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Amartumur S, Nguyen H, Huynh T, Kim TS, Woo RS, Oh E, Kim KK, Lee LP, Heo C. Neuropathogenesis-on-chips for neurodegenerative diseases. Nat Commun 2024; 15:2219. [PMID: 38472255 PMCID: PMC10933492 DOI: 10.1038/s41467-024-46554-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Developing diagnostics and treatments for neurodegenerative diseases (NDs) is challenging due to multifactorial pathogenesis that progresses gradually. Advanced in vitro systems that recapitulate patient-like pathophysiology are emerging as alternatives to conventional animal-based models. In this review, we explore the interconnected pathogenic features of different types of ND, discuss the general strategy to modelling NDs using a microfluidic chip, and introduce the organoid-on-a-chip as the next advanced relevant model. Lastly, we overview how these models are being applied in academic and industrial drug development. The integration of microfluidic chips, stem cells, and biotechnological devices promises to provide valuable insights for biomedical research and developing diagnostic and therapeutic solutions for NDs.
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Affiliation(s)
- Sarnai Amartumur
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea
| | - Huong Nguyen
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea
| | - Thuy Huynh
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea
| | - Testaverde S Kim
- Center for Integrated Nanostructure Physics (CINAP), Institute for Basic Science (IBS), Suwon, 16419, Korea
| | - Ran-Sook Woo
- Department of Anatomy and Neuroscience, College of Medicine, Eulji University, Daejeon, 34824, Korea
| | - Eungseok Oh
- Department of Neurology, Chungnam National University Hospital, Daejeon, 35015, Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Luke P Lee
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea.
- Harvard Medical School, Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, 94720, USA.
| | - Chaejeong Heo
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea.
- Center for Integrated Nanostructure Physics (CINAP), Institute for Basic Science (IBS), Suwon, 16419, Korea.
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2
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Sturchio A, Duker AP, Muñoz-Sanjuan I, Espay AJ. Subtyping monogenic disorders: Huntington disease. HANDBOOK OF CLINICAL NEUROLOGY 2023; 193:171-184. [PMID: 36803810 DOI: 10.1016/b978-0-323-85555-6.00003-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Huntington disease is a highly disabling neurodegenerative disease characterized by psychiatric, cognitive, and motor deficits. The causal genetic mutation in huntingtin (Htt, also known as IT15), located on chromosome 4p16.3, leads to an expansion of a triplet coding for polyglutamine. The expansion is invariably associated with the disease when >39 repeats. Htt encodes for the protein huntingtin (HTT), which carries out many essential biological functions in the cell, in particular in the nervous system. The precise mechanism of toxicity is not known. Based on a one-gene-one-disease framework, the prevailing hypothesis ascribes toxicity to the universal aggregation of HTT. However, the aggregation process into mutant huntingtin (mHTT) is associated with a reduction of the levels of wild-type HTT. A loss of wild-type HTT may plausibly be pathogenic, contributing to the disease onset and progressive neurodegeneration. Moreover, many other biological pathways are altered in Huntington disease, such as in the autophagic system, mitochondria, and essential proteins beyond HTT, potentially explaining biological and clinical differences among affected individuals. As one gene does not mean one disease, future efforts at identifying specific Huntington subtypes are important to design biologically tailored therapeutic approaches that correct the corresponding biological pathways-rather than continuing to exclusively target the common denominator of HTT aggregation for elimination.
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Affiliation(s)
- Andrea Sturchio
- James J. and Joan A. Gardner Family Center for Parkinson's disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States; Department of Clinical Neuroscience, Neuro Svenningsson, Karolinska Institutet, Stockholm, Sweden.
| | - Andrew P Duker
- James J. and Joan A. Gardner Family Center for Parkinson's disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
| | | | - Alberto J Espay
- James J. and Joan A. Gardner Family Center for Parkinson's disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States.
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The nuclease activity of DNA2 promotes exonuclease 1-independent mismatch repair. J Biol Chem 2022; 298:101831. [PMID: 35300981 PMCID: PMC9036127 DOI: 10.1016/j.jbc.2022.101831] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/03/2022] Open
Abstract
The DNA mismatch repair (MMR) system is a major DNA repair system that corrects DNA replication errors. In eukaryotes, the MMR system functions via mechanisms both dependent on and independent of exonuclease 1 (EXO1), an enzyme that has multiple roles in DNA metabolism. Although the mechanism of EXO1-dependent MMR is well understood, less is known about EXO1-independent MMR. Here, we provide genetic and biochemical evidence that the DNA2 nuclease/helicase has a role in EXO1-independent MMR. Biochemical reactions reconstituted with purified human proteins demonstrated that the nuclease activity of DNA2 promotes an EXO1-independent MMR reaction via a mismatch excision-independent mechanism that involves DNA polymerase δ. We show that DNA polymerase ε is not able to replace DNA polymerase δ in the DNA2-promoted MMR reaction. Unlike its nuclease activity, the helicase activity of DNA2 is dispensable for the ability of the protein to enhance the MMR reaction. Further examination established that DNA2 acts in the EXO1-independent MMR reaction by increasing the strand-displacement activity of DNA polymerase δ. These data reveal a mechanism for EXO1-independent mismatch repair.
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Luteran EM, Paukstelis PJ. The parallel-stranded d(CGA) duplex is a highly predictable structural motif with two conformationally distinct strands. Acta Crystallogr D Struct Biol 2022; 78:299-309. [PMID: 35234144 PMCID: PMC8900823 DOI: 10.1107/s2059798322000304] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/10/2022] [Indexed: 11/10/2022] Open
Abstract
DNA can adopt noncanonical structures that have important biological functions while also providing structural diversity for applications in nanotechnology. Here, the crystal structures of two oligonucleotides composed of d(CGA) triplet repeats in the parallel-stranded duplex form are described. The structure determination of four unique d(CGA)-based parallel-stranded duplexes across two crystal structures has allowed the structural parameters of d(CGA) triplets in the parallel-stranded duplex form to be characterized and established. These results show that d(CGA) units are highly uniform, but that each strand in the duplex is structurally unique and has a distinct role in accommodating structural asymmetries induced by the C-CH+ base pair.
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Affiliation(s)
- Emily M. Luteran
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Paul J. Paukstelis
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA,Correspondence e-mail:
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Schor NF, Bianchi DW. Neurodevelopmental Clues to Neurodegeneration. Pediatr Neurol 2021; 123:67-76. [PMID: 34399111 PMCID: PMC10040214 DOI: 10.1016/j.pediatrneurol.2021.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/19/2021] [Accepted: 07/21/2021] [Indexed: 12/17/2022]
Abstract
Neurodegenerative disorders are characterized by neuronal loss, usually in late life. But recently, abnormalities of proteins implicated in neurodegenerative disorders have been identified in disorders of childhood, raising the possibility that clues to susceptibility to and prevention of neurodegenerative disorders may be identifiable before symptoms of disease arise. This review leverages these new and evolving findings to test our hypothesis, first proposed in 2010, that proteins implicated in neurodegenerative disorders play important roles in brain development by examining evidence in the peer-reviewed literature published in the past five years for the relevance of these proteins in normal and disease-associated brain development.
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Affiliation(s)
- Nina F Schor
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland.
| | - Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
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Do HA, Baek KH. Cellular functions regulated by deubiquitinating enzymes in neurodegenerative diseases. Ageing Res Rev 2021; 69:101367. [PMID: 34023421 DOI: 10.1016/j.arr.2021.101367] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 12/24/2022]
Abstract
Neurodegenerative diseases are one of the most common diseases in mankind. Although there are reports of several candidates that cause neurodegenerative diseases, the exact mechanism of pathogenesis is poorly understood. The ubiquitin-proteasome system (UPS) is an important posttranslational modification for protein degradation and control of homeostasis. Enzymes such as E1, E2, E3 ligases, and deubiquitinating enzymes (DUBs) participating in UPS, regulate disease-inducing proteins by controlling the degree of ubiquitination. Therefore, the development of treatments targeting enzymes for degenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS), is emerging as an attractive perspective. In particular, as DUBs are able to regulate one or more degenerative disease-related proteins, the potential as a therapeutic target is even more evident. DUBs influence the regulation of toxic proteins that cause neurodegenerative diseases by not only their removal, but also by regulating signals associated with mitophagy, autophagy, and endoplasmic reticulum-associated degradation (ERAD). In this review, we analyze not only the cellular processes of DUBs, which control neurodegenerative disease-inducing proteins, but also their potentials as a therapeutic agent for neurodegenerative diseases.
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Dent P, Booth L, Roberts JL, Poklepovic A, Cridebring D, Reiman EM. Inhibition of heat shock proteins increases autophagosome formation, and reduces the expression of APP, Tau, SOD1 G93A and TDP-43. Aging (Albany NY) 2021; 13:17097-17117. [PMID: 34252884 PMCID: PMC8312464 DOI: 10.18632/aging.203297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022]
Abstract
Aberrant expression and denaturation of Tau, amyloid-beta and TDP-43 can lead to cell death and is a major component of pathologies such as Alzheimer’s Disease (AD). AD neurons exhibit a reduced ability to form autophagosomes and degrade proteins via autophagy. Using genetically manipulated colon cancer cells we determined whether drugs that directly inhibit the chaperone ATPase activity or cause chaperone degradation and endoplasmic reticulum stress signaling leading to macroautophagy could reduce the levels of these proteins. The antiviral chaperone ATPase inhibitor AR12 reduced the ATPase activities and total expression of GRP78, HSP90, and HSP70, and of Tau, Tau 301L, APP, APP692, APP715, SOD1 G93A and TDP-43. In parallel, it increased the phosphorylation of ATG13 S318 and eIF2A S51 and caused eIF2A-dependent autophagosome formation and autophagic flux. Knock down of Beclin1 or ATG5 prevented chaperone, APP and Tau degradation. Neratinib, used to treat HER2+ breast cancer, reduced chaperone levels and expression of Tau and APP via macroautophagy, and neratinib interacted with AR12 to cause further reductions in protein levels. The autophagy-regulatory protein ATG16L1 is expressed as two isoforms, T300 or A300: Africans trend to express T300 and Europeans A300. We observed higher basal expression of Tau in T300 cells when compared to isogenic A300 cells. ATG16L1 isoform expression did not alter basal levels of HSP90, HSP70 or HSP27, however, basal levels of GRP78 were reduced in A300 cells. The abilities of both AR12 and neratinib to stimulate ATG13 S318 and eIF2A S51 phosphorylation and autophagic flux was also reduced in A300 cells. Our data support further evaluation of AR12 and neratinib in neuronal cells as repurposed treatments for AD.
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Affiliation(s)
- Paul Dent
- Department of Biochemistry and Molecular Biology, Richmond, VA 23298, USA
| | - Laurence Booth
- Department of Biochemistry and Molecular Biology, Richmond, VA 23298, USA
| | - Jane L Roberts
- Department of Pharmacology and Toxicology, Richmond, VA 23298, USA
| | - Andrew Poklepovic
- Department of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Derek Cridebring
- Translational Genomics Research Institute (TGEN), Phoenix, AZ 85004, USA
| | - Eric M Reiman
- Translational Genomics Research Institute (TGEN), Phoenix, AZ 85004, USA.,Banner Alzheimer's Institute, Phoenix, AZ 85006, USA
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Richard GF. The Startling Role of Mismatch Repair in Trinucleotide Repeat Expansions. Cells 2021; 10:cells10051019. [PMID: 33925919 PMCID: PMC8145212 DOI: 10.3390/cells10051019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/26/2022] Open
Abstract
Trinucleotide repeats are a peculiar class of microsatellites whose expansions are responsible for approximately 30 human neurological or developmental disorders. The molecular mechanisms responsible for these expansions in humans are not totally understood, but experiments in model systems such as yeast, transgenic mice, and human cells have brought evidence that the mismatch repair machinery is involved in generating these expansions. The present review summarizes, in the first part, the role of mismatch repair in detecting and fixing the DNA strand slippage occurring during microsatellite replication. In the second part, key molecular differences between normal microsatellites and those that show a bias toward expansions are extensively presented. The effect of mismatch repair mutants on microsatellite expansions is detailed in model systems, and in vitro experiments on mismatched DNA substrates are described. Finally, a model presenting the possible roles of the mismatch repair machinery in microsatellite expansions is proposed.
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Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, CNRS UMR3525, 25 rue du Docteur Roux, 75015 Paris, France
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Neuronal Signaling: A reflection on the Biochemical Society's newest journal and an exciting outlook on its next steps. Neuronal Signal 2021; 5:NS20210007. [PMID: 33585040 PMCID: PMC7871031 DOI: 10.1042/ns20210007] [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: 01/29/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 11/17/2022] Open
Abstract
The inaugural Editor-in-Chief of Neuronal Signaling, Aideen M. Sullivan, reflects on the journal's journey so far and welcomes the new Editor-in-Chief, Clare Stanford, as she shares some of the exciting initiatives and plans for its future.
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