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Du Y, Fan X, Song C, Chang W, Xiong J, Deng L, Ji WK. Sec23IP recruits VPS13B/COH1 to ER exit site-Golgi interface for tubular ERGIC formation. J Cell Biol 2024; 223:e202402083. [PMID: 39352497 PMCID: PMC11457499 DOI: 10.1083/jcb.202402083] [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: 02/13/2024] [Revised: 06/25/2024] [Accepted: 08/07/2024] [Indexed: 10/09/2024] Open
Abstract
VPS13B/COH1 is the only known causative factor for Cohen syndrome, an early-onset autosomal recessive developmental disorder with intellectual inability, developmental delay, joint hypermobility, myopia, and facial dysmorphism as common features, but the molecular basis of VPS13B/COH1 in pathogenesis remains largely unclear. Here, we identify Sec23 interacting protein (Sec23IP) at the ER exit site (ERES) as a VPS13B adaptor that recruits VPS13B to ERES-Golgi interfaces. VPS13B interacts directly with Sec23IP via the VPS13 adaptor binding domain (VAB), and the interaction promotes the association between ERES and the Golgi. Disease-associated missense mutations of VPS13B-VAB impair the interaction with Sec23IP. Knockout of VPS13B or Sec23IP blocks the formation of tubular ERGIC, an unconventional cargo carrier that expedites ER-to-Golgi transport. In addition, depletion of VPS13B or Sec23IP delays ER export of procollagen, suggesting a link between procollagen secretion and joint laxity in patients with Cohen disease. Together, our study reveals a crucial role of VPS13B-Sec23IP interaction at the ERES-Golgi interface in the pathogenesis of Cohen syndrome.
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Affiliation(s)
- Yuanjiao Du
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Xinyu Fan
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | | | | | - Juan Xiong
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Deng
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Wei-Ke Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, China
- Shenzhen Bay Laboratory, Shenzhen, China
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2
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Wang J, Zhang F, Luo Z, Zhang H, Yu C, Xu Z. VPS13D affects epileptic seizures by regulating mitochondrial fission and autophagy in epileptic rats. Genes Dis 2024; 11:101266. [PMID: 39286655 PMCID: PMC11402929 DOI: 10.1016/j.gendis.2024.101266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 01/30/2024] [Accepted: 02/28/2024] [Indexed: 09/19/2024] Open
Abstract
Abnormal mitochondrial dynamics can lead to seizures, and improved mitochondrial dynamics can alleviate seizures. Vacuolar protein sorting 13D (VPS13D) is closely associated with regulating mitochondrial homeostasis and autophagy. However, further investigation is required to determine whether VPS13D affects seizures by influencing mitochondrial dynamics and autophagy. We aimed to investigate the influence of VPS13D on behavior in a rat model of acute epileptic seizures. Hence, we established an acute epileptic seizure rat model and employed the CRISPR/CAS9 technology to construct a lentivirus to silence the Vps13d gene. Furthermore, we used the HT22 mouse hippocampal neuron cell line to establish a stable strain with suppressed expression of Vps13d in vitro. Then, we performed quantitative proteomic and bioinformatics analyses to confirm the mechanism by which VPS13D influences mitochondrial dynamics and autophagy, both in vitro and in vivo using the experimental acute epileptic seizure model. We found that knockdown of Vps13d resulted in reduced seizure latency and increased seizure frequency in the experimental rats. Immunofluorescence staining and western blot analysis revealed a significant increase in mitochondrial dynamin-related protein 1 expression following Vps13d knockdown. Moreover, we observed a significant reduction in LC3II protein expression levels and the LC3II/LC3I ratio (indicators for autophagy) accompanied by a significant increase in P62 expression (an autophagy adaptor protein). The proteomic analysis confirmed the up-regulation of P62 protein expression. Therefore, we propose that VPS13D plays a role in modulating seizures by influencing mitochondrial dynamics and autophagy.
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Affiliation(s)
- Jian Wang
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
- Department of Neurology, Affiliated Aerospace Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Fan Zhang
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
- Department of Clinical Medicine, Zunyi Medical and Pharmaceutical College, Zunyi, Guizhou 563000, China
| | - Zhong Luo
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Haiqing Zhang
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Changyin Yu
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Zucai Xu
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
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3
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Hanna MG, Rodriguez Cruz HO, Fujise K, Li Z, Monetti M, De Camilli P. Bridge-like lipid transfer protein 3A (BLTP3A) is associated with membranes of the late endocytic pathway and is an effector of CASM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.28.615015. [PMID: 39386594 PMCID: PMC11463362 DOI: 10.1101/2024.09.28.615015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Recent studies have identified a family of rod-shaped proteins which includes VPS13 and ATG2 and are thought to mediate unidirectional lipid transport at intracellular membrane contacts by a bridge-like mechanism. Here, we show that one such protein, BLTP3A/UHRF1BP1, associates with VAMP7-positive vesicles via its C-terminal region and anchors them to lysosomes via the binding of its chorein domain containing N-terminal region to Rab7. Upon damage of lysosomal membranes and resulting mATG8 recruitment to their surface by CASM, BLTP3A first dissociates from lysosomes but then reassociates with them via an interaction of its LIR motif with mATG8. Such interaction is mutually exclusive to the binding of BLTP3A to vesicles and leaves its N-terminal chorein domain, i.e. the proposed entry site of lipids into this family of proteins, available for binding to another membrane, possibly the ER. Our findings reveal that BLTP3A is an effector CASM, potentially as part of a mechanism to help repair or minimize lysosome damage by delivering lipids.
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4
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Harada S, Azuma Y, Misumi Y, Hayashi H, Matsubara S, Nakahara K, Miyatake S, Matsumoto N, Ueda M. A Novel Mutation of VPS13D-related Disorders with Parkinsonism. Intern Med 2024; 63:2551-2553. [PMID: 38369353 DOI: 10.2169/internalmedicine.3101-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/20/2024] Open
Abstract
We herein report a case of VPS13D-related disorder with a novel homogeneous variant. A 58-year-old Japanese woman was referred to our hospital with slowly progressive gait disturbance and cognitive impairment. A neurological examination revealed decreased spontaneity, recent memory impairment, parkinsonism, cerebellar ataxia, pyramidal signs, and autonomic dysfunction. Dopamine transporter single-photon-emission computed tomography showed a markedly reduced uptake in the striatum bilaterally. Whole-exome sequencing revealed a novel homozygous missense variant of the VPS13D gene (Arg3267Pro). Our case suggests that mutations in VPS13D may cause parkinsonism, in addition to the previously reported cerebellar ataxia and spastic paraplegia.
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Affiliation(s)
- Shizuka Harada
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Yoshiteru Azuma
- Department of Pediatrics, Aichi Medical University, Japan
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Yohei Misumi
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Hirotaka Hayashi
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Soichiro Matsubara
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Keiichi Nakahara
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Mitsuharu Ueda
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
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5
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Otegui MS, Steelheart C, Ma W, Ma J, Kang BH, De Medina Hernandez VS, Dagdas Y, Gao C, Goto-Yamada S, Oikawa K, Nishimura M. Vacuolar degradation of plant organelles. THE PLANT CELL 2024; 36:3036-3056. [PMID: 38657116 PMCID: PMC11371181 DOI: 10.1093/plcell/koae128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Plants continuously remodel and degrade their organelles due to damage from their metabolic activities and environmental stressors, as well as an integral part of their cell differentiation programs. Whereas certain organelles use local hydrolytic enzymes for limited remodeling, most of the pathways that control the partial or complete dismantling of organelles rely on vacuolar degradation. Specifically, selective autophagic pathways play a crucial role in recognizing and sorting plant organelle cargo for vacuolar clearance, especially under cellular stress conditions induced by factors like heat, drought, and damaging light. In these short reviews, we discuss the mechanisms that control the vacuolar degradation of chloroplasts, mitochondria, endoplasmic reticulum, Golgi, and peroxisomes, with an emphasis on autophagy, recently discovered selective autophagy receptors for plant organelles, and crosstalk with other catabolic pathways.
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Affiliation(s)
- Marisa S Otegui
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Charlotte Steelheart
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wenlong Ma
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Juncai Ma
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Byung-Ho Kang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | | | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Shino Goto-Yamada
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow 30-348, Poland
| | - Kazusato Oikawa
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Mikio Nishimura
- Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
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6
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Restrepo LJ, Baehrecke EH. Regulation and Functions of Autophagy During Animal Development. J Mol Biol 2024; 436:168473. [PMID: 38311234 PMCID: PMC11260256 DOI: 10.1016/j.jmb.2024.168473] [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: 12/12/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Autophagy is used to degrade cytoplasmic materials, and is critical to maintain cell and organismal health in diverse animals. Here we discuss the regulation, utilization and impact of autophagy on development, including roles in oogenesis, spermatogenesis and embryogenesis in animals. We also describe how autophagy influences postembryonic development in the context of neuronal and cardiac development, wound healing, and tissue regeneration. We describe recent studies of selective autophagy during development, including mitochondria-selective autophagy and endoplasmic reticulum (ER)-selective autophagy. Studies of developing model systems have also been used to discover novel regulators of autophagy, and we explain how studies of autophagy in these physiologically relevant systems are advancing our understanding of this important catabolic process.
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Affiliation(s)
- Lucas J Restrepo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA.
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7
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Dong Y, Jia M, Tan S, Li XY, Song Y, Wang X, Wang Z, Wang C. Clinical, genetic, and neuroimaging profiles of autosomal recessive spinocerebellar ataxia type 4 caused by novel VPS13D variants in Chinese. Am J Med Genet A 2024:e63828. [PMID: 39058251 DOI: 10.1002/ajmg.a.63828] [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: 02/27/2024] [Revised: 05/20/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024]
Abstract
Autosomal recessive spinocerebellar ataxias (SCARs) are a heterogeneous group of neurodegenerative disorders. VPS13D gene is currently the only gene associated with autosomal recessive spinocerebellar ataxia type 4 (SCAR4), also known as VPS13D dyskinesia. SCAR4 is a rare inherited disease, with only 34 reported cases reported worldwide. In this study, we reported three independent SCAR4 cases with adolescent onsets caused by five novel variants of the VPS13D gene. Each patient carried one frameshift and one missense variant: Patient 1 with c.10474del and c.9734C > A (p.Leu3492Tyrfs*43 and p.Thr3245Asn), Patient 2 with c.6094_6107delGTTCTCTTGATCCC and c.9734C > A (p.Val2032Argfs*7 and p.Thr3245Asn), and Patient 3 with c.11954_11963del and c.9833 T > G (p.Phe3985Serfs*10 and p.Ile3278Ser). Two of the three patients shared nystagmus with an identical variant c.9734C > A. Magnetic resonance imaging indicated thoracic spinal atrophy in all three patients and corpus callosum atrophy in one patient, along with other typical manifestations of white matter degradation, cerebral atrophy, and cerebellar atrophy. These findings expanded the genetic, clinical, and neuroimaging spectrum of SCAR4, and provided new insights into the genetic counseling, molecular mechanisms, and differential diagnosis of the disease.
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Affiliation(s)
- Yue Dong
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Milan Jia
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Shuang Tan
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Xu-Ying Li
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Yang Song
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Xianling Wang
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Zhanjun Wang
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Chaodong Wang
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
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8
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Lee J, Pye N, Ellis L, Vos KD, Mortiboys H. Evidence of mitochondrial dysfunction in ALS and methods for measuring in model systems. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2024; 176:269-325. [PMID: 38802177 DOI: 10.1016/bs.irn.2024.04.006] [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: 05/29/2024]
Abstract
Metabolic dysfunction is a hallmark of multiple amyotrophic lateral sclerosis (ALS) models with a majority of ALS patients exhibiting hypermetabolism. The central sites of metabolism in the cell are mitochondria, capable of utilising a multitude of cellular substrates in an array of ATP-generating reactions. With reactive oxygen species (ROS) production occurring during some of these reactions, mitochondria can contribute considerably to oxidative stress. Mitochondria are also very dynamic organelles, interacting with other organelles, undergoing fusion/fission in response to changing metabolic states and being turned over by the cell regularly. Disruptions to many of these mitochondrial functions and processes have been reported in ALS models, largely indicating compromised mitochondrial function, increased ROS production by mitochondria, disrupted interactions with the endoplasmic reticulum and reduced turnover. This chapter summarises methods routinely used to assess mitochondria in ALS models and the alterations that have been reported in these models.
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Affiliation(s)
- James Lee
- Sheffield Institute for Translational Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom
| | - Natalie Pye
- Sheffield Institute for Translational Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom
| | - Laura Ellis
- Sheffield Institute for Translational Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom
| | - Kurt De Vos
- Sheffield Institute for Translational Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom.
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9
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Kistol D, Tsygankova P, Bostanova F, Orlova M, Zakharova E. New Case of Spinocerebellar Ataxia, Autosomal Recessive 4, Due to VPS13D Variants. Int J Mol Sci 2024; 25:5127. [PMID: 38791166 PMCID: PMC11121673 DOI: 10.3390/ijms25105127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Movement disorders such as bradykinesia, tremor, dystonia, chorea, and myoclonus most often arise in several neurodegenerative diseases with basal ganglia and white matter involvement. While the pathophysiology of these disorders remains incompletely understood, dysfunction of the basal ganglia and related brain regions is often implicated. The VPS13D gene, part of the VPS13 family, has emerged as a crucial player in neurological pathology, implicated in diverse phenotypes ranging from movement disorders to Leigh syndrome. We present a clinical case of VPS13D-associated disease with two variants in the VPS13D gene in an adult female. This case contributes to our evolving understanding of VPS13D-related diseases and underscores the importance of genetic screening in diagnosing and managing such conditions.
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Affiliation(s)
- Denis Kistol
- Research Centre for Medical Genetics, 115522 Moscow, Russia
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10
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Sultan T, Scorrano G, Panciroli M, Christoforou M, Raza Alvi J, Di Ludovico A, Qureshi S, Efthymiou S, Salpietro V, Houlden H. Clinical and molecular heterogeneity of VPS13D-related neurodevelopmental and movement disorders. Gene 2024; 899:148119. [PMID: 38160741 DOI: 10.1016/j.gene.2023.148119] [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: 09/18/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The VPS13 family of proteins has been implicated in lipid transport and trafficking between endoplasmic reticulum and organelles, to maintain homeostasis of subcellular membranes. Recently, pathogenic variants in each human VPS13S gene, have been linked to distinct human neurodevelopmental or neurodegenerative disorders. Within the VPS13 family of genes, VPS13D is known to be implicated in mitochondria homeostasis and function. METHODS We investigated a Pakistani sibship affected with neurodevelopmental impairment and severe hyperkinetic (choreoathetoid) movements. Whole exome sequencing (WES) and Sanger sequencing were performed to identify potential candidate variants segregating in the family. We described clinical phenotypes and natural history of the disease during a 3-year clinical follow-up and summarized literature data related to previously identified patients with VPS13D-related neurological disorders. RESULTS We identified by WES an homozygous non-synonymous variant in VPS13D (c.5723 T > C; p.Ile1908Thr) as the potential underlying cause of the disease in our family. Two young siblings developed an early-onset neurological impairment characterized by global developmental delay, with impaired speech and motor milestones, associated to hyperkinetic movement disorders as well as progressive and non-progressive neurological abnormalities. CONCLUSION In this study we delineated the heterogeneity of VPS13D-related clinical phenotypes and described a novel VPS13D homozygous variant associated with severe neurological impairment. Further studies will be pivotal to understand the exact VPS13D function and its impact on mitochondria homeostasis, brain development and regulation of movements, to further clarify genotype-phenotype correlations and provide crucial prognostic information and potential therapeutic implications.
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Affiliation(s)
- Tipu Sultan
- Department of Pediatric Neurology, Children Hospital Lahore, Main Boulevard Gulberg, Nishtar Town, Lahore, Punjab 54000, Pakistan
| | | | - Marta Panciroli
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Marilena Christoforou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Javeria Raza Alvi
- Department of Pediatric Neurology, Children Hospital Lahore, Main Boulevard Gulberg, Nishtar Town, Lahore, Punjab 54000, Pakistan
| | | | - Sameen Qureshi
- Department of Pediatric Neurology, Children Hospital Lahore, Main Boulevard Gulberg, Nishtar Town, Lahore, Punjab 54000, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom.
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
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11
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Hu X, Cai Y, Ji WK. Recent Advances on Synaptotagmin-Like Mitochondrial-Lipid Binding Protein Domain Containing Lipid Transfer Proteins. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2024; 7:25152564241273646. [PMID: 39139576 PMCID: PMC11320393 DOI: 10.1177/25152564241273646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/09/2024] [Accepted: 07/09/2024] [Indexed: 08/15/2024]
Abstract
The Synaptotagmin-like mitochondrial-lipid binding protein (SMP) domain is found in a group of ER-resident lipid transfer proteins that are recruited to membrane contact sites (MCSs) by adaptors. Deciphering the molecular basis underlying the recruitment of SMP proteins to specific MCS sheds light not only on their cellular localization but also on their biological functions at these sites. Here we summarize recent advances in SMP domain-containing lipid transfer proteins, focusing on a recent study showing the localization, regulation and cellular function of a specific SMP protein named testis expressed protein 2 (Tex2). TMEM55, a potential PIP phosphatase on late endosome/lysosomal (LE/lys) membranes, was identified as an adaptor that enables the recruitment of Tex2 to ER- LE/lys MCS. In addition, we have summarized several important questions about the regulation and physiological functions of Tex2 that remained unanswered.
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Affiliation(s)
- Xuewen Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Yirui Cai
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Wei-Ke Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
- Cell Architecture Research Center; Huazhong University of Science and Technology, Wuhan, China
- Shenzhen Bay Laboratory, Shenzhen, China
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12
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Wang R, Velentzas PD, Baehrecke EH. Mass isolation of staged Drosophila pupal intestines for analysis of protein ubiquitylation. STAR Protoc 2023; 4:102713. [PMID: 37950865 PMCID: PMC10682243 DOI: 10.1016/j.xpro.2023.102713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/04/2023] [Accepted: 10/26/2023] [Indexed: 11/13/2023] Open
Abstract
Large quantities of developmentally synchronized pupal intestines are required for biochemistry experiments. Here, we present a protocol for the mass isolation of staged pupal intestines during Drosophila melanogaster development based on buoyancy in sucrose for biochemical evaluation of protein ubiquitylation. We describe steps for crossing flies, preparation of samples, immunoprecipitation of proteins from staged isolated tissues, and analysis of samples by western blot. This protocol can be extended to investigate biochemical changes in other tissues. For complete details on the use and execution of this protocol, please refer to Wang et al. (2023).1.
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Affiliation(s)
- Ruoxi Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
| | - Panagiotis D Velentzas
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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13
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Neiman AM. Pharmacological interventions for lipid transport disorders. Front Neurosci 2023; 17:1321250. [PMID: 38156273 PMCID: PMC10752963 DOI: 10.3389/fnins.2023.1321250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/29/2023] [Indexed: 12/30/2023] Open
Abstract
The recent discovery that defects in inter-organelle lipid transport are at the heart of several neurological and neurodegenerative disorders raises the challenge of identifying therapeutic strategies to correct lipid transport defects. This perspective highlights two potential strategies suggested by the study of lipid transport in budding yeast. In the first approach, small molecules are proposed that enhance the lipid transfer activity of VPS13 proteins and thereby compensate for reduced transport. In the second approach, molecules that act as inter-organelle tethers could be used to create artificial contact sites and bypass the loss of endogenous contacts.
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Affiliation(s)
- Aaron M. Neiman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States
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14
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Chang YM, Pan YW, Chou YY, Yu WH, Tsai MC. A boy with a progressive neurologic decline harboring two coexisting mutations in KMT2D and VPS13D. Brain Dev 2023; 45:603-607. [PMID: 37599126 DOI: 10.1016/j.braindev.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/25/2023] [Accepted: 08/05/2023] [Indexed: 08/22/2023]
Abstract
INTRODUCTION Kabuki syndrome (KS) and spinocerebellar ataxia (SCA) are both rare conditions with neurodevelopmental abnormalities. Approaching a patient with complex phenotypes and differentiating the role of mutations may be beneficial but challenging in predicting the disease prognosis. CASE PRESENTATION A boy presented with progressive ataxia, developmental regression, and myoclonus since 4 years of age. Additional features included growth hormone deficiency, excessive body hair, dysmorphic facies, hypoparathyroidism, and bilateral sensorineural hearing impairment. Brain magnetic resonance imaging depicted T2-weighted hyperintensities over bilateral globus pallidus, thalamus, subcortical white matter, and brainstem. The results of tandem mass spectrometry, mitochondrial deletion, and mitochondrial DNA sequencing were inconclusive. Whole-exome sequencing (WES) on genomic DNA obtained from peripheral blood cells revealed a known pathogenic variant at KMT2D gene (c.5993A > G, p.Tyr1998Cys) related to KS and two compound heterozygous, likely pathogenic variants at VPS13D gene (c.908G > A, p.Arg303Gln and c.8561T > G, p.Leu2854Arg) related to autosomal recessive SCA type 4 (SCAR4). DISCUSSION SCAR4 is mainly adult-onset, but a few pediatric cases have recently been reported with progressive gait instability and developmental delay. The VPS13D gene has been suggested to play a role in mitochondrial size, autophagy, and clearance, thus explaining the clinical and imaging phenotypes. CONCLUSION Our case showed a rare co-existence of KS and SCAR4, highlighting the utility of WES in atypical cases that a single-gene disease cannot fully explain.
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Affiliation(s)
- Yu-Ming Chang
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Wen Pan
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yen-Yin Chou
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Genomic Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Hao Yu
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Meng-Che Tsai
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Genomic Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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15
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Hanna M, Guillén-Samander A, De Camilli P. RBG Motif Bridge-Like Lipid Transport Proteins: Structure, Functions, and Open Questions. Annu Rev Cell Dev Biol 2023; 39:409-434. [PMID: 37406299 DOI: 10.1146/annurev-cellbio-120420-014634] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The life of eukaryotic cells requires the transport of lipids between membranes, which are separated by the aqueous environment of the cytosol. Vesicle-mediated traffic along the secretory and endocytic pathways and lipid transfer proteins (LTPs) cooperate in this transport. Until recently, known LTPs were shown to carry one or a few lipids at a time and were thought to mediate transport by shuttle-like mechanisms. Over the last few years, a new family of LTPs has been discovered that is defined by a repeating β-groove (RBG) rod-like structure with a hydrophobic channel running along their entire length. This structure and the localization of these proteins at membrane contact sites suggest a bridge-like mechanism of lipid transport. Mutations in some of these proteins result in neurodegenerative and developmental disorders. Here we review the known properties and well-established or putative physiological roles of these proteins, and we highlight the many questions that remain open about their functions.
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Affiliation(s)
- Michael Hanna
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Andrés Guillén-Samander
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
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16
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Wang R, Fortier TM, Chai F, Miao G, Shen JL, Restrepo LJ, DiGiacomo JJ, Velentzas PD, Baehrecke EH. PINK1, Keap1, and Rtnl1 regulate selective clearance of endoplasmic reticulum during development. Cell 2023; 186:4172-4188.e18. [PMID: 37633267 PMCID: PMC10530463 DOI: 10.1016/j.cell.2023.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/27/2023] [Accepted: 08/07/2023] [Indexed: 08/28/2023]
Abstract
Selective clearance of organelles, including endoplasmic reticulum (ER) and mitochondria, by autophagy plays an important role in cell health. Here, we describe a developmentally programmed selective ER clearance by autophagy. We show that Parkinson's disease-associated PINK1, as well as Atl, Rtnl1, and Trp1 receptors, regulate ER clearance by autophagy. The E3 ubiquitin ligase Parkin functions downstream of PINK1 and is required for mitochondrial clearance while having the opposite function in ER clearance. By contrast, Keap1 and the E3 ubiquitin ligase Cullin3 function downstream of PINK1 to regulate ER clearance by influencing Rtnl1 and Atl. PINK1 regulates a change in Keap1 localization and Keap1-dependent ubiquitylation of the ER-phagy receptor Rtnl1 to facilitate ER clearance. Thus, PINK1 regulates the selective clearance of ER and mitochondria by influencing the balance of Keap1- and Parkin-dependent ubiquitylation of substrates that determine which organelle is removed by autophagy.
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Affiliation(s)
- Ruoxi Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Tina M Fortier
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Fei Chai
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Guangyan Miao
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James L Shen
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Lucas J Restrepo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jeromy J DiGiacomo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Panagiotis D Velentzas
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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17
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Muñoz JP, Basei FL, Rojas ML, Galvis D, Zorzano A. Mechanisms of Modulation of Mitochondrial Architecture. Biomolecules 2023; 13:1225. [PMID: 37627290 PMCID: PMC10452872 DOI: 10.3390/biom13081225] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial network architecture plays a critical role in cellular physiology. Indeed, alterations in the shape of mitochondria upon exposure to cellular stress can cause the dysfunction of these organelles. In this scenario, mitochondrial dynamics proteins and the phospholipid composition of the mitochondrial membrane are key for fine-tuning the modulation of mitochondrial architecture. In addition, several factors including post-translational modifications such as the phosphorylation, acetylation, SUMOylation, and o-GlcNAcylation of mitochondrial dynamics proteins contribute to shaping the plasticity of this architecture. In this regard, several studies have evidenced that, upon metabolic stress, mitochondrial dynamics proteins are post-translationally modified, leading to the alteration of mitochondrial architecture. Interestingly, several proteins that sustain the mitochondrial lipid composition also modulate mitochondrial morphology and organelle communication. In this context, pharmacological studies have revealed that the modulation of mitochondrial shape and function emerges as a potential therapeutic strategy for metabolic diseases. Here, we review the factors that modulate mitochondrial architecture.
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Affiliation(s)
- Juan Pablo Muñoz
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), 28029 Madrid, Spain
- Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), 08041 Barcelona, Spain
| | - Fernanda Luisa Basei
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, 13083-871 Campinas, SP, Brazil
| | - María Laura Rojas
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
| | - David Galvis
- Programa de Química Farmacéutica, Universidad CES, Medellín 050031, Colombia
| | - Antonio Zorzano
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), 28029 Madrid, Spain
- Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
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18
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Dabrowski R, Tulli S, Graef M. Parallel phospholipid transfer by Vps13 and Atg2 determines autophagosome biogenesis dynamics. J Cell Biol 2023; 222:e202211039. [PMID: 37115156 PMCID: PMC10148235 DOI: 10.1083/jcb.202211039] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/30/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
During autophagy, rapid membrane assembly expands small phagophores into large double-membrane autophagosomes. Theoretical modeling predicts that the majority of autophagosomal phospholipids are derived from highly efficient non-vesicular phospholipid transfer (PLT) across phagophore-ER contacts (PERCS). Currently, the phagophore-ER tether Atg2 is the only PLT protein known to drive phagophore expansion in vivo. Here, our quantitative live-cell imaging analysis reveals a poor correlation between the duration and size of forming autophagosomes and the number of Atg2 molecules at PERCS of starving yeast cells. Strikingly, we find that Atg2-mediated PLT is non-rate limiting for autophagosome biogenesis because membrane tether and the PLT protein Vps13 localizes to the rim and promotes the expansion of phagophores in parallel with Atg2. In the absence of Vps13, the number of Atg2 molecules at PERCS determines the duration and size of forming autophagosomes with an apparent in vivo transfer rate of ∼200 phospholipids per Atg2 molecule and second. We propose that conserved PLT proteins cooperate in channeling phospholipids across organelle contact sites for non-rate-limiting membrane assembly during autophagosome biogenesis.
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Affiliation(s)
- Rahel Dabrowski
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Susanna Tulli
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Martin Graef
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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19
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Rozich E, Randolph LK, Insolera R. An optimized temporally controlled Gal4 system in Drosophila reveals degeneration caused by adult-onset neuronal Vps13D knockdown. Front Neurosci 2023; 17:1204068. [PMID: 37457002 PMCID: PMC10339317 DOI: 10.3389/fnins.2023.1204068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Mutations in the human gene VPS13D cause the adult-onset neurodegenerative disease ataxia. Our previous work showed that disruptions in the Vps13D gene in Drosophila neurons causes mitochondrial defects. However, developmental lethality caused by Vps13D loss limited our understanding of the long-term physiological effects of Vps13D perturbation in neurons. Here, we optimized a previously generated system to temporally knock down Vps13D expression precisely in adult Drosophila neurons using a modification to the Gal4/UAS system. Adult-onset activation of Gal4 was enacted using the chemically-inducible tool which fuses a destabilization-domain to the Gal4 repressor Gal80 (Gal80-DD). Optimization of the Gal80-DD tool shows that feeding animals the DD-stabilizing drug trimethoprim (TMP) during development and rearing at a reduced temperature maximally represses Gal4 activity. Temperature shift and removal of TMP from the food after eclosion robustly activates Gal4 expression in adult neurons. Using the optimized Gal80-DD system, we find that adult-onset Vps13D RNAi expression in neurons causes the accumulation of mitophagy intermediates, progressive deficits in locomotor activity, early lethality, and brain vacuolization characteristic of neurodegeneration. The development of this optimized system allows us to more precisely examine the degenerative phenotypes caused by Vps13D disruption, and can likely be utilized in the future for other genes associated with neurological diseases whose manipulation causes developmental lethality in Drosophila.
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Affiliation(s)
- Emily Rozich
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, United States
| | - Lynsey K. Randolph
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Ryan Insolera
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, United States
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20
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Goldstein O, Gana-Weisz M, Banfi S, Nigro V, Bar-Shira A, Thaler A, Gurevich T, Mirelman A, Giladi N, Alcalay RN, Orr-Urtreger A. Novel variants in genes related to vesicle-mediated-transport modify Parkinson's disease risk. Mol Genet Metab 2023; 139:107608. [PMID: 37201419 DOI: 10.1016/j.ymgme.2023.107608] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
OBJECTIVES VPS35 and VPS13 have been associated with Parkinson's disease (PD), and their shared phenotype in yeast when reduced in function is abnormal vacuolar transport. We aim to test if additional potentially deleterious variants in other genes that share this phenotype can modify the risk for PD. METHODS 77 VPS and VPS-related genes were analyzed using whole-genome-sequencing data from 202 PD patients of Ashkenazi Jewish (AJ) ancestry. Filtering was done based on quality and functionality scores. Ten variants in nine genes were further genotyped in 1200 consecutively recruited unrelated AJ-PD patients, and allele frequencies and odds ratio calculated compared to gnomAD-AJ-non-neuro database, in un-stratified (n = 1200) and stratified manner (LRRK2-G2019S-PD patients (n = 145), GBA-PD patients (n = 235), and non-carriers of these mutations (NC, n = 787)). RESULTS Five variants in PIK3C3, VPS11, AP1G2, HGS and VPS13D were significantly associated with PD-risk. PIK3C3-R768W showed a significant association in an un-stratified (all PDs) analysis, as well as in stratified (LRRK2, GBA, and NC) analyses (Odds ratios = 2.71, 5.32, 3.26. and 2.19 with p = 0.0015, 0.002, 0.0287, and 0.0447, respectively). AP1G2-R563W was significantly associated in LRRK2-carriers (OR = 3.69, p = 0.006) while VPS13D-D2932N was significantly associated in GBA-carriers (OR = 5.45, p = 0.0027). VPS11-C846G and HGS-S243Y were significantly associated in NC (OR = 2.48 and 2.06, with p = 0.022 and 0.0163, respectively). CONCLUSIONS Variants in genes involved in vesicle-mediated protein transport and recycling pathways, including autophagy and mitophagy, may differentially modify PD-risk in LRRK2-carriers, GBA carriers, or NC. Specifically, PIK3C3-R768W is a PD-risk allele, with the highest effect size in LRRK2-G2019S carriers. These results suggest oligogenic effect that may depends on the genetic background of the patient. An unbiased burden of mutations approach in these genes should be evaluated in additional PD and control groups. The mechanisms by which these novel variants interact and increase PD-risk should be researched in depth for better tailoring therapeutic intervention for PD prevention or slowing disease progression.
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Affiliation(s)
- Orly Goldstein
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Mali Gana-Weisz
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, NA, Italy; Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, NA, Italy; Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Anat Bar-Shira
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Avner Thaler
- Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Tanya Gurevich
- Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Anat Mirelman
- Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Nir Giladi
- Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Roy N Alcalay
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Avi Orr-Urtreger
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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21
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Kim BH, Koh HC. The role of CK2 in the regulation of mitochondrial autophagy induced by rotenone. Toxicol Lett 2023; 382:1-12. [PMID: 37156403 DOI: 10.1016/j.toxlet.2023.05.002] [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: 01/13/2023] [Revised: 04/17/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
CK2 regulates receptor-mediated mitophagy that removes damaged mitochondria. The PINK1/Parkin pathways also involve mitochondrial clearance through mitophagy. However, it is not clear whether CK2 regulates PINK1/Parkin-dependent mitophagy in response to stress. Rotenone treatment showed a decrease of FUNDC1 expression in the mitochondrial fraction of SH-SY5Y and HeLa cells, but an increase of PINK1/Parkin expression only in SH-SY5Y cells. Interestingly, CK2 inhibition increased mitochondrial LC3II expression in rotenone-treated HeLa cells, whereas it decreased in SH-SY5Y cells, indicating that CK2 mediates rotenone-induced mitophagy in dopaminergic neurons. Furthermore, FUNDC1 expression increased in rotenone-treated SH-SY5Y cells by CK2 inhibition, whereas it decreased in HeLa cells. CK2 inhibition also blocked the increase of Drp1, PINK1 and Parkin translocation into mitochondria and decrease of PGAM5 expression in rotenone-treated SH-SY5Y cells. As expected, rotenone treatment in PGAM5-knockdown cells reduced the expression of PINK1 and Parkin and decrease of LC3II expression. Interestingly, we observed that knockdown of CK2α or PGAM5 induced a further increase in caspase-3 expression. These results suggest that PINK1/Parkin-dependent mitophagy was dominant over FUNDC1 receptor-mediated mitophagy. Collectively, our findings suggest that CK2 can positively induce PINK1/Parkin-dependent mitophagy, and that mitophagy regulates cytoprotective effects by CK2 signaling in dopaminergic neurons. DATA AVAILABILITY STATEMENT: All data generated or analyzed during this study are available upon request.
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Affiliation(s)
- Beom Hee Kim
- Department of Pharmacology, College of Medicine, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, 04763, Seoul, Republic of Korea; Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, 04763, Seoul, Republic of Korea
| | - Hyun Chul Koh
- Department of Pharmacology, College of Medicine, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, 04763, Seoul, Republic of Korea; Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, 04763, Seoul, Republic of Korea; Hanyang Biomedical Research Institute, 222 Wangsimni-ro, Seongdong-gu, 04763, Seoul, Republic of Korea.
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22
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Guillén-Samander A, De Camilli P. Endoplasmic Reticulum Membrane Contact Sites, Lipid Transport, and Neurodegeneration. Cold Spring Harb Perspect Biol 2023; 15:a041257. [PMID: 36123033 PMCID: PMC10071438 DOI: 10.1101/cshperspect.a041257] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Endoplasmic Reticulum (ER) is an endomembrane system that plays a multiplicity of roles in cell physiology and populates even the most distal cell compartments, including dendritic tips and axon terminals of neurons. Some of its functions are achieved by a cross talk with other intracellular membranous organelles and with the plasma membrane at membrane contacts sites (MCSs). As the ER synthesizes most membrane lipids, lipid exchanges mediated by lipid transfer proteins at MCSs are a particularly important aspect of this cross talk, which synergizes with the cross talk mediated by vesicular transport. Several mutations of genes that encode proteins localized at ER MCSs result in familial neurodegenerative diseases, emphasizing the importance of the normal lipid traffic within cells for a healthy brain. Here, we provide an overview of such diseases, with a specific focus on proteins that directly or indirectly impact lipid transport.
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Affiliation(s)
- Andrés Guillén-Samander
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland 20815, USA
| | - Pietro De Camilli
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland 20815, USA
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23
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Subra M, Dezi M, Bigay J, Lacas-Gervais S, Di Cicco A, Araújo ARD, Abélanet S, Fleuriot L, Debayle D, Gautier R, Patel A, Roussi F, Antonny B, Lévy D, Mesmin B. VAP-A intrinsically disordered regions enable versatile tethering at membrane contact sites. Dev Cell 2023; 58:121-138.e9. [PMID: 36693319 DOI: 10.1016/j.devcel.2022.12.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/21/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023]
Abstract
Membrane contact sites (MCSs) are heterogeneous in shape, composition, and dynamics. Despite this diversity, VAP proteins act as receptors for multiple FFAT motif-containing proteins and drive the formation of most MCSs that involve the endoplasmic reticulum (ER). Although the VAP-FFAT interaction is well characterized, no model explains how VAP adapts to its partners in various MCSs. We report that VAP-A localization to different MCSs depends on its intrinsically disordered regions (IDRs) in human cells. VAP-A interaction with PTPIP51 and VPS13A at ER-mitochondria MCS conditions mitochondria fusion by promoting lipid transfer and cardiolipin buildup. VAP-A also enables lipid exchange at ER-Golgi MCS by interacting with oxysterol-binding protein (OSBP) and CERT. However, removing IDRs from VAP-A restricts its distribution and function to ER-mitochondria MCS. Our data suggest that IDRs do not modulate VAP-A preference toward specific partners but do adjust their geometry to MCS organization and lifetime constraints. Thus, IDR-mediated VAP-A conformational flexibility ensures membrane tethering plasticity and efficiency.
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Affiliation(s)
- Mélody Subra
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Manuela Dezi
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, 75005 Paris, France
| | - Joëlle Bigay
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Sandra Lacas-Gervais
- Université Côte d'Azur, Centre Commun de Microscopie Appliquée, Parc Valrose, 06000 Nice, France
| | - Aurélie Di Cicco
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, 75005 Paris, France
| | - Ana Rita Dias Araújo
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Sophie Abélanet
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Lucile Fleuriot
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Delphine Debayle
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Romain Gautier
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Amanda Patel
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Fanny Roussi
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Bruno Antonny
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Daniel Lévy
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, 75005 Paris, France
| | - Bruno Mesmin
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France.
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24
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Chen P, Levy DL. Regulation of organelle size and organization during development. Semin Cell Dev Biol 2023; 133:53-64. [PMID: 35148938 PMCID: PMC9357868 DOI: 10.1016/j.semcdb.2022.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/20/2022] [Accepted: 02/01/2022] [Indexed: 12/11/2022]
Abstract
During early embryogenesis, as cells divide in the developing embryo, the size of intracellular organelles generally decreases to scale with the decrease in overall cell size. Organelle size scaling is thought to be important to establish and maintain proper cellular function, and defective scaling may lead to impaired development and disease. However, how the cell regulates organelle size and organization are largely unanswered questions. In this review, we summarize the process of size scaling at both the cell and organelle levels and discuss recently discovered mechanisms that regulate this process during early embryogenesis. In addition, we describe how some recently developed techniques and Xenopus as an animal model can be used to investigate the underlying mechanisms of size regulation and to uncover the significance of proper organelle size scaling and organization.
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Affiliation(s)
- Pan Chen
- Institute of Biochemistry and Molecular Biology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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25
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Du Y, Hu X, Chang W, Deng L, Ji WK, Xiong J. A Possible Role of VPS13B in the Formation of Golgi-Lipid Droplet Contacts Associating with the ER. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231195718. [PMID: 38090145 PMCID: PMC10714374 DOI: 10.1177/25152564231195718] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 02/18/2024]
Abstract
While the physical interactions between the Golgi apparatus (Golgi) and lipid droplets (LDs) have been suggested through system-level imaging, the Golgi-LD membrane contact sites (MCSs) remain largely uncharacterized. Here, we show evidence to support the existence of Golgi-LD MCSs in HEK293 cells. We further suggest that vacuolar protein sorting-associated protein 13B (VPS13B) localizes to and promotes the formation of Golgi-LD contacts upon oleic acid (OA) stimulation using 3D high-resolution microscopy. Depletion of VPS13B moderately affects the formation of Golgi-LD contacts upon OA treatment in addition to the fragmentation of the Golgi. Although cellular functions of VPS13B-mediated contacts are still elusive, these findings may provide a new insight into related diseases caused by loss-of-function mutations of VPS13B.
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Affiliation(s)
- Yuanjiao Du
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xuewen Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | | | - Lin Deng
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Wei-Ke Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cell Architecture Research Center; Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Juan Xiong
- Department of Anesthesiology, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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26
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Ye H, Sun A, Xiao W, Zhang T, Xu Z, Shi L, Sha X, Yang H. Differential Circular RNA Expression Profiling of Orbital Connective Tissue From Patients With Type I and Type II Thyroid-Associated Ophthalmopathy. Invest Ophthalmol Vis Sci 2022; 63:27. [DOI: 10.1167/iovs.63.12.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Huijing Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Anqi Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Wei Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Te Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhihui Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Lu Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xiaotong Sha
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Huasheng Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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27
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McEwan DG, Ryan KM. ATG2 and VPS13 proteins: molecular highways transporting lipids to drive membrane expansion and organelle communication. FEBS J 2022; 289:7113-7127. [PMID: 34783437 DOI: 10.1111/febs.16280] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 01/13/2023]
Abstract
Communication between organelles is an essential process that helps maintain cellular homeostasis and organelle contact sites have recently emerged as crucial mediators of this communication. The emergence of a class of molecular bridges that span the inter-organelle gaps has now been shown to direct the flow of lipid traffic from one lipid bilayer to another. One of the key components of these molecular bridges is the presence of an N-terminal Chorein/VPS13 domain. This is an evolutionarily conserved domain present in multiple proteins within the endocytic and autophagy trafficking pathways. Herein, we discuss the current state-of-the-art of this class of proteins, focusing on the role of these lipid transporters in the autophagy and endocytic pathways. We discuss the recent biochemical and structural advances that have highlighted the essential role Chorein-N domain containing ATG2 proteins play in driving the formation of the autophagosome and how lipids are transported from the endoplasmic reticulum to the growing phagophore. We also consider the VPS13 proteins, their role in organelle contacts and the endocytic pathway and highlight how disease-causing mutations disrupt these contact sites. Finally, we open the door to discuss other Chorein_N domain containing proteins, for instance, UHRF1BP1/1L, their role in disease and look towards prokaryote examples of Chorein_N-like domains. Taken together, recent advances have highlighted an exciting opportunity to delve deeper into inter-organelle communication and understand how lipids are transported between membrane bilayers and how this process is disrupted in multiple diseases.
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Affiliation(s)
| | - Kevin M Ryan
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
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28
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Neuman SD, Levine TP, Bashirullah A. A novel superfamily of bridge-like lipid transfer proteins. Trends Cell Biol 2022; 32:962-974. [PMID: 35491307 PMCID: PMC9588498 DOI: 10.1016/j.tcb.2022.03.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 01/21/2023]
Abstract
Lipid transfer proteins mediate nonvesicular transport of lipids at membrane contact sites to regulate the lipid composition of organelle membranes. Recently, a new type of bridge-like lipid transfer protein has emerged; these proteins contain a long hydrophobic groove and can mediate bulk transport of lipids between organelles. Here, we review recent insights into the structure of these proteins and identify a repeating modular unit that we propose to name the repeating β-groove (RBG) domain. This new structural understanding conceptually unifies all the RBG domain-containing lipid transfer proteins as members of an RBG protein superfamily. We also examine the biological functions of these lipid transporters in normal physiology and disease and speculate on the evolutionary origins of RBG proteins in bacteria.
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Affiliation(s)
- Sarah D Neuman
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA
| | - Tim P Levine
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK.
| | - Arash Bashirullah
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA.
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29
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VPS13D-based disease: Expansion of the clinical phenotype in two brothers and mutation diversity in the Turkish population. Rev Neurol (Paris) 2022; 178:907-913. [PMID: 36156252 DOI: 10.1016/j.neurol.2022.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 03/13/2022] [Accepted: 05/06/2022] [Indexed: 10/14/2022]
Abstract
VPS13D is a recently described gene. Worldwide, only 15 families with 23 affected individuals have been reported with a VPS13D-based disease. Mutated VPS13D causes a complex phenotype with a hyperkinetic movement disorder and ataxia, especially in childhood onset disease. The clinical phenotype of the rare adult-onset cases consists of cerebellar ataxia and/or spastic paraplegia. Here, we report the extensive clinical, laboratory and genetic findings of two offspring from consanguineous parents, with ages of disease onset at 57 and 49 with VPS13D-based ataxia. Although conventional magnetic resonance imaging showed mild cerebellar and cerebral atrophy, diffusion tensor imaging, applied for the first time for VPS13D patients, revealed prominent atrophy in U fibers and cerebellopontine tracts. Whole exome sequencing analysis revealed a biallelic Ala4210Val mutation in the VPS13D, reported only once in the literature. Complementary screening of our in-house database consisting of 295 ataxia and hereditary spastic paraplegia patients revealed two further ataxia patients with novel VPS13D variants. Screening the control cohort for VPS13D variants revealed one asymptomatic individual carrying a novel VPS13D variant. In this study, the phenotypic spectrum of VPS13D-based disease is expanded with the description of pre-senile onset predominant ataxia. Further, with the additional novel mutations described, the report is expected to contribute to the understanding of the yet elusive phenotype-genotype correlations in the rare VPS13D-based movement disorder.
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30
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Rani L, Ranjan Sahu M, Chandra Mondal A. Age-related Mitochondrial Dysfunction in Parkinson's Disease: New Insights Into the Disease Pathology. Neuroscience 2022; 499:152-169. [PMID: 35839924 DOI: 10.1016/j.neuroscience.2022.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/13/2022] [Accepted: 07/07/2022] [Indexed: 12/14/2022]
Abstract
Aging is a progressive loss of physiological function that increases risk of disease and death. Among the many factors that contribute to human aging, mitochondrial dysfunction has emerged as one of the most prominent features of the aging process. It has been linked to the development of various age-related pathologies, including Parkinson's disease (PD). Mitochondria has a complex quality control system that ensures mitochondrial integrity and function. Perturbations in these mitochondrial mechanisms have long been linked to various age-related neurological disorders. Even though research has shed light on several aspects of the disease pathology, the underlying mechanism of age-related factors responsible for individuals developing this disease is still unknown. This review article aims to discuss the role of mitochondria in the transition from normal brain aging to pathological brain aging, which leads to the progression of PD. We have discussed the emerging evidence on how age-related disruption of mitochondrial quality control mechanisms contributes to the development of PD-related pathophysiology.
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Affiliation(s)
- Linchi Rani
- Laboratory of Cellular and Molecular Neurobiology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Manas Ranjan Sahu
- Laboratory of Cellular and Molecular Neurobiology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Amal Chandra Mondal
- Laboratory of Cellular and Molecular Neurobiology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India.
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31
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Zhao L, Sun X, Wang X, Qin S, Kong Y, Li M. Bombyx mori Vps13d is a key gene affecting silk yield. PLoS One 2022; 17:e0270840. [PMID: 35797274 PMCID: PMC9262180 DOI: 10.1371/journal.pone.0270840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/20/2022] [Indexed: 11/18/2022] Open
Abstract
Bombyx mori is an important economic insect, its economic value mainly reflected in the silk yield. The major functional genes affecting the silk yield of B. mori have not been determined yet. Bombyx mori vacuolar protein sorting-associated protein 13d (BmVps13d) has been identified, but its function is not reported. In this study, BmVps13d protein shared 30.84% and 34.35% identity with that of in Drosophila melanogaster and Homo. sapiens, respectively. The expressions of BmVps13d were significantly higher in the midgut and silk gland of JS (high silk yield) than in that of L10 (low silk yield). An insertion of 9 bp nucleotides and two deficiencies of adenine ribonucleotides in the putative promoter region of BmVps13d gene in L10 resulted in the decline of promoter activity was confirmed using dual luciferase assay. Finally, the functions of BmVps13d in B. mori were studied using the CRISPR/Cas9 system, and the mutation of BmVps13d resulted in a 24.7% decline in weight of larvae, as well as a 27.1% (female) decline and a 11.8% (male) decline in the silk yield. This study provides a foundation for studying the molecular mechanism of silk yield and breeding the silkworm with high silk yield.
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Affiliation(s)
- Luochao Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
| | - Xia Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, 212018, Jiangsu, China
| | - Xueyang Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, 212018, Jiangsu, China
| | - Sheng Qin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, 212018, Jiangsu, China
| | - Yunhui Kong
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, 212018, Jiangsu, China
| | - Muwang Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, 212018, Jiangsu, China
- * E-mail:
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32
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Chen J, Li Z, Zhang Y, Zhang X, Zhang S, Liu Z, Yuan H, Pang X, Liu Y, Tao W, Chen X, Zhang P, Chen GQ. Mechanism of reduced muscle atrophy via ketone body (D)-3-hydroxybutyrate. Cell Biosci 2022; 12:94. [PMID: 35725651 PMCID: PMC9208164 DOI: 10.1186/s13578-022-00826-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/03/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Muscle atrophy is an increasingly global health problem affecting millions, there is a lack of clinical drugs or effective therapy. Excessive loss of muscle mass is the typical characteristic of muscle atrophy, manifesting as muscle weakness accompanied by impaired metabolism of protein and nucleotide. (D)-3-hydroxybutyrate (3HB), one of the main components of the ketone body, has been reported to be effective for the obvious hemodynamic effects in atrophic cardiomyocytes and exerts beneficial metabolic reprogramming effects in healthy muscle. This study aims to exploit how the 3HB exerts therapeutic effects for treating muscle atrophy induced by hindlimb unloaded mice. RESULTS Anabolism/catabolism balance of muscle protein was maintained with 3HB via the Akt/FoxO3a and the mTOR/4E-BP1 pathways; protein homeostasis of 3HB regulation includes pathways of ubiquitin-proteasomal, autophagic-lysosomal, responses of unfolded-proteins, heat shock and anti-oxidation. Metabolomic analysis revealed the effect of 3HB decreased purine degradation and reduced the uric acid in atrophied muscles; enhanced utilization from glutamine to glutamate also provides evidence for the promotion of 3HB during the synthesis of proteins and nucleotides. CONCLUSIONS 3HB significantly inhibits the loss of muscle weights, myofiber sizes and myofiber diameters in hindlimb unloaded mouse model; it facilitates positive balance of proteins and nucleotides with enhanced accumulation of glutamate and decreased uric acid in wasting muscles, revealing effectiveness for treating muscle atrophy.
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Affiliation(s)
- Jin Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zihua Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yudian Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Shujie Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zonghan Liu
- National Key Laboratory of Human Factors Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Huimei Yuan
- National Key Laboratory of Human Factors Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Xiangsheng Pang
- National Key Laboratory of Human Factors Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Yaxuan Liu
- National Key Laboratory of Human Factors Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Wuchen Tao
- National Key Laboratory of Human Factors Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Xiaoping Chen
- National Key Laboratory of Human Factors Engineering, China Astronaut Research and Training Center, Beijing, 100094, China.
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, 100094, China.
| | - Peng Zhang
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, 100094, China.
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
- MOE Key Lab of Industrial Biocatalysis, Dept of Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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33
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Zhao J, Zhang H, Fan X, Yu X, Huai J. Lipid Dyshomeostasis and Inherited Cerebellar Ataxia. Mol Neurobiol 2022; 59:3800-3828. [PMID: 35420383 PMCID: PMC9148275 DOI: 10.1007/s12035-022-02826-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/01/2022] [Indexed: 12/04/2022]
Abstract
Cerebellar ataxia is a form of ataxia that originates from dysfunction of the cerebellum, but may involve additional neurological tissues. Its clinical symptoms are mainly characterized by the absence of voluntary muscle coordination and loss of control of movement with varying manifestations due to differences in severity, in the site of cerebellar damage and in the involvement of extracerebellar tissues. Cerebellar ataxia may be sporadic, acquired, and hereditary. Hereditary ataxia accounts for the majority of cases. Hereditary ataxia has been tentatively divided into several subtypes by scientists in the field, and nearly all of them remain incurable. This is mainly because the detailed mechanisms of these cerebellar disorders are incompletely understood. To precisely diagnose and treat these diseases, studies on their molecular mechanisms have been conducted extensively in the past. Accumulating evidence has demonstrated that some common pathogenic mechanisms exist within each subtype of inherited ataxia. However, no reports have indicated whether there is a common mechanism among the different subtypes of inherited cerebellar ataxia. In this review, we summarize the available references and databases on neurological disorders characterized by cerebellar ataxia and show that a subset of genes involved in lipid homeostasis form a new group that may cause ataxic disorders through a common mechanism. This common signaling pathway can provide a valuable reference for future diagnosis and treatment of ataxic disorders.
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Affiliation(s)
- Jin Zhao
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China
| | - Huan Zhang
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China
| | - Xueyu Fan
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China
| | - Xue Yu
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China
| | - Jisen Huai
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China.
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China.
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34
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Ogawa S, Darhan H, Suzuki K. Genetic and genomic analysis of oxygen consumption in mice. J Anim Breed Genet 2022; 139:596-610. [PMID: 35608337 DOI: 10.1111/jbg.12721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/07/2022] [Indexed: 12/16/2022]
Abstract
We estimated genetic parameters for oxygen consumption (OC), OC per metabolic body weight (OCMBW) and body weight at three through 8 weeks of age in divergently selected mice populations, with an animal model considering maternal genetic, common litter environmental and cytoplasmic inheritance effects. Cytoplasmic inheritance was considered based on maternal lineage information. With respect to OC, estimated direct heritability was moderate (0.32) and the estimated proportion of the variance of cytoplasmic inheritance effects to the phenotypic variance was very low (0.01), implying that causal genes for OC could be located on autosomes. To assess this hypothesis, we attempted to identify possible candidate causal genes through selective signature detection with the results of pooled whole-genome resequencing using pooled DNA samples from high and low OC mice. We made a list of possible candidate causal genes for OC, including those relating to electron transport chain and ATP-binding proteins (Ndufa12, Sdhc, Atp10b, etc.), Prr16 encoding Largen protein, Cry1 encoding a key component of the circadian core oscillator and so on. The results, although careful interpretation must be required, could contribute to elucidate the genetic mechanism of OC, an indicator for maintenance energy requirement, and therefore feed efficiency.
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Affiliation(s)
- Shinichiro Ogawa
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Hongyu Darhan
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Keiichi Suzuki
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
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35
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Kaminska J, Soczewka P, Rzepnikowska W, Zoladek T. Yeast as a Model to Find New Drugs and Drug Targets for VPS13-Dependent Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23095106. [PMID: 35563497 PMCID: PMC9104724 DOI: 10.3390/ijms23095106] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 12/10/2022] Open
Abstract
Mutations in human VPS13A-D genes result in rare neurological diseases, including chorea-acanthocytosis. The pathogenesis of these diseases is poorly understood, and no effective treatment is available. As VPS13 genes are evolutionarily conserved, the effects of the pathogenic mutations could be studied in model organisms, including yeast, where one VPS13 gene is present. In this review, we summarize advancements obtained using yeast. In recent studies, vps13Δ and vps13-I2749 yeast mutants, which are models of chorea-acanthocytosis, were used to screen for multicopy and chemical suppressors. Two of the suppressors, a fragment of the MYO3 and RCN2 genes, act by downregulating calcineurin activity. In addition, vps13Δ suppression was achieved by using calcineurin inhibitors. The other group of multicopy suppressors were genes: FET4, encoding iron transporter, and CTR1, CTR3 and CCC2, encoding copper transporters. Mechanisms of their suppression rely on causing an increase in the intracellular iron content. Moreover, among the identified chemical suppressors were copper ionophores, which require a functional iron uptake system for activity, and flavonoids, which bind iron. These findings point at areas for further investigation in a higher eukaryotic model of VPS13-related diseases and to new therapeutic targets: calcium signalling and copper and iron homeostasis. Furthermore, the identified drugs are interesting candidates for drug repurposing for these diseases.
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Affiliation(s)
- Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Piotr Soczewka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Weronika Rzepnikowska
- Neuromuscular Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
- Correspondence:
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36
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Abstract
Endosomal sorting complex required for transport (ESCRT) proteins can promote extreme membrane deformations, including scission and sealing. New work uncovers a link between these proteins and the early secretory pathway that is functionally important for programmed autophagy during Drosophila development.
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Affiliation(s)
- Leticia Lemus
- Department of Genetics, University of Seville, Av. Reina Mercedes 6, 41012 Seville, Spain.
| | - Veit Goder
- Department of Genetics, University of Seville, Av. Reina Mercedes 6, 41012 Seville, Spain.
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37
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Jetto CT, Nambiar A, Manjithaya R. Mitophagy and Neurodegeneration: Between the Knowns and the Unknowns. Front Cell Dev Biol 2022; 10:837337. [PMID: 35392168 PMCID: PMC8981085 DOI: 10.3389/fcell.2022.837337] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/24/2022] [Indexed: 12/11/2022] Open
Abstract
Macroautophagy (henceforth autophagy) an evolutionary conserved intracellular pathway, involves lysosomal degradation of damaged and superfluous cytosolic contents to maintain cellular homeostasis. While autophagy was initially perceived as a bulk degradation process, a surfeit of studies in the last 2 decades has revealed that it can also be selective in choosing intracellular constituents for degradation. In addition to the core autophagy machinery, these selective autophagy pathways comprise of distinct molecular players that are involved in the capture of specific cargoes. The diverse organelles that are degraded by selective autophagy pathways are endoplasmic reticulum (ERphagy), lysosomes (lysophagy), mitochondria (mitophagy), Golgi apparatus (Golgiphagy), peroxisomes (pexophagy) and nucleus (nucleophagy). Among these, the main focus of this review is on the selective autophagic pathway involved in mitochondrial turnover called mitophagy. The mitophagy pathway encompasses diverse mechanisms involving a complex interplay of a multitude of proteins that confers the selective recognition of damaged mitochondria and their targeting to degradation via autophagy. Mitophagy is triggered by cues that signal the mitochondrial damage such as disturbances in mitochondrial fission-fusion dynamics, mitochondrial membrane depolarisation, enhanced ROS production, mtDNA damage as well as developmental cues such as erythrocyte maturation, removal of paternal mitochondria, cardiomyocyte maturation and somatic cell reprogramming. As research on the mechanistic aspects of this complex pathway is progressing, emerging roles of new players such as the NIPSNAP proteins, Miro proteins and ER-Mitochondria contact sites (ERMES) are being explored. Although diverse aspects of this pathway are being investigated in depth, several outstanding questions such as distinct molecular players of basal mitophagy, selective dominance of a particular mitophagy adapter protein over the other in a given physiological condition, molecular mechanism of how specific disease mutations affect this pathway remain to be addressed. In this review, we aim to give an overview with special emphasis on molecular and signalling pathways of mitophagy and its dysregulation in neurodegenerative disorders.
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Affiliation(s)
- Cuckoo Teresa Jetto
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Akshaya Nambiar
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Ravi Manjithaya
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
- *Correspondence: Ravi Manjithaya,
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38
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Fleming A, Bourdenx M, Fujimaki M, Karabiyik C, Krause GJ, Lopez A, Martín-Segura A, Puri C, Scrivo A, Skidmore J, Son SM, Stamatakou E, Wrobel L, Zhu Y, Cuervo AM, Rubinsztein DC. The different autophagy degradation pathways and neurodegeneration. Neuron 2022; 110:935-966. [PMID: 35134347 PMCID: PMC8930707 DOI: 10.1016/j.neuron.2022.01.017] [Citation(s) in RCA: 171] [Impact Index Per Article: 85.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/31/2021] [Accepted: 01/11/2022] [Indexed: 12/11/2022]
Abstract
The term autophagy encompasses different pathways that route cytoplasmic material to lysosomes for degradation and includes macroautophagy, chaperone-mediated autophagy, and microautophagy. Since these pathways are crucial for degradation of aggregate-prone proteins and dysfunctional organelles such as mitochondria, they help to maintain cellular homeostasis. As post-mitotic neurons cannot dilute unwanted protein and organelle accumulation by cell division, the nervous system is particularly dependent on autophagic pathways. This dependence may be a vulnerability as people age and these processes become less effective in the brain. Here, we will review how the different autophagic pathways may protect against neurodegeneration, giving examples of both polygenic and monogenic diseases. We have considered how autophagy may have roles in normal CNS functions and the relationships between these degradative pathways and different types of programmed cell death. Finally, we will provide an overview of recently described strategies for upregulating autophagic pathways for therapeutic purposes.
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Affiliation(s)
- Angeleen Fleming
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK; UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Mathieu Bourdenx
- Université de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France
| | - Motoki Fujimaki
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK; UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Cansu Karabiyik
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK; UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Gregory J Krause
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ana Lopez
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK; UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Adrián Martín-Segura
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Claudia Puri
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK; UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Aurora Scrivo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John Skidmore
- The ALBORADA Drug Discovery Institute, University of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, UK
| | - Sung Min Son
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK; UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Eleanna Stamatakou
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK; UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Lidia Wrobel
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK; UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Ye Zhu
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK; UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - David C Rubinsztein
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK; UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
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39
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Melia TJ, Reinisch KM. A possible role for VPS13-family proteins in bulk lipid transfer, membrane expansion and organelle biogenesis. J Cell Sci 2022; 135:jcs259357. [PMID: 35267021 PMCID: PMC8976877 DOI: 10.1242/jcs.259357] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
At organelle-organelle contact sites, proteins have long been known to facilitate the rapid movement of lipids. Classically, this lipid transport involves the extraction of single lipids into a hydrophobic pocket on a lipid transport protein. Recently, a new class of lipid transporter has been described with physical characteristics that suggest these proteins are likely to function differently. They possess long hydrophobic tracts that can bind many lipids at once and physically span the entire gulf between membranes at contact sites, suggesting that they may act as bridges to facilitate bulk lipid flow. Here, we review what has been learned regarding the structure and function of this class of lipid transporters, whose best characterized members are VPS13 and ATG2 proteins, and their apparent coordination with other lipid-mobilizing proteins on organelle membranes. We also discuss the prevailing hypothesis in the field, that this type of lipid transport may facilitate membrane expansion through the bulk delivery of lipids, as well as other emerging hypotheses and questions surrounding these novel lipid transport proteins.
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Affiliation(s)
- Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Karin M. Reinisch
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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40
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Whole-exome sequencing confirms implication of VPS13D as a potential cause of progressive spastic ataxia. BMC Neurol 2022; 22:53. [PMID: 35151251 PMCID: PMC8840315 DOI: 10.1186/s12883-022-02553-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/09/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
VPS13D is a large ubiquitin-binding protein playing an essential role in mitophagy by regulating mitochondrial fission. Recently, VPS13D biallelic pathogenic variants have been reported in patients displaying variable neurological phenotypes, with an autosomic recessive inheritance.
The objectives of the study were to determine the genetic etiology of a patient with early onset sporadic progressive spastic ataxia, and to investigate the pathogenicity of VPS13D variants through functional studies on patient’s skin fibroblasts.
Case presentation
We report the case of a 51-year-old patient with spastic ataxia, with an acute onset of the disease at age 7. Walking difficulties slowly worsened over time, with the use of a wheelchair since age 26. We have used trio-based whole-exome sequencing (WES) to identify genes associated with spastic ataxia. The impact of the identified variants on mitochondrial function was assessed in patient’s fibroblasts by imaging mitochondrial network and measuring level of individual OXPHOS complex subunits. Compound heterozygous variants were identified in VPS13D: c.946C > T, p.Arg316* and c.12416C > T, p.(Ala4139Val). Primary fibroblasts obtained from this patient revealed an altered mitochondrial morphology, and a decrease in levels of proteins from complex I, III and IV.
Conclusions
Our findings confirmed implication of VPS13D in spastic ataxia and provided further support for mitochondrial defects in patient’s skin fibroblasts with VPS13D variants. This report of long-term follow up showed a slowly progressive course of the spastic paraplegia with cerebellar features. Furthermore, the performed functional studies could be used as biomarker helping diagnosis of VPS13D-related neurological disorders when molecular results are uneasy to interpret.
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41
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Wang R, Miao G, Shen JL, Fortier TM, Baehrecke EH. ESCRT dysfunction compromises endoplasmic reticulum maturation and autophagosome biogenesis in Drosophila. Curr Biol 2022; 32:1262-1274.e4. [PMID: 35134326 PMCID: PMC8969116 DOI: 10.1016/j.cub.2022.01.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/09/2021] [Accepted: 01/13/2022] [Indexed: 12/20/2022]
Abstract
Autophagy targets cytoplasmic materials for degradation and influences cell health. Organelle contact and trafficking systems provide membranes for autophagosome formation, but how different membrane systems are selected for use during autophagy remains unclear. Here, we report a novel function of the endosomal sorting complex required for transport (ESCRT) in the regulation of endoplasmic reticulum (ER) coat protein complex II (COPII) vesicle formation that influences autophagy. The ESCRT functions in a pathway upstream of Vps13D to influence COPII vesicle transport, ER-Golgi intermediate compartment (ERGIC) assembly, and autophagosome formation. Atg9 functions downstream of the ESCRT to facilitate ERGIC and autophagosome formation. Interestingly, cells lacking either ESCRT or Vps13D functions exhibit dilated ER structures that are similar to cranio-lenticulo-sutural dysplasia patient cells with SEC23A mutations, which encodes a component of COPII vesicles. Our data reveal a novel ESCRT-dependent pathway that influences the ERGIC and autophagosome formation.
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Affiliation(s)
- Ruoxi Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Guangyan Miao
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James L Shen
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Tina M Fortier
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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42
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Huang X, Fan DS. Autosomal recessive spinocerebellar ataxia type 4 with a VPS13D mutation: A case report. World J Clin Cases 2022; 10:703-708. [PMID: 35097097 PMCID: PMC8771376 DOI: 10.12998/wjcc.v10.i2.703] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/03/2021] [Accepted: 12/03/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Autosomal recessive spinocerebellar ataxia type 4 (SCAR4) is a type of SCA that is a group of hereditary diseases characterized by gait ataxia. The main clinical features of SCAR4 are progressive cerebellar ataxia, pyramidal signs, neuropathy, and macrosaccadic intrusions. To date, many gene dysfunctions have been reported to be associated with SCAR4.
CASE SUMMARY Here, we report a novel compound heterozygous mutation, c.3288delA (p.Asp1097ThrfsTer6), in the VPS13D gene in a young female Chinese patient. The patient found something wrong with her legs about 10 years ago and presented with the typical characteristics of SCAR4 when she came to the hospital, including ataxia, neuropathy, and positive pyramidal signs. She was then diagnosed with SCAR4 and went home with symptomatic schemes.
CONCLUSION SCAR4 is a hereditary disease characterized by ataxia, pyramidal signs, neuropathy, and macrosaccadic intrusions. We report a novel compound heterozygous mutation, c.3288delA (p.Asp1097ThrfsTer6), in the VPS13D gene, which enriches the gene mutation spectrum and provides additional information about SCAR4.
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Affiliation(s)
- Xin Huang
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China
- Municipal Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing 100191, China
| | - Dong-Sheng Fan
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China
- Municipal Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing 100191, China
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43
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Levine TP. Sequence Analysis and Structural Predictions of Lipid Transfer Bridges in the Repeating Beta Groove (RBG) Superfamily Reveal Past and Present Domain Variations Affecting Form, Function and Interactions of VPS13, ATG2, SHIP164, Hobbit and Tweek. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:251525642211343. [PMID: 36571082 PMCID: PMC7613979 DOI: 10.1177/25152564221134328] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Lipid transfer between organelles requires proteins that shield the hydrophobic portions of lipids as they cross the cytoplasm. In the last decade a new structural form of lipid transfer protein (LTP) has been found: long hydrophobic grooves made of beta-sheet that bridge between organelles at membrane contact sites. Eukaryotes have five families of bridge-like LTPs: VPS13, ATG2, SHIP164, Hobbit and Tweek. These are unified into a single superfamily through their bridges being composed of just one domain, called the repeating beta groove (RBG) domain, which builds into rod shaped multimers with a hydrophobic-lined groove and hydrophilic exterior. Here, sequences and predicted structures of the RBG superfamily were analyzed in depth. Phylogenetics showed that the last eukaryotic common ancestor contained all five RBG proteins, with duplicated VPS13s. The current set of long RBG protein appears to have arisen in even earlier ancestors from shorter forms with 4 RBG domains. The extreme ends of most RBG proteins have amphipathic helices that might be an adaptation for direct or indirect bilayer interaction, although this has yet to be tested. The one exception to this is the C-terminus of SHIP164, which instead has a coiled-coil. Finally, the exterior surfaces of the RBG bridges are shown to have conserved residues along most of their length, indicating sites for partner interactions almost all of which are unknown. These findings can inform future cell biological and biochemical experiments.
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Lei Y, Wen X, Klionsky DJ. Vps13 is required for efficient autophagy in Saccharomyces cerevisiae. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:25152564221136388. [PMID: 37151407 PMCID: PMC10162780 DOI: 10.1177/25152564221136388] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/14/2022] [Indexed: 05/09/2023]
Abstract
Vps13 is a large, conserved protein that transports lipids between membranes. Its localization at multiple organelle membranes and membrane contact sites suggests its important physiological roles. In addition, the high correlation of mutant VPS13 with certain diseases, especially those involving neurodegeneration, makes this protein of considerable biomedical interest. Taking advantage of the fact that yeasts only have one Vps13 protein, the roles of yeast Vps13 have been well studied. However, whether and how Vps13 functions in macroautophagy/autophagy, a process of degradation of cytoplasmic cargoes, have been elusive questions. In this paper, we investigated the role of Vps13 in both non-selective and selective autophagy and found that this protein participates in non-selective autophagy, reticulophagy and pexophagy, but not mitophagy, and that Vps13 plays a role in the late stage of autophagy.
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Affiliation(s)
- Yuchen Lei
- Life Sciences Institute, and the Department
of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xin Wen
- Life Sciences Institute, and the Department
of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J Klionsky
- Life Sciences Institute, and the Department
of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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45
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Naruse M, Ishigamori R, Imai T. The Unique Genetic and Histological Characteristics of DMBA-Induced Mammary Tumors in an Organoid-Based Carcinogenesis Model. Front Genet 2021; 12:765131. [PMID: 34912374 PMCID: PMC8666664 DOI: 10.3389/fgene.2021.765131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/29/2021] [Indexed: 01/23/2023] Open
Abstract
Here, we report a model system using in vitro 7,12-dimethylbenz[a]anthracene (DMBA; 0.6 μM)-treated mammary tissue-derived organoids generated from heterozygous BALB/c-Trp53 knockout mice to induce tumors after injection into the nude mouse subcutis. In parallel, a single oral dose of DMBA (50 mg/kg bodyweight) to the same murine strain induced mammary adenocarcinomas, characterized by biphasic structures differentiated into luminal and myoepithelial lineages and frequent Hras mutations at codon 61. In the present study, the genetic and histological characteristics of DMBA-induced tumors in the organoid-based model were evaluated to validate its similarities to the in vivo study. The organoid-derived tumors were low-grade adenocarcinomas composed of luminal and basal/myoepithelial cells. When the organoid-derived carcinomas were passaged to other nude mice, they partly progressed to squamous cell carcinomas (SCCs). Whole exome sequencing revealed no mutations at Hras codon 61 in the organoid-derived tumors. However, various mutations were detected in other genes such as Tusc3 and Tgfbr2, which have been reported as cancer-associated or homeostatic squamous cell genes. The most common mutational pattern observed in these genes were the G:C to T:A transversions and G:C to A:T transitions, which are not typical of the mutations caused by DMBA treatment. In conclusion, DMBA exhibited carcinogenicity in the both the ex vivo and in vivo mammary carcinogenesis models, albeit with distinct histological and genetical alterations. Further studies are needed to clarify whether organoid-based carcinogenesis models generated following chemical treatment in vitro could be applied to the clarification of the novel mode of action of chemical carcinogenesis.
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Affiliation(s)
- Mie Naruse
- Central Animal Division, National Cancer Center Research Institute, Tokyo, Japan
| | - Rikako Ishigamori
- Central Animal Division, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshio Imai
- Central Animal Division, National Cancer Center Research Institute, Tokyo, Japan
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46
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Tzou FY, Wen JK, Yeh JY, Huang SY, Chen GC, Chan CC. Drosophila as a model to study autophagy in neurodegenerative diseases and digestive tract. IUBMB Life 2021; 74:339-360. [PMID: 34874101 DOI: 10.1002/iub.2583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/08/2021] [Accepted: 11/15/2021] [Indexed: 12/20/2022]
Abstract
Autophagy regulates cellular homeostasis by degrading and recycling cytosolic components and damaged organelles. Disruption of autophagic flux has been shown to induce or facilitate neurodegeneration and accumulation of autophagic vesicles is overt in neurodegenerative diseases. The fruit fly Drosophila has been used as a model system to identify new factors that regulate physiology and disease. Here we provide a historical perspective of how the fly models have offered mechanistic evidence to understand the role of autophagy in neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, Charcot-Marie-Tooth neuropathy, and polyglutamine disorders. Autophagy also plays a pivotal role in maintaining tissue homeostasis and protecting organism health. The gastrointestinal tract regulates organism health by modulating food intake, energy balance, and immunity. Growing evidence is strengthening the link between autophagy and digestive tract health in recent years. Here, we also discuss how the fly models have advanced the understanding of digestive physiology regulated by autophagy.
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Affiliation(s)
- Fei-Yang Tzou
- Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan
| | - Jung-Kun Wen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Jui-Yu Yeh
- Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan
| | - Shu-Yi Huang
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Guang-Chao Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chih-Chiang Chan
- Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan
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47
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Shen JL, Fortier TM, Wang R, Baehrecke EH. Vps13D functions in a Pink1-dependent and Parkin-independent mitophagy pathway. J Cell Biol 2021; 220:212607. [PMID: 34459871 PMCID: PMC8406608 DOI: 10.1083/jcb.202104073] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/27/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022] Open
Abstract
Defects in autophagy cause problems in metabolism, development, and disease. The autophagic clearance of mitochondria, mitophagy, is impaired by the loss of Vps13D. Here, we discover that Vps13D regulates mitophagy in a pathway that depends on the core autophagy machinery by regulating Atg8a and ubiquitin localization. This process is Pink1 dependent, with loss of pink1 having similar autophagy and mitochondrial defects as loss of vps13d. The role of Pink1 has largely been studied in tandem with Park/Parkin, an E3 ubiquitin ligase that is widely considered to be crucial in Pink1-dependent mitophagy. Surprisingly, we find that loss of park does not exhibit the same autophagy and mitochondrial deficiencies as vps13d and pink1 mutant cells and contributes to mitochondrial clearance through a pathway that is parallel to vps13d. These findings provide a Park-independent pathway for Pink1-regulated mitophagy and help to explain how Vps13D regulates autophagy and mitochondrial morphology and contributes to neurodegenerative diseases.
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Affiliation(s)
- James L Shen
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Tina M Fortier
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Ruoxi Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
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48
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Lechado Terradas A, Zittlau KI, Macek B, Fraiberg M, Elazar Z, Kahle PJ. Regulation of mitochondrial cargo-selective autophagy by posttranslational modifications. J Biol Chem 2021; 297:101339. [PMID: 34688664 PMCID: PMC8591368 DOI: 10.1016/j.jbc.2021.101339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/18/2022] Open
Abstract
Mitochondria are important organelles in eukaryotes. Turnover and quality control of mitochondria are regulated at the transcriptional and posttranslational level by several cellular mechanisms. Removal of defective mitochondrial proteins is mediated by mitochondria resident proteases or by proteasomal degradation of individual proteins. Clearance of bulk mitochondria occurs via a selective form of autophagy termed mitophagy. In yeast and some developing metazoan cells (e.g., oocytes and reticulocytes), mitochondria are largely removed by ubiquitin-independent mechanisms. In such cases, the regulation of mitophagy is mediated via phosphorylation of mitochondria-anchored autophagy receptors. On the other hand, ubiquitin-dependent recruitment of cytosolic autophagy receptors occurs in situations of cellular stress or disease, where dysfunctional mitochondria would cause oxidative damage. In mammalian cells, a well-studied ubiquitin-dependent mitophagy pathway induced by mitochondrial depolarization is regulated by the mitochondrial protein kinase PINK1, which upon activation recruits the ubiquitin ligase parkin. Here, we review mechanisms of mitophagy with an emphasis on posttranslational modifications that regulate various mitophagy pathways. We describe the autophagy components involved with particular emphasis on posttranslational modifications. We detail the phosphorylations mediated by PINK1 and parkin-mediated ubiquitylations of mitochondrial proteins that can be modulated by deubiquitylating enzymes. We also discuss the role of accessory factors regulating mitochondrial fission/fusion and the interplay with pro- and antiapoptotic Bcl-2 family members. Comprehensive knowledge of the processes of mitophagy is essential for the understanding of vital mitochondrial turnover in health and disease.
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Affiliation(s)
- Anna Lechado Terradas
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | | | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Milana Fraiberg
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Zvulun Elazar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Philipp J Kahle
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
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Hirano T, Suzuki N, Ikenaka Y, Hoshi N, Tabuchi Y. Neurotoxicity of a pyrethroid pesticide deltamethrin is associated with the imbalance in proteolytic systems caused by mitophagy activation and proteasome inhibition. Toxicol Appl Pharmacol 2021; 430:115723. [PMID: 34520793 DOI: 10.1016/j.taap.2021.115723] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 12/23/2022]
Abstract
Pyrethroids are one of the most commonly used classes of synthetic pesticides in the world. Recent laboratory and epidemiological evidence suggested that pyrethroids have potential adverse effects in the mammalian brain; however, the underlying mechanisms of the neurotoxic effects of pyrethroids have not been fully elucidated. In the present study, we investigated the mechanisms of effects of a type II pyrethroid deltamethrin (DM) in a neuronal cell model focusing on the proteolytic function, including autophagy and the ubiquitin-proteasome system. We confirmed that a micromolar concentration of DM dose-dependently decreased the cell viability and induced apoptotic cell death. Our results showed that DM enhanced autophagy in association with an accumulation of autophagosomes and increase in the levels of autophagy markers LC3-II/LC3-I ratio and p62 which were much elevated in the presence of lysosomal inhibitors bafilomycin A1 and chloroquine. We also found that DM caused a dysfunction of mitochondria with a decrease of mitochondrial membrane potential and mitochondrial DNA copy number as well as colocalization with autophagosomes. Moreover, a decrease in the activities of three major proteasomal enzymes and an accumulation of ubiquitinated proteins were observed by the exposure to DM. Transcriptome analysis revealed that up-regulated genes supported the activation of autophagy with induction of cellular stress responses including oxidative stress and endoplasmic reticulum stress, while down-regulated genes related to the cell cycle and DNA replication. These findings provide novel insights into the neurotoxicity of DM which underlie the imbalance in proteolytic function caused by mitophagy activation and proteasome inhibition.
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Affiliation(s)
- Tetsushi Hirano
- Life Science Research Center, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0194, Japan.
| | - Nihei Suzuki
- Life Science Research Center, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0194, Japan
| | - Yoshinori Ikenaka
- Translational Research Unit, Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Kita 18, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-0818, Japan; Water Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa; One Health Research Center, Hokkaido University, Kita 18, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-0818, Japan; Laboratory of Toxicology, Department of Environmental Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita 18, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-0818, Japan
| | - Nobuhiko Hoshi
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Kobe, Hyogo 657-8501, Japan
| | - Yoshiaki Tabuchi
- Life Science Research Center, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0194, Japan
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DRP1-Mediated Mitochondrial Fission Regulates Lung Epithelial Response to Allergen. Int J Mol Sci 2021; 22:ijms222011125. [PMID: 34681784 PMCID: PMC8540036 DOI: 10.3390/ijms222011125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/11/2021] [Indexed: 12/17/2022] Open
Abstract
Mitochondria regulate a myriad of cellular functions. Dysregulation of mitochondrial control within airway epithelial cells has been implicated in the pro-inflammatory response to allergens in asthma patients. Because of their multifaceted nature, mitochondrial structure must be tightly regulated through fission and fusion. Dynamin Related Protein 1 (DRP1) is a key driver of mitochondrial fission. During allergic asthma, airway epithelial mitochondria appear smaller and structurally altered. The role of DRP1-mediated mitochondrial fission, however, has not been fully elucidated in epithelial response to allergens. We used a Human Bronchial Epithelial Cell line (HBECs), primary Mouse Tracheal Epithelial Cells (MTECs), and conditional DRP1 ablation in lung epithelial cells to investigate the impact of mitochondrial fission on the pro-inflammatory response to house dust mite (HDM) in vitro and in vivo. Our data suggest that, following HDM challenge, mitochondrial fission is rapidly upregulated in airway epithelial cells and precedes production of pro-inflammatory cytokines and chemokines. Further, deletion of Drp1 in lung epithelial cells leads to decreased fission and enhanced pro-inflammatory signaling in response to HDM in vitro, as well as enhanced airway hyper-responsiveness (AHR), inflammation, differential mucin transcription, and epithelial cell death in vivo. Mitochondrial fission, therefore, regulates the lung epithelial pro-inflammatory response to HDM.
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