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Abyadeh M, Mirshahvaladi S, Kashani SA, Paulo JA, Amirkhani A, Mehryab F, Seydi H, Moradpour N, Jodeiryjabarzade S, Mirzaei M, Gupta V, Shekari F, Salekdeh GH. Proteomic profiling of mesenchymal stem cell-derived extracellular vesicles: Impact of isolation methods on protein cargo. JOURNAL OF EXTRACELLULAR BIOLOGY 2024; 3:e159. [PMID: 38947171 PMCID: PMC11212298 DOI: 10.1002/jex2.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/01/2024] [Accepted: 05/15/2024] [Indexed: 07/02/2024]
Abstract
Extracellular vesicles (EVs) are nanosized vesicles with a lipid bilayer that are secreted by cells and play a critical role in cell-to-cell communication. Despite the promising reports regarding their diagnostic and therapeutic potential, the utilization of EVs in the clinical setting is limited due to insufficient information about their cargo and a lack of standardization in isolation and analysis methods. Considering protein cargos in EVs as key contributors to their therapeutic potency, we conducted a tandem mass tag (TMT) quantitative proteomics analysis of three subpopulations of mesenchymal stem cell (MSC)-derived EVs obtained through three different isolation techniques: ultracentrifugation (UC), high-speed centrifugation (HS), and ultracentrifugation on sucrose cushion (SU). Subsequently, we checked EV marker expression, size distribution, and morphological characterization, followed by bioinformatic analysis. The bioinformatic analysis of the proteome results revealed that these subpopulations exhibit distinct molecular and functional characteristics. The choice of isolation method impacts the proteome of isolated EVs by isolating different subpopulations of EVs. Specifically, EVs isolated through the high-speed centrifugation (HS) method exhibited a higher abundance of ribosomal and mitochondrial proteins. Functional apoptosis assays comparing isolated mitochondria with EVs isolated through different methods revealed that HS-EVs, but not other EVs, induced early apoptosis in cancer cells. On the other hand, EVs isolated using the sucrose cushion (SU) and ultracentrifugation (UC) methods demonstrated a higher abundance of proteins primarily involved in the immune response, cell-cell interactions and extracellular matrix interactions. Our analyses unveil notable disparities in proteins and associated biological functions among EV subpopulations, underscoring the importance of meticulously selecting isolation methods and resultant EV subpopulations based on the intended application.
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Affiliation(s)
- Morteza Abyadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
| | - Shahab Mirshahvaladi
- Macquarie Medical School, School of MedicineHealth and Human Sciences, Macquarie UniversitySydneyNew South WalesAustralia
| | - Sara Assar Kashani
- Department of Stem Cells and Developmental Biology, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
- Motor Neuron Disease Research Centre, Faculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Joao A. Paulo
- Department of Cell BiologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Ardeshir Amirkhani
- Australian Proteome Analysis FacilityMacquarie UniversitySydneyNew South WalesAustralia
| | - Fatemeh Mehryab
- Advanced Therapy Medicinal Product Technology Development Center, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
| | - Homeyra Seydi
- Advanced Therapy Medicinal Product Technology Development Center, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
- Department of BiologyUniversity of Science and CultureTehranIran
| | | | | | - Mehdi Mirzaei
- Macquarie Medical School, School of MedicineHealth and Human Sciences, Macquarie UniversitySydneyNew South WalesAustralia
| | - Vivek Gupta
- Macquarie Medical School, School of MedicineHealth and Human Sciences, Macquarie UniversitySydneyNew South WalesAustralia
| | - Faezeh Shekari
- Department of Stem Cells and Developmental Biology, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
- Advanced Therapy Medicinal Product Technology Development Center, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
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Abyadeh M, Gupta V, Paulo JA, Mahmoudabad AG, Shadfar S, Mirshahvaladi S, Gupta V, Nguyen CTO, Finkelstein DI, You Y, Haynes PA, Salekdeh GH, Graham SL, Mirzaei M. Amyloid-beta and tau protein beyond Alzheimer's disease. Neural Regen Res 2024; 19:1262-1276. [PMID: 37905874 DOI: 10.4103/1673-5374.386406] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 09/07/2023] [Indexed: 11/02/2023] Open
Abstract
ABSTRACT The aggregation of amyloid-beta peptide and tau protein dysregulation are implicated to play key roles in Alzheimer's disease pathogenesis and are considered the main pathological hallmarks of this devastating disease. Physiologically, these two proteins are produced and expressed within the normal human body. However, under pathological conditions, abnormal expression, post-translational modifications, conformational changes, and truncation can make these proteins prone to aggregation, triggering specific disease-related cascades. Recent studies have indicated associations between aberrant behavior of amyloid-beta and tau proteins and various neurological diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis, as well as retinal neurodegenerative diseases like Glaucoma and age-related macular degeneration. Additionally, these proteins have been linked to cardiovascular disease, cancer, traumatic brain injury, and diabetes, which are all leading causes of morbidity and mortality. In this comprehensive review, we provide an overview of the connections between amyloid-beta and tau proteins and a spectrum of disorders.
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Affiliation(s)
| | - Vivek Gupta
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW, Australia
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | | | - Sina Shadfar
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW, Australia
| | - Shahab Mirshahvaladi
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW, Australia
| | - Veer Gupta
- School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Christine T O Nguyen
- Department of Optometry and Vision Sciences, School of Health Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - David I Finkelstein
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Yuyi You
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW, Australia
| | - Paul A Haynes
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW, Australia
| | - Ghasem H Salekdeh
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW, Australia
| | - Stuart L Graham
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW, Australia
| | - Mehdi Mirzaei
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW, Australia
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Abyadeh M, Kaya A. Application of Multiomics Approach to Investigate the Therapeutic Potentials of Stem Cell-derived Extracellular Vesicle Subpopulations for Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593647. [PMID: 38798317 PMCID: PMC11118424 DOI: 10.1101/2024.05.10.593647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Alzheimer's disease (AD) presents a complex interplay of molecular alterations, yet understanding its pathogenesis remains a challenge. In this study, we delved into the intricate landscape of proteome and transcriptome changes in AD brains compared to healthy controls, examining 788 brain samples revealing common alterations at both protein and mRNA levels. Moreover, our analysis revealed distinct protein-level changes in aberrant energy metabolism pathways in AD brains that were not evident at the mRNA level. This suggests that the changes in protein expression could provide a deeper molecular representation of AD pathogenesis. Subsequently, using a comparative proteomic approach, we explored the therapeutic potential of mesenchymal stem cell-derived extracellular vehicles (EVs), isolated through various methods, in mitigating AD-associated changes at the protein level. Our analysis revealed a particular EV-subtype that can be utilized for compensating dysregulated mitochondrial proteostasis in the AD brain. By using network biology approaches, we further revealed the potential regulators of key therapeutic proteins. Overall, our study illuminates the significance of proteome alterations in AD pathogenesis and identifies the therapeutic promise of a specific EV subpopulation with reduced pro-inflammatory protein cargo and enriched proteins to target mitochondrial proteostasis.
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Affiliation(s)
- Morteza Abyadeh
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284 USA
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284 USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA
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Kanwal H, Sangineto M, Ciarnelli M, Castaldo P, Villani R, Romano AD, Serviddio G, Cassano T. Potential Therapeutic Targets to Modulate the Endocannabinoid System in Alzheimer's Disease. Int J Mol Sci 2024; 25:4050. [PMID: 38612861 PMCID: PMC11012768 DOI: 10.3390/ijms25074050] [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: 02/27/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Alzheimer's disease (AD), the most common neurodegenerative disease (NDD), is characterized by chronic neuronal cell death through progressive loss of cognitive function. Amyloid beta (Aβ) deposition, neuroinflammation, oxidative stress, and hyperphosphorylated tau proteins are considered the hallmarks of AD pathology. Different therapeutic approaches approved by the Food and Drug Administration can only target a single altered pathway instead of various mechanisms that are involved in AD pathology, resulting in limited symptomatic relief and almost no effect in slowing down the disease progression. Growing evidence on modulating the components of the endocannabinoid system (ECS) proclaimed their neuroprotective effects by reducing neurochemical alterations and preventing cellular dysfunction. Recent studies on AD mouse models have reported that the inhibitors of the fatty acid amide hydrolase (FAAH) and monoacylglycerol (MAGL), hydrolytic enzymes for N-arachidonoyl ethanolamine (AEA) and 2-arachidonoylglycerol (2-AG), respectively, might be promising candidates as therapeutical intervention. The FAAH and MAGL inhibitors alone or in combination seem to produce neuroprotection by reversing cognitive deficits along with Aβ-induced neuroinflammation, oxidative responses, and neuronal death, delaying AD progression. Their exact signaling mechanisms need to be elucidated for understanding the brain intrinsic repair mechanism. The aim of this review was to shed light on physiology and pathophysiology of AD and to summarize the experimental data on neuroprotective roles of FAAH and MAGL inhibitors. In this review, we have also included CB1R and CB2R modulators with their diverse roles to modulate ECS mediated responses such as anti-nociceptive, anxiolytic, and anti-inflammatory actions in AD. Future research would provide the directions in understanding the molecular mechanisms and development of new therapeutic interventions for the treatment of AD.
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Affiliation(s)
- Hina Kanwal
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (M.S.); (M.C.); (R.V.); (A.D.R.); (G.S.); (T.C.)
| | - Moris Sangineto
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (M.S.); (M.C.); (R.V.); (A.D.R.); (G.S.); (T.C.)
| | - Martina Ciarnelli
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (M.S.); (M.C.); (R.V.); (A.D.R.); (G.S.); (T.C.)
| | - Pasqualina Castaldo
- Department of Biomedical Sciences and Public Health, School of Medicine, University “Politecnica delle Marche”, 60126 Ancona, Italy;
| | - Rosanna Villani
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (M.S.); (M.C.); (R.V.); (A.D.R.); (G.S.); (T.C.)
| | - Antonino Davide Romano
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (M.S.); (M.C.); (R.V.); (A.D.R.); (G.S.); (T.C.)
| | - Gaetano Serviddio
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (M.S.); (M.C.); (R.V.); (A.D.R.); (G.S.); (T.C.)
| | - Tommaso Cassano
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (M.S.); (M.C.); (R.V.); (A.D.R.); (G.S.); (T.C.)
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Wang X, Tang X, Zhu P, Hua D, Xie Z, Guo M, Que M, Yan J, Li X, Xia Q, Luo X, Bi J, Zhao Y, Zhou Z, Li S, Luo A. CircAKT3 alleviates postoperative cognitive dysfunction by stabilizing the feedback cycle of miR-106a-5p/HDAC4/MEF2C axis in hippocampi of aged mice. Cell Mol Life Sci 2024; 81:138. [PMID: 38478029 PMCID: PMC10937803 DOI: 10.1007/s00018-024-05156-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/10/2024] [Accepted: 02/05/2024] [Indexed: 03/17/2024]
Abstract
Circular RNAs (circRNAs) have garnered significant attention in the field of neurodegenerative diseases including Alzheimer's diseases due to their covalently closed loop structure. However, the involvement of circRNAs in postoperative cognitive dysfunction (POCD) is still largely unexplored. To identify the genes differentially expressed between non-POCD (NPOCD) and POCD mice, we conducted the whole transcriptome sequencing initially in this study. According to the expression profiles, we observed that circAKT3 was associated with hippocampal neuronal apoptosis in POCD mice. Moreover, we found that circAKT3 overexpression reduced apoptosis of hippocampal neurons and alleviated POCD. Subsequently, through bioinformatics analysis, our data showed that circAKT3 overexpression in vitro and in vivo elevated the abundance of miR-106a-5p significantly, resulting in a decrease of HDAC4 protein and an increase of MEF2C protein. Additionally, this effect of circAKT3 was blocked by miR-106a-5p inhibitor. Interestingly, MEF2C could activate the transcription of miR-106a-5p promoter and form a positive feedback loop. Therefore, our findings revealed more potential modulation ways between circRNA-miRNA and miRNA-mRNA, providing different directions and targets for preclinical studies of POCD.
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Affiliation(s)
- Xuan Wang
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Xiaole Tang
- State Key Laboratory of Oncology in Southern China, Department of Anesthesiology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, China
| | - Pengfei Zhu
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Dongyu Hua
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Zheng Xie
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Mingke Guo
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Mengxin Que
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Jing Yan
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Xing Li
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Qian Xia
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Xiaoxiao Luo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jiangjiang Bi
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Yilin Zhao
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Zhiqiang Zhou
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Shiyong Li
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China.
| | - Ailin Luo
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China.
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Zhang Z, Liu X, Zhang S, Song Z, Lu K, Yang W. A review and analysis of key biomarkers in Alzheimer's disease. Front Neurosci 2024; 18:1358998. [PMID: 38445255 PMCID: PMC10912539 DOI: 10.3389/fnins.2024.1358998] [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: 12/20/2023] [Accepted: 02/02/2024] [Indexed: 03/07/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that affects over 50 million elderly individuals worldwide. Although the pathogenesis of AD is not fully understood, based on current research, researchers are able to identify potential biomarker genes and proteins that may serve as effective targets against AD. This article aims to present a comprehensive overview of recent advances in AD biomarker identification, with highlights on the use of various algorithms, the exploration of relevant biological processes, and the investigation of shared biomarkers with co-occurring diseases. Additionally, this article includes a statistical analysis of key genes reported in the research literature, and identifies the intersection with AD-related gene sets from databases such as AlzGen, GeneCard, and DisGeNet. For these gene sets, besides enrichment analysis, protein-protein interaction (PPI) networks utilized to identify central genes among the overlapping genes. Enrichment analysis, protein interaction network analysis, and tissue-specific connectedness analysis based on GTEx database performed on multiple groups of overlapping genes. Our work has laid the foundation for a better understanding of the molecular mechanisms of AD and more accurate identification of key AD markers.
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Affiliation(s)
- Zhihao Zhang
- School of Computer Science and Technology, Xinjiang University, Ürümqi, China
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
| | - Xiangtao Liu
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
| | - Suixia Zhang
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | - Zhixin Song
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
| | - Ke Lu
- School of Computer Science and Technology, Xinjiang University, Ürümqi, China
| | - Wenzhong Yang
- School of Computer Science and Technology, Xinjiang University, Ürümqi, China
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7
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Iskusnykh IY, Zakharova AA, Kryl’skii ED, Popova TN. Aging, Neurodegenerative Disorders, and Cerebellum. Int J Mol Sci 2024; 25:1018. [PMID: 38256091 PMCID: PMC10815822 DOI: 10.3390/ijms25021018] [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: 12/13/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
An important part of the central nervous system (CNS), the cerebellum is involved in motor control, learning, reflex adaptation, and cognition. Diminished cerebellar function results in the motor and cognitive impairment observed in patients with neurodegenerative disorders such as Alzheimer's disease (AD), vascular dementia (VD), Parkinson's disease (PD), Huntington's disease (HD), spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), Friedreich's ataxia (FRDA), and multiple sclerosis (MS), and even during the normal aging process. In most neurodegenerative disorders, impairment mainly occurs as a result of morphological changes over time, although during the early stages of some disorders such as AD, the cerebellum also serves a compensatory function. Biological aging is accompanied by changes in cerebellar circuits, which are predominantly involved in motor control. Despite decades of research, the functional contributions of the cerebellum and the underlying molecular mechanisms in aging and neurodegenerative disorders remain largely unknown. Therefore, this review will highlight the molecular and cellular events in the cerebellum that are disrupted during the process of aging and the development of neurodegenerative disorders. We believe that deeper insights into the pathophysiological mechanisms of the cerebellum during aging and the development of neurodegenerative disorders will be essential for the design of new effective strategies for neuroprotection and the alleviation of some neurodegenerative disorders.
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Affiliation(s)
- Igor Y. Iskusnykh
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Anastasia A. Zakharova
- Department of Medical Biochemistry, Faculty of Biomedicine, Pirogov Russian National Research Medical University, Ostrovitianov St. 1, Moscow 117997, Russia
| | - Evgenii D. Kryl’skii
- Department of Medical Biochemistry, Molecular and Cell Biology, Voronezh State University, Universitetskaya Sq. 1, Voronezh 394018, Russia; (E.D.K.)
| | - Tatyana N. Popova
- Department of Medical Biochemistry, Molecular and Cell Biology, Voronezh State University, Universitetskaya Sq. 1, Voronezh 394018, Russia; (E.D.K.)
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8
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Abyadeh M, Alikhani M, Mirzaei M, Gupta V, Shekari F, Salekdeh GH. Proteomics provides insights into the theranostic potential of extracellular vesicles. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:101-133. [PMID: 38220422 DOI: 10.1016/bs.apcsb.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Extracellular vesicles (EVs) encompass a diverse range of membranous structures derived from cells, including exosomes and microvesicles. These vesicles are present in biological fluids and play vital roles in various physiological and pathological processes. They facilitate intercellular communication by enabling the exchange of proteins, lipids, and genetic material between cells. Understanding the cellular processes that govern EV biology is essential for unraveling their physiological and pathological functions and their potential clinical applications. Despite significant advancements in EV research in recent years, there is still much to learn about these vesicles. The advent of improved mass spectrometry (MS)-based techniques has allowed for a deeper characterization of EV protein composition, providing valuable insights into their roles in different physiological and pathological conditions. In this chapter, we provide an overview of proteomics studies conducted to identify the protein contents of EVs, which contribute to their therapeutic and pathological features. We also provided evidence on the potential of EV proteome contents as biomarkers for early disease diagnosis, progression, and treatment response, as well as factors that influence their composition. Additionally, we discuss the available databases containing information on EV proteome contents, and finally, we highlight the need for further research to pave the way toward their utilization in clinical settings.
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Affiliation(s)
- Morteza Abyadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Alikhani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Mirzaei
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW, Australia
| | - Vivek Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW, Australia
| | - Faezeh Shekari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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9
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Abyadeh M, Gupta V, Liu X, Rossio V, Mirzaei M, Cornish J, Paulo JA, Haynes PA. Proteome-Wide Profiling Using Sample Multiplexing of a Human Cell Line Treated with Cannabidiol (CBD) and Tetrahydrocannabinol (THC). Proteomes 2023; 11:36. [PMID: 37987316 PMCID: PMC10661330 DOI: 10.3390/proteomes11040036] [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: 08/29/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
Cannabis has been used historically for both medicinal and recreational purposes, with the most notable cannabinoids being cannabidiol (CBD) and tetrahydrocannabinol (THC). Although their therapeutic effects have been well studied and their recreational use is highly debated, the underlying mechanisms of their biological effects remain poorly defined. In this study, we use isobaric tag-based sample multiplexed proteome profiling to investigate protein abundance differences in the human neuroblastoma SH-SY5Y cell line treated with CBD and THC. We identified significantly regulated proteins by each treatment and performed a pathway classification and associated protein-protein interaction analysis. Our findings suggest that these treatments may lead to mitochondrial dysfunction and induce endoplasmic reticulum stress. These data can potentially be interrogated further to investigate the potential role of CBD and THC in various biological and disease contexts, providing a foundation for future studies.
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Affiliation(s)
- Morteza Abyadeh
- ProGene Technologies Pty Ltd., Macquarie Park, NSW 2113, Australia;
| | - Vivek Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (V.G.); (M.M.)
| | - Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; (X.L.); (V.R.); (J.A.P.)
| | - Valentina Rossio
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; (X.L.); (V.R.); (J.A.P.)
| | - Mehdi Mirzaei
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (V.G.); (M.M.)
| | - Jennifer Cornish
- School of Psychological Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia;
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; (X.L.); (V.R.); (J.A.P.)
| | - Paul A. Haynes
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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10
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Hashemi KS, Aliabadi MK, Mehrara A, Talebi E, Hemmati AA, Rezaeiye RD, Ghanbary MJ, Motealleh M, Dayeri B, Alashti SK. A meta-analysis of microarray datasets to identify biological regulatory networks in Alzheimer's disease. Front Genet 2023; 14:1225196. [PMID: 37705610 PMCID: PMC10497115 DOI: 10.3389/fgene.2023.1225196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023] Open
Abstract
Background: Alzheimer's Disease (AD) is an age-related progressive neurodegenerative disorder characterized by mental deterioration, memory deficit, and multiple cognitive abnormalities, with an overall prevalence of ∼2% among industrialized countries. Although a proper diagnosis is not yet available, identification of miRNAs and mRNAs could offer valuable insights into the molecular pathways underlying AD's prognosis. Method: This study aims to utilize microarray bioinformatic analysis to identify potential biomarkers of AD, by analyzing six microarray datasets (GSE4757, GSE5281, GSE16759, GSE28146, GSE12685, and GSE1297) of AD patients, and control groups. Furthermore, this study conducted gene ontology, pathways analysis, and protein-protein interaction network to reveal major pathways linked to probable biological events. The datasets were meta-analyzed using bioinformatics tools, to identify significant differentially expressed genes (DEGs) and hub genes and their targeted miRNAs'. Results: According to the findings, CXCR4, TGFB1, ITGB1, MYH11, and SELE genes were identified as hub genes in this study. The analysis of DEGs using GO (gene ontology) revealed that these genes were significantly enriched in actin cytoskeleton regulation, ECM-receptor interaction, and hypertrophic cardiomyopathy. Eventually, hsa-mir-122-5p, hsa-mir-106a-5p, hsa-mir-27a-3p, hsa-mir16-5p, hsa-mir-145-5p, hsa-mir-12-5p, hsa-mir-128-3p, hsa-mir 3200-3p, hsa-mir-103a-3p, and hsa-mir-9-3p exhibited significant interactions with most of the hub genes. Conclusion: Overall, these genes can be considered as pivotal biomarkers for diagnosing the pathogenesis and molecular functions of AD.
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Affiliation(s)
- Kimia Sadat Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohadese Koohi Aliabadi
- Faculty of Interdisciplinary Science and Technology, Tarbiat Modares University, Tehran, Iran
| | - Arian Mehrara
- School of Pharmacy, Ramsar International Campus, Mazandaran University of Medical Sciences, Ramsar, Iran
| | - Elham Talebi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ali Akbar Hemmati
- Department of Biology and Biotechnology, Molecular Biology, and Genetics, Pavia University, Lombardi, Italy
| | | | | | - Maryam Motealleh
- Department of System Biology Lab, University of Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Behnaz Dayeri
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Biotechnology, University of Milan, Milan, Italy
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11
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Abyadeh M, Gupta V, Paulo JA, Sheriff S, Shadfar S, Fitzhenry M, Amirkhani A, Gupta V, Salekdeh GH, Haynes PA, Graham SL, Mirzaei M. Apolipoprotein ε in Brain and Retinal Neurodegenerative Diseases. Aging Dis 2023; 14:1311-1330. [PMID: 37199411 PMCID: PMC10389820 DOI: 10.14336/ad.2023.0312-1] [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: 01/11/2023] [Accepted: 03/12/2023] [Indexed: 05/19/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia that remains incurable and has become a major medical, social, and economic challenge worldwide. AD is characterized by pathological hallmarks of senile plaques (SP) and neurofibrillary tangles (NFTs) that damage the brain up to twenty years before a clinical diagnosis is made. Interestingly these pathological features have also been observed in retinal neurodegenerative diseases including age related macular degeneration (ARMD), glaucoma and diabetic retinopathy (DR). An association of AD with these diseases has been suggested in epidemiological studies and several common pathological events and risk factors have been identified between these diseases. The E4 allele of Apolipoprotein E (APOE) is a well-established genetic risk factor for late onset AD. The ApoE ε4 allele is also associated with retinal neurodegenerative diseases however in contrast to AD, it is considered protective in AMD, likewise ApoE E2 allele, which is a protective factor for AD, has been implicated as a risk factor for AMD and glaucoma. This review summarizes the evidence on the effects of ApoE in retinal neurodegenerative diseases and discusses the overlapping molecular pathways in AD. The involvement of ApoE in regulating amyloid beta (Aβ) and tau pathology, inflammation, vascular integrity, glucose metabolism and vascular endothelial growth factor (VEGF) signaling is also discussed.
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Affiliation(s)
| | - Vivek Gupta
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW 2109, Australia.
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Samran Sheriff
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW 2109, Australia.
| | - Sina Shadfar
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW 2109, Australia.
| | - Matthew Fitzhenry
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW 2113, Australia.
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW 2113, Australia.
| | - Veer Gupta
- School of Medicine, Deakin University, VIC, Australia.
| | - Ghasem H Salekdeh
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia.
| | - Paul A Haynes
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia.
| | - Stuart L Graham
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW 2109, Australia.
| | - Mehdi Mirzaei
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW 2109, Australia.
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12
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Abyadeh M, Yadav VK, Kaya A. Common molecular signatures between coronavirus infection and Alzheimer's disease reveal targets for drug development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544970. [PMID: 37398415 PMCID: PMC10312734 DOI: 10.1101/2023.06.14.544970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cognitive decline has been reported as a common consequence of COVID-19, and studies have suggested a link between COVID-19 infection and Alzheimer's disease (AD). However, the molecular mechanisms underlying this association remain unclear. To shed light on this link, we conducted an integrated genomic analysis using a novel Robust Rank Aggregation method to identify common transcriptional signatures of the frontal cortex, a critical area for cognitive function, between individuals with AD and COVID-19. We then performed various analyses, including the KEGG pathway, GO ontology, protein-protein interaction, hub gene, gene-miRNA, and gene-transcription factor interaction analyses to identify molecular components of biological pathways that are associated with AD in the brain also show similar changes in severe COVID-19. Our findings revealed the molecular mechanisms underpinning the association between COVID-19 infection and AD development and identified several genes, miRNAs, and TFs that may be targeted for therapeutic purposes. However, further research is needed to investigate the diagnostic and therapeutic applications of these findings.
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Affiliation(s)
- Morteza Abyadeh
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284 USA
| | - Vijay K. Yadav
- Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284 USA
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13
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Jiang C, Geng L, Wang J, Liang Y, Guo X, Liu C, Zhao Y, Jin J, Liu Z, Mu Y. Multiplexed Gene Engineering Based on dCas9 and gRNA-tRNA Array Encoded on Single Transcript. Int J Mol Sci 2023; 24:ijms24108535. [PMID: 37239880 DOI: 10.3390/ijms24108535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Simultaneously, multiplexed genome engineering and targeting multiple genomic loci are valuable to elucidating gene interactions and characterizing genetic networks that affect phenotypes. Here, we developed a general CRISPR-based platform to perform four functions and target multiple genome loci encoded in a single transcript. To establish multiple functions for multiple loci targets, we fused four RNA hairpins, MS2, PP7, com and boxB, to stem-loops of gRNA (guide RNA) scaffolds, separately. The RNA-hairpin-binding domains MCP, PCP, Com and λN22 were fused with different functional effectors. These paired combinations of cognate-RNA hairpins and RNA-binding proteins generated the simultaneous, independent regulation of multiple target genes. To ensure that all proteins and RNAs are expressed in one transcript, multiple gRNAs were constructed in a tandemly arrayed tRNA (transfer RNA)-gRNA architecture, and the triplex sequence was cloned between the protein-coding sequences and the tRNA-gRNA array. By leveraging this system, we illustrate the transcriptional activation, transcriptional repression, DNA methylation and DNA demethylation of endogenous targets using up to 16 individual CRISPR gRNAs delivered on a single transcript. This system provides a powerful platform to investigate synthetic biology questions and engineer complex-phenotype medical applications.
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Affiliation(s)
- Chaoqian Jiang
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Lishuang Geng
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jinpeng Wang
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Yingjuan Liang
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Xiaochen Guo
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Chang Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Yunjing Zhao
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Junxue Jin
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yanshuang Mu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
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14
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Vallelunga A, Iannitti T, Somma G, Russillo MC, Picillo M, De Micco R, Vacca L, Cilia R, Cicero CE, Zangaglia R, Lazzeri G, Galantucci S, Radicati FG, De Rosa A, Amboni M, Scaglione C, Tessitore A, Stocchi F, Eleopra R, Nicoletti A, Pacchetti C, Di Fonzo A, Volontè MA, Barone P, Pellecchia MT. Gender differences in microRNA expression in levodopa-naive PD patients. J Neurol 2023:10.1007/s00415-023-11707-0. [PMID: 37052669 DOI: 10.1007/s00415-023-11707-0] [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: 02/21/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023]
Abstract
Gender is an important factor influencing epidemiological and clinical features of Parkinson's disease (PD). We aimed to evaluate gender differences in the expression of a panel of miRNAs (miR-34a-5p, miR-146a, miR-155, miR-29a, miR-106a) possibly involved in the pathophysiology or progression of disease. Serum samples were obtained from 104 PD patients (58 men and 46 women) never treated with levodopa. We measured levels of miRNAs using quantitative PCR. Correlations between miRNA expression and clinical data were assessed using the Spearman's correlation test. We used STRING to evaluate co-expression relationship among target genes. MiR-34a-5p was significantly upregulated in PD male patients compared to PD female patients (fc: 1.62; p < 0.0001). No correlation was found with age, BMI, and disease severity, assessed by UPDRS III scale, in male and female patients. MiR-146a-5p was significantly upregulated in female as compared to male patients (fc: 3.44; p < 0.0001) and a significant correlation was also observed between disease duration and mir-146a-5p. No differences were found in the expression of miR-29a, miR-106a-5p and miR-155 between genders. Predicted target genes for miR-34a-5p and miR-146-5p and protein interactions in biological processes were reported. Our study supports the hypothesis that there are gender-specific differences in serum miRNAs expression in PD patients. Follow-up of this cohort is needed to understand if these differences may affect disease progression and response to treatment.
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Affiliation(s)
- A Vallelunga
- Department of Life Sciences and Biotechnologies, Section of Medicines and Health Products, University of Ferrara, Ferrara, Italy
| | - T Iannitti
- Department of Medical Sciences, Section of Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - G Somma
- Department of Medicine Surgery and Dentistry "Scuola Medica Salernitana", Neuroscience Section, University of Salerno, Fisciano, Italy
| | - M C Russillo
- Department of Medicine Surgery and Dentistry "Scuola Medica Salernitana", Neuroscience Section, University of Salerno, Fisciano, Italy
| | - M Picillo
- Department of Medicine Surgery and Dentistry "Scuola Medica Salernitana", Neuroscience Section, University of Salerno, Fisciano, Italy
| | - R De Micco
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - L Vacca
- IRCCS San Raffaele, Rome, Italy
| | - R Cilia
- Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - C E Cicero
- Neurologic Unit, AOU "Policlinico-San Marco", Department of Medical, Surgical Sciences and Advanced Technologies, GF Ingrassia, University of Catania, Catania, Italy
| | - R Zangaglia
- Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - G Lazzeri
- IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - S Galantucci
- IRCCS San Raffaele Scientific Institute, Neurology Unit, Milan, Italy
| | | | - A De Rosa
- IRCCS San Raffaele, Rome, Italy
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, Federico II University, Naples, Italy
| | - M Amboni
- Department of Medicine Surgery and Dentistry "Scuola Medica Salernitana", Neuroscience Section, University of Salerno, Fisciano, Italy
| | - C Scaglione
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - A Tessitore
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - F Stocchi
- IRCCS San Raffaele, Rome, Italy
- University San Raffaele, Roma, Italy
| | - R Eleopra
- Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - A Nicoletti
- Neurologic Unit, AOU "Policlinico-San Marco", Department of Medical, Surgical Sciences and Advanced Technologies, GF Ingrassia, University of Catania, Catania, Italy
| | - C Pacchetti
- Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - A Di Fonzo
- IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - M A Volontè
- IRCCS San Raffaele Scientific Institute, Neurology Unit, Milan, Italy
| | - P Barone
- Department of Medicine Surgery and Dentistry "Scuola Medica Salernitana", Neuroscience Section, University of Salerno, Fisciano, Italy
| | - M T Pellecchia
- Department of Medicine Surgery and Dentistry "Scuola Medica Salernitana", Neuroscience Section, University of Salerno, Fisciano, Italy.
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15
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Deng L, Gupta V, Abyadeh M, Chitranshi N, Pushpitha K, Wu Y, Gupta V, You Y, Paulo JA, Graham SL, Mirzaei M, Haynes PA. Oxidative Stress Induced Dysfunction of Protein Synthesis in 661W Mice Photoreceptor Cells. Proteomes 2023; 11:12. [PMID: 37092453 PMCID: PMC10123756 DOI: 10.3390/proteomes11020012] [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: 12/05/2022] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
Photoreceptor cells are highly susceptible to oxidative-stress-induced damage due to their high metabolic rate. Oxidative stress plays a key role in driving pathological events in several different ocular diseases, which lead to retinal degeneration and ultimately blindness. A growing number of studies have been performed to understand downstream events caused by ROS induced oxidative stress in photoreceptor cells; however, the underlying mechanisms of ROS toxicity are not fully understood. To shed light on ROS induced downstream pathological events, we employed a tandem mass tag (TMT) labelling-based quantitative mass-spectrometric approach to determine proteome changes in 661W photoreceptor cells following oxidative stress induction via the application of different concentrations of H2O2 at different time points. Overall, 5920 proteins were identified and quantified, and 450 differentially expressed proteins (DEPs) were identified, which were altered in a dose and time dependent manner in all treatment groups compared to the control group. These proteins were involved in several biological pathways, including spliceosome and ribosome response, activated glutathione metabolism, decreased ECM-receptor interaction, oxidative phosphorylation, abnormally regulated lysosome, apoptosis, and ribosome biogenesis. Our results highlighted ECM receptor interaction, oxidative phosphorylation and spliceosome pathways as the major targets of oxidative stress that might mediate vascular dysfunction and cellular senescence.
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Affiliation(s)
- Liting Deng
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Vivek Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | | | - Nitin Chitranshi
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Kanishka Pushpitha
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Yunqi Wu
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Veer Gupta
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
| | - Yuyi You
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stuart L. Graham
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Mehdi Mirzaei
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Paul A. Haynes
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Macquarie Park, NSW 2109, Australia
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16
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Abyadeh M, Yadav VK, Kaya A. Common Molecular Signatures Between Coronavirus Infection and Alzheimer's Disease Reveal Targets for Drug Development. J Alzheimers Dis 2023; 95:995-1011. [PMID: 37638446 DOI: 10.3233/jad-230684] [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] [Indexed: 08/29/2023]
Abstract
BACKGROUND Cognitive decline is a common consequence of COVID-19, and studies suggest a link between COVID-19 and Alzheimer's disease (AD). However, the molecular mechanisms underlying this association remain unclear. OBJECTIVE To understand the potential molecular mechanisms underlying the association between COVID-19 and AD development, and identify the potential genetic targets for pharmaceutical approaches to reduce the risk or delay the development of COVID-19-related neurological pathologies. METHODS We analyzed transcriptome datasets of 638 brain samples using a novel Robust Rank Aggregation method, followed by functional enrichment, protein-protein, hub genes, gene-miRNA, and gene-transcription factor (TF) interaction analyses to identify molecular markers altered in AD and COVID-19 infected brains. RESULTS Our analyses of frontal cortex from COVID-19 and AD patients identified commonly altered genes, miRNAs and TFs. Functional enrichment and hub gene analysis of these molecular changes revealed commonly altered pathways, including downregulation of the cyclic adenosine monophosphate (cAMP) signaling and taurine and hypotaurine metabolism, alongside upregulation of neuroinflammatory pathways. Furthermore, gene-miRNA and gene-TF network analyses provided potential up- and downstream regulators of identified pathways. CONCLUSION We found that downregulation of cAMP signaling pathway, taurine metabolisms, and upregulation of neuroinflammatory related pathways are commonly altered in AD and COVID-19 pathogenesis, and may make COVID-19 patients more susceptible to cognitive decline and AD. We also identified genetic targets, regulating these pathways that can be targeted pharmaceutically to reduce the risk or delay the development of COVID-19-related neurological pathologies and AD.
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Affiliation(s)
- Morteza Abyadeh
- Department of Biology, Virginia Common wealth University, Richmond, VA, USA
| | - Vijay K Yadav
- Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Alaattin Kaya
- Department of Biology, Virginia Common wealth University, Richmond, VA, USA
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17
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López-Cepeda L, Castro JD, Aristizábal-Pachón AF, González-Giraldo Y, Pinzón A, Puentes-Rozo PJ, González J. Modulation of Small RNA Signatures by Astrocytes on Early Neurodegeneration Stages; Implications for Biomarker Discovery. Life (Basel) 2022; 12:1720. [PMID: 36362875 PMCID: PMC9696502 DOI: 10.3390/life12111720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/01/2022] [Accepted: 10/12/2022] [Indexed: 04/04/2024] Open
Abstract
Diagnosis of neurodegenerative disease (NDD) is complex, therefore simpler, less invasive, more accurate biomarkers are needed. small non-coding RNA (sncRNA) dysregulates in NDDs and sncRNA signatures have been explored for the diagnosis of NDDs, however, the performance of previous biomarkers is still better. Astrocyte dysfunction promotes neurodegeneration and thus derived scnRNA signatures could provide a more precise way to identify of changes related to NDD course and pathogenesis, and it could be useful for the dissection of mechanistic insights operating in NDD. Often sncRNA are transported outside the cell by the action of secreted particles such as extracellular vesicles (EV), which protect sncRNA from degradation. Furthermore, EV associated sncRNA can cross the BBB to be found in easier to obtain peripheral samples, EVs also inherit cell-specific surface markers that can be used for the identification of Astrocyte Derived Extracellular Vesicles (ADEVs) in a peripheral sample. By the study of the sncRNA transported in ADEVs it is possible to identify astrocyte specific sncRNA signatures that could show astrocyte dysfunction in a more simpler manner than previous methods. However, sncRNA signatures in ADEV are not a copy of intracellular transcriptome and methodological aspects such as the yield of sncRNA produced in ADEV or the variable amount of ADEV captured after separation protocols must be considered. Here we review the role as signaling molecules of ADEV derived sncRNA dysregulated in conditions associated with risk of neurodegeneration, providing an explanation of why to choose ADEV for the identification of astrocyte-specific transcriptome. Finally, we discuss possible limitations of this approach and the need to improve the detection limits of sncRNA for the use of ADEV derived sncRNA signatures.
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Affiliation(s)
- Leonardo López-Cepeda
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Juan David Castro
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | | | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Andrés Pinzón
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Pedro J. Puentes-Rozo
- Grupo de Neurociencias del Caribe, Unidad de Neurociencias Cognitivas, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Grupo de Neurociencias del Caribe, Universidad del Atlántico, Barranquilla 080007, Colombia
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
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18
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Mirzaei M, Abyadeh M, Turner AJ, Wall RV, Chick JM, Paulo JA, Gupta VK, Basavarajappa D, Chitranshi N, Mirshahvaladi SSO, You Y, Fitzhenry MJ, Amirkhani A, Haynes PA, Klistorner A, Gupta V, Graham SL. Fingolimod effects on the brain are mediated through biochemical modulation of bioenergetics, autophagy, and neuroinflammatory networks. Proteomics 2022; 22:e2100247. [PMID: 35866514 PMCID: PMC9786555 DOI: 10.1002/pmic.202100247] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/30/2022] [Accepted: 07/18/2022] [Indexed: 12/30/2022]
Abstract
Fingolimod (FTY720) is an oral drug approved by the Food and Drug Administration (FDA) for management of multiple sclerosis (MS) symptoms, which has also shown beneficial effects against Alzheimer's (AD) and Parkinson's (PD) diseases pathologies. Although an extensive effort has been made to identify mechanisms underpinning its therapeutic effects, much remains unknown. Here, we investigated Fingolimod induced proteome changes in the cerebellum (CB) and frontal cortex (FC) regions of the brain which are known to be severely affected in MS, using a tandem mass tag (TMT) isobaric labeling-based quantitative mass-spectrometric approach to investigate the mechanism of action of Fingolimod. This study identified 6749 and 6319 proteins in CB and FC, respectively, and returned 2609 and 3086 differentially expressed proteins in mouse CB and FC, respectively, between Fingolimod treated and control groups. Subsequent bioinformatics analyses indicated a metabolic reprogramming in both brain regions of the Fingolimod treated group, where oxidative phosphorylation was upregulated while glycolysis and pentose phosphate pathway were downregulated. In addition, modulation of neuroinflammation in the Fingolimod treated group was indicated by upregulation of retrograde endocannabinoid signaling and autophagy pathways, and downregulation of neuroinflammation related pathways including neutrophil degranulation and the IL-12 mediated signaling pathway. Our findings suggest that Fingolimod may exert its protective effects on the brain by inducing metabolic reprogramming and neuroinflammation pathway modulation.
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Affiliation(s)
- Mehdi Mirzaei
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | | | - Anita J. Turner
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Roshana Vander Wall
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Joel M. Chick
- Department of Cell BiologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Joao A. Paulo
- Department of Cell BiologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Veer K. Gupta
- School of MedicineDeakin UniversityGeelongVICAustralia
| | - Devaraj Basavarajappa
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Nitin Chitranshi
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Seyed Shahab Oddin Mirshahvaladi
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Yuyi You
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | | | - Ardeshir Amirkhani
- Australian Proteome Analysis FacilityMacquarie UniversitySydneyNSWAustralia
| | - Paul A. Haynes
- School of Natural SciencesMacquarie UniversityMacquarie ParkNSWAustralia
- Biomolecular Discovery Research CentreMacquarie UniversitySydneyNSWAustralia
| | - Alexander Klistorner
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Vivek Gupta
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Stuart L. Graham
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
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