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Wang Y, Wang Z, Yu X, Wang X, Song J, Yu DJ, Ge F. MORE: a multi-omics data-driven hypergraph integration network for biomedical data classification and biomarker identification. Brief Bioinform 2024; 26:bbae658. [PMID: 39692449 DOI: 10.1093/bib/bbae658] [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: 08/19/2024] [Revised: 11/18/2024] [Accepted: 12/04/2024] [Indexed: 12/19/2024] Open
Abstract
High-throughput sequencing methods have brought about a huge change in omics-based biomedical study. Integrating various omics data is possibly useful for identifying some correlations across data modalities, thus improving our understanding of the underlying biological mechanisms and complexity. Nevertheless, most existing graph-based feature extraction methods overlook the complementary information and correlations across modalities. Moreover, these methods tend to treat the features of each omics modality equally, which contradicts current biological principles. To solve these challenges, we introduce a novel approach for integrating multi-omics data termed Multi-Omics hypeRgraph integration nEtwork (MORE). MORE initially constructs a comprehensive hyperedge group by extensively investigating the informative correlations within and across modalities. Subsequently, the multi-omics hypergraph encoding module is employed to learn the enriched omics-specific information. Afterward, the multi-omics self-attention mechanism is then utilized to adaptatively aggregate valuable correlations across modalities for representation learning and making the final prediction. We assess MORE's performance on datasets characterized by message RNA (mRNA) expression, Deoxyribonucleic Acid (DNA) methylation, and microRNA (miRNA) expression for Alzheimer's disease, invasive breast carcinoma, and glioblastoma. The results from three classification tasks highlight the competitive advantage of MORE in contrast with current state-of-the-art (SOTA) methods. Moreover, the results also show that MORE has the capability to identify a greater variety of disease-related biomarkers compared to existing methods, highlighting its advantages in biomedical data mining and interpretation. Overall, MORE can be investigated as a valuable tool for facilitating multi-omics analysis and novel biomarker discovery. Our code and data can be publicly accessed at https://github.com/Wangyuhanxx/MORE.
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Affiliation(s)
- Yuhan Wang
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
| | - Zhikang Wang
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Wellington Rd, Clayton, Melbourne, VIC 3800, Australia
| | - Xuan Yu
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong 999077, China
| | - Xiaoyu Wang
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Wellington Rd, Clayton, Melbourne, VIC 3800, Australia
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Wellington Rd, Clayton, Melbourne, VIC 3800, Australia
- Monash Data Futures Institute, Monash University, Wellington Rd, Clayton, Melbourne, VIC 3800, Australia
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
| | - Fang Ge
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan, Nanjing 210023, China
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Çalışkan H, Önal D, Nalçacı E. Darbepoetin alpha has an anxiolytic and anti-neuroinflammatory effect in male rats. BMC Immunol 2024; 25:75. [PMID: 39523336 PMCID: PMC11552158 DOI: 10.1186/s12865-024-00665-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 10/28/2024] [Indexed: 11/16/2024] Open
Abstract
AIMS We aimed to investigate the anxiolytic effect of darbepoetin alpha (DEPO), an erythropoietin derivative, in a neuroinflammation model regarding different behaviors and biological pathways. METHODS Forty adult male Wistar albino rats were divided into four groups (control, LPS, DEPO, and DEPO + LPS). The rats were treated with 5 µg /kg DEPO once a week for four weeks, after which neuroinflammation was induced with 2 mg/kg lipopolysaccharide (LPS). The elevated plus maze, open-field, and light‒dark box tests were conducted to assess anxiety levels. Harderian gland secretions were scored via observation. Tumor necrosis factor alpha (TNF-α), Interleukin-1-beta (IL-1β), brain-derived growth factor (BDNF), serotonin, cortisol, total antioxidant/oxidant (TAS/TOS), and total/free thiol levels were measured in the prefrontal cortex, striatum, and serum. RESULTS DEPO had a potent anxiolytic effect on both DEPO and DEPO + LPS groups. Compared to the control group, DEPO administration caused an increase in serotonin and BDNF levels and decreased basal cortisol and TNF-α levels in naive rats. IL-1β did not alter after DEPO administration in naive rats. Prophylactic DEPO treatment remarkably downregulated cortisol, IL-1β, and TNF-α in the DEPO + LPS group. In addition, prophylactic DEPO administration significantly attenuated the decrease in serotonin and BDNF levels in the DEPO + LPS group. Furthermore, DEPO ameliorated excessive harderian gland secretion in the DEPO + LPS group. Compared with those in the control group, the free thiol content in the serum increased after DEPO administration. No similar effect was seen in the DEPO + LPS group receiving prophylactic DEPO. TAS showed no difference among all experimental groups. DEPO administration increased TOS and OSI in the serum and prefrontal cortex but not in the striatum. This effect was not seen in the DEPO + LPS group. CONCLUSION Darbepoetin alpha had an anxiolytic effect on many physiological mechanisms in a neuroinflammation model and naive rats.
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Affiliation(s)
- Hasan Çalışkan
- Physiology Department, Balıkesir University Medicine Faculty, Balıkesir, Turkey.
| | - Deniz Önal
- Physiology Department, Balıkesir University Medicine Faculty, Balıkesir, Turkey
| | - Erhan Nalçacı
- Physiology Department, Ankara University Medicine Faculty , Ankara, Turkey
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Kalluru PKR, Bhavanthi S, Vashist S, Gopavaram RR, Mamilla M, Sharma S, Gundoji CR, Goguri SR. Role of erythropoietin in the treatment of Alzheimer's disease: the story so far. Ann Med Surg (Lond) 2024; 86:3608-3614. [PMID: 38846819 PMCID: PMC11152865 DOI: 10.1097/ms9.0000000000002113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 04/17/2024] [Indexed: 06/09/2024] Open
Abstract
This review aims to explore the potential of erythropoietin, a glycopeptide hormone, as a treatment option for Alzheimer's disease, which is the commonest cause of dementia. Despite years of focus and research, therapeutic options for Alzheimer's disease are not yet completely satisfactory. And as people age, they are likely to develop Alzheimer's Disease, further pressuring the healthcare system. So, it is definite to develop treatment options that meet superior outcomes with minimal negative effects. A comprehensive review of the literature was conducted in PubMed and Google Scholar using a combination of keywords, including Alzheimer's disease, dementia, erythropoietin, and neuroprotection. Search results were assessed for relevance before using the data for this study. The beneficial implications of erythropoietin as a therapeutic option have been explored, along with the side effects and mechanisms of erythropoietin in Alzheimer's disease. Overall, the authors' review indicates that erythropoietin presents a promising avenue for mitigating the progression of Alzheimer's disease, with minimal associated side effects.
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Affiliation(s)
| | | | | | | | | | - Shriya Sharma
- Internal Medicine, Dnipropetrovsk Medical Academy of Health Ministry of Ukraine, Dnipro, Ukraine
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Lin JZ, Duan MR, Lin N, Zhao WJ. The emerging role of the chondroitin sulfate proteoglycan family in neurodegenerative diseases. Rev Neurosci 2021; 32:737-750. [PMID: 33655733 DOI: 10.1515/revneuro-2020-0146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/07/2021] [Indexed: 02/05/2023]
Abstract
Chondroitin sulfate (CS) is a kind of linear polysaccharide that is covalently linked to proteins to form proteoglycans. Chondroitin sulfate proteoglycans (CSPGs) consist of a core protein, with one or more CS chains covalently attached. CSPGs are precisely regulated and they exert a variety of physiological functions by binding to adhesion molecules and growth factors. Widely distributed in the nervous system in human body, CSPGs contribute to the major component of extracellular matrix (ECM), where they play an important role in the development and maturation of the nervous system, as well as in the pathophysiological response to damage to the central nervous system (CNS). While there are more than 30 types of CSPGs, this review covers the roles of the most important ones, including versican, aggrecan, neurocan and NG2 in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and multiple sclerosis. The updated reports of the treatment of neurodegenerative diseases are involving CSPGs.
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Affiliation(s)
- Jia-Zhe Lin
- Neurosurgical Department, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
- Center for Neuroscience, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Ming-Rui Duan
- Center for Neuroscience, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Nuan Lin
- Obstetrics and Gynecology Department, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Wei-Jiang Zhao
- Center for Neuroscience, Shantou University Medical College, Shantou 515041, Guangdong, China
- Cell Biology Department, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, China
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Lai SW, Chen JH, Lin HY, Liu YS, Tsai CF, Chang PC, Lu DY, Lin C. Regulatory Effects of Neuroinflammatory Responses Through Brain-Derived Neurotrophic Factor Signaling in Microglial Cells. Mol Neurobiol 2018; 55:7487-7499. [PMID: 29427085 DOI: 10.1007/s12035-018-0933-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 01/25/2018] [Indexed: 11/26/2022]
Abstract
Inhibition of microglial over-activation is an important strategy to counter balance neurodegenerative progression. We previously demonstrated that the adenosine monophosphate-activated protein kinase (AMPK) may be a therapeutic target in mediating anti-neuroinflammatory responses in microglia. Brain-derived neurotrophic factor (BDNF) is one of the major neurotrophic factors produced by astrocytes to maintain the development and survival of neurons in the brain, and have recently been shown to modulate homeostasis of neuroinflammation. Therefore, the present study focused on BDNF-mediated neuroinflammatory responses and may provide an endogenous regulation of neuroinflammation. Among the tested neuroinflammation, epigallocatechin gallate (EGCG) and minocycline exerted BDNF upregulation to inhibit COX-2 and proinflammatory mediator expressions. Furthermore, both EGCG and minocycline upregulated BDNF expression in microglia through AMPK signaling. In addition, minocycline and EGCG also increased expressions of erythropoietin (EPO) and sonic hedgehog (Shh). In the endogenous modulation of neuroinflammation, astrocyte-conditioned medium (AgCM) also decreased the expression of COX-2 and upregulated BDNF expression in microglia. The anti-inflammatory effects of BDNF were mediated through EPO/Shh in microglia. Our results indicated that the BDNF-EPO-Shh novel-signaling pathway underlies the regulation of inflammatory responses and may be regarded as a potential therapeutic target in neurodegenerative diseases. This study also reveals a better understanding of an endogenous crosstalk between astrocytes and microglia to regulate anti-inflammatory actions, which could provide a novel strategy for the treatment of neuroinflammation and neurodegenerative diseases.
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Affiliation(s)
- Sheng-Wei Lai
- Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan
| | - Jia-Hong Chen
- Department of General Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Hsiao-Yun Lin
- Department of Pharmacology, School of Medicine, China Medical University, No.91 Hsueh-Shih Road, Taichung, Taiwan
| | - Yu-Shu Liu
- Department of Pharmacology, School of Medicine, China Medical University, No.91 Hsueh-Shih Road, Taichung, Taiwan
- Department of Biotechnology, Asia University, Taichung, Taiwan
| | - Cheng-Fang Tsai
- Department of Biotechnology, Asia University, Taichung, Taiwan
| | - Pei-Chun Chang
- Department of Bioinformatics, Asia University, Taichung, Taiwan
| | - Dah-Yuu Lu
- Department of Pharmacology, School of Medicine, China Medical University, No.91 Hsueh-Shih Road, Taichung, Taiwan.
- Department of Photonics and Communication Engineering, Asia University, Taichung, Taiwan.
| | - Chingju Lin
- Department of Physiology, School of Medicine, China Medical University, Taichung, Taiwan.
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Parry SM, Peeples ES. The impact of hypoxic-ischemic brain injury on stem cell mobilization, migration, adhesion, and proliferation. Neural Regen Res 2018; 13:1125-1135. [PMID: 30028311 PMCID: PMC6065219 DOI: 10.4103/1673-5374.235012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neonatal hypoxic-ischemic encephalopathy continues to be a significant cause of death or neurodevelopmental delays despite standard use of therapeutic hypothermia. The use of stem cell transplantation has recently emerged as a promising supplemental therapy to further improve the outcomes of infants with hypoxic-ischemic encephalopathy. After the injury, the brain releases several chemical mediators, many of which communicate directly with stem cells to encourage mobilization, migration, cell adhesion and differentiation. This manuscript reviews the biomarkers that are released from the injured brain and their interactions with stem cells, providing insight regarding how their upregulation could improve stem cell therapy by maximizing cell delivery to the injured tissue.
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Affiliation(s)
- Stephanie M Parry
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Eric S Peeples
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA
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Maadawi ZME. Conditioned Medium Derived from Salidroside-Pretreated Mesenchymal Stem Cell Culture Ameliorates Mouse Lipopolysaccharide-Induced Cerebral Neuroinflammation- Histological and Immunohistochemical Study. Int J Stem Cells 2017; 10:60-68. [PMID: 28446004 PMCID: PMC5488777 DOI: 10.15283/ijsc16055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2016] [Indexed: 12/18/2022] Open
Abstract
Background and Objectives Neuroinflammation is involved in the pathogenesis of neurodegenerative disorders. Conditioned medium (CM) derived from bone marrow mesenchymal stem cells (MSCs) revealed substantial benefits due to its rich content of trophic factors. Salidroside (Sal), extracted from Rhodiola rosea, is known for its anti-inflammatory and neuroprotective effects. This study was designed to investigate the effect of Sal pretreated CM (CM-Sal) derived from bone marrow MSCs in lipopolysaccharide (LPS) induced neuroinflammation. Material and Methods Fifty adult male mice were equally divided into 5 groups: Group I (Normal Control), Group II (LPS): single 0.8 mg/kg LPS intraperitoneally; Group III (LPS-DMEM), Group IV (LPS-CM) and Group V (LPS-CM-Sal): LPS was injected as group II followed, 24 hours later, by intranasal injection of 50 μl of filtered serum- free Dulbecco's Modified Eagle's medium (DMEM), CM or CM-Sal, respectively, twice daily for 4 days. Animals were sacrificed at day 6 and paraffin cerebral sections were subjected to Hematoxylin and Eosin staining and immunohistochemistry with caspase 3 (apoptosis), glial fibrillary acidic protein GFAP (astrocytes) and CD68 (active microglia) followed by quantitative morphometric study. Results Examination of LPS and LPS-DMEM groups revealed neuronal apoptosis with reactive astrogliosis and increased active microglia. LPS-CM and LPS-CM-Sal groups showed less apoptosis, less astrocytes and less active microglia. The regression in neuroinflammation was more evident in LPS-CM-Sal group and the difference was statistically significant compared to other groups. Conclusion CM-Sal derived from MSCs culture elicited significant histopathological improvement in LPS induced neuroinflammation which could be used as new therapeutic modality.
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Affiliation(s)
- Zeinab M El Maadawi
- Department of Histology and Cell Biology, Faculty of Medicine, Cairo University, Cairo, Egypt
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