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Yang YH, Yan F, Yuan W, Shi PS, Wu SM, Cui DJ. High-altitude hypoxia promotes BRD4-mediated activation of the Wnt/β-catenin pathway and disruption of intestinal barrier. Cell Signal 2024; 120:111187. [PMID: 38648894 DOI: 10.1016/j.cellsig.2024.111187] [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: 10/24/2023] [Revised: 04/03/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Hypobaric hypoxia, commonly experienced at elevated altitudes, presents significant physiological challenges. Our investigation is centered on the impact of the bromodomain protein 4 (BRD4) under these conditions, especially its interaction with the Wnt/β-Catenin pathway and resultant effects on glycolytic inflammation and intestinal barrier stability. By combining transcriptome sequencing with bioinformatics, we identified BRD4's key role in hypoxia-related intestinal anomalies. Clinical parameters of altitude sickness patients, including serum BRD4 levels, inflammatory markers, and barrier integrity metrics, were scrutinized. In vitro studies using CCD 841 CoN cells depicted expression changes in BRD4, Interleukin (IL)-1β, IL-6, and β-Catenin. Transepithelial electrical resistance (TEER) and FD4 analyses assessed barrier resilience. Hypoxia-induced mouse models, analyzed via H&E staining and Western blot, provided insights into barrier and protein alterations. Under hypoxic conditions, marked BRD4 expression variations emerged. Elevated serum BRD4 in patients coincided with intensified Wnt signaling, inflammation, and barrier deterioration. In vitro, findings showed hypoxia-induced upregulation of BRD4 and inflammatory markers but a decline in Occludin and ZO1, affecting barrier strength-effects mitigated by BRD4 inhibition. Mouse models echoed these patterns, linking BRD4 upregulation in hypoxia to barrier perturbations. Hypobaric hypoxia-induced BRD4 upregulation disrupts the Wnt/β-Catenin signaling, sparking glycolysis-fueled inflammation and weakening intestinal tight junctions and barrier degradation.
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Affiliation(s)
- Yun-Han Yang
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Fang Yan
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Wenqiang Yuan
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Peng-Shuang Shi
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Shi-Min Wu
- Graduate School, Zunyi Medical University, Zunyi, China
| | - De-Jun Cui
- Department of Gastroenterology, Guizhou Provincial People's Hospital, No. 83, Zhongshan East Road, Guiyang 550002, Guizhou Province, China.
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2
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Bo Y, Zhang Y, Wei L, Pei X, Zhu B, Zanoli L, Kalantar-Zadeh K, Gao F, Yong Z, Zhang T, Zhao W, Wu J. BRD4 plays an antiaging role in the senescence of renal tubular epithelial cells. Transl Androl Urol 2024; 13:1014-1023. [PMID: 38983468 PMCID: PMC11228682 DOI: 10.21037/tau-24-214] [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: 04/29/2024] [Accepted: 06/25/2024] [Indexed: 07/11/2024] Open
Abstract
Background Age-related kidney failure is often induced by a decrease in the bioavailability of tubular epithelial cells in elderly chronic kidney disease (CKD) patients. BRD4, an epigenetic regulator and a member of the bromodomain and extraterminal (BET) protein family, acts as a super-enhancer (SE) organizing and regulating genes expression during embryogenesis and cancer development. But the physiological function of BRD4 in normal cells has been less studied. This study aimed to research certain biological roles of BRD4 in the process of normal cell aging and discuss the potential mechanisms. Methods In this study, we investigated the biological functions of BRD4 proteins in the aging of renal tubular cells. At first, we used a D-galactose (D-gal) and BRD4 inhibitor (Abbv-075) to replicate kidney senescence in vivo. D-gal and Abbv-075 were then used to measure the aging-related changes, such as changes in cell cycle, β-galactosidase activity, cell migration, and p16 protein expression in vitro. At last, we knocked down and over-expressed BRD4 to investigate the aging-related physiological phenomena in renal tubular cells. Results In vitro, D-gal treatment induced noticeable aging-related changes such as inducing cell apoptosis and cell cycle arrest, increasing β-galactosidase activity as well as up-regulating p16 protein expression in primary human tubular epithelial cells. In the aging mice model, D-gal significantly induced renal function impairment and attenuated BRD4 protein expression. At the same time, the BRD4 inhibitor (Abbv-075) was able to mimic D-gal-induced cell senescence. In vivo, Abbv-075 also decreased kidney function and up-regulated p21 protein expression. When we knocked down the expression of BRD4, the senescence-associated β-galactosidase (SA-β-gal) activity increased dramatically, cell migration was inhibited, and the proportion of cells in the G0/G1 phase increased. Additionally, the knockdown also promoted the expression of the senescence-related proteins p16. When the renal tubular cells were overexpressed with BRD4, cell aging-related indicators were reversed in the D-gal-induced cell aging model. Conclusions BRD4 appears to have an active role in the aging of renal tubular cells in vivo and in vitro. The findings also suggest that BRD4 inhibitors have potential nephrotoxic effects for oncology treatment. BRD4 may be a potential therapeutic biomarker and drug target for aging-related kidney diseases, which warrants additional studies.
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Affiliation(s)
- Yun Bo
- Department of Geriatrics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yu Zhang
- Department of Geriatrics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lu Wei
- Department of Geriatrics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaohua Pei
- Department of Geriatrics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Bei Zhu
- Department of Geriatrics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Luca Zanoli
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Kamyar Kalantar-Zadeh
- Division of Nephrology, Tibor Rubin VA Medical Center, Long Beach, CA, USA
- Division of Nephrology, Hypertension, and Kidney Transplantation, University of California, Irvine, Orange, CA, USA
| | - Fei Gao
- Department of Geriatrics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhenzhu Yong
- Department of Geriatrics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tao Zhang
- Department of Geriatrics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Weihong Zhao
- Department of Geriatrics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jianqing Wu
- Department of Geriatrics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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3
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Wang F, Fan Y, Li Y, Zhou Y, Wang X, Zhu M, Chen X, Xue Y, Shen C. Identification of differentially expressed genes of blood leukocytes for Schizophrenia. Front Genet 2024; 15:1398240. [PMID: 38988837 PMCID: PMC11233772 DOI: 10.3389/fgene.2024.1398240] [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: 03/13/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024] Open
Abstract
Background Schizophrenia (SCZ) is a severe neurodevelopmental disorder with brain dysfunction. This study aimed to use bioinformatic analysis to identify candidate blood biomarkers for SCZ. Methods The study collected peripheral blood leukocyte samples of 9 SCZ patients and 20 healthy controls for RNA sequencing analysis. Bioinformatic analyses included differentially expressed genes (DEGs) analysis, pathway enrichment analysis, and weighted gene co-expression network analysis (WGCNA). Results This study identified 1,205 statistically significant DEGs, of which 623 genes were upregulated and 582 genes were downregulated. Functional enrichment analysis showed that DEGs were mainly enriched in cell chemotaxis, cell surface, and serine peptidase activity, as well as involved in Natural killer cell-mediated cytotoxicity. WGCNA identified 16 gene co-expression modules, and five modules were significantly correlated with SCZ (p < 0.05). There were 106 upregulated genes and 90 downregulated genes in the five modules. The top ten genes sorted by the Degree algorithm were RPS28, BRD4, FUS, PABPC1, PCBP1, PCBP2, RPL27A, RPS21, RAG1, and RPL27. RAG1 and the other nine genes belonged to the turquoise and pink module respectively. Pathway enrichment analysis indicated that these 10 genes were mainly involved in processes such as Ribosome, cytoplasmic translation, RNA binding, and protein binding. Conclusion This study finds that the gene functions in key modules and related enrichment pathways may help to elucidate the molecular pathogenesis of SCZ, and the potential of key genes to become blood biomarkers for SCZ warrants further validation.
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Affiliation(s)
- Feifan Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yao Fan
- Department of Clinical Epidemiology, Jiangsu Province Geriatric Institute, Geriatric Hospital of Nanjing Medical University, Nanjing, China
| | - Yinghui Li
- Department of Medical Psychology, Huai'an Third Hospital, Huai'an, China
| | - Yuan Zhou
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xin Wang
- Department of Medical Laboratory, Huai'an Third Hospital, Huai'an, China
| | - Mengya Zhu
- Department of Medical Laboratory, Huai'an Third Hospital, Huai'an, China
| | - Xuefei Chen
- Department of Medical Laboratory, Huai'an Third Hospital, Huai'an, China
| | - Yong Xue
- Department of Medical Laboratory, Huai'an Third Hospital, Huai'an, China
| | - Chong Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
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4
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Gudmundsdottir V, Frick E, Emilsson V, Jonmundsson T, Steindorsdottir A, Johnson ECB, Puerta R, Dammer E, Shantaraman A, Cano A, Boada M, Valero S, Garcia-Gonzalez P, Gudmundsson E, Gudjonsson A, Pitts R, Qiu X, Finkel N, Loureiro J, Orth A, Seyfried N, Levey A, Ruiz A, Aspelund T, Jennings L, Launer L, Gudnason V. Serum proteomics reveals APOE dependent and independent protein signatures in Alzheimer's disease. RESEARCH SQUARE 2024:rs.3.rs-3706206. [PMID: 38260284 PMCID: PMC10802738 DOI: 10.21203/rs.3.rs-3706206/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The current demand for early intervention, prevention, and treatment of late onset Alzheimer's disease (LOAD) warrants deeper understanding of the underlying molecular processes which could contribute to biomarker and drug target discovery. Utilizing high-throughput proteomic measurements in serum from a prospective population-based cohort of older adults (n = 5,294), we identified 303 unique proteins associated with incident LOAD (median follow-up 12.8 years). Over 40% of these proteins were associated with LOAD independently of APOE-ε4 carrier status. These proteins were implicated in neuronal processes and overlapped with protein signatures of LOAD in brain and cerebrospinal fluid. We found 17 proteins which LOAD-association was strongly dependent on APOE-ε4 carrier status. Most of them showed consistent associations with LOAD in cerebrospinal fluid and a third had brain-specific gene expression. Remarkably, four proteins in this group (TBCA, ARL2, S100A13 and IRF6) were downregulated by APOE-ε4 yet upregulated as a consequence of LOAD as determined in a bi-directional Mendelian randomization analysis, reflecting a potential response to the disease onset. Accordingly, the direct association of these proteins to LOAD was reversed upon APOE-ε4 genotype adjustment, a finding which we replicate in an external cohort (n = 719). Our findings provide an insight into the dysregulated pathways that may lead to the development and early detection of LOAD, including those both independent and dependent on APOE-ε4. Importantly, many of the LOAD-associated proteins we find in the circulation have been found to be expressed - and have a direct link with AD - in brain tissue. Thus, the proteins identified here, and their upstream modulating pathways, provide a new source of circulating biomarker and therapeutic target candidates for LOAD.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Merce Boada
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades-UIC, Barcelona
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lenore Launer
- National Institute on Aging, National Institutes of Health
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Mondal P, Bai P, Gomm A, Bakiasi G, Lin CJ, Wang Y, Choi SH, Tanzi RE, Wang C, Zhang C. Structure-Based Discovery of A Small Molecule Inhibitor of Histone Deacetylase 6 (HDAC6) that Significantly Reduces Alzheimer's Disease Neuropathology. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304545. [PMID: 37990786 PMCID: PMC10767396 DOI: 10.1002/advs.202304545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/27/2023] [Indexed: 11/23/2023]
Abstract
Histone deacetylase 6 (HDAC6) is one of the key histone deacetylases (HDACs) that regulates various cellular functions including clearance of misfolded protein and immunological responses. Considerable evidence suggests that HDAC6 is closely related to amyloid and tau pathology, the two primary hallmarks of Alzheimer's disease (AD). It is still unclear whether HDAC6 expression changes with amyloid deposition in AD during disease progression or HDAC6 may be regulating amyloid phagocytosis or neuroinflammation or other neuropathological changes in AD. In this work, the pathological accumulation of HDAC6 in AD brains over age as well as the relationship of its regulatory activity - with amyloid pathogenesis and pathophysiological alterations is aimed to be enlightened using the newly developed HDAC6 inhibitor (HDAC6i) PB118 in microglia BV2 cell and 3D-AD human neural culture model. Results suggest that the structure-based rational design led to biologically compelling HDAC6i PB118 with multiple mechanisms that clear Aβ deposits by upregulating phagocytosis, improve tubulin/microtubule network by enhancing acetyl α-tubulin levels, regulate different cytokines and chemokines responsible for inflammation, and significantly reduce phospho-tau (p-tau) levels associated with AD. These findings indicate that HDAC6 plays key roles in the pathophysiology of AD and potentially serves as a suitable pharmacological target through chemical biology-based drug discovery in AD.
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Affiliation(s)
- Prasenjit Mondal
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
| | - Ping Bai
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General HospitalHarvard Medical SchoolBuilding 149, CharlestownBostonMA02129USA
| | - Ashley Gomm
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
| | - Grisilda Bakiasi
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
| | - Chih‐Chung Jerry Lin
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
| | - Yanli Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General HospitalHarvard Medical SchoolBuilding 149, CharlestownBostonMA02129USA
| | - Se Hoon Choi
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
| | - Rudolph E. Tanzi
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
| | - Changning Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General HospitalHarvard Medical SchoolBuilding 149, CharlestownBostonMA02129USA
| | - Can Zhang
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
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Kubat Oktem E. BMP4, SGSH, and SLC11A2 are Predicted to Be Biomarkers of Aging Associated with Programmed Cell Death. J Mol Neurosci 2023; 73:713-723. [PMID: 37632651 DOI: 10.1007/s12031-023-02148-5] [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: 07/12/2023] [Accepted: 08/10/2023] [Indexed: 08/28/2023]
Abstract
Most neurodegenerative diseases are exacerbated by aging, with symptoms often worsening over time. Programmed cell death (PCD) is a controlled cell suicide mechanism that is essential for the stability, growth, and homeostasis of organisms. Understanding the effects of aging at the level of systems biology could lead to new therapeutic approaches for a broad spectrum of neurodegenerative diseases. In the absence of comprehensive functional studies on the relationship between PCD and aging of the prefrontal cortex, this study provides prefrontal brain biomarkers of aging associated with PCD that could open the way for improved therapeutic techniques for age-related neurodegenerative diseases. To this end, publicly available transcriptome data were subjected to bioinformatic analyses such as differential gene expression, functional enrichment, and the weighted gene coexpression network analysis (WGCNA). The diagnostic utility of the biomarkers was tested using a logistic regression-based prediction model. Three genes, namely BMP4, SGSH, and SLC11A2, were found to be aging biomarkers associated with PCD. Finally, a multifactorial regulatory network with interacting proteins, transcription factors (TFs), competing endogenous RNAs (ceRNAs), and microRNAs (miRNAs) was constructed around these biomarkers. The elements of this multifactorial regulatory network were mainly enriched in BMP signaling. Further exploration of these three biomarkers and their regulatory elements would enable the development of 3PM (predictive, preventive, and personalized) medicine for the treatment of age-related neurodegenerative diseases.
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Affiliation(s)
- Elif Kubat Oktem
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Istanbul Medeniyet University, Kuzey Yerleşkesi H Blok, Ünalan Mah. Ünalan Sk. D100 Karayolu Yanyol 34700, Üsküdar, Istanbul, Turkey.
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Martella N, Pensabene D, Varone M, Colardo M, Petraroia M, Sergio W, La Rosa P, Moreno S, Segatto M. Bromodomain and Extra-Terminal Proteins in Brain Physiology and Pathology: BET-ing on Epigenetic Regulation. Biomedicines 2023; 11:biomedicines11030750. [PMID: 36979729 PMCID: PMC10045827 DOI: 10.3390/biomedicines11030750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
BET proteins function as histone code readers of acetylated lysins that determine the positive regulation in transcription of genes involved in cell cycle progression, differentiation, inflammation, and many other pathways. In recent years, thanks to the development of BET inhibitors, interest in this protein family has risen for its relevance in brain development and function. For example, experimental evidence has shown that BET modulation affects neuronal activity and the expression of genes involved in learning and memory. In addition, BET inhibition strongly suppresses molecular pathways related to neuroinflammation. These observations suggest that BET modulation may play a critical role in the onset and during the development of diverse neurodegenerative and neuropsychiatric disorders, such as Alzheimer’s disease, fragile X syndrome, and Rett syndrome. In this review article, we summarize the most recent evidence regarding the involvement of BET proteins in brain physiology and pathology, as well as their pharmacological potential as targets for therapeutic purposes.
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Affiliation(s)
- Noemi Martella
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Daniele Pensabene
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
- Department of Science, University Roma Tre, Viale Marconi 446, 00146 Rome, Italy
- Laboratory of Neurodevelopment, Neurogenetics and Neuromolecular Biology, IRCCS Santa Lucia Foundation, 64 via del Fosso di Fiorano, 00179 Rome, Italy
| | - Michela Varone
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Mayra Colardo
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Michele Petraroia
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - William Sergio
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, via dei Marsi 78, 00185 Rome, Italy
| | - Sandra Moreno
- Department of Science, University Roma Tre, Viale Marconi 446, 00146 Rome, Italy
- Laboratory of Neurodevelopment, Neurogenetics and Neuromolecular Biology, IRCCS Santa Lucia Foundation, 64 via del Fosso di Fiorano, 00179 Rome, Italy
| | - Marco Segatto
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
- Correspondence:
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Zhang J, Li X, Xiao J, Xiang Y, Ye F. Analysis of gene expression profiles in Alzheimer's disease patients with different lifespan: A bioinformatics study focusing on the disease heterogeneity. Front Aging Neurosci 2023; 15:1072184. [PMID: 36909942 PMCID: PMC9995587 DOI: 10.3389/fnagi.2023.1072184] [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: 10/17/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
Objective Alzheimer's disease (AD) as the most frequent neurodegenerative disease is featured by gradual decline of cognition and social function in the elderly. However, there have been few studies focusing on AD heterogeneity which exists both genetically and clinically, leading to the difficulties of AD researches. As one major kind of clinical heterogeneity, the lifespan of AD patients varies significantly. Aiming to investigate the potential driving factors, the current research identified the differentially expressed genes (DEGs) between longer-lived AD patients and shorter-lived ones via bioinformatics analyses. Methods Qualified datasets of gene expression profiles were identified in National Center of Biotechnology Information Gene Expression Omnibus (NCBI-GEO). The data of the temporal lobes of patients above 60 years old were used. Two groups were divided according to the lifespan: the group ≥85 years old and the group <85 years old. Then GEO2R online software and R package of Robust Rank Aggregation (RRA) were used to screen DEGs. Bioinformatic tools were adopted to identify possible pathways and construct protein-protein interaction network. Result Sixty-seven AD cases from four qualified datasets (GSE28146, GSE5281, GSE48350, and GSE36980) were included in this study. 740 DEGs were identified with 361 upregulated and 379 downregulated when compared longer-lived AD patients with shorter-lived ones. These DEGs were primarily involved in the pathways directly or indirectly associated with the regulation of neuroinflammation and cancer pathogenesis, as shown by pathway enrichment analysis. Among the DEGs, the top 15 hub genes were identified from the PPI network. Notably, the same bioinformatic procedures were conducted in 62 non-AD individuals (serving as controls of AD patients in the four included studies) with distinctly different findings from AD patients, indicating different regulatory mechanisms of lifespan between non-AD controls and AD, reconfirming the necessity of the present study. Conclusion These results shed some lights on lifespan-related regulatory mechanisms in AD patients, which also indicated that AD heterogeneity should be more taken into account in future investigations.
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Affiliation(s)
- Ji Zhang
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaojia Li
- Department of Neurology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China.,Department of Neurology, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Jun Xiao
- Department of Neurology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China.,Department of Neurology, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Yang Xiang
- Department of Neurology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China.,Department of Neurology, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Fang Ye
- Department of Neurology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China.,Department of Neurology, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
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9
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He YJ, Cong L, Liang SL, Ma X, Tian JN, Li H, Wu Y. Discovery and validation of Ferroptosis-related molecular patterns and immune characteristics in Alzheimer's disease. Front Aging Neurosci 2022; 14:1056312. [PMID: 36506471 PMCID: PMC9727409 DOI: 10.3389/fnagi.2022.1056312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Abstract
Background To date, the pathogenesis of Alzheimer's disease is still not fully elucidated. Much evidence suggests that Ferroptosis plays a crucial role in the pathogenesis of AD, but little is known about its molecular immunological mechanisms. Therefore, this study aims to comprehensively analyse and explore the molecular mechanisms and immunological features of Ferroptosis-related genes in the pathogenesis of AD. Materials and methods We obtained the brain tissue dataset for AD from the GEO database and downloaded the Ferroptosis-related gene set from FerrDb for analysis. The most relevant Hub genes for AD were obtained using two machine learning algorithms (Least absolute shrinkage and selection operator (LASSO) and multiple support vector machine recursive feature elimination (mSVM-RFE)). The study of the Hub gene was divided into two parts. In the first part, AD patients were genotyped by unsupervised cluster analysis, and the different clusters' immune characteristics were analysed. A PCA approach was used to quantify the FRGscore. In the second part: we elucidate the biological functions involved in the Hub genes and their role in the immune microenvironment by integrating algorithms (GSEA, GSVA and CIBERSORT). Analysis of Hub gene-based drug regulatory networks and mRNA-miRNA-lncRNA regulatory networks using Cytoscape. Hub genes were further analysed using logistic regression models. Results Based on two machine learning algorithms, we obtained a total of 10 Hub genes. Unsupervised clustering successfully identified two different clusters, and immune infiltration analysis showed a significantly higher degree of immune infiltration in type A than in type B, indicating that type A may be at the peak of AD neuroinflammation. Secondly, a Hub gene-based Gene-Drug regulatory network and a ceRNA regulatory network were successfully constructed. Finally, a logistic regression algorithm-based AD diagnosis model and Nomogram diagram were developed. Conclusion Our study provides new insights into the role of Ferroptosis-related molecular patterns and immune mechanisms in AD, as well as providing a theoretical basis for the addition of diagnostic markers for AD.
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10
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Sfera A, Thomas KG, Andronescu CV, Jafri N, Sfera DO, Sasannia S, Zapata-Martín del Campo CM, Maldonado JC. Bromodomains in Human-Immunodeficiency Virus-Associated Neurocognitive Disorders: A Model of Ferroptosis-Induced Neurodegeneration. Front Neurosci 2022; 16:904816. [PMID: 35645713 PMCID: PMC9134113 DOI: 10.3389/fnins.2022.904816] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus (HIV)-associated neurocognitive disorders (HAND) comprise a group of illnesses marked by memory and behavioral dysfunction that can occur in up to 50% of HIV patients despite adequate treatment with combination antiretroviral drugs. Iron dyshomeostasis exacerbates HIV-1 infection and plays a major role in Alzheimer's disease pathogenesis. In addition, persons living with HIV demonstrate a high prevalence of neurodegenerative disorders, indicating that HAND provides a unique opportunity to study ferroptosis in these conditions. Both HIV and combination antiretroviral drugs increase the risk of ferroptosis by augmenting ferritin autophagy at the lysosomal level. As many viruses and their proteins exit host cells through lysosomal exocytosis, ferroptosis-driving molecules, iron, cathepsin B and calcium may be released from these organelles. Neurons and glial cells are highly susceptible to ferroptosis and neurodegeneration that engenders white and gray matter damage. Moreover, iron-activated microglia can engage in the aberrant elimination of viable neurons and synapses, further contributing to ferroptosis-induced neurodegeneration. In this mini review, we take a closer look at the role of iron in the pathogenesis of HAND and neurodegenerative disorders. In addition, we describe an epigenetic compensatory system, comprised of bromodomain-containing protein 4 (BRD4) and microRNA-29, that may counteract ferroptosis by activating cystine/glutamate antiporter, while lowering ferritin autophagy and iron regulatory protein-2. We also discuss potential interventions for lysosomal fitness, including ferroptosis blockers, lysosomal acidification, and cathepsin B inhibitors to achieve desirable therapeutic effects of ferroptosis-induced neurodegeneration.
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Affiliation(s)
- Adonis Sfera
- Patton State Hospital, San Bernardino, CA, United States
- Department of Psychiatry, University of California, Riverside, Riverside, CA, United States
| | | | | | - Nyla Jafri
- Patton State Hospital, San Bernardino, CA, United States
| | - Dan O. Sfera
- Patton State Hospital, San Bernardino, CA, United States
| | | | | | - Jose C. Maldonado
- Department of Medicine, The University of Texas Rio Grande Valley, Edinburg, TX, United States
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