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Chen J, Xu J, Gou L, Zhu Y, Zhong W, Guo H, Du Y. Integrating transcriptomic and proteomic data for a comprehensive molecular perspective on the association between sarcopenia and osteoporosis. Arch Gerontol Geriatr 2024; 125:105486. [PMID: 38761527 DOI: 10.1016/j.archger.2024.105486] [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: 12/02/2023] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND Osteoporosis and sarcopenia are common age-related conditions characterized by the progressive loss of bone density and muscle mass, respectively. Their co-occurrence, often referred to as osteosarcopenia, presents significant challenges in elderly care due to increased fragility and functional impairment. Existing studies have identified shared pathological mechanisms between these conditions, including inflammation, hormonal imbalances, and metabolic dysregulation, but a comprehensive understanding of their molecular interplay remains incomplete. OBJECTIVE This study aims to deepen our understanding of the molecular interactions between sarcopenia and osteoporosis through an integrated omics approach, revealing potential therapeutic targets and biomarkers. METHODS Employing a combination of proteomics and transcriptomics analyses, this study analyzed bone and muscle tissue samples from patients diagnosed with osteoporosis and osteosarcopenia. Techniques included high-throughput sequencing and label-free proteomics, supported by advanced bioinformatics tools for data analysis and functional annotation of genes and proteins. RESULTS The study found marked differences in gene and protein expressions between osteoporosis and osteosarcopenia tissues. Specifically, genes like PDIA5, TUBB1, and CYFIP2 in bone, along with MYH7 and NCAM1 in muscle, exhibited differential expression at both mRNA and protein levels. Pathway analyses revealed the significance of oxidative-reduction balance, cellular metabolism, and immune response in the progression of these conditions. Importantly, the study pinpointed osteoclast differentiation and NF-kappa B signaling pathways as critical in the molecular dynamics of osteosarcopenia, suggesting potential targets for therapy. CONCLUSIONS This study utilized transcriptomics and proteomics to identify key genes and proteins impacting sarcopenia and osteoporosis, employing advanced network tools to delineate interaction networks and crucial signaling pathways. It highlighted genes like PDIA5 and TUBB1, consistently expressed in both analyses, involved in pathways such as osteoclast differentiation and cytokine interactions. These insights enhance understanding of the molecular interplay in bone and muscle degeneration with aging, suggesting directions for future research into therapeutic interventions and prevention strategies for age-related degenerative diseases.
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Affiliation(s)
- Jincheng Chen
- The Third Affiliated Hospital of Guangxi University of Chinese Medicine, Liuzhou, 545000, PR China; Department of Orthopedics, Fujian Provincial Hospital, Fujian Medical University, Fuzhou, 350000, PR China.
| | - Jie Xu
- Department of Orthopedics, Fujian Provincial Hospital, Fujian Medical University, Fuzhou, 350000, PR China; Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350000, PR China
| | - Lingyun Gou
- The Third Affiliated Hospital of Guangxi University of Chinese Medicine, Liuzhou, 545000, PR China
| | - Yong Zhu
- The Third Affiliated Hospital of Guangxi University of Chinese Medicine, Liuzhou, 545000, PR China
| | - Weihua Zhong
- The Third Affiliated Hospital of Guangxi University of Chinese Medicine, Liuzhou, 545000, PR China
| | - Hai Guo
- The Third Affiliated Hospital of Guangxi University of Chinese Medicine, Liuzhou, 545000, PR China
| | - Yujuan Du
- The Second People's Hospital of Kunming, Kunming, 650000, PR China
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Kim Y, Ma R, Zhang Y, Kang HR, Kim US, Han K. Cell-autonomous reduction of CYFIP2 changes dendrite length, dendritic protrusion morphology, and inhibitory synapse density in the hippocampal CA1 pyramidal neurons of 17-month-old mice. Anim Cells Syst (Seoul) 2024; 28:294-302. [PMID: 38832126 PMCID: PMC11146249 DOI: 10.1080/19768354.2024.2360740] [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: 04/17/2024] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
The cytoplasmic FMR1-interacting protein 2 (CYFIP2) have diverse molecular functions in neurons, including the regulation of actin polymerization, mRNA translation, and mitochondrial morphology and function. Mutations in the CYFIP2 gene are associated with early-onset epilepsy and neurodevelopmental disorders, while decreases in its protein levels are linked to Alzheimer's disease (AD). Notably, previous research has revealed AD-like phenotypes, such as dendritic spine loss, in the hippocampal CA1 pyramidal neurons of 12-month-old Cyfip2 heterozygous mice but not of age-matched CA1 pyramidal neuron-specific Cyfip2 conditional knock-out (cKO) mice. This study aims to investigate whether dendritic spine loss in Cyfip2 cKO mice is merely delayed compared to Cyfip2 heterozygous mice, and to explore further neuronal phenotypes regulated by CYFIP2 in aged mice. We characterized dendrite and dendritic protrusion morphologies, along with excitatory/inhibitory synapse densities in CA1 pyramidal neurons of 17-month-old Cyfip2 cKO mice. Overall dendritic branching was normal, with a reduction in the length of basal, not apical, dendrites in CA1 pyramidal neurons of Cyfip2 cKO mice. Furthermore, while dendritic protrusion density remained normal, alterations were observed in the length of mushroom spines and the head volume of stubby spines in basal, not apical, dendrites of Cyfip2 cKO mice. Although excitatory synapse density remained unchanged, inhibitory synapse density increased in apical, not basal, dendrites of Cyfip2 cKO mice. Consequently, a cell-autonomous reduction of CYFIP2 appears insufficient to induce dendritic spine loss in CA1 pyramidal neurons of aged mice. However, CYFIP2 is required to maintain normal dendritic length, dendritic protrusion morphology, and inhibitory synapse density.
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Affiliation(s)
- Yoonhee Kim
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ruiying Ma
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Yinhua Zhang
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyae Rim Kang
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - U Suk Kim
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kihoon Han
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
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3
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Xie PL, Zheng MY, Han R, Chen WX, Mao JH. Pharmacological mTOR inhibitors in ameliorating Alzheimer's disease: current review and perspectives. Front Pharmacol 2024; 15:1366061. [PMID: 38873415 PMCID: PMC11169825 DOI: 10.3389/fphar.2024.1366061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/25/2024] [Indexed: 06/15/2024] Open
Abstract
Traditionally, pharmacological mammalian/mechanistic targets of rapamycin (mTOR) kinase inhibitors have been used during transplantation and tumor treatment. Emerging pre-clinical evidence from the last decade displayed the surprising effectiveness of mTOR inhibitors in ameliorating Alzheimer's Disease (AD), a common neurodegenerative disorder characterized by progressive cognitive function decline and memory loss. Research shows mTOR activation as an early event in AD development, and inhibiting mTOR may promote the resolution of many hallmarks of Alzheimer's. Aberrant protein aggregation, including amyloid-beta (Aβ) deposition and tau filaments, and cognitive defects, are reversed upon mTOR inhibition. A closer inspection of the evidence highlighted a temporal dependence and a hallmark-specific nature of such beneficial effects. Time of administration relative to disease progression, and a maintenance of a functional lysosomal system, could modulate its effectiveness. Moreover, mTOR inhibition also exerts distinct effects between neurons, glial cells, and endothelial cells. Different pharmacological properties of the inhibitors also produce different effects based on different blood-brain barrier (BBB) entry capacities and mTOR inhibition sites. This questions the effectiveness of mTOR inhibition as a viable AD intervention strategy. In this review, we first summarize the different mTOR inhibitors available and their characteristics. We then comprehensively update and discuss the pre-clinical results of mTOR inhibition to resolve many of the hallmarks of AD. Key pathologies discussed include Aβ deposition, tauopathies, aberrant neuroinflammation, and neurovascular system breakdowns.
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Affiliation(s)
- Pei-Lun Xie
- University College London, London, United Kingdom
| | | | - Ran Han
- Dongfang Hospital of Beijing University of Chinese Medicine, Beijing, China
| | - Wei-Xin Chen
- Dongfang Hospital of Beijing University of Chinese Medicine, Beijing, China
| | - Jin-Hua Mao
- Beijing University of Chinese Medicine, Beijing, China
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4
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Mall R, Singh A, Patel CN, Guirimand G, Castiglione F. VISH-Pred: an ensemble of fine-tuned ESM models for protein toxicity prediction. Brief Bioinform 2024; 25:bbae270. [PMID: 38842509 PMCID: PMC11154842 DOI: 10.1093/bib/bbae270] [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: 02/29/2024] [Revised: 05/06/2024] [Accepted: 05/23/2024] [Indexed: 06/07/2024] Open
Abstract
Peptide- and protein-based therapeutics are becoming a promising treatment regimen for myriad diseases. Toxicity of proteins is the primary hurdle for protein-based therapies. Thus, there is an urgent need for accurate in silico methods for determining toxic proteins to filter the pool of potential candidates. At the same time, it is imperative to precisely identify non-toxic proteins to expand the possibilities for protein-based biologics. To address this challenge, we proposed an ensemble framework, called VISH-Pred, comprising models built by fine-tuning ESM2 transformer models on a large, experimentally validated, curated dataset of protein and peptide toxicities. The primary steps in the VISH-Pred framework are to efficiently estimate protein toxicities taking just the protein sequence as input, employing an under sampling technique to handle the humongous class-imbalance in the data and learning representations from fine-tuned ESM2 protein language models which are then fed to machine learning techniques such as Lightgbm and XGBoost. The VISH-Pred framework is able to correctly identify both peptides/proteins with potential toxicity and non-toxic proteins, achieving a Matthews correlation coefficient of 0.737, 0.716 and 0.322 and F1-score of 0.759, 0.696 and 0.713 on three non-redundant blind tests, respectively, outperforming other methods by over $10\%$ on these quality metrics. Moreover, VISH-Pred achieved the best accuracy and area under receiver operating curve scores on these independent test sets, highlighting the robustness and generalization capability of the framework. By making VISH-Pred available as an easy-to-use web server, we expect it to serve as a valuable asset for future endeavors aimed at discerning the toxicity of peptides and enabling efficient protein-based therapeutics.
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Affiliation(s)
- Raghvendra Mall
- Biotechnology Research Center, Technology Innovation Institute, P.O. Box 9639, Abu Dhabi, United Arab Emirates
| | - Ankita Singh
- Biotechnology Research Center, Technology Innovation Institute, P.O. Box 9639, Abu Dhabi, United Arab Emirates
| | - Chirag N Patel
- Biotechnology Research Center, Technology Innovation Institute, P.O. Box 9639, Abu Dhabi, United Arab Emirates
| | - Gregory Guirimand
- Biotechnology Research Center, Technology Innovation Institute, P.O. Box 9639, Abu Dhabi, United Arab Emirates
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Filippo Castiglione
- Biotechnology Research Center, Technology Innovation Institute, P.O. Box 9639, Abu Dhabi, United Arab Emirates
- Institute for Applied Computing, National Research Council of Italy, Via dei Taurini, 19, 00185, Rome, Italy
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Li H, Khang TF. SIEVE: One-stop differential expression, variability, and skewness analyses using RNA-Seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588804. [PMID: 38645120 PMCID: PMC11030344 DOI: 10.1101/2024.04.09.588804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Motivation RNA-Seq data analysis is commonly biased towards detecting differentially expressed genes and insufficiently conveys the complexity of gene expression changes between biological conditions. This bias arises because discrete models of RNA-Seq count data cannot fully characterize the mean, variance, and skewness of gene expression distribution using independent model parameters. A unified framework that simultaneously tests for differential expression, variability, and skewness is needed to realize the full potential of RNA-Seq data analysis in a systems biology context. Results We present SIEVE, a statistical methodology that provides the desired unified framework. SIEVE embraces a compositional data analysis framework that transforms discrete RNA-Seq counts to a continuous form with a distribution that is well-fitted by a skew-normal distribution. Simulation results show that SIEVE controls the false discovery rate and probability of Type II error better than existing methods for differential expression analysis. Analysis of the Mayo RNA-Seq dataset for Alzheimer's disease using SIEVE reveals that a gene set with significant expression difference in mean, standard deviation and skewness between the control and the Alzheimer's disease group strongly predicts a subject's disease state. Furthermore, functional enrichment analysis shows that relying solely on differentially expressed genes detects only a segment of a much broader spectrum of biological aspects associated with Alzheimer's disease. The latter aspects can only be revealed using genes that show differential variability and skewness. Thus, SIEVE enables fresh perspectives for understanding the intricate changes in gene expression that occur in complex diseases. Availability The SIEVE R package and source codes are available at https://github.com/Divo-Lee/SIEVE .
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Ge J, Wang Z, Wu J. NAT10-mediated ac 4C modification promotes ectoderm differentiation of human embryonic stem cells via acetylating NR2F1 mRNA. Cell Prolif 2024; 57:e13577. [PMID: 38041497 PMCID: PMC10984107 DOI: 10.1111/cpr.13577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/11/2023] [Accepted: 11/01/2023] [Indexed: 12/03/2023] Open
Abstract
Cell fate determination in mammalian development is complex and precisely controlled and accumulating evidence indicates that epigenetic mechanisms are crucially involved. N4-acetylcytidine (ac4C) is a recently identified modification of messenger RNA (mRNA); however, its functions are still elusive in mammalian. Here, we show that N-acetyltransferase 10 (NAT10)-mediated ac4C modification promotes ectoderm differentiation of human embryonic stem cells (hESCs) by acetylating nuclear receptor subfamily 2 group F member 1 (NR2F1) mRNA to enhance translation efficiency (TE). Acetylated RNA immunoprecipitation sequencing (acRIP-seq) revealed that levels of ac4C modification were higher in ectodermal neuroepithelial progenitor (NEP) cells than in hESCs or mesoendoderm cells. In addition, integrated analysis of acRIP-seq and ribosome profiling sequencing revealed that NAT10 catalysed ac4C modification to improve TE in NEP cells. RIP-qRT-PCR analysis identified an interaction between NAT10 and NR2F1 mRNA in NEP cells and NR2F1 accelerated the nucleus-to-cytoplasm translocation of yes-associated protein 1, which contributed to ectodermal differentiation of hESCs. Collectively, these findings point out the novel regulatory role of ac4C modification in the early ectodermal differentiation of hESCs and will provide a new strategy for the treatment of neuroectodermal defects diseases.
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Affiliation(s)
- Junbang Ge
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
| | - Zhaoxia Wang
- Laboratory Animal Center of Instrumental Analysis CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Ji Wu
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, School of Basic Medical SciencesNingxia Medical UniversityYinchuanChina
- Shanghai Key Laboratory of Reproductive MedicineShanghaiChina
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7
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Di Liegro CM, Schiera G, Schirò G, Di Liegro I. Role of Post-Transcriptional Regulation in Learning and Memory in Mammals. Genes (Basel) 2024; 15:337. [PMID: 38540396 PMCID: PMC10970538 DOI: 10.3390/genes15030337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 06/14/2024] Open
Abstract
After many decades, during which most molecular studies on the regulation of gene expression focused on transcriptional events, it was realized that post-transcriptional control was equally important in order to determine where and when specific proteins were to be synthesized. Translational regulation is of the most importance in the brain, where all the steps of mRNA maturation, transport to different regions of the cells and actual expression, in response to specific signals, constitute the molecular basis for neuronal plasticity and, as a consequence, for structural stabilization/modification of synapses; notably, these latter events are fundamental for the highest brain functions, such as learning and memory, and are characterized by long-term potentiation (LTP) of specific synapses. Here, we will discuss the molecular bases of these fundamental events by considering both the role of RNA-binding proteins (RBPs) and the effects of non-coding RNAs involved in controlling splicing, editing, stability and translation of mRNAs. Importantly, it has also been found that dysregulation of mRNA metabolism/localization is involved in many pathological conditions, arising either during brain development or in the adult nervous system.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (C.M.D.L.); (G.S.)
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (C.M.D.L.); (G.S.)
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy;
- Neurology and Multiple Sclerosis Center, Unità Operativa Complessa (UOC), Foundation Institute “G. Giglio”, 90015 Cefalù, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy;
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8
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Lawer A, Schulz L, Sawyer R, Liu X. Harmony of Protein Tags and Chimeric Molecules Empowers Targeted Protein Ubiquitination and Beyond. Cells 2024; 13:426. [PMID: 38474390 DOI: 10.3390/cells13050426] [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: 01/26/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Post-translational modifications (PTMs) are crucial mechanisms that underlie the intricacies of biological systems and disease mechanisms. This review focuses on the latest advancements in the design of heterobifunctional small molecules that hijack PTM machineries for target-specific modifications in living systems. A key innovation in this field is the development of proteolysis-targeting chimeras (PROTACs), which promote the ubiquitination of target proteins for proteasomal degradation. The past decade has seen several adaptations of the PROTAC concept to facilitate targeted (de)phosphorylation and acetylation. Protein fusion tags have been particularly vital in these proof-of-concept studies, aiding in the investigation of the functional roles of post-translationally modified proteins linked to diseases. This overview delves into protein-tagging strategies that enable the targeted modulation of ubiquitination, phosphorylation, and acetylation, emphasizing the synergies and challenges of integrating heterobifunctional molecules with protein tags in PTM research. Despite significant progress, many PTMs remain to be explored, and protein tag-assisted PTM-inducing chimeras will continue to play an important role in understanding the fundamental roles of protein PTMs and in exploring the therapeutic potential of manipulating protein modifications, particularly for targets not yet addressed by existing drugs.
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Affiliation(s)
- Aggie Lawer
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW 2050, Australia
- Heart Research Institute, The University of Sydney, Newtown, NSW 2042, Australia
| | - Luke Schulz
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Renata Sawyer
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW 2050, Australia
- Heart Research Institute, The University of Sydney, Newtown, NSW 2042, Australia
| | - Xuyu Liu
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW 2050, Australia
- Heart Research Institute, The University of Sydney, Newtown, NSW 2042, Australia
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Zammit AR, Bennett DA, Buchman AS. From theory to practice: translating the concept of cognitive resilience to novel therapeutic targets that maintain cognition in aging adults. Front Aging Neurosci 2024; 15:1303912. [PMID: 38283067 PMCID: PMC10811007 DOI: 10.3389/fnagi.2023.1303912] [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: 09/28/2023] [Accepted: 12/06/2023] [Indexed: 01/30/2024] Open
Abstract
While the concept of cognitive resilience is well-established it has not been defined in a way that can be measured. This has been an impediment to studying its underlying biology and to developing instruments for its clinical assessment. This perspective highlights recent work that has quantified the expression of cortical proteins associated with cognitive resilience, thus facilitating studies of its complex underlying biology and the full range of its clinical effects in aging adults. These initial studies provide empirical support for the conceptualization of resilience as a continuum. Like other conventional risk factors, some individuals manifest higher-than-average cognitive resilience and other individuals manifest lower-than-average cognitive resilience. These novel approaches for advancing studies of cognitive resilience can be generalized to other aging phenotypes and can set the stage for the development of clinical tools that might have the potential to measure other mechanisms of resilience in aging adults. These advances also have the potential to catalyze a complementary therapeutic approach that focuses on augmenting resilience via lifestyle changes or therapies targeting its underlying molecular mechanisms to maintain cognition and brain health even in the presence of untreatable stressors like brain pathologies that accumulate in aging adults.
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Affiliation(s)
- Andrea R. Zammit
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
- Department of Psychiatry and Behavioral Sciences, Rush University Medical Center, Chicago, IL, United States
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Aron S. Buchman
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
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10
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Peng X, Wellard N, Ghosh A, Troakes C, Giese KP. Different dysregulations of CYFIP1 and CYFIP2 in distinct types of dementia. Brain Res Bull 2024; 206:110849. [PMID: 38128786 DOI: 10.1016/j.brainresbull.2023.110849] [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: 11/03/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
In humans, the cytoplasmic FMR1 interacting protein (CYFIP) family consists of two members, namely CYFIP1 and CYFIP2. Both CYFIP1 and CYFIP2 function in the WAVE regulatory complex (WRC), which regulates actin polymerization. Additionally, these two proteins form a posttranscriptional regulatory complex with the fragile X mental retardation protein (FMRP), which suppresses mRNA translation. Thus, CYFIP1 and CYFIP2 are important signalling regulators at synapses, and mutations in their genes are associated with neurodevelopmental and neuropsychiatric disorders, including intellectual disabilities. Moreover, dysregulation of the CYFIP protein family is involved in Alzheimer's disease (AD). However, the relevance of the CYFIP family in other dementias is largely unknown. Here, we compared CYFIP1/2 protein levels in the post-mortem hippocampus from patients with AD, dementia with Lewy bodies (DLB), vascular dementia (VaD) and frontotemporal lobar degeneration with TDP-43 pathology (FTLD-TDP). Consistent with previous findings, CYFIP2 was reduced in AD hippocampus. In DLB and VaD hippocampus, the protein level of CYFIP2 and CYFIP1 was unaltered. Finally, an increase in the protein level of both CYFIP1 and CYFIP2 was noted in FTLD-TDP hippocampus. These findings reveal that the protein levels of the CYFIP family is distinct in different types of dementia, suggesting that the pathogenesis of these neurodegenerative disorders has divergent impacts on hippocampal synaptic function.
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Affiliation(s)
- Xianhui Peng
- Department of Basic and Clinical Neuroscience, King's College London, 125 Coldharbour Lane, London SE5 9NU, United Kingdom
| | - Natalie Wellard
- Department of Basic and Clinical Neuroscience, King's College London, 125 Coldharbour Lane, London SE5 9NU, United Kingdom
| | - Anshua Ghosh
- Department of Basic and Clinical Neuroscience, King's College London, 125 Coldharbour Lane, London SE5 9NU, United Kingdom
| | - Claire Troakes
- Department of Basic and Clinical Neuroscience, King's College London, 125 Coldharbour Lane, London SE5 9NU, United Kingdom
| | - K Peter Giese
- Department of Basic and Clinical Neuroscience, King's College London, 125 Coldharbour Lane, London SE5 9NU, United Kingdom.
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11
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Shao S, Ye X, Su W, Wang Y. Curcumin alleviates Alzheimer's disease by inhibiting inflammatory response, oxidative stress and activating the AMPK pathway. J Chem Neuroanat 2023; 134:102363. [PMID: 37989445 DOI: 10.1016/j.jchemneu.2023.102363] [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: 08/18/2023] [Revised: 11/10/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is a common degenerative brain disorder with limited therapeutic options. Curcumin (Cur) exhibits neuroprotective function in many diseases. We aimed to explore the role and mechanism of Cur in AD. MATERIALS AND METHODS Firstly, we established AD mice by injecting amyloid-β1-42 (Aβ1-42) solution into the hippocampus. Then, the AD mice received 150 mg/kg/d Cur for 10 consecutive days. The Morris water maze test was conducted to evaluate the cognitive function of the mice by hidden platform training and probe trials. To assess the spatial memory of the mice, spontaneous alternation behavior, the number of crossing the novel arm and the time spent in the novel arm during the Y-maze test was recorded. Hematoxylin and eosin (H&E) staining and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNAL) assay were performed to assess the pathological damage and apoptosis of brain tissues. The number of damaged neurons was inspected by Nissl staining. Immunohistochemical staining was then performed to detect Aβ1-42 deposition. The levels of tumor necrosis factor-α (TNF-a), interleukin-6 (IL-6) and interleukin-1β (IL-1β) in serum and hippocampus, the contents of super oxide dismutase (SOD) and malondialdehyde (MDA) in brain tissues were assessed by enzyme-linked immunosorbent assay (ELISA). Additionally, B-cell lymphoma-2 (Bcl-2), Bcl-2 associated X protein (Bax), RelA (p65) protein expressions and Adenosine 5'-monophosphate-activated protein kinase (AMPK) phosphorylation were tested using Western blot. RESULTS Cur not only improved cognitive function and spatial memory, but also alleviated the pathological damage and apoptosis of brain tissues for AD mice. Meanwhile, upon Cur treatment, the number of damaged neurons in AD mice was decreased, the level of Aβ1-42 in AD mice was significantly decreased. Furthermore, the AD mice treated with Cur exhibited lower TNF-a, IL-6, IL-1β and MDA levels and a higher SOD content. Besides, Cur also downregulated p65 expression and upregulated AMPK phosphorylation. CONCLUSION Cur may improve AD via suppressing the inflammatory response, oxidative stress and activating the AMPK pathway, suggesting that Cur may be a potential drug for AD.
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Affiliation(s)
- Sen Shao
- Department of Neurology, The Xixi Hospital of Hangzhou Affiliated to Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaojun Ye
- Department of Neurology, the Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Wenwen Su
- Department of Internal Medicine, CiXi Seventh People's Hospital, Ningbo, China
| | - Yanbo Wang
- Department of Neurology, the Third Affiliated Hospital of Zhejiang Chinese Medicine University, Hangzhou, China.
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12
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Margvelani G, Welden JR, Maquera AA, Van Eyk JE, Murray C, Miranda Sardon SC, Stamm S. Influence of FTDP-17 mutants on circular Tau RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.08.556913. [PMID: 37786725 PMCID: PMC10541600 DOI: 10.1101/2023.09.08.556913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
At least 53 mutations in the microtubule associated protein tau gene (MAPT) have been identified that cause frontotemporal dementia. 47 of these mutations are localized between exons 7 and 13. They could thus affect the formation of circular RNAs (circRNAs) from the MAPT gene that occur through backsplicing from exon 12 to either exon 10 or exon 7. We analyzed representative mutants and found that five FTDP-17 mutations increase the formation of 12➔7 circRNA and three different mutations increase the amount of 12➔10 circRNA. CircRNAs are translated after undergoing adenosine to inosine RNA editing, catalyzed by ADAR enzymes. We found that the interferon induced ADAR1-p150 isoform has the strongest effect on circTau RNA translation. ADAR1-p150 activity had a stronger effect on circTau RNA expression and strongly decreased 12➔7 circRNA, but unexpectedly increased 12➔10 circRNA. In both cases, ADAR-activity strongly promoted translation of circTau RNAs. Unexpectedly, we found that the 12➔7 circTau protein interacts with eukaryotic initiation factor 4B (eIF4B), which is reduced by four FTDP-17 mutations located in the second microtubule domain. These are the first studies of the effect of human mutations on circular RNA formation and translation. They show that point mutations influence circRNA expression levels, likely through changes in the secondary pre-mRNA structures. The effect of the mutations is surpassed by editing of the circular RNAs, leading to their translation. Thus, circular RNAs and their editing status should be considered when analyzing FTDP-17 mutations. Highlights 47/53 known FTDP-17 mutations are located in regions that could influence generation of circular RNAs from the MAPT geneCircular Tau RNAs are translated after adenosine to inosine RNA editing, most effectively caused by ADAR1-p150FTDP-17 mutations influence both circTau RNA and circTau protein expression levelsCircTau protein expression levels do not correlate with circTau RNA expression levelsCircTau proteins bind to eukaryotic initiation factor 4B, which is antagonized by FTDP-17 mutations in exon 10. Graphic Abstract
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13
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Varesi A, Campagnoli LIM, Barbieri A, Rossi L, Ricevuti G, Esposito C, Chirumbolo S, Marchesi N, Pascale A. RNA binding proteins in senescence: A potential common linker for age-related diseases? Ageing Res Rev 2023; 88:101958. [PMID: 37211318 DOI: 10.1016/j.arr.2023.101958] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/09/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023]
Abstract
Aging represents the major risk factor for the onset and/or progression of various disorders including neurodegenerative diseases, metabolic disorders, and bone-related defects. As the average age of the population is predicted to exponentially increase in the coming years, understanding the molecular mechanisms underlying the development of aging-related diseases and the discovery of new therapeutic approaches remain pivotal. Well-reported hallmarks of aging are cellular senescence, genome instability, autophagy impairment, mitochondria dysfunction, dysbiosis, telomere attrition, metabolic dysregulation, epigenetic alterations, low-grade chronic inflammation, stem cell exhaustion, altered cell-to-cell communication and impaired proteostasis. With few exceptions, however, many of the molecular players implicated within these processes as well as their role in disease development remain largely unknown. RNA binding proteins (RBPs) are known to regulate gene expression by dictating at post-transcriptional level the fate of nascent transcripts. Their activity ranges from directing primary mRNA maturation and trafficking to modulation of transcript stability and/or translation. Accumulating evidence has shown that RBPs are emerging as key regulators of aging and aging-related diseases, with the potential to become new diagnostic and therapeutic tools to prevent or delay aging processes. In this review, we summarize the role of RBPs in promoting cellular senescence and we highlight their dysregulation in the pathogenesis and progression of the main aging-related diseases, with the aim of encouraging further investigations that will help to better disclose this novel and captivating molecular scenario.
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Affiliation(s)
- Angelica Varesi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
| | | | - Annalisa Barbieri
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy
| | - Lorenzo Rossi
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | | | - Ciro Esposito
- Department of Internal Medicine and Therapeutics, University of Pavia, Italy; Nephrology and dialysis unit, ICS S. Maugeri SPA SB Hospital, Pavia, Italy; High School in Geriatrics, University of Pavia, Italy
| | | | - Nicoletta Marchesi
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy
| | - Alessia Pascale
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy.
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14
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Fernandez A, Monsen PJ, Platanias LC, Schiltz GE. Medicinal chemistry approaches to target the MNK-eIF4E axis in cancer. RSC Med Chem 2023; 14:1060-1087. [PMID: 37360400 PMCID: PMC10285747 DOI: 10.1039/d3md00121k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
Aberrant translation of proteins that promote cell proliferation is an essential factor that defines oncogenic processes and cancer. The process for ribosomal translation of proteins from mRNA requires an essential initiation step which is controlled by the protein eIF4E, which binds the RNA 5'-cap and forms the eIF4F complex that subsequently translates protein. Typically, eIF4E is activated by phosphorylation on Ser209 by MNK1 and MNK2 kinases. Substantial work has shown that eIF4E and MNK1/2 are dysregulated in many cancers and this axis has therefore become an active area of interest for developing new cancer therapeutics. This review summarizes and discusses recent work to develop small molecules that target different steps in the MNK-eIF4E axis as potential cancer therapeutics. The aim of this review is to cover the breadth of different molecular approaches being taken and the medicinal chemistry basis for their optimization and testing as new cancer therapeutics.
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Affiliation(s)
- Ann Fernandez
- Department of Chemistry, Northwestern University Evanston IL 60208 USA
| | - Paige J Monsen
- Department of Chemistry, Northwestern University Evanston IL 60208 USA
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center Chicago IL 60611 USA
- Division of Hematology-Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University Chicago IL 60611 USA
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center Chicago IL 60612 USA
| | - Gary E Schiltz
- Department of Chemistry, Northwestern University Evanston IL 60208 USA
- Robert H. Lurie Comprehensive Cancer Center Chicago IL 60611 USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine Chicago IL 60611 USA
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15
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Vijay Kumar MJ, Morales R, Tsvetkov AS. G-quadruplexes and associated proteins in aging and Alzheimer's disease. FRONTIERS IN AGING 2023; 4:1164057. [PMID: 37323535 PMCID: PMC10267416 DOI: 10.3389/fragi.2023.1164057] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Aging is a prominent risk factor for many neurodegenerative disorders, such as Alzheimer's disease (AD). Alzheimer's disease is characterized by progressive cognitive decline, memory loss, and neuropsychiatric and behavioral symptoms, accounting for most of the reported dementia cases. This disease is now becoming a major challenge and burden on modern society, especially with the aging population. Over the last few decades, a significant understanding of the pathophysiology of AD has been gained by studying amyloid deposition, hyperphosphorylated tau, synaptic dysfunction, oxidative stress, calcium dysregulation, and neuroinflammation. This review focuses on the role of non-canonical secondary structures of DNA/RNA G-quadruplexes (G4s, G4-DNA, and G4-RNA), G4-binding proteins (G4BPs), and helicases, and their roles in aging and AD. Being critically important for cellular function, G4s are involved in the regulation of DNA and RNA processes, such as replication, transcription, translation, RNA localization, and degradation. Recent studies have also highlighted G4-DNA's roles in inducing DNA double-strand breaks that cause genomic instability and G4-RNA's participation in regulating stress granule formation. This review emphasizes the significance of G4s in aging processes and how their homeostatic imbalance may contribute to the pathophysiology of AD.
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Affiliation(s)
- M. J. Vijay Kumar
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
| | - Rodrigo Morales
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Andrey S. Tsvetkov
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX, United States
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16
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Kim HS, Pickering AM. Protein translation paradox: Implications in translational regulation of aging. Front Cell Dev Biol 2023; 11:1129281. [PMID: 36711035 PMCID: PMC9880214 DOI: 10.3389/fcell.2023.1129281] [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: 12/21/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
Protein translation is an essential cellular process playing key roles in growth and development. Protein translation declines over the course of age in multiple animal species, including nematodes, fruit flies, mice, rats, and even humans. In all these species, protein translation transiently peaks in early adulthood with a subsequent drop over the course of age. Conversely, lifelong reductions in protein translation have been found to extend lifespan and healthspan in multiple animal models. These findings raise the protein synthesis paradox: age-related declines in protein synthesis should be detrimental, but life-long reductions in protein translation paradoxically slow down aging and prolong lifespan. This article discusses the nature of this paradox and complies an extensive body of work demonstrating protein translation as a modulator of lifespan and healthspan.
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Affiliation(s)
- Harper S. Kim
- Center for Neurodegeneration and Experimental Therapeutics (CNET), Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Medical Scientist Training Program, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Andrew M. Pickering
- Center for Neurodegeneration and Experimental Therapeutics (CNET), Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
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Ma R, Zhang Y, Li H, Kang HR, Kim Y, Han K. Cell-autonomous reduction of CYFIP2 is insufficient to induce Alzheimer's disease-like pathologies in the hippocampal CA1 pyramidal neurons of aged mice. Anim Cells Syst (Seoul) 2023; 27:93-101. [PMID: 36999135 PMCID: PMC10044167 DOI: 10.1080/19768354.2023.2192263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
Abstract
Cytoplasmic FMR1-interacting protein 2 (CYFIP2) is an evolutionarily conserved multifunctional protein that regulates the neuronal actin cytoskeleton, mRNA translation and transport, and mitochondrial morphology and function. Supporting its critical roles in proper neuronal development and function, human genetic studies have repeatedly identified variants of the CYFIP2 gene in individuals diagnosed with neurodevelopmental disorders. Notably, a few recent studies have also suggested a mechanistic link between reduced CYFIP2 level and Alzheimer's disease (AD). Specifically, in the hippocampus of 12-month-old Cyfip2 heterozygous mice, several AD-like pathologies were identified, including increased levels of Tau phosphorylation and gliosis, and loss of dendritic spines in CA1 pyramidal neurons. However, detailed pathogenic mechanisms, such as cell types and their circuits where the pathologies originate, remain unknown for AD-like pathologies caused by CYFIP2 reduction. In this study, we aimed to address this issue by examining whether the cell-autonomous reduction of CYFIP2 in CA1 excitatory pyramidal neurons is sufficient to induce AD-like phenotypes in the hippocampus. We performed immunohistochemical, morphological, and biochemical analyses in 12-month-old Cyfip2 conditional knock-out mice, which have postnatally reduced CYFIP2 expression level in CA1, but not in CA3, excitatory pyramidal neurons of the hippocampus. Unexpectedly, we could not find any significant AD-like phenotype, suggesting that the CA1 excitatory neuron-specific reduction of CYFIP2 level is insufficient to lead to AD-like pathologies in the hippocampus. Therefore, we propose that CYFIP2 reduction in other neurons and/or their synaptic connections with CA1 pyramidal neurons may be critically involved in the hippocampal AD-like phenotypes of Cyfip2 heterozygous mice.
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Affiliation(s)
- Ruiying Ma
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Yinhua Zhang
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Huiling Li
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyae Rim Kang
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Yoonhee Kim
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kihoon Han
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
- Kihoon Han
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18
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Felsky D, Santa-Maria I, Cosacak MI, French L, Schneider JA, Bennett DA, De Jager PL, Kizil C, Tosto G. The Caribbean-Hispanic Alzheimer's disease brain transcriptome reveals ancestry-specific disease mechanisms. Neurobiol Dis 2023; 176:105938. [PMID: 36462719 PMCID: PMC10039465 DOI: 10.1016/j.nbd.2022.105938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/21/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
Identifying ancestry-specific molecular profiles of late-onset Alzheimer's Disease (LOAD) in brain tissue is crucial to understand novel mechanisms and develop effective interventions in non-European, high-risk populations. We performed gene differential expression (DE) and consensus network-based analyses in RNA-sequencing data of postmortem brain tissue from 39 Caribbean Hispanics (CH). To identify ancestry-concordant and -discordant expression profiles, we compared our results to those from two independent non-Hispanic White (NHW) samples (n = 731). In CH, we identified 2802 significant DE genes, including several LOAD known-loci. DE effects were highly concordant across ethnicities, with 373 genes transcriptome-wide significant in all three cohorts. Cross-ancestry meta-analysis found NPNT to be the top DE gene. We replicated over 82% of meta-analyses genome-wide signals in single-nucleus RNA-seq data (including NPNT and LOAD known-genes SORL1, FBXL7, CLU, ABCA7). Increasing representation in genetic studies will allow for deeper understanding of ancestry-specific mechanisms and improving precision treatment options in understudied groups.
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Affiliation(s)
- Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, 250 College St., M5T 1R8, Canada; Department of Psychiatry, University of Toronto, 27 King's College Circle, Toronto, Ontario M5S 1A1, Canada; Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Ismael Santa-Maria
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Mehmet Ilyas Cosacak
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Tatzberg 41, 01307 Dresden, Germany
| | - Leon French
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, 250 College St., M5T 1R8, Canada; Department of Psychiatry, University of Toronto, 27 King's College Circle, Toronto, Ontario M5S 1A1, Canada
| | - Julie A Schneider
- Department of Neurology, Rush University Medical Center, 1653 West Congress Parkway, Chicago, IL 60612, USA; Rush Alzheimer's Disease Center, Rush University Medical Center, 1653 West Congress Parkway, Chicago, IL 60612, USA
| | - David A Bennett
- Department of Neurology, Rush University Medical Center, 1653 West Congress Parkway, Chicago, IL 60612, USA; Rush Alzheimer's Disease Center, Rush University Medical Center, 1653 West Congress Parkway, Chicago, IL 60612, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Caghan Kizil
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA; German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Tatzberg 41, 01307 Dresden, Germany; The Department of Neurology, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Giuseppe Tosto
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA; The Department of Neurology, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA; Gertrude H. Sergievsky Centre, Columbia University Medical Center, 630 West 168th St., New York, NY 10032, USA.
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19
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Kang D, Baek Y, Lee JS. Mechanisms of RNA and Protein Quality Control and Their Roles in Cellular Senescence and Age-Related Diseases. Cells 2022; 11:cells11244062. [PMID: 36552825 PMCID: PMC9777292 DOI: 10.3390/cells11244062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/04/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Cellular senescence, a hallmark of aging, is defined as irreversible cell cycle arrest in response to various stimuli. It plays both beneficial and detrimental roles in cellular homeostasis and diseases. Quality control (QC) is important for the proper maintenance of cellular homeostasis. The QC machineries regulate the integrity of RNA and protein by repairing or degrading them, and are dysregulated during cellular senescence. QC dysfunction also contributes to multiple age-related diseases, including cancers and neurodegenerative, muscle, and cardiovascular diseases. In this review, we describe the characters of cellular senescence, discuss the major mechanisms of RNA and protein QC in cellular senescence and aging, and comprehensively describe the involvement of these QC machineries in age-related diseases. There are many open questions regarding RNA and protein QC in cellular senescence and aging. We believe that a better understanding of these topics could propel the development of new strategies for addressing age-related diseases.
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Affiliation(s)
- Donghee Kang
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Republic of Korea
| | - Yurim Baek
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Jae-Seon Lee
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea
- Correspondence: ; Tel.: +82-32-860-9832; Fax: +82-32-885-8302
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20
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Gardner OK, Van Booven D, Wang L, Gu T, Hofmann NK, Whitehead PL, Nuytemans K, Hamilton-Nelson KL, Adams LD, Starks TD, Cuccaro ML, Martin ER, Vance JM, Bush WS, Byrd GS, Haines JL, Beecham GW, Pericak-Vance MA, Griswold AJ. Genetic architecture of RNA editing regulation in Alzheimer's disease across diverse ancestral populations. Hum Mol Genet 2022; 31:2876-2886. [PMID: 35383839 PMCID: PMC9433728 DOI: 10.1093/hmg/ddac075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/24/2022] [Accepted: 03/27/2022] [Indexed: 11/14/2022] Open
Abstract
Most Alzheimer's disease (AD)-associated genetic variants do not change protein coding sequence and thus likely exert their effects through regulatory mechanisms. RNA editing, the post-transcriptional modification of RNA bases, is a regulatory feature that is altered in AD patients that differs across ancestral backgrounds. Editing QTLs (edQTLs) are DNA variants that influence the level of RNA editing at a specific site. To study the relationship of DNA variants genome-wide, and particularly in AD-associated loci, with RNA editing, we performed edQTL analyses in self-reported individuals of African American (AF) or White (EU) race with corresponding global genetic ancestry averaging 82.2% African ancestry (AF) and 96.8% European global ancestry (EU) in the two groups, respectively. We used whole-genome genotyping array and RNA sequencing data from peripheral blood of 216 AD cases and 212 age-matched, cognitively intact controls. We identified 2144 edQTLs in AF and 3579 in EU, of which 1236 were found in both groups. Among these, edQTLs in linkage disequilibrium (r2 > 0.5) with AD-associated genetic variants in the SORL1, SPI1 and HLA-DRB1 loci were associated with sites that were differentially edited between AD cases and controls. While there is some shared RNA editing regulatory architecture, most edQTLs had distinct effects on the rate of RNA editing in different ancestral populations suggesting a complex architecture of RNA editing regulation. Altered RNA editing may be one possible mechanism for the functional effect of AD-associated variants and may contribute to observed differences in the genetic etiology of AD between ancestries.
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Affiliation(s)
- Olivia K Gardner
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Lily Wang
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Tianjie Gu
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Natalia K Hofmann
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Takiyah D Starks
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, Dr. John T Macdonald Foundation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, Dr. John T Macdonald Foundation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, Dr. John T Macdonald Foundation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - William S Bush
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
- Cleveland Institute for Computational Biology, Cleveland, OH 44106, USA
| | - Goldie S Byrd
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Jonathan L Haines
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
- Cleveland Institute for Computational Biology, Cleveland, OH 44106, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, Dr. John T Macdonald Foundation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, Dr. John T Macdonald Foundation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, Dr. John T Macdonald Foundation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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21
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Early Changes in Transcriptomic Profiles in Synaptodendrosomes Reveal Aberrant Synaptic Functions in Alzheimer’s Disease. Int J Mol Sci 2022; 23:ijms23168888. [PMID: 36012153 PMCID: PMC9408306 DOI: 10.3390/ijms23168888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/29/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Alzheimer’s disease (AD) is one of the most prevalent neurodegenerative disorders characterized by the progressive decline of cognitive functions, and is closely associated with the dysfunction of synapses, which comprise the basic structure that mediates the communication between neurons. Although the protein architecture and machinery for protein translation at synapses are extensively studied, the impact that local changes in the mRNA reservoir have on AD progression is largely unknown. Here, we investigated the changes in transcriptomic profiles in the synaptodendrosomes purified from the cortices of AD mice at ages 3 and 6 months, a stage when early signatures of synaptic dysfunction are revealed. The transcriptomic profiles of synaptodendrosomes showed a greater number of localized differentially expressed genes (DEGs) in 6-month-old AD mice compared with mice 3 months of age. Gene Ontology (GO) analysis showed that these DEGs are majorly enriched in mitochondrial biogenesis and metabolic activity. More specifically, we further identified three representative DEGs in mitochondrial and metabolic pathways—Prnp, Cst3, and Cox6c—that regulate the dendritic spine density and morphology in neurons. Taken together, this study provides insights into the transcriptomic changes in synaptodendrosomes during AD progression, which may facilitate the development of intervention strategies targeting local translation to ameliorate the pathological progression of AD.
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22
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You Y, Hersh SW, Aslebagh R, Shaffer SA, Ikezu S, Mez J, Lunetta KL, Logue MW, Farrer LA, Ikezu T. Alzheimer's disease associated AKAP9 I2558M mutation alters posttranslational modification and interactome of tau and cellular functions in CRISPR-edited human neuronal cells. Aging Cell 2022; 21:e13617. [PMID: 35567427 PMCID: PMC9197405 DOI: 10.1111/acel.13617] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 02/28/2022] [Accepted: 04/04/2022] [Indexed: 12/01/2022] Open
Abstract
Alzheimer's disease (AD) is a pervasive neurodegeneration disease with high heritability. In this study, we employed CRISPR-Cas9-engineered technology to investigate the effects of a rare mutation (rs144662445) in the A kinase anchoring protein 9 (AKAP9) gene, which is associated with AD in African Americans (AA), on tau pathology and the tau interactome in SH-SY5Y P301L neuron-like cells. The mutation significantly increased the level of phosphorylated tau, specifically at the site Ser396/Ser404. Moreover, analyses of the tau interactome measured by affinity purification-mass spectrometry revealed that differentially expressed tau-interacting proteins in AKAP9 mutant cells were associated with RNA translation, RNA localization and oxidative activity, recapitulating the tau interactome signature previously reported with human AD brain samples. Importantly, these results were further validated by functional studies showing a significant reduction in protein synthesis activity and excessive oxidative stress in AKAP9 mutant compared with wild type cells in a tau-dependent manner, which are mirrored with pathological phenotype frequently seen in AD. Our results demonstrated specific effects of rs14462445 on mis-processing of tau and suggest a potential role of AKAP9 in AD pathogenesis.
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Affiliation(s)
- Yang You
- Departments of Pharmacology & Experimental TherapeuticsBoston University School of MedicineBostonMassachusettsUSA
- Department of NeuroscienceMayo Clinic FloridaJacksonvilleFloridaUSA
| | - Samuel W. Hersh
- Departments of Pharmacology & Experimental TherapeuticsBoston University School of MedicineBostonMassachusettsUSA
| | - Roshanak Aslebagh
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical SchoolWorcesterMassachusettsUSA
- Mass Spectrometry FacilityUniversity of Massachusetts Medical SchoolShrewsburyMassachusettsUSA
| | - Scott A. Shaffer
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical SchoolWorcesterMassachusettsUSA
- Mass Spectrometry FacilityUniversity of Massachusetts Medical SchoolShrewsburyMassachusettsUSA
| | - Seiko Ikezu
- Departments of Pharmacology & Experimental TherapeuticsBoston University School of MedicineBostonMassachusettsUSA
| | - Jesse Mez
- Department of NeurologyBoston University School of MedicineBostonMassachusettsUSA
| | - Kathryn L. Lunetta
- Department of BiostatisticsBoston University School of Public HealthBostonMassachusettsUSA
| | - Mark W. Logue
- Department of BiostatisticsBoston University School of Public HealthBostonMassachusettsUSA
- Department of PsychiatryBoston University School of MedicineBostonMassachusettsUSA
- Department of Medicine (Biomedical Genetics)Boston University School of MedicineBostonMassachusettsUSA
- National Center for PTSDBehavioral Sciences DivisionVA Boston Healthcare SystemBostonMassachusettsUSA
| | - Lindsay A. Farrer
- Department of NeurologyBoston University School of MedicineBostonMassachusettsUSA
- Department of BiostatisticsBoston University School of Public HealthBostonMassachusettsUSA
- Department of Medicine (Biomedical Genetics)Boston University School of MedicineBostonMassachusettsUSA
- Department of OphthalmologyBoston University School of MedicineBostonMassachusettsUSA
- Department of EpidemiologyBoston University School of Public HealthBostonMassachusettsUSA
| | - Tsuneya Ikezu
- Departments of Pharmacology & Experimental TherapeuticsBoston University School of MedicineBostonMassachusettsUSA
- Department of NeuroscienceMayo Clinic FloridaJacksonvilleFloridaUSA
- Center for Systems NeuroscienceBoston UniversityBostonMassachusettsUSA
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23
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Lizarazo S, Yook Y, Tsai N. Amyloid beta induces
Fmr1
‐dependent translational suppression and hyposynchrony of neural activity via phosphorylation of eIF2α and eEF2. J Cell Physiol 2022; 237:2929-2942. [PMID: 35434801 PMCID: PMC9283232 DOI: 10.1002/jcp.30754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 01/02/2023]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia, with the accumulation of amyloid beta peptide (Aβ) being one of the main causes of the disease. Fragile X mental retardation protein (FMRP), encoded by fragile X mental retardation 1 (Fmr1), is an RNA‐binding protein that represses translation of its bound mRNAs or exerts other indirect mechanisms that result in translational suppression. Because the accumulation of Aβ has been shown to cause translational suppression resulting from the elevated cellular stress response, in this study we asked whether and how Fmr1 is involved in Aβ‐induced translational regulation. Our data first showed that the application of synthetic Aβ peptide induces the expression of Fmr1 in cultured primary neurons. We followed by showing that Fmr1 is required for Aβ‐induced translational suppression, hyposynchrony of neuronal firing activity, and loss of excitatory synapses. Mechanistically, we revealed that Fmr1 functions to repress the expression of phosphatases including protein phosphatase 2A (PP2A) and protein phosphatase 1 (PP1), leading to elevated phosphorylation of eukaryotic initiation factor 2‐α (eIF2α) and eukaryotic elongation factor 2 (eEF2), and subsequent translational suppression. Finally, our data suggest that such translational suppression is critical to Aβ‐induced hyposynchrony of firing activity, but not the loss of synapses. Altogether, our study uncovers a novel mechanism by which Aβ triggers translational suppression and we reveal the participation of Fmr1 in altered neural plasticity associated with Aβ pathology. Our study may also provide information for a better understanding of Aβ‐induced cellular stress responses in AD.
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Affiliation(s)
- Simon Lizarazo
- Department of Molecular and Integrative Physiology, School of Molecular and Cellular Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - Yeeun Yook
- Department of Molecular and Integrative Physiology, School of Molecular and Cellular Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - Nien‐Pei Tsai
- Department of Molecular and Integrative Physiology, School of Molecular and Cellular Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Neuroscience Program University of Illinois at Urbana‐Champaign Urbana Illinois USA
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24
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Pomilio AB, Vitale AA, Lazarowski AJ. Uncommon Noninvasive Biomarkers for the Evaluation and Monitoring of the Etiopathogenesis of Alzheimer's Disease. Curr Pharm Des 2022; 28:1152-1169. [DOI: 10.2174/1381612828666220413101929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/25/2022] [Indexed: 11/22/2022]
Abstract
Background:
Alzheimer´s disease (AD) is the most widespread dementia in the world, followed by vascular dementia. Since AD is a heterogeneous disease that shows several varied phenotypes, it is not easy to make an accurate diagnosis, so it arises when the symptoms are clear and the disease is already very advanced. Therefore, it is important to find out biomarkers for AD early diagnosis that facilitate treatment or slow down the disease. Classic biomarkers are obtained from cerebrospinal fluid and plasma, along with brain imaging by positron emission tomography. Attempts have been made to discover uncommon biomarkers from other body fluids, which are addressed in this update.
Objective:
This update aims to describe recent biomarkers from minimally invasive body fluids for the patients, such as saliva, urine, eye fluid or tears.
Methods:
Biomarkers were determined in patients versus controls by single tandem mass spectrometry, and immunoassays. Metabolites were identified by nuclear magnetic resonance, and microRNAs with genome-wide high-throughput real-time polymerase chain reaction-based platforms.
Results:
Biomarkers from urine, saliva, and eye fluid were described, including peptides/proteins, metabolites, and some microRNAs. The association with AD neuroinflammation and neurodegeneration was analyzed, highlighting the contribution of matrix metalloproteinases, the immune system and microglia, as well as the vascular system.
Conclusion:
Unusual biomarkers have been developed, which distinguish each stage and progression of the disease, and are suitable for the early AD diagnosis. An outstanding relationship of biomarkers with neuroinflammation and neurodegeneration was assessed, clearing up concerns of the etiopathogenesis of AD.
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Affiliation(s)
- Alicia B. Pomilio
- Departamento de Bioquímica Clínica, Área Hematología, Hospital de Clínicas “José de San Martín”, Universidad de Buenos Aires, Av. Córdoba 2351, C1120AAF Buenos Aires, Argentina
| | - Arturo A. Vitale
- Departamento de Bioquímica Clínica, Área Hematología, Hospital de Clínicas “José de San Martín”, Universidad de Buenos Aires, Av. Córdoba 2351, C1120AAF Buenos Aires, Argentina
| | - Alberto J. Lazarowski
- Departamento de Bioquímica Clínica, Facultad de Farmacia y Bioquímica, Instituto de Fisiopatología y Bioquímica Clínica (INFIBIOC), Universidad de Buenos Aires, Córdoba 2351, C1120AAF Buenos Aires, Argentina
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25
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Tan S, Li S, Tang C, Bai X, Ran X, Qu Q, Li L, Yang L. A regenerable and reducing false-positive fluorescent switch for detection of β-amyloid 1−42 oligomers. Talanta 2022; 246:123461. [DOI: 10.1016/j.talanta.2022.123461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 11/24/2022]
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26
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Saeedi M, Mehranfar F. Challenges and approaches of drugs such as Memantine, Donepezil, Rivastigmine and Aducanumab in the treatment, control and management of Alzheimer's disease. Recent Pat Biotechnol 2022; 16:102-121. [PMID: 35236274 DOI: 10.2174/1872208316666220302115901] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/20/2021] [Accepted: 12/28/2021] [Indexed: 11/22/2022]
Abstract
Alzheimer's disease (AD) is a kinds of neuropsychiatric illnesses that affect the central nervous system. In this disease, the accumulation of amyloid-beta increases, and phosphorylated tau (P-tau) protein, one of the ways to treat this disease is to reduce the accumulation of amyloid-beta. Various studies have demonstrated that pharmacological approaches have considerable effects in the treatment of AD, despite the side effects and challenges. Cholinesterase inhibitors and the NMDA receptor antagonist memantine are presently authorized therapies for AD. Memantine and Donepezil are the most common drugs for the prevention and therapy of AD with mechanisms such as lessened β-amyloid plaque, effect on N-Methyl-D-aspartate (NMDA) receptors. Diminution glutamate and elevated acetylcholine are some of the influences of medications administrated to treat AD, and drugs can also play a role in slowing the progression of cognitive and memory impairment. A new pharmacological approach and strategy is required to control the future of AD. This review appraises the effects of memantine, donepezil, rivastigmine, and aducanumab in clinical trials, in vitro and animal model studies that have explored how these drugs versus AD development and also discuss possible mechanisms of influence on the brain. Research in clinical trials has substantial findings that support the role of these medications in AD treatment and ameliorate the safety and efficacy of AD therapy, although more clinical trials are required to prove their effectiveness.
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Affiliation(s)
- Mohammad Saeedi
- Department of Laboratory Science, Faculty of medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Fatemeh Mehranfar
- Department of Laboratory Science, Faculty of medicine, Semnan University of Medical Sciences, Semnan, Iran
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27
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Recent Advances in Our Molecular and Mechanistic Understanding of Misfolded Cellular Proteins in Alzheimer’s Disease (AD) and Prion Disease (PrD). Biomolecules 2022; 12:biom12020166. [PMID: 35204666 PMCID: PMC8961532 DOI: 10.3390/biom12020166] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 12/29/2022] Open
Abstract
Naturally occurring neuron-abundant proteins including amyloid Aβ42 peptide and the microtubule-associated protein tau (MAPT) can, over time and under pathological situations, assume atypical conformations, altering their normal biological structure and function, and causing them to aggregate into insoluble and neurotoxic intracellular inclusions. These misfolded proteins ultimately contribute to the pathogenesis of several progressive, age-related and ultimately lethal human neurodegenerative disorders. The molecular mechanism of this pathological phenomenon of neuronal protein misfolding lends support to the ‘prion hypothesis’, which predicts that the aberrant folding of endogenous natural protein structures into unusual pathogenic isoforms can induce the atypical folding of other similar brain-abundant proteins, underscoring the age-related, progressive nature and potential transmissible and spreading capabilities of the aberrant protein isoforms that drive these invariably fatal neurological syndromes. The abnormal folding and aggregation of host proteins is a consistent feature of both amyloidopathies and tauopathies that encompass a continuous spectrum of brain diseases that include Alzheimer’s disease (AD), prion disorders (PrD) such as scrapie in sheep and goats (Bovidae), experimental prion infection of rodents (Muridae), Creutzfeldt–Jakob disease (CJD) and Gerstmann–Sträussler–Scheinker syndrome (GSS) in humans (Hominidae), and other fatal prion-driven neurological disorders. Because AD patients accumulate both misfolded tau and Aβ peptides, AD may be somewhat unique as the first example of a ‘double prion disorder’. This commentary will examine current research trends in this fascinating research area, with a special emphasis on AD and PrD, and the novel pathological misfolded protein processes common to both intractable neurological disorders.
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28
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Discovery of a dual-action small molecule that improves neuropathological features of Alzheimer's disease mice. Proc Natl Acad Sci U S A 2022; 119:2115082119. [PMID: 35027452 PMCID: PMC8784098 DOI: 10.1073/pnas.2115082119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 12/28/2022] Open
Abstract
Since Alzheimer’s disease (AD) is a multifaceted neurodegenerative disease, multitargeted therapeutic approaches are likely required for effective AD treatment. The importance of acid sphingomyelinase (ASM) activation in the various neuropathological features of AD is well-known. Therefore, in this study, we focused on identifying an efficient, direct inhibitor of ASM activity. We found that KARI 201 was a highly selective ASM activity inhibitor without any off-target effects. Through RNA-sequencing analysis in brains of AD mice, we also unexpectedly uncovered the role of KARI 201 as a ghrelin receptor agonist. This dual role of KARI 201 in neurons led to improvement of Aβ accumulation, neuroinflammation, synapse loss, hippocampal neurogenesis, and memory dysfunction in AD mice. Alzheimer’s disease (AD) is characterized by complex, multifactorial neuropathology, suggesting that small molecules targeting multiple neuropathological factors are likely required to successfully impact clinical progression. Acid sphingomyelinase (ASM) activation has been recognized as an important contributor to these neuropathological features in AD, leading to the concept of using ASM inhibitors for the treatment of this disorder. Here we report the identification of KARI 201, a direct ASM inhibitor evaluated for AD treatment. KARI 201 exhibits highly selective inhibition effects on ASM, with excellent pharmacokinetic properties, especially with regard to brain distribution. Unexpectedly, we found another role of KARI 201 as a ghrelin receptor agonist, which also has therapeutic potential for AD treatment. This dual role of KARI 201 in neurons efficiently rescued neuropathological features in AD mice, including amyloid beta deposition, autophagy dysfunction, neuroinflammation, synaptic loss, and decreased hippocampal neurogenesis and synaptic plasticity, leading to an improvement in memory function. Our data highlight the possibility of potential clinical application of KARI 201 as an innovative and multifaceted drug for AD treatment.
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29
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Eastman G, Sharlow ER, Lazo JS, Bloom GS, Sotelo-Silveira JR. Transcriptome and Translatome Regulation of Pathogenesis in Alzheimer's Disease Model Mice. J Alzheimers Dis 2022; 86:365-386. [PMID: 35034904 DOI: 10.3233/jad-215357] [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] [Indexed: 12/13/2022]
Abstract
BACKGROUND Defining cellular mechanisms that drive Alzheimer's disease (AD) pathogenesis and progression will be aided by studies defining how gene expression patterns change during pre-symptomatic AD and ensuing periods of declining cognition. Previous studies have emphasized changes in transcriptome, but not translatome regulation, leaving the ultimate results of gene expression alterations relatively unexplored in the context of AD. OBJECTIVE To identify genes whose expression might be regulated at the transcriptome and translatome levels in AD, we analyzed gene expression in cerebral cortex of two AD model mouse strains, CVN (APPSwDI;NOS2 -/- ) and Tg2576 (APPSw), and their companion wild type (WT) strains at 6 months of age by tandem RNA-Seq and Ribo-Seq (ribosome profiling). METHODS Identical starting pools of bulk RNA were used for RNA-Seq and Ribo-Seq. Differential gene expression analysis was performed at the transcriptome, translatome, and translational efficiency levels. Regulated genes were functionally evaluated by gene ontology tools. RESULTS Compared to WT mice, AD model mice had similar levels of transcriptome regulation, but differences in translatome regulation. A microglial signature associated with early stages of Aβ accumulation was upregulated at both levels in CVN mice. Although the two mice strains did not share many regulated genes, they showed common regulated pathways related to AβPP metabolism associated with neurotoxicity and neuroprotection. CONCLUSION This work represents the first genome-wide study of brain translatome regulation in animal models of AD and provides evidence of a tight and early translatome regulation of gene expression controlling the balance between neuroprotective and neurodegenerative processes in brain.
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Affiliation(s)
- Guillermo Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay.,Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Elizabeth R Sharlow
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA
| | - John S Lazo
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA.,Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - George S Bloom
- Department of Biology, University of Virginia, Charlottesville, VA, USA.,Department of Cell Biology, University of Virginia, Charlottesville, VA, USA.,Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - José R Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay.,Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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30
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Bleuzé L, Triaca V, Borreca A. FMRP-Driven Neuropathology in Autistic Spectrum Disorder and Alzheimer's disease: A Losing Game. Front Mol Biosci 2021; 8:699613. [PMID: 34760921 PMCID: PMC8573832 DOI: 10.3389/fmolb.2021.699613] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/24/2021] [Indexed: 12/28/2022] Open
Abstract
Fragile X mental retardation protein (FMRP) is an RNA binding protein (RBP) whose absence is essentially associated to Fragile X Syndrome (FXS). As an RNA Binding Protein (RBP), FMRP is able to bind and recognize different RNA structures and the control of specific mRNAs is important for neuronal synaptic plasticity. Perturbations of this pathway have been associated with the autistic spectrum. One of the FMRP partners is the APP mRNA, the main protagonist of Alzheimer’s disease (AD), thereby regulating its protein level and metabolism. Therefore FMRP is associated to two neurodevelopmental and age-related degenerative conditions, respectively FXS and AD. Although these pathologies are characterized by different features, they have been reported to share a number of common molecular and cellular players. The aim of this review is to describe the double-edged sword of FMRP in autism and AD, possibly allowing the elucidation of key shared underlying mechanisms and neuronal circuits. As an RBP, FMRP is able to regulate APP expression promoting the production of amyloid β fragments. Indeed, FXS patients show an increase of amyloid β load, typical of other neurological disorders, such as AD, Down syndrome, Parkinson’s Disease, etc. Beyond APP dysmetabolism, the two neurodegenerative conditions share molecular targets, brain circuits and related cognitive deficits. In this review, we will point out the potential common neuropathological pattern which needs to be addressed and we will hopefully contribute to clarifying the complex phenotype of these two neurorological disorders, in order to pave the way for a novel, common disease-modifying therapy.
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Affiliation(s)
- Louis Bleuzé
- University de Rennes 1, Rennes, France.,Humanitas Clinical and Research Center-IRCCS, Rozzano (Mi), Italy
| | - Viviana Triaca
- Institute of Biochemistry and Cell Biology, National Research Council (CNR-IBBC), International Campus A. Buzzati Traverso, Monterotondo, Italy
| | - Antonella Borreca
- Humanitas Clinical and Research Center-IRCCS, Rozzano (Mi), Italy.,Institute of Neuroscience-National Research Council (CNR-IN), Milan, Italy
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31
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Biembengut ÍV, Silva ILZ, Souza TDACBD, Shigunov P. Cytoplasmic FMR1 interacting protein (CYFIP) family members and their function in neural development and disorders. Mol Biol Rep 2021; 48:6131-6143. [PMID: 34327661 DOI: 10.1007/s11033-021-06585-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/20/2021] [Indexed: 11/25/2022]
Abstract
In humans, the cytoplasmic FMR1 interacting protein (CYFIP) family is composed of CYFIP1 and CYFIP2. Despite their high similarity and shared interaction with many partners, CYFIP1 and CYFIP2 act at different points in cellular processes. CYFIP1 and CYFIP2 have different expression levels in human tissues, and knockout animals die at different time points of development. CYFIP1, similar to CYFIP2, acts in the WAVE regulatory complex (WRC) and plays a role in actin dynamics through the activation of the Arp2/3 complex and in a posttranscriptional regulatory complex with the fragile X mental retardation protein (FMRP). Previous reports have shown that CYFIP1 and CYFIP2 may play roles in posttranscriptional regulation in different ways. While CYFIP1 is involved in translation initiation via the 5'UTR, CYFIP2 may regulate mRNA expression via the 3'UTR. In addition, this CYFIP protein family is involved in neural development and maturation as well as in different neural disorders, such as intellectual disabilities, autistic spectrum disorders, and Alzheimer's disease. In this review, we map diverse studies regarding the functions, regulation, and implications of CYFIP proteins in a series of molecular pathways. We also highlight mutations and their structural effects both in functional studies and in neural diseases.
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Affiliation(s)
- Ísis Venturi Biembengut
- Carlos Chagas Institute-FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, 3775, CIC, Curitiba, Paraná, 81830-010, Brazil
| | | | | | - Patrícia Shigunov
- Carlos Chagas Institute-FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, 3775, CIC, Curitiba, Paraná, 81830-010, Brazil.
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32
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Jęśko H, Wieczorek I, Wencel PL, Gąssowska-Dobrowolska M, Lukiw WJ, Strosznajder RP. Age-Related Transcriptional Deregulation of Genes Coding Synaptic Proteins in Alzheimer's Disease Murine Model: Potential Neuroprotective Effect of Fingolimod. Front Mol Neurosci 2021; 14:660104. [PMID: 34305524 PMCID: PMC8299068 DOI: 10.3389/fnmol.2021.660104] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Alzheimer's disease (AD) induces time-dependent changes in sphingolipid metabolism, which may affect transcription regulation and neuronal phenotype. We, therefore, analyzed the influence of age, amyloid β precursor protein (AβPP), and the clinically approved, bioavailable sphingosine-1-phosphate receptor modulator fingolimod (FTY720) on the expression of synaptic proteins. RNA was isolated, reverse-transcribed, and subjected to real-time PCR. Expression of mutant (V717I) AβPP led to few changes at 3 months of age but reduced multiple mRNA coding for synaptic proteins in a 12-month-old mouse brain. Complexin 1 (Cplx1), SNAP25 (Snap25), syntaxin 1A (Stx1a), neurexin 1 (Nrxn1), neurofilament light (Nefl), and synaptotagmin 1 (Syt1) in the hippocampus, and VAMP1 (Vamp1) and neurexin 1 (Nrxn1) in the cortex were all significantly reduced in 12-month-old mice. Post mortem AD samples from the human hippocampus and cortex displayed lower expression of VAMP, synapsin, neurofilament light (NF-L) and synaptophysin. The potentially neuroprotective FTY720 reversed most AβPP-induced changes in gene expression (Cplx1, Stx1a, Snap25, and Nrxn1) in the 12-month-old hippocampus, which is thought to be most sensitive to early neurotoxic insults, but it only restored Vamp1 in the cortex and had no influence in 3-month-old brains. Further study may reveal the potential usefulness of FTY720 in the modulation of deregulated neuronal phenotype in AD brains.
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Affiliation(s)
- Henryk Jęśko
- Department of Cellular Signalling, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Iga Wieczorek
- Laboratory of Preclinical Research and Environmental Agents, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Przemysław Leonard Wencel
- Laboratory of Preclinical Research and Environmental Agents, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | | | - Walter J. Lukiw
- LSU Neuroscience Center, Departments of Neurology and Ophthalmology, Louisiana State University School of Medicine, New Orleans, LA, United States
| | - Robert Piotr Strosznajder
- Laboratory of Preclinical Research and Environmental Agents, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
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33
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Jishi A, Qi X, Miranda HC. Implications of mRNA translation dysregulation for neurological disorders. Semin Cell Dev Biol 2021; 114:11-19. [PMID: 34024497 PMCID: PMC8144541 DOI: 10.1016/j.semcdb.2020.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/30/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023]
Abstract
The translation of information encoded in the DNA into functional proteins is one of the tenets of cellular biology. Cell survival and function depend on the tightly controlled processes of transcription and translation. Growing evidence suggests that dysregulation in mRNA translation plays an important role in the pathogenesis of several neurodevelopmental diseases, such as autism spectrum disorder (ASD) and fragile X syndrome (FXS) as well as neurodegenerative disorders, such as Alzheimer's disease (AD), Parkinson's disease (PD) and amyotrophic lateral sclerosis (ALS). In this review, we provide an overview of mRNA translation and its modes of regulation that have been implicated in neurological disease.
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Affiliation(s)
- Aya Jishi
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Xin Qi
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Helen C Miranda
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Neurosciences, School of Medicine Case Western Reserve University, Cleveland, OH, USA.
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34
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Mofatteh M. Neurodegeneration and axonal mRNA transportation. AMERICAN JOURNAL OF NEURODEGENERATIVE DISEASE 2021; 10:1-12. [PMID: 33815964 PMCID: PMC8012751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
The prevalence of neurodegenerative diseases is accelerating in rapidly aging global population. Novel and effective diagnostic and therapeutic methods are required to tackle the global issue of neurodegeneration in the future. A better understanding of the potential molecular mechanism causing neurodegeneration can shed light on dysfunctional processes in diseased neurons, which can pave the way to design and synthesize novel targets for early diagnosis during the asymptomatic phase of the disease. Abnormal protein aggregation is a hallmark of neurodegenerative diseases which can hamper transportation of cargoes into axons. Recent evidence suggests that disruption of local protein synthesis has been observed in neurodegenerative diseases. Because of their highly asymmetric structure, highly polarized neurons require trafficking of cargoes from the cell body to different subcellular regions to meet the extensive demands of cellular physiology. Localization of mRNAs and subsequent local translation to corresponding proteins in axons is a mechanism which allows neurons to rapidly respond to external stimuli as well as establishing neuronal networks by synthesizing proteins on demand. Axonal protein synthesis is required for axon guidance, synapse formation and plasticity, axon maintenance and regeneration in response to injury. Different types of excitatory and inhibitory neurons in the central and peripheral nervous systems have been shown to localize mRNA. Rising evidence suggests that the repertoire of localizing mRNA in axons can change during aging, indicating a connection between axonal mRNA trafficking and aging diseases such as neurodegeneration. Here, I briefly review the latest findings on the importance of mRNA localization and local translation in neurons and the consequences of their disruption in neurodegenerative diseases. In addition, I discuss recent evidence that dysregulation of mRNA localization and local protein translation can contribute to the formation of neurodegenerative diseases such as Alzheimer's disease, Amyotrophic Lateral Sclerosis, and Spinal Muscular Atrophy. In addition, I discuss recent findings on mRNAs localizing to mitochondria in neurodegeneration.
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Affiliation(s)
- Mohammad Mofatteh
- Lincoln College, University of OxfordOxford, UK
- Sir William Dunn School of Pathology, Medical Sciences Division, University of OxfordOxford, UK
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Evans HT, Blackmore D, Götz J, Bodea LG. De novo proteomic methods for examining the molecular mechanisms underpinning long-term memory. Brain Res Bull 2021; 169:94-103. [PMID: 33465403 DOI: 10.1016/j.brainresbull.2020.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/07/2020] [Accepted: 12/21/2020] [Indexed: 01/19/2023]
Abstract
Memory formation is a fundamental function of the nervous system that enables the experience-based adaptation of behaviour. The formation, recall and updating of long-term memory (LTM) requires new protein synthesis through its direct involvement in neuronal processes, such as long-term potentiation (LTP), long-term depression (LTD) and synaptic scaling. We discuss the advantages and limitations of several emerging techniques which enable the tagging of newly synthesised proteins, including stable isotope labelling with amino acids in cell culture (SILAC), puromycin labelling, and non-canonical amino acid (NCAA) labelling. We further present how these methods allow for the identification and visualisation of proteins which are newly synthesised during different stages of memory formation. These emerging techniques will continue to expand our understanding of how memories are formed, consolidated and retrieved.
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Affiliation(s)
- Harrison Tudor Evans
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia
| | - Daniel Blackmore
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia.
| | - Liviu-Gabriel Bodea
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia.
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Kozlova I, Sah S, Keable R, Leshchyns'ka I, Janitz M, Sytnyk V. Cell Adhesion Molecules and Protein Synthesis Regulation in Neurons. Front Mol Neurosci 2020; 13:592126. [PMID: 33281551 PMCID: PMC7689008 DOI: 10.3389/fnmol.2020.592126] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/16/2020] [Indexed: 12/18/2022] Open
Abstract
Cell adhesion molecules (CAMs) mediate interactions of neurons with the extracellular environment by forming adhesive bonds with CAMs on adjacent membranes or via binding to proteins of the extracellular matrix. Binding of CAMs to their extracellular ligands results in the activation of intracellular signaling cascades, leading to changes in neuronal structure and the molecular composition and function of neuronal contacts. Ultimately, many of these changes depend on the synthesis of new proteins. In this review, we summarize the evidence showing that CAMs regulate protein synthesis by modulating the activity of transcription factors, gene expression, protein translation, and the structure and distribution of organelles involved in protein synthesis and transport.
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Affiliation(s)
- Irina Kozlova
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Saroj Sah
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Ryan Keable
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Iryna Leshchyns'ka
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Vladimir Sytnyk
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
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Bisht I, Ambasta RK, Kumar P. An integrated approach to unravel a putative crosstalk network in Alzheimer's disease and Parkinson's disease. Neuropeptides 2020; 83:102078. [PMID: 32807513 DOI: 10.1016/j.npep.2020.102078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 12/31/2022]
Abstract
Integration of multiple profiling data and construction of functional regulatory networks provide a powerful approach to uncover functional relationships and significant molecular entities from transcriptomic data, highlighting the molecular mechanisms of complex diseases. Despite having an overlap in the neuropathologies of AD and PD, the molecular entities overlapped and mechanisms behind them are less known. Here we used an integrated strategy to analyze miRNA and gene transcriptomic data to understand the role of miRNAs and genes in regulatory activities taking place in cells, and find transcriptomic signatures linking AD and PD. We preprocessed and analyzed publicly available microarray datasets and identified 97 DEGs and 21 DEmiRs that may be involved in the overlapped mechanisms between these two disorders. Among the DEGs, we found HSPA9, PGK1, SDHC, FH, DLD, YWHAZ and ACLY as the major protein-coding genes involved in the crosstalk for AD-PD pathogenesis. Further we integrated these DEGs and DEmiRs with regulatory TFs to construct an overlapped dysregulated network of AD and PD. In the network, miR-27a-3p, miR-148a-3p and miR-15a-5p were found to be the most relevant with maximum interactions, describing their significance in the potential crosstalk. We also looked into the dysregulated biological processes and pathways overlapped in AD and PD. In conclusion, we highlighted the DEGs, DEmiRs, their interactions and related pathways overlapped in AD and PD pathogenesis, also describing a potential crosstalk at molecular level. Besides, our findings can further be used for molecular studies to reveal an assured AD-PD crosstalk.
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Affiliation(s)
- Indu Bisht
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly DCE), Delhi, 110042, India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly DCE), Delhi, 110042, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly DCE), Delhi, 110042, India.
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