1
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Holzer E, Martens S, Tulli S. The Role of ATG9 Vesicles in Autophagosome Biogenesis. J Mol Biol 2024; 436:168489. [PMID: 38342428 DOI: 10.1016/j.jmb.2024.168489] [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: 12/19/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/13/2024]
Abstract
Autophagy mediates the degradation and recycling of cellular material in the lysosomal system. Dysfunctional autophagy is associated with a plethora of diseases including uncontrolled infections, cancer and neurodegeneration. In macroautophagy (hereafter autophagy) this material is encapsulated in double membrane vesicles, the autophagosomes, which form upon induction of autophagy. The precursors to autophagosomes, referred to as phagophores, first appear as small flattened membrane cisternae, which gradually enclose the cargo material as they grow. The assembly of phagophores during autophagy initiation has been a major subject of investigation over the past decades. A special focus has been ATG9, the only conserved transmembrane protein among the core machinery. The majority of ATG9 localizes to small Golgi-derived vesicles. Here we review the recent advances and breakthroughs regarding our understanding of how ATG9 and the vesicles it resides in serve to assemble the autophagy machinery and to establish membrane contact sites for autophagosome biogenesis. We also highlight open questions in the field that need to be addressed in the years to come.
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Affiliation(s)
- Elisabeth Holzer
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria; University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Campus-Vienna-Biocenter 1, Vienna, Austria.
| | - Sascha Martens
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria; University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria.
| | - Susanna Tulli
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria; University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria.
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2
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Diarra S, Ghosh S, Cissé L, Coulibaly T, Yalcouyé A, Harmison G, Diallo S, Diallo SH, Coulibaly O, Schindler A, Cissé CAK, Maiga AB, Bamba S, Samassekou O, Khokha MK, Mis EK, Lakhani SA, Donovan FX, Jacobson S, Blackstone C, Guinto CO, Landouré G, Bonifacino JS, Fischbeck KH, Grunseich C. AP2A2 mutation and defective endocytosis in a Malian family with hereditary spastic paraplegia. Neurobiol Dis 2024; 198:106537. [PMID: 38772452 PMCID: PMC11209852 DOI: 10.1016/j.nbd.2024.106537] [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: 01/13/2024] [Revised: 04/17/2024] [Accepted: 05/17/2024] [Indexed: 05/23/2024] Open
Abstract
Hereditary spastic paraplegia (HSP) comprises a large group of neurogenetic disorders characterized by progressive lower extremity spasticity. Neurological evaluation and genetic testing were completed in a Malian family with early-onset HSP. Three children with unaffected consanguineous parents presented with symptoms consistent with childhood-onset complicated HSP. Neurological evaluation found lower limb weakness, spasticity, dysarthria, seizures, and intellectual disability. Brain MRI showed corpus callosum thinning with cortical and spinal cord atrophy, and an EEG detected slow background in the index patient. Whole exome sequencing identified a homozygous missense variant in the adaptor protein (AP) complex 2 alpha-2 subunit (AP2A2) gene. Western blot analysis showed reduced levels of AP2A2 in patient-iPSC derived neuronal cells. Endocytosis of transferrin receptor (TfR) was decreased in patient-derived neurons. In addition, we observed increased axon initial segment length in patient-derived neurons. Xenopus tropicalis tadpoles with ap2a2 knockout showed cerebral edema and progressive seizures. Immunoprecipitation of the mutant human AP-2-appendage alpha-C construct showed defective binding to accessory proteins. We report AP2A2 as a novel genetic entity associated with HSP and provide functional data in patient-derived neuron cells and a frog model. These findings expand our understanding of the mechanism of HSP and improve the genetic diagnosis of this condition.
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Affiliation(s)
- Salimata Diarra
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States; Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
| | - Saikat Ghosh
- Neurosciences and Cellular and Structural Biology Division, NICHD, NIH, Bethesda, MD, United States
| | - Lassana Cissé
- Service de Neurologie, CHU du Point "G", Bamako, Mali
| | - Thomas Coulibaly
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Neurosciences and Cellular and Structural Biology Division, NICHD, NIH, Bethesda, MD, United States
| | - Abdoulaye Yalcouyé
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - George Harmison
- Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | | | | | - Oumar Coulibaly
- Service de Chirurgie Pédiatrique, CHU du Gabriel Touré, Bamako, Mali
| | - Alice Schindler
- Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | - Cheick A K Cissé
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Alassane B Maiga
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Service de Neurologie, CHU du Point "G", Bamako, Mali
| | - Salia Bamba
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Oumar Samassekou
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Mustafa K Khokha
- Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
| | - Emily K Mis
- Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
| | - Saquib A Lakhani
- Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
| | - Frank X Donovan
- Cancer Genetics and Comparative Genomics Branch, NHGRI, NIH, Bethesda, MD, United States
| | - Steve Jacobson
- Neuroimmunology Division, NINDS, NIH, Bethesda, MD, United States
| | - Craig Blackstone
- Movement Disorders Division, Department of Neurology, Harvard Medicine School, Massachusetts General Hospital, Boston, MA, United States
| | - Cheick O Guinto
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Service de Neurologie, CHU du Point "G", Bamako, Mali
| | - Guida Landouré
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States; Service de Neurologie, CHU du Point "G", Bamako, Mali
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, NICHD, NIH, Bethesda, MD, United States
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3
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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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4
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Wallace NS, Gadbery JE, Cohen CI, Kendall AK, Jackson LP. Tepsin binds LC3B to promote ATG9A trafficking and delivery. Mol Biol Cell 2024; 35:ar56. [PMID: 38381558 PMCID: PMC11064669 DOI: 10.1091/mbc.e23-09-0359-t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024] Open
Abstract
Tepsin is an established accessory protein found in Adaptor Protein 4 (AP-4) coated vesicles, but the biological role of tepsin remains unknown. AP-4 vesicles originate at the trans-Golgi network (TGN) and target the delivery of ATG9A, a scramblase required for autophagosome biogenesis, to the cell periphery. Using in silico methods, we identified a putative LC3-Interacting Region (LIR) motif in tepsin. Biochemical experiments using purified recombinant proteins indicate tepsin directly binds LC3B preferentially over other members of the mammalian ATG8 family. Calorimetry and structural modeling data indicate this interaction occurs with micromolar affinity using the established LC3B LIR docking site. Loss of tepsin in cultured cells dysregulates ATG9A export from the TGN as well as ATG9A distribution at the cell periphery. Tepsin depletion in a mRFP-GFP-LC3B HeLa reporter cell line using siRNA knockdown increases autophagosome volume and number, but does not appear to affect flux through the autophagic pathway. Reintroduction of wild-type tepsin partially rescues ATG9A cargo trafficking defects. In contrast, reintroducing tepsin with a mutated LIR motif or missing N-terminus drives diffuse ATG9A subcellular distribution. Together, these data suggest roles for tepsin in cargo export from the TGN; ensuring delivery of ATG9A-positive vesicles; and in overall maintenance of autophagosome structure.
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Affiliation(s)
- Natalie S. Wallace
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - John E. Gadbery
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Cameron I. Cohen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
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5
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Orlowski A, Karippaparambil J, Paumier JM, Ghanta S, Pallares E, Tandukar J, Gao R, Gowrishankar S. Axonal organelle buildup from loss of AP-4 complex function causes exacerbation of amyloid plaque pathology and gliosis in Alzheimer's disease mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.587499. [PMID: 38617351 PMCID: PMC11014495 DOI: 10.1101/2024.03.31.587499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Lysosomes and related precursor organelles robustly build up in swollen axons that surround amyloid plaques and disrupted axonal lysosome transport has been implicated in worsening Alzheimer's pathology. Our prior studies have revealed that loss of Adaptor protein-4 (AP-4) complex function, linked primarily to Spastic Paraplegia (HSP), leads to a similar build of lysosomes in structures we term "AP-4 dystrophies". Surprisingly, these AP-4 dystrophies were also characterized by enrichment of components of APP processing machinery, β-site cleaving enzyme 1 (BACE1) and Presenilin 2. Our studies examining whether the abnormal axonal lysosome build up resulting from AP-4 loss could lead to amyloidogenesis revealed that the loss of AP-4 complex function in an Alzheimer's disease model resulted in a strong increase in size and abundance of amyloid plaques in the hippocampus and corpus callosum as well as increased microglial association with the plaques. Interestingly, we found a further increase in enrichment of the secretase, BACE1, in the axonal swellings of the plaques of Alzheimer model mice lacking AP-4 complex compared to those having normal AP-4 complex function, suggestive of increased amyloidogenic processing under this condition. Additionally, the exacerbation of plaque pathology was region-specific as it did not increase in the cortex. The burden of the AP-4 linked axonal dystrophies/AP-4 dystrophies was higher in the corpus callosum and hippocampus compared to the cortex, establishing the critical role of AP-4 -dependent axonal lysosome transport and maturation in regulating amyloidogenic amyloid precursor protein processing.
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Affiliation(s)
- Alex Orlowski
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Joseph Karippaparambil
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Jean-Michel Paumier
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Shraddha Ghanta
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Eduardo Pallares
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Jamuna Tandukar
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL 60607 USA
| | - Ruixuan Gao
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL 60607 USA
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL 60607 USA
| | - Swetha Gowrishankar
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
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6
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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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7
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Yamaguchi F, Sakane H, Akasaki K. Comparative study of the steady-state subcellular distribution of lysosome-associated membrane glycoprotein-2 (LAMP-2) isoforms with GYXXΦ-type tyrosine-based motifs that interact differently with four adaptor protein (AP) complexes. J Biochem 2024; 175:275-287. [PMID: 37983719 DOI: 10.1093/jb/mvad096] [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: 08/08/2023] [Revised: 10/23/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023] Open
Abstract
Lysosome-associated membrane protein-1 and -2 (LAMP-1 and LAMP-2, respectively) are type I transmembrane proteins. LAMP-2 comprises three splice isoforms (LAMP-2A, -B and-C) with different cytoplasmic tails (CTs). These three CTs possess different tyrosine-based motifs (GYXXΦ, where Φ is a bulky hydrophobic amino acid) at their C-termini. Interactions between tyrosine-based motifs and μ-subunits of four tetrameric adaptor protein (AP) complexes are necessary for their vesicular transport to lysosomes. Little is known about how the interaction strengths of these tyrosine motifs with μ-subunits affect the localization of isoforms to lysosomes. The interactions were first investigated using a yeast two-hybrid system to address this question. LAMP-2A-CT interacted with all four μ-subunits (μ1, μ2, μ3A and μ4 of AP-1, AP-2, AP-3 and AP-4, respectively). The interaction with μ3A was more robust than that with other μ-subunits. LAMP-2B-CT interacted exclusively and moderately with μ3A. LAMP-2C-CT did not detectably interact with any of the four μ-subunits. Immunofluorescence microscopy showed that all isoforms were localized in late endosomes and lysosomes. LAMP-2C was present in the plasma membrane and early endosomes; however, LAMP-2A and -2B were barely detectable in these organelles. In cell fractionation, LAMP-2A was the most abundant in the dense lysosomes, whereas LAMP-2C was significantly present in the low-density fraction containing the plasma membrane and early endosomes, in addition to the dense lysosomes. LAMP-2B considerably existed in the low-density late endosomal fraction. These data strongly suggest that the LAMP-2 isoforms are distributed differently in endocytic organelles depending on their interaction strengths with AP-3.
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Affiliation(s)
- Fumiaki Yamaguchi
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University, Fukuyama, Hiroshima 729-0292, Japan
| | - Hiroshi Sakane
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University, Fukuyama, Hiroshima 729-0292, Japan
| | - Kenji Akasaki
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University, Fukuyama, Hiroshima 729-0292, Japan
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8
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Damiani D, Baggiani M, Della Vecchia S, Naef V, Santorelli FM. Pluripotent Stem Cells as a Preclinical Cellular Model for Studying Hereditary Spastic Paraplegias. Int J Mol Sci 2024; 25:2615. [PMID: 38473862 DOI: 10.3390/ijms25052615] [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: 01/08/2024] [Revised: 02/12/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Hereditary spastic paraplegias (HSPs) comprise a family of degenerative diseases mostly hitting descending axons of corticospinal neurons. Depending on the gene and mutation involved, the disease could present as a pure form with limb spasticity, or a complex form associated with cerebellar and/or cortical signs such as ataxia, dysarthria, epilepsy, and intellectual disability. The progressive nature of HSPs invariably leads patients to require walking canes or wheelchairs over time. Despite several attempts to ameliorate the life quality of patients that have been tested, current therapeutical approaches are just symptomatic, as no cure is available. Progress in research in the last two decades has identified a vast number of genes involved in HSP etiology, using cellular and animal models generated on purpose. Although unanimously considered invaluable tools for basic research, those systems are rarely predictive for the establishment of a therapeutic approach. The advent of induced pluripotent stem (iPS) cells allowed instead the direct study of morphological and molecular properties of the patient's affected neurons generated upon in vitro differentiation. In this review, we revisited all the present literature recently published regarding the use of iPS cells to differentiate HSP patient-specific neurons. Most studies have defined patient-derived neurons as a reliable model to faithfully mimic HSP in vitro, discovering original findings through immunological and -omics approaches, and providing a platform to screen novel or repurposed drugs. Thereby, one of the biggest hopes of current HSP research regards the use of patient-derived iPS cells to expand basic knowledge on the disease, while simultaneously establishing new therapeutic treatments for both generalized and personalized approaches in daily medical practice.
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Affiliation(s)
- Devid Damiani
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris, Via dei Giacinti 2, 56128 Pisa, Italy
| | - Matteo Baggiani
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris, Via dei Giacinti 2, 56128 Pisa, Italy
| | - Stefania Della Vecchia
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris, Via dei Giacinti 2, 56128 Pisa, Italy
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Viale Pieraccini, 6, 50139 Florence, Italy
| | - Valentina Naef
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris, Via dei Giacinti 2, 56128 Pisa, Italy
| | - Filippo Maria Santorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris, Via dei Giacinti 2, 56128 Pisa, Italy
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9
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Saffari A, Brechmann B, Böger C, Saber WA, Jumo H, Whye D, Wood D, Wahlster L, Alecu JE, Ziegler M, Scheffold M, Winden K, Hubbs J, Buttermore ED, Barrett L, Borner GHH, Davies AK, Ebrahimi-Fakhari D, Sahin M. High-content screening identifies a small molecule that restores AP-4-dependent protein trafficking in neuronal models of AP-4-associated hereditary spastic paraplegia. Nat Commun 2024; 15:584. [PMID: 38233389 PMCID: PMC10794252 DOI: 10.1038/s41467-023-44264-1] [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: 06/07/2023] [Accepted: 12/06/2023] [Indexed: 01/19/2024] Open
Abstract
Unbiased phenotypic screens in patient-relevant disease models offer the potential to detect therapeutic targets for rare diseases. In this study, we developed a high-throughput screening assay to identify molecules that correct aberrant protein trafficking in adapter protein complex 4 (AP-4) deficiency, a rare but prototypical form of childhood-onset hereditary spastic paraplegia characterized by mislocalization of the autophagy protein ATG9A. Using high-content microscopy and an automated image analysis pipeline, we screened a diversity library of 28,864 small molecules and identified a lead compound, BCH-HSP-C01, that restored ATG9A pathology in multiple disease models, including patient-derived fibroblasts and induced pluripotent stem cell-derived neurons. We used multiparametric orthogonal strategies and integrated transcriptomic and proteomic approaches to delineate potential mechanisms of action of BCH-HSP-C01. Our results define molecular regulators of intracellular ATG9A trafficking and characterize a lead compound for the treatment of AP-4 deficiency, providing important proof-of-concept data for future studies.
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Affiliation(s)
- Afshin Saffari
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Child Neurology and Inherited Metabolic Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Barbara Brechmann
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Cedric Böger
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Wardiya Afshar Saber
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Hellen Jumo
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Dosh Whye
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Delaney Wood
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lara Wahlster
- Department of Hematology & Oncology, Boston Children's Hospital & Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Julian E Alecu
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marvin Ziegler
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marlene Scheffold
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kellen Winden
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jed Hubbs
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Elizabeth D Buttermore
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lee Barrett
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, 82152, Germany
| | - Alexandra K Davies
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, 82152, Germany
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK
| | - Darius Ebrahimi-Fakhari
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Movement Disorders Program, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Mustafa Sahin
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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10
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Peng Y, Li X, Kang K, Zhou Y. AP4M1 as a prognostic biomarker associated with cell proliferation, migration and immune regulation in hepatocellular carcinoma. Cancer Cell Int 2023; 23:235. [PMID: 37821948 PMCID: PMC10568912 DOI: 10.1186/s12935-023-03089-0] [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: 06/29/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND AP4M1 is a protein-coding gene that plays a crucial role in transporter activity, recognition, and hereditary-associated diseases, but it's largely unknown in cancers. METHODS The expression level of AP4M1 in cancers was investigated by The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and the correlation between AP4M1 and hepatocellular carcinoma (HCC) clinicopathological parameters were analyzed. Univariate and multifactorial COX regression analyses were performed to clarify the prognostic value of AP4M1 in HCC. The correlation between AP4M1 and immune cell infiltration was analyzed using single-sample Gene Set Enrichment Analysis (ssGSEA). Besides, we verified the biological function of AP4M1 by applying Cell Counting Kit-8 (CCK8), colony formation, and transwell assays. RESULTS The expression of AP4M1 was significantly elevated in HCC and was correlated with patients' pathological grades, AFP, and BMI. Kaplan-Meier survival curves indicated that patients with AP4M1 overexpression had worse overall survival. Univariate and multivariate COX regression analyses showed that AP4M1 was an independent risk factor affecting the prognosis of HCC. In addition, we observed that AP4M1 positively correlated with most immune checkpoint suppressor genes in HCC. Moreover, in vitro experiments further confirmed that AP4M1 could promote the proliferation and invasion of HCC. CONCLUSIONS AP4M1 is highly expressed and associated with poor prognosis in HCC. AP4M1 is closely related to cancer-immune regulation and could be a novel target for HCC, and guiding new strategies for the diagnosis and treatment of HCC patients.
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Affiliation(s)
- Yuanhao Peng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis, Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xuanxuan Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Kuo Kang
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Xiangya Hospital Central South University, Changsha, 410008, Hunan, China
| | - Yangying Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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11
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Wallace NS, Gadbery JE, Cohen CI, Kendall AK, Jackson LP. Tepsin binds LC3B to promote ATG9A export and delivery at the cell periphery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549521. [PMID: 37502979 PMCID: PMC10370099 DOI: 10.1101/2023.07.18.549521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Tepsin is an established accessory protein found in Adaptor Protein 4 (AP-4) coated vesicles, but the biological role of tepsin remains unknown. AP-4 vesicles originate at the trans -Golgi network (TGN) and target the delivery of ATG9A, a scramblase required for autophagosome biogenesis, to the cell periphery. Using in silico methods, we identified a putative L C3-Interacting R egion (LIR) motif in tepsin. Biochemical experiments using purified recombinant proteins indicate tepsin directly binds LC3B, but not other members, of the mammalian ATG8 family. Calorimetry and structural modeling data indicate this interaction occurs with micromolar affinity using the established LC3B LIR docking site. Loss of tepsin in cultured cells dysregulates ATG9A export from the TGN as well as ATG9A distribution at the cell periphery. Tepsin depletion in a mRFP-GFP-LC3B HeLa reporter cell line using siRNA knockdown increases autophagosome volume and number, but does not appear to affect flux through the autophagic pathway. Re-introduction of wild-type tepsin partially rescues ATG9A cargo trafficking defects. In contrast, re-introducing tepsin with a mutated LIR motif or missing N-terminus does not fully rescue altered ATG9A subcellular distribution. Together, these data suggest roles for tepsin in cargo export from the TGN; delivery of ATG9A-positive vesicles at the cell periphery; and in overall maintenance of autophagosome structure.
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12
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Saffari A, Brechmann B, Boeger C, Saber WA, Jumo H, Whye D, Wood D, Wahlster L, Alecu J, Ziegler M, Scheffold M, Winden K, Hubbs J, Buttermore E, Barrett L, Borner G, Davies A, Sahin M, Ebrahimi-Fakhari D. High-Content Small Molecule Screen Identifies a Novel Compound That Restores AP-4-Dependent Protein Trafficking in Neuronal Models of AP-4-Associated Hereditary Spastic Paraplegia. RESEARCH SQUARE 2023:rs.3.rs-3036166. [PMID: 37398196 PMCID: PMC10312991 DOI: 10.21203/rs.3.rs-3036166/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Unbiased phenotypic screens in patient-relevant disease models offer the potential to detect novel therapeutic targets for rare diseases. In this study, we developed a high-throughput screening assay to identify molecules that correct aberrant protein trafficking in adaptor protein complex 4 (AP-4) deficiency, a rare but prototypical form of childhood-onset hereditary spastic paraplegia, characterized by mislocalization of the autophagy protein ATG9A. Using high-content microscopy and an automated image analysis pipeline, we screened a diversity library of 28,864 small molecules and identified a lead compound, C-01, that restored ATG9A pathology in multiple disease models, including patient-derived fibroblasts and induced pluripotent stem cell-derived neurons. We used multiparametric orthogonal strategies and integrated transcriptomic and proteomic approaches to delineate putative molecular targets of C-01 and potential mechanisms of action. Our results define molecular regulators of intracellular ATG9A trafficking and characterize a lead compound for the treatment of AP-4 deficiency, providing important proof-of-concept data for future Investigational New Drug (IND)-enabling studies.
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Affiliation(s)
| | | | | | | | | | - Dosh Whye
- Boston Children's Hospital, Harvard Medical School
| | - Delaney Wood
- Boston Children's Hospital, Harvard Medical School
| | | | - Julian Alecu
- Boston Children's Hospital, Harvard Medical School
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13
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Bhatnagar P, Bajpai P, Shrinet J, Kaja MK, Chandele A, Sitaraman R. Prediction of human protein interactome of dengue virus non-structural protein 5 (NS5) and its downstream immunological implications. 3 Biotech 2023; 13:180. [PMID: 37193327 PMCID: PMC10182223 DOI: 10.1007/s13205-023-03569-0] [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: 10/06/2022] [Accepted: 04/19/2023] [Indexed: 05/18/2023] Open
Abstract
The non-structural protein 5 (NS5) is the most conserved protein among flaviviruses, a family that includes the dengue virus. It functions both as an RNA-dependent RNA polymerase and an RNA-methyltransferase and is therefore essential for the replication of viral RNA. The discovery that dengue virus NS5 protein (DENV-NS5) can also localize to the nucleus has resulted in renewed interest in its potential roles at the host-virus interface. In this study, we have used two complementary computational approaches in parallel - one based on linear motifs (ELM) and another based on tertiary structure of the protein (DALI) - to predict the host proteins that DENV-NS5 might interact with. Of the 42 human proteins predicted by both these methods, 34 are novel. Pathway analysis of these 42 human proteins shows that they are involved in key host cellular processes related to cell cycle regulation, proliferation, protein degradation, apoptosis, and immune responses. A focused analysis of transcription factors that directly interact with the predicted DENV-NS5 interacting proteins was performed, followed by the identification of downstream genes that are differentially expressed after dengue infection using previously published RNA-seq data. Our study provides unique insights into the DENV-NS5 interaction network and delineates mechanisms whereby DENV-NS5 could impact the host-virus interface. The novel interactors identified in this study could be potentially targeted by NS5 to modulate the host cellular environment in general, and the immune response in particular, thereby extending the role of DENV-NS5 beyond its known enzymatic functions. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03569-0.
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Affiliation(s)
- Priya Bhatnagar
- Department of Biotechnology, TERI School of Advanced Studies, New Delhi, India
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Jatin Shrinet
- Department of Biological Science, Florida State University, Tallahassee, FL 32306 USA
| | - Murali Krishna Kaja
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- Department of Pediatrics and Emory Vaccine Centre, Emory University School of Medicine, Atlanta, GA USA
| | - Anmol Chandele
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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14
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Chen X, Dong T, Hu Y, De Pace R, Mattera R, Eberhardt K, Ziegler M, Pirovolakis T, Sahin M, Bonifacino JS, Ebrahimi-Fakhari D, Gray SJ. Intrathecal AAV9/AP4M1 gene therapy for hereditary spastic paraplegia 50 shows safety and efficacy in preclinical studies. J Clin Invest 2023; 133:e164575. [PMID: 36951961 PMCID: PMC10178841 DOI: 10.1172/jci164575] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/14/2023] [Indexed: 03/24/2023] Open
Abstract
Spastic paraplegia 50 (SPG50) is an ultrarare childhood-onset neurological disorder caused by biallelic loss-of-function variants in the AP4M1 gene. SPG50 is characterized by progressive spastic paraplegia, global developmental delay, and subsequent intellectual disability, secondary microcephaly, and epilepsy. We preformed preclinical studies evaluating an adeno-associated virus (AAV)/AP4M1 gene therapy for SPG50 and describe in vitro studies that demonstrate transduction of patient-derived fibroblasts with AAV2/AP4M1, resulting in phenotypic rescue. To evaluate efficacy in vivo, Ap4m1-KO mice were intrathecally (i.t.) injected with 5 × 1011, 2.5 × 1011, or 1.25 × 1011 vector genome (vg) doses of AAV9/AP4M1 at P7-P10 or P90. Age- and dose-dependent effects were observed, with early intervention and higher doses achieving the best therapeutic benefits. In parallel, three toxicology studies in WT mice, rats, and nonhuman primates (NHPs) demonstrated that AAV9/AP4M1 had an acceptable safety profile up to a target human dose of 1 × 1015 vg. Of note, similar degrees of minimal-to-mild dorsal root ganglia (DRG) toxicity were observed in both rats and NHPs, supporting the use of rats to monitor DRG toxicity in future i.t. AAV studies. These preclinical results identify an acceptably safe and efficacious dose of i.t.-administered AAV9/AP4M1, supporting an investigational gene transfer clinical trial to treat SPG50.
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Affiliation(s)
- Xin Chen
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Thomas Dong
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Yuhui Hu
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Raffaella De Pace
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Rafael Mattera
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Kathrin Eberhardt
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marvin Ziegler
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Mustafa Sahin
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Juan S. Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Darius Ebrahimi-Fakhari
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven J. Gray
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
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15
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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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16
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Maciejowski WJ, Gile GH, Jerlström-Hultqvist J, Dacks JB. Ancient and pervasive expansion of adaptin-related vesicle coat machinery across Parabasalia. Int J Parasitol 2023; 53:233-245. [PMID: 36898426 DOI: 10.1016/j.ijpara.2023.01.002] [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: 10/10/2022] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 03/11/2023]
Abstract
The eukaryotic phylum Parabasalia is composed primarily of anaerobic, endobiotic organisms such as the veterinary parasite Tritrichomonas foetus and the human parasite Trichomonas vaginalis, the latter causing the most prevalent, non-viral, sexually transmitted disease world-wide. Although a parasitic lifestyle is generally associated with a reduction in cell biology, T. vaginalis provides a striking counter-example. The 2007 T. vaginalis genome paper reported a massive and selective expansion of encoded proteins involved in vesicle trafficking, particularly those implicated in the late secretory and endocytic systems. Chief amongst these were the hetero-tetrameric adaptor proteins or 'adaptins', with T. vaginalis encoding ∼3.5 times more such proteins than do humans. The provenance of such a complement, and how it relates to the transition from a free-living or endobiotic state to parasitism, remains unclear. In this study, we performed a comprehensive bioinformatic and molecular evolutionary investigation of the heterotetrameric cargo adaptor-derived coats, comparing the molecular complement and evolution of these proteins between T. vaginalis, T. foetus and the available diversity of endobiotic parabasalids. Notably, with the recent discovery of Anaeramoeba spp. as the free-living sister lineage to all parabasalids, we were able to delve back to time points earlier in the lineage's history than ever before. We found that, although T. vaginalis still encodes the most HTAC subunits amongst parabasalids, the duplications giving rise to the complement took place more deeply and at various stages across the lineage. While some duplications appear to have convergently shaped the parasitic lineages, the largest jump is in the transition from free-living to endobiotic lifestyle with both gains and losses shaping the encoded complement. This work details the evolution of a cellular system across an important lineage of parasites and provides insight into the evolutionary dynamics of an example of expansion of protein machinery, counter to the more common trends observed in many parasitic systems.
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Affiliation(s)
- William J Maciejowski
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Canada; Women and Children's Health Research Institute, University of Alberta, Edmonton, Canada
| | - Gillian H Gile
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, Arizona, USA
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, BMC, Box 586, Uppsala Universitet, SE-751 24 Uppsala, Sweden. https://twitter.com/jon_hultqvist
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Canada; Women and Children's Health Research Institute, University of Alberta, Edmonton, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
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17
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Fink JK. The hereditary spastic paraplegias. HANDBOOK OF CLINICAL NEUROLOGY 2023; 196:59-88. [PMID: 37620092 DOI: 10.1016/b978-0-323-98817-9.00022-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
The hereditary spastic paraplegias (HSPs) are a group of more than 90 genetic disorders in which lower extremity spasticity and weakness are either the primary neurologic impairments ("uncomplicated HSP") or when accompanied by other neurologic deficits ("complicated HSP"), important features of the clinical syndrome. Various genetic types of HSP are inherited such as autosomal dominant, autosomal recessive, X-linked, and maternal (mitochondrial) traits. Symptoms that begin in early childhood may be nonprogressive and resemble spastic diplegic cerebral palsy. Symptoms that begin later, typically progress insidiously over a number of years. Genetic testing is able to confirm the diagnosis for many subjects. Insights from gene discovery indicate that abnormalities in diverse molecular processes underlie various forms of HSP, including disturbance in axon transport, endoplasmic reticulum morphogenesis, vesicle transport, lipid metabolism, and mitochondrial function. Pathologic studies in "uncomplicated" HSP have shown axon degeneration particularly involving the distal ends of corticospinal tracts and dorsal column fibers. Treatment is limited to symptom reduction including amelioration of spasticity, reducing urinary urgency, proactive physical therapy including strengthening, stretching, balance, and agility exercise.
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Affiliation(s)
- John K Fink
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States.
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18
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Barlow LD, Maciejowski W, More K, Terry K, Vargová R, Záhonová K, Dacks JB. Comparative Genomics for Evolutionary Cell Biology Using AMOEBAE: Understanding the Golgi and Beyond. Methods Mol Biol 2022; 2557:431-452. [PMID: 36512230 DOI: 10.1007/978-1-0716-2639-9_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Taking an evolutionary approach to cell biology can yield important new information about how the cell works and how it evolved to do so. This is true of the Golgi apparatus, as it is of all systems within the cell. Comparative genomics is one of the crucial first steps to this line of research, but comes with technical challenges that must be overcome for rigor and robustness. We here introduce AMOEBAE, a workflow for mid-range scale comparative genomic analyses. It allows for customization of parameters, queries, and taxonomic sampling of genomic and transcriptomics data. This protocol article covers the rationale for an evolutionary approach to cell biological study (i.e., when would AMOEBAE be useful), how to use AMOEBAE, and discussion of limitations. It also provides an example dataset, which demonstrates that the Golgi protein AP4 Epsilon is present as the sole retained subunit of the AP4 complex in basidiomycete fungi. AMOEBAE can facilitate comparative genomic studies by balancing reproducibility and speed with user-input and interpretation. It is hoped that AMOEBAE or similar tools will encourage cell biologists to incorporate an evolutionary context into their research.
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Affiliation(s)
- Lael D Barlow
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada. .,Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK.
| | - William Maciejowski
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Kiran More
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Kara Terry
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Romana Vargová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Kristína Záhonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Joel B Dacks
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada. .,Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, AB, Canada. .,Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia. .,Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College of London, London, UK.
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19
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Bonifacino JS. Getting where you want to go. Mol Biol Cell 2022; 33:ae4. [PMID: 36399622 PMCID: PMC9727807 DOI: 10.1091/mbc.e22-08-0362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In 1956, referring to the emerging application of electron microscopy to the study of eukaryotic cells, Keith R. Porter wrote, "For those of us who are fortunate to be part of this new development, these are days of great interest and opportunity." Those early days left us a rich legacy of knowledge on the internal organization of eukaryotic cells that provides a framework for current research on cell structure and function. In this vein, my long-time quest has been to understand how proteins and organelles travel through the cytoplasm to reach their respective destinations within the cell. This research has led us to elucidate various mechanisms of protein sorting and organelle transport and how defects in these mechanisms cause human disease.
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Affiliation(s)
- Juan S. Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892,*Address correspondence to: Juan S. Bonifacino ()
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20
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Salayev K, Rocca C, Kaiyrzhanov R, Guliyeva U, Guliyeva S, Mursalova A, Rahman F, Anwar N, Zafar F, Jan F, Rana N, Maqbool S, Efthymiou S, Houlden H. AP4B1-associated hereditary spastic paraplegia: Expansion of clinico-genetic phenotype and geographic range. Eur J Med Genet 2022; 65:104620. [PMID: 36122674 DOI: 10.1016/j.ejmg.2022.104620] [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: 11/17/2021] [Revised: 05/22/2022] [Accepted: 09/12/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND Hereditary spastic paraplegias (HSP) are a group of neurodegenerative diseases that present with weakness and stiffness in the lower limb muscles and lead to progressive neurological decline. Bi-allelic loss-of-function variants in genes that encode subunits of the adaptor protein complex 4 (AP-4) lead to complex HSP. This study aimed to identify causative genetic variants in consanguineous families with HSP from Azerbaijan and Pakistan. METHODS We performed a thorough clinical and neuroradiological characterization followed by exome sequencing in 7 patients from 3 unrelated families. Segregation analysis was subsequently performed by Sanger sequencing. RESULTS We describe 7 patients (4 males, 2-31 years of age) with developmental delay and spasticity. Similar to the previously reported cases with AP4B1-associated HSP, cases in the present report besides spasticity in the lower limbs had additional features including microcephaly, facial dysmorphism, infantile hypotonia, and epilepsy. The imaging findings included thin corpus callosum, white matter loss, and ventriculomegaly. CONCLUSION In this study, we report 7 novel cases of HSP caused by bi-allelic variants in AP4B1 in Azerbaijani and Pakistani families. Our observations will help clinicians observe and compare common and unique clinical features of AP4B1-associated HSP patients, further improving our current understanding of HSP.
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Affiliation(s)
- Kamran Salayev
- Azerbaijan Medical University, Department of Neurology, Baku, AZ, 1010, Azerbaijan
| | - Clarissa Rocca
- University College London, Institute of Neurology, Department of Neuromuscular Disorders, Queen Square, WC1N 3BG, London, UK
| | - Rauan Kaiyrzhanov
- University College London, Institute of Neurology, Department of Neuromuscular Disorders, Queen Square, WC1N 3BG, London, UK
| | - Ulviyya Guliyeva
- MediClub Hospital, 45, Uzeyir Hajibeyli Str., Baku, AZ, 1010, Azerbaijan
| | - Sughra Guliyeva
- MediClub Hospital, 45, Uzeyir Hajibeyli Str., Baku, AZ, 1010, Azerbaijan
| | - Aytan Mursalova
- Baku City Gerontologic Centre, Azadliq Ave., Baku, Azerbaijan
| | - Fatima Rahman
- Development and Behavioral Pediatrics Department, Institute of Child Health and the Children Hospital, Lahore, 54000, Pakistan
| | - Najwa Anwar
- Development and Behavioral Pediatrics Department, Institute of Child Health and the Children Hospital, Lahore, 54000, Pakistan
| | - Faisal Zafar
- Department of Paediatric Neurology, Children's Hospital and Institute of Child Health, Multan, Pakistan
| | - Farida Jan
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Nuzhat Rana
- Department of Paediatric Neurology, Children's Hospital and Institute of Child Health, Multan, Pakistan
| | - Shazia Maqbool
- Development and Behavioral Pediatrics Department, Institute of Child Health and the Children Hospital, Lahore, 54000, Pakistan
| | - Stephanie Efthymiou
- University College London, Institute of Neurology, Department of Neuromuscular Disorders, Queen Square, WC1N 3BG, London, UK
| | - Henry Houlden
- University College London, Institute of Neurology, Department of Neuromuscular Disorders, Queen Square, WC1N 3BG, London, UK.
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21
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Hooy RM, Iwamoto Y, Tudorica DA, Ren X, Hurley JH. Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat. SCIENCE ADVANCES 2022; 8:eadd3914. [PMID: 36269825 PMCID: PMC9586487 DOI: 10.1126/sciadv.add3914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/01/2022] [Indexed: 05/28/2023]
Abstract
The adaptor protein (AP) complexes not only form the inner layer of clathrin coats but also have clathrin-independent roles in membrane traffic whose mechanisms are unknown. HIV-1 Nef hijacks AP-1 to sequester major histocompatibility complex class I (MHC-I), evading immune detection. We found that AP-1:Arf1:Nef:MHC-I forms a coat on tubulated membranes without clathrin and determined its structure. The coat assembles via Arf1 dimer interfaces. AP-1-positive tubules are enriched in cells upon clathrin knockdown. Nef localizes preferentially to AP-1 tubules in cells, explaining how Nef sequesters MHC-I. Coat contact residues are conserved across Arf isoforms and the Arf-dependent AP complexes AP-1, AP-3, and AP-4. Thus, AP complexes can self-assemble with Arf1 into tubular coats without clathrin or other scaffolding factors. The AP-1:Arf1 coat defines the structural basis of a broader class of tubulovesicular membrane coats as an intermediate in clathrin vesicle formation from internal membranes and as an MHC-I sequestration mechanism in HIV-1 infection.
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Affiliation(s)
- Richard M. Hooy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yuichiro Iwamoto
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dan A. Tudorica
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xuefeng Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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22
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Crook OM, Davies CTR, Breckels LM, Christopher JA, Gatto L, Kirk PDW, Lilley KS. Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE. Nat Commun 2022; 13:5948. [PMID: 36216816 PMCID: PMC9550814 DOI: 10.1038/s41467-022-33570-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/20/2022] [Indexed: 11/08/2022] Open
Abstract
The steady-state localisation of proteins provides vital insight into their function. These localisations are context specific with proteins translocating between different subcellular niches upon perturbation of the subcellular environment. Differential localisation, that is a change in the steady-state subcellular location of a protein, provides a step towards mechanistic insight of subcellular protein dynamics. High-accuracy high-throughput mass spectrometry-based methods now exist to map the steady-state localisation and re-localisation of proteins. Here, we describe a principled Bayesian approach, BANDLE, that uses these data to compute the probability that a protein differentially localises upon cellular perturbation. Extensive simulation studies demonstrate that BANDLE reduces the number of both type I and type II errors compared to existing approaches. Application of BANDLE to several datasets recovers well-studied translocations. In an application to cytomegalovirus infection, we obtain insights into the rewiring of the host proteome. Integration of other high-throughput datasets allows us to provide the functional context of these data.
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Affiliation(s)
- Oliver M Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK.
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK.
| | - Colin T R Davies
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Josie A Christopher
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Laurent Gatto
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200, Brussels, Belgium
| | - Paul D W Kirk
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK.
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK.
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23
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Kha QH, Tran TO, Nguyen TTD, Nguyen VN, Than K, Le NQK. An interpretable deep learning model for classifying adaptor protein complexes from sequence information. Methods 2022; 207:90-96. [PMID: 36174933 DOI: 10.1016/j.ymeth.2022.09.007] [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: 05/08/2022] [Revised: 08/19/2022] [Accepted: 09/22/2022] [Indexed: 11/15/2022] Open
Abstract
Adaptor proteins (APs) are a family of proteins that aids in intracellular membrane trafficking, and their impairments or defects are closely related to various disorders. Traditional methods to identify and classify APs require time and complex techniques, which were then advanced by machine learning and computational approaches to facilitate the APs recognition task. However, most studies focused on recognizing separate ones in the APs family or the APs in general with non-APs, lacking one comprehensive strategy to distinguish the complexes of AP subtypes. Herein, we proposed a novel method to implement one novel task as discriminating the AP complexes in the APs family, utilizing an interpretable deep neural network architecture on sequence-based encoding features. This work also introduced a benchmark data set of AP complexes originating from the UniProt and GeneOntology databases. To assess the robustness of our proposed method, we compared our performance to various machine learning algorithms and feature extraction strategies. Furthermore, the interpretation of the model's prediction performance was implemented using t-distributed stochastic neighbor embedding (t-SNE), uniform manifold approximation and projection (UMAP), and SHapley Additive exPlanations (SHAP) analysis to show the distribution of AP complexes on optimal features. The promising performance of our architecture can assist scientists not only in AP complexes distinction but also in general protein sequences. Moreover, we have also made our work publicly on GitHub https://github.com/khanhlee/adaptor-dnn.
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Affiliation(s)
- Quang-Hien Kha
- International Master/Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Thi-Oanh Tran
- International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Trinh-Trung-Duong Nguyen
- Personalised Medicine Cluster, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Van-Nui Nguyen
- University of Information and Communication Technology, Thai Nguyen University, Thai Nguyen, Viet Nam
| | - Khoat Than
- School of Information and Communication Technology, Hanoi University of Science and Technology, Viet Nam
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 106, Taiwan; Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei 106, Taiwan; Translational Imaging Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan.
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24
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Spastic paraplegia 51: phenotypic spectrum related to novel homozygous AP4E1 mutation. J Genet 2022. [DOI: 10.1007/s12041-022-01385-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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25
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Majumder P, Edmison D, Rodger C, Patel S, Reid E, Gowrishankar S. AP-4 regulates neuronal lysosome composition, function, and transport via regulating export of critical lysosome receptor proteins at the trans-Golgi network. Mol Biol Cell 2022; 33:ar102. [PMID: 35976706 PMCID: PMC9635302 DOI: 10.1091/mbc.e21-09-0473] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The adaptor protein complex-4 or AP-4 is known to mediate autophagosome maturation through regulating sorting of transmembrane cargo such as ATG9A at the Golgi. There is a need to understand AP-4 function in neurons, as mutations in any of its four subunits cause a complex form of hereditary spastic paraplegia (HSP) with intellectual disability. While AP-4 has been implicated in regulating trafficking and distribution of cargo such as ATG9A and APP, little is known about its effect on neuronal lysosomal protein traffic, lysosome biogenesis and function. In this study, we demonstrate that in human iPSC-derived neurons AP-4 regulates lysosome composition, function and transport via regulating export of critical lysosomal receptors, including Sortilin 1, from the trans-Golgi network to endo-lysosomes. Additionally, loss of AP-4 causes endo-lysosomes to stall and build up in axonal swellings potentially through reduced recruitment of retrograde transport machinery to the organelle. These findings of axonal lysosome build-up are highly reminiscent of those observed in Alzheimer's disease as well as in neurons modelling the most common form of HSP, caused by spastin mutations. Our findings implicate AP-4 as a critical regulator of neuronal lysosome biogenesis and altered lysosome function and axonal endo-lysosome transport as an underlying defect in AP-4 deficient HSP. Additionally, our results also demonstrate the utility of the human i3Neuronal model system in investigating neuronal phenotypes observed in AP-4 deficient mice and/or the human AP-4 deficiency syndrome. [Media: see text] [Media: see text].
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Affiliation(s)
- Piyali Majumder
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Daisy Edmison
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Catherine Rodger
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England, UK
| | - Sruchi Patel
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Evan Reid
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England, UK
| | - Swetha Gowrishankar
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
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26
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Mattera R, De Pace R, Bonifacino JS. The adaptor protein chaperone AAGAB stabilizes AP-4 complex subunits. Mol Biol Cell 2022; 33:ar109. [PMID: 35976721 DOI: 10.1091/mbc.e22-05-0177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Adaptor protein 4 (AP-4) is a heterotetrameric complex composed of ε, β4, μ4 and σ4 subunits that mediates export of a subset of transmembrane cargos, including autophagy protein 9A (ATG9A), from the trans-Golgi network (TGN). AP-4 has received particular attention in recent years because mutations in any of its subunits cause a complicated form of hereditary spastic paraplegia (HSP or SPG) referred to as "AP-4-deficiency syndrome." The identification of proteins that interact with AP-4 has shed light on the mechanisms of AP-4-dependent cargo sorting and distribution within the cell. However, the mechanisms by which the AP-4 complex itself is assembled have remained unknown. Herein, we report that the alpha- and gamma-adaptin-binding protein (AAGAB, also known as p34) binds to and stabilizes the AP-4 ε-and σ4 subunits, thus promoting complex assembly. The importance of this binding is underscored by the observation that AAGAB-knockout cells exhibit reduced levels of AP-4 subunits and accumulation of ATG9A at the TGN like those in cells, mice, or patients with mutations in AP-4-subunit genes. These findings demonstrate that AP-4 assembly is not spontaneous but AAGAB-assisted, thus contributing to the understanding of an adaptor protein complex that is critically involved in development of the central nervous system.
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Affiliation(s)
- Rafael Mattera
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Raffaella De Pace
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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27
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Dahhan DA, Reynolds GD, Cárdenas JJ, Eeckhout D, Johnson A, Yperman K, Kaufmann WA, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek SY. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. THE PLANT CELL 2022; 34:2150-2173. [PMID: 35218346 PMCID: PMC9134090 DOI: 10.1093/plcell/koac071] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/22/2022] [Indexed: 05/26/2023]
Abstract
In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.
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Affiliation(s)
| | | | - Jessica J Cárdenas
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Alexander Johnson
- Institute of Science and Technology (IST Austria), Klosterneuburg 3400, Austria
| | | | - Walter A Kaufmann
- Institute of Science and Technology (IST Austria), Klosterneuburg 3400, Austria
| | - Nou Vang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Xu Yan
- College Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science & Technology, Pohang 37673, Korea
| | - Antje Heese
- Division of Biochemistry, Interdisciplinary Plant Group, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Jiří Friml
- Institute of Science and Technology (IST Austria), Klosterneuburg 3400, Austria
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Jianwei Pan
- College Life Sciences, Lanzhou University, Lanzhou 730000, China
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28
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Dahhan DA, Reynolds GD, Cárdenas JJ, Eeckhout D, Johnson A, Yperman K, Kaufmann WA, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek SY. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. THE PLANT CELL 2022; 34:2150-2173. [PMID: 35218346 DOI: 10.1101/2021.09.16.460678] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/22/2022] [Indexed: 05/26/2023]
Abstract
In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.
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Affiliation(s)
- Dana A Dahhan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Gregory D Reynolds
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jessica J Cárdenas
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Alexander Johnson
- Institute of Science and Technology (IST Austria), Klosterneuburg 3400, Austria
| | - Klaas Yperman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Walter A Kaufmann
- Institute of Science and Technology (IST Austria), Klosterneuburg 3400, Austria
| | - Nou Vang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Xu Yan
- College Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science & Technology, Pohang 37673, Korea
| | - Antje Heese
- Division of Biochemistry, Interdisciplinary Plant Group, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Jiří Friml
- Institute of Science and Technology (IST Austria), Klosterneuburg 3400, Austria
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Jianwei Pan
- College Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Sebastian Y Bednarek
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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29
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Davies AK, Alecu JE, Ziegler M, Vasilopoulou CG, Merciai F, Jumo H, Afshar-Saber W, Sahin M, Ebrahimi-Fakhari D, Borner GHH. AP-4-mediated axonal transport controls endocannabinoid production in neurons. Nat Commun 2022; 13:1058. [PMID: 35217685 PMCID: PMC8881493 DOI: 10.1038/s41467-022-28609-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 01/08/2022] [Indexed: 01/20/2023] Open
Abstract
The adaptor protein complex AP-4 mediates anterograde axonal transport and is essential for axon health. AP-4-deficient patients suffer from a severe neurodevelopmental and neurodegenerative disorder. Here we identify DAGLB (diacylglycerol lipase-beta), a key enzyme for generation of the endocannabinoid 2-AG (2-arachidonoylglycerol), as a cargo of AP-4 vesicles. During normal development, DAGLB is targeted to the axon, where 2-AG signalling drives axonal growth. We show that DAGLB accumulates at the trans-Golgi network of AP-4-deficient cells, that axonal DAGLB levels are reduced in neurons from a patient with AP-4 deficiency, and that 2-AG levels are reduced in the brains of AP-4 knockout mice. Importantly, we demonstrate that neurite growth defects of AP-4-deficient neurons are rescued by inhibition of MGLL (monoacylglycerol lipase), the enzyme responsible for 2-AG hydrolysis. Our study supports a new model for AP-4 deficiency syndrome in which axon growth defects arise through spatial dysregulation of endocannabinoid signalling. Davies et al. identify a putative mechanism underlying the childhood neurological disorder AP-4 deficiency syndrome. In the absence of AP-4, an enzyme that makes 2-AG is not transported to the axon, leading to axonal growth defects, which can be rescued by inhibition of 2-AG breakdown.
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Affiliation(s)
- Alexandra K Davies
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.
| | - Julian E Alecu
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marvin Ziegler
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Department of Functional Neuroanatomy, Institute of Anatomy and Cell Biology, Heidelberg University, INF 307, Heidelberg, 69120, Germany
| | - Catherine G Vasilopoulou
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Fabrizio Merciai
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.,Department of Pharmacy and PhD Program in Drug Discovery and Development, University of Salerno, 84084, Fisciano, SA, Italy
| | - Hellen Jumo
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Wardiya Afshar-Saber
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Mustafa Sahin
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Darius Ebrahimi-Fakhari
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.
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30
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Law KC, Chung KK, Zhuang X. An Update on Coat Protein Complexes for Vesicle Formation in Plant Post-Golgi Trafficking. FRONTIERS IN PLANT SCIENCE 2022; 13:826007. [PMID: 35283904 PMCID: PMC8905187 DOI: 10.3389/fpls.2022.826007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/11/2022] [Indexed: 05/13/2023]
Abstract
Endomembrane trafficking is an evolutionarily conserved process for all eukaryotic organisms. It is a fundamental and essential process for the transportation of proteins, lipids, or cellular metabolites. The aforementioned cellular components are sorted across multiple membrane-bounded organelles. In plant cells, the endomembrane mainly consists of the nuclear envelope, endoplasmic reticulum (ER), Golgi apparatus, trans-Golgi network or early endosome (TGN/EE), prevacuolar compartments or multivesicular bodies (PVCs/MVBs), and vacuole. Among them, Golgi apparatus and TGN represent two central sorting intermediates for cargo secretion and recycling from other compartments by anterograde or retrograde trafficking. Several protein sorting machineries have been identified to function in these pathways for cargo recognition and vesicle assembly. Exciting progress has been made in recent years to provide novel insights into the sorting complexes and also the underlying sorting mechanisms in plants. Here, we will highlight the recent findings for the adaptor protein (AP) complexes, retromer, and retriever complexes, and also their functions in the related coated vesicle formation in post-Golgi trafficking.
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Affiliation(s)
| | | | - Xiaohong Zhuang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
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31
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Zhou X, Dai W, Qin Y, Qi S, Zhang Y, Tian W, Gu X, Zheng B, Xiao J, Yu W, Chen X, Su D. Electroacupuncture relieves neuropathic pain by inhibiting degradation of the ecto-nucleotidase PAP in the dorsal root ganglions of CCI mice. Eur J Pain 2022; 26:991-1005. [PMID: 35138669 DOI: 10.1002/ejp.1923] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 01/31/2022] [Accepted: 02/05/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Although electroacupuncture is widely used in chronic pain management, it is quite controversial due to its unclear mechanism. We hypothesised that EA alleviates pain by inhibiting degradation of the ecto-nucleotidase prostatic acid phosphatase (PAP) and facilitating ATP dephosphorylation in dorsal root ganglions (DRGs). METHODS We applied EA in male C57 mice subjected to chronic constriction injury (CCI) and assessed extracellular ATP and 5'-nucleotidease expression in DRGs. Specifically, we used a luminescence assay, quantitative reverse transcriptase-polymerase chain reaction, western blotting, immunohistochemistry and nociceptive-related behavioural changes to gather data, and we tested for effects after PAP expression was inhibited with an adeno-associated virus (AAV). Moreover, membrane PAP degradation was investigated in cultured DRG neurons and the inhibitory effects of EA on this degradation were assessed using immunoprecipitation. RESULTS EA treatment alleviated CCI surgery induced mechanical pain hypersensitivity. Furthermore, extracellular ATP decreased significantly in both the DRGs and dorsal horn of EA-treated mice. PAP protein but not mRNA increased in L4-L5 DRGs, and inhibition of PAP expression via AAV microinjection reversed the analgesic effect of EA. Membrane PAP degradation occurred through a clathrin-mediated endocytosis pathway in cultured DRG neurons; EA treatment inhibited the phosphorylation of adaptor protein complex 2, which subsequently reduced the endocytosis of membrane PAP. CONCLUSIONS EA treatment alleviated peripheral nerve injury-induced mechanical pain hypersensitivity in mice by inhibiting membrane PAP degradation via reduced endocytosis and subsequently promote ATP dephosphorylation in DRGs.
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Affiliation(s)
- Xiaoxin Zhou
- Department of Anaesthesiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China, Postal Code: 200127
| | - Wanbing Dai
- Department of Anaesthesiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China, Postal Code: 200127
| | - Yi Qin
- Department of Anaesthesiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China, Postal Code: 200127
| | - Siyi Qi
- Department of Anaesthesiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China, Postal Code: 200127
| | - Yizhe Zhang
- Department of Anaesthesiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China, Postal Code: 200127
| | - Weitian Tian
- Department of Anaesthesiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China, Postal Code: 200127
| | - Xiyao Gu
- Department of Anaesthesiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China, Postal Code: 200127
| | - Beijie Zheng
- Department of Anaesthesiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China, Postal Code: 200127
| | - Jie Xiao
- Department of Anaesthesiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China, Postal Code: 200127
| | - Weifeng Yu
- Department of Anaesthesiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China, Postal Code: 200127
| | - Xuemei Chen
- Department of Anaesthesiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China, Postal Code: 200127
| | - Diansan Su
- Department of Anaesthesiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China, Postal Code: 200127
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32
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Shin J, Nile A, Oh JW. Role of adaptin protein complexes in intracellular trafficking and their impact on diseases. Bioengineered 2021; 12:8259-8278. [PMID: 34565296 PMCID: PMC8806629 DOI: 10.1080/21655979.2021.1982846] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023] Open
Abstract
Adaptin proteins (APs) play a crucial role in intracellular cell trafficking. The 'classical' role of APs is carried out by AP1‒3, which bind to clathrin, cargo, and accessory proteins. Accordingly, AP1-3 are crucial for both vesicle formation and sorting. All APs consist of four subunits that are indispensable for their functions. In fact, based on studies using cells, model organism knockdown/knock-out, and human variants, each subunit plays crucial roles and contributes to the specificity of each AP. These studies also revealed that the sorting and intracellular trafficking function of AP can exert varying effects on pathology by controlling features such as cell development, signal transduction related to the apoptosis and proliferation pathways in cancer cells, organelle integrity, receptor presentation, and viral infection. Although the roles and functions of AP1‒3 are relatively well studied, the functions of the less abundant and more recently identified APs, AP4 and AP5, are still to be investigated. Further studies on these APs may enable a better understanding and targeting of specific diseases.APs known or suggested locations and functions.
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Affiliation(s)
- Juhyun Shin
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
| | - Arti Nile
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
| | - Jae-Wook Oh
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
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33
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Guardia CM, Jain A, Mattera R, Friefeld A, Li Y, Bonifacino JS. RUSC2 and WDR47 oppositely regulate kinesin-1-dependent distribution of ATG9A to the cell periphery. Mol Biol Cell 2021; 32:ar25. [PMID: 34432492 PMCID: PMC8693955 DOI: 10.1091/mbc.e21-06-0295] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 01/12/2023] Open
Abstract
Autophagy-related protein 9 (ATG9) is a transmembrane protein component of the autophagy machinery that cycles between the trans-Golgi network (TGN) in the perinuclear area and other compartments in the peripheral area of the cell. In mammalian cells, export of the ATG9A isoform from the TGN into ATG9A-containing vesicles is mediated by the adaptor protein 4 (AP-4) complex. However, the mechanisms responsible for the subsequent distribution of these vesicles to the cell periphery are unclear. Herein we show that the AP-4-accessory protein RUSC2 couples ATG9A-containing vesicles to the plus-end-directed microtubule motor kinesin-1 via an interaction between a disordered region of RUSC2 and the kinesin-1 light chain. This interaction is counteracted by the microtubule-associated protein WDR47. These findings uncover a mechanism for the peripheral distribution of ATG9A-containing vesicles involving the function of RUSC2 as a kinesin-1 adaptor and WDR47 as a negative regulator of this function.
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Affiliation(s)
- Carlos M. Guardia
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
| | - Akansha Jain
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
| | - Rafael Mattera
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
| | - Alex Friefeld
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
| | - Juan S. Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
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34
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Ebrahimi-Fakhari D, Alecu JE, Brechmann B, Ziegler M, Eberhardt K, Jumo H, D’Amore A, Habibzadeh P, Faghihi MA, De Bleecker JL, Vuillaumier-Barrot S, Auvin S, Santorelli FM, Neuser S, Popp B, Yang E, Barrett L, Davies AK, Saffari A, Hirst J, Sahin M. High-throughput imaging of ATG9A distribution as a diagnostic functional assay for adaptor protein complex 4-associated hereditary spastic paraplegia. Brain Commun 2021; 3:fcab221. [PMID: 34729478 PMCID: PMC8557665 DOI: 10.1093/braincomms/fcab221] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/05/2021] [Accepted: 08/19/2021] [Indexed: 01/09/2023] Open
Abstract
Adaptor protein complex 4-associated hereditary spastic paraplegia is caused by biallelic loss-of-function variants in AP4B1, AP4M1, AP4E1 or AP4S1, which constitute the four subunits of this obligate complex. While the diagnosis of adaptor protein complex 4-associated hereditary spastic paraplegia relies on molecular testing, the interpretation of novel missense variants remains challenging. Here, we address this diagnostic gap by using patient-derived fibroblasts to establish a functional assay that measures the subcellular localization of ATG9A, a transmembrane protein that is sorted by adaptor protein complex 4. Using automated high-throughput microscopy, we determine the ratio of the ATG9A fluorescence in the trans-Golgi-network versus cytoplasm and ascertain that this metric meets standards for screening assays (Z'-factor robust >0.3, strictly standardized mean difference >3). The 'ATG9A ratio' is increased in fibroblasts of 18 well-characterized adaptor protein complex 4-associated hereditary spastic paraplegia patients [mean: 1.54 ± 0.13 versus 1.21 ± 0.05 (standard deviation) in controls] and receiver-operating characteristic analysis demonstrates robust diagnostic power (area under the curve: 0.85, 95% confidence interval: 0.849-0.852). Using fibroblasts from two individuals with atypical clinical features and novel biallelic missense variants of unknown significance in AP4B1, we show that our assay can reliably detect adaptor protein complex 4 function. Our findings establish the 'ATG9A ratio' as a diagnostic marker of adaptor protein complex 4-associated hereditary spastic paraplegia.
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Affiliation(s)
- Darius Ebrahimi-Fakhari
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Julian E Alecu
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Barbara Brechmann
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Neuropediatrics and Inherited Metabolic Diseases, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Marvin Ziegler
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Ruprecht-Karls University Heidelberg, Medical School, 69120 Heidelberg, Germany
| | - Kathrin Eberhardt
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hellen Jumo
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Angelica D’Amore
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Parham Habibzadeh
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, 71347 Shiraz, Iran
| | - Mohammad Ali Faghihi
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL 33136, USA
| | - Jan L De Bleecker
- Department of Neurology, Ghent University Hospital, 9000 Ghent, Belgium
| | | | - Stéphane Auvin
- Pediatric Neurology Department, AP-HP, Robert Debré Hospital, 75019 Paris, France
| | - Filippo M Santorelli
- Department of Molecular Medicine, IRCCS Fondazione Stella Maris, 56128 Pisa, Italy
| | - Sonja Neuser
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Edward Yang
- Division of Neuroradiology, Department of Radiology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lee Barrett
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Alexandra K Davies
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Afshin Saffari
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Neuropediatrics and Inherited Metabolic Diseases, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Mustafa Sahin
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
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35
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Degrandmaison J, Grisé O, Parent JL, Gendron L. Differential barcoding of opioid receptors trafficking. J Neurosci Res 2021; 100:99-128. [PMID: 34559903 DOI: 10.1002/jnr.24949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 07/25/2021] [Accepted: 08/05/2021] [Indexed: 11/09/2022]
Abstract
Over the past several years, studies have highlighted the δ-opioid receptor (DOPr) as a promising therapeutic target for chronic pain management. While exhibiting milder undesired effects than most currently prescribed opioids, its specific agonists elicit effective analgesic responses in numerous animal models of chronic pain, including inflammatory, neuropathic, diabetic, and cancer-related pain. However, as compared with the extensively studied μ-opioid receptor, the molecular mechanisms governing its trafficking remain elusive. Recent advances have denoted several significant particularities in the regulation of DOPr intracellular routing, setting it apart from the other members of the opioid receptor family. Although they share high homology, each opioid receptor subtype displays specific amino acid patterns potentially involved in the regulation of its trafficking. These precise motifs or "barcodes" are selectively recognized by regulatory proteins and therefore dictate several aspects of the itinerary of a receptor, including its anterograde transport, internalization, recycling, and degradation. With a specific focus on the regulation of DOPr trafficking, this review will discuss previously reported, as well as potential novel trafficking barcodes within the opioid and nociceptin/orphanin FQ opioid peptide receptors, and their impact in determining distinct interactomes and physiological responses.
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Affiliation(s)
- Jade Degrandmaison
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Institut de Pharmacologie de Sherbrooke, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Quebec Network of Junior Pain Investigators, QC, Canada
| | - Olivier Grisé
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Institut de Pharmacologie de Sherbrooke, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Luc Parent
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Institut de Pharmacologie de Sherbrooke, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Louis Gendron
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Institut de Pharmacologie de Sherbrooke, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Quebec Pain Research Network, QC, Canada
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36
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Justo BL, Jasiulionis MG. Characteristics of TIMP1, CD63, and β1-Integrin and the Functional Impact of Their Interaction in Cancer. Int J Mol Sci 2021; 22:9319. [PMID: 34502227 PMCID: PMC8431149 DOI: 10.3390/ijms22179319] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 01/03/2023] Open
Abstract
Tissue Inhibitor of Metalloproteases 1, also known as TIMP-1, is named for its well-established function of inhibiting the proteolytic activity of matrix metalloproteases. Given this function, many studies were carried out to verify if TIMP-1 was able to interrupt processes such as tumor cell invasion and metastasis. In contrast, many studies have shown that TIMP-1 expression is increased in several types of tumors, and this increase was correlated with a poor prognosis and lower survival in cancer patients. Later, it was shown that TIMP-1 is also able to modulate cell behavior through the induction of signaling pathways involved in cell growth, proliferation, and survival. The mechanisms involved in the regulation of the pleiotropic functions of TIMP-1 are still poorly understood. Thus, this review aimed to present literature data that show its ability to form a membrane complex with CD63 and β1-integrin, and point to N-glycosylation as a potential regulatory mechanism of the functions exerted by TIMP-1. This article reviewed the characteristics and functions performed individually by TIMP1, CD63, and β1-integrin, the roles of the TIMP-1/CD63/β1-integrin complex, both in a physiological context and in cancer, and the regulatory mechanisms involved in its assembly.
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Affiliation(s)
| | - Miriam Galvonas Jasiulionis
- Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), Rua Pedro de Toledo 669, 5 Floor, São Paulo 04039-032, Brazil;
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37
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Lujan P, Campelo F. Should I stay or should I go? Golgi membrane spatial organization for protein sorting and retention. Arch Biochem Biophys 2021; 707:108921. [PMID: 34038703 DOI: 10.1016/j.abb.2021.108921] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/12/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022]
Abstract
The Golgi complex is the membrane-bound organelle that lies at the center of the secretory pathway. Its main functions are to maintain cellular lipid homeostasis, to orchestrate protein processing and maturation, and to mediate protein sorting and export. These functions are not independent of one another, and they all require that the membranes of the Golgi complex have a well-defined biochemical composition. Importantly, a finely-regulated spatiotemporal organization of the Golgi membrane components is essential for the correct performance of the organelle. In here, we review our current mechanistic and molecular understanding of how Golgi membranes are spatially organized in the lateral and axial directions to fulfill their functions. In particular, we highlight the current evidence and proposed models of intra-Golgi transport, as well as the known mechanisms for the retention of Golgi residents and for the sorting and export of transmembrane cargo proteins. Despite the controversies, conflicting evidence, clashes between models, and technical limitations, the field has moved forward and we have gained extensive knowledge in this fascinating topic. However, there are still many important questions that remain to be completely answered. We hope that this review will help boost future investigations on these issues.
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Affiliation(s)
- Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860, Barcelona, Spain.
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860, Barcelona, Spain.
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38
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Fang S, Kirk PDW, Bantscheff M, Lilley KS, Crook OM. A Bayesian semi-parametric model for thermal proteome profiling. Commun Biol 2021; 4:810. [PMID: 34188175 PMCID: PMC8241860 DOI: 10.1038/s42003-021-02306-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
The thermal stability of proteins can be altered when they interact with small molecules, other biomolecules or are subject to post-translation modifications. Thus monitoring the thermal stability of proteins under various cellular perturbations can provide insights into protein function, as well as potentially determine drug targets and off-targets. Thermal proteome profiling is a highly multiplexed mass-spectrommetry method for monitoring the melting behaviour of thousands of proteins in a single experiment. In essence, thermal proteome profiling assumes that proteins denature upon heating and hence become insoluble. Thus, by tracking the relative solubility of proteins at sequentially increasing temperatures, one can report on the thermal stability of a protein. Standard thermodynamics predicts a sigmoidal relationship between temperature and relative solubility and this is the basis of current robust statistical procedures. However, current methods do not model deviations from this behaviour and they do not quantify uncertainty in the melting profiles. To overcome these challenges, we propose the application of Bayesian functional data analysis tools which allow complex temperature-solubility behaviours. Our methods have improved sensitivity over the state-of-the art, identify new drug-protein associations and have less restrictive assumptions than current approaches. Our methods allows for comprehensive analysis of proteins that deviate from the predicted sigmoid behaviour and we uncover potentially biphasic phenomena with a series of published datasets.
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Affiliation(s)
- Siqi Fang
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Paul D W Kirk
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | | | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
| | - Oliver M Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
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39
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Arora D, Damme DV. Motif-based endomembrane trafficking. PLANT PHYSIOLOGY 2021; 186:221-238. [PMID: 33605419 PMCID: PMC8154067 DOI: 10.1093/plphys/kiab077] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 05/08/2023]
Abstract
Endomembrane trafficking, which allows proteins and lipids to flow between the different endomembrane compartments, largely occurs by vesicle-mediated transport. Transmembrane proteins intended for transport are concentrated into a vesicle or carrier by undulation of a donor membrane. This is followed by vesicle scission, uncoating, and finally, fusion at the target membrane. Three major trafficking pathways operate inside eukaryotic cells: anterograde, retrograde, and endocytic. Each pathway involves a unique set of machinery and coat proteins that pack the transmembrane proteins, along with their associated lipids, into specific carriers. Adaptor and coatomer complexes are major facilitators that function in anterograde transport and in endocytosis. These complexes recognize the transmembrane cargoes destined for transport and recruit the coat proteins that help form the carriers. These complexes use either linear motifs or posttranslational modifications to recognize the cargoes, which are then packaged and delivered along the trafficking pathways. In this review, we focus on the different trafficking complexes that share a common evolutionary branch in Arabidopsis (Arabidopsis thaliana), and we discuss up-to-date knowledge about the cargo recognition motifs they use.
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Affiliation(s)
- Deepanksha Arora
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent 9052, Belgium
| | - Daniёl Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent 9052, Belgium
- Author for communication:
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40
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Russell T, Samolej J, Hollinshead M, Smith GL, Kite J, Elliott G. Novel Role for ESCRT-III Component CHMP4C in the Integrity of the Endocytic Network Utilized for Herpes Simplex Virus Envelopment. mBio 2021; 12:e02183-20. [PMID: 33975940 PMCID: PMC8262985 DOI: 10.1128/mbio.02183-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/31/2021] [Indexed: 12/29/2022] Open
Abstract
Enveloped viruses exploit cellular trafficking pathways for their morphogenesis, providing potential scope for the development of new antiviral therapies. We have previously shown that herpes simplex virus 1 (HSV1) utilizes recycling endocytic membranes as the source of its envelope, in a process involving four Rab GTPases. To identify novel factors involved in HSV1 envelopment, we have screened a small interfering RNA (siRNA) library targeting over 80 human trafficking proteins, including coat proteins, adaptor proteins, fusion factors, fission factors, and Rab effectors. The depletion of 11 factors reduced virus yields by 20- to 100-fold, including three early secretory pathway proteins, four late secretory pathway proteins, and four endocytic pathway proteins, three of which are membrane fission factors. Five of the 11 targets were chosen for further analysis in virus infection, where it was found that the absence of only 1, the fission factor CHMP4C, but not the CHMP4A or CHMP4B paralogues, reduced virus production at the final stage of morphogenesis. Ultrastructural and confocal microscopy of CHMP4C-depleted, HSV1-infected cells showed an accumulation of endocytic membranes; extensive tubulation of recycling, transferrin receptor-positive endosomes indicative of aberrant fission; and a failure in virus envelopment. No effect on the late endocytic pathway was detected, while exogenous CHMP4C was shown to localize to recycling endosomes. Taken together, these data reveal a novel role for the CHMP4C fission factor in the integrity of the recycling endosomal network, which has been unveiled through the dependence of HSV1 on these membranes for the acquisition of their envelopes.IMPORTANCE Cellular transport pathways play a fundamental role in secretion and membrane biogenesis. Enveloped viruses exploit these pathways to direct their membrane proteins to sites of envelopment and, as such, are powerful tools for unraveling subtle activities of trafficking factors, potentially pinpointing therapeutic targets. Using the sensitive biological readout of virus production, over 80 trafficking factors involved in diverse and poorly defined cellular processes have been screened for involvement in the complex process of HSV1 envelopment. Out of 11 potential targets, CHMP4C, a key component in the cell cycle abscission checkpoint, stood out as being required for the process of virus wrapping in endocytic tubules, where it localized. In the absence of CHMP4C, recycling endocytic membranes failed to undergo scission in infected cells, causing transient tubulation and accumulation of membranes and unwrapped virus. These data reveal a new role for this important cellular factor in the biogenesis of recycling endocytic membranes.
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Affiliation(s)
- Tiffany Russell
- Department of Microbial Sciences, University of Surrey, Guildford, United Kingdom
| | - Jerzy Samolej
- Department of Microbial Sciences, University of Surrey, Guildford, United Kingdom
| | | | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Joanne Kite
- Department of Microbial Sciences, University of Surrey, Guildford, United Kingdom
| | - Gillian Elliott
- Department of Microbial Sciences, University of Surrey, Guildford, United Kingdom
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A novel loss of function mutation in adaptor protein complex 4, subunit mu-1 causing autosomal recessive spastic paraplegia 50. Neurol Sci 2021; 42:5311-5319. [PMID: 33884525 DOI: 10.1007/s10072-021-05262-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/16/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Spastic paraplegia 50 (SPG50) is a rare autosomal recessive inherited disorder characterized by spasticity, severe intellectual disability and delayed or absent speech. Loss-of-function pathogenic mutations in the AP4M1 gene cause SPG50. METHODS In this study, we investigated the clinical and genetic characteristics of a consanguineous family with two male siblings who had infantile hypotonia that progressed to spasticity, paraplegia in one and quadriplegia in the other patient. In addition, the patients also exhibited neurodevelopmental phenotypes including severe intellectual disability, developmental delay, microcephaly and dysmorphism. RESULTS In order to identify the genetic cause, we performed cytogenetics, whole-exome sequencing and Sanger sequencing. Whole-exome sequencing of the affected siblings and unaffected parents revealed a novel exonic frameshift insertion of eight nucleotides (c.341_342insTGAAGTGC) on exon 4 of the AP4M1 gene. CONCLUSION Insertion of these eight nucleotides in the AP4M1 gene is predicted to result in a premature protein product of 132 amino acids. The truncated protein product lacks a signal binding domain which is essential for protein-protein interactions and the transport of cargo proteins to the membrane. Thus, the identified variant is pathogenic and our study expands the knowledge of clinical and genetic features of SPG50.
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Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa. Int J Mol Sci 2021; 22:ijms22073477. [PMID: 33801727 PMCID: PMC8036860 DOI: 10.3390/ijms22073477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 01/26/2023] Open
Abstract
Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.
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Edmison D, Wang L, Gowrishankar S. Lysosome Function and Dysfunction in Hereditary Spastic Paraplegias. Brain Sci 2021; 11:152. [PMID: 33498913 PMCID: PMC7911997 DOI: 10.3390/brainsci11020152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/15/2021] [Accepted: 01/21/2021] [Indexed: 12/13/2022] Open
Abstract
Hereditary Spastic Paraplegias (HSPs) are a genetically diverse group of inherited neurological diseases with over 80 associated gene loci. Over the last decade, research into mechanisms underlying HSPs has led to an emerging interest in lysosome dysfunction. In this review, we highlight the different classes of HSPs that have been linked to lysosome defects: (1) a subset of complex HSPs where mutations in lysosomal genes are causally linked to the diseases, (2) other complex HSPs where mutation in genes encoding membrane trafficking adaptors lead to lysosomal defects, and (3) a subset of HSPs where mutations affect genes encoding proteins whose function is primarily linked to a different cellular component or organelle such as microtubule severing and Endoplasmic Reticulum-shaping, while also altering to lysosomes. Interestingly, aberrant axonal lysosomes, associated with the latter two subsets of HSPs, are a key feature observed in other neurodegenerative diseases such as Alzheimer's disease. We discuss how altered lysosome function and trafficking may be a critical contributor to HSP pathology and highlight the need for examining these features in the cortico-spinal motor neurons of HSP mutant models.
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Affiliation(s)
| | | | - Swetha Gowrishankar
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA; (D.E.); (L.W.)
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Cross-Kingdom Activation of Vibrio Toxins by ADP-Ribosylation Factor Family GTPases. J Bacteriol 2020; 202:JB.00278-20. [PMID: 32900828 DOI: 10.1128/jb.00278-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogenic Vibrio species use many different approaches to subvert, attack, and undermine the host response. The toxins they produce are often responsible for the devastating effects associated with their diseases. These toxins target a variety of host proteins, which leads to deleterious effects, including dissolution of cell organelle integrity and inhibition of protein secretion. Becoming increasingly prevalent as cofactors for Vibrio toxins are proteins of the small GTPase families. ADP-ribosylation factor small GTPases (ARFs) in particular are emerging as a common host cofactor necessary for full activation of Vibrio toxins. While ARFs are not the direct target of Vibrio cholerae cholera toxin (CT), ARF binding is required for its optimal activity as an ADP-ribosyltransferase. The makes caterpillars floppy (MCF)-like and the domain X (DmX) effectors of the Vibrio vulnificus multifunctional autoprocessing repeats-in-toxin (MARTX) toxin also both require ARFs to initiate autoprocessing and activation as independent effectors. ARFs are ubiquitously expressed in eukaryotes and are key regulators of many cellular processes, and as such they are ideal cofactors for Vibrio pathogens that infect many host species. In this review, we cover in detail the known Vibrio toxins that use ARFs as cross-kingdom activators to both stimulate and optimize their activity. We further discuss how these contrast to toxins and effectors from other bacterial species that coactivate, stimulate, or directly modify host ARFs as their mechanisms of action.
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The role of AP-4 in cargo export from the trans-Golgi network and hereditary spastic paraplegia. Biochem Soc Trans 2020; 48:1877-1888. [PMID: 33084855 DOI: 10.1042/bst20190664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 01/02/2023]
Abstract
Heterotetrameric adaptor protein (AP) complexes play key roles in protein sorting and transport vesicle formation in the endomembrane system of eukaryotic cells. One of these complexes, AP-4, was identified over 20 years ago but, up until recently, its function remained unclear. AP-4 associates with the trans-Golgi network (TGN) through interaction with small GTPases of the ARF family and recognizes transmembrane proteins (i.e. cargos) having specific sorting signals in their cytosolic domains. Recent studies identified accessory proteins (tepsin, RUSC2 and the FHF complex) that co-operate with AP-4, and cargos (amyloid precursor protein, ATG9A and SERINC3/5) that are exported from the TGN in an AP-4-dependent manner. Defective export of ATG9A from the TGN in AP-4-deficient cells was shown to reduce ATG9A delivery to pre-autophagosomal structures, impairing autophagosome formation and/or maturation. In addition, mutations in AP-4-subunit genes were found to cause neurological dysfunction in mice and a form of complicated hereditary spastic paraplegia referred to as 'AP-4-deficiency syndrome' in humans. These findings demonstrated that mammalian AP-4 is required for the development and function of the central nervous system, possibly through its role in the sorting of ATG9A for the maintenance of autophagic homeostasis. In this article, we review the properties and functions of AP-4, and discuss how they might explain the clinical features of AP-4 deficiency.
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Ebrahimi-Fakhari D, Teinert J, Behne R, Wimmer M, D'Amore A, Eberhardt K, Brechmann B, Ziegler M, Jensen DM, Nagabhyrava P, Geisel G, Carmody E, Shamshad U, Dies KA, Yuskaitis CJ, Salussolia CL, Ebrahimi-Fakhari D, Pearson TS, Saffari A, Ziegler A, Kölker S, Volkmann J, Wiesener A, Bearden DR, Lakhani S, Segal D, Udwadia-Hegde A, Martinuzzi A, Hirst J, Perlman S, Takiyama Y, Xiromerisiou G, Vill K, Walker WO, Shukla A, Dubey Gupta R, Dahl N, Aksoy A, Verhelst H, Delgado MR, Kremlikova Pourova R, Sadek AA, Elkhateeb NM, Blumkin L, Brea-Fernández AJ, Dacruz-Álvarez D, Smol T, Ghoumid J, Miguel D, Heine C, Schlump JU, Langen H, Baets J, Bulk S, Darvish H, Bakhtiari S, Kruer MC, Lim-Melia E, Aydinli N, Alanay Y, El-Rashidy O, Nampoothiri S, Patel C, Beetz C, Bauer P, Yoon G, Guillot M, Miller SP, Bourinaris T, Houlden H, Robelin L, Anheim M, Alamri AS, Mahmoud AAH, Inaloo S, Habibzadeh P, Faghihi MA, Jansen AC, Brock S, Roubertie A, Darras BT, Agrawal PB, Santorelli FM, Gleeson J, Zaki MS, Sheikh SI, Bennett JT, Sahin M. Defining the clinical, molecular and imaging spectrum of adaptor protein complex 4-associated hereditary spastic paraplegia. Brain 2020; 143:2929-2944. [PMID: 32979048 PMCID: PMC7780481 DOI: 10.1093/brain/awz307] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/25/2019] [Accepted: 08/16/2019] [Indexed: 12/21/2022] Open
Abstract
Bi-allelic loss-of-function variants in genes that encode subunits of the adaptor protein complex 4 (AP-4) lead to prototypical yet poorly understood forms of childhood-onset and complex hereditary spastic paraplegia: SPG47 (AP4B1), SPG50 (AP4M1), SPG51 (AP4E1) and SPG52 (AP4S1). Here, we report a detailed cross-sectional analysis of clinical, imaging and molecular data of 156 patients from 101 families. Enrolled patients were of diverse ethnic backgrounds and covered a wide age range (1.0-49.3 years). While the mean age at symptom onset was 0.8 ± 0.6 years [standard deviation (SD), range 0.2-5.0], the mean age at diagnosis was 10.2 ± 8.5 years (SD, range 0.1-46.3). We define a set of core features: early-onset developmental delay with delayed motor milestones and significant speech delay (50% non-verbal); intellectual disability in the moderate to severe range; mild hypotonia in infancy followed by spastic diplegia (mean age: 8.4 ± 5.1 years, SD) and later tetraplegia (mean age: 16.1 ± 9.8 years, SD); postnatal microcephaly (83%); foot deformities (69%); and epilepsy (66%) that is intractable in a subset. At last follow-up, 36% ambulated with assistance (mean age: 8.9 ± 6.4 years, SD) and 54% were wheelchair-dependent (mean age: 13.4 ± 9.8 years, SD). Episodes of stereotypic laughing, possibly consistent with a pseudobulbar affect, were found in 56% of patients. Key features on neuroimaging include a thin corpus callosum (90%), ventriculomegaly (65%) often with colpocephaly, and periventricular white-matter signal abnormalities (68%). Iron deposition and polymicrogyria were found in a subset of patients. AP4B1-associated SPG47 and AP4M1-associated SPG50 accounted for the majority of cases. About two-thirds of patients were born to consanguineous parents, and 82% carried homozygous variants. Over 70 unique variants were present, the majority of which are frameshift or nonsense mutations. To track disease progression across the age spectrum, we defined the relationship between disease severity as measured by several rating scales and disease duration. We found that the presence of epilepsy, which manifested before the age of 3 years in the majority of patients, was associated with worse motor outcomes. Exploring genotype-phenotype correlations, we found that disease severity and major phenotypes were equally distributed among the four subtypes, establishing that SPG47, SPG50, SPG51 and SPG52 share a common phenotype, an 'AP-4 deficiency syndrome'. By delineating the core clinical, imaging, and molecular features of AP-4-associated hereditary spastic paraplegia across the age spectrum our results will facilitate early diagnosis, enable counselling and anticipatory guidance of affected families and help define endpoints for future interventional trials.
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Affiliation(s)
- Darius Ebrahimi-Fakhari
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Julian Teinert
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Child Neurology and Metabolic Medicine, Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Robert Behne
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, University Hospital Würzburg, Würzburg, Germany
| | - Miriam Wimmer
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Angelica D'Amore
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Kathrin Eberhardt
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Barbara Brechmann
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marvin Ziegler
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dana M Jensen
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Premsai Nagabhyrava
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gregory Geisel
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Erin Carmody
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Uzma Shamshad
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kira A Dies
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher J Yuskaitis
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Catherine L Salussolia
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel Ebrahimi-Fakhari
- Pediatric Neurology, Saarland University Medical Center, Homburg/Saar, Germany
- Department of General Pediatrics, University Children's Hospital Muenster, Muenster, Germany
| | - Toni S Pearson
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Afshin Saffari
- Division of Child Neurology and Metabolic Medicine, Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas Ziegler
- Division of Child Neurology and Metabolic Medicine, Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Kölker
- Division of Child Neurology and Metabolic Medicine, Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Jens Volkmann
- Department of Neurology, University Hospital Würzburg, Würzburg, Germany
| | - Antje Wiesener
- Institute of Human Genetics, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - David R Bearden
- Child Neurology, University of Rochester School of Medicine, Rochester, NY, USA
| | - Shenela Lakhani
- Center for Neurogenetics, Weill Cornell Medical College, New York, NY, USA
| | - Devorah Segal
- Center for Neurogenetics, Weill Cornell Medical College, New York, NY, USA
- Division of Child Neurology, Weill Cornell Medicine, New York City, NY, USA
| | - Anaita Udwadia-Hegde
- Department of Pediatric Neurology, Jaslok Hospital and Research Centre, Mumbai, India
| | - Andrea Martinuzzi
- Scientific Institute, IRCCS E. Medea, Unità Operativa Conegliano, Treviso, Italy
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Seth Perlman
- Division of Neurology, Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | | | | | - Katharina Vill
- Pediatric Neurology and Developmental Medicine, Dr. v. Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - William O Walker
- Department of Pediatrics, Seattle Children's Hospital, University of Washington School of Medicine, Seattle, WA, USA
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | | | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ayse Aksoy
- Pediatric Neurology, Dr. Sami Ulus Hospital, Ankara, Turkey
| | - Helene Verhelst
- Pediatric Neurology, Ghent University Hospital, Ghent, Belgium
| | - Mauricio R Delgado
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Radka Kremlikova Pourova
- Department of Biology and Medical Genetics, Second Medical Faculty, Charles University and UH Motol, Prague, Czech Republic
| | - Abdelrahim A Sadek
- Pediatric Neurology, Faculty of Medicine, Sohag University, Sohag, Egypt
| | | | - Lubov Blumkin
- Movement Disorders Clinic, Pediatric Neurology Unit, Wolfson Medical Center, Holon, Sackler School of Medicine, Tel-Aviv University, Israel
| | | | - David Dacruz-Álvarez
- Neurología Pediátrica, Complexo Hospitalario Universitario, Santiago de Compostela, Spain
| | - Thomas Smol
- CHU Lille, Institut de Génétique Médicale, RADEME, Lille, France
| | - Jamal Ghoumid
- CHU Lille, Institut de Génétique Médicale, RADEME, Lille, France
| | - Diego Miguel
- Serviço de Genética Médica, Universidade Federal da Bahia, Salvador, Brazil
| | - Constanze Heine
- Institute of Human Genetics, University Hospital Leipzig, Leipzig, Germany
| | | | | | - Jonathan Baets
- Neurogenetics Group and Neuromuscular Reference Center, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Saskia Bulk
- Medical Genetics, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - Hossein Darvish
- Cancer Research Center and Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Elizabeth Lim-Melia
- Pediatric Medical Genetics, Maria Fareri Children's Hospital, Valhalla, NY, USA
| | - Nur Aydinli
- Pediatric Genetics, Department of Pediatrics, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Yasemin Alanay
- Pediatric Neurology, Istanbul Medical Faculty, Istanbul, Turkey
| | | | | | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | | | | | - Grace Yoon
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Mireille Guillot
- Department of Paediatrics, The Hospital for Sick Children and The University of Toronto, Toronto, Canada
| | - Steven P Miller
- Department of Paediatrics, The Hospital for Sick Children and The University of Toronto, Toronto, Canada
| | - Thomas Bourinaris
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Laura Robelin
- Service de Neurologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Mathieu Anheim
- Service de Neurologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Abdullah S Alamri
- Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Adel A H Mahmoud
- Pediatrics, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Soroor Inaloo
- Neonatal Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parham Habibzadeh
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Ali Faghihi
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Anna C Jansen
- Pediatric Neurology Unit, Department of Pediatrics, UZ Brussel, Brussels, Belgium
| | - Stefanie Brock
- Pediatric Neurology Unit, Department of Pediatrics, UZ Brussel, Brussels, Belgium
| | | | - Basil T Darras
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Pankaj B Agrawal
- Divisions of Newborn Medicine and Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Joseph Gleeson
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Maha S Zaki
- Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | | | - James T Bennett
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Mustafa Sahin
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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EPSIN1 and MTV1 define functionally overlapping but molecularly distinct trans-Golgi network subdomains in Arabidopsis. Proc Natl Acad Sci U S A 2020; 117:25880-25889. [PMID: 32989160 DOI: 10.1073/pnas.2004822117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The plant trans-Golgi network (TGN) is a central trafficking hub where secretory, vacuolar, recycling, and endocytic pathways merge. Among currently known molecular players involved in TGN transport, three different adaptor protein (AP) complexes promote vesicle generation at the TGN with different cargo specificity and destination. Yet, it remains unresolved how sorting into diverging vesicular routes is spatially organized. Here, we study the family of Arabidopsis thaliana Epsin-like proteins, which are accessory proteins to APs facilitating vesicle biogenesis. By comprehensive molecular, cellular, and genetic analysis of the EPSIN gene family, we identify EPSIN1 and MODIFIED TRANSPORT TO THE VACUOLE1 (MTV1) as its only TGN-associated members. Despite their large phylogenetic distance, they perform overlapping functions in vacuolar and secretory transport. By probing their relationship with AP complexes, we find that they define two molecularly independent pathways: While EPSIN1 associates with AP-1, MTV1 interacts with AP-4, whose function is required for MTV1 recruitment. Although both EPSIN1/AP-1 and MTV1/AP-4 pairs reside at the TGN, high-resolution microscopy reveals them as spatially separate entities. Our results strongly support the hypothesis of molecularly, functionally, and spatially distinct subdomains of the plant TGN and suggest that functional redundancy can be achieved through parallelization of molecularly distinct but functionally overlapping pathways.
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Mattera R, Williamson CD, Ren X, Bonifacino JS. The FTS-Hook-FHIP (FHF) complex interacts with AP-4 to mediate perinuclear distribution of AP-4 and its cargo ATG9A. Mol Biol Cell 2020; 31:963-979. [PMID: 32073997 PMCID: PMC7185972 DOI: 10.1091/mbc.e19-11-0658] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/05/2020] [Accepted: 02/12/2020] [Indexed: 01/08/2023] Open
Abstract
The heterotetrameric adaptor protein complex 4 (AP-4) is a component of a protein coat associated with the trans-Golgi network (TGN). Mutations in AP-4 subunits cause a complicated form of autosomal-recessive hereditary spastic paraplegia termed AP-4-deficiency syndrome. Recent studies showed that AP-4 mediates export of the transmembrane autophagy protein ATG9A from the TGN to preautophagosomal structures. To identify additional proteins that cooperate with AP-4 in ATG9A trafficking, we performed affinity purification-mass spectrometry followed by validation of the hits by biochemical and functional analyses. This approach resulted in the identification of the fused toes homolog-Hook-FHIP (FHF) complex as a novel AP-4 accessory factor. We found that the AP-4-FHF interaction is mediated by direct binding of the AP-4 μ4 subunit to coiled-coil domains in the Hook1 and Hook2 subunits of FHF. Knockdown of FHF subunits resulted in dispersal of AP-4 and ATG9A from the perinuclear region of the cell, consistent with the previously demonstrated role of the FHF complex in coupling organelles to the microtubule (MT) retrograde motor dynein-dynactin. These findings thus uncover an additional mechanism for the distribution of ATG9A within cells and provide further evidence for a role of protein coats in coupling transport vesicles to MT motors.
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Affiliation(s)
- Rafael Mattera
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Chad D. Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Xuefeng Ren
- Department of Molecular and Cell Biology and California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - Juan S. Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
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49
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Birnbaum J, Scharf S, Schmidt S, Jonscher E, Hoeijmakers WAM, Flemming S, Toenhake CG, Schmitt M, Sabitzki R, Bergmann B, Fröhlke U, Mesén-Ramírez P, Blancke Soares A, Herrmann H, Bártfai R, Spielmann T. A Kelch13-defined endocytosis pathway mediates artemisinin resistance in malaria parasites. Science 2020; 367:51-59. [PMID: 31896710 DOI: 10.1126/science.aax4735] [Citation(s) in RCA: 228] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 09/19/2019] [Accepted: 10/30/2019] [Indexed: 01/20/2023]
Abstract
Artemisinin and its derivatives (ARTs) are the frontline drugs against malaria, but resistance is jeopardizing their effectiveness. ART resistance is mediated by mutations in the parasite's Kelch13 protein, but Kelch13 function and its role in resistance remain unclear. In this study, we identified proteins located at a Kelch13-defined compartment. Inactivation of eight of these proteins, including Kelch13, rendered parasites resistant to ART, revealing a pathway critical for resistance. Functional analysis showed that these proteins are required for endocytosis of hemoglobin from the host cell. Parasites with inactivated Kelch13 or a resistance-conferring Kelch13 mutation displayed reduced hemoglobin endocytosis. ARTs are activated by degradation products of hemoglobin. Hence, reduced activity of Kelch13 and its interactors diminishes hemoglobin endocytosis and thereby ART activation, resulting in parasite resistance.
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Affiliation(s)
- Jakob Birnbaum
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Sarah Scharf
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Sabine Schmidt
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Ernst Jonscher
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | | | - Sven Flemming
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Christa Geeke Toenhake
- Department of Molecular Biology, Radboud University, Geert Grooteplein 26-28, 6525 GA Nijmegen, Netherlands
| | - Marius Schmitt
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Ricarda Sabitzki
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Bärbel Bergmann
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Ulrike Fröhlke
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Paolo Mesén-Ramírez
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | | | - Hendrik Herrmann
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Richárd Bártfai
- Department of Molecular Biology, Radboud University, Geert Grooteplein 26-28, 6525 GA Nijmegen, Netherlands
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany.
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50
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Jiang D, Burger CA, Casasent A, Albrecht NE, Li F, Samuel MA. Spatiotemporal gene expression patterns reveal molecular relatedness between retinal laminae. J Comp Neurol 2020; 528:729-755. [PMID: 31609468 PMCID: PMC7147688 DOI: 10.1002/cne.24784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/28/2019] [Accepted: 09/13/2019] [Indexed: 12/16/2022]
Abstract
In several areas of the central nervous system, neurons are regionally organized into groups or layers that carry out specific activities. In this form of patterning, neurons of distinct types localize their cell bodies to just one or a few of the layers within a structure. However, little is known about whether diverse neuron types within a lamina share molecular features that coordinate their organization. To begin to identify such candidates, we used the laminated murine retina to screen 92 lacZ reporter lines available through the Knockout Mouse Project. Thirty-two of these displayed reporter expression in restricted subsets of inner retina neurons. We then identified the spatiotemporal expression patterns of these genes at key developmental stages. This uncovered several that were heavily enriched in development but reduced in adulthood, including the transcriptional regulator Hmga1. An additional set of genes displayed maturation associated laminar enrichment. Among these, we identified Bbox1 as a novel gene that specifically labels all neurons in the ganglion cell layer but is largely excluded from otherwise molecularly similar neurons in the inner retina. Finally, we established Dbn1 as a new marker enriched in amacrines and Fmnl3 as a marker for subsets of αRGCs. Together, these data provide a spatiotemporal map for laminae-specific molecules and suggest that diverse neuron types within a lamina share coordinating molecular features that may inform their fate or function.
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Affiliation(s)
- Danye Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030
| | - Courtney A. Burger
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030
| | - Anna Casasent
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030
| | - Nicholas E. Albrecht
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030
| | - Fenge Li
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030
| | - Melanie A. Samuel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030
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