied Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Hisazumi Tsutsui
- Faculty of Science, Department of Applied Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Daiki Usukura
- Faculty of Science, Department of Applied Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Takatsugu Murata
- Faculty of Science, Department of Applied Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Ryo Abe
- Tokyo University of Science, Noda, Chiba, Japan
| | - Motoyuki Shimonaka
- Faculty of Science, Department of Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Toshirou Nishida
- National Cancer Center Hospital, Chuo-ku, Tokyo, Japan; Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Isamu Shiina
- Faculty of Science, Department of Applied Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Yuuki Obata
- Laboratory of Intracellular Traffic & Oncology, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan.
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11
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Yang L, Zhang S, Zheng L, Kong F, Pu P, Li X, Jia L. Association of ADP‑ribosylation factor family genes with prognosis and immune infiltration of breast cancer. Oncol Lett 2024; 27:280. [PMID: 38699662 PMCID: PMC11063756 DOI: 10.3892/ol.2024.14413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/19/2024] [Indexed: 05/05/2024] Open
Abstract
Breast cancer (BC) is the most common type of cancer found in women. ADP-ribosylation factors (ARFs) are a group of small proteins that bind to GTP and are involved in controlling different cellular functions. The function and evolution of multiple ARFs in BC have remained to be fully elucidated, despite existing studies on this protein family in Homo sapiens and other species. In the present study, a systematic analysis of ARF expression levels in BC tissues compared to normal breast tissues was performed using data from The Cancer Genome Atlas database. The analysis revealed significantly higher expression of ARFs in BC tissues. In addition, the prognostic significance of ARF1 and ARF3-6 expression levels was assessed in patients with BC. Of note, elevated ARF1 expression was associated with reduced rates of distant metastasis-free survival (DMFS), overall survival (OS) and recurrence-free survival (RFS) in affected individuals. Similarly, patients with high expression levels of ARF3 had lower post-progression survival (PPS) rates. In addition, patients with higher ARF4 expression had worse PPS and patients with high ARF5 expression exhibited lower DMFS. Patients with high ARF6 expression had worse DMFS, OS, RFS and predictive power score values. Furthermore, the expression of ARF was found to be strongly linked to the infiltration of various immune cell types, namely dendritic cells, macrophages, neutrophils, CD8+ T cells and B cells. These significant associations offer a solid foundation for the potential utilization of new therapeutic targets and predictive markers for the treatment of BC.
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Affiliation(s)
- Lixian Yang
- Department of Breast Surgery, Xingtai People's Hospital, Xingtai, Hebei 054000, P.R. China
| | - Shiyu Zhang
- Department of Breast Surgery, Xingtai People's Hospital, Xingtai, Hebei 054000, P.R. China
| | - Lei Zheng
- Department of Breast Surgery, Xingtai People's Hospital, Xingtai, Hebei 054000, P.R. China
| | - Fanting Kong
- Department of Breast Surgery, Xingtai People's Hospital, Xingtai, Hebei 054000, P.R. China
| | - Pengpeng Pu
- Department of Breast Surgery, Xingtai People's Hospital, Xingtai, Hebei 054000, P.R. China
| | - Xiaowei Li
- Department of Breast Surgery, Xingtai People's Hospital, Xingtai, Hebei 054000, P.R. China
| | - Lining Jia
- Department of Breast Surgery, Xingtai People's Hospital, Xingtai, Hebei 054000, P.R. China
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12
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O'Donoghue L, Smolenski A. Roles of G proteins and their GTPase-activating proteins in platelets. Biosci Rep 2024; 44:BSR20231420. [PMID: 38808367 PMCID: PMC11139668 DOI: 10.1042/bsr20231420] [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: 11/17/2023] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024] Open
Abstract
Platelets are small anucleate blood cells supporting vascular function. They circulate in a quiescent state monitoring the vasculature for injuries. Platelets adhere to injury sites and can be rapidly activated to secrete granules and to form platelet/platelet aggregates. These responses are controlled by signalling networks that include G proteins and their regulatory guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Recent proteomics studies have revealed the complete spectrum of G proteins, GEFs, and GAPs present in platelets. Some of these proteins are specific for platelets and very few have been characterised in detail. GEFs and GAPs play a major role in setting local levels of active GTP-bound G proteins in response to activating and inhibitory signals encountered by platelets. Thus, GEFs and GAPs are highly regulated themselves and appear to integrate G protein regulation with other cellular processes. This review focuses on GAPs of small G proteins of the Arf, Rab, Ras, and Rho families, as well as of heterotrimeric G proteins found in platelets.
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Affiliation(s)
- Lorna O'Donoghue
- UCD School of Medicine, University College Dublin, UCD Conway Institute, Belfield, Dublin 4, Ireland
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green 123, Dublin 2, Ireland
| | - Albert Smolenski
- UCD School of Medicine, University College Dublin, UCD Conway Institute, Belfield, Dublin 4, Ireland
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green 123, Dublin 2, Ireland
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13
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Mohr I, Mirzaiebadizi A, Sanyal SK, Chuenban P, Ahmadian MR, Ivanov R, Bauer P. Characterization of the small Arabidopsis thaliana GTPase and ADP-ribosylation factor-like 2 protein TITAN 5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.27.538563. [PMID: 37162876 PMCID: PMC10168340 DOI: 10.1101/2023.04.27.538563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Small GTPases function by conformational switching ability between GDP- and GTP-bound states in rapid cell signaling events. The ADP-ribosylation factor (ARF) family is involved in vesicle trafficking. Though evolutionarily well conserved, little is known about ARF and ARF-like GTPases in plants. Here, we characterized biochemical properties and cellular localization of the essential small ARF-like GTPase TITAN 5/HALLIMASCH/ARL2/ARLC1 (hereafter termed TTN5) from Arabidopsis thaliana. Two TTN5 variants were included in the study with point mutations at conserved residues, suspected to be functional for nucleotide exchange and GTP hydrolysis, TTN5T30N and TTN5Q70L. We found that TTN5 had a very rapid intrinsic nucleotide exchange capacity with a conserved nucleotide switching mechanism. TTN5 acted as a non-classical small GTPase with a remarkably low GTP hydrolysis activity, suggesting it is likely present in GTP-loaded active form in the cell. We analyzed signals from yellow fluorescent protein (YFP)-tagged TTN5 and from in situ immunolocalization of hemagglutine-tagged HA3-TTN5 in Arabidopsis seedlings and in a transient expression system. Together with colocalization using endomembrane markers and pharmacological treatments the microscopic analysis suggests that TTN5 can be present at the plasma membrane and dynamically associated with membranes of vesicles, Golgi stacks and multivesicular bodies. While the TTN5Q70L variant showed similar GTPase activities and localization behavior as wild-type TTN5, the TTN5T30N mutant differed in some aspects. Hence, the unusual capacity of rapid nucleotide exchange activity of TTN5 is linked with cell membrane dynamics, likely associated with vesicle transport pathways in the endomembrane system.
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Affiliation(s)
- Inga Mohr
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Amin Mirzaiebadizi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Sibaji K Sanyal
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Pichaporn Chuenban
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Mohammad R Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Rumen Ivanov
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Heinrich Heine University, 40225 Düsseldorf, Germany
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14
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Suzuki K, Okawa Y, Akter S, Ito H, Shiba Y. Arf GTPase-Activating proteins ADAP1 and ARAP1 regulate incorporation of CD63 in multivesicular bodies. Biol Open 2024; 13:bio060338. [PMID: 38682696 PMCID: PMC11103404 DOI: 10.1242/bio.060338] [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: 01/26/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024] Open
Abstract
Arf GTPase-activating proteins (ArfGAPs) mediate the hydrolysis of GTP bound to ADP-ribosylation factors. ArfGAPs are critical for cargo sorting in the Golgi-to-ER traffic. However, the role of ArfGAPs in sorting into intralumenal vesicles (ILVs) in multivesicular bodies (MVBs) in post-Golgi traffic remains unclear. Exosomes are extracellular vesicles (EVs) of endosomal origin. CD63 is an EV marker. CD63 is enriched ILVs in MVBs of cells. However, the secretion of CD63 positive EVs has not been consistent with the data on CD63 localization in MVBs, and how CD63-containing EVs are formed is yet to be understood. To elucidate the mechanism of CD63 transport to ILVs, we focused on CD63 localization in MVBs and searched for the ArfGAPs involved in CD63 localization. We observed that ADAP1 and ARAP1 depletion inhibited CD63 localization to enlarged endosomes after Rab5Q79L overexpression. We tested epidermal growth factor (EGF) and CD9 localization in MVBs. We observed that ADAP1 and ARAP1 depletion inhibited CD9 localization in enlarged endosomes but not EGF. Our results indicate ADAP1 and ARAP1, regulate incorporation of CD63 and CD9, but not EGF, in overlapped and different MVBs. Our work will contribute to distinguish heterogenous ILVs and exosomes by ArfGAPs.
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Affiliation(s)
- Kasumi Suzuki
- Graduate course of Biological Sciences, Division of Science and Engineering, Graduate School of Arts and Sciences, Iwate University, 020-8551, Morioka, Japan
| | - Yoshitaka Okawa
- Graduate course of Biological Sciences, Division of Science and Engineering, Graduate School of Arts and Sciences, Iwate University, 020-8551, Morioka, Japan
| | - Sharmin Akter
- Graduate course of Biological Sciences, Division of Science and Engineering, Graduate School of Arts and Sciences, Iwate University, 020-8551, Morioka, Japan
| | - Haruki Ito
- Biological Sciences Course, Faculty of Science and Engineering, Iwate University, 020-8551, Morioka, Japan
| | - Yoko Shiba
- Graduate course of Biological Sciences, Division of Science and Engineering, Graduate School of Arts and Sciences, Iwate University, 020-8551, Morioka, Japan
- Biological Sciences Course, Faculty of Science and Engineering, Iwate University, 020-8551, Morioka, Japan
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15
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López-Landavery EA, Urquizo-Rosado Á, Saavedra-Flores A, Tapia-Morales S, Fernandino JI, Zelada-Mázmela E. Cellular and transcriptomic response to pathogenic and non-pathogenic Vibrio parahaemolyticus strains causing acute hepatopancreatic necrosis disease (AHPND) in Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2024; 148:109472. [PMID: 38438059 DOI: 10.1016/j.fsi.2024.109472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
The shrimp industry has historically been affected by viral and bacterial diseases. One of the most recent emerging diseases is Acute Hepatopancreatic Necrosis Disease (AHPND), which causes severe mortality. Despite its significance to sanitation and economics, little is known about the molecular response of shrimp to this disease. Here, we present the cellular and transcriptomic responses of Litopenaeus vannamei exposed to two Vibrio parahaemolyticus strains for 98 h, wherein one is non-pathogenic (VpN) and the other causes AHPND (VpP). Exposure to the VpN strain resulted in minor alterations in hepatopancreas morphology, including reductions in the size of R and B cells and detachments of small epithelial cells from 72 h onwards. On the other hand, exposure to the VpP strain is characterized by acute detachment of epithelial cells from the hepatopancreatic tubules and infiltration of hemocytes in the inter-tubular spaces. At the end of exposure, RNA-Seq analysis revealed functional enrichment in biological processes, such as the toll3 receptor signaling pathway, apoptotic processes, and production of molecular mediators involved in the inflammatory response of shrimp exposed to VpN treatment. The biological processes identified in the VpP treatment include superoxide anion metabolism, innate immune response, antimicrobial humoral response, and toll3 receptor signaling pathway. Furthermore, KEGG enrichment analysis revealed metabolic pathways associated with survival, cell adhesion, and reactive oxygen species, among others, for shrimp exposed to VpP. Our study proves the differential immune responses to two strains of V. parahaemolyticus, one pathogenic and the other nonpathogenic, enlarges our knowledge on the evolution of AHPND in L. vannamei, and uncovers unique perspectives on establishing genomic resources that may function as a groundwork for detecting probable molecular markers linked to the immune system in shrimp.
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Affiliation(s)
- Edgar A López-Landavery
- Laboratorio de Genética, Fisiología y Reproducción, Facultad de Ciencias, Universidad Nacional del Santa, Nuevo Chimbote, Ancash, Peru.
| | - Ángela Urquizo-Rosado
- Laboratorio de Genética, Fisiología y Reproducción, Facultad de Ciencias, Universidad Nacional del Santa, Nuevo Chimbote, Ancash, Peru
| | - Anaid Saavedra-Flores
- Laboratorio de Genética, Fisiología y Reproducción, Facultad de Ciencias, Universidad Nacional del Santa, Nuevo Chimbote, Ancash, Peru
| | - Sandra Tapia-Morales
- Laboratorio de Genética, Fisiología y Reproducción, Facultad de Ciencias, Universidad Nacional del Santa, Nuevo Chimbote, Ancash, Peru
| | - Juan I Fernandino
- Laboratorio de Genética, Fisiología y Reproducción, Facultad de Ciencias, Universidad Nacional del Santa, Nuevo Chimbote, Ancash, Peru; Laboratorio de Biología del Desarrollo - Instituto Tecnológico de Chascomús. INTECH (CONICET-UNSAM), Argentina; Escuela de Bio y Nanotecnologías (UNSAM). Chascomús, Argentina.
| | - Eliana Zelada-Mázmela
- Laboratorio de Genética, Fisiología y Reproducción, Facultad de Ciencias, Universidad Nacional del Santa, Nuevo Chimbote, Ancash, Peru.
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16
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Quirion L, Robert A, Boulais J, Huang S, Bernal Astrain G, Strakhova R, Jo CH, Kherdjemil Y, Faubert D, Thibault MP, Kmita M, Baskin JM, Gingras AC, Smith MJ, Côté JF. Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways. J Cell Sci 2024; 137:jcs262140. [PMID: 38606629 PMCID: PMC11166204 DOI: 10.1242/jcs.262140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024] Open
Abstract
The ADP-ribosylation factors (ARFs) and ARF-like (ARL) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we used proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ∼3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely, SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.
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Affiliation(s)
- Laura Quirion
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Amélie Robert
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Jonathan Boulais
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Shiying Huang
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Gabriela Bernal Astrain
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Regina Strakhova
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Chang Hwa Jo
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Yacine Kherdjemil
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Denis Faubert
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | | | - Marie Kmita
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Experimental Medicine, McGill University, Montréal, QC H3G 2M1, Canada
| | - Jeremy M. Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Matthew J. Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Jean-François Côté
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
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17
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Wong HN, Chen T, Wang PJ, Holzman LB. ARF6, a component of intercellular bridges, is essential for spermatogenesis in mice. Dev Biol 2024; 508:46-63. [PMID: 38242343 DOI: 10.1016/j.ydbio.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
Male germ cells are connected by intercellular bridges (ICBs) in a syncytium due to incomplete cytokinesis. Syncytium is thought to be important for synchronized germ cell development by interchange of cytoplasmic factors via ICBs. Mammalian ADP-ribosylation factor 6 (ARF6) is a small GTPase that is involved in many cellular mechanisms including but not limited to regulating cellular structure, motility, vesicle trafficking and cytokinesis. ARF6 localizes to ICBs in spermatogonia and spermatocytes in mice. Here we report that mice with global depletion of ARF6 in adulthood using Ubc-CreERT2 display no observable phenotypes but are male sterile. ARF6-deficient males display a progressive loss of germ cells, including LIN28A-expressing spermatogonia, and ultimately develop Sertoli-cell-only syndrome. Specifically, intercellular bridges are lost in ARF6-deficient testis. Furthermore, germ cell-specific inactivation using the Ddx4-CreERT2 results in the same testicular morphological phenotype, showing the germ cell-intrinsic requirement of ARF6. Therefore, ARF6 is essential for spermatogenesis in mice and this function is conserved from Drosophila to mammals.
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Affiliation(s)
- Hetty N Wong
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Tingfang Chen
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - P Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19104, USA
| | - Lawrence B Holzman
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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18
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Quirion L, Robert A, Boulais J, Huang S, Bernal Astrain G, Strakhova R, Jo CH, Kherdjemil Y, Thibault MP, Faubert D, Kmita M, Baskin JM, Gingras AC, Smith MJ, Cote JF. Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.01.530598. [PMID: 36909472 PMCID: PMC10002736 DOI: 10.1101/2023.03.01.530598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The ADP-ribosylation factors (ARFs) and ARF-like (ARLs) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we utilized proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ~3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.
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19
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Koike S, Jahn R. Rab GTPases and phosphoinositides fine-tune SNAREs dependent targeting specificity of intracellular vesicle traffic. Nat Commun 2024; 15:2508. [PMID: 38509070 PMCID: PMC10954720 DOI: 10.1038/s41467-024-46678-x] [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: 02/06/2023] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
In the secretory pathway the destination of trafficking vesicles is determined by specific proteins that, with the notable exception of SNAREs, are recruited from soluble pools. Previously we have shown that microinjected proteoliposomes containing early or late endosomal SNAREs, respectively, are targeted to the corresponding endogenous compartments, with targeting specificity being dependent on the recruitment of tethering factors by some of the SNAREs. Here, we show that targeting of SNARE-containing liposomes is refined upon inclusion of polyphosphoinositides and Rab5. Intriguingly, targeting specificity is dependent on the concentration of PtdIns(3)P, and on the recruitment of PtdIns(3)P binding proteins such as rabenosyn-5 and PIKfyve, with conversion of PtdIns(3)P into PtdIns(3,5)P2 re-routing the liposomes towards late endosomes despite the presence of GTP-Rab5 and early endosomal SNAREs. Our data reveal a complex interplay between permissive and inhibitory targeting signals that sharpen a basic targeting and fusion machinery for conveying selectivity in intracellular membrane traffic.
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Affiliation(s)
- Seiichi Koike
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- University of Toyama, Laboratory of Molecular and Cellular Biology, Department of Life Sciences and Bioengineering, 3190 Gofuku, Toyama City, 930-8555, Japan
| | - Reinhard Jahn
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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20
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Ferreira A, Castanheira P, Escrevente C, Barral DC, Barona T. Membrane trafficking alterations in breast cancer progression. Front Cell Dev Biol 2024; 12:1350097. [PMID: 38533085 PMCID: PMC10963426 DOI: 10.3389/fcell.2024.1350097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/12/2024] [Indexed: 03/28/2024] Open
Abstract
Breast cancer (BC) is the most common type of cancer in women, and remains one of the major causes of death in women worldwide. It is now well established that alterations in membrane trafficking are implicated in BC progression. Indeed, membrane trafficking pathways regulate BC cell proliferation, migration, invasion, and metastasis. The 22 members of the ADP-ribosylation factor (ARF) and the >60 members of the rat sarcoma (RAS)-related in brain (RAB) families of small GTP-binding proteins (GTPases), which belong to the RAS superfamily, are master regulators of membrane trafficking pathways. ARF-like (ARL) subfamily members are involved in various processes, including vesicle budding and cargo selection. Moreover, ARFs regulate cytoskeleton organization and signal transduction. RABs are key regulators of all steps of membrane trafficking. Interestingly, the activity and/or expression of some of these proteins is found dysregulated in BC. Here, we review how the processes regulated by ARFs and RABs are subverted in BC, including secretion/exocytosis, endocytosis/recycling, autophagy/lysosome trafficking, cytoskeleton dynamics, integrin-mediated signaling, among others. Thus, we provide a comprehensive overview of the roles played by ARF and RAB family members, as well as their regulators in BC progression, aiming to lay the foundation for future research in this field. This research should focus on further dissecting the molecular mechanisms regulated by ARFs and RABs that are subverted in BC, and exploring their use as therapeutic targets or prognostic markers.
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21
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Sulimenko V, Sládková V, Sulimenko T, Dráberová E, Vosecká V, Dráberová L, Skalli O, Dráber P. Regulation of microtubule nucleation in mouse bone marrow-derived mast cells by ARF GTPase-activating protein GIT2. Front Immunol 2024; 15:1321321. [PMID: 38370406 PMCID: PMC10870779 DOI: 10.3389/fimmu.2024.1321321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/16/2024] [Indexed: 02/20/2024] Open
Abstract
Aggregation of high-affinity IgE receptors (FcϵRIs) on granulated mast cells triggers signaling pathways leading to a calcium response and release of inflammatory mediators from secretory granules. While microtubules play a role in the degranulation process, the complex molecular mechanisms regulating microtubule remodeling in activated mast cells are only partially understood. Here, we demonstrate that the activation of bone marrow mast cells induced by FcϵRI aggregation increases centrosomal microtubule nucleation, with G protein-coupled receptor kinase-interacting protein 2 (GIT2) playing a vital role in this process. Both endogenous and exogenous GIT2 were associated with centrosomes and γ-tubulin complex proteins. Depletion of GIT2 enhanced centrosomal microtubule nucleation, and phenotypic rescue experiments revealed that GIT2, unlike GIT1, acts as a negative regulator of microtubule nucleation in mast cells. GIT2 also participated in the regulation of antigen-induced degranulation and chemotaxis. Further experiments showed that phosphorylation affected the centrosomal localization of GIT2 and that during antigen-induced activation, GIT2 was phosphorylated by conventional protein kinase C, which promoted microtubule nucleation. We propose that GIT2 is a novel regulator of microtubule organization in activated mast cells by modulating centrosomal microtubule nucleation.
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Affiliation(s)
- Vadym Sulimenko
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Vladimíra Sládková
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Tetyana Sulimenko
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Eduarda Dráberová
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Věra Vosecká
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Lubica Dráberová
- Laboratory of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Omar Skalli
- Department of Biological Sciences, The University of Memphis, Memphis, TN, United States
| | - Pavel Dráber
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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22
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Kumar R, Khan M, Francis V, Aguila A, Kulasekaran G, Banks E, McPherson PS. DENND6A links Arl8b to a Rab34/RILP/dynein complex, regulating lysosomal positioning and autophagy. Nat Commun 2024; 15:919. [PMID: 38296963 PMCID: PMC10830484 DOI: 10.1038/s41467-024-44957-1] [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: 08/21/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024] Open
Abstract
Lysosomes help maintain cellular proteostasis, and defects in lysosomal positioning and function can cause disease, including neurodegenerative disorders. The spatiotemporal distribution of lysosomes is regulated by small GTPases including Rabs, which are activated by guanine nucleotide exchange factors (GEFs). DENN domain proteins are the largest family of Rab GEFs. Using a cell-based assay, we screened DENND6A, a member of the DENN domain protein family against all known Rabs and identified it as a potential GEF for 20 Rabs, including Rab34. Here, we demonstrate that DENND6A activates Rab34, which recruits a RILP/dynein complex to lysosomes, promoting lysosome retrograde transport. Further, we identify DENND6A as an effector of Arl8b, a major regulatory GTPase on lysosomes. We demonstrate that Arl8b recruits DENND6A to peripheral lysosomes to activate Rab34 and initiate retrograde transport, regulating nutrient-dependent lysosomal juxtanuclear repositioning. Loss of DENND6A impairs autophagic flux. Our findings support a model whereby Arl8b/DENND6A/Rab34-dependent lysosomal retrograde trafficking controls autophagy.
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Affiliation(s)
- Rahul Kumar
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada.
| | - Maleeha Khan
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada
| | - Vincent Francis
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada
| | - Adriana Aguila
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada
| | - Gopinath Kulasekaran
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada
| | - Emily Banks
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada
| | - Peter S McPherson
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada.
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23
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Matsuki T, Hamada N, Ito H, Sugawara R, Iwamoto I, Nakayama A, Nagata KI. Expression analysis of type I ARF small GTPases ARF1-3 during mouse brain development. Mol Biol Rep 2024; 51:106. [PMID: 38227057 DOI: 10.1007/s11033-023-09142-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND ARF (ADP-ribosylation factor) GTPases are major regulators of intracellular trafficking, and classified into 3 groups (Type I - III), among which the type I group members, ARF1 and 3, are responsible genes for neurodevelopmental disorders. METHODS In this study, we analysed the expression of Type I ARFs ARF1-3 during mouse brain development using biochemical and morphological methods. RESULTS Western blotting analyses revealed that ARF1-3 are weakly expressed in the mouse brain at embryonic day 13 and gradually increase until postnatal day 30. ARF1-3 appear to be abundantly expressed in various telencephalon regions. Biochemical fractionation studies detected ARF1-3 in the synaptosome fraction of cortical neurons containing both pre- and post-synapses, however ARF1-3 were not observed in post-synaptic compartments. In immunohistochemical analyses, ARF1-3 appeared to be distributed in the cytoplasm and dendrites of cortical and hippocampal neurons as well as in the cerebellar molecular layer including dendrites of Purkinje cells and granule cell axons. Immunofluorescence in primary cultured hippocampal neurons revealed that ARF1-3 are diffusely distributed in the cytoplasm and dendrites with partial colocalization with a pre-synaptic marker, synaptophysin. CONCLUSIONS Overall, our results support the notion that ARF1-3 could participate in vesicle trafficking both in the dendritic shaft (excluding spines) and axon terminals (pre-synaptic compartments).
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Affiliation(s)
- Tohru Matsuki
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan
| | - Nanako Hamada
- Department of Molecular Neurobiology Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan
| | - Hidenori Ito
- Department of Molecular Neurobiology Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan
| | - Ryota Sugawara
- Department of Molecular Neurobiology Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan
| | - Ikuko Iwamoto
- Department of Molecular Neurobiology Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan
| | - Atsuo Nakayama
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan
- Department of Neurochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Nagoya, 466-8550, Japan
| | - Koh-Ichi Nagata
- Department of Molecular Neurobiology Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan.
- Department of Neurochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Nagoya, 466-8550, Japan.
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24
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Sun X, Li Y, He Y, Cheng L, Wei J, Du L, Shen Z, Yoshida S. GTPase-activating protein ARAP1 regulates circular dorsal ruffles as a nutrient uptake mechanism in the Hep3B hepatocellular carcinoma cell line. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573800. [PMID: 38260345 PMCID: PMC10802275 DOI: 10.1101/2023.12.31.573800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Circular dorsal ruffles (CDRs), large-scale rounded membrane ruffles, function as precursors of macropinocytosis. We recently reported that CDRs are exposed in the Hep3B hepatocellular carcinoma cell line, while not in other hepatocellular carcinoma cell lines, indicating that the CDRs in Hep3B are associated with malignant potential. In this study, we investigated the cellular function of CDRs in Hep3B cells by focusing on the molecular mechanisms of the GTPase-activating protein ARAP1. ARAP1 was localized to the CDRs, the sizes of which were reduced by deletion of this protein. High-resolution scanning electron micrographs revealed that CDRs comprise small vertical lamellipodia, the expression pattern of which was disrupted in ARAP1 KO cells. Extracellular solute uptake, rate of cell growth, and malignant potential were attenuated in the KO cells. ARAP1 is also localized in Hep3B cell mitochondria, although not in those of the Huh7 hepatocellular carcinoma cell line. On the basis of these findings, we propose that the aberrant expression of ARAP1 in Hep3B cells modulates CDRs, thereby resulting in an excess uptake of nutrients as an initial event in cancer development. SUMMARY STATEMENT ARAP1 regulates circular dorsal ruffles (CDRs) in the Hep3B HCC cell line and deletion of this protein attenuates malignant potential, thereby indicating the involvement of CDRs in cancer development.
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25
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Tsong H, Holzbaur ELF, Stavoe AKH. Aging Differentially Affects Axonal Autophagosome Formation and Maturation. Autophagy 2023; 19:3079-3095. [PMID: 37464898 PMCID: PMC10621248 DOI: 10.1080/15548627.2023.2236485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 06/21/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
Misregulation of neuronal macroautophagy/autophagy has been implicated in age-related neurodegenerative diseases. We compared autophagosome formation and maturation in primary murine neurons during development and through aging to elucidate how aging affects neuronal autophagy. We observed an age-related decrease in the rate of autophagosome formation leading to a significant decrease in the density of autophagosomes along the axon. Next, we identified a surprising increase in the maturation of autophagic vesicles in neurons from aged mice. While we did not detect notable changes in endolysosomal content in the distal axon during early aging, we did observe a significant loss of acidified vesicles in the distal axon during late aging. Interestingly, we found that autophagic vesicles were transported more efficiently in neurons from adult mice than in neurons from young mice. This efficient transport of autophagic vesicles in both the distal and proximal axon is maintained in neurons during early aging, but is lost during late aging. Our data indicate that early aging does not negatively impact autophagic vesicle transport nor the later stages of autophagy. However, alterations in autophagic vesicle transport efficiency during late aging reveal that aging differentially impacts distinct aspects of neuronal autophagy.Abbreviations: ACAP3: ArfGAP with coiled-coil, ankyrin repeat and PH domains 3; ARF6: ADP-ribosylation factor 6; ATG: autophagy related; AVs: autophagic vesicles; DCTN1/p150Glued: dynactin 1; DRG: dorsal root ganglia; GAP: GTPase activating protein; GEF: guanine nucleotide exchange factor; LAMP2: lysosomal-associated protein 2; LysoT: LysoTracker; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MAPK8IP1/JIP1: mitogen-activated protein kinase 8 interacting protein 1; MAPK8IP3/JIP3: mitogen-activated protein kinase 8 interacting protein 3; mCh: mCherry; PE: phosphatidylethanolamine.
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Affiliation(s)
- Heather Tsong
- Department of Neurobiology & Anatomy, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Erika LF Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrea KH Stavoe
- Department of Neurobiology & Anatomy, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
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26
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Georgiou X, Dimou S, Diallinas G, Samiotaki M. The interactome of the UapA transporter reveals putative new players in anterograde membrane cargo trafficking. Fungal Genet Biol 2023; 169:103840. [PMID: 37730157 DOI: 10.1016/j.fgb.2023.103840] [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: 07/21/2023] [Revised: 09/01/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
Neosynthesized plasma membrane (PM) proteins co-translationally translocate to the ER, concentrate at regions called ER-exit sites (ERes) and pack into COPII secretory vesicles which are sorted to the early-Golgi through membrane fusion. Following Golgi maturation, membrane cargoes reach the late-Golgi, from where they exit in clathrin-coated vesicles destined to the PM, directly or through endosomes. Post-Golgi membrane cargo trafficking also involves the cytoskeleton and the exocyst. The Golgi-dependent secretory pathway is thought to be responsible for the trafficking of all major membrane proteins. However, our recent findings in Aspergillus nidulans showed that several plasma membrane cargoes, such as transporters and receptors, follow a sorting route that seems to bypass Golgi functioning. To gain insight on membrane trafficking and specifically Golgi-bypass, here we used proximity dependent biotinylation (PDB) coupled with data-independent acquisition mass spectrometry (DIA-MS) for identifying transient interactors of the UapA transporter. Our assays, which included proteomes of wild-type and mutant strains affecting ER-exit or endocytosis, identified both expected and novel interactions that might be physiologically relevant to UapA trafficking. Among those, we validated, using reverse genetics and fluorescence microscopy, that COPI coatomer is essential for ER-exit and anterograde trafficking of UapA and other membrane cargoes. We also showed that ArfAArf1 GTPase activating protein (GAP) Glo3 contributes to UapA trafficking at increased temperature. This is the first report addressing the identification of transient interactions during membrane cargo biogenesis using PDB and proteomics coupled with fungal genetics. Our work provides a basis for dissecting dynamic membrane cargo trafficking via PDB assays.
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Affiliation(s)
- Xenia Georgiou
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens 15784, Greece
| | - Sofia Dimou
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens 15784, Greece
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens 15784, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion 70013, Greece.
| | - Martina Samiotaki
- Biomedical Sciences Research Center "Alexander Fleming", Institute for Bioinnovation, Vari 16672, Greece.
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27
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Hornigold K, Baker MJ, Machin PA, Chetwynd SA, Johnsson AK, Pantarelli C, Islam P, Stammers M, Crossland L, Oxley D, Okkenhaug H, Walker S, Walker R, Segonds-Pichon A, Fukui Y, Malliri A, Welch HCE. The Rac-GEF Tiam1 controls integrin-dependent neutrophil responses. Front Immunol 2023; 14:1223653. [PMID: 38077328 PMCID: PMC10703174 DOI: 10.3389/fimmu.2023.1223653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/20/2023] [Indexed: 12/18/2023] Open
Abstract
Rac GTPases are required for neutrophil adhesion and migration, and for the neutrophil effector responses that kill pathogens. These Rac-dependent functions are impaired when neutrophils lack the activators of Rac, Rac-GEFs from the Prex, Vav, and Dock families. In this study, we demonstrate that Tiam1 is also expressed in neutrophils, governing focal complexes, actin cytoskeletal dynamics, polarisation, and migration, in a manner depending on the integrin ligand to which the cells adhere. Tiam1 is dispensable for the generation of reactive oxygen species but mediates degranulation and NETs release in adherent neutrophils, as well as the killing of bacteria. In vivo, Tiam1 is required for neutrophil recruitment during aseptic peritonitis and for the clearance of Streptococcus pneumoniae during pulmonary infection. However, Tiam1 functions differently to other Rac-GEFs. Instead of promoting neutrophil adhesion to ICAM1 and stimulating β2 integrin activity as could be expected, Tiam1 restricts these processes. In accordance with these paradoxical inhibitory roles, Tiam1 limits the fMLP-stimulated activation of Rac1 and Rac2 in adherent neutrophils, rather than activating Rac as expected. Tiam1 promotes the expression of several regulators of small GTPases and cytoskeletal dynamics, including αPix, Psd4, Rasa3, and Tiam2. It also controls the association of Rasa3, and potentially αPix, Git2, Psd4, and 14-3-3ζ/δ, with Rac. We propose these latter roles of Tiam1 underlie its effects on Rac and β2 integrin activity and on cell responses. Hence, Tiam1 is a novel regulator of Rac-dependent neutrophil responses that functions differently to other known neutrophil Rac-GEFs.
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Affiliation(s)
- Kirsti Hornigold
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | - Martin J. Baker
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
- Cell Signalling Group, Cancer Research UK Manchester Institute, University of Manchester, Macclesfield, United Kingdom
| | - Polly A. Machin
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | | | | | | | - Priota Islam
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | | | | | - David Oxley
- Mass Spectrometry Facility, Babraham Institute, Cambridge, United Kingdom
| | | | - Simon Walker
- Imaging Facility, Babraham Institute, Cambridge, United Kingdom
| | - Rachael Walker
- Flow Cytometry Facility, Babraham Institute, Cambridge, United Kingdom
| | | | - Yoshinori Fukui
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Angeliki Malliri
- Cell Signalling Group, Cancer Research UK Manchester Institute, University of Manchester, Macclesfield, United Kingdom
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28
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Hirschenberger M, Lepelley A, Rupp U, Klute S, Hunszinger V, Koepke L, Merold V, Didry-Barca B, Wondany F, Bergner T, Moreau T, Rodero MP, Rösler R, Wiese S, Volpi S, Gattorno M, Papa R, Lynch SA, Haug MG, Houge G, Wigby KM, Sprague J, Lenberg J, Read C, Walther P, Michaelis J, Kirchhoff F, de Oliveira Mann CC, Crow YJ, Sparrer KMJ. ARF1 prevents aberrant type I interferon induction by regulating STING activation and recycling. Nat Commun 2023; 14:6770. [PMID: 37914730 PMCID: PMC10620153 DOI: 10.1038/s41467-023-42150-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
Type I interferon (IFN) signalling is tightly controlled. Upon recognition of DNA by cyclic GMP-AMP synthase (cGAS), stimulator of interferon genes (STING) translocates along the endoplasmic reticulum (ER)-Golgi axis to induce IFN signalling. Termination is achieved through autophagic degradation or recycling of STING by retrograde Golgi-to-ER transport. Here, we identify the GTPase ADP-ribosylation factor 1 (ARF1) as a crucial negative regulator of cGAS-STING signalling. Heterozygous ARF1 missense mutations cause a previously unrecognized type I interferonopathy associated with enhanced IFN-stimulated gene expression. Disease-associated, GTPase-defective ARF1 increases cGAS-STING dependent type I IFN signalling in cell lines and primary patient cells. Mechanistically, mutated ARF1 perturbs mitochondrial morphology, causing cGAS activation by aberrant mitochondrial DNA release, and leads to accumulation of active STING at the Golgi/ERGIC due to defective retrograde transport. Our data show an unexpected dual role of ARF1 in maintaining cGAS-STING homeostasis, through promotion of mitochondrial integrity and STING recycling.
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Affiliation(s)
| | - Alice Lepelley
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, F-75015, Paris, France
| | - Ulrich Rupp
- Central Facility for Electron Microscopy, Ulm University, 89081, Ulm, Germany
| | - Susanne Klute
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Victoria Hunszinger
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Veronika Merold
- Institute of Virology, Technical University of Munich, 81675, Munich, Germany
| | - Blaise Didry-Barca
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, F-75015, Paris, France
| | - Fanny Wondany
- Institute of Biophysics, Ulm University, 89081, Ulm, Germany
| | - Tim Bergner
- Central Facility for Electron Microscopy, Ulm University, 89081, Ulm, Germany
| | - Tatiana Moreau
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, F-75015, Paris, France
| | - Mathieu P Rodero
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, F-75015, Paris, France
| | - Reinhild Rösler
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081, Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081, Ulm, Germany
| | - Stefano Volpi
- UOC Reumatologia e Malattie Autoinfiammatorie, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Università degli Studi di Genova, Genoa, Italy
| | - Marco Gattorno
- UOC Reumatologia e Malattie Autoinfiammatorie, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Riccardo Papa
- UOC Reumatologia e Malattie Autoinfiammatorie, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Sally-Ann Lynch
- Children's Health Ireland, Crumlin, Dublin, Eire
- University College Dublin, Dublin, Eire
| | - Marte G Haug
- Department of Medical Genetics, St. Olav's Hospital, Trondheim, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Kristen M Wigby
- Division of Genomic Medicine, Department of Pediatrics, University of California, Davis in Sacramento, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Jessica Sprague
- Division of Pediatric and Adolescent Dermatology, Rady Children's Hospital San Diego, San Diego, CA, USA
- Department of Dermatology, University of California San Diego School of Medicine, La Jolla, USA
| | - Jerica Lenberg
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Clarissa Read
- Central Facility for Electron Microscopy, Ulm University, 89081, Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, 89081, Ulm, Germany
| | - Jens Michaelis
- Institute of Biophysics, Ulm University, 89081, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | | | - Yanick J Crow
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, F-75015, Paris, France.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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29
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Sasazawa Y, Hattori N, Saiki S. JNK-interacting protein 4 is a central molecule for lysosomal retrograde trafficking. Bioessays 2023; 45:e2300052. [PMID: 37559169 DOI: 10.1002/bies.202300052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
Lysosomal positioning is an important factor in regulating cellular responses, including autophagy. Because proteins encoded by disease-responsible genes are involved in lysosomal trafficking, proper intracellular lysosomal trafficking is thought to be essential for cellular homeostasis. In the past few years, the mechanisms of lysosomal trafficking have been elucidated with a focus on adapter proteins linking motor proteins to lysosomes. Here, we outline recent findings on the mechanisms of lysosomal trafficking by focusing on adapter protein c-Jun NH2 -terminal kinase-interacting protein (JIP) 4, which plays a central role in this process, and other JIP4 functions and JIP family proteins. Additionally, we discuss neuronal diseases associated with aberrance in the JIP family protein. Accumulating evidence suggests that chemical manipulation of lysosomal positioning may be a therapeutic approach for these neuronal diseases.
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Affiliation(s)
- Yukiko Sasazawa
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
- Department of Neurology, Juntendo University Faculty of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University Faculty of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Shinji Saiki
- Department of Neurology, Juntendo University Faculty of Medicine, Bunkyo-ku, Tokyo, Japan
- Department of Neurology, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Wee Y, Wang J, Wilson EC, Rich CP, Rogers A, Tong Z, DeGroot E, Gopal YV, Davies MA, Ekiz HA, Tay JK, Stubben C, Boucher KM, Oviedo JM, Fairfax KC, Williams MA, Holmen SL, Wolff RK, Grossmann AH. ARF6-dependent endocytic trafficking of the Interferon-γ receptor drives adaptive immune resistance in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560199. [PMID: 37873189 PMCID: PMC10592860 DOI: 10.1101/2023.09.29.560199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Adaptive immune resistance (AIR) is a protective process used by cancer to escape elimination by CD8+ T cells. Inhibition of immune checkpoints PD-1 and CTLA-4 specifically target Interferon-gamma (IFNγ)-driven AIR. AIR begins at the plasma membrane where tumor cell-intrinsic cytokine signaling is initiated. Thus, plasma membrane remodeling by endomembrane trafficking could regulate AIR. Herein we report that the trafficking protein ADP-Ribosylation Factor 6 (ARF6) is critical for IFNγ-driven AIR. ARF6 prevents transport of the receptor to the lysosome, augmenting IFNγR expression, tumor intrinsic IFNγ signaling and downstream expression of immunosuppressive genes. In murine melanoma, loss of ARF6 causes resistance to immune checkpoint blockade (ICB). Likewise, low expression of ARF6 in patient tumors correlates with inferior outcomes with ICB. Our data provide new mechanistic insights into tumor immune escape, defined by ARF6-dependent AIR, and support that ARF6-dependent endomembrane trafficking of the IFNγ receptor influences outcomes of ICB.
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Affiliation(s)
- Yinshen Wee
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- These authors contributed equally
- current contact information: School of Dentistry, Taipei Medical University, Taiwan
| | - Junhua Wang
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- These authors contributed equally
| | - Emily C. Wilson
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Coulson P. Rich
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Aaron Rogers
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Zongzhong Tong
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Evelyn DeGroot
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Y.N. Vashisht Gopal
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - H. Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir institute of Technology, Gulbahce, Urla, 35430, Izmir, Turkey
| | - Joshua K.H. Tay
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Chris Stubben
- Bioinformatics Shared Resource, Huntsman Cancer Institute, Salt Lake City, Utah
| | - Kenneth M. Boucher
- Cancer Biostatistics Shared Resource, Huntsman Cancer Institute, Salt Lake City, Utah
| | - Juan M. Oviedo
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Keke C. Fairfax
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Matthew A. Williams
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Sheri L. Holmen
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Surgery, University of Utah, Salt Lake City, Utah
| | - Roger K. Wolff
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Allie H. Grossmann
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- Lead contact
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Sun D, Guo Y, Tang P, Li H, Chen L. Arf6 as a therapeutic target: Structure, mechanism, and inhibitors. Acta Pharm Sin B 2023; 13:4089-4104. [PMID: 37799386 PMCID: PMC10547916 DOI: 10.1016/j.apsb.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/28/2023] [Accepted: 06/02/2023] [Indexed: 10/07/2023] Open
Abstract
ADP-ribosylation factor 6 (Arf6), a small G-protein of the Ras superfamily, plays pivotal roles in multiple cellular events, including exocytosis, endocytosis, actin remodeling, plasma membrane reorganization and vesicular transport. Arf6 regulates the progression of cancer through the activation of cell motility and invasion. Aberrant Arf6 activation is a potential therapeutic target. This review aims to understand the comprehensive function of Arf6 for future cancer therapy. The Arf6 GEFs, protein structure, and roles in cancer have been summarized. Comprehending the mechanism underlying Arf6-mediated cancer cell growth and survival is essential. The structural features of Arf6 and its efforts are discussed and may be contributed to the discovery of future novel protein-protein interaction inhibitors. In addition, Arf6 inhibitors and mechanism of action are listed in the table. This review further emphasizes the crucial roles in drug resistance and attempts to offer an outlook of Arf6 in cancer therapy.
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Affiliation(s)
- Dejuan Sun
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yuanyuan Guo
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Piyu Tang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
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de Sainte Agathe JM, Pode-Shakked B, Naudion S, Michaud V, Arveiler B, Fergelot P, Delmas J, Keren B, Poirsier C, Alkuraya FS, Tabarki B, Bend E, Davis K, Bebin M, Thompson ML, Bryant EM, Wagner M, Hannibal I, Lenberg J, Krenn M, Wigby KM, Friedman JR, Iascone M, Cereda A, Miao T, LeGuern E, Argilli E, Sherr E, Caluseriu O, Tidwell T, Bayrak-Toydemir P, Hagedorn C, Brugger M, Vill K, Morneau-Jacob FD, Chung W, Weaver KN, Owens JW, Husami A, Chaudhari BP, Stone BS, Burns K, Li R, de Lange IM, Biehler M, Ginglinger E, Gérard B, Stottmann RW, Trimouille A. ARF1-related disorder: phenotypic and molecular spectrum. J Med Genet 2023; 60:999-1005. [PMID: 37185208 PMCID: PMC10579487 DOI: 10.1136/jmg-2022-108803] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 04/07/2023] [Indexed: 05/17/2023]
Abstract
PURPOSE ARF1 was previously implicated in periventricular nodular heterotopia (PVNH) in only five individuals and systematic clinical characterisation was not available. The aim of this study is to provide a comprehensive description of the phenotypic and genotypic spectrum of ARF1-related neurodevelopmental disorder. METHODS We collected detailed phenotypes of an international cohort of individuals (n=17) with ARF1 variants assembled through the GeneMatcher platform. Missense variants were structurally modelled, and the impact of several were functionally validated. RESULTS De novo variants (10 missense, 1 frameshift, 1 splice altering resulting in 9 residues insertion) in ARF1 were identified among 17 unrelated individuals. Detailed phenotypes included intellectual disability (ID), microcephaly, seizures and PVNH. No specific facial characteristics were consistent across all cases, however microretrognathia was common. Various hearing and visual defects were recurrent, and interestingly, some inflammatory features were reported. MRI of the brain frequently showed abnormalities consistent with a neuronal migration disorder. CONCLUSION We confirm the role of ARF1 in an autosomal dominant syndrome with a phenotypic spectrum including severe ID, microcephaly, seizures and PVNH due to impaired neuronal migration.
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Affiliation(s)
| | - Ben Pode-Shakked
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sophie Naudion
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Vincent Michaud
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- Maladies Rares : Génétique et Métabolisme (MRGM), U1211, INSERM, Bordeaux, France
| | - Benoit Arveiler
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- Maladies Rares : Génétique et Métabolisme (MRGM), U1211, INSERM, Bordeaux, France
| | - Patricia Fergelot
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- Maladies Rares : Génétique et Métabolisme (MRGM), U1211, INSERM, Bordeaux, France
| | - Jean Delmas
- Pediatric and Prenatal Imaging Department, Centre Hospitalier Universitaire de Bordeaux Groupe hospitalier Pellegrin, Bordeaux, France
| | - Boris Keren
- Department of Medical Genetics, Groupe Hospitalo-Universitaire Pitié-Salpêtrière, AP-HP.Sorbonne Université, Paris, France
| | | | - Fowzan S Alkuraya
- Department of Translational Genomic, Center for Genomic Medicine, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Brahim Tabarki
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military and Medical City, Riyadh, Saudi Arabia
| | - Eric Bend
- PreventionGenetics LLC, Marshfield, Wisconsin, USA
| | - Kellie Davis
- Division of Medical Genetics, Royal University Hospital, Saskatoon, Saskatchewan, Canada
| | - Martina Bebin
- UAB Epilepsy Center, The University of Alabama at Birmingham Hospital, Birmingham, Alabama, USA
| | - Michelle L Thompson
- Greg Cooper's Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Emily M Bryant
- Gillette Children's Specialty Healthcare, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Matias Wagner
- Institute of Human Genetics, Technische Universitat Munchen, Munchen, Germany
- Institute of Neurogenomics, Helmholtz Zentrum Munchen Deutsches Forschungszentrum fur Umwelt und Gesundheit, Neuherberg, Germany
| | - Iris Hannibal
- Department of Pediatrics, University Hospital Munich, Munchen, Germany
| | - Jerica Lenberg
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Martin Krenn
- Department of Neurology, Medizinische Universitat Wien, Wien, Austria
| | - Kristen M Wigby
- Rady Children's Hospital-San Diego, University of California, San Diego, California, USA
| | - Jennifer R Friedman
- Department of Neuroscience, Rady Children's Institute for Genomic Medicine, San Diego, California, USA
- Division of Neurology, Rady Children's Hospital San Diego, San Diego, California, USA
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Anna Cereda
- Pediatric Department, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Térence Miao
- Department of Medical Genetics, Groupe Hospitalo-Universitaire Pitié-Salpêtrière, AP-HP.Sorbonne Université, Paris, France
- École d'ingénieurs biotechnologies Paris - SupBiotech, Sup'Biotech, Paris, France
| | - Eric LeGuern
- Department of Medical Genetics, Groupe Hospitalo-Universitaire Pitié-Salpêtrière, AP-HP.Sorbonne Université, Paris, France
- ICM, INSERM, Paris, France
| | - Emanuela Argilli
- Department of Neurology, University of California San Francisco Division of Hospital Medicine, San Francisco, California, USA
| | - Elliott Sherr
- Department of Neurology, University of California San Francisco Division of Hospital Medicine, San Francisco, California, USA
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta Hospital, Edmonton, Alberta, Canada
| | | | | | - Caroline Hagedorn
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munchen, Germany
| | - Katharina Vill
- Fachbereich Neuromuskuläre Erkrankungen und klinische Neurophysiologie, Dr. v. Hauner Children's Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | | | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University, New York City, New York, USA
| | - Kathryn N Weaver
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Joshua W Owens
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ammar Husami
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Bimal P Chaudhari
- Divisions of Neonatology, Genetics and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Brandon S Stone
- Divisions of Genetics and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Katie Burns
- Sanford Children's Specialty Clinic, Sioux Falls, South Dakota, USA
| | - Rachel Li
- Department of Pediatrics, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA
| | - Iris M de Lange
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Margaux Biehler
- Laboratories of Genetic Diagnosis, Institut de Génétique Médicale d'Alsace (IGMA), Strasbourg University Hospitals, Strasbourg, France
| | | | - Bénédicte Gérard
- Laboratories of Genetic Diagnosis, Institut de Génétique Médicale d'Alsace (IGMA), Strasbourg University Hospitals, Strasbourg, France
| | - Rolf W Stottmann
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
| | - Aurélien Trimouille
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- Maladies Rares : Génétique et Métabolisme (MRGM), U1211, INSERM, Bordeaux, France
- Service de Pathologie, University Hospital Centre Bordeaux Pellegrin Hospital Group, Bordeaux, France
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Liang J, Fang D, Yao F, Chen L, Zou Z, Tang X, Feng L, Zhuang Y, Xie T, Wei P, Li P, Zheng H, Zhang S. Analysis of shared ceRNA networks and related-hub genes in rats with primary and secondary photoreceptor degeneration. Front Neurosci 2023; 17:1259622. [PMID: 37811327 PMCID: PMC10552924 DOI: 10.3389/fnins.2023.1259622] [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: 07/20/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Photoreceptor degenerative diseases are characterized by the progressive death of photoreceptor cells, resulting in irreversible visual impairment. However, the role of competing endogenous RNA (ceRNA) in photoreceptor degeneration is unclear. We aimed to explore the shared ceRNA regulation network and potential molecular mechanisms between primary and secondary photoreceptor degenerations. Methods We established animal models for both types of photoreceptor degenerations and conducted retina RNA sequencing to identify shared differentially expressed long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs). Using ceRNA regulatory principles, we constructed a shared ceRNA network and performed function enrichment and protein-protein interaction (PPI) analyses to identify hub genes and key pathways. Immune cell infiltration and drug-gene interaction analyses were conducted, and hub gene expression was validated by quantitative real-time polymerase chain reaction (qRT-PCR). Results We identified 37 shared differentially expressed lncRNAs, 34 miRNAs, and 247 mRNAs and constructed a ceRNA network consisting of 3 lncRNAs, 5 miRNAs, and 109 mRNAs. Furthermore, we examined 109 common differentially expressed genes (DEGs) through functional annotation, PPI analysis, and regulatory network analysis. We discovered that these diseases shared the complement and coagulation cascades pathway. Eight hub genes were identified and enriched in the immune system process. Immune infiltration analysis revealed increased T cells and decreased B cells in both photoreceptor degenerations. The expression of hub genes was closely associated with the quantities of immune cell types. Additionally, we identified 7 immune therapeutical drugs that target the hub genes. Discussion Our findings provide new insights and directions for understanding the common mechanisms underlying the development of photoreceptor degeneration. The hub genes and related ceRNA networks we identified may offer new perspectives for elucidating the mechanisms and hold promise for the development of innovative treatment strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Shaochong Zhang
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Jinan University, Shenzhen, Guangdong, China
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Hu Y, Huang Y, Xie X, Li L, Zhang Y, Zhang X. ARF6 promotes hepatocellular carcinoma proliferation through activating STAT3 signaling. Cancer Cell Int 2023; 23:205. [PMID: 37716993 PMCID: PMC10505330 DOI: 10.1186/s12935-023-03053-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/03/2023] [Indexed: 09/18/2023] Open
Abstract
BACKGROUND Hepatocellular Carcinoma (HCC) possesses the high mortality in cancers worldwide. Nevertheless, the concrete mechanism underlying HCC proliferation remains obscure. In this study, we show that high expression of ARF6 is associated with a poor clinical prognosis, which could boost the proliferation of HCC. METHODS Immunohistochemistry and western blotting were used to detect the expression level of ARF6 in HCC tissues. We analyzed the clinical significance of ARF6 in primary HCC patients. We estimated the effect of ARF6 on tumor proliferation with in vitro CCK8, colony formation assay, and in vivo nude mouse xenograft models. Immunofluorescence was conducted to investigate the ARF6 localization. western blotting was used to detect the cell cycle-related proteins with. Additionally, we examined the correlation between ARF6 and STAT3 signaling in HCC with western blotting, immunohistochemistry and xenograft assay. RESULTS ARF6 was upregulated in HCC tissues compared to adjacent normal liver tissues. The increased expression of ARF6 correlated with poor tumor differentiation, incomplete tumor encapsulation, advanced tumor TNM stage and poor prognosis. ARF6 obviously promoted HCC cell proliferation, colony formation, and cell cycle progression. In vivo nude mouse xenograft models showed that ARF6 enhanced tumor growth. Furthermore, ARF6 activated the STAT3 signaling and ARF6 expression was positively correlated with phosphorylated STAT3 level in HCC tissues. Furthermore, after intervening of STAT3, the effect of ARF6 on tumor-promoting was weakened, which demonstrated ARF6 functioned through STAT3 signaling in HCC. CONCLUSIONS Our results indicate that ARF6 promotes HCC proliferation through activating STAT3 signaling, suggesting that ARF6 may serve as potential prognostic and therapeutic targets for HCC patients.
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Affiliation(s)
- Yabing Hu
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Laboratory Medicine, Wuhan No.1 Hospital, Wuhan, China
| | - Yongchu Huang
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaohang Xie
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Longshan Li
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Zhang
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaochao Zhang
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Viktorova EG, Gabaglio S, Moghimi S, Zimina A, Wynn BG, Sztul E, Belov GA. The development of resistance to an inhibitor of a cellular protein reveals a critical interaction between the enterovirus protein 2C and a small GTPase Arf1. PLoS Pathog 2023; 19:e1011673. [PMID: 37721955 PMCID: PMC10538752 DOI: 10.1371/journal.ppat.1011673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/28/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
The cellular protein GBF1, an activator of Arf GTPases (ArfGEF: Arf guanine nucleotide exchange factor), is recruited to the replication organelles of enteroviruses through interaction with the viral protein 3A, and its ArfGEF activity is required for viral replication, however how GBF1-dependent Arf activation supports the infection remains enigmatic. Here, we investigated the development of resistance of poliovirus, a prototype enterovirus, to increasing concentrations of brefeldin A (BFA), an inhibitor of GBF1. High level of resistance required a gradual accumulation of multiple mutations in the viral protein 2C. The 2C mutations conferred BFA resistance even in the context of a 3A mutant previously shown to be defective in the recruitment of GBF1 to replication organelles, and in cells depleted of GBF1, suggesting a GBF1-independent replication mechanism. Still, activated Arfs accumulated on the replication organelles of this mutant even in the presence of BFA, its replication was inhibited by a pan-ArfGEF inhibitor LM11, and the BFA-resistant phenotype was compromised in Arf1-knockout cells. Importantly, the mutations strongly increased the interaction of 2C with the activated form of Arf1. Analysis of other enteroviruses revealed a particularly strong interaction of 2C of human rhinovirus 1A with activated Arf1. Accordingly, the replication of this virus was significantly less sensitive to BFA than that of poliovirus. Thus, our data demonstrate that enterovirus 2Cs may behave like Arf1 effector proteins and that GBF1 but not Arf activation can be dispensable for enterovirus replication. These findings have important implications for the development of host-targeted anti-viral therapeutics.
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Affiliation(s)
- Ekaterina G. Viktorova
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Samuel Gabaglio
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Seyedehmahsa Moghimi
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Anna Zimina
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Bridge G. Wynn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - George A. Belov
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
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Powis G, Meuillet EJ, Indarte M, Booher G, Kirkpatrick L. Pleckstrin Homology [PH] domain, structure, mechanism, and contribution to human disease. Biomed Pharmacother 2023; 165:115024. [PMID: 37399719 DOI: 10.1016/j.biopha.2023.115024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/14/2023] [Indexed: 07/05/2023] Open
Abstract
The pleckstrin homology [PH] domain is a structural fold found in more than 250 proteins making it the 11th most common domain in the human proteome. 25% of family members have more than one PH domain and some PH domains are split by one, or several other, protein domains although still folding to give functioning PH domains. We review mechanisms of PH domain activity, the role PH domain mutation plays in human disease including cancer, hyperproliferation, neurodegeneration, inflammation, and infection, and discuss pharmacotherapeutic approaches to regulate PH domain activity for the treatment of human disease. Almost half PH domain family members bind phosphatidylinositols [PIs] that attach the host protein to cell membranes where they interact with other membrane proteins to give signaling complexes or cytoskeleton scaffold platforms. A PH domain in its native state may fold over other protein domains thereby preventing substrate access to a catalytic site or binding with other proteins. The resulting autoinhibition can be released by PI binding to the PH domain, or by protein phosphorylation thus providing fine tuning of the cellular control of PH domain protein activity. For many years the PH domain was thought to be undruggable until high-resolution structures of human PH domains allowed structure-based design of novel inhibitors that selectively bind the PH domain. Allosteric inhibitors of the Akt1 PH domain have already been tested in cancer patients and for proteus syndrome, with several other PH domain inhibitors in preclinical development for treatment of other human diseases.
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Affiliation(s)
- Garth Powis
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA.
| | | | - Martin Indarte
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| | - Garrett Booher
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| | - Lynn Kirkpatrick
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
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Nikolatou K, Bryant DM, Sandilands E. The ARF GTPase regulatory network in collective invasion and metastasis. Biochem Soc Trans 2023; 51:1559-1569. [PMID: 37622523 PMCID: PMC10586773 DOI: 10.1042/bst20221355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
The ability to remodel and move cellular membranes, and the cargoes regulated by these membranes, allows for specialised functions to occur in distinct regions of the cell in a process known as cellular polarisation. The ability to collectively co-ordinate such polarisation between cells allows for the genesis of multicellularity, such as the formation of organs. During tumourigenesis, the rules for such tissue polarisation become dysregulated, allowing for collective polarity rearrangements that can drive metastasis. In this review, we focus on how membrane trafficking underpins collective cell invasion and metastasis in cancer. We examine this through the lens of the ADP-ribosylation factor (ARF) subfamily of small GTPases, focusing on how the ARF regulatory network - ARF activators, inactivators, effectors, and modifications - controls ARF GTPase function.
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Affiliation(s)
- Konstantina Nikolatou
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1HQ, U.K
- The CRUK Beatson Institute, Glasgow G61 1BD, U.K
| | - David M. Bryant
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1HQ, U.K
- The CRUK Beatson Institute, Glasgow G61 1BD, U.K
| | - Emma Sandilands
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1HQ, U.K
- The CRUK Beatson Institute, Glasgow G61 1BD, U.K
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Rossi S, Di Salvio M, Balì M, De Simone A, Apolloni S, D’Ambrosi N, Arisi I, Cipressa F, Cozzolino M, Cestra G. C9orf72 Toxic Species Affect ArfGAP-1 Function. Cells 2023; 12:2007. [PMID: 37566088 PMCID: PMC10416972 DOI: 10.3390/cells12152007] [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: 07/15/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/12/2023] Open
Abstract
Compelling evidence indicates that defects in nucleocytoplasmic transport contribute to the pathogenesis of amyotrophic lateral sclerosis (ALS). In particular, hexanucleotide (G4C2) repeat expansions in C9orf72, the most common cause of genetic ALS, have a widespread impact on the transport machinery that regulates the nucleocytoplasmic distribution of proteins and RNAs. We previously reported that the expression of G4C2 hexanucleotide repeats in cultured human and mouse cells caused a marked accumulation of poly(A) mRNAs in the cell nuclei. To further characterize the process, we set out to systematically identify the specific mRNAs that are altered in their nucleocytoplasmic distribution in the presence of C9orf72-ALS RNA repeats. Interestingly, pathway analysis showed that the mRNAs involved in membrane trafficking are particularly enriched among the identified mRNAs. Most importantly, functional studies in cultured cells and Drosophila indicated that C9orf72 toxic species affect the membrane trafficking route regulated by ADP-Ribosylation Factor 1 GTPase Activating Protein (ArfGAP-1), which exerts its GTPase-activating function on the small GTPase ADP-ribosylation factor 1 to dissociate coat proteins from Golgi-derived vesicles. We demonstrate that the function of ArfGAP-1 is specifically affected by expanded C9orf72 RNA repeats, as well as by C9orf72-related dipeptide repeat proteins (C9-DPRs), indicating the retrograde Golgi-to-ER vesicle-mediated transport as a target of C9orf72 toxicity.
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Affiliation(s)
- Simona Rossi
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), 00133 Rome, Italy; (S.R.); (I.A.)
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy;
| | - Michela Di Salvio
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), 00185 Rome, Italy;
| | - Marilisa Balì
- Department of Biology and Biotechnology, University of Rome “La Sapienza”, 00185 Rome, Italy; (M.B.); (A.D.S.)
| | - Assia De Simone
- Department of Biology and Biotechnology, University of Rome “La Sapienza”, 00185 Rome, Italy; (M.B.); (A.D.S.)
| | - Savina Apolloni
- Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy;
| | - Nadia D’Ambrosi
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy;
- Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy;
| | - Ivan Arisi
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), 00133 Rome, Italy; (S.R.); (I.A.)
- European Brain Research Institute “Rita Levi-Montalcini”, 00161 Rome, Italy
| | - Francesca Cipressa
- Department of Ecological and Biological Science, University of Tuscia, 01100 Viterbo, Italy;
| | - Mauro Cozzolino
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), 00133 Rome, Italy; (S.R.); (I.A.)
| | - Gianluca Cestra
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy;
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), 00185 Rome, Italy;
- Department of Biology and Biotechnology, University of Rome “La Sapienza”, 00185 Rome, Italy; (M.B.); (A.D.S.)
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Van Sciver RE, Long AB, Katz HG, Gigante ED, Caspary T. Ciliary ARL13B inhibits developmental kidney cystogenesis in mouse. Dev Biol 2023; 500:1-9. [PMID: 37209936 PMCID: PMC10330881 DOI: 10.1016/j.ydbio.2023.05.004] [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: 02/08/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/22/2023]
Abstract
ARL13B is a small GTPase enriched in cilia. Deletion of Arl13b in mouse kidney results in renal cysts and an associated absence of primary cilia. Similarly, ablation of cilia leads to kidney cysts. To investigate whether ARL13B functions from within cilia to direct kidney development, we examined kidneys of mice expressing an engineered cilia-excluded ARL13B variant, ARL13BV358A. These mice retained renal cilia and developed cystic kidneys. Because ARL13B functions as a guanine nucleotide exchange factor (GEF) for ARL3, we examined kidneys of mice expressing an ARL13B variant that lacks ARL3 GEF activity, ARL13BR79Q. We found normal kidney development with no evidence of cysts in these mice. Taken together, our results show that ARL13B functions within cilia to inhibit renal cystogenesis during mouse development, and that this function does not depend on its role as a GEF for ARL3.
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Affiliation(s)
- Robert E Van Sciver
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA, 30322, USA.
| | - Alyssa B Long
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA, 30322, USA.
| | - Harrison G Katz
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA, 30322, USA; Department of Biology, Brown University, Providence, RI, 02912, USA.
| | - Eduardo D Gigante
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA, 30322, USA; Graduate Program in Neuroscience, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA, 30322, USA; Department of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA, 30322, USA.
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40
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Motiwala Z, Sandholu AS, Sengupta D, Kulkarni K. Wavelet coherence phase analysis decodes the universal switching mechanism of Ras GTPase superfamily. iScience 2023; 26:107031. [PMID: 37448564 PMCID: PMC10336170 DOI: 10.1016/j.isci.2023.107031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/06/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
The Ras superfamily of GTPases regulate critical cellular processes by shuttling between GTP-bound ON and GDP-bound OFF states. This switching mechanism is attributed to the conformational changes in two loops, SWI and SWII, upon GTP binding and hydrolysis. Since these conformational changes vary across the Ras superfamily, there is no generic parameter to define their functional states. A unique wavelet coherence (WC) analysis-based approach developed here shows that the structural changes in switch regions could be mapped onto the wavelet coherence phase couplings (WPCs). Thus, WPCs could serve as unique parameters to define their functional states. Disentanglement of WPCs in oncogenic GTPases shows how breakdown of structural allostery leads to their aberrant function. These observations stand out even for simulated ensemble of switch region conformers. Overall, for the first time, we show that WPCs could unravel the latent structural deviations in Ras proteins to decode their universal switching mechanism.
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Affiliation(s)
- Zenia Motiwala
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anand S. Sandholu
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Durba Sengupta
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Division of Physical and Material Chemistry, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Kiran Kulkarni
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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41
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Mahbub L, Kozlov G, Zong P, Lee EL, Tetteh S, Nethramangalath T, Knorn C, Jiang J, Shahsavan A, Yue L, Runnels L, Gehring K. Structural insights into regulation of CNNM-TRPM7 divalent cation uptake by the small GTPase ARL15. eLife 2023; 12:e86129. [PMID: 37449820 PMCID: PMC10348743 DOI: 10.7554/elife.86129] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/02/2023] [Indexed: 07/18/2023] Open
Abstract
Cystathionine-β-synthase (CBS)-pair domain divalent metal cation transport mediators (CNNMs) are an evolutionarily conserved family of magnesium transporters. They promote efflux of Mg2+ ions on their own and influx of divalent cations when expressed with the transient receptor potential ion channel subfamily M member 7 (TRPM7). Recently, ADP-ribosylation factor-like GTPase 15 (ARL15) has been identified as CNNM-binding partner and an inhibitor of divalent cation influx by TRPM7. Here, we characterize ARL15 as a GTP and CNNM-binding protein and demonstrate that ARL15 also inhibits CNNM2 Mg2+ efflux. The crystal structure of a complex between ARL15 and CNNM2 CBS-pair domain reveals the molecular basis for binding and allowed the identification of mutations that specifically block binding. A binding deficient ARL15 mutant, R95A, failed to inhibit CNNM and TRPM7 transport of Mg2+ and Zn2+ ions. Structural analysis and binding experiments with phosphatase of regenerating liver 2 (PRL2 or PTP4A2) showed that ARL15 and PRLs compete for binding CNNM to coordinate regulation of ion transport by CNNM and TRPM7.
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Affiliation(s)
- Luba Mahbub
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
| | - Guennadi Kozlov
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
| | - Pengyu Zong
- Department of Cell Biology, UCONN Health CenterFarmingtonUnited States
| | - Emma L Lee
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
| | - Sandra Tetteh
- Rutgers-Robert Wood Johnson Medical SchoolPiscatawayUnited States
| | | | - Caroline Knorn
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
| | - Jianning Jiang
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
| | - Ashkan Shahsavan
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
| | - Lixia Yue
- Department of Cell Biology, UCONN Health CenterFarmingtonUnited States
| | - Loren Runnels
- Rutgers-Robert Wood Johnson Medical SchoolPiscatawayUnited States
| | - Kalle Gehring
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
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Wong-Dilworth L, Rodilla-Ramirez C, Fox E, Restel SD, Stockhammer A, Adarska P, Bottanelli F. STED imaging of endogenously tagged ARF GTPases reveals their distinct nanoscale localizations. J Cell Biol 2023; 222:e202205107. [PMID: 37102998 PMCID: PMC10140647 DOI: 10.1083/jcb.202205107] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 01/10/2023] [Accepted: 04/05/2023] [Indexed: 04/28/2023] Open
Abstract
ADP-ribosylation factor (ARF) GTPases are major regulators of cellular membrane homeostasis. High sequence similarity and multiple, possibly redundant functions of the five human ARFs make investigating their function a challenging task. To shed light on the roles of the different Golgi-localized ARF members in membrane trafficking, we generated CRISPR-Cas9 knockins (KIs) of type I (ARF1 and ARF3) and type II ARFs (ARF4 and ARF5) and mapped their nanoscale localization with stimulated emission depletion (STED) super-resolution microscopy. We find ARF1, ARF4, and ARF5 on segregated nanodomains on the cis-Golgi and ER-Golgi intermediate compartments (ERGIC), revealing distinct roles in COPI recruitment on early secretory membranes. Interestingly, ARF4 and ARF5 define Golgi-tethered ERGIC elements decorated by COPI and devoid of ARF1. Differential localization of ARF1 and ARF4 on peripheral ERGICs suggests the presence of functionally different classes of intermediate compartments that could regulate bi-directional transport between the ER and the Golgi. Furthermore, ARF1 and ARF3 localize to segregated nanodomains on the trans-Golgi network (TGN) and are found on TGN-derived post-Golgi tubules, strengthening the idea of distinct roles in post-Golgi sorting. This work provides the first map of the nanoscale organization of human ARF GTPases on cellular membranes and sets the stage to dissect their numerous cellular roles.
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Affiliation(s)
| | | | - Eleanor Fox
- Institut für Biochemie, Freie Universität Berlin, Berlin, Germany
| | | | | | - Petia Adarska
- Institut für Biochemie, Freie Universität Berlin, Berlin, Germany
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43
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Li FL, Guan KL. The Arf family GTPases: Regulation of vesicle biogenesis and beyond. Bioessays 2023; 45:e2200214. [PMID: 36998106 PMCID: PMC10282109 DOI: 10.1002/bies.202200214] [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: 11/05/2022] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 04/01/2023]
Abstract
The Arf family proteins are best known for their roles in the vesicle biogenesis. However, they also play fundamental roles in a wide range of cellular regulation besides vesicular trafficking, such as modulation of lipid metabolic enzymes, cytoskeleton remodeling, ciliogenesis, lysosomal, and mitochondrial morphology and functions. Growing studies continue to expand the downstream effector landscape of Arf proteins, especially for the less-studied members, revealing new biological functions, such as amino acid sensing. Experiments with cutting-edge technologies and in vivo functional studies in the last decade help to provide a more comprehensive view of Arf family functions. In this review, we summarize the cellular functions that are regulated by at least two different Arf members with an emphasis on those beyond vesicle biogenesis.
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Affiliation(s)
- Fu-Long Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kun-Liang Guan
- Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
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44
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Yin G, Huang J, Petela J, Jiang H, Zhang Y, Gong S, Wu J, Liu B, Shi J, Gao Y. Targeting small GTPases: emerging grasps on previously untamable targets, pioneered by KRAS. Signal Transduct Target Ther 2023; 8:212. [PMID: 37221195 DOI: 10.1038/s41392-023-01441-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/28/2023] [Accepted: 04/14/2023] [Indexed: 05/25/2023] Open
Abstract
Small GTPases including Ras, Rho, Rab, Arf, and Ran are omnipresent molecular switches in regulating key cellular functions. Their dysregulation is a therapeutic target for tumors, neurodegeneration, cardiomyopathies, and infection. However, small GTPases have been historically recognized as "undruggable". Targeting KRAS, one of the most frequently mutated oncogenes, has only come into reality in the last decade due to the development of breakthrough strategies such as fragment-based screening, covalent ligands, macromolecule inhibitors, and PROTACs. Two KRASG12C covalent inhibitors have obtained accelerated approval for treating KRASG12C mutant lung cancer, and allele-specific hotspot mutations on G12D/S/R have been demonstrated as viable targets. New methods of targeting KRAS are quickly evolving, including transcription, immunogenic neoepitopes, and combinatory targeting with immunotherapy. Nevertheless, the vast majority of small GTPases and hotspot mutations remain elusive, and clinical resistance to G12C inhibitors poses new challenges. In this article, we summarize diversified biological functions, shared structural properties, and complex regulatory mechanisms of small GTPases and their relationships with human diseases. Furthermore, we review the status of drug discovery for targeting small GTPases and the most recent strategic progress focused on targeting KRAS. The discovery of new regulatory mechanisms and development of targeting approaches will together promote drug discovery for small GTPases.
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Affiliation(s)
- Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
| | - Jing Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Johnny Petela
- Wake Forest University School of Medicine, Winston-Salem, NC, 27101, USA
| | - Hongmei Jiang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Yuetong Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Siqi Gong
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Jiaxin Wu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Bei Liu
- National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, 100871, China
| | - Jianyou Shi
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, 610072, China.
| | - Yijun Gao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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Nguyen QA, Chou WH, Hsieh MC, Chang CM, Luo WT, Tai YT, Chang WC. Genetic alterations in peritoneal metastatic tumors predicted the outcomes for hyperthermic intraperitoneal chemotherapy. Front Oncol 2023; 13:1054406. [PMID: 37182141 PMCID: PMC10170308 DOI: 10.3389/fonc.2023.1054406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/27/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction Cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) are considered for patients with peritoneal metastasis (PM). However, patients selection that relies on conventional prognostic factors is not yet optimal. In this study, we performed whole exome sequencing (WES) to establish tumor molecular characteristics and expect to identify prognosis profiles for PM management. Methods In this study, blood and tumor samples were collected from patients with PM before HIPEC. Tumor molecular signatures were determined using WES. Patient cohort was divided into responders and non-responders according to 12-month progression-free survival (PFS). Genomic characteristics between the two cohorts were compared to study potential targets. Results In total, 15 patients with PM were enrolled in this study. Driver genes and enriched pathways were identified from WES results. AGAP5 mutation was found in all responders. This mutation was significantly associated with better OS (p = 0.00652). Conclusions We identified prognostic markers that might be useful to facilitate decision-making before CRS/HIPEC.
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Affiliation(s)
- Quynh-Anh Nguyen
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Wan-Hsuan Chou
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Mao-Chih Hsieh
- Department of General Surgery, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Che-Mai Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Wei-Tzu Luo
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Yu-Ting Tai
- Department of Anesthesiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Anesthesiology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
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Caswell PT. ARF3 weights the balance for prostate cancer metastasis. J Cell Biol 2023; 222:e202303037. [PMID: 36920439 PMCID: PMC10040632 DOI: 10.1083/jcb.202303037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Patrick T. Caswell discusses work from Bryant and colleagues (2023. J. Cell Biol.https://doi.org/10.1083/jcb.202206115) which shows how ARF3 impacts metastasis in prostate cancer by regulating a switch between modes of collective invasion.
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Affiliation(s)
- Patrick T. Caswell
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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47
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Sandilands E, Freckmann EC, Cumming EM, Román-Fernández A, McGarry L, Anand J, Galbraith L, Mason S, Patel R, Nixon C, Cartwright J, Leung HY, Blyth K, Bryant DM. The small GTPase ARF3 controls invasion modality and metastasis by regulating N-cadherin levels. J Cell Biol 2023; 222:e202206115. [PMID: 36880595 PMCID: PMC9997661 DOI: 10.1083/jcb.202206115] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/13/2022] [Accepted: 01/20/2023] [Indexed: 03/04/2023] Open
Abstract
ARF GTPases are central regulators of membrane trafficking that control local membrane identity and remodeling facilitating vesicle formation. Unraveling their function is complicated by the overlapping association of ARFs with guanine nucleotide exchange factors (GEFs), GTPase-activating proteins (GAPs), and numerous interactors. Through a functional genomic screen of three-dimensional (3D) prostate cancer cell behavior, we explore the contribution of ARF GTPases, GEFs, GAPs, and interactors to collective invasion. This revealed that ARF3 GTPase regulates the modality of invasion, acting as a switch between leader cell-led chains of invasion or collective sheet movement. Functionally, the ability of ARF3 to control invasion modality is dependent on association and subsequent control of turnover of N-cadherin. In vivo, ARF3 levels acted as a rheostat for metastasis from intraprostatic tumor transplants and ARF3/N-cadherin expression can be used to identify prostate cancer patients with metastatic, poor-outcome disease. Our analysis defines a unique function for the ARF3 GTPase in controlling how cells collectively organize during invasion and metastasis.
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Affiliation(s)
- Emma Sandilands
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- The CRUK Beatson Institute, Glasgow, UK
| | - Eva C. Freckmann
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- The CRUK Beatson Institute, Glasgow, UK
| | - Erin M. Cumming
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- The CRUK Beatson Institute, Glasgow, UK
| | - Alvaro Román-Fernández
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- The CRUK Beatson Institute, Glasgow, UK
| | | | | | | | | | | | | | | | - Hing Y. Leung
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- The CRUK Beatson Institute, Glasgow, UK
| | - Karen Blyth
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- The CRUK Beatson Institute, Glasgow, UK
| | - David M. Bryant
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- The CRUK Beatson Institute, Glasgow, UK
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48
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Ishida M, Otero MG, Freeman C, Sánchez-Lara PA, Guardia CM, Pierson TM, Bonifacino JS. A neurodevelopmental disorder associated with an activating de novo missense variant in ARF1. Hum Mol Genet 2023; 32:1162-1174. [PMID: 36345169 PMCID: PMC10026249 DOI: 10.1093/hmg/ddac279] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
ADP-ribosylation factor 1 (ARF1) is a small GTPase that regulates membrane traffic at the Golgi apparatus and endosomes through recruitment of several coat proteins and lipid-modifying enzymes. Here, we report a pediatric patient with an ARF1-related disorder because of a monoallelic de novo missense variant (c.296 G > A; p.R99H) in the ARF1 gene, associated with developmental delay, hypotonia, intellectual disability and motor stereotypies. Neuroimaging revealed a hypoplastic corpus callosum and subcortical white matter abnormalities. Notably, this patient did not exhibit periventricular heterotopias previously observed in other patients with ARF1 variants (including p.R99H). Functional analysis of the R99H-ARF1 variant protein revealed that it was expressed at normal levels and properly localized to the Golgi apparatus; however, the expression of this variant caused swelling of the Golgi apparatus, increased the recruitment of coat proteins such as coat protein complex I, adaptor protein complex 1 and GGA3 and altered the morphology of recycling endosomes. In addition, we observed that the expression of R99H-ARF1 prevented dispersal of the Golgi apparatus by the ARF1-inhibitor brefeldin A. Finally, protein interaction analyses showed that R99H-ARF1 bound more tightly to the ARF1-effector GGA3 relative to wild-type ARF1. These properties were similar to those of the well-characterized constitutively active Q71L-ARF1 mutant, indicating that the pathogenetic mechanism of the R99H-ARF1 variant involves constitutive activation with resultant Golgi and endosomal alterations. The absence of periventricular nodular heterotopias in this R99H-ARF1 subject also indicates that this finding may not be a consistent phenotypic expression of all ARF1-related disorders.
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Affiliation(s)
- Morié Ishida
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - María G Otero
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Christina Freeman
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Pedro A Sánchez-Lara
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Carlos M Guardia
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27703, USA
| | - Tyler Mark Pierson
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Pediatric Neurology, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Center for the Undiagnosed Patient, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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49
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Mahajan D, Madugula V, Lu L. Rab8 and TNPO1 are ciliary transport adaptors for GTPase Arl13b by interacting with its RVEP motif-containing ciliary targeting sequence. J Biol Chem 2023; 299:104604. [PMID: 36907439 PMCID: PMC10124946 DOI: 10.1016/j.jbc.2023.104604] [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: 08/24/2022] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Arl13b, an ARF/Arl-family GTPase, is highly enriched in the cilium. Recent studies have established Arl13b as one of the most crucial regulators for ciliary organization, trafficking, and signaling. The ciliary localization of Arl13b is known to require the RVEP motif. However, its cognitive ciliary transport adaptor has been elusive. Here, by imaging the ciliary localization of truncation and point mutations, we defined the ciliary targeting sequence (CTS) of Arl13b as a C-terminal stretch of 17 amino acids containing the RVEP motif. We found Rab8-GDP, but not Rab8-GTP, and TNPO1 simultaneously and directly bind to the CTS of Arl13b in pull-down assays using cell lysates or purified recombinant proteins. Furthermore, Rab8-GDP substantially enhances the interaction between TNPO1 and CTS. Additionally, we determined that the RVEP motif is an essential element as its mutation abolishes the interaction of the CTS with Rab8-GDP and TNPO1 in pull-down and TurboID-based proximity ligation assays. Finally, knockdown of endogenous Rab8 or TNPO1 decreases the ciliary localization of endogenous Arl13b. Therefore, our results suggest Rab8 and TNPO1 might function together as a ciliary transport adaptor for Arl13b by interacting with its RVEP-containing CTS.
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Affiliation(s)
- Divyanshu Mahajan
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Viswanadh Madugula
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Lei Lu
- School of Biological Sciences, Nanyang Technological University, Singapore.
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50
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Rosenberg EM, Jian X, Soubias O, Yoon HY, Yadav MP, Hammoudeh S, Pallikkuth S, Akpan I, Chen PW, Maity TK, Jenkins LM, Yohe ME, Byrd RA, Randazzo PA. The small molecule inhibitor NAV-2729 has a complex target profile including multiple ADP-ribosylation factor regulatory proteins. J Biol Chem 2023; 299:102992. [PMID: 36758799 PMCID: PMC10023970 DOI: 10.1016/j.jbc.2023.102992] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/11/2023] Open
Abstract
The ADP-ribosylation factor (Arf) GTPases and their regulatory proteins are implicated in cancer progression. NAV-2729 was previously identified as a specific inhibitor of Arf6 that reduced progression of uveal melanoma in an orthotopic xenograft. Here, our goal was to assess the inhibitory effects of NAV-2729 on the proliferation of additional cell types. We found NAV-2729 inhibited proliferation of multiple cell lines, but Arf6 expression did not correlate with NAV-2729 sensitivity, and knockdown of Arf6 affected neither cell viability nor sensitivity to NAV-2729. Furthermore, binding to native Arf6 was not detected; however, we determined that NAV-2729 inhibited both Arf exchange factors and Arf GTPase-activating proteins. ASAP1, a GTPase-activating protein linked to cancer progression, was further investigated. We demonstrated that NAV-2729 bound to the PH domain of ASAP1 and changed ASAP1 cellular distribution. However, ASAP1 knockdown did not fully recapitulate the cytoskeletal effects of NAV-2729 nor affect cell proliferation. Finally, our screens identified 48 other possible targets of NAV-2729. These results illustrate the complexities of defining targets of small molecules and identify NAV-2729 as a model PH domain-binding inhibitor.
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Affiliation(s)
- Eric M Rosenberg
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Olivier Soubias
- Center for Structural Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Hye-Young Yoon
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Mukesh P Yadav
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sarah Hammoudeh
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sandeep Pallikkuth
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Itoro Akpan
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Pei-Wen Chen
- Department of Biology, Williams College, Williamstown, Massachusetts, USA
| | - Tapan K Maity
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Marielle E Yohe
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA; Laboratory of Cell and Developmental Signaling, Center for Cancer Research, Frederick, Maryland, USA
| | - R Andrew Byrd
- Center for Structural Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
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