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Lin K, Cai J, Guo J, Zhang H, Sun G, Wang X, Zhu K, Xue Q, Zhu F, Wang P, Yuan G, Sun Y, Wang S, Ai J, Zhang W. Multi-omics landscapes reveal heterogeneity in long COVID patients characterized with enhanced neutrophil activity. J Transl Med 2024; 22:753. [PMID: 39135185 PMCID: PMC11318262 DOI: 10.1186/s12967-024-05560-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/30/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Omicron variant impacts populations with its rapid contagiousness, and part of patients suffered from persistent symptoms termed as long COVID. The molecular and immune mechanisms of this currently dominant global variant leading to long COVID remain unclear, due to long COVID heterogeneity across populations. METHODS We recruited 66 participants in total, 22 out of 66 were healthy control without COVID-19 infection history, and 22 complaining about long COVID symptoms 6 months after first infection of Omicron, referred as long COVID (LC) Group. The left ones were defined as non-long COVID (NLC) Group. We profiled them via plasma neutralizing antibody titer, SARS-CoV-2 viral load, transcriptomic and proteomics screening, and machine learning. RESULTS No serum residual SARS-CoV-2 was observed in the participants 6 months post COVID-19 infection. No significant difference in neutralizing antibody titers was found between the long COVID (LC) Group and the non-long COVID (NLC) Group. Transcriptomic and proteomic profiling allow the stratification of long COVID into neutrophil function upregulated (NU-LC) and downregulated types (ND-LC). The NU-LC, identifiable through a refined set of 5 blood gene markers (ABCA13, CEACAM6, CRISP3, CTSG and BPI), displays evidence of relatively higher neutrophil counts and function of degranulation than the ND-LC at 6 months after infection, while recovered at 12 months post COVID-19. CONCLUSION The transcriptomic and proteomic profiling revealed heterogeneity among long COVID patients. We discovered a subgroup of long COVID population characterized by neutrophil activation, which might associate with the development of psychiatric symptoms and indicate a higher inflammatory state. Meanwhile, a cluster of 5 genes was manually curated as the most potent discriminators of NU-LC from long COVID population. This study can serve as a foundational exploration of the heterogeneity in the pathogenesis of long COVID and assist in therapeutic targeting and detailed epidemiological investigation of long COVID.
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Affiliation(s)
- Ke Lin
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianpeng Cai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingxin Guo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China
- Institute of Infection and Health, Fudan University, Shanghai, China
| | - Haocheng Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gangqiang Sun
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xun Wang
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Kun Zhu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Quanlin Xue
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Feng Zhu
- Department of Respiratory and Critical Care Medicine, Affiliated Wuxi Fifth Hospital of Jiangnan University, Wuxi Fifth People's Hospital, Wuxi, People's Republic of China
| | - Pengfei Wang
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Guanmin Yuan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuhan Sun
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Sen Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China.
- Institute of Infection and Health, Fudan University, Shanghai, China.
| | - Jingwen Ai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China.
- Institute of Infection and Health, Fudan University, Shanghai, China.
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China
- Institute of Infection and Health, Fudan University, Shanghai, China
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Yang Y, Lu K, Qian J, Guo J, Xu H, Lu Z. Identification and characterization of ABC proteins in an important rice insect pest, Cnaphalocrocis medinalis unveil their response to Cry1C toxin. Int J Biol Macromol 2023; 237:123949. [PMID: 36894061 DOI: 10.1016/j.ijbiomac.2023.123949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023]
Abstract
Rice leaffolder (Cnaphalocrocis medinalis) is an important insect pest in paddy fields. Due to their essential role in the physiology and insecticidal resistance, ATP-binding cassette (ABC) proteins were studied in many insects. In this study, we identified the ABC proteins in C. medinalis through genomic data and analyzed their molecular characteristics. A total of 37 sequences with nucleotide-binding domain (NBD) were identified as ABC proteins and belonged to eight families (ABCA-ABCH). Four structure styles of ABC proteins were found in C. medinalis, including full structure, half structure, single structure, and ABC2 structure. In addition to these structures, TMD-NBD-TMD, NBD-TMD-NBD, and NBD-TMD-NBD-NBD were found in C. medinalis ABC proteins. Docking studies suggested that in addition to the soluble ABC proteins, other ABC proteins including ABCC4, ABCH1, ABCG3, ABCB5, ABCG1, ABCC7, ABCB3, ABCA3, and ABCC5 binding with Cry1C had higher weighted scores. The upregulation of ABCB1 and downregulation of ABCB3, ABCC1, ABCC7, ABCG1, ABCG3, and ABCG6 were associated with the C. medinalis response to Cry1C toxin. Collectively, these results help elucidate the molecular characteristics of C. medinalis ABC proteins, pave the way for further functional studies of C. medinalis ABC proteins, including their interaction with Cry1C toxin, and provide potential insecticide targets.
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Affiliation(s)
- Yajun Yang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agriculture Sciences, Hangzhou 310021, China
| | - Ke Lu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agriculture Sciences, Hangzhou 310021, China; Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianing Qian
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agriculture Sciences, Hangzhou 310021, China
| | - Jiawen Guo
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agriculture Sciences, Hangzhou 310021, China
| | - Hongxing Xu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agriculture Sciences, Hangzhou 310021, China.
| | - Zhongxian Lu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agriculture Sciences, Hangzhou 310021, China.
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3
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Katzeff JS, Lok HC, Bhatia S, Fu Y, Halliday GM, Kim WS. ATP-binding cassette transporter expression is widely dysregulated in frontotemporal dementia with TDP-43 inclusions. Front Mol Neurosci 2022; 15:1043127. [PMID: 36385764 PMCID: PMC9663841 DOI: 10.3389/fnmol.2022.1043127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/11/2022] [Indexed: 10/17/2023] Open
Abstract
The human brain is highly enriched in lipids and increasing evidence indicates that dysregulation of lipids in the brain is associated with neurodegeneration. ATP-binding cassette subfamily A (ABCA) transporters control the movement of lipids across cellular membranes and are implicated in a number of neurodegenerative diseases. However, very little is known about the role of ABCA transporters in frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), which is a common form of younger-onset dementia. We therefore undertook a comprehensive analysis of the expression of ABCA transporters (ABCA1-13) in five key brain regions (amygdala, inferior temporal cortex, superior frontal cortex, cerebellum and parietal cortex) in FTLD-TDP and controls. We found that the expression of ABCA2, ABCA3, ABCA4, ABCA7, ABCA9, ABCA10 and ABCA13 was significantly altered in FTLD-TDP in a region-specific manner. In addition, the expression of ABCA transporters correlated specifically to different neural markers and TARDBP. These results suggest substantial dysregulation of ABCA transporters and lipid metabolism in FTLD-TDP and these changes are associated with neuroinflammation.
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Affiliation(s)
| | | | | | | | | | - Woojin Scott Kim
- Brain and Mind Centre & School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
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4
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Liu Y, Castano D, Girolamo F, Trigueros-Motos L, Bae HG, Neo SP, Oh J, Narayanaswamy P, Torta F, Rye KA, Jo DG, Gunaratne J, Jung S, Virgintino D, Singaraja RR. Loss of ABCA8B decreases myelination by reducing oligodendrocyte precursor cells in mice. J Lipid Res 2022; 63:100147. [PMID: 34752805 PMCID: PMC8953628 DOI: 10.1016/j.jlr.2021.100147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 01/29/2023] Open
Abstract
The myelin sheath, which is wrapped around axons, is a lipid-enriched structure produced by mature oligodendrocytes. Disruption of the myelin sheath is observed in several neurological diseases, such as multiple sclerosis. A crucial component of myelin is sphingomyelin, levels of which can be increased by ABCA8, a member of the ATP-binding cassette transporter family. ABCA8 is highly expressed in the cerebellum, specifically in oligodendroglia. However, whether ABCA8 plays a role in myelination and mechanisms that would underlie this role remain unknown. Here, we found that the absence of Abca8b, a mouse ortholog of ABCA8, led to decreased numbers of cerebellar oligodendrocyte precursor cells (OPCs) and mature oligodendrocytes in mice. We show that in oligodendrocytes, ABCA8 interacts with chondroitin sulfate proteoglycan 4 (CSPG4), a molecule essential for OPC proliferation, migration, and myelination. In the absence of Abca8b, localization of CSPG4 to the plasma membrane was decreased, contributing to reduced cerebellar CSPG4 expression. Cerebellar CSPG4+ OPCs were also diminished, leading to decreased mature myelinating oligodendrocyte numbers and cerebellar myelination levels in Abca8b-/- mice. In addition, electron microscopy analyses showed that the number of nonmyelinated cerebellar axons was increased, whereas cerebellar myelin thickness (g-ratio), myelin sheath periodicity, and axonal diameter were all decreased, indicative of disordered myelin ultrastructure. In line with disrupted cerebellar myelination, Abca8b-/- mice showed lower cerebellar conduction velocity and disturbed locomotion. In summary, ABCA8 modulates cerebellar myelination, in part through functional regulation of the ABCA8-interacting protein CSPG4. Our findings suggest that ABCA8 disruption may contribute to the pathophysiology of myelin disorders.
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Affiliation(s)
- Yiran Liu
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Cardiovascular Research Institute, National University Health System, Singapore, Singapore
| | - David Castano
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Cardiovascular Research Institute, National University Health System, Singapore, Singapore
| | - Francesco Girolamo
- Department of Basic Medical Sciences, Neurosciences, and Sensory Organs, Human Anatomy and Histology Unit, University of Bari School of Medicine, Bari, Italy
| | - Laia Trigueros-Motos
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore, Singapore
| | - Han-Gyu Bae
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, Singapore, Singapore
| | - Suat Peng Neo
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jeongah Oh
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Pradeep Narayanaswamy
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kerry Anne Rye
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Dong-Gyu Jo
- School of Pharmacy, Sungkyunkwan University, Suwon, Korea
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Sangyong Jung
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, Singapore, Singapore
| | - Daniela Virgintino
- Department of Basic Medical Sciences, Neurosciences, and Sensory Organs, Human Anatomy and Histology Unit, University of Bari School of Medicine, Bari, Italy
| | - Roshni R Singaraja
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Cardiovascular Research Institute, National University Health System, Singapore, Singapore.
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5
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Stepler KE, Gillyard TR, Reed CB, Avery TM, Davis JS, Robinson RA. ABCA7, a Genetic Risk Factor Associated with Alzheimer's Disease Risk in African Americans. J Alzheimers Dis 2022; 86:5-19. [PMID: 35034901 PMCID: PMC10984370 DOI: 10.3233/jad-215306] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
African American/Black adults are twice as likely to have Alzheimer's disease (AD) compared to non-Hispanic White adults. Genetics partially contributes to this disparity in AD risk, among other factors, as there are several genetic variants associated with AD that are more prevalent in individuals of African or European ancestry. The phospholipid-transporting ATPase ABCA7 (ABCA7) gene has stronger associations with AD risk in individuals with African ancestry than in individuals with European ancestry. In fact, ABCA7 has been shown to have a stronger effect size than the apolipoprotein E (APOE) ɛ4 allele in African American/Black adults. ABCA7 is a transmembrane protein involved in lipid homeostasis and phagocytosis. ABCA7 dysfunction is associated with increased amyloid-beta production, reduced amyloid-beta clearance, impaired microglial response to inflammation, and endoplasmic reticulum stress. This review explores the impact of ABCA7 mutations that increase AD risk in African American/Black adults on ABCA7 structure and function and their contributions to AD pathogenesis. The combination of biochemical/biophysical and 'omics-based studies of these variants needed to elucidate their downstream impact and molecular contributions to AD pathogenesis is highlighted.
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Affiliation(s)
| | - Taneisha R. Gillyard
- Meharry Medical College Department of Biochemistry and Cancer Biology, Nashville, TN, USA
| | - Calla B. Reed
- Vanderbilt University Department of Chemistry, Nashville, TN, USA
| | - Tyra M. Avery
- Fisk University Department of Life and Physical Sciences, Nashville, TN, USA
| | - Jamaine S. Davis
- Meharry Medical College Department of Biochemistry and Cancer Biology, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer’s Center Vanderbilt University Medical Center, Nashville, TN, USA
| | - Renã A.S. Robinson
- Vanderbilt University Department of Chemistry, Nashville, TN, USA
- Vanderbilt University Medical Center Department of Neurology, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer’s Center Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute of Chemical Biology, Nashville, TN, USA
- Vanderbilt Brain Institute, Nashville, TN, USA
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6
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Molday RS, Garces FA, Scortecci JF, Molday LL. Structure and function of ABCA4 and its role in the visual cycle and Stargardt macular degeneration. Prog Retin Eye Res 2021; 89:101036. [PMID: 34954332 DOI: 10.1016/j.preteyeres.2021.101036] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 12/17/2022]
Abstract
ABCA4 is a member of the superfamily of ATP-binding cassette (ABC) transporters that is preferentially localized along the rim region of rod and cone photoreceptor outer segment disc membranes. It uses the energy from ATP binding and hydrolysis to transport N-retinylidene-phosphatidylethanolamine (N-Ret-PE), the Schiff base adduct of retinal and phosphatidylethanolamine, from the lumen to the cytoplasmic leaflet of disc membranes. This ensures that all-trans-retinal and excess 11-cis-retinal are efficiently cleared from photoreceptor cells thereby preventing the accumulation of toxic retinoid compounds. Loss-of-function mutations in the gene encoding ABCA4 cause autosomal recessive Stargardt macular degeneration, also known as Stargardt disease (STGD1), and related autosomal recessive retinopathies characterized by impaired central vision and an accumulation of lipofuscin and bis-retinoid compounds. High resolution structures of ABCA4 in its substrate and nucleotide free state and containing bound N-Ret-PE or ATP have been determined by cryo-electron microscopy providing insight into the molecular architecture of ABCA4 and mechanisms underlying substrate recognition and conformational changes induced by ATP binding. The expression and functional characterization of a large number of disease-causing missense ABCA4 variants have been determined. These studies have shed light into the molecular mechanisms underlying Stargardt disease and a classification that reliably predicts the effect of a specific missense mutation on the severity of the disease. They also provide a framework for developing rational therapeutic treatments for ABCA4-associated diseases.
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Affiliation(s)
- Robert S Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada; Department of Ophthalmology & Visual Sciences, University of British Columbia, Vancouver, B.C., Canada.
| | - Fabian A Garces
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
| | | | - Laurie L Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
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7
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Namasivayam V, Stefan K, Pahnke J, Stefan SM. Binding mode analysis of ABCA7 for the prediction of novel Alzheimer's disease therapeutics. Comput Struct Biotechnol J 2021; 19:6490-6504. [PMID: 34976306 PMCID: PMC8666613 DOI: 10.1016/j.csbj.2021.11.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 12/17/2022] Open
Abstract
The adenosine-triphosphate-(ATP)-binding cassette (ABC) transporter ABCA7 is a genetic risk factor for Alzheimer's disease (AD). Defective ABCA7 promotes AD development and/or progression. Unfortunately, ABCA7 belongs to the group of 'under-studied' ABC transporters that cannot be addressed by small-molecules. However, such small-molecules would allow for the exploration of ABCA7 as pharmacological target for the development of new AD diagnostics and therapeutics. Pan-ABC transporter modulators inherit the potential to explore under-studied ABC transporters as novel pharmacological targets by potentially binding to the proposed 'multitarget binding site'. Using the recently reported cryogenic-electron microscopy (cryo-EM) structures of ABCA1 and ABCA4, a homology model of ABCA7 has been generated. A set of novel, diverse, and potent pan-ABC transporter inhibitors has been docked to this ABCA7 homology model for the discovery of the multitarget binding site. Subsequently, application of pharmacophore modelling identified the essential pharmacophore features of these compounds that may support the rational drug design of innovative diagnostics and therapeutics against AD.
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Key Words
- ABC transporter (ABCA1, ABCA4, ABCA7)
- ABC, ATP-binding cassette
- AD, Alzheimer’s disease
- APP, amyloid precursor protein
- ATP, Adenosine-triphosphate
- Alzheimer’s disease (AD)
- BBB, blood-brain barrier
- BODIPY-cholesterol, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene-cholesterol
- ECD, extracellular domain
- EH, extracellular helix
- GSH, reduced glutathione
- HTS, high-throughput screening
- IC, intracellular helix
- MOE, Molecular Operating Environment
- MSD, membrane spanning domain
- Multitarget modulation (PANABC)
- NBD, nucleotide binding domain
- NBD-cholesterol, 7-nitro-2-1,3-benzoxadiazol-4-yl-cholesterol
- PDB, protein data bank
- PET tracer (PETABC)
- PET, positron emission tomography
- PLIF, protein ligand interaction
- PSO, particle swarm optimization
- Polypharmacology
- R-domain/region, regulatory domain/region
- RMSD, root mean square distance
- Rational drug design and development
- SNP, single-nucleotide polymorphism
- TM, transmembrane helix
- cryo-EM, cryogenic-electron microscopy
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Affiliation(s)
- Vigneshwaran Namasivayam
- Department of Pharmaceutical and Cellbiological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Katja Stefan
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab (www.pahnkelab.eu), University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway
| | - Jens Pahnke
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab (www.pahnkelab.eu), University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway
- LIED, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
- Department of Pharmacology, Faculty of Medicine, University of Latvia, Jelgavas iela 1, 1004 Rīga, Latvia
| | - Sven Marcel Stefan
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab (www.pahnkelab.eu), University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway
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8
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Sharma P, Singh N, Sharma S. ATP binding cassette transporters and cancer: revisiting their controversial role. Pharmacogenomics 2021; 22:1211-1235. [PMID: 34783261 DOI: 10.2217/pgs-2021-0116] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The expression of ATP-binding cassette transporter (ABC transporters) has been reported in various tissues such as the lung, liver, kidney, brain and intestine. These proteins account for the efflux of different compounds and metabolites across the membrane, thus decreasing the concentration of the toxic compounds. ABC transporter genes play a vital role in the development of multidrug resistance, which is the main obstacle that hinders the success of chemotherapy. Preclinical and clinical trials have investigated the probability of overcoming drug-associated resistance and substantial toxicities. The focus has been put on several strategies to overcome multidrug resistance. These strategies include the development of modulators that can modulate ABC transporters. This knowledge can be translated for clinical oncology treatment in the future.
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Affiliation(s)
- Parul Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, India
| | - Navneet Singh
- Department of Pulmonary medicine, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, India
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9
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Scortecci JF, Molday LL, Curtis SB, Garces FA, Panwar P, Van Petegem F, Molday RS. Cryo-EM structures of the ABCA4 importer reveal mechanisms underlying substrate binding and Stargardt disease. Nat Commun 2021; 12:5902. [PMID: 34625547 PMCID: PMC8501128 DOI: 10.1038/s41467-021-26161-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/20/2021] [Indexed: 12/04/2022] Open
Abstract
ABCA4 is an ATP-binding cassette (ABC) transporter that flips N-retinylidene-phosphatidylethanolamine (N-Ret-PE) from the lumen to the cytoplasmic leaflet of photoreceptor membranes. Loss-of-function mutations cause Stargardt disease (STGD1), a macular dystrophy associated with severe vision loss. To define the mechanisms underlying substrate binding and STGD1, we determine the cryo-EM structure of ABCA4 in its substrate-free and bound states. The two structures are similar and delineate an elongated protein with the two transmembrane domains (TMD) forming an outward facing conformation, extended and twisted exocytoplasmic domains (ECD), and closely opposed nucleotide binding domains. N-Ret-PE is wedged between the two TMDs and a loop from ECD1 within the lumen leaflet consistent with a lateral access mechanism and is stabilized through hydrophobic and ionic interactions with residues from the TMDs and ECDs. Our studies provide a framework for further elucidating the molecular mechanism associated with lipid transport and disease and developing promising disease interventions.
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Affiliation(s)
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Susan B Curtis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Fabian A Garces
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Pankaj Panwar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC, Canada.
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10
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Carregosa D, Mota S, Ferreira S, Alves-Dias B, Loncarevic-Vasiljkovic N, Crespo CL, Menezes R, Teodoro R, dos Santos CN. Overview of Beneficial Effects of (Poly)phenol Metabolites in the Context of Neurodegenerative Diseases on Model Organisms. Nutrients 2021; 13:2940. [PMID: 34578818 PMCID: PMC8464690 DOI: 10.3390/nu13092940] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/18/2022] Open
Abstract
The rise of neurodegenerative diseases in an aging population is an increasing problem of health, social and economic consequences. Epidemiological and intervention studies have demonstrated that diets rich in (poly)phenols can have potent health benefits on cognitive decline and neurodegenerative diseases. Meanwhile, the role of gut microbiota is ever more evident in modulating the catabolism of (poly)phenols to dozens of low molecular weight (poly)phenol metabolites that have been identified in plasma and urine. These metabolites can reach circulation in higher concentrations than parent (poly)phenols and persist for longer periods of time. However, studies addressing their potential brain effects are still lacking. In this review, we will discuss different model organisms that have been used to study how low molecular weight (poly)phenol metabolites affect neuronal related mechanisms gathering critical insight on their potential to tackle the major hallmarks of neurodegeneration.
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Affiliation(s)
- Diogo Carregosa
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 1169-056 Lisboa, Portugal; (D.C.); (S.M.); (S.F.); (B.A.-D.); (N.L.-V.); (C.L.C.); (R.M.); (R.T.)
| | - Sara Mota
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 1169-056 Lisboa, Portugal; (D.C.); (S.M.); (S.F.); (B.A.-D.); (N.L.-V.); (C.L.C.); (R.M.); (R.T.)
- iBET, Institute of Experimental and Technological Biology, Apartado 12, 2781-901 Oeiras, Portugal
| | - Sofia Ferreira
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 1169-056 Lisboa, Portugal; (D.C.); (S.M.); (S.F.); (B.A.-D.); (N.L.-V.); (C.L.C.); (R.M.); (R.T.)
- CBIOS, University Lusófona’s Research Center for Biosciences & Health Technologies, Campo Grande 376, 1749-024 Lisboa, Portugal
| | - Beatriz Alves-Dias
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 1169-056 Lisboa, Portugal; (D.C.); (S.M.); (S.F.); (B.A.-D.); (N.L.-V.); (C.L.C.); (R.M.); (R.T.)
| | - Natasa Loncarevic-Vasiljkovic
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 1169-056 Lisboa, Portugal; (D.C.); (S.M.); (S.F.); (B.A.-D.); (N.L.-V.); (C.L.C.); (R.M.); (R.T.)
- Department of Neurobiology, Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia
| | - Carolina Lage Crespo
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 1169-056 Lisboa, Portugal; (D.C.); (S.M.); (S.F.); (B.A.-D.); (N.L.-V.); (C.L.C.); (R.M.); (R.T.)
| | - Regina Menezes
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 1169-056 Lisboa, Portugal; (D.C.); (S.M.); (S.F.); (B.A.-D.); (N.L.-V.); (C.L.C.); (R.M.); (R.T.)
- iBET, Institute of Experimental and Technological Biology, Apartado 12, 2781-901 Oeiras, Portugal
- CBIOS, University Lusófona’s Research Center for Biosciences & Health Technologies, Campo Grande 376, 1749-024 Lisboa, Portugal
| | - Rita Teodoro
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 1169-056 Lisboa, Portugal; (D.C.); (S.M.); (S.F.); (B.A.-D.); (N.L.-V.); (C.L.C.); (R.M.); (R.T.)
| | - Cláudia Nunes dos Santos
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 1169-056 Lisboa, Portugal; (D.C.); (S.M.); (S.F.); (B.A.-D.); (N.L.-V.); (C.L.C.); (R.M.); (R.T.)
- iBET, Institute of Experimental and Technological Biology, Apartado 12, 2781-901 Oeiras, Portugal
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11
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ATP-binding cassette transporters and neurodegenerative diseases. Essays Biochem 2021; 65:1013-1024. [PMID: 34415015 DOI: 10.1042/ebc20210012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022]
Abstract
ATP-binding cassette (ABC) transporters are one of the largest groups of transporter families in humans. ABC transporters mediate the translocation of a diverse range of substrates across cellular membranes, including amino acids, nucleosides, lipids, sugars and xenobiotics. Neurodegenerative diseases are a group of brain diseases that detrimentally affect neurons and other brain cells and are usually associated with deposits of pathogenic proteins in the brain. Major neurodegenerative diseases include Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. ABC transporters are highly expressed in the brain and have been implicated in a number of pathological processes underlying neurodegenerative diseases. This review outlines the current understanding of the role of ABC transporters in neurodegenerative diseases, focusing on some of the most important pathways, and also suggests future directions for research in this field.
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Kotlyarov S, Kotlyarova A. The Role of ABC Transporters in Lipid Metabolism and the Comorbid Course of Chronic Obstructive Pulmonary Disease and Atherosclerosis. Int J Mol Sci 2021; 22:6711. [PMID: 34201488 PMCID: PMC8269124 DOI: 10.3390/ijms22136711] [Citation(s) in RCA: 9] [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: 05/12/2021] [Revised: 06/12/2021] [Accepted: 06/18/2021] [Indexed: 12/11/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) ranks among the leading causes of morbidity and mortality worldwide. COPD rarely occurs in isolation and is often combined with various diseases. It is considered that systemic inflammation underlies the comorbid course of COPD. The data obtained in recent years have shown the importance of violations of the cross-links of lipid metabolism and the immune response, which are links in the pathogenesis of both COPD and atherosclerosis. The role of lipid metabolism disorders in the pathogenesis of the comorbid course of COPD and atherosclerosis and the participation of ATP-binding cassette (ABC) transporters in these processes is discussed in this article. It is known that about 20 representatives of a large family of ABC transporters provide lipid homeostasis of cells by moving lipids inside the cell and in its plasma membrane, as well as removing lipids from the cell. It was shown that some representatives of the ABC-transporter family are involved in various links of the pathogenesis of COPD and atherosclerosis, which can determine their comorbid course.
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Affiliation(s)
- Stanislav Kotlyarov
- Department of Nursing, Ryazan State Medical University, 390026 Ryazan, Russia
| | - Anna Kotlyarova
- Department of Pharmacology and Pharmacy, Ryazan State Medical University, 390026 Ryazan, Russia;
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13
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García‐Sanz P, M.F.G. Aerts J, Moratalla R. The Role of Cholesterol in α-Synuclein and Lewy Body Pathology in GBA1 Parkinson's Disease. Mov Disord 2021; 36:1070-1085. [PMID: 33219714 PMCID: PMC8247417 DOI: 10.1002/mds.28396] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disease where dopaminergic neurons in the substantia nigra are lost, resulting in a decrease in striatal dopamine and, consequently, motor control. Dopaminergic degeneration is associated with the appearance of Lewy bodies, which contain membrane structures and proteins, including α-synuclein (α-Syn), in surviving neurons. PD displays a multifactorial pathology and develops from interactions between multiple elements, such as age, environmental conditions, and genetics. Mutations in the GBA1 gene represent one of the major genetic risk factors for PD. This gene encodes an essential lysosomal enzyme called β-glucocerebrosidase (GCase), which is responsible for degrading the glycolipid glucocerebroside into glucose and ceramide. GCase can generate glucosylated cholesterol via transglucosylation and can also degrade the sterol glucoside. Although the molecular mechanisms that predispose an individual to neurodegeneration remain unknown, the role of cholesterol in PD pathology deserves consideration. Disturbed cellular cholesterol metabolism, as reflected by accumulation of lysosomal cholesterol in GBA1-associated PD cellular models, could contribute to changes in lipid rafts, which are necessary for synaptic localization and vesicle cycling and modulation of synaptic integrity. α-Syn has been implicated in the regulation of neuronal cholesterol, and cholesterol facilitates interactions between α-Syn oligomers. In this review, we integrate the results of previous studies and describe the cholesterol landscape in cellular homeostasis and neuronal function. We discuss its implication in α-Syn and Lewy body pathophysiological mechanisms underlying PD, focusing on the role of GCase and cholesterol. © 2020 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Patricia García‐Sanz
- Instituto Cajal, CSICMadridSpain
- Centro de Investigación Biomédica en Red sobre Enfermedades NeurodegenerativasInstituto de Salud Carlos IIIMadridSpain
| | - Johannes M.F.G. Aerts
- Medical Biochemistry, Leiden Institute of Chemistry, Leiden UniversityFaculty of ScienceLeidenthe Netherlands
| | - Rosario Moratalla
- Instituto Cajal, CSICMadridSpain
- Centro de Investigación Biomédica en Red sobre Enfermedades NeurodegenerativasInstituto de Salud Carlos IIIMadridSpain
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14
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Nakato M, Shiranaga N, Tomioka M, Watanabe H, Kurisu J, Kengaku M, Komura N, Ando H, Kimura Y, Kioka N, Ueda K. ABCA13 dysfunction associated with psychiatric disorders causes impaired cholesterol trafficking. J Biol Chem 2021; 296:100166. [PMID: 33478937 PMCID: PMC7948424 DOI: 10.1074/jbc.ra120.015997] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 01/22/2023] Open
Abstract
ATP-binding cassette subfamily A member 13 (ABCA13) is predicted to be the largest ABC protein, consisting of 5058 amino acids and a long N-terminal region. Mutations in the ABCA13 gene were reported to increase the susceptibility to schizophrenia, bipolar disorder, and major depression. However, little is known about the molecular functions of ABCA13 or how they associate with psychiatric disorders. Here, we examined the biochemical activity of ABCA13 using HEK293 cells transfected with mouse ABCA13. The expression of ABCA13 induced the internalization of cholesterol and gangliosides from the plasma membrane to intracellular vesicles. Cholesterol internalization by ABCA13 required the long N-terminal region and ATP hydrolysis. To examine the physiological roles of ABCA13, we generated Abca13 KO mice using CRISPR/Cas and found that these mice exhibited deficits of prepulse inhibition. Vesicular cholesterol accumulation and synaptic vesicle endocytosis were impaired in primary cultures of Abca13 KO cortical neurons. Furthermore, mutations in ABCA13 gene associated with psychiatric disorders disrupted the protein's subcellular localization and impaired cholesterol trafficking. These findings suggest that ABCA13 accelerates cholesterol internalization by endocytic retrograde transport in neurons and that loss of this function is associated with the pathophysiology of psychiatric disorders.
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Affiliation(s)
- Mitsuhiro Nakato
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
| | - Naoko Shiranaga
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Maiko Tomioka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hitomi Watanabe
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Junko Kurisu
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Mineko Kengaku
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Naoko Komura
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan; Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu, Japan
| | - Hiromune Ando
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan; Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu, Japan
| | - Yasuhisa Kimura
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Noriyuki Kioka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kazumitsu Ueda
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan.
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15
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Dvorak P, Hlavac V, Soucek P. 5' Untranslated Region Elements Show High Abundance and Great Variability in Homologous ABCA Subfamily Genes. Int J Mol Sci 2020; 21:ijms21228878. [PMID: 33238634 PMCID: PMC7700387 DOI: 10.3390/ijms21228878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 11/16/2022] Open
Abstract
The 12 members of the ABCA subfamily in humans are known for their ability to transport cholesterol and its derivatives, vitamins, and xenobiotics across biomembranes. Several ABCA genes are causatively linked to inborn diseases, and the role in cancer progression and metastasis is studied intensively. The regulation of translation initiation is implicated as the major mechanism in the processes of post-transcriptional modifications determining final protein levels. In the current bioinformatics study, we mapped the features of the 5' untranslated regions (5'UTR) known to have the potential to regulate translation, such as the length of 5'UTRs, upstream ATG codons, upstream open-reading frames, introns, RNA G-quadruplex-forming sequences, stem loops, and Kozak consensus motifs, in the DNA sequences of all members of the subfamily. Subsequently, the conservation of the features, correlations among them, ribosome profiling data as well as protein levels in normal human tissues were examined. The 5'UTRs of ABCA genes contain above-average numbers of upstream ATGs, open-reading frames and introns, as well as conserved ones, and these elements probably play important biological roles in this subfamily, unlike RG4s. Although we found significant correlations among the features, we did not find any correlation between the numbers of 5'UTR features and protein tissue distribution and expression scores. We showed the existence of single nucleotide variants in relation to the 5'UTR features experimentally in a cohort of 105 breast cancer patients. 5'UTR features presumably prepare a complex playground, in which the other elements such as RNA binding proteins and non-coding RNAs play the major role in the fine-tuning of protein expression.
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Affiliation(s)
- Pavel Dvorak
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (V.H.); (P.S.)
- Correspondence: ; Tel.: +420-377593263
| | - Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (V.H.); (P.S.)
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (V.H.); (P.S.)
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
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16
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Wang H, Vanyukov MM, Xing EP, Wu W. Discovering weaker genetic associations guided by known associations. BMC Med Genomics 2020; 13:19. [PMID: 32093702 PMCID: PMC7038505 DOI: 10.1186/s12920-020-0667-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 01/20/2020] [Indexed: 12/05/2022] Open
Abstract
Background The current understanding of the genetic basis of complex human diseases is that they are caused and affected by many common and rare genetic variants. A considerable number of the disease-associated variants have been identified by Genome Wide Association Studies, however, they can explain only a small proportion of heritability. One of the possible reasons for the missing heritability is that many undiscovered disease-causing variants are weakly associated with the disease. This can pose serious challenges to many statistical methods, which seems to be only capable of identifying disease-associated variants with relatively stronger coefficients. Results In order to help identify weaker variants, we propose a novel statistical method, Constrained Sparse multi-locus Linear Mixed Model (CS-LMM) that aims to uncover genetic variants of weaker associations by incorporating known associations as a prior knowledge in the model. Moreover, CS-LMM accounts for polygenic effects as well as corrects for complex relatednesses. Our simulation experiments show that CS-LMM outperforms other competing existing methods in various settings when the combinations of MAFs and coefficients reflect different scenarios in complex human diseases. Conclusions We also apply our method to the GWAS data of alcoholism and Alzheimer’s disease and exploratively discover several SNPs. Many of these discoveries are supported through literature survey. Furthermore, our association results strengthen the belief in genetic links between alcoholism and Alzheimer’s disease.
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Affiliation(s)
- Haohan Wang
- Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Michael M Vanyukov
- Department of Pharmaceutical Sciences, Departments of Psychiatry, and Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eric P Xing
- Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.,Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Wei Wu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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17
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Castanho I, Murray TK, Hannon E, Jeffries A, Walker E, Laing E, Baulf H, Harvey J, Bradshaw L, Randall A, Moore K, O'Neill P, Lunnon K, Collier DA, Ahmed Z, O'Neill MJ, Mill J. Transcriptional Signatures of Tau and Amyloid Neuropathology. Cell Rep 2020; 30:2040-2054.e5. [PMID: 32049030 PMCID: PMC7016505 DOI: 10.1016/j.celrep.2020.01.063] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 11/21/2019] [Accepted: 01/21/2020] [Indexed: 12/31/2022] Open
Abstract
Alzheimer's disease (AD) is associated with the intracellular aggregation of hyperphosphorylated tau and the accumulation of β-amyloid in the neocortex. We use transgenic mice harboring human tau (rTg4510) and amyloid precursor protein (J20) mutations to investigate transcriptional changes associated with the progression of tau and amyloid pathology. rTg4510 mice are characterized by widespread transcriptional differences in the entorhinal cortex with changes paralleling neuropathological burden across multiple brain regions. Differentially expressed transcripts overlap with genes identified in genetic studies of familial and sporadic AD. Systems-level analyses identify discrete co-expression networks associated with the progressive accumulation of tau that are enriched for genes and pathways previously implicated in AD pathology and overlap with co-expression networks identified in human AD cortex. Our data provide further evidence for an immune-response component in the accumulation of tau and reveal molecular pathways associated with the progression of AD neuropathology.
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Affiliation(s)
- Isabel Castanho
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Tracey K Murray
- Eli Lilly & Co., Erl Wood Manor, Sunninghill Road, Windlesham GU20 6PH, UK
| | - Eilis Hannon
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Aaron Jeffries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Emma Walker
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Emma Laing
- Eli Lilly & Co., Erl Wood Manor, Sunninghill Road, Windlesham GU20 6PH, UK
| | - Hedley Baulf
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Joshua Harvey
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Lauren Bradshaw
- Eli Lilly & Co., Erl Wood Manor, Sunninghill Road, Windlesham GU20 6PH, UK
| | - Andrew Randall
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Karen Moore
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Paul O'Neill
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Katie Lunnon
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - David A Collier
- Eli Lilly & Co., Erl Wood Manor, Sunninghill Road, Windlesham GU20 6PH, UK
| | - Zeshan Ahmed
- Eli Lilly & Co., Erl Wood Manor, Sunninghill Road, Windlesham GU20 6PH, UK
| | - Michael J O'Neill
- Eli Lilly & Co., Erl Wood Manor, Sunninghill Road, Windlesham GU20 6PH, UK
| | - Jonathan Mill
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK.
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18
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Novel genetic link between the ATP-binding cassette subfamily A gene and hippo gene in Drosophila. Exp Cell Res 2020; 386:111733. [DOI: 10.1016/j.yexcr.2019.111733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/16/2019] [Accepted: 11/16/2019] [Indexed: 11/21/2022]
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19
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Ueoka I, Pham HTN, Matsumoto K, Yamaguchi M. Autism Spectrum Disorder-Related Syndromes: Modeling with Drosophila and Rodents. Int J Mol Sci 2019; 20:E4071. [PMID: 31438473 PMCID: PMC6747505 DOI: 10.3390/ijms20174071] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/17/2019] [Accepted: 08/18/2019] [Indexed: 12/11/2022] Open
Abstract
Whole exome analyses have identified a number of genes associated with autism spectrum disorder (ASD) and ASD-related syndromes. These genes encode key regulators of synaptogenesis, synaptic plasticity, cytoskeleton dynamics, protein synthesis and degradation, chromatin remodeling, transcription, and lipid homeostasis. Furthermore, in silico studies suggest complex regulatory networks among these genes. Drosophila is a useful genetic model system for studies of ASD and ASD-related syndromes to clarify the in vivo roles of ASD-associated genes and the complex gene regulatory networks operating in the pathogenesis of ASD and ASD-related syndromes. In this review, we discuss what we have learned from studies with vertebrate models, mostly mouse models. We then highlight studies with Drosophila models. We also discuss future developments in the related field.
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Affiliation(s)
- Ibuki Ueoka
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 603-8585, Japan
| | - Hang Thi Nguyet Pham
- Department of Pharmacology and Biochemistry, National Institute of Medicinal Materials, Hanoi 110100, Vietnam
| | - Kinzo Matsumoto
- Division of Medicinal Pharmacology, Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Masamitsu Yamaguchi
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 603-8585, Japan.
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20
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Hagos FT, Adams SM, Poloyac SM, Kochanek PM, Horvat CM, Clark RSB, Empey PE. Membrane transporters in traumatic brain injury: Pathological, pharmacotherapeutic, and developmental implications. Exp Neurol 2019; 317:10-21. [PMID: 30797827 DOI: 10.1016/j.expneurol.2019.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/12/2019] [Accepted: 02/20/2019] [Indexed: 12/12/2022]
Abstract
Membrane transporters regulate the trafficking of endogenous and exogenous molecules across biological barriers and within the neurovascular unit. In traumatic brain injury (TBI), they moderate the dynamic movement of therapeutic drugs and injury mediators among neurons, endothelial cells and glial cells, thereby becoming important determinants of pathogenesis and effective pharmacotherapy after TBI. There are three ways transporters may impact outcomes in TBI. First, transporters likely play a key role in the clearance of injury mediators. Second, genetic association studies suggest transporters may be important in the transition of TBI from acute brain injury to a chronic neurological disease. Third, transporters dynamically control the brain penetration and efflux of many drugs and their distribution within and elimination from the brain, contributing to pharmacoresistance and possibly in some cases pharmacosensitivity. Understanding the nature of drugs or candidate drugs in development with respect to whether they are a transporter substrate or inhibitor is relevant to understand whether they distribute to their target in sufficient concentrations. Emerging data provide evidence of altered expression and function of transporters in humans after TBI. Genetic variability in expression and/or function of key transporters adds an additional dynamic, as shown in recent clinical studies. In this review, evidence supporting the role of individual membrane transporters in TBI are discussed as well as novel strategies for their modulation as possible therapeutic targets. Since data specifically targeting pediatric TBI are sparse, this review relies mainly on experimental studies using adult animals and clinical studies in adult patients.
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Affiliation(s)
- Fanuel T Hagos
- Center for Clinical Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, PA, United States of America
| | - Solomon M Adams
- Center for Clinical Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, PA, United States of America
| | - Samuel M Poloyac
- Center for Clinical Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, PA, United States of America; Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Patrick M Kochanek
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, United States of America; Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America; UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States of America
| | - Christopher M Horvat
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, United States of America; Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America; UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States of America
| | - Robert S B Clark
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, United States of America; Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America; UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States of America.
| | - Philip E Empey
- Center for Clinical Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, PA, United States of America; Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, United States of America.
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Leukocyte expression profiles reveal gene sets with prognostic value for seizure-free outcome following stereotactic laser amygdalohippocampotomy. Sci Rep 2019; 9:1086. [PMID: 30705324 PMCID: PMC6355811 DOI: 10.1038/s41598-018-37763-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/13/2018] [Indexed: 02/08/2023] Open
Abstract
Among patients with intractable epilepsy, the most commonly performed surgical procedure is craniotomy for amygdalohippocampectomy (AH). Stereotactic laser amygdalohippocampotomy (SLAH) has also been recently employed as a minimally invasive treatment for intractable temporal lobe epilepsy (TLE). Among patients treated with AH and SLAH approximately 65% and 54% of patients become seizure-free, respectively. Therefore, selection criteria for surgical candidates with improved prognostic value for post-operative seizure-free outcome are greatly needed. In this study, we perform RNA sequencing (RNA-Seq) on whole blood leukocyte samples taken from 16 patients with intractable TLE prior to SLAH to test the hypothesis that pre-operative leukocyte RNA expression profiles are prognostic for post-operative seizure outcome. Multidimensional scaling analysis of the RNA expression data indicated separate clustering of patients with seizure free (SF) and non-seizure-free (NSF) outcomes. Differential expression (DE) analysis performed on SF versus NSF groups revealed 24 significantly differentially expressed genes (≥2.0-fold change, p-value < 0.05, FDR <0.05). Network and pathway analyses identified differential activation of pathways involved in lipid metabolism, morphology of oligodendrocytes, inflammatory response, and development of astrocytes. These results suggest that pre-operative leukocyte expression profiles have prognostic value for seizure outcome following SLAH.
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Iritani S, Torii Y, Habuchi C, Sekiguchi H, Fujishiro H, Yoshida M, Go Y, Iriki A, Isoda M, Ozaki N. The neuropathological investigation of the brain in a monkey model of autism spectrum disorder with ABCA13 deletion. Int J Dev Neurosci 2018; 71:130-139. [PMID: 30201574 DOI: 10.1016/j.ijdevneu.2018.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/31/2018] [Accepted: 09/03/2018] [Indexed: 02/06/2023] Open
Abstract
The precise biological etiology of autism spectrum disorder (ASD) remains unknown. In this study, we investigated the neuropathology of a monkey model of autism Human ABCA13 is the largest ABC transporter protein, with a length of 5058 amino acids and a predicted molecular weight of >450 kDa. However, the function of this protein remains to be elucidated. This protein is thought to be associated with major psychiatric disease. Using this monkey model of autism with an ABCA13 deletion and a mutation of 5HT2c, we neuropathologically investigated the changes in the neuronal formation in the frontal cortex. As a result, the neuronal formation in the cortex was found to be disorganized with regard to the neuronal size and laminal distribution in the ABCA13 deletion monkey. The catecholaminergic and GABAergic neuronal systems, serotoninergic neuronal formation (5HT2c) were also found to be impaired by an immunohistochemical evaluation. This study suggested that ABCA13 deficit induces the impairment of neuronal maturation or migration, and the function of the neuronal network. This protein might thus play a role in the neurodevelopmental function of the central nervous system and the dysfunction of this protein may be a pathophysiological cause of mental disorders including autism.
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Affiliation(s)
- Shuji Iritani
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.
| | - Youta Torii
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Chikako Habuchi
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Hirotaka Sekiguchi
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Hiroshige Fujishiro
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Mari Yoshida
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Aichi, Japan
| | - Yasuhiro Go
- Department of Brain Sciences, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Developmental Physiology, National Institute for Physiological Sciences, Okazaki, Japan; The Graduate University for Advanced Studies (Sokendai), Okazaki, Japan
| | - Astushi Iriki
- Laboratory for Symbolic Cognitive Developmen RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Masaki Isoda
- Department of System Neuroscience, National Institute for Physiological Sciences, Okazaki, Aichi, Japan; Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute, Wako, Saitama, Japan; Department of Physiology, Kansai Medical University School of Medicine, Hirakata, Osaka, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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Tachikawa M, Toki H, Watanabe M, Tomi M, Hosoya KI, Terasaki T. Gene expression of A6-like subgroup of ATP-binding cassette transporters in mouse brain parenchyma and microvessels. Anat Sci Int 2018. [DOI: 10.1007/s12565-018-0435-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Davis W. The ATP-Binding Cassette Transporter-2 (ABCA2) Overexpression Modulates Sphingosine Levels and Transcription of the Amyloid Precursor Protein (APP) Gene. Curr Alzheimer Res 2016; 12:847-59. [PMID: 26510981 DOI: 10.2174/156720501209151019105834] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/06/2015] [Accepted: 06/17/2015] [Indexed: 01/04/2023]
Abstract
The ATP-binding cassette transporter-2 (ABCA2) is a member of a family of multipass transmembrane proteins that use the energy of ATP hydrolysis to transport substrates across membrane bilayers. ABCA2 has also been genetically linked with Alzheimer's disease but the molecular mechanisms are unknown. In this report, we hypothesized that ABCA2 modulation of sphingolipid metabolism activates a signaling pathway that regulates amyloid precursor protein transcription. We found that ABCA2 overexpression in N2a cells was associated with increased mass of the sphingolipid sphingosine, derived from the catabolism of ceramide. ABCA2 overexpression increased in vitro alkaline and acid ceramidase activity. Sphingosine is a physiological inhibitor of protein kinase C (PKC) activity. Pharmacological inhibition of ceramidase activity or activation PKC activity with 12-myristate 13-acetate (PMA) or diacylglycerol (DAG) decreased endogenous APP mRNA levels in ABCA2 overexpressing cells. Treatment with PMA also decreased the expression of a transfected human APP promoter reporter construct, while treatment with a general PKC inhibitor, GF109203x, increased APP promoter activity. In N2a cells, chromatin immunoprecipitation experiments revealed that a repressive complex forms at the AP-1 site in the human APP promoter, consisting of c-jun, c-jun dimerization protein 2 (JDP2) and HDAC3 and this complex was reduced in ABCA2 overexpressing cells. Activation of the human APP promoter in A2 cells was directed by the upstream stimulatory factors USF-1 and USF-2 that bound to an E-box element in vivo. These findings indicate that ABCA2 overexpression modulates sphingosine levels and regulates transcription of the endogenous APP gene.
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Affiliation(s)
- Warren Davis
- Medical University of South Carolina, 173 Ashley Avenue, BSB 358, MSC 505, Charleston, SC, 29403, USA.
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25
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Rezaei F, Shafiei M, Shariati G, Dehdashtian A, Mohebbi M, Galehdari H. Novel Mutation in the ATP-Binding Cassette Transporter A3 (ABCA3) Encoding Gene Causes Respiratory Distress Syndrome in A Term Newborn in Southwest Iran. IRANIAN JOURNAL OF PEDIATRICS 2016; 26:e2493. [PMID: 27437095 PMCID: PMC4939234 DOI: 10.5812/ijp.2493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 11/01/2015] [Accepted: 11/14/2015] [Indexed: 11/16/2022]
Abstract
INTRODUCTION ABCA3 glycoprotein belongs to the ATP-binding cassette (ABC) superfamily of transporters, which utilize the energy derived from hydrolysis of ATP for the translocation of a wide variety of substrates across the plasma membrane. Mutations in the ABCA3 gene are knowingly causative for fatal surfactant deficiency, particularly respiratory distress syndrome (RDS) in term babies. CASE PRESENTATION In this study, Sanger sequencing of the whole ABCA3 gene (NCBI NM_001089) was performed in a neonatal boy with severe RDS. A homozygous mutation has been identified in the patient. Parents were heterozygous for the same missense mutation GGA > AGA at position 202 in exon 6 of the ABCA3 gene (c.604G > A; p.G202R). Furthermore, 70 normal individuals have been analyzed for the mentioned change with negative results. CONCLUSIONS Regarding Human Genome Mutation Database (HGMD) and other literature recherche, the detected change is a novel mutation and has not been reported before. Bioinformatics mutation predicting tools prefer it as pathogenic.
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Affiliation(s)
- Farideh Rezaei
- Deptartment of Genetics, Faculty of Science, Shahid Chamran University, Ahvaz, IR Iran
| | - Mohammad Shafiei
- Deptartment of Genetics, Faculty of Science, Shahid Chamran University, Ahvaz, IR Iran
| | - Gholamreza Shariati
- Narges Medical Genetic Laboratory, Ahvaz, IR Iran
- Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | | | - Maryam Mohebbi
- Narges Medical Genetic Laboratory, Ahvaz, IR Iran
- Jundishapur University of Medical Sciences, Ahvaz, IR Iran
- Corresponding author: Maryam Mohebbi, Jundishapur University of Medical Sciences, Ahvaz, IR Iran. Tel: +98-9126433468, E-mail:
| | - Hamid Galehdari
- Deptartment of Genetics, Faculty of Science, Shahid Chamran University, Ahvaz, IR Iran
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26
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Schengrund CL. Gangliosides: glycosphingolipids essential for normal neural development and function. Trends Biochem Sci 2015; 40:397-406. [DOI: 10.1016/j.tibs.2015.03.007] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 11/25/2022]
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Greenberg RM. Schistosome ABC multidrug transporters: From pharmacology to physiology. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2014; 4:301-9. [PMID: 25516841 PMCID: PMC4266782 DOI: 10.1016/j.ijpddr.2014.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The genuine and hypothesized roles of schistosome ABC transporters are reviewed. Evidence suggesting a role for transporters in schistosome drug susceptibility is discussed. Potential roles of ABC transporters in normal schistosome biology are outlined.
Praziquantel (PZQ) is essentially the only drug currently available for treatment and control of schistosomiasis, a disease affecting hundreds of millions worldwide. Though highly effective overall, PZQ has limitations, most notably its significant lack of activity against immature schistosomes. Furthermore, the availability of only a single drug for a disease of this magnitude makes reports of PZQ-resistant isolates particularly troubling. ATP-binding cassette (ABC) multidrug transporters such as P-glycoprotein (Pgp; ABCB1) are efflux transporters that underlie multidrug resistance (MDR); changes in their expression or structure are also associated with drug resistance in parasites, including helminths. This review will discuss the role these transporters might play in modulating schistosome susceptibility to PZQ, and the implications for developing new or repurposed treatments that enhance the efficacy of PZQ. However, in addition to influencing drug susceptibility, ABC transporters play important roles in several critical physiological functions such as excretion and maintenance of permeability barriers. They also transport signaling molecules with high affinity, and several lines of evidence implicate mammalian transporters in a diverse array of physiological functions, including regulation of immune responses. Like their mammalian counterparts, schistosome ABC transporters appear to be involved in functions critical to the parasite, including excretory activity and reproduction, and we hypothesize that they underlie at least some aspects of parasite–host interactions. Thus, in addition to their potential as targets for enhancers of PZQ susceptibility, these transporters might also serve as candidate targets for agents that disrupt the parasite life cycle and act as antischistosomals on their own.
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Affiliation(s)
- Robert M Greenberg
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, PA 19104, USA
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Tsybovsky Y, Palczewski K. Expression, purification and structural properties of ABC transporter ABCA4 and its individual domains. Protein Expr Purif 2014; 97:50-60. [PMID: 24583180 DOI: 10.1016/j.pep.2014.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 12/13/2022]
Abstract
ABCA4 is a member of the A subfamily of ATP-binding cassette transporters that consists of large integral membrane proteins implicated in inherited human diseases. ABCA4 assists in the clearance of N-retinylidene-phosphatidylethanolamine, a potentially toxic by-product of the visual cycle formed in photoreceptor cells during light perception. Structural and functional studies of this protein have been hindered by its large size, membrane association, and domain complexity. Although mammalian, insect and bacterial systems have been used for expression of ABCA4 and its individual domains, the structural relevance of resulting proteins to the native transporter has yet to be established. We produced soluble domains of ABCA4 in Escherichia coli and Saccharomyces cerevisiae and the full-length transporter in HEK293 cells. Electron microscopy and size exclusion chromatography were used to assess the conformational homogeneity and structure of these proteins. We found that isolated ABCA4 domains formed large, heterogeneous oligomers cross-linked with non-specific disulphide bonds. Incomplete folding of cytoplasmic domain 2 was proposed based on fluorescence spectroscopy results. In contrast, full-length human ABCA4 produced in mammalian cells was found structurally equivalent to the native protein obtained from bovine photoreceptors. These findings offer recombinantly expressed full-length ABCA4 as an appropriate object for future detailed structural and functional characterization.
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Affiliation(s)
- Yaroslav Tsybovsky
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Krzysztof Palczewski
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA.
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29
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Quazi F, Molday RS. Differential phospholipid substrates and directional transport by ATP-binding cassette proteins ABCA1, ABCA7, and ABCA4 and disease-causing mutants. J Biol Chem 2013; 288:34414-26. [PMID: 24097981 DOI: 10.1074/jbc.m113.508812] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
ABCA1, ABCA7, and ABCA4 are members of the ABCA subfamily of ATP-binding cassette transporters that share extensive sequence and structural similarity. Mutations in ABCA1 cause Tangier disease characterized by defective cholesterol homeostasis and high density lipoprotein (HDL) deficiency. Mutations in ABCA4 are responsible for Stargardt disease, a degenerative disorder associated with severe loss in central vision. Although cell-based studies have implicated ABCA proteins in lipid transport, the substrates and direction of transport have not been firmly established. We have purified and reconstituted ABCA1, ABCA7, and ABCA4 into liposomes for fluorescent-lipid transport studies. ABCA1 actively exported or flipped phosphatidylcholine, phosphatidylserine, and sphingomyelin from the cytoplasmic to the exocytoplasmic leaflet of membranes, whereas ABCA7 preferentially exported phosphatidylserine. In contrast, ABCA4 transported phosphatidylethanolamine in the reverse direction. The same phospholipids stimulated the ATPase activity of these ABCA transporters. The transport and ATPase activities of ABCA1 and ABCA4 were reduced by 25% in the presence of 20% cholesterol. Nine ABCA1 Tangier mutants and the corresponding ABCA4 Stargardt mutants showed significantly reduced phospholipid transport activity and subcellular mislocalization. These studies provide the first direct evidence for ABCA1 and ABCA7 functioning as phospholipid transporters and suggest that this activity is an essential step in the loading of apoA-1 with phospholipids for HDL formation.
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Affiliation(s)
- Faraz Quazi
- From the Department of Biochemistry and Molecular Biology, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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30
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Pahnke J, Fröhlich C, Krohn M, Schumacher T, Paarmann K. Impaired mitochondrial energy production and ABC transporter function-A crucial interconnection in dementing proteopathies of the brain. Mech Ageing Dev 2013; 134:506-15. [PMID: 24012632 DOI: 10.1016/j.mad.2013.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 06/21/2013] [Accepted: 08/24/2013] [Indexed: 01/07/2023]
Abstract
Ageing is the main risk factor for the development of dementing neurodegenerative diseases (NDs) and it is accompanied by the accumulation of variations in mitochondrial DNA. The resulting tissue-specific alterations in ATP production and availability cause deteriorations of cerebral clearance mechanisms that are important for the removal of toxic peptides and its aggregates. ABC transporters were shown to be the most important exporter superfamily for toxic peptides, e.g. β-amyloid and α-synuclein. Their activity is highly dependent on the availability of ATP and forms a directed energy-exporter network, linking decreased mitochondrial function with highly impaired ABC transporter activity and disease progression. In this paper, we describe a network based on interactions between ageing, energy metabolism, regeneration, accumulation of toxic peptides and the development of proteopathies of the brain with a focus on Alzheimer's disease (AD). Additionally, we provide new experimental evidence for interactions within this network in regenerative processes in AD.
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Affiliation(s)
- Jens Pahnke
- Neurodegeneration Research Lab (NRL), Department of Neurology, University of Magdeburg, Leipziger Str. 44, H64, 39120 Magdeburg, Germany; German Center for Neurodegenerative Diseases (DZNE) Magdeburg, Leipziger Str. 44, H64, 39120 Magdeburg, Germany.
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31
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Tsybovsky Y, Orban T, Molday RS, Taylor D, Palczewski K. Molecular organization and ATP-induced conformational changes of ABCA4, the photoreceptor-specific ABC transporter. Structure 2013; 21:854-60. [PMID: 23562398 DOI: 10.1016/j.str.2013.03.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 02/04/2013] [Accepted: 03/01/2013] [Indexed: 02/03/2023]
Abstract
ATP-binding cassette (ABC) transporters use ATP to translocate various substrates across cellular membranes. Several members of subfamily A of mammalian ABC transporters are associated with severe health disorders, but their unusual complexity and large size have so far precluded structural characterization. ABCA4 is localized to the discs of vertebrate photoreceptor outer segments. This protein transports N-retinylidene-phosphatidylethanolamine to the outer side of disc membranes to prevent formation of toxic compounds causing macular degeneration. An 18 Å-resolution structure of ABCA4 isolated from bovine rod outer segments was determined using electron microscopy and single-particle reconstruction. Significant conformational changes in the cytoplasmic and transmembrane regions were observed upon binding of a nonhydrolyzable ATP analog and accompanied by altered hydrogen/deuterium exchange in the Walker A motif of one of the nucleotide-binding domains. These findings provide an initial view of the molecular organization and functional rearrangements for any member of the ABCA subfamily of ABC transporters.
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Affiliation(s)
- Yaroslav Tsybovsky
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
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32
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Greenberg RM. ABC multidrug transporters in schistosomes and other parasitic flatworms. Parasitol Int 2013; 62:647-53. [PMID: 23474413 DOI: 10.1016/j.parint.2013.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 02/14/2013] [Accepted: 02/18/2013] [Indexed: 12/19/2022]
Abstract
Schistosomiasis, a neglected tropical disease affecting hundreds of millions, is caused by parasitic flatworms of the genus Schistosoma. Treatment and control of schistosomiasis relies almost exclusively on a single drug, praziquantel (PZQ), a dangerous situation for a disease of this magnitude. Though PZQ is highly effective overall, it has drawbacks, and reports of worms showing PZQ resistance, either induced in the laboratory or isolated from the field, are disconcerting. Multidrug transporters underlie multidrug resistance (MDR), a phenomenon in which resistance to a single drug is accompanied by unexpected cross-resistance to several structurally unrelated compounds. Some of the best studied multidrug transporters are members of the ancient and very large ATP-binding cassette (ABC) superfamily of efflux transporters. ABC multidrug transporters such as P-glycoprotein (Pgp; ABCB1) are also associated with drug resistance in parasites, including helminths such as schistosomes. In addition to their association with drug resistance, however, ABC transporters also function in a wide variety of physiological processes in metazoans. In this review, we examine recent studies that help define the role of schistosome ABC transporters in regulating drug susceptibility, and in normal schistosome physiology, including reproduction and excretory activity. We postulate that schistosome ABC transporters could be useful targets for compounds that enhance the effectiveness of current therapeutics as well as for agents that act as antischistosomals on their own.
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Affiliation(s)
- Robert M Greenberg
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104, USA.
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Ohtsuki S, Ikeda C, Uchida Y, Sakamoto Y, Miller F, Glacial F, Decleves X, Scherrmann JM, Couraud PO, Kubo Y, Tachikawa M, Terasaki T. Quantitative targeted absolute proteomic analysis of transporters, receptors and junction proteins for validation of human cerebral microvascular endothelial cell line hCMEC/D3 as a human blood-brain barrier model. Mol Pharm 2012; 10:289-96. [PMID: 23137377 DOI: 10.1021/mp3004308] [Citation(s) in RCA: 168] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Human cerebral microvascular endothelial cell line hCMEC/D3 is an established model of the human blood-brain barrier (BBB). The purpose of the present study was to determine, by means of quantitative targeted absolute proteomics, the protein expression levels in hCMEC/D3 cells of multiple transporters, receptors and junction proteins for comparison with our previously reported findings in isolated human brain microvessels. Among 91 target molecules, 12 transporters, 2 receptors, 1 junction protein and 1 membrane marker were present at quantifiable levels in plasma membrane fraction of hCMEC/D3 cells. ABCA2, MDR1, MRP4, BCRP, GLUT1, 4F2hc, MCT1, ENT1, transferrin and insulin receptors and claudin-5 were detected in both hCMEC/D3 cells and human brain microvessels. After normalization based on Na(+)/K(+) ATPase expression, the differences in protein expression levels between hCMEC/D3 cells and human brain microvessels were within 4-fold for these proteins, with the exceptions of ENT1, transferrin receptor and claudin-5. ABCA8, LAT1, LRP1 and γ-GTP were below the limit of quantification in the cells, but were found in human brain microvessels. ABCA3, ABCA6, MRP1 and ATA1 were found only in hCMEC/D3 cells. Furthermore, compared with human umbilical vein endothelial cells (HUVECs) as reference nonbrain endothelial cells, MDR1 was found only in hCMEC/D3 cells, and GLUT1 expression was 15-fold higher in hCMEC/D3 cells than in HUVECs. In conclusion, this is the first study to examine the suitability and limitations of the hCMEC/D3 cell line as a BBB functional model in terms of quantitative expression levels of transporters, receptors and tight junction proteins.
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Affiliation(s)
- Sumio Ohtsuki
- Division of Membrane Transport and Drug Targeting, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
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The effects of neurological disorder-related codon variations of ABCA13 on the function of the ABC protein. Biosci Biotechnol Biochem 2012; 76:2289-93. [PMID: 23221702 DOI: 10.1271/bbb.120563] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Rare coding variants of ATP-binding cassette protein A13 (ABCA13) contribute to the risk of neurological disorders, but little is known about the physiological function of ABCA13 and how single nucleotide polymorphisms (SNPs) affect it. Here, we examined the effects of neurological disorder-related SNPs ABCA13, T4031A and R4843C in the context of ABCA1, and found that the former SNP (T1088A in ABCA1) severely impaired the ABCA1 functions of apolipoprotein A-I (apoA-I) binding and cholesterol efflux. The antibody against mouse ABCA13 reacted with neurons in the cerebral cortex, hippocampus, and cerebellum. These results suggest that the T4031A replacement affects the function of ABCA13 in the brain.
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