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Ceylan B, Düz E, Çakir T. Personalized Protein-Protein Interaction Networks Towards Unraveling the Molecular Mechanisms of Alzheimer's Disease. Mol Neurobiol 2024; 61:2120-2135. [PMID: 37855983 DOI: 10.1007/s12035-023-03690-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
Alzheimer's disease (AD) is a highly heterogenous neurodegenerative disease, and several omic-based datasets were generated in the last decade from the patients with the disease. However, the vast majority of studies evaluate these datasets in bulk by considering all the patients as a single group, which obscures the molecular differences resulting from the heterogeneous nature of the disease. In this study, we adopted a personalized approach and analyzed the transcriptome data from 403 patients individually by mapping the data on a human protein-protein interaction network. Patient-specific subnetworks were discovered and analyzed in terms of the genes in the subnetworks, enriched functional terms, and known AD genes. We identified several affected pathways that could not be captured by the bulk comparison. We also showed that our personalized findings point to patterns of alterations consistent with the recently suggested AD subtypes.
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Affiliation(s)
- Betül Ceylan
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Elif Düz
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Tunahan Çakir
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey.
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2
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Karandikar PV, Suh L, Gerstl JVE, Blitz SE, Qu QR, Won SY, Gessler FA, Arnaout O, Smith TR, Peruzzi PP, Yang W, Friedman GK, Bernstock JD. Positioning SUMO as an immunological facilitator of oncolytic viruses for high-grade glioma. Front Cell Dev Biol 2023; 11:1271575. [PMID: 37860820 PMCID: PMC10582965 DOI: 10.3389/fcell.2023.1271575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Oncolytic viral (OV) therapies are promising novel treatment modalities for cancers refractory to conventional treatment, such as glioblastoma, within the central nervous system (CNS). Although OVs have received regulatory approval for use in the CNS, efficacy is hampered by obstacles related to delivery, under-/over-active immune responses, and the "immune-cold" nature of most CNS malignancies. SUMO, the Small Ubiquitin-like Modifier, is a family of proteins that serve as a high-level regulator of a large variety of key physiologic processes including the host immune response. The SUMO pathway has also been implicated in the pathogenesis of both wild-type viruses and CNS malignancies. As such, the intersection of OV biology with the SUMO pathway makes SUMOtherapeutics particularly interesting as adjuvant therapies for the enhancement of OV efficacy alone and in concert with other immunotherapeutic agents. Accordingly, the authors herein provide: 1) an overview of the SUMO pathway and its role in CNS malignancies; 2) describe the current state of CNS-targeted OVs; and 3) describe the interplay between the SUMO pathway and the viral lifecycle and host immune response.
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Affiliation(s)
- Paramesh V. Karandikar
- T. H. Chan School of Medicine, University of Massachusetts, Worcester, MA, United States
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Lyle Suh
- T. H. Chan School of Medicine, University of Massachusetts, Worcester, MA, United States
| | - Jakob V. E. Gerstl
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Sarah E. Blitz
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Qing Rui Qu
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Sae-Yeon Won
- Department of Neurosurgery, University of Rostock, Rostock, Germany
| | | | - Omar Arnaout
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Timothy R. Smith
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Pier Paolo Peruzzi
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Wei Yang
- Department of Anesthesiology, Multidisciplinary Brain Protection Program, Duke University Medical Center, Durham, NC, United States
| | - Gregory K. Friedman
- Department of Neuro-Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX, United States
| | - Joshua D. Bernstock
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
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Li S, Liang Y, Zou J, Cai Z, Yang H, Yang J, Zhang Y, Lin H, Zhang G, Tan M. SUMOylation of microtubule-cleaving enzyme KATNA1 promotes microtubule severing and neurite outgrowth. J Biol Chem 2022; 298:102292. [PMID: 35868557 PMCID: PMC9403493 DOI: 10.1016/j.jbc.2022.102292] [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: 06/15/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022] Open
Abstract
Katanin p60 ATPase-containing subunit A1 (KATNA1) is a microtubule-cleaving enzyme that regulates the development of neural protrusions through cytoskeletal rearrangements. However, the mechanism underlying the linkage of the small ubiquitin-like modifier (SUMO) protein to KATNA1 and how this modification regulates the development of neural protrusions is unclear. Here we discovered, using mass spectrometry analysis, that SUMO-conjugating enzyme UBC9, an enzyme necessary for the SUMOylation process, was present in the KATNA1 interactome. Moreover, GST-pull down and co-immunoprecipitation assays confirmed that KATNA1 and SUMO interact. We further demonstrated using immunofluorescence experiments that KATNA1 and the SUMO2 isoform colocalized in hippocampal neurites. We also performed a bioinformatics analysis of KATNA1 protein sequences to identify three potentially conserved SUMOylation sites (K77, K157, and K330) among vertebrates. Mutation of K330, but not K77 or K157, abolished KATNA1-induced microtubule severing and decreased the level of binding observed for KATNA1 and SUMO2. Cotransfection of SUMO2 and wildtype KATNA1 in COS7 cells increased microtubule severing, whereas no effect was observed after cotransfection with the K330R KATNA1 mutant. Furthermore, in cultured hippocampal neurons, overexpression of wildtype KATNA1 significantly promoted neurite outgrowth, whereas the K330R mutant eliminated this effect. Taken together, our results demonstrate that the K330 site in KATNA1 is modified by SUMOylation and SUMOylation of KATNA1 promotes microtubule dynamics and hippocampal neurite outgrowth.
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Affiliation(s)
- Shaojin Li
- Department of Orthopaedics, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Yaozhong Liang
- Department of Orthopaedics, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Jianyu Zou
- Department of Orthopaedics, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Zhenbin Cai
- Department of Orthopaedics, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Hua Yang
- Department of Orthopaedics, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Jie Yang
- Department of Orthopaedics, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Yunlong Zhang
- Department of Orthopaedics, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Hongsheng Lin
- Department of Orthopaedics, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China.
| | - Guowei Zhang
- Department of Orthopaedics, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China.
| | - Minghui Tan
- Department of Orthopaedics, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China.
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Long Y, Cheng Y, Yang J, Yang T, Lai Y. Abeta-induced Presynaptic Release of UBC9 through Extracellular Vesicles involves SNAP23. Neurosci Lett 2022; 785:136771. [DOI: 10.1016/j.neulet.2022.136771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/20/2022] [Accepted: 06/30/2022] [Indexed: 11/26/2022]
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Liu Y, Tian X, Ke P, Gu J, Ma Y, Guo Y, Xu X, Chen Y, Yang M, Wang X, Xiao F. KIF17 Modulates Epileptic Seizures and Membrane Expression of the NMDA Receptor Subunit NR2B. Neurosci Bull 2022; 38:841-856. [PMID: 35678994 PMCID: PMC9352834 DOI: 10.1007/s12264-022-00888-9] [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: 09/12/2021] [Accepted: 04/01/2022] [Indexed: 10/18/2022] Open
Abstract
Epilepsy is a common and severe brain disease affecting >65 million people worldwide. Recent studies have shown that kinesin superfamily motor protein 17 (KIF17) is expressed in neurons and is involved in regulating the dendrite-targeted transport of N-methyl-D-aspartate receptor subtype 2B (NR2B). However, the effect of KIF17 on epileptic seizures remains to be explored. We found that KIF17 was mainly expressed in neurons and that its expression was increased in epileptic brain tissue. In the kainic acid (KA)-induced epilepsy mouse model, KIF17 overexpression increased the severity of epileptic activity, whereas KIF17 knockdown had the opposite effect. In electrophysiological tests, KIF17 regulated excitatory synaptic transmission, potentially due to KIF17-mediated NR2B membrane expression. In addition, this report provides the first demonstration that KIF17 is modified by SUMOylation (SUMO, small ubiquitin-like modifier), which plays a vital role in the stabilization and maintenance of KIF17 in epilepsy.
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Affiliation(s)
- Yan Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing, 400016, China
| | - Xin Tian
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing, 400016, China
| | - Pingyang Ke
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing, 400016, China
| | - Juan Gu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing, 400016, China
| | - Yuanlin Ma
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing, 400016, China
| | - Yi Guo
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing, 400016, China
| | - Xin Xu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing, 400016, China
| | - Yuanyuan Chen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing, 400016, China
| | - Min Yang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing, 400016, China
| | - Xuefeng Wang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing, 400016, China.
| | - Fei Xiao
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing, 400016, China.
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Chakrabarty R, Yousuf S, Singh MP. Contributive Role of Hyperglycemia and Hypoglycemia Towards the Development of Alzheimer's Disease. Mol Neurobiol 2022; 59:4274-4291. [PMID: 35503159 DOI: 10.1007/s12035-022-02846-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/20/2022] [Indexed: 11/30/2022]
Abstract
Alzheimer's disease (AD) is one of the causes of dementia that results from several infections/biological conditions leading to either cell disruption or loss of neuronal communication. Studies have documented the accumulation of two proteins, beta-amyloid (Aβ), which accumulates on the exteriors of neurons, and tau (Tau), which assembles at the interiors of brain cells and is chiefly liable for the progression of the disease. Several molecular and cellular pathways account for the accumulation of amyloid-β and the formation of neurofibrillary tangles, which are phosphorylated variants of Tau protein. Moreover, research has revealed a potential connection between AD and diabetes. It has also been demonstrated that both hypoglycemia and hyperglycemia have a significant role in the development of AD. In addition, SUMO (small ubiquitin-like modifier protein) plays a crucial role in the pathogenesis of AD. SUMOylation is the process by which modification of amyloid precursor protein (APP) and Tau takes place. Furthermore, Drosophila melanogaster has proven to be an efficient model organism in studies to establish the relationship between AD and variations in blood glucose levels. In addition, the review successfully identifies the common pathway that links the effects of fluctuations in glucose levels on AD pathogenesis and advancements.
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Affiliation(s)
- Riya Chakrabarty
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Ludhiana National Highway, Phagwara, Punjab, 144411, India
| | - Sumaira Yousuf
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Ludhiana National Highway, Phagwara, Punjab, 144411, India
| | - Mahendra P Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Ludhiana National Highway, Phagwara, Punjab, 144411, India.
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E3 ligases: a potential multi-drug target for different types of cancers and neurological disorders. Future Med Chem 2022; 14:187-201. [DOI: 10.4155/fmc-2021-0157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ubiquitylation is a posttranslational modification of proteins that is necessary for a variety of cellular processes. E1 ubiquitin activating enzyme, E2 ubiquitin conjugating enzyme, and E3 ubiquitin ligase are all involved in transferring ubiquitin to the target substrate to regulate cellular function. The objective of this review is to provide an overview of different aspects of E3 ubiquitin ligases that can lead to major biological system failure in several deadly diseases. The first part of this review covers the important characteristics of E3 ubiquitin ligases and their classification based on structural domains. Further, the authors provide some online resources that help researchers explore the data relevant to the enzyme. The following section delves into the involvement of E3 ubiquitin ligases in various diseases and biological processes, including different types of cancer and neurological disorders.
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Chang KC. Influence of Sox protein SUMOylation on neural development and regeneration. Neural Regen Res 2022; 17:477-481. [PMID: 34380874 PMCID: PMC8504373 DOI: 10.4103/1673-5374.320968] [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] [Indexed: 11/04/2022] Open
Abstract
SRY-related HMG-box (Sox) transcription factors are known to regulate central nervous system development and are involved in several neurological diseases. Post-translational modification of Sox proteins is known to alter their functions in the central nervous system. Among the different types of post-translational modification, small ubiquitin-like modifier (SUMO) modification of Sox proteins has been shown to modify their transcriptional activity. Here, we review the mechanisms of three Sox proteins in neuronal development and disease, along with their transcriptional changes under SUMOylation. Across three species, lysine is the conserved residue for SUMOylation. In Drosophila, SUMOylation of SoxN plays a repressive role in transcriptional activity, which impairs central nervous system development. However, deSUMOylation of SoxE and Sox11 plays neuroprotective roles, which promote neural crest precursor formation in Xenopus and retinal ganglion cell differentiation as well as axon regeneration in the rodent. We further discuss a potential translational therapy by SUMO site modification using AAV gene transduction and Clustered regularly interspaced short palindromic repeats-Cas9 technology. Understanding the underlying mechanisms of Sox SUMOylation, especially in the rodent system, may provide a therapeutic strategy to address issues associated with neuronal development and neurodegeneration.
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Affiliation(s)
- Kun-Che Chang
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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