1
|
Morito M, Yasuda H, Matsufuji T, Kinoshita M, Matsumori N. Identification of lipid-specific proteins with high-density lipid-immobilized beads. Analyst 2024. [PMID: 38829210 DOI: 10.1039/d4an00579a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
In biological membranes, lipids often interact with membrane proteins (MPs), regulating the localization and activity of MPs in cells. Although elucidating lipid-MP interactions is critical to comprehend the physiological roles of lipids, a systematic and comprehensive identification of lipid-binding proteins has not been adequately established. Therefore, we report the development of lipid-immobilized beads where lipid molecules were covalently immobilized. Owing to the detergent tolerance, these beads enable screening of water-soluble proteins and MPs, the latter of which typically necessitate surfactants for solubilization. Herein, two sphingolipid species-ceramide and sphingomyelin-which are major constituents of lipid rafts, were immobilized on the beads. We first showed that the density of immobilized lipid molecules on the beads was as high as that of biological lipid membranes. Subsequently, we confirmed that these beads enabled the selective pulldown of known sphingomyelin- or ceramide-binding proteins (lysenin, p24, and CERT) from protein mixtures, including cell lysates. In contrast, commercial sphingomyelin beads, on which lipid molecules are sparsely immobilized through biotin-streptavidin linkage, failed to capture lysenin, a well-known protein that recognizes clustered sphingomyelin molecules. This clearly demonstrates the applicability of our beads for obtaining proteins that recognize not only a single lipid molecule but also lipid clusters or lipid membranes. Finally, we demonstrated the screening of lipid-binding proteins from Neuro2a cell lysates using these beads. This method is expected to significantly contribute to the understanding of interactions between lipids and proteins and to unravel the complexities of lipid diversity.
Collapse
Affiliation(s)
- Masayuki Morito
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Hiroki Yasuda
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Takaaki Matsufuji
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Masanao Kinoshita
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| |
Collapse
|
2
|
Smith DM, Liu BY, Wolfgang MJ. Rab30 facilitates lipid homeostasis during fasting. Nat Commun 2024; 15:4469. [PMID: 38796472 PMCID: PMC11127972 DOI: 10.1038/s41467-024-48959-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: 08/15/2023] [Accepted: 05/17/2024] [Indexed: 05/28/2024] Open
Abstract
To facilitate inter-tissue communication and the exchange of proteins, lipoproteins, and metabolites with the circulation, hepatocytes have an intricate and efficient intracellular trafficking system regulated by small Rab GTPases. Here, we show that Rab30 is induced in the mouse liver by fasting, which is amplified in liver-specific carnitine palmitoyltransferase 2 knockout mice (Cpt2L-/-) lacking the ability to oxidize fatty acids, in a Pparα-dependent manner. Live-cell super-resolution imaging and in vivo proximity labeling demonstrates that Rab30-marked vesicles are highly dynamic and interact with proteins throughout the secretory pathway. Rab30 whole-body, liver-specific, and Rab30; Cpt2 liver-specific double knockout (DKO) mice are viable with intact Golgi ultrastructure, although Rab30 deficiency in DKO mice suppresses the serum dyslipidemia observed in Cpt2L-/- mice. Corresponding with decreased serum triglyceride and cholesterol levels, DKO mice exhibit decreased circulating but not hepatic ApoA4 protein, indicative of a trafficking defect. Together, these data suggest a role for Rab30 in the selective sorting of lipoproteins to influence hepatocyte and circulating triglyceride levels, particularly during times of excessive lipid burden.
Collapse
Affiliation(s)
- Danielle M Smith
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Brian Y Liu
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Michael J Wolfgang
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| |
Collapse
|
3
|
Sittewelle M, Royle SJ. Passive diffusion accounts for the majority of intracellular nanovesicle transport. Life Sci Alliance 2024; 7:e202302406. [PMID: 37857498 PMCID: PMC10587482 DOI: 10.26508/lsa.202302406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023] Open
Abstract
During membrane trafficking, a vesicle formed at the donor compartment must travel to the acceptor membrane before fusing. For large carriers, it is established that this transport is motor-driven; however, the mode by which small vesicles, which outnumber larger carriers, are transported is poorly characterized. Here, we show that intracellular nanovesicles (INVs), a substantial class of small vesicles, are highly mobile within cells and that this mobility depends almost entirely on passive diffusion (0.1-0.3 μm2 s-1). Using single particle tracking, we describe how other small trafficking vesicles have a similar diffusive mode of transport that contrasts with the motor-dependent movement of larger endolysosomal carriers. We also demonstrate that a subset of INVs is involved in exocytosis and that delivery of cargo to the plasma membrane during exocytosis is decreased when diffusion of INVs is specifically restricted. Our results suggest that passive diffusion is sufficient to explain the majority of small vesicle transport.
Collapse
Affiliation(s)
- Méghane Sittewelle
- https://ror.org/01a77tt86 Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Stephen J Royle
- https://ror.org/01a77tt86 Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| |
Collapse
|
4
|
Wilson B, Flett C, Gemperle J, Lawless C, Hartshorn M, Hinde E, Harrison T, Chastney M, Taylor S, Allen J, Norman JC, Zacharchenko T, Caswell PT. Proximity labelling identifies pro-migratory endocytic recycling cargo and machinery of the Rab4 and Rab11 families. J Cell Sci 2023; 136:jcs260468. [PMID: 37232246 PMCID: PMC10323252 DOI: 10.1242/jcs.260468] [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: 07/28/2022] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
Endocytic recycling controls the return of internalised cargoes to the plasma membrane to coordinate their positioning, availability and downstream signalling. The Rab4 and Rab11 small GTPase families regulate distinct recycling routes, broadly classified as fast recycling from early endosomes (Rab4) and slow recycling from perinuclear recycling endosomes (Rab11), and both routes handle a broad range of overlapping cargoes to regulate cell behaviour. We adopted a proximity labelling approach, BioID, to identify and compare the protein complexes recruited by Rab4a, Rab11a and Rab25 (a Rab11 family member implicated in cancer aggressiveness), revealing statistically robust protein-protein interaction networks of both new and well-characterised cargoes and trafficking machinery in migratory cancer cells. Gene ontological analysis of these interconnected networks revealed that these endocytic recycling pathways are intrinsically connected to cell motility and cell adhesion. Using a knock-sideways relocalisation approach, we were further able to confirm novel links between Rab11, Rab25 and the ESCPE-1 and retromer multiprotein sorting complexes, and identify new endocytic recycling machinery associated with Rab4, Rab11 and Rab25 that regulates cancer cell migration in the 3D matrix.
Collapse
Affiliation(s)
- Beverley Wilson
- 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, M13 9PT, UK
| | - Chloe Flett
- 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, M13 9PT, UK
| | - Jakub Gemperle
- 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, M13 9PT, UK
| | - Craig Lawless
- 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, M13 9PT, UK
| | - Matthew Hartshorn
- 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, M13 9PT, UK
| | - Eleanor Hinde
- 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, M13 9PT, UK
| | - Tess Harrison
- 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, M13 9PT, UK
| | - Megan Chastney
- 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, M13 9PT, UK
| | - Sarah Taylor
- 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, M13 9PT, UK
| | - Jennifer Allen
- 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, M13 9PT, UK
| | - Jim C. Norman
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Thomas Zacharchenko
- 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, M13 9PT, UK
| | - 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, M13 9PT, UK
| |
Collapse
|
5
|
Sittewelle M, Ferrandiz N, Fesenko M, Royle SJ. Genetically encoded imaging tools for investigating cell dynamics at a glance. J Cell Sci 2023; 136:jcs260783. [PMID: 37039102 DOI: 10.1242/jcs.260783] [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] [Indexed: 04/12/2023] Open
Abstract
The biology of a cell is the sum of many highly dynamic processes, each orchestrated by a plethora of proteins and other molecules. Microscopy is an invaluable approach to spatially and temporally dissect the molecular details of these processes. Hundreds of genetically encoded imaging tools have been developed that allow cell scientists to determine the function of a protein of interest in the context of these dynamic processes. Broadly, these tools fall into three strategies: observation, inhibition and activation. Using examples for each strategy, in this Cell Science at a Glance and the accompanying poster, we provide a guide to using these tools to dissect protein function in a given cellular process. Our focus here is on tools that allow rapid modification of proteins of interest and how observing the resulting changes in cell states is key to unlocking dynamic cell processes. The aim is to inspire the reader's next set of imaging experiments.
Collapse
Affiliation(s)
- Méghane Sittewelle
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Nuria Ferrandiz
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Mary Fesenko
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| |
Collapse
|
6
|
Integrin receptor trafficking in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 196:271-302. [PMID: 36813362 DOI: 10.1016/bs.pmbts.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Integrins are a family of 24 different heterodimers that are indispensable for multicellular life. Cell polarity, adhesion and migration are controlled by integrins delivered to the cell surface which in turn is regulated by the exo- and endocytic trafficking of integrins. The deep integration between trafficking and cell signaling determines the spatial and temporal output from any biochemical cue. Integrin trafficking plays a key role in development and many pathological conditions, especially cancer. Several novel regulators of integrin traffic have been discovered in recent times, including a novel class of integrin carrying vesicles, the intracellular nanovesicles (INVs). The tight regulation of trafficking pathways by cell signaling, where kinases phosphorylate key small GTPases in the trafficking pathway enable coordination of cell response to the extracellular milieu. Integrin heterodimer expression and trafficking differ in different tissues and contexts. In this Chapter, we discuss recent studies on integrin trafficking and its contribution to normal physiological and pathophysiological states.
Collapse
|
7
|
Luo S, Wang H, Wang Z, Xu W, Tian R, Zhou J. Internalization of myriocin involved in energy and affected expression of genes and proteins in the endocytosis pathway in Fusarium oxysporum f. sp. niveum. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2100721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Shiqi Luo
- Department of Horticulture, College of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang, PR China
- Department of Biology, Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, Heilongjiang, PR China
| | - Hengxu Wang
- Department of Horticulture, College of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang, PR China
- Department of Biology, Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, Heilongjiang, PR China
| | - Zhigang Wang
- Department of Horticulture, College of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang, PR China
- Department of Biology, Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, Heilongjiang, PR China
| | - Weihui Xu
- Department of Horticulture, College of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang, PR China
- Department of Biology, Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, Heilongjiang, PR China
| | - Renmao Tian
- Department of Food Safety, Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL, USA
| | - Jiaxin Zhou
- Department of Horticulture, College of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang, PR China
- Department of Biology, Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, Heilongjiang, PR China
| |
Collapse
|
8
|
Investigation of Transcript Variant 6 of TPD52L2 as a Prognostic and Predictive Biomarker in Basal-Like MDA-MB-231 and MDA-MB-453 Cell Lines for Breast Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7078787. [PMID: 36071863 PMCID: PMC9444471 DOI: 10.1155/2022/7078787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/10/2022] [Indexed: 12/02/2022]
Abstract
Background Basal-like breast cancer (BLBC) exhibits worse pathological features than other breast cancer subtypes, and patients diagnosed with BLBC have short disease-free and overall survival times. Thus, the identification of novel biomarkers and therapeutic targets for BLBC is of upmost importance. Although TPD52L2 is upregulated in multiple cancers, little is known about its roles in BLBC. Methods RNA levels were analyzed between breast cancer tissues and paired adjacent normal tissues using RNA-seq data from The Cancer Genome Atlas (TCGA). TPD52L2 stable knockdown and inducible knockout cell lines were established using basal-like MDA-MB-231 and MDA-MB-453 cell lines. Cell proliferation assays in vitro and tumor growth analysis in vivo were performed to determine the function of TPD52L2 during BLBC progression. Transwell assays were used to estimate the regulatory effect of TPD52L2 on BLBC cell migration. The expression profile of all tpd52l2 transcripts was analyzed to assess the functional protein isoform. Association of transcript variant 6 (V6) expression with pathological parameters was carried out using the clinical data of the BRCA cohort. Results We identified V6 of TPD52L2 as a novel biomarker and regulator of BLBC progression. TPD52L2 is upregulated in BLBCs and associated with patient outcomes. TPD52L2 knockdown suppresses tumor growth, and V6 correlates with cancer-related phenotypes in BLBC. Clinical data further proved that V6 is associated with different pathological features, such as pathological stage and pathological tumor status, and independently predicts patient outcomes and responses to therapies. Conclusions Our findings demonstrate that V6 of TPD52L2 is a novel biomarker for BLBC patients. V6 promotes cell proliferation and migration and has marked oncogenic roles in determining the malignant phenotypes of BLBC.
Collapse
|
9
|
Ferrandiz N, Downie L, Starling GP, Royle SJ. Endomembranes promote chromosome missegregation by ensheathing misaligned chromosomes. J Cell Biol 2022; 221:e202203021. [PMID: 35486148 PMCID: PMC9066052 DOI: 10.1083/jcb.202203021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 01/29/2023] Open
Abstract
Errors in mitosis that cause chromosome missegregation lead to aneuploidy and micronucleus formation, which are associated with cancer. Accurate segregation requires the alignment of all chromosomes by the mitotic spindle at the metaphase plate, and any misalignment must be corrected before anaphase is triggered. The spindle is situated in a membrane-free "exclusion zone"; beyond this zone, endomembranes (mainly endoplasmic reticulum) are densely packed. We investigated what happens to misaligned chromosomes localized beyond the exclusion zone. Here we show that such chromosomes become ensheathed in multiple layers of endomembranes. Chromosome ensheathing delays mitosis and increases the frequency of chromosome missegregation and micronucleus formation. We use an induced organelle relocalization strategy in live cells to show that clearance of endomembranes allows for the rescue of chromosomes that were destined for missegregation. Our findings indicate that endomembranes promote the missegregation of misaligned chromosomes that are outside the exclusion zone and therefore constitute a risk factor for aneuploidy.
Collapse
Affiliation(s)
- Nuria Ferrandiz
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, UK
| | - Laura Downie
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, UK
| | | | - Stephen J. Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, UK
| |
Collapse
|
10
|
Manivannan SN, Roovers J, Smal N, Myers CT, Turkdogan D, Roelens F, Kanca O, Chung HL, Scholz T, Hermann K, Bierhals T, Caglayan HS, Stamberger H, Mefford H, de Jonghe P, Yamamoto S, Weckhuysen S, Bellen HJ. De novo FZR1 loss-of-function variants cause developmental and epileptic encephalopathies. Brain 2022; 145:1684-1697. [PMID: 34788397 PMCID: PMC9166542 DOI: 10.1093/brain/awab409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/21/2021] [Accepted: 10/18/2021] [Indexed: 01/18/2023] Open
Abstract
FZR1, which encodes the Cdh1 subunit of the anaphase-promoting complex, plays an important role in neurodevelopment by regulating the cell cycle and by its multiple post-mitotic functions in neurons. In this study, evaluation of 250 unrelated patients with developmental and epileptic encephalopathies and a connection on GeneMatcher led to the identification of three de novo missense variants in FZR1. Whole-exome sequencing in 39 patient-parent trios and subsequent targeted sequencing in an additional cohort of 211 patients was performed to identify novel genes involved in developmental and epileptic encephalopathy. Functional studies in Drosophila were performed using three different mutant alleles of the Drosophila homologue of FZR1 fzr. All three individuals carrying de novo variants in FZR1 had childhood-onset generalized epilepsy, intellectual disability, mild ataxia and normal head circumference. Two individuals were diagnosed with the developmental and epileptic encephalopathy subtype myoclonic atonic epilepsy. We provide genetic-association testing using two independent statistical tests to support FZR1 association with developmental and epileptic encephalopathies. Further, we provide functional evidence that the missense variants are loss-of-function alleles using Drosophila neurodevelopment assays. Using three fly mutant alleles of the Drosophila homologue fzr and overexpression studies, we show that patient variants can affect proper neurodevelopment. With the recent report of a patient with neonatal-onset with microcephaly who also carries a de novo FZR1 missense variant, our study consolidates the relationship between FZR1 and developmental and epileptic encephalopathy and expands the associated phenotype. We conclude that heterozygous loss-of-function of FZR1 leads to developmental and epileptic encephalopathies associated with a spectrum of neonatal to childhood-onset seizure types, developmental delay and mild ataxia. Microcephaly can be present but is not an essential feature of FZR1-encephalopathy. In summary, our approach of targeted sequencing using novel gene candidates and functional testing in Drosophila will help solve undiagnosed myoclonic atonic epilepsy or developmental and epileptic encephalopathy cases.
Collapse
Affiliation(s)
- Sathiya N Manivannan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston 77030, USA
| | - Jolien Roovers
- Neurogenetics Group, VIB Centre for Molecular Neurology, Antwerp 2610, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp 2610, Belgium
| | - Noor Smal
- Applied and Translational Neurogenomics Group, VIB Centre for Molecular Neurology, VIB, Antwerp 2610, Belgium
| | - Candace T Myers
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology St. Jude Children's Research Hospital, Memphis, TN 30105, USA
| | - Dilsad Turkdogan
- Division of Child Neurology, Department of Paediatrics, Marmara University, Faculty of Medicine, Turkey
| | | | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston 77030, USA
| | - Hyung-Lok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston 77030, USA
| | - Tasja Scholz
- Institute of Human Genetics, University Medical Centre Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Katharina Hermann
- Department of Paediatrics, University Medical Centre Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Centre Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Hande S Caglayan
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
| | - Hannah Stamberger
- Applied and Translational Neurogenomics Group, VIB Centre for Molecular Neurology, VIB, Antwerp 2610, Belgium.,Department of Neurology, University Hospital Antwerp, Antwerp 2650, Belgium
| | | | - Heather Mefford
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology St. Jude Children's Research Hospital, Memphis, TN 30105, USA
| | - Peter de Jonghe
- Neurogenetics Group, VIB Centre for Molecular Neurology, Antwerp 2610, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp 2610, Belgium.,Department of Neurology, University Hospital Antwerp, Antwerp 2650, Belgium
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston 77030, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Weckhuysen
- Applied and Translational Neurogenomics Group, VIB Centre for Molecular Neurology, VIB, Antwerp 2610, Belgium.,Department of Neurology, University Hospital Antwerp, Antwerp 2650, Belgium.,Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp 2650, Belgium.,µNEURO Research Centre of Excellence, University of Antwerp, Antwerp 2610, Belgium
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston 77030, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
11
|
Larocque G, Royle SJ. Integrating intracellular nanovesicles into integrin trafficking pathways and beyond. Cell Mol Life Sci 2022; 79:335. [PMID: 35657500 PMCID: PMC9166830 DOI: 10.1007/s00018-022-04371-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022]
Abstract
Membrane traffic controls the movement of proteins and lipids from one cellular compartment to another using a system of transport vesicles. Intracellular nanovesicles (INVs) are a newly described class of transport vesicles. These vesicles are small, carry diverse cargo, and are involved in multiple trafficking steps including anterograde traffic and endosomal recycling. An example of a biological process that they control is cell migration and invasion, due to their role in integrin recycling. In this review, we describe what is known so far about these vesicles. We discuss how INVs may integrate into established membrane trafficking pathways using integrin recycling as an example. We speculate where in the cell INVs have the potential to operate and we identify key questions for future investigation.
Collapse
Affiliation(s)
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill Road, Coventry, CV4 7AL, UK.
| |
Collapse
|
12
|
The Antitumor Effect of TPD52L2 Silencing on Oxaliplatin-Resistant Gastric Carcinoma Is Related to Endoplasmic Reticulum Stress In Vitro. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4451178. [PMID: 35087592 PMCID: PMC8789433 DOI: 10.1155/2022/4451178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 12/01/2021] [Accepted: 12/17/2021] [Indexed: 11/17/2022]
Abstract
Tumor protein D52-like 2 or simply TPD52L2 belongs to the TPD52 family which has been implicated in a variety of human carcinomas. However, the TPD52L2 function in the gastric carcinoma oxaliplatin (OXA) resistance remains elusive. The main objective of this study is to evaluate the TPD52L2 effect in OXA-resistant gastric carcinoma cells in vitro. Oxaliplatin-resistant gastric carcinoma cells were generated in MGC-803 and SGC-7901 cells. siRNA-mediated knockdown of TPD52L2 was investigated in OXA-resistant MGC-803-OXA and SGC-7901-OXA cells. qRT-PCR was performed to assess the expression level of TPD52L2 mRNA. TPD52L2 protein expression level, apoptosis, and endoplasmic reticulum (ER) stress-associated proteins were identified via immunoblotting analysis. MTT assay was conducted for the evaluation of cell viability, while colony-forming activity was carried out via crystal violet staining. SGC-7901-OXA and MGC-803-OXA cells were found to be more resistant to OXA, as compared to the parental cell lines. The expression of TPD52L2 was found to be upregulated in OXA-resistant cells. Knockdown of TPD52L2 suppressed cell colony-forming potency, cell growth, and development in OXA-resistant cells. TPD52L2 knockdown also enhanced the PARP and caspase-3 cleavage. ER-associated proteins such as PERK, GRP78, CHOP, and IRE1α were found to be elevated in TPD52L2 knockdown cells. ER stress might be involved in TPD52L2 knockdown-induced apoptosis in OXA-resistant gastric carcinoma cells.
Collapse
|
13
|
Larocque G, Moore DJ, Sittewelle M, Kuey C, Hetmanski JHR, La-Borde PJ, Wilson BJ, Clarke NI, Caswell PT, Royle SJ. Intracellular nanovesicles mediate α5β1 integrin trafficking during cell migration. J Cell Biol 2021; 220:212493. [PMID: 34287617 PMCID: PMC8298100 DOI: 10.1083/jcb.202009028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 05/29/2021] [Accepted: 06/30/2021] [Indexed: 12/30/2022] Open
Abstract
Membrane traffic is an important regulator of cell migration through the endocytosis and recycling of cell surface receptors such as integrin heterodimers. Intracellular nanovesicles (INVs) are transport vesicles that are involved in multiple membrane trafficking steps, including the recycling pathway. The only known marker for INVs is tumor protein D54 (TPD54/TPD52L2), a member of the TPD52-like protein family. Overexpression of TPD52-like family proteins in cancer has been linked to poor prognosis and an aggressive metastatic phenotype, which suggests cell migration may be altered under these conditions. Here, we show that TPD54 directly binds membrane and associates with INVs via a conserved positively charged motif in its C terminus. We describe how other TPD52-like proteins are also associated with INVs, and we document the Rab GTPase complement of all INVs. Depletion of TPD52-like proteins inhibits cell migration and invasion, while their overexpression boosts motility. We show that inhibition of migration is likely due to altered recycling of α5β1 integrins in INVs.
Collapse
Affiliation(s)
- Gabrielle Larocque
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, UK
| | - Daniel J Moore
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, UK
| | - Méghane Sittewelle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, UK
| | - Cansu Kuey
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, UK
| | - Joseph H R Hetmanski
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Penelope J La-Borde
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, UK
| | - Beverley J Wilson
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Nicholas I Clarke
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, UK
| | - Patrick T Caswell
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, UK
| |
Collapse
|
14
|
Haspinger DC, Klinge S, Holzapfel GA. Numerical analysis of the impact of cytoskeletal actin filament density alterations onto the diffusive vesicle-mediated cell transport. PLoS Comput Biol 2021; 17:e1008784. [PMID: 33939706 PMCID: PMC8130967 DOI: 10.1371/journal.pcbi.1008784] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 05/18/2021] [Accepted: 02/09/2021] [Indexed: 11/21/2022] Open
Abstract
The interior of a eukaryotic cell is a highly complex composite material which consists of water, structural scaffoldings, organelles, and various biomolecular solutes. All these components serve as obstacles that impede the motion of vesicles. Hence, it is hypothesized that any alteration of the cytoskeletal network may directly impact or even disrupt the vesicle transport. A disruption of the vesicle-mediated cell transport is thought to contribute to several severe diseases and disorders, such as diabetes, Parkinson’s and Alzheimer’s disease, emphasizing the clinical relevance. To address the outlined objective, a multiscale finite element model of the diffusive vesicle transport is proposed on the basis of the concept of homogenization, owed to the complexity of the cytoskeletal network. In order to study the microscopic effects of specific nanoscopic actin filament network alterations onto the vesicle transport, a parametrized three-dimensional geometrical model of the actin filament network was generated on the basis of experimentally observed filament densities and network geometries in an adenocarcinomic human alveolar basal epithelial cell. Numerical analyzes of the obtained effective diffusion properties within two-dimensional sampling domains of the whole cell model revealed that the computed homogenized diffusion coefficients can be predicted statistically accurate by a simple two-parameter power law as soon as the inaccessible area fraction, due to the obstacle geometries and the finite size of the vesicles, is known. This relationship, in turn, leads to a massive reduction in computation time and allows to study the impact of a variety of different cytoskeletal alterations onto the vesicle transport. Hence, the numerical simulations predicted a 35% increase in transport time due to a uniformly distributed four-fold increase of the total filament amount. On the other hand, a hypothetically reduced expression of filament cross-linking proteins led to sparser filament networks and, thus, a speed up of the vesicle transport. Many vital processes in our eukaryotic cells and organs require an astonishingly precise routing of intermediate products to various intra- and extracellular destinations using vesicles as transporters. This can be illustrated by numerous examples, such as the production and destruction of proteins, the export of neurotransmitters or insulin to the extracellular domain, etc. However, the inside of a cell is tightly packed with numerous structural scaffoldings (filaments), which serve as obstacles and impede the vesicle motion. It is thought that any disturbances of the vesicle-mediated cell transport contribute to numerous degenerative diseases and disorders, which highlights the clinical relevance for investigating this intracellular transport mechanism by developing computational models and performing experimental studies. In this study, we numerically quantified how different specific alterations of the filament density inside a human lung cell—due to changed mechanical loadings or genetic disorders of proteins being responsible for filament branching—affect the diffusion of vesicles inside the intracellular fluid. Therefore, based on the concept of homogenization, a computationally efficient numerical method was developed and utilized to simulate the diffusion of vesicles inside the whole cell, considering the detailed structural information of the filament network.
Collapse
Affiliation(s)
| | - Sandra Klinge
- Chair of Structural Mechanics and Analysis, TU Berlin, Berlin, Germany
| | - Gerhard A. Holzapfel
- Institute of Biomechanics, Graz University of Technology, Graz, Austria
- Faculty of Engineering Science and Technology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- * E-mail:
| |
Collapse
|
15
|
Stalder D, Gershlick DC. Direct trafficking pathways from the Golgi apparatus to the plasma membrane. Semin Cell Dev Biol 2020; 107:112-125. [PMID: 32317144 PMCID: PMC7152905 DOI: 10.1016/j.semcdb.2020.04.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/19/2022]
Abstract
In eukaryotic cells, protein sorting is a highly regulated mechanism important for many physiological events. After synthesis in the endoplasmic reticulum and trafficking to the Golgi apparatus, proteins sort to many different cellular destinations including the endolysosomal system and the extracellular space. Secreted proteins need to be delivered directly to the cell surface. Sorting of secreted proteins from the Golgi apparatus has been a topic of interest for over thirty years, yet there is still no clear understanding of the machinery that forms the post-Golgi carriers. Most evidence points to these post-Golgi carriers being tubular pleomorphic structures that bud from the trans-face of the Golgi. In this review, we present the background studies and highlight the key components of this pathway, we then discuss the machinery implicated in the formation of these carriers, their translocation across the cytosol, and their fusion at the plasma membrane.
Collapse
Key Words
- ATP, adenosine triphosphate
- BFA, Brefeldin A
- CARTS, CARriers of the TGN to the cell Surface
- CI-MPR, cation-independent mannose-6 phosphate receptor
- Constitutive Secretion
- CtBP3/BARS, C-terminus binding protein 3/BFA adenosine diphosphate–ribosylated substrate
- ER, endoplasmic reticulum
- GPI-anchored proteins, glycosylphosphatidylinositol-anchored proteins
- GlcCer, glucosylceramidetol
- Golgi to plasma membrane sorting
- PAUF, pancreatic adenocarcinoma up-regulated factor
- PKD, Protein Kinase D
- RUSH, retention using selective hooks
- SBP, streptavidin-binding peptide
- SM, sphingomyelin
- SNARE, soluble N-ethylmaleimide sensitive fusion protein attachment protein receptor
- SPCA1, secretory pathway calcium ATPase 1
- Secretion
- TGN, trans-Golgi Network
- TIRF, total internal reflection fluorescence
- VSV, vesicular stomatitis virus
- pleomorphic tubular carriers
- post-Golgi carriers
- ts, temperature sensitive
Collapse
Affiliation(s)
- Danièle Stalder
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - David C Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.
| |
Collapse
|
16
|
Miaczynska M, Munson M. Membrane trafficking: vesicle formation, cargo sorting and fusion. Mol Biol Cell 2020; 31:399-400. [PMID: 32163346 PMCID: PMC7185893 DOI: 10.1091/mbc.e19-12-0680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- Marta Miaczynska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Mary Munson
- University of Massachusetts Medical School, Worcester, MA 01605
| |
Collapse
|
17
|
Abstract
Cells are complex machines with tremendous potential for applications in medicine and biotechnology. Although much effort has been devoted to engineering the metabolic, genetic, and signaling pathways of cells, methods for systematically engineering the physical structure of cells are less developed. Here we consider how coarse-grained models for cellular geometry at the organelle level can be used to build computer-aided design (CAD) tools for cellular structure.
Collapse
Affiliation(s)
- Simone Bianco
- Center for Cellular Construction, San Francisco, CA, United States of America. IBM Almaden Research Center, San Jose, CA, United States of America
| | | | | |
Collapse
|
18
|
Küey C, Larocque G, Clarke NI, Royle SJ. Unintended perturbation of protein function using GFP nanobodies in human cells. J Cell Sci 2019; 132:jcs234955. [PMID: 31601614 PMCID: PMC6857592 DOI: 10.1242/jcs.234955] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/03/2019] [Indexed: 12/28/2022] Open
Abstract
Tagging a protein of interest with GFP using genome editing is a popular approach to study protein function in cell and developmental biology. To avoid re-engineering cell lines or organisms in order to introduce additional tags, functionalized nanobodies that bind GFP can be used to extend the functionality of the GFP tag. We developed functionalized nanobodies, which we termed 'dongles', that could add, for example, an FKBP tag to a GFP-tagged protein of interest, enabling knocksideways experiments in GFP knock-in cell lines. The power of knocksideways is that it allows investigators to rapidly switch the protein from an active to an inactive state. We show that dongles allow for effective knocksideways of GFP-tagged proteins in genome-edited human cells. However, we discovered that nanobody binding to dynamin-2-GFP caused inhibition of dynamin function prior to knocksideways. The function of GFP-tagged tumor protein D54 (TPD54, also known as TPD52L2) in anterograde traffic was also perturbed by dongles. While these issues potentially limit the application of dongles, we discuss strategies for their deployment as cell biological tools.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Cansu Küey
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Gabrielle Larocque
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Nicholas I Clarke
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| |
Collapse
|