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Hernández-Contreras KA, Martínez-Díaz JA, Hernández-Aguilar ME, Herrera-Covarrubias D, Rojas-Durán F, Chi-Castañeda LD, García-Hernández LI, Aranda-Abreu GE. Alterations of mRNAs and Non-coding RNAs Associated with Neuroinflammation in Alzheimer's Disease. Mol Neurobiol 2024; 61:5826-5840. [PMID: 38236345 DOI: 10.1007/s12035-023-03908-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 12/27/2023] [Indexed: 01/19/2024]
Abstract
Alzheimer's disease is a neurodegenerative pathology whose pathognomonic hallmarks are increased generation of β-amyloid (Aβ) peptide, production of hyperphosphorylated (pTau), and neuroinflammation. The last is an alteration closely related to the progression of AD and although it is present in multiple neurodegenerative diseases, the pathophysiological events that characterize neuroinflammatory processes vary depending on the disease. In this article, we focus on mRNA and non-coding RNA alterations as part of the pathophysiological events characteristic of neuroinflammation in AD and the influence of these alterations on the course of the disease through interaction with multiple RNAs related to the generation of Aβ, pTau, and neuroinflammation itself.
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Affiliation(s)
- Karla Aketzalli Hernández-Contreras
- Doctorado en Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Jorge Antonio Martínez-Díaz
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - María Elena Hernández-Aguilar
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Deissy Herrera-Covarrubias
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Fausto Rojas-Durán
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Lizbeth Donají Chi-Castañeda
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Luis Isauro García-Hernández
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Gonzalo Emiliano Aranda-Abreu
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México.
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2
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Swanson MJ, Lewis KN, Carpenter R, Whetzel A, Bae NS. The human RAP1 and GFAPɛ proteins increase γ-secretase activity in a yeast model system. G3 (BETHESDA, MD.) 2023; 13:jkad057. [PMID: 36929840 PMCID: PMC10411568 DOI: 10.1093/g3journal/jkad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/24/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023]
Abstract
Alzheimer's disease (AD) is an age-related disorder that results in progressive cognitive impairment and memory loss. Deposition of amyloid β (Aβ) peptides in senile plaques is a hallmark of AD. γ-secretase produces Aβ peptides, mostly as the soluble Aβ40 with fewer insoluble Aβ42 peptides. Rare, early-onset AD (EOAD) occurs in individuals under 60 years of age. Most EOAD cases are due to unknown genetic causes, but a subset is due to mutations in the genes encoding the amyloid precursor protein that is processed into Aβ peptides or the presenilins (PS1 and PS2) that process APP. PS1 interacts with the epsilon isoform of glial fibrillary acidic protein (GFAPɛ), a protein found in the subventricular zone of the brain. We have found that GFAPɛ interacts with the telomere protection factor RAP1 (TERF2IP). RAP1 can also interact with PS1 alone or with GFAPɛ in vitro. Our data show that the nuclear protein RAP1 has an extratelomeric role in the cytoplasm through its interactions with GFAPɛ and PS1. GFAPɛ coprecipitated with RAP1 from human cell extracts. RAP1, GFAPɛ, and PS1 all colocalized in human SH-SY5Y cells. Using a genetic model of the γ-secretase complex in Saccharomyces cerevisiae, RAP1 increased γ-secretase activity, and this was potentiated by GFAPɛ. Our studies are the first to connect RAP1 with an age-related disorder.
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Affiliation(s)
- Mark J Swanson
- Department of Biochemistry and Molecular Genetics, Midwestern University, Glendale, AZ 85308, USA
| | - Kelsey N Lewis
- Department of Biochemistry and Molecular Genetics, Midwestern University, Glendale, AZ 85308, USA
| | - Robert Carpenter
- Department of Biomedical Sciences, College of Graduate Studies, Midwestern University, Glendale, AZ 85308, USA
| | - Alexis Whetzel
- Department of Biochemistry and Molecular Genetics, Midwestern University, Glendale, AZ 85308, USA
| | - Nancy S Bae
- Department of Biochemistry and Molecular Genetics, Midwestern University, Glendale, AZ 85308, USA
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3
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Specific Mutations near the Amyloid Precursor Protein Cleavage Site Increase γ-Secretase Sensitivity and Modulate Amyloid-β Production. Int J Mol Sci 2023; 24:ijms24043970. [PMID: 36835396 PMCID: PMC9959964 DOI: 10.3390/ijms24043970] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/16/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Amyloid-β peptides (Aβs) are produced via cleavage of the transmembrane region of the amyloid precursor protein (APP) by γ-secretase and are responsible for Alzheimer's disease. Familial Alzheimer's disease (FAD) is associated with APP mutations that disrupt the cleavage reaction and increase the production of neurotoxic Aβs, i.e., Aβ42 and Aβ43. Study of the mutations that activate and restore the cleavage of FAD mutants is necessary to understand the mechanism of Aβ production. In this study, using a yeast reconstruction system, we revealed that one of the APP FAD mutations, T714I, severely reduced the cleavage, and identified secondary APP mutations that restored the cleavage of APP T714I. Some mutants were able to modulate Aβ production by changing the proportions of Aβ species when introduced into mammalian cells. Secondary mutations include proline and aspartate residues; proline mutations are thought to act through helical structural destabilization, while aspartate mutations are thought to promote interactions in the substrate binding pocket. Our results elucidate the APP cleavage mechanism and could facilitate drug discovery.
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Specific Mutations in Aph1 Cause γ-Secretase Activation. Int J Mol Sci 2022; 23:ijms23010507. [PMID: 35008932 PMCID: PMC8745412 DOI: 10.3390/ijms23010507] [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: 12/10/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 01/25/2023] Open
Abstract
Amyloid beta peptides (Aβs) are generated from amyloid precursor protein (APP) through multiple cleavage steps mediated by γ-secretase, including endoproteolysis and carboxypeptidase-like trimming. The generation of neurotoxic Aβ42/43 species is enhanced by familial Alzheimer's disease (FAD) mutations within the catalytic subunit of γ-secretase, presenilin 1 (PS1). FAD mutations of PS1 cause partial loss-of-function and decrease the cleavage activity. Activating mutations, which have the opposite effect of FAD mutations, are important for studying Aβ production. Aph1 is a regulatory subunit of γ-secretase; it is presumed to function as a scaffold of the complex. In this study, we identified Aph1 mutations that are active in the absence of nicastrin (NCT) using a yeast γ-secretase assay. We analyzed these Aph1 mutations in the presence of NCT; we found that the L30F/T164A mutation is activating. When introduced in mouse embryonic fibroblasts, the mutation enhanced cleavage. The Aph1 mutants produced more short and long Aβs than did the wild-type Aph1, without an apparent modulatory function. The mutants did not change the amount of γ-secretase complex, suggesting that L30F/T164A enhances catalytic activity. Our results provide insights into the regulatory function of Aph1 in γ-secretase activity.
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Suzuki T, Sobu Y, Hata S. γ-Secretase structure and activity are modified by alterations in its membrane localization and ambient environment. J Biochem 2021; 171:253-256. [PMID: 34865063 DOI: 10.1093/jb/mvab132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/29/2021] [Indexed: 01/25/2023] Open
Abstract
γ-Secretase cleaves type I transmembrane proteins in a hydrophobic membrane environment following ectodomain shedding. Mutations in PSEN genes, encoding the catalytic subunits of γ-secretase, presenilins, are the most common cause of familial Alzheimer's disease (AD). Pathogenic mutations in PSEN genes increase production of longer and neurotoxic amyloid-β (Aβ) by intramembrane cleavage of membrane-associated amyloid-β protein precursor (APP) carboxy-terminal fragment β (APP CTFβ), which is generated via primary cleavage of APP by β-site APP cleaving enzyme 1. The longer Aβ is prone to aggregate and accumulate in the brain, however, the accumulation of Aβ in brain is also a pathological feature of sporadic AD. Increased pathogenic Aβ generation, even in the absence of pathogenic PSEN gene mutations, is one of proposed mechanisms for sporadic AD pathogenesis. γ-Secretase digests substrates in the transmembrane region, generating Aβ peptide intermediates of various lengths. The end-products, shorter Aβ40 and Aβ38 peptides, are less neurotoxic, whereas PSEN gene mutations increase the production ratio of longer, neurotoxic Aβ species such as Aβ42, an intermediate in Aβ38 production. γ-Secretase activity or structures is altered because of its aberrant membrane localization or changes in the ambient environment such as luminal acidification. Interestingly, γ-secretase has a pH sensor in presenilins.
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Affiliation(s)
- Toshiharu Suzuki
- Advanced Prevention and Research Laboratory for Dementia, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.,Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Yuriko Sobu
- Advanced Prevention and Research Laboratory for Dementia, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.,Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Saori Hata
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
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6
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Liu L, Lauro BM, Wolfe MS, Selkoe DJ. Hydrophilic loop 1 of Presenilin-1 and the APP GxxxG transmembrane motif regulate γ-secretase function in generating Alzheimer-causing Aβ peptides. J Biol Chem 2021; 296:100393. [PMID: 33571524 PMCID: PMC7961089 DOI: 10.1016/j.jbc.2021.100393] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/22/2021] [Accepted: 02/04/2021] [Indexed: 02/06/2023] Open
Abstract
γ-Secretase is responsible for the proteolysis of amyloid precursor protein (APP) into amyloid-beta (Aβ) peptides, which are centrally implicated in the pathogenesis of Alzheimer’s disease (AD). The biochemical mechanism of how processing by γ-secretase is regulated, especially as regards the interaction between enzyme and substrate, remains largely unknown. Here, mutagenesis reveals that the hydrophilic loop-1 (HL-1) of presenilin-1 (PS1) is critical for both γ-secretase step-wise cleavages (processivity) and its allosteric modulation by heterocyclic γ-modulatory compounds. Systematic mutagenesis of HL-1, including all of its familial AD mutations and additional engineered variants, and quantification of the resultant Aβ products show that HL-1 is necessary for proper sequential γ-secretase processivity. We identify Y106, L113, and Y115 in HL-1 as key targets for heterocyclic γ-secretase modulators (GSMs) to stimulate processing of pathogenic Aβ peptides. Further, we confirm that the GxxxG domain in the APP transmembrane region functions as a critical substrate motif for γ-secretase processivity: a G29A substitution in APP-C99 mimics the beneficial effects of GSMs. Together, these findings provide a molecular basis for the structural regulation of γ-processivity by enzyme and substrate, facilitating the rational design of new GSMs that lower AD-initiating amyloidogenic Aβ peptides.
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Affiliation(s)
- Lei Liu
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bianca M Lauro
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael S Wolfe
- Department of Medical Chemistry, University of Kansas School of Pharmacy, Lawrence, Kansas, USA
| | - Dennis J Selkoe
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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Escamilla-Ayala A, Wouters R, Sannerud R, Annaert W. Contribution of the Presenilins in the cell biology, structure and function of γ-secretase. Semin Cell Dev Biol 2020; 105:12-26. [DOI: 10.1016/j.semcdb.2020.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/06/2020] [Accepted: 02/17/2020] [Indexed: 01/25/2023]
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Cai T, Tomita T. Structure-activity relationship of presenilin in γ-secretase-mediated intramembrane cleavage. Semin Cell Dev Biol 2020; 105:102-109. [PMID: 32171519 DOI: 10.1016/j.semcdb.2020.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 01/12/2023]
Abstract
Genetic research on familial cases of Alzheimer disease have identified presenilin (PS) as an important membrane protein in the pathomechanism of this disease. PS is the catalytic subunit of γ-secretase, which is responsible for the generation of amyloid-β peptide deposited in the brains of Alzheimer disease patients. γ-Secretase is an atypical protease composed of four membrane proteins (i.e., presenilin, nicastrin, anterior pharynx defective-1 (Aph-1), and presenilin enhancer-2 (Pen-2)) and mediates intramembrane proteolysis. Numerous investigations have been conducted toward understanding the structural features of γ-secretase components as well as the cleavage mechanism of γ-secretase. In this review, we summarize our current understanding of the structure and activity relationship of the γ-secretase complex.
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Affiliation(s)
- Tetsuo Cai
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Taisuke Tomita
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
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Cai T, Morishima K, Takagi-Niidome S, Tominaga A, Tomita T. Conformational Dynamics of Transmembrane Domain 3 of Presenilin 1 Is Associated with the Trimming Activity of γ-Secretase. J Neurosci 2019; 39:8600-8610. [PMID: 31527118 PMCID: PMC6807281 DOI: 10.1523/jneurosci.0838-19.2019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 08/16/2019] [Accepted: 08/30/2019] [Indexed: 12/26/2022] Open
Abstract
γ-Secretase is an intramembrane-cleaving protease that generates the toxic species of the amyloid-β peptide (Aβ) that is responsible for the pathology of Alzheimer disease. The catalytic subunit of γ-secretase is presenilin 1 (PS1), which is a polytopic membrane protein with a hydrophilic catalytic pore. The length of the C terminus of Aβ is proteolytically determined by its processive trimming by γ-secretase, although the precise mechanism still remains largely unknown. Here, we identified that transmembrane domain (TMD) 3 of human PS1 is involved in the formation of the intramembranous hydrophilic pore. Notably, the water accessibility of TMD3 was greatly altered by point mutations and compounds, which modify γ-secretase activity. The changes in the water accessibility of TMD3 was also correlated with Aβ42 production. Moreover, crosslinking between TMD3 and TMD7 resulted in a loss of sensitivity to a γ-secretase modulator that reduces Aβ42 production. Therefore, our findings indicate that the conformational dynamics of TMD3 is a prerequisite for regulation of the Aβ trimming activity of γ-secretase.SIGNIFICANCE STATEMENT Modulation of γ-secretase activity to reduce the level of toxic amyloid-β species is thought to be a therapeutic strategy for Alzheimer disease. However, the detailed mechanism of the regulation of amyloid-β production, as well as the structure-and-activity relationship of γ-secretase remains unclear. Here we identified that the water accessibility around transmembrane domain 3 in presenilin 1 was increased along with a reduction in toxic amyloid-β production. Our findings demonstrate how the structure of presenilin 1 dynamically changes during amyloid-β production, and provides insights toward the development of treatments against Alzheimer disease.
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Affiliation(s)
- Tetsuo Cai
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, and
| | - Kanan Morishima
- Laboratory of Neuropathology and Neuroscience, Faculty of Pharmaceutical Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shizuka Takagi-Niidome
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, and
| | - Aya Tominaga
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, and
| | - Taisuke Tomita
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, and
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G. N. S HS, Ganesan Rajalekshmi S, Murahari M, Burri RR. Reappraisal of FDA approved drugs against Alzheimer’s disease based on differential gene expression and protein interaction network analysis: an in silico approach. J Biomol Struct Dyn 2019; 38:3972-3989. [DOI: 10.1080/07391102.2019.1671231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hema Sree G. N. S
- Pharmacological Modelling and Simulation Centre, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Saraswathy Ganesan Rajalekshmi
- Pharmacological Modelling and Simulation Centre, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
- Department of Pharmacy Practice, Faculty of Pharmacy, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Manikanta Murahari
- Pharmacological Modelling and Simulation Centre, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
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