1
|
Islam MR, Rabbi MA, Hossain T, Sultana S, Uddin S. Mechanistic Approach to Immunity and Immunotherapy of Alzheimer's Disease: A Review. ACS Chem Neurosci 2024. [PMID: 39173186 DOI: 10.1021/acschemneuro.4c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024] Open
Abstract
Alzheimer's disease (AD) is a debilitating neurodegenerative condition characterized by progressive cognitive decline and memory loss, affecting millions of people worldwide. Traditional treatments, such as cholinesterase inhibitors and NMDA receptor antagonists, offer limited symptomatic relief without addressing the underlying disease mechanisms. These limitations have driven the development of more potent and effective therapies. Recent advances in immunotherapy present promising avenues for AD treatment. Immunotherapy strategies, including both active and passive approaches, harness the immune system to target and mitigate AD-related pathology. Active immunotherapy stimulates the patient's immune response to produce antibodies against AD-specific antigens, while passive immunotherapy involves administering preformed antibodies or immune cells that specifically target amyloid-β (Aβ) or tau proteins. Monoclonal antibodies, such as aducanumab and lecanemab, have shown potential in reducing Aβ plaques and slowing cognitive decline in clinical trials, despite challenges related to adverse immune responses and the need for precise targeting. This comprehensive review explores the role of the immune system in AD, evaluates the current successes and limitations of immunotherapeutic approaches, and discusses future directions for enhancing the treatment efficacy.
Collapse
Affiliation(s)
- Md Rubiath Islam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Md Afser Rabbi
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Tanbir Hossain
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Sadia Sultana
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Shihab Uddin
- Department of Bioengineering, King Fahad University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
- Interdisciplinary Research Center for Bio Systems and Machines, King Fahad University of Petroleum & Minerals, Dhahran-31261, Saudi Arabia
| |
Collapse
|
2
|
Cao D, Zhang S, Zhang Y, Shao M, Yang Q, Wang P. Association between gynecologic cancer and Alzheimer's disease: a bidirectional mendelian randomization study. BMC Cancer 2024; 24:1032. [PMID: 39169299 PMCID: PMC11337634 DOI: 10.1186/s12885-024-12787-5] [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: 01/02/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) manifests with a higher rate of occurrence in women. Previous epidemiological studies have suggested a potential association between AD and gynecological cancers, but the causal relationship between them remains unclear. This study aims to explore the causal link between 12 types of gynecological cancers and AD using a bidirectional Mendelian randomization (MR) approach. METHODS We obtained genetic correlation tools for AD using data from the most extensive genome-wide association study. Genetic correlation data for 12 types of gynecological cancers were also sourced from the Finnish Biobank. These cancers include breast cancer (BC), cervical adenocarcinoma (CA), cervical squamous cell carcinoma (CSCC), cervical cancer (CC), endometrial cancer (EC), ovarian endometrioid carcinoma (OEC), ovarian cancer (OC), ovarian serous carcinoma (OSC), breast carcinoma in situ (BCIS), cervical carcinoma in situ (CCIS), endometrial carcinoma in situ (ECIS), and vulvar carcinoma in situ (VCIS). We used the inverse-variance weighted (IVW) model for causal analysis and conducted horizontal pleiotropy tests, heterogeneity tests, MR-PRESSO tests, and leave-one-out analyses to ensure the robustness of our results. We also applied replication analysis and meta-analysis to further validate our experimental results. RESULTS The study found that EC (P_IVW =0.037, OR [95% CI] = 1.032 [1.002, 1.064]) and CCIS (P_IVW = 0.046, OR [95% CI] = 1.032 [1.011, 1.064]) increase the risk of AD, whereas OC was negatively correlated with AD (P_IVW = 0.016, OR [95% CI] = 0.974[0.954, 0.995]). In reverse MR analysis, AD increased the risk of CC (P_IVW = 0.039, OR [95% CI] = 1.395 [1.017, 1.914]) and VCIS (P_IVW = 0.041, OR [95% CI] = 1.761 [1.027, 2.021]), but was negatively correlated with OEC (P_IVW = 0.034, OR [95% CI] = 0.634 [0.417, 0.966]). Sensitivity analysis results demonstrated robustness. These findings were further substantiated through replication and meta-analyses. CONCLUSIONS Our MR study supports a causal relationship between AD and gynecological cancers. This encourages further research into the incidence of gynecological cancers in female Alzheimer's patients and the active prevention of AD.
Collapse
Affiliation(s)
- Di Cao
- Hubei University of Chinese Medicine, Wuhan, Hubei, 430065, China
- Engineering Research Center of TCM Protection Technology and New Product Development for the Elderly Brain Health, Ministry of Education, Wuhan, Hubei, 430065, China
| | - Shaobo Zhang
- Changchun University of Chinese Medicine, Changchun, Jilin, 130000, China
| | - Yini Zhang
- Hubei University of Chinese Medicine, Wuhan, Hubei, 430065, China
- Engineering Research Center of TCM Protection Technology and New Product Development for the Elderly Brain Health, Ministry of Education, Wuhan, Hubei, 430065, China
| | - Ming Shao
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 210000, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 210000, China
| | - Qiguang Yang
- The Second Affiliated Hospital of Changchun University of Chinese Medicine, Changchun Hospital of Chinese Medicine, Changchun, Jilin, 130000, China
| | - Ping Wang
- Hubei University of Chinese Medicine, Wuhan, Hubei, 430065, China.
- Engineering Research Center of TCM Protection Technology and New Product Development for the Elderly Brain Health, Ministry of Education, Wuhan, Hubei, 430065, China.
| |
Collapse
|
3
|
Weijie Z, Meng Z, Chunxiao W, Lingjie M, Anguo Z, Yan Z, Xinran C, Yanjiao X, Li S. Obesity-induced chronic low-grade inflammation in adipose tissue: A pathway to Alzheimer's disease. Ageing Res Rev 2024; 99:102402. [PMID: 38977081 DOI: 10.1016/j.arr.2024.102402] [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: 03/11/2024] [Revised: 06/19/2024] [Accepted: 06/30/2024] [Indexed: 07/10/2024]
Abstract
Alzheimer's disease (AD) is a leading cause of cognitive impairment worldwide. Overweight and obesity are strongly associated with comorbidities, such as hypertension, diabetes, and insulin resistance (IR), which contribute substantially to the development of AD and subsequent morbidity and mortality. Adipose tissue (AT) is a highly dynamic organ composed of a diverse array of cell types, which can be classified based on their anatomic localization or cellular composition. The expansion and remodeling of AT in the context of obesity involves immunometabolic and functional shifts steered by the intertwined actions of multiple immune cells and cytokine signaling within AT, which contribute to the development of metabolic disorders, IR, and systemic markers of chronic low-grade inflammation. Chronic low-grade inflammation, a prolonged, low-dose stimulation by specific immunogens that can progress from localized sites and affect multiple organs throughout the body, leads to neurodystrophy, increased apoptosis, and disruption of homeostasis, manifesting as brain atrophy and AD-related pathology. In this review, we sought to elucidate the mechanisms by which AT contributes to the onset and progression of AD in obesity through the mediation of chronic low-grade inflammation, particularly focusing on the roles of adipokines and AT-resident immune cells.
Collapse
Affiliation(s)
- Zhai Weijie
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun, China; Cognitive Center, Department of Neurology, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Zhao Meng
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun, China; Cognitive Center, Department of Neurology, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Wei Chunxiao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun, China; Cognitive Center, Department of Neurology, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Meng Lingjie
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun, China; Cognitive Center, Department of Neurology, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Zhao Anguo
- Department of Urology, Dushu Lake Hospital Affiliated to Soochow University, Medical Center of Soochow University, Suzhou Dushu Lake Hospital, Suzhou 215000 China
| | - Zhang Yan
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun, China; Cognitive Center, Department of Neurology, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Cui Xinran
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun, China; Cognitive Center, Department of Neurology, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Xu Yanjiao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun, China; Cognitive Center, Department of Neurology, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Sun Li
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun, China; Cognitive Center, Department of Neurology, The First Hospital of Jilin University, Jilin University, Changchun, China.
| |
Collapse
|
4
|
Weng W, Fu J, Cheng F, Wang Y, Zhang J. Integrated Bulk and Single-Cell RNA-Sequencing Reveals the Effects of Circadian Rhythm Disruption on the Metabolic Reprogramming of CD4+ T Cells in Alzheimer's Disease. Mol Neurobiol 2024; 61:6013-6030. [PMID: 38265551 DOI: 10.1007/s12035-023-03907-6] [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: 03/14/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024]
Abstract
Although growing evidence suggests close correlations between Alzheimer's disease (AD) and circadian rhythm disruption (CRD), few studies have focused on the influence of circadian rhythm on levels of immune cells in AD. We aimed to delineate the mechanism underlying the effects of circadian related genes on T cell immune function in AD. A total of 112 brain samples were used to construct the CRD-related model by performing weighted gene co-expression network analysis and machine learning algorithms (LASSO, SVM-RFE, and RF). The ssGSEA method was used to calculate the CRDscore in order to quantify CRD status. Using single-cell transcriptome data of CSF cells, we investigated the CD4+ T cell metabolism and cell-cell communication in high- and low-risk CRD groups. Connectivity map (CMap) was applied to explore small molecule drugs targeting CRD, and the expression of the signature gene GPR4 was further validated in AD. The CRDscore algorithm, which is based on 23 circadian-related genes, can effectively classify the CRD status in AD datasets. The single-cell analysis revealed that the CD4+ T cells with high CRDscore were characterized by hypometabolism. Cell communication analysis revealed that CD4+ T cells might be involved in promoting CD8+ T cell adhesion under CRD, which may facilitate T cell infiltration into the brain parenchyma. Overall, this study indicates the potential connotation of circadian rhythm in AD, providing insights into understanding T cell metabolic reprogramming under CRD.
Collapse
Affiliation(s)
- Weipin Weng
- Department of Neurology, The Second Xiangya Hospital of Central South University, Changsha, China
- Department of Neurology, Center for Cognitive Neurology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jianhan Fu
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Fan Cheng
- Department of Neurology, The Second Xiangya Hospital of Central South University, Changsha, China
- Clinical Medical Research Center for Stroke Prevention and Treatment of Hunan Province, Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Yixuan Wang
- Department of Neurology, The Second Xiangya Hospital of Central South University, Changsha, China
- Clinical Medical Research Center for Stroke Prevention and Treatment of Hunan Province, Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Jie Zhang
- Department of Neurology, The Second Xiangya Hospital of Central South University, Changsha, China.
- Clinical Medical Research Center for Stroke Prevention and Treatment of Hunan Province, Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, China.
- Department of Neurology, Turpan City People's Hospital, Tulufan, China.
| |
Collapse
|
5
|
Lüleci HB, Jones A, Çakır T. Multi-omics analyses highlight molecular differences between clinical and neuropathological diagnoses in Alzheimer's disease. Eur J Neurosci 2024. [PMID: 39072881 DOI: 10.1111/ejn.16482] [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: 02/11/2024] [Revised: 05/14/2024] [Accepted: 07/13/2024] [Indexed: 07/30/2024]
Abstract
Both clinical diagnosis and neuropathological diagnosis are commonly used in literature to categorize individuals as Alzheimer's disease (AD) or non-AD in omics analyses. Whether these diagnostic strategies result in distinct profiles of molecular abnormalities is poorly understood. Here, we analysed one of the most commonly used AD omics datasets in the literature from the Religious Orders Study and Memory and Aging Project (ROSMAP) cohort and compared the two diagnosis strategies using brain transcriptome and metabolome by grouping individuals as non-AD and AD according to clinical or neuropathological diagnosis separately. Differentially expressed genes, associated pathways related with AD hallmarks and AD-related genes showed that the categorization based on neuropathological diagnosis more accurately reflects the disease state at the molecular level than the categorization based on clinical diagnosis. We further identified consensus biomarker candidates between the two diagnosis strategies such as 5-hydroxylysine, sphingomyelin and 1-myristoyl-2-palmitoyl-GPC as metabolite biomarkers and sphingolipid metabolism as a pathway biomarker, which could be robust AD biomarkers since they are independent of diagnosis strategies. We also used consensus AD and consensus non-AD individuals between the two diagnostic strategies to train a machine-learning based model, which we used to classify the individuals who were cognitively normal but diagnosed as AD based on neuropathological diagnosis (asymptomatic AD individuals). The majority of these individuals were classified as consensus AD patients for both omics data types. Our study provides a detailed characterization of both diagnostic strategies in terms of the association of the corresponding multi-omics profiles with AD.
Collapse
Affiliation(s)
| | - Attila Jones
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
| |
Collapse
|
6
|
Qiao Y, Mei Y, Xia M, Luo D, Gao L. The role of m6A modification in the risk prediction and Notch1 pathway of Alzheimer's disease. iScience 2024; 27:110235. [PMID: 39040060 PMCID: PMC11261416 DOI: 10.1016/j.isci.2024.110235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 03/17/2024] [Accepted: 05/19/2024] [Indexed: 07/24/2024] Open
Abstract
N6-methyladenosine (m6A) methylation and abnormal immune responses are implicated in neurodegenerative diseases, yet their relationship in Alzheimer's disease (AD) remains unclear. We obtained AD datasets from GEO databases and used AD mouse and cell models, observing abnormal expression of m6A genes in the AD group, alongside disruptions in the immune microenvironment. Key m6A genes (YTHDF2, LRPPRC, and FTO) selected by machine learning were associated with the Notch pathway, with FTO and Notch1 displaying the strongest correlation. Specifically, FTO expression decreased and m6A methylation of Notch1 increased in AD mouse and cell models. We further silenced FTO expression in HT22 cells, resulting in upregulation of the Notch1 signaling pathway. Additionally, increased Notch1 expression in dendritic cells heightened inflammatory cytokine secretion in vitro. These results suggest that reduced FTO expression may contribute to the pathogenesis of AD by activating the Notch1 pathway to interfere with the immune response.
Collapse
Affiliation(s)
- Yingdan Qiao
- Department of Endocrinology & Metabolism, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| | - Yingna Mei
- Department of Endocrinology & Metabolism, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| | - Minqi Xia
- Department of Endocrinology & Metabolism, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| | - Deng Luo
- Department of Endocrinology & Metabolism, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| | - Ling Gao
- Department of Endocrinology & Metabolism, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| |
Collapse
|
7
|
Liao J, Zhang Y, Tang Z, Liu P, He L. Causal relationships between peripheral immune cells and Alzheimer's disease: a two-sample Mendelian randomization study. Neurol Sci 2024; 45:3117-3124. [PMID: 38267604 DOI: 10.1007/s10072-024-07324-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/08/2024] [Indexed: 01/26/2024]
Abstract
OBJECTIVE Previous research suggests that peripheral immune cells may play a role in the development of Alzheimer's disease (AD). Our study aims to determine if the composition of peripheral immune cells directly contributes to the occurrence of AD. METHODS We utilized a two-sample Mendelian randomization (MR) approach to examine the association between peripheral immune cells and AD.The primary analysis method used was the inverse variance weighted (IVW) method, and we also conducted analyses using MR Egger, weighted median, simple mode, and weighted mode methods to ensure the accuracy of the results.Heterogeneity and horizontal pleiotropy were evaluated using Cochran's Q statistics and the MR Egger intercept, respectively. RESULTS The study found a significant correlation between increased IgD + CD24- AC cells (Odds Ratio [OR] = 1.03, 95% Confidence Interval [CI] = 1.01-1.06, P = 0.0172), increased CD4 + %leukocyte (OR = 1.08, 95% CI = 1.02-1.14, P = 0.0086), and increased CD4 + CD8dim AC cells (OR = 1.06, 95% CI = 1.01-1.11, P = 0.0218), with an increased susceptibility to AD. Conversely, an increase in EM DN (CD4-CD8-) %T cells (OR = 0.95, 95% CI = 0.92-0.99, P = 0.0164) and an increase in DN (CD4-CD8-) AC cells (OR = 0.93, 95% CI = 0.88-0.99, P = 0.0145) were associated with a protective effect against AD. CONCLUSION Our findings establish a causal link between peripheral immune cells and AD. This study is the first to examine the relationship between peripheral immune cells and AD using MR, offering valuable insights for early diagnosis and treatment decisions.
Collapse
Affiliation(s)
- Jing Liao
- Ruikang Hospital, Affiliated to Guangxi University of Chinese Medicine, 10 Huadong Road, Xingning District, Nanning City, Guangxi, 53000, China.
| | - Yongquan Zhang
- Ruikang Hospital, Affiliated to Guangxi University of Chinese Medicine, 10 Huadong Road, Xingning District, Nanning City, Guangxi, 53000, China
| | - Zhanhong Tang
- First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning City, Guangxi, 530021, China
| | - Pinjing Liu
- Ruikang Hospital, Affiliated to Guangxi University of Chinese Medicine, 10 Huadong Road, Xingning District, Nanning City, Guangxi, 53000, China
| | - Luoyi He
- Ruikang Hospital, Affiliated to Guangxi University of Chinese Medicine, 10 Huadong Road, Xingning District, Nanning City, Guangxi, 53000, China
| |
Collapse
|
8
|
Zhuang X, Xia Y, Liu Y, Guo T, Xia Z, Wang Z, Zhang G. SCG5 and MITF may be novel markers of copper metabolism immunorelevance in Alzheimer's disease. Sci Rep 2024; 14:13619. [PMID: 38871989 DOI: 10.1038/s41598-024-64599-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024] Open
Abstract
The slow-developing neurological disorder Alzheimer's disease (AD) has no recognized etiology. A bioinformatics investigation verified copper metabolism indicators for AD development. GEO contributed AD-related datasets GSE1297 and GSE5281. Differential expression analysis and WGCNA confirmed biomarker candidate genes. Each immune cell type in AD and control samples was scored using single sample gene set enrichment analysis. Receiver Operating Characteristic (ROC) analysis, short Time-series Expression Miner (STEM) grouping, and expression analysis between control and AD samples discovered copper metabolism indicators that impacted AD progression. We test clinical samples and cellular function to ensure study correctness. Biomarker-targeting miRNAs and lncRNAs were predicted by starBase. Trust website anticipated biomarker-targeting transcription factors. In the end, Cytoscape constructed the TF/miRNA-mRNA and lncRNA-miRNA networks. The DGIdb database predicted biomarker-targeted drugs. We identified 57 differentially expressed copper metabolism-related genes (DE-CMRGs). Next, fourteen copper metabolism indicators impacting AD progression were identified: CCK, ATP6V1E1, SYT1, LDHA, PAM, HPRT1, SCG5, ATP6V1D, GOT1, NFKBIA, SPHK1, MITF, BRCA1, and CD38. A TF/miRNA-mRNA regulation network was then established with two miRNAs (hsa-miR-34a-5p and 34c-5p), six TFs (NFKB1, RELA, MYC, HIF1A, JUN, and SP1), and four biomarkers. The DGIdb database contained 171 drugs targeting ten copper metabolism-relevant biomarkers (BRCA1, MITF, NFKBIA, CD38, CCK2, HPRT1, SPHK1, LDHA, SCG5, and SYT1). Copper metabolism biomarkers CCK, ATP6V1E1, SYT1, LDHA, PAM, HPRT1, SCG5, ATP6V1D, GOT1, NFKBIA, SPHK1, MITF, BRCA1, and CD38 alter AD progression, laying the groundwork for disease pathophysiology and novel AD diagnostic and treatment.
Collapse
Affiliation(s)
- Xianbo Zhuang
- Department of Neurology, Liaocheng People's Hospital and Liaocheng Hospital affiliated to Shandong First Medical University, Liaocheng, China
| | - Yitong Xia
- School of Rehabilitation Medicine, Jining Medical University, Jining, China
| | - Yingli Liu
- Department of Neurology, Liaocheng People's Hospital and Liaocheng Hospital affiliated to Shandong First Medical University, Liaocheng, China
| | - Tingting Guo
- Department of Neurology, Liaocheng People's Hospital and Liaocheng Hospital affiliated to Shandong First Medical University, Liaocheng, China
| | - Zhangyong Xia
- Department of Neurology, Liaocheng People's Hospital and Liaocheng Hospital affiliated to Shandong First Medical University, Liaocheng, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Shandong Sub-Centre, Liaocheng, China
- Department of Neurology, the Second People's Hospital of Liaocheng, Liaocheng, China
| | - Zheng Wang
- Department of Neurosurgery, Liaocheng Traditional Chinese Medicine Hospital, Liaocheng, China.
| | - Guifeng Zhang
- Department of Neurology, Liaocheng People's Hospital and Liaocheng Hospital affiliated to Shandong First Medical University, Liaocheng, China.
| |
Collapse
|
9
|
Benjamin KJM, Chen Q, Eagles NJ, Huuki-Myers LA, Collado-Torres L, Stolz JM, Pertea G, Shin JH, Paquola ACM, Hyde TM, Kleinman JE, Jaffe AE, Han S, Weinberger DR. Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry. Nat Neurosci 2024; 27:1064-1074. [PMID: 38769152 PMCID: PMC11156587 DOI: 10.1038/s41593-024-01636-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 03/29/2024] [Indexed: 05/22/2024]
Abstract
Ancestral differences in genomic variation affect the regulation of gene expression; however, most gene expression studies have been limited to European ancestry samples or adjusted to identify ancestry-independent associations. Here, we instead examined the impact of genetic ancestry on gene expression and DNA methylation in the postmortem brain tissue of admixed Black American neurotypical individuals to identify ancestry-dependent and ancestry-independent contributions. Ancestry-associated differentially expressed genes (DEGs), transcripts and gene networks, while notably not implicating neurons, are enriched for genes related to the immune response and vascular tissue and explain up to 26% of heritability for ischemic stroke, 27% of heritability for Parkinson disease and 30% of heritability for Alzheimer's disease. Ancestry-associated DEGs also show general enrichment for the heritability of diverse immune-related traits but depletion for psychiatric-related traits. We also compared Black and non-Hispanic white Americans, confirming most ancestry-associated DEGs. Our results delineate the extent to which genetic ancestry affects differences in gene expression in the human brain and the implications for brain illness risk.
Collapse
Affiliation(s)
- Kynon J M Benjamin
- Lieber Institute for Brain Development, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Qiang Chen
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | | | | | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Joshua M Stolz
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Geo Pertea
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Apuã C M Paquola
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew E Jaffe
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Neumora Therapeutics, Watertown, MA, USA
| | - Shizhong Han
- Lieber Institute for Brain Development, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
10
|
Hodgson L, Li Y, Iturria-Medina Y, Stratton JA, Wolf G, Krishnaswamy S, Bennett DA, Bzdok D. Supervised latent factor modeling isolates cell-type-specific transcriptomic modules that underlie Alzheimer's disease progression. Commun Biol 2024; 7:591. [PMID: 38760483 PMCID: PMC11101463 DOI: 10.1038/s42003-024-06273-8] [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: 12/18/2023] [Accepted: 05/01/2024] [Indexed: 05/19/2024] Open
Abstract
Late onset Alzheimer's disease (AD) is a progressive neurodegenerative disease, with brain changes beginning years before symptoms surface. AD is characterized by neuronal loss, the classic feature of the disease that underlies brain atrophy. However, GWAS reports and recent single-nucleus RNA sequencing (snRNA-seq) efforts have highlighted that glial cells, particularly microglia, claim a central role in AD pathophysiology. Here, we tailor pattern-learning algorithms to explore distinct gene programs by integrating the entire transcriptome, yielding distributed AD-predictive modules within the brain's major cell-types. We show that these learned modules are biologically meaningful through the identification of new and relevant enriched signaling cascades. The predictive nature of our modules, especially in microglia, allows us to infer each subject's progression along a disease pseudo-trajectory, confirmed by post-mortem pathological brain tissue markers. Additionally, we quantify the interplay between pairs of cell-type modules in the AD brain, and localized known AD risk genes to enriched module gene programs. Our collective findings advocate for a transition from cell-type-specificity to gene modules specificity to unlock the potential of unique gene programs, recasting the roles of recently reported genome-wide AD risk loci.
Collapse
Affiliation(s)
- Liam Hodgson
- School of Computer Science, McGill University, Montréal, QC, Canada
- Mila - Quebec Artificial Intelligence Institute, Montréal, QC, Canada
| | - Yue Li
- School of Computer Science, McGill University, Montréal, QC, Canada
| | - Yasser Iturria-Medina
- McConnell Brain Imaging Centre (BIC), MNI, Faculty of Medicine, McGill University, Montréal, Canada
- Neurology and Neurosurgery Department, Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montréal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montréal, Canada
| | - Jo Anne Stratton
- Neurology and Neurosurgery Department, Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montréal, Canada
| | - Guy Wolf
- Mila - Quebec Artificial Intelligence Institute, Montréal, QC, Canada
- Department of Mathematics & Statistics, Université de Montréal, Montréal, Canada
| | - Smita Krishnaswamy
- Department of Computer Science, Department of Genetics, Yale University, New Haven, CT, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Danilo Bzdok
- Mila - Quebec Artificial Intelligence Institute, Montréal, QC, Canada.
- Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montréal, QC, Canada.
- The Neuro - Montréal Neurological Institute, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, QC, Canada.
| |
Collapse
|
11
|
Duchateau L, Wawrzyniak N, Sleegers K. The ABC's of Alzheimer risk gene ABCA7. Alzheimers Dement 2024; 20:3629-3648. [PMID: 38556850 PMCID: PMC11095487 DOI: 10.1002/alz.13805] [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: 01/03/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 04/02/2024]
Abstract
Alzheimer's disease (AD) is a growing problem worldwide. Since ABCA7's identification as a risk gene, it has been extensively researched for its role in the disease. We review its recently characterized structure and what the mechanistic insights teach us about its function. We furthermore provide an overview of identified ABCA7 mutations, their presence in different ancestries and protein domains and how they might cause AD. For ABCA7 PTC variants and a VNTR expansion, haploinsufficiency is proposed as the most likely mode-of-action, although splice events could further influence disease risk. Overall, the need to better understand expression of canonical ABCA7 and its isoforms in disease is indicated. Finally, ABCA7's potential functions in lipid metabolism, phagocytosis, amyloid deposition, and the interplay between these three, is described. To conclude, in this review, we provide a comprehensive overview and discussion about the current knowledge on ABCA7 in AD, and what research questions remain. HIGHLIGHTS: Alzheimer's risk-increasing variants in ABCA7 can be found in up to 7% of AD patients. We review the recently characterized protein structure of ABCA7. We present latest insights in genetics, expression patterns, and functions of ABCA7.
Collapse
Affiliation(s)
- Lena Duchateau
- Complex Genetics of Alzheimer's Disease group, VIB‐UAntwerp Center for Molecular NeurologyWilrijkAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpWilrijkAntwerpBelgium
| | - Nicole Wawrzyniak
- Complex Genetics of Alzheimer's Disease group, VIB‐UAntwerp Center for Molecular NeurologyWilrijkAntwerpBelgium
- Chávez‐Gutiérrez Lab, VIB‐KU Leuven Center for Brain and Disease Research, VIBLeuvenBelgium
| | - Kristel Sleegers
- Complex Genetics of Alzheimer's Disease group, VIB‐UAntwerp Center for Molecular NeurologyWilrijkAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpWilrijkAntwerpBelgium
| |
Collapse
|
12
|
Sun Y, Xiao Y, Tang Q, Chen W, Lin L. Genetic markers associated with ferroptosis in Alzheimer's disease. Front Aging Neurosci 2024; 16:1364605. [PMID: 38711596 PMCID: PMC11073811 DOI: 10.3389/fnagi.2024.1364605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
Objective Ferroptosis is implicated in the pathogenesis of neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and vascular dementia, implying that it may have a regulatory effect on the progression of these diseases. However, the specific role of ferroptosis-related genes (FRGs) in Alzheimer's disease (AD) is not yet fully understood. The aim of the study was to detect ferroptosis related genes with regulatory functions in the disease and explore potential mechanisms in AD. Methods Hub FRGs were obtained through multiple algorithms based on the GSE5281 dataset. The screening process was implemented by R packages including limma, WGCNA, glm and SVM-RFE. Gene Ontology classification and pathway enrichment analysis were performed based on FRGs. Biological processes involved with hub FRGs were investigated through GSVA and GSEA methods. Immune infiltration analysis was performed by the R package CIBERSORT. Receiver operating characteristic curve (ROC) was utilized to validate the accuracy of hub FRGs. The CeRNA network attempted to find non-coding RNA transcripts which may play a role in disease progression. Results DDIT4, MUC1, KLHL24, CD44, and RB1 were identified as hub FRGs. As later revealed by enrichment analysis, the hub FRGs had important effects on AD through involvement in diverse AD pathogenesis-related pathways such as autophagy and glutathione metabolism. The immune microenvironment in AD shows increased numbers of resting NK cells, macrophages, and mast cells, with decreased levels of CD8 T cells when compared to healthy samples. Regulatory T cells were positively correlated with MUC1, KLHL24, and DDIT4 expression, while RB1 showed negative correlations with eosinophils and CD8 T cells, suggesting potential roles in modulating the immune environment in AD. Conclusion Our research has identified five hub FRGs in AD. We concluded that ferroptosis may be involved in the disease.
Collapse
Affiliation(s)
- Yuting Sun
- Department of Clinical Laboratory, The Fourth People’s Hospital of Chengdu, Chengdu, China
- Department of Clinical Laboratory, The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Yu Xiao
- Psychosomatic Medicine Center, The Fourth People’s Hospital of Chengdu, Chengdu, China
- Psychosomatic Medicine Center, The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Qin Tang
- Department of Clinical Laboratory, The Fourth People’s Hospital of Chengdu, Chengdu, China
- Department of Clinical Laboratory, The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Wei Chen
- Department of Clinical Laboratory, The Fourth People’s Hospital of Chengdu, Chengdu, China
- Department of Clinical Laboratory, The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Lu Lin
- Department of Clinical Laboratory, The Fourth People’s Hospital of Chengdu, Chengdu, China
- Department of Clinical Laboratory, The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
13
|
Xu Z, Hu J, Wei Z, Lei Y, Afewerky HK, Gao Y, Wan L, Li L, Lei L, Liu Y, Huang F, Yu T, Wang J, Li H, Liu R, Wang X. Dynamic changes in lysosome-related pathways in APP/PS1 mice with aging. MedComm (Beijing) 2024; 5:e540. [PMID: 38606360 PMCID: PMC11006716 DOI: 10.1002/mco2.540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 04/13/2024] Open
Abstract
Senile plaque, composed of amyloid β protein (Aβ) aggregates, is a critical pathological feature in Alzheimer's disease (AD), leading to cognitive dysfunction. However, how Aβ aggregates exert age-dependent toxicity and temporal cognitive dysfunction in APP/PS1 mice remains incompletely understood. In this study, we investigated AD pathogenesis and dynamic alterations in lysosomal pathways within the hippocampus of age-gradient male mice using transcriptome sequencing, molecular biology assays, and histopathological analyses. We observed high levels of β-amyloid precursor protein (APP) protein expression in the hippocampus at an early stage and age-dependent Aβ deposition. Transcriptome sequencing revealed the enrichment of differential genes related to the lysosome pathway. Furthermore, the protein expression of ATP6V0d2 and CTSD associated with lysosomal functions exhibited dynamic changes with age, increasing in the early stage and decreasing later. Similar age-dependent patterns were observed for the endosome function, autophagy pathway, and SGK1/FOXO3a pathway. Nissl and Golgi staining in the hippocampal region showed age-dependent neuronal loss and synaptic damage, respectively. These findings clearly define the age-gradient changes in the autophagy-lysosome system, the endosome/lysosome system, and the SGK1/FOXO3a pathway in the hippocampus of APP/PS1 mice, providing new perspectives and clues for understanding the possible mechanisms of AD, especially the transition from compensatory to decompensated state.
Collapse
Affiliation(s)
- Zhendong Xu
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Jichang Hu
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Zhen Wei
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Yu Lei
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Henok Kessete Afewerky
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Yang Gao
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Lu Wan
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Longfei Li
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Ling Lei
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Yi Liu
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Fang Huang
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Tong Yu
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Jian‐Zhi Wang
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Co‐innovation Center of NeuroregenerationNantong UniversityNantongChina
| | - Hong‐Lian Li
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Rong Liu
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Xiaochuan Wang
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Education Ministry/Hubei Province of China for Neurological DisordersTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Co‐innovation Center of NeuroregenerationNantong UniversityNantongChina
| |
Collapse
|
14
|
Shen M, Zhang L, Chen C, Wei X, Ma Y, Ma Y. Investigating the causal relationship between immune cell and Alzheimer's disease: a mendelian randomization analysis. BMC Neurol 2024; 24:98. [PMID: 38500057 PMCID: PMC10946133 DOI: 10.1186/s12883-024-03599-y] [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: 12/22/2023] [Accepted: 03/12/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Complex interactions between the immune system and the brain may affect neural development, survival, and function, with etiological and therapeutic implications for neurodegenerative diseases. However, previous studies investigating the association between immune inflammation and Alzheimer's disease (AD) have yielded inconsistent results. METHODS We applied Mendelian randomization (MR) to examine the causal relationship between immune cell traits and AD risk using genetic variants as instrumental variables. MR is an epidemiological study design based on genetic information that reduces the effects of confounding and reverse causation. We analyzed the causal associations between 731 immune cell traits and AD risk based on publicly available genetic data. RESULTS We observed that 5 immune cell traits conferred protection against AD, while 7 immune cell traits increased the risk of AD. These immune cell traits mainly involved T cell regulation, monocyte activation and B cell differentiation. Our findings suggest that immune regulation may influence the development of AD and provide new insights into potential targets for AD prevention and treatment. We also conducted various sensitivity analyses to test the validity and robustness of our results, which revealed no evidence of pleiotropy or heterogeneity. CONCLUSION Our research shows that immune regulation is important for AD and provides new information on potential targets for AD prevention and treatment. However, this study has limitations, including the possibility of reverse causality, lack of validation in independent cohorts, and potential confounding by population stratification. Further research is needed to validate and amplify these results and to elucidate the potential mechanisms of the immune cell-AD association.
Collapse
Affiliation(s)
- Min Shen
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - Linlin Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - Chen Chen
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - Xiaocen Wei
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - Yuning Ma
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China.
| | - Yuxia Ma
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China.
| |
Collapse
|
15
|
Castellanos-Perilla N, Borda MG, Aarsland D, Barreto GE. An analysis of omega-3 clinical trials and a call for personalized supplementation for dementia prevention. Expert Rev Neurother 2024; 24:313-324. [PMID: 38379273 PMCID: PMC11090157 DOI: 10.1080/14737175.2024.2313547] [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: 05/25/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024]
Abstract
INTRODUCTION Targeted interventions are needed to delay or prevent the onset of neurodegenerative diseases. Poor dietary habits are associated with cognitive decline, highlighting the benefits of a healthy diet with fish and polyunsaturated fatty acids (PUFAs). Intake of omega-3 PUFAs docosahexaenoic acid (DHA), α-linolenic acid (ALA) and eicosapentaenoic acid (EPA) is linked with healthy aging, cardiovascular benefits, and reduced risk of Alzheimer's disease. Although omega-3 has health benefits, its intake is often inadequate and insufficient in modern diets. Although fish oil supplements offer an alternative source, inconsistent results from clinical trials raise questions about the factors determining their success. AREAS COVERED In this this review, the authors discuss the aforementioned determining factors and highlight strategies that could enhance the effectiveness of omega-3 PUFAs interventions for dementia and cognitive decline. Moreover, the authors provide suggestions for potential future research. EXPERT OPINION Factors such as diet, lifestyle, and genetic predisposition can all influence the effectiveness of omega-3 supplementation. When implementing clinical trials, it is crucial to consider these factors and recognize their potential impact on the interpretation of results. It is important to study each variable independently and the interactions between them.
Collapse
Affiliation(s)
- Nicolás Castellanos-Perilla
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Centre for Age-Related Medicine (SESAM), Stavanger University Hospital, Stavanger, Norway
- Semillero de Neurociencias y Envejecimiento, Ageing Institute, Medical School, Pontificia Universidad Javeriana, Bogotá, Colombia
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Miguel Germán Borda
- Centre for Age-Related Medicine (SESAM), Stavanger University Hospital, Stavanger, Norway
- Semillero de Neurociencias y Envejecimiento, Ageing Institute, Medical School, Pontificia Universidad Javeriana, Bogotá, Colombia
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Dag Aarsland
- Centre for Age-Related Medicine (SESAM), Stavanger University Hospital, Stavanger, Norway
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London, UK
| | - George E. Barreto
- Department of Biological Sciences, University of Limerick, Limerick, Ireland
| |
Collapse
|
16
|
Chen BR, Wu T, Chen TH, Wang Y. Neuroimmune interactions and their roles in neurodegenerative diseases. FUNDAMENTAL RESEARCH 2024; 4:251-261. [PMID: 38933502 PMCID: PMC11197660 DOI: 10.1016/j.fmre.2023.04.002] [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: 07/21/2022] [Revised: 02/10/2023] [Accepted: 04/03/2023] [Indexed: 06/28/2024] Open
Abstract
The nervous system possesses bidirectional, sophisticated and delicate communications with the immune system. These neuroimmune interactions play a vitally important role in the initiation and development of many disorders, especially neurodegenerative diseases. Although scientific advancements have made tremendous progress in this field during the last few years, neuroimmune communications are still far from being elucidated. By organizing recent research, in this review, we discuss the local and intersystem neuroimmune interactions and their roles in Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. Unveiling these will help us gain a better understanding of the process of interplay inside the body and how the organism maintains homeostasis. It will also facilitate a view of the diseases from a holistic, pluralistic and interconnected perspective, thus providing a basis of developing novel and effective methods to diagnose, intervene and treat diseases.
Collapse
Affiliation(s)
- Bai-Rong Chen
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100083, China
| | - Ting Wu
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100083, China
| | - Ting-Hui Chen
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100083, China
| | - Yun Wang
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100083, China
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| |
Collapse
|
17
|
Zhang C, Qi H, Jia D, Zhao J, Xu C, Liu J, Cui Y, Zhang J, Wang M, Chen M, Tang B. Cognitive impairment in Alzheimer's disease FAD 4T mouse model: Synaptic loss facilitated by activated microglia via C1qA. Life Sci 2024; 340:122457. [PMID: 38266812 DOI: 10.1016/j.lfs.2024.122457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/09/2024] [Accepted: 01/20/2024] [Indexed: 01/26/2024]
Abstract
Alzheimer's disease (AD) is a chronic and progressive neurodegenerative disorder characterized by cognitive dysfunction. The connection between neuroinflammation and abnormal synaptic function in AD is recognized, but the underlying mechanisms remain unclear. In this study, we utilized a mouse model of AD, FAD4T mice aged 6-7 months, to investigate the molecular changes affecting cognitive impairment. Behavior tests showed that FAD4T mice exhibited impaired spatial memory compared with their wild-type littermates. Immunofluorescence staining revealed the presence of Aβ plaques and abnormal glial cell activation as well as changes in microglial morphology in the cortex and hippocampus of FAD4T mice. Synaptic function was impaired in FAD4T mice. Patch clamp recordings of hippocampal neurons revealed reduced amplitude of miniature excitatory postsynaptic currents. Additionally, Golgi staining showed decreased dendritic spine density in the cortex and hippocampus of FAD4T mice, indicating aberrant synapse morphology. Moreover, hippocampal PSD-95 and NMDAR1 protein levels decreased in FAD4T mice. RNA-seq analysis revealed elevated expression of immune system and proinflammatory genes, including increased C1qA protein and mRNA levels, as well as higher expression of TNF-α and IL-18. Taken together, our findings suggest that excessive microglia activation mediated by complement factor C1qA may contribute to aberrant synaptic pruning, resulting in synapse loss and disrupted synaptic transmission, ultimately leading to AD pathogenesis and behavioral impairments in the FAD4T mouse model. Our study provides valuable insights into the underlying mechanisms of cognitive impairments and preliminarily explores a potentially effective treatment approach targeting on C1qA for AD.
Collapse
Affiliation(s)
- Cui Zhang
- Center for Rehabilitation Medicine, Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Department of Rehabilitation Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China; Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Hao Qi
- GemPharmatech Inc., 12 Xuefu Road, Jiangbei New Area, Nanjing 210061, China
| | - Dongjing Jia
- GemPharmatech Inc., 12 Xuefu Road, Jiangbei New Area, Nanjing 210061, China
| | - Jingting Zhao
- Center for Rehabilitation Medicine, Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Department of Rehabilitation Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Chengyuan Xu
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Jing Liu
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Yangfeng Cui
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Jiajian Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Minzhe Wang
- Center for Rehabilitation Medicine, Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Department of Rehabilitation Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ming Chen
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China.
| | - Binliang Tang
- Center for Rehabilitation Medicine, Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Department of Rehabilitation Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China; Interdisciplinary Institute of Neuroscience and Technology, Zhejiang University School of Medicine, Hangzhou 310029, China.
| |
Collapse
|
18
|
Zhang Y, Shen S, Li X, Wang S, Xiao Z, Cheng J, Li R. A multiclass extreme gradient boosting model for evaluation of transcriptomic biomarkers in Alzheimer's disease prediction. Neurosci Lett 2024; 821:137609. [PMID: 38157927 DOI: 10.1016/j.neulet.2023.137609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/30/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Patients with young-onset Alzheimer's disease (AD) (before the age of 50 years old) often lack obvious imaging changes and amyloid protein deposition, which can lead to misdiagnosis with other cognitive impairments. Considering the association between immunological dysfunction and progression of neurodegenerative disease, recent research has focused on identifying blood transcriptomic signatures for precise prediction of AD. METHODS In this study, we extracted blood biomarkers from large-scale transcriptomics to construct multiclass eXtreme Gradient Boosting models (XGBoost), and evaluated their performance in distinguishing AD from cognitive normal (CN) and mild cognitive impairment (MCI). RESULTS Independent testing with external dataset revealed that the combination of blood transcriptomic signatures achieved an area under the receiver operating characteristic curve (AUC of ROC) of 0.81 for multiclass classification (sensitivity = 0.81; specificity = 0.63), 0.83 for classification of AD vs. CN (sensitivity = 0.72; specificity = 0.73), and 0.85 for classification of AD vs. MCI (sensitivity = 0.77; specificity = 0.73). These candidate signatures were significantly enriched in 62 chromosome regions, such as Chr.19p12-19p13.3, Chr.1p22.1-1p31.1, and Chr.1q21.2-1p23.1 (adjusted p < 0.05), and significantly overrepresented by 26 transcription factors, including E2F2, FOXO3, and GATA1 (adjusted p < 0.05). Biological analysis of these signatures pointed to systemic dysregulation of immune responses, hematopoiesis, exocytosis, and neuronal support in neurodegenerative disease (adjusted p < 0.05). CONCLUSIONS Blood transcriptomic biomarkers hold great promise in clinical use for the accurate assessment and prediction of AD.
Collapse
Affiliation(s)
- Yi Zhang
- Institute of Neuroscience, Panzhihua University, Panzhihua 617000, China.
| | - Shasha Shen
- Institute of Neuroscience, Panzhihua University, Panzhihua 617000, China
| | - Xiaokai Li
- Institute of Neuroscience, Panzhihua University, Panzhihua 617000, China
| | - Songlin Wang
- Medical College, Panzhihua University, Panzhihua 617000, China
| | - Zongni Xiao
- Medical College, Panzhihua University, Panzhihua 617000, China
| | - Jun Cheng
- Medical College, Panzhihua University, Panzhihua 617000, China
| | - Ruifeng Li
- Institute of Neuroscience, Panzhihua University, Panzhihua 617000, China
| |
Collapse
|
19
|
Alavez-Rubio JS, Juarez-Cedillo T. Microglia as a Possible Alternative Therapeutic for Dementia. J Alzheimers Dis Rep 2024; 8:43-56. [PMID: 38229830 PMCID: PMC10789290 DOI: 10.3233/adr-230112] [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: 08/21/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024] Open
Abstract
Dementia is a syndrome in which there is deterioration in memory, behavior, and the ability to perform everyday activities. Alzheimer's disease and vascular dementia are the most common forms of dementia. There is evidence supporting the hypothesis that inflammatory and immune mechanisms are involved in dementia. Microglia, the resident macrophage tissues in the central nervous system, play a significant role in neuroinflammation and play an important role in amyloid-β clearance in the brain, and impaired microglial clearance of amyloid-β has also been shown to be involved in the pathogenesis of Alzheimer's disease. However, there is also abundant evidence that microglia have harmful actions in dementia. Once activated, they can mediate uptake at neuronal synapses. They can also exacerbate tau pathology and secrete deleterious inflammatory factors that can directly or indirectly damage neurons. Thus, depending on the stage of the disease, microglia can act both protectively and detrimentally. Therefore, it is still necessary to continue with studies to better understand the role of microglia in the pathology of dementia. Currently available drugs can only improve cognitive symptoms, have no impact on progression and are not curative, so identifying and studying new therapeutic approaches is important. Considering the role played by microglia in this pathology, it has been pointed out as a possible therapeutic approach. This manuscript aims to address the relationship between microglia and dementia and how this relationship could be used for therapeutic purposes.
Collapse
Affiliation(s)
| | - Teresa Juarez-Cedillo
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Área de Envejecimiento, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico
| |
Collapse
|
20
|
Wang Y, Jiang R, Li M, Wang Z, Yang Y, Sun L. Characteristics of T Cells in Single-Cell Datasets of Peripheral Blood and Cerebrospinal Fluid in Alzheimer's Disease Patients. J Alzheimers Dis 2024; 99:S265-S280. [PMID: 38043012 PMCID: PMC11091562 DOI: 10.3233/jad-230784] [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] [Accepted: 09/27/2023] [Indexed: 12/04/2023]
Abstract
Background Alzheimer's disease (AD) is the most common type of dementia, causing a huge socioeconomic burden. In parallel with the widespread uptake of single-cell RNA sequencing (scRNA-seq) technology, there has been a rapid accumulation of data produced by researching AD at single-cell resolution, which is more conductive to explore the neuroimmune-related mechanism of AD. Objective To explore the potential features of T cells in the peripheral blood and cerebrospinal fluid of AD patients. Methods Two datasets, GSE181279 and GSE134578, were integrated from GEO database. Seurat, Monocle, CellChat, scRepertoire, and singleR packages were mainly employed for data analysis. Results Our analysis demonstrated that in peripheral blood, T cells were significantly expanded, and these expanded T cells were possessed effector function, such as CD8+TEMRA, CD4+TEMRA, and CD8+TEM. Interestingly, CD8+TEMRA and CD4+TEMRA cells positioned adjacently after dimensions reduction and clustering. Notably, we identified that the expanded T cells were developed from Naïve T cells and TCM cells, and TEM cells was in the intermediate state of this developing process. Additionally, in cerebrospinal fluid of AD patients, the amplified T cells were mainly CD8+TEMRA cells, and the number and strength of communication between CD4+TEM, CD8+TEM, and CD8+TEMRA were decreased in AD patients. Conclusions Our comprehensive analyses identified the cells in cerebrospinal fluid from AD patients are expanded TEMRA or TEM cells and the TEMRA cells communicating with other immune cells is weakened, which may be an important immune feature that leads to AD.
Collapse
Affiliation(s)
- Yongchun Wang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun, China
- Department of Neurology, Cognitive Center, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Richeng Jiang
- Department of Otolaryngology Head and Neck Surgery, The First Hospital of Jilin University, Changchun, China
| | - Mingxi Li
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun, China
- Department of Neurology, Cognitive Center, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Zicheng Wang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun, China
- Department of Neurology, Cognitive Center, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Yu Yang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun, China
- Department of Neurology, Cognitive Center, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Li Sun
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun, China
- Department of Neurology, Cognitive Center, The First Hospital of Jilin University, Jilin University, Changchun, China
| |
Collapse
|
21
|
Cervellati C, Zuliani G, Valacchi G. OxInflammation in Alzheimer's disease. Neural Regen Res 2023; 18:2709-2710. [PMID: 37449634 DOI: 10.4103/1673-5374.374144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Affiliation(s)
- Carlo Cervellati
- Department of Translational Medicine and for Romagna, University of Ferrara, Ferrara, Italy
| | - Giovanni Zuliani
- Department of Translational Medicine and for Romagna, University of Ferrara, Ferrara, Italy
| | - Giuseppe Valacchi
- Department of Environmental Sciences and Prevention, University of Ferrara, Ferrara, Italy; Plants for Human Health Institute, Animal Science Department, NC State University, Kannapolis, NC, USA; Department of Food and Nutrition, Kyung Hee University, Seoul, South Korea
| |
Collapse
|
22
|
Duchateau L, Küҫükali F, De Roeck A, Wittens MMJ, Temmerman J, Weets I, Timmers M, Engelborghs S, Bjerke M, Sleegers K. CSF biomarker analysis of ABCA7 mutation carriers suggests altered APP processing and reduced inflammatory response. Alzheimers Res Ther 2023; 15:195. [PMID: 37946268 PMCID: PMC10634183 DOI: 10.1186/s13195-023-01338-y] [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: 08/11/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND The Alzheimer's disease (AD) risk gene ABCA7 has suggested functions in lipid metabolism and the immune system. Rare premature termination codon (PTC) mutations and an expansion of a variable number of tandem repeats (VNTR) polymorphism in the gene, both likely cause a lower ABCA7 expression and hereby increased risk for AD. However, the exact mechanism of action remains unclear. By studying CSF biomarkers reflecting different types of AD-related pathological processes, we aim to get a better insight in those processes and establish a biomarker profile of mutation carriers. METHODS The study population consisted of 229 AD patients for whom CSF was available and ABCA7 sequencing and VNTR genotyping had been performed. This included 28 PTC mutation and 16 pathogenic expansion carriers. CSF levels of Aβ1-42, Aβ1-40, P-tau181, T-tau, sAPPα, sAPPβ, YKL-40, and hFABP were determined using ELISA and Meso Scale Discovery assays. We compared differences in levels of these biomarkers and the Aβ ratio between AD patients with or without an ABCA7 PTC mutation or expansion using linear regression on INT-transformed data with APOE-status, age and sex as covariates. RESULTS Carriers of ABCA7 expansion mutations had significantly lower Aβ1-42 levels (P = 0.022) compared with non-carrier patients. The effect of the presence of ABCA7 mutations on CSF levels was especially pronounced in APOE ε4-negative carriers. In addition, VNTR expansion carriers had reduced Aβ1-40 (P = 0.023), sAPPα (P = 0.047), sAPPβ (P = 0.016), and YKL-40 (P = 0.0036) levels. CONCLUSIONS Our results are suggestive for an effect on APP processing by repeat expansions given the changes in the amyloid-related CSF biomarkers that were found in carriers. The decrease in YKL-40 levels in expansion carriers moreover suggests that these patients potentially have a reduced inflammatory response to AD damage. Moreover, our findings suggest the existence of a mechanism, independent of lowered expression, affecting neuropathology in expansion carriers.
Collapse
Affiliation(s)
- Lena Duchateau
- Complex Genetics of Alzheimer's Disease Group, VIB-UAntwerp Center for Molecular Neurology, VIB, Building V, Universiteitsplein 1, Wilrijk, Antwerp, B-2610, Belgium
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, Antwerp, 2610, Belgium
| | - Fahri Küҫükali
- Complex Genetics of Alzheimer's Disease Group, VIB-UAntwerp Center for Molecular Neurology, VIB, Building V, Universiteitsplein 1, Wilrijk, Antwerp, B-2610, Belgium
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, Antwerp, 2610, Belgium
| | - Arne De Roeck
- Complex Genetics of Alzheimer's Disease Group, VIB-UAntwerp Center for Molecular Neurology, VIB, Building V, Universiteitsplein 1, Wilrijk, Antwerp, B-2610, Belgium
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, Antwerp, 2610, Belgium
- Present Address: Argenx, Ghent, Belgium
| | - Mandy M J Wittens
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, Antwerp, 2610, Belgium
- Clinical Neurochemistry Laboratory, Department of Clinical Biology, University Hospital Brussels, Generaal Jacqueslaan 137, Elsene, Brussels, 1050, Belgium
| | - Joke Temmerman
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, Antwerp, 2610, Belgium
- Neuroprotection & Neuromodulation (NEUR) Research Group, Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Jette, Brussels, 1090, Belgium
| | - Ilse Weets
- Clinical Neurochemistry Laboratory, Department of Clinical Biology, University Hospital Brussels, Generaal Jacqueslaan 137, Elsene, Brussels, 1050, Belgium
- Experimental Pharmacology (EFAR) Research Group, Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels, 1090, Belgium
| | - Maarten Timmers
- Reference Center for Biological Markers of Dementia, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, Antwerp, 2610, Belgium
- Janssen Research and Development, a Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Sebastiaan Engelborghs
- Neuroprotection & Neuromodulation (NEUR) Research Group, Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Jette, Brussels, 1090, Belgium
- Reference Center for Biological Markers of Dementia, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, Antwerp, 2610, Belgium
- Department of Neurology and Bru-BRAIN, University Hospital Brussels, Generaal Jacqueslaan 137, Elsene, Brussels, 1050, Belgium
| | - Maria Bjerke
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, Antwerp, 2610, Belgium
- Clinical Neurochemistry Laboratory, Department of Clinical Biology, University Hospital Brussels, Generaal Jacqueslaan 137, Elsene, Brussels, 1050, Belgium
- Neuroprotection & Neuromodulation (NEUR) Research Group, Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Jette, Brussels, 1090, Belgium
| | - Kristel Sleegers
- Complex Genetics of Alzheimer's Disease Group, VIB-UAntwerp Center for Molecular Neurology, VIB, Building V, Universiteitsplein 1, Wilrijk, Antwerp, B-2610, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, Antwerp, 2610, Belgium.
| |
Collapse
|
23
|
Benjamin KJM, Chen Q, Eagles NJ, Huuki-Myers LA, Collado-Torres L, Stolz JM, Pertea G, Shin JH, Paquola ACM, Hyde TM, Kleinman JE, Jaffe AE, Han S, Weinberger DR. Genetic and environmental contributions to ancestry differences in gene expression in the human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534458. [PMID: 37034760 PMCID: PMC10081196 DOI: 10.1101/2023.03.28.534458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Ancestral differences in genomic variation are determining factors in gene regulation; however, most gene expression studies have been limited to European ancestry samples or adjusted for ancestry to identify ancestry-independent associations. We instead examined the impact of genetic ancestry on gene expression and DNA methylation (DNAm) in admixed African/Black American neurotypical individuals to untangle effects of genetic and environmental factors. Ancestry-associated differentially expressed genes (DEGs), transcripts, and gene networks, while notably not implicating neurons, are enriched for genes related to immune response and vascular tissue and explain up to 26% of heritability for ischemic stroke, 27% of heritability for Parkinson's disease, and 30% of heritability for Alzhemier's disease. Ancestry-associated DEGs also show general enrichment for heritability of diverse immune-related traits but depletion for psychiatric-related traits. The cell-type enrichments and direction of effects vary by brain region. These DEGs are less evolutionarily constrained and are largely explained by genetic variations; roughly 15% are predicted by DNAm variation implicating environmental exposures. We also compared Black and White Americans, confirming most of these ancestry-associated DEGs. Our results highlight how environment and genetic background affect genetic ancestry differences in gene expression in the human brain and affect risk for brain illness.
Collapse
Affiliation(s)
- Kynon J M Benjamin
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Qiang Chen
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | | | | | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Joshua M Stolz
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Geo Pertea
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Apuã C M Paquola
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew E Jaffe
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Neumora Therapeutics, Watertown, MA, USA
| | - Shizhong Han
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
24
|
Plaschke K, Kopitz J, Gebert J, Wolf ND, Wolf RC. Proteomic Analysis Reveals Potential Exosomal Biomarkers in Patients With Sporadic Alzheimer Disease. Alzheimer Dis Assoc Disord 2023; 37:315-321. [PMID: 38015424 DOI: 10.1097/wad.0000000000000589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 09/18/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Despite substantial progress made in the past decades, the pathogenesis of sporadic Alzheimer disease (sAD) and related biological markers of the disease are still controversially discussed. Cerebrospinal fluid and functional brain imaging markers have been established to support the clinical diagnosis of sAD. Yet, due to the invasiveness of such diagnostics, less burdensome markers have been increasingly investigated in the past years. Among such markers, extracellular vesicles may yield promise in (early) diagnostics and treatment monitoring in sAD. MATERIALS AND METHODS In this pilot study, we collected the blood plasma of 18 patients with sAD and compared the proteome of extracted extracellular vesicles with the proteome of 11 age-matched healthy controls. The resulting proteomes were characterized by Gene Ontology terms and between-group statistics. RESULTS Ten distinct proteins were found to significantly differ between sAD patients and controls (P<0.05, False Discovery Rate, corrected). These proteins included distinct immunoglobulins, fibronectin, and apolipoproteins. CONCLUSIONS These findings lend further support for exosomal changes in neurodegenerative disorders, and particularly in sAD. Further proteomic research could decisively advance our knowledge of sAD pathophysiology as much as it could foster the development of clinically meaningful biomarkers.
Collapse
Affiliation(s)
| | | | | | - Nadine D Wolf
- Center for Psychosocial Medicine, Department of General Psychiatry, University Hospital Heidelberg, Heidelberg, Germany
| | - Robert Christian Wolf
- Center for Psychosocial Medicine, Department of General Psychiatry, University Hospital Heidelberg, Heidelberg, Germany
| |
Collapse
|
25
|
Zhu Y, Kong L, Han T, Yan Q, Liu J. Machine learning identification and immune infiltration of disulfidptosis-related Alzheimer's disease molecular subtypes. Immun Inflamm Dis 2023; 11:e1037. [PMID: 37904698 PMCID: PMC10566450 DOI: 10.1002/iid3.1037] [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: 05/09/2023] [Revised: 09/08/2023] [Accepted: 09/09/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a common neurodegenerative disorder. Disulfidptosis is a newly discovered form of programmed cell death that holds promise as a therapeutic strategy for various disorders. However, the functional roles of disulfidptosis-related genes (DRGs) in AD remain unknown. METHODS Microarray data and clinical information from patients with AD and healthy controls were downloaded from the Gene Expression Omnibus database. A thorough examination of DRG expression and immune characteristics in both groups was performed. Based on the identified DRGs, we performed an unsupervised clustering analysis to categorize the AD samples into various disulfidptosis-related molecular clusters. Weighted gene co-expression network analysis was performed to select hub genes specific to disulfidptosis-related AD clusters. The performances of various machine learning models were compared to determine the optimal predictive model. The predictive ability of the optimal model was assessed using nomogram analysis and five external datasets. RESULTS Eight DRGs showed differential expression between the AD and control samples. Two different molecular clusters were identified. The immune cell infiltration analysis revealed distinct differences in the immune microenvironment of the two clusters. The support vector machine model showed the highest performance, and a panel of five signature genes was identified, which showed excellent performance on the external validation datasets. The nomogram analysis also showed high accuracy in predicting AD. CONCLUSION We identified disulfidptosis-related molecular clusters in AD and established a novel risk model to assess the likelihood of developing AD. These findings revealed a complex association between disulfidptosis and AD, which may aid in identifying potential therapeutic targets for this debilitating disorder.
Collapse
Affiliation(s)
- Yidong Zhu
- Department of Traditional Chinese Medicine, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Lingyue Kong
- Department of Traditional Chinese Medicine, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Tianxiong Han
- Department of Traditional Chinese Medicine, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Qiongzhi Yan
- Department of Traditional Chinese Medicine, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Jun Liu
- Department of Traditional Chinese Medicine, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| |
Collapse
|
26
|
Clement M. The association of microbial infection and adaptive immune cell activation in Alzheimer's disease. DISCOVERY IMMUNOLOGY 2023; 2:kyad015. [PMID: 38567070 PMCID: PMC10917186 DOI: 10.1093/discim/kyad015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/31/2023] [Accepted: 09/04/2023] [Indexed: 04/04/2024]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the most common form of dementia. Early symptoms include the loss of memory and mild cognitive ability; however, as the disease progresses, these symptoms can present with increased severity manifesting as mood and behaviour changes, disorientation, and a loss of motor/body control. AD is one of the leading causes of death in the UK, and with an ever-increasing ageing society, patient numbers are predicted to rise posing a significant global health emergency. AD is a complex neurophysiological disorder where pathology is characterized by the deposition and aggregation of misfolded amyloid-beta (Aβ)-protein that in-turn promotes excessive tau-protein production which together drives neuronal cell dysfunction, neuroinflammation, and neurodegeneration. It is widely accepted that AD is driven by a combination of both genetic and immunological processes with recent data suggesting that adaptive immune cell activity within the parenchyma occurs throughout disease. The mechanisms behind these observations remain unclear but suggest that manipulating the adaptive immune response during AD may be an effective therapeutic strategy. Using immunotherapy for AD treatment is not a new concept as the only two approved treatments for AD use antibody-based approaches to target Aβ. However, these have been shown to only temporarily ease symptoms or slow progression highlighting the urgent need for newer treatments. This review discusses the role of the adaptive immune system during AD, how microbial infections may be contributing to inflammatory immune activity and suggests how adaptive immune processes can pose as therapeutic targets for this devastating disease.
Collapse
Affiliation(s)
- Mathew Clement
- Division of Infection and Immunity, Systems Immunity University Research Institute, Cardiff University, Cardiff, UK
| |
Collapse
|
27
|
Zhang Y, Miao Y, Tan J, Chen F, Lei P, Zhang Q. Identification of mitochondrial related signature associated with immune microenvironment in Alzheimer's disease. J Transl Med 2023; 21:458. [PMID: 37434203 DOI: 10.1186/s12967-023-04254-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/07/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common neurodegenerative disease. Mitochondrial dysfunction and immune responses are important factors in the pathogenesis of AD, but their crosstalk in AD has not been studied. In this study, the independent role and interaction of mitochondria-related genes and immune cell infiltration in AD were investigated using bioinformatics methods. METHODS The datasets of AD were obtained from NCBI Gene Expression Omnibus (GEO), and the data of mitochondrial genes was from MitoCarta3.0 database. Subsequently, differential expression genes (DEGs) screening and GSEA functional enrichment analysis were performed. The intersection of DEGs and mitochondrial related genes was used to obtain MitoDEGs. The MitoDEGs most relevant to AD were determined by Least absolute shrinkage and selection operator and multiple support vector machine recursive feature elimination, as well as protein-protein interactions (PPI) network and random forest. The infiltration of 28 kinds of immune cells in AD was analyzed by ssGSEA, and the relationship between hub MitoDEGs and the proportion of immune infiltration was studied. The expression levels of hub MitoDEGs were verified in cell models and AD mice, and the role of OPA1 in mitochondrial damage and neuronal apoptosis was investigated. RESULTS The functions and pathways of DEGs were significantly enriched in AD, including immune response activation, IL1R pathway, mitochondrial metabolism, oxidative damage response and electron transport chain-oxphos system in mitochondria. Hub MitoDEGs closely related to AD were obtained based on PPI network, random forest and two machine learning algorithms. Five hub MitoDEGs associated with neurological disorders were identified by biological function examination. The hub MitoDEGs were found to be correlated with memory B cell, effector memory CD8 T cell, activated dendritic cell, natural killer T cell, type 17 T helper cell, Neutrophil, MDSC, plasmacytoid dendritic cell. These genes can also be used to predict the risk of AD and have good diagnostic efficacy. In addition, the mRNA expression levels of BDH1, TRAP1, OPA1, DLD in cell models and AD mice were consistent with the results of bioinformatics analysis, and expression levels of SPG7 showed a downward trend. Meanwhile, OPA1 overexpression alleviated mitochondrial damage and neuronal apoptosis induced by Aβ1-42. CONCLUSIONS Five potential hub MitoDEGs most associated with AD were identified. Their interaction with immune microenvironment may play a crucial role in the occurrence and prognosis of AD, which provides a new insight for studying the potential pathogenesis of AD and exploring new targets.
Collapse
Affiliation(s)
- Yaodan Zhang
- Department of Geriatrics, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, China
- Tianjin Geriatrics Institute, Anshan Road No. 154, Tianjin, 300052, China
| | - Yuyang Miao
- Department of Geriatrics, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, China
- Tianjin Geriatrics Institute, Anshan Road No. 154, Tianjin, 300052, China
| | - Jin Tan
- Department of Geriatrics, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, China
- Tianjin Geriatrics Institute, Anshan Road No. 154, Tianjin, 300052, China
| | - Fanglian Chen
- Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Ping Lei
- Department of Geriatrics, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, China.
- Tianjin Geriatrics Institute, Anshan Road No. 154, Tianjin, 300052, China.
- Haihe Laboratory of Cell Ecosystem, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, China.
| | - Qiang Zhang
- Department of Geriatrics, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, China.
- Tianjin Geriatrics Institute, Anshan Road No. 154, Tianjin, 300052, China.
| |
Collapse
|
28
|
Zhang Y, Chen H, Li R, Sterling K, Song W. Amyloid β-based therapy for Alzheimer's disease: challenges, successes and future. Signal Transduct Target Ther 2023; 8:248. [PMID: 37386015 PMCID: PMC10310781 DOI: 10.1038/s41392-023-01484-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 07/01/2023] Open
Abstract
Amyloid β protein (Aβ) is the main component of neuritic plaques in Alzheimer's disease (AD), and its accumulation has been considered as the molecular driver of Alzheimer's pathogenesis and progression. Aβ has been the prime target for the development of AD therapy. However, the repeated failures of Aβ-targeted clinical trials have cast considerable doubt on the amyloid cascade hypothesis and whether the development of Alzheimer's drug has followed the correct course. However, the recent successes of Aβ targeted trials have assuaged those doubts. In this review, we discussed the evolution of the amyloid cascade hypothesis over the last 30 years and summarized its application in Alzheimer's diagnosis and modification. In particular, we extensively discussed the pitfalls, promises and important unanswered questions regarding the current anti-Aβ therapy, as well as strategies for further study and development of more feasible Aβ-targeted approaches in the optimization of AD prevention and treatment.
Collapse
Affiliation(s)
- Yun Zhang
- National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China.
| | - Huaqiu Chen
- National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Ran Li
- The Second Affiliated Hospital and Yuying Children's Hospital, Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Keenan Sterling
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Weihong Song
- National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China.
- The Second Affiliated Hospital and Yuying Children's Hospital, Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang, China.
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, China.
| |
Collapse
|
29
|
Shigemizu D, Akiyama S, Suganuma M, Furutani M, Yamakawa A, Nakano Y, Ozaki K, Niida S. Classification and deep-learning-based prediction of Alzheimer disease subtypes by using genomic data. Transl Psychiatry 2023; 13:232. [PMID: 37386009 DOI: 10.1038/s41398-023-02531-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023] Open
Abstract
Late-onset Alzheimer's disease (LOAD) is the most common multifactorial neurodegenerative disease among elderly people. LOAD is heterogeneous, and the symptoms vary among patients. Genome-wide association studies (GWAS) have identified genetic risk factors for LOAD but not for LOAD subtypes. Here, we examined the genetic architecture of LOAD based on Japanese GWAS data from 1947 patients and 2192 cognitively normal controls in a discovery cohort and 847 patients and 2298 controls in an independent validation cohort. Two distinct groups of LOAD patients were identified. One was characterized by major risk genes for developing LOAD (APOC1 and APOC1P1) and immune-related genes (RELB and CBLC). The other was characterized by genes associated with kidney disorders (AXDND1, FBP1, and MIR2278). Subsequent analysis of albumin and hemoglobin values from routine blood test results suggested that impaired kidney function could lead to LOAD pathogenesis. We developed a prediction model for LOAD subtypes using a deep neural network, which achieved an accuracy of 0.694 (2870/4137) in the discovery cohort and 0.687 (2162/3145) in the validation cohort. These findings provide new insights into the pathogenic mechanisms of LOAD.
Collapse
Affiliation(s)
- Daichi Shigemizu
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan.
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
| | - Shintaro Akiyama
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| | - Mutsumi Suganuma
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| | - Motoki Furutani
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
- Department of Cardiovascular Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, 734-8553, Japan
| | - Akiko Yamakawa
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| | - Yukiko Nakano
- Department of Cardiovascular Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, 734-8553, Japan
| | - Kouichi Ozaki
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
- Department of Cardiovascular Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, 734-8553, Japan
| | - Shumpei Niida
- Core Facility Administration, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| |
Collapse
|
30
|
Ma C, Li J, Chi Y, Sun X, Yang M, Sui X. Identification and prediction of m7G-related Alzheimer's disease subtypes: insights from immune infiltration and machine learning models. Front Aging Neurosci 2023; 15:1161068. [PMID: 37396662 PMCID: PMC10312082 DOI: 10.3389/fnagi.2023.1161068] [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: 02/07/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction Alzheimer's disease (AD) is a complex and progressive neurodegenerative disorder that primarily affects older individuals. N7-methylguanosine (m7G) is a common RNA chemical modification that impacts the development of numerous diseases. Thus, our work investigated m7G-related AD subtypes and established a predictive model. Methods The datasets for AD patients, including GSE33000 and GSE44770, were obtained from the Gene Expression Omnibus (GEO) database, which were derived from the prefrontal cortex of the brain. We performed differential analysis of m7G regulators and examined the immune signatures differences between AD and matched-normal samples. Consensus clustering was employed to identify AD subtypes based on m7G-related differentially expressed genes (DEGs), and immune signatures were explored among different clusters. Furthermore, we developed four machine learning models based on the expression profiles of m7G-related DEGs and identified five important genes from the optimal model. We evaluated the predictive power of the 5-gene-based model using an external AD dataset (GSE44770). Results A total of 15 genes related to m7G were found to be dysregulated in patients with AD compared to non-AD patients. This finding suggests that there are differences in immune characteristics between these two groups. Based on the differentially expressed m7G regulators, we categorized AD patients into two clusters and calculated the ESTIMATE score for each cluster. Cluster 2 exhibited a higher ImmuneScore than Cluster 1. We performed the receiver operating characteristic (ROC) analysis to compare the performance of four models, and we found that the Random Forest (RF) model had the highest AUC value of 1.000. Furthermore, we tested the predictive efficacy of a 5-gene-based RF model on an external AD dataset and obtained an AUC value of 0.968. The nomogram, calibration curve, and decision curve analysis (DCA) confirmed the accuracy of our model in predicting AD subtypes. Conclusion The present study systematically examines the biological significance of m7G methylation modification in AD and investigates its association with immune infiltration characteristics. Furthermore, the study develops potential predictive models to assess the risk of m7G subtypes and the pathological outcomes of patients with AD, which can facilitate risk classification and clinical management of AD patients.
Collapse
Affiliation(s)
- Chao Ma
- Department of General Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
- School of Clinical Medicine, Weifang Medical University, Weifang, Shandong, China
| | - Jian Li
- Department of Neurology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Yuhua Chi
- Department of General Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Xuan Sun
- Department of General Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Maoquan Yang
- School of Clinical Medicine, Weifang Medical University, Weifang, Shandong, China
| | - Xueqin Sui
- Department of General Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| |
Collapse
|
31
|
Su Y, Huang Y, Kou Q, Lu L, Jiang H, Li X, Gui R, Huang R, Huang X, Ma J, Li J, Nie X. Study on the Role of an Erythrocyte Membrane-Coated Nanotheranostic System in Targeted Immune Regulation of Alzheimer's Disease. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301361. [PMID: 37075744 PMCID: PMC10288270 DOI: 10.1002/advs.202301361] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/18/2023] [Indexed: 05/03/2023]
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative diseases in the elderly population. Despite significant advances in studies of the pathobiology on AD, there is still no effective treatment. Here, an erythrocyte membrane-camouflaged nanodrug delivery system (TR-ZRA) modified with transferrin receptor aptamers that can be targeted across the blood-brain barrier to ameliorate AD immune environment is established. Based on metal-organic framework (Zn-CA), TR-ZRA is loaded with CD22shRNA plasmid to silence the abnormally high expression molecule CD22 in aging microglia. Most importantly, TR-ZRA can enhance the ability of microglia to phagocytose Aβ and alleviate complement activation, which can promote neuronal activity and decrease inflammation level in the AD brain. Moreover, TR-ZRA is also loaded with Aβ aptamers, which allow rapid and low-cost monitoring of Aβ plaques in vitro. After treatment with TR-ZRA, learning, and memory abilities are enhanced in AD mice. In conclusion, the biomimetic delivery nanosystem TR-ZRA in this study provides a promising strategy and novel immune targets for AD therapy.
Collapse
Affiliation(s)
- Yanrong Su
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Yufen Huang
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Qinjie Kou
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Lu Lu
- Department of Blood TransfusionThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Haiye Jiang
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Xisheng Li
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Rong Gui
- Department of Blood TransfusionThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Rong Huang
- Department of Blood TransfusionThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Xueyuan Huang
- Department of Blood TransfusionThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Jinqi Ma
- Department of Blood TransfusionThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Jian Li
- Department of Blood TransfusionThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Xinmin Nie
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
- Hunan Engineering Technology Research Center of Optoelectronic Health DetectionChangshaHunan410000China
| |
Collapse
|
32
|
Jin B, Fei G, Sang S, Zhong C. Identification of biomarkers differentiating Alzheimer's disease from other neurodegenerative diseases by integrated bioinformatic analysis and machine-learning strategies. Front Mol Neurosci 2023; 16:1152279. [PMID: 37234685 PMCID: PMC10205980 DOI: 10.3389/fnmol.2023.1152279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Background Alzheimer's disease (AD) is the most common neurodegenerative disease, imposing huge mental and economic burdens on patients and society. The specific molecular pathway(s) and biomarker(s) that distinguish AD from other neurodegenerative diseases and reflect the disease progression are still not well studied. Methods Four frontal cortical datasets of AD were integrated to conduct differentially expressed genes (DEGs) and functional gene enrichment analyses. The transcriptional changes after the integrated frontal cortical datasets subtracting the cerebellar dataset of AD were further compared with frontal cortical datasets of frontotemporal dementia and Huntingdon's disease to identify AD-frontal-associated gene expression. Integrated bioinformatic analysis and machine-learning strategies were applied for screening and determining diagnostic biomarkers, which were further validated in another two frontal cortical datasets of AD by receiver operating characteristic (ROC) curves. Results Six hundred and twenty-six DEGs were identified as AD frontal associated, including 580 downregulated genes and 46 upregulated genes. The functional enrichment analysis revealed that immune response and oxidative stress were enriched in AD patients. Decorin (DCN) and regulator of G protein signaling 1 (RGS1) were screened as diagnostic biomarkers in distinguishing AD from frontotemporal dementia and Huntingdon's disease of AD. The diagnostic effects of DCN and RGS1 for AD were further validated in another two datasets of AD: the areas under the curve (AUCs) reached 0.8148 and 0.8262 in GSE33000, and 0.8595 and 0.8675 in GSE44770. There was a better value for AD diagnosis when combining performances of DCN and RGS1 with the AUCs of 0.863 and 0.869. Further, DCN mRNA level was correlated to CDR (Clinical Dementia Rating scale) score (r = 0.5066, p = 0.0058) and Braak staging (r = 0.3348, p = 0.0549). Conclusion DCN and RGS1 associated with the immune response may be useful biomarkers for diagnosing AD and distinguishing the disease from frontotemporal dementia and Huntingdon's disease. DCN mRNA level reflects the development of the disease.
Collapse
Affiliation(s)
- Boru Jin
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Guoqiang Fei
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Shaoming Sang
- Shanghai Raising Pharmaceutical Technology Co., Ltd., Shanghai, China
| | - Chunjiu Zhong
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| |
Collapse
|
33
|
Li Y, Chang J, Chen X, Liu J, Zhao L. Advances in the Study of APOE and Innate Immunity in Alzheimer's Disease. J Alzheimers Dis 2023:JAD230179. [PMID: 37182889 DOI: 10.3233/jad-230179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Alzheimer's disease (AD) is a progressive degenerative disease of the nervous system (CNS) with an insidious onset. Clinically, it is characterized by a full range of dementia manifestations including memory impairment, aphasia, loss of speech, loss of use, loss of recognition, impairment of visuospatial skills, and impairment of executive function, as well as changes in personality and behavior. The exact cause of AD has not yet been identified. Nevertheless, modern research indicates that genetic factors contribute to 70% of human's risk of AD. Apolipoprotein (APOE) accounts for up to 90% of the genetic predisposition. APOE is a crucial gene that cannot be overstated. In addition, innate immunity plays a significant role in the etiology and treatment of AD. Understanding the different subtypes of APOE and their interconnections is of paramount importance. APOE and innate immunity, along with their relationship to AD, are primary research motivators for in-depth research and clinical trials. The exploration of novel technologies has led to an increasing trend in the study of AD at the cellular and molecular levels and continues to make more breakthroughs and progress. As of today, there is no effective treatment available for AD around the world. This paper aims to summarize and analyze the role of APOE and innate immunity, as well as development trends in recent years. It is anticipated that APOE and innate immunity will provide a breakthrough for humans to hinder AD progression in the near future.
Collapse
Affiliation(s)
- Yujiao Li
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Jun Chang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Xi Chen
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Jianwei Liu
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lan Zhao
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| |
Collapse
|
34
|
Aghamohammad S, Hafezi A, Rohani M. Probiotics as functional foods: How probiotics can alleviate the symptoms of neurological disabilities. Biomed Pharmacother 2023; 163:114816. [PMID: 37150033 DOI: 10.1016/j.biopha.2023.114816] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/09/2023] Open
Abstract
Neurological disorders are diseases of the central nervous system with progressive loss of nervous tissue. One of the most difficult problems associated with neurological disorders is that there is no clear treatment for these diseases. In this review, the physiopathology of some neurodegenerative diseases, etiological causes, drugs used and their side effects, and finally the role of probiotics in controlling the symptoms of these neurodegenerative diseases are presented. Recently, researchers have focused more on the microbiome and the gut-brain axis, which may play a critical role in maintaining brain health. Probiotics are among the most important bacteria that have positive effects on the balance of homeostasis via influencing the microbiome. Other important functions of probiotics in alleviating symptoms of neurological disorders include anti-inflammatory properties, short-chain fatty acid production, and the production of various neurotransmitters. The effects of probiotics on the control of abnormalities seen in neurological disorders led to probiotics being referred to as "psychobiotic. Given the important role of the gut-brain axis and the imbalance of the gut microbiome in the etiology and symptoms of neurological disorders, probiotics could be considered safe agents that positively affect the balance of the microbiome as complementary treatment options for neurological disorders.
Collapse
Affiliation(s)
| | - Asal Hafezi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Mahdi Rohani
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
35
|
Marsool MDM, Prajjwal P, Reddy YB, Marsool ADM, Lam JR, Nandwana V. Newer modalities in the management of Alzheimer's dementia along with the role of aducanumab and lecanemab in the treatment of its refractory cases. Dis Mon 2023; 69:101547. [PMID: 36931947 DOI: 10.1016/j.disamonth.2023.101547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Alzheimer's disease (AD) is a common neurological condition characterized by a gradual and progressive decline in memory, language, emotion, and cognition. It mainly affects elderly people. Due to the effects of AD, pharmaceutical medications and anticholinesterases have been vigorously promoted and approved by the FDA as a form of AD therapy. However, it was progressively found that these drugs did not address the underlying causes of AD pathogenesis; rather, they focused on the symptoms in order to enhance patients' cognitive outcomes. Consequently, a hunt for superior disease-modifying options is launched. Designing new therapeutic agents requires a thorough understanding of the neuroprotective processes and varied functions carried out by certain genes, and antibodies. In this comprehensive review article, we give an overview of the history of Alzheimer's disease, the significance of the blood-brain barrier in determining the scope of treatment options, as well as the advantages and disadvantages of the current therapeutic treatment options for stem cell therapy, immunotherapy, regenerative therapy, and improved Alzheimer's disease care and diagnosis. We have also included a discussion on the potential role of aducanumab and Lecanemab as a cutting-edge therapy in refractory Alzheimer's disease patients. Lecanemab has been recently approved by the FDA for the treatment of Alzheimer's disease.
Collapse
Affiliation(s)
| | | | | | | | - Justin Riley Lam
- Internal Medicine, Cebu Institute of Medicine, Cebu, Philippines
| | - Varsha Nandwana
- Neurology, Virginia Tech Carilion School of Medicine, Virginia, USA
| |
Collapse
|
36
|
Huang J, Song Z, Wei B, Li Q, Lin P, Li H, Dong K. Immunological evaluation of patients with Alzheimer's disease based on mitogen-stimulated cytokine productions and mitochondrial DNA indicators. BMC Psychiatry 2023; 23:145. [PMID: 36890488 PMCID: PMC9993804 DOI: 10.1186/s12888-023-04634-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/27/2023] [Indexed: 03/10/2023] Open
Abstract
BACKGROUND Based on its objective characteristics, laboratory markers have always been the research direction of clinical diagnosis and assessment of mental disorders including Alzheimer's disease. METHODS MTT Colorimetric Assay, ELISA, and quantitative PCR were used to investigate the responsiveness of peripheral blood mononuclear cells (PBMCs) to mitogen Lipopolysaccharides (LPS) and Phytohemagglutinin (PHA), PBMCs genomic methylation and hydroxymethylation levels, nuclear DNA and mitochondrial DNA damage, respiratory chain enzyme activities, and circulating cell-free mitochondrial DNA levels were detected in 90 patients with Alzheimer's disease. RESULTS In the Alzheimer's disease group, LPS stimulated PBMCs viability, TNF-α secretion, PHA stimulated IL-10 secretion, genomic DNA methylation levels, circulating cell-free mitochondrial DNA copies, citrate synthase activity were reduced compared to the control; while the LPS stimulated PBMCs IL-1α secretion, PHA stimulated IL-1α and IFN-γ secretion, plasma IL-6 and TNF-α, mitochondrial DNA damages were increased compared to the control. CONCLUSIONS The reactivity of peripheral blood mononuclear cells to mitogens, mitochondrial DNA integrity characteristics, and cell-free mitochondrial DNA copies may be used as candidate laboratory biomarkers to help clinical management of Alzheimer's disease.
Collapse
Affiliation(s)
- Jiewen Huang
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Zhen Song
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Beiwen Wei
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingtian Li
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Lin
- Department of Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Hui Li
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Ke Dong
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China.
| |
Collapse
|
37
|
Zhou S, Li Y, Zhang Z, Yuan Y. An insight into the TAM system in Alzheimer's disease. Int Immunopharmacol 2023; 116:109791. [PMID: 36738678 DOI: 10.1016/j.intimp.2023.109791] [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: 12/02/2022] [Revised: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
The TAM receptors may help delay the progression of Alzheimer's disease (AD). AD is the most common neurodegenerative disease associated with human aging. The TAM receptors, derived from the first letter of its three constituents -Tyro3, Axl, and Mertk, are associated with immune responses, cellular differentiation and migration, and clearance of apoptotic cells and debris, with the two canonical ligands, Growth Arrest Specific 6 (Gas6) and ProS1. Several kinds of research have indicated the participation of the TAM system in AD pathology. Also, the TAMs regulate multiple features of microglia, the significant sensors of disorder in the central nervous system (CNS). In this review, we describe the biology of the TAM receptors and ligands in the CNS. Then, we discuss the relationship between the TAM system and AD, specially focusing on its functional expression in the microglia. Finally, we also summarize some agents that could interfere with the TAM signaling pathways and discuss potential difficulties and strategies for drug development.
Collapse
Affiliation(s)
- Shiqi Zhou
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Yanyan Li
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Zhao Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Yuhe Yuan
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| |
Collapse
|
38
|
Qiu Z, Bai X, Han X, Wang P, Wang X, Lv Y, An Y. Clinical and biological significance of RNA N6-methyladenosine regulators in Alzheimer disease. Medicine (Baltimore) 2023; 102:e32945. [PMID: 36800593 PMCID: PMC9936051 DOI: 10.1097/md.0000000000032945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
RNA N6-methyladenosine (m6A) regulators are essential for a variety of biological functions, such as early development, viral infections, and cancer. However, their roles in Alzheimer disease (AD) are still not very clear. Here, 16 significant m6A regulators were identified using difference analysis between AD patients and non-demented controls based on the GSE132903 dataset from the Gene Expression Omnibus database. Using these 16 m6A regulators, a nomogram model was established to predict the prevalence of AD. We found that patients could obtain a good clinical benefit based on this model. In addition, we revealed 2 distinct m6A patterns and 2 distinct m6A gene patterns in AD and demonstrated their prognostic and risk assessment significance. This present work comprehensively evaluated the functions of m6A regulators in the diagnosis and subtype classification of AD. These results suggested they have potential prognostic and risk assessment significance in AD.
Collapse
Affiliation(s)
- Zhiqiang Qiu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Xuanyang Bai
- School of Public Health, China Medical University, Shenyang, Liaoning Province, China
| | - Xinye Han
- Department of Research and Development, Beijing Yihua Biotechnology Co., Ltd, Beijing, China
| | - Peishen Wang
- Department of Research and Development, Beijing Yihua Biotechnology Co., Ltd, Beijing, China
| | - Xiang Wang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yuxia Lv
- Medical Supply Center of Chinese PLA General Hospital, Beijing, China
- * Correspondence: Yuxia Lv, Medical Supply Center of Chinese PLA General Hospital, Beijing 100093, China (e-mail: )
| | - Yihua An
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
39
|
He CY, Tian DY, Chen SH, Jin WS, Cheng Y, Xin JY, Li WW, Zeng GH, Tan CR, Jian JM, Fan DY, Ren JR, Liu YH, Wang YJ, Zeng F. Elevated Levels of Naturally-Occurring Autoantibodies Against the Extracellular Domain of p75NTR Aggravate the Pathology of Alzheimer's Disease. Neurosci Bull 2023; 39:261-272. [PMID: 35974288 PMCID: PMC9905456 DOI: 10.1007/s12264-022-00936-4] [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: 03/01/2022] [Accepted: 05/24/2022] [Indexed: 10/15/2022] Open
Abstract
The extracellular domain (p75ECD) of p75 neurotrophin receptor (p75NTR) antagonizes Aβ neurotoxicity and promotes Aβ clearance in Alzheimer's disease (AD). The impaired shedding of p75ECD is a key pathological process in AD, but its regulatory mechanism is largely unknown. This study was designed to investigate the presence and alterations of naturally-occurring autoantibodies against p75ECD (p75ECD-NAbs) in AD patients and their effects on AD pathology. We found that the cerebrospinal fluid (CSF) level of p75ECD-NAbs was increased in AD, and negatively associated with the CSF levels of p75ECD. Transgenic AD mice actively immunized with p75ECD showed a lower level of p75ECD and more severe AD pathology in the brain, as well as worse cognitive functions than the control groups, which were immunized with Re-p75ECD (the reverse sequence of p75ECD) and phosphate-buffered saline, respectively. These findings demonstrate the impact of p75ECD-NAbs on p75NTR/p75ECD imbalance, providing a novel insight into the role of autoimmunity and p75NTR in AD.
Collapse
Affiliation(s)
- Chen-Yang He
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
- Department of Neurology, The General Hospital of Western Theater Command, Chengdu, 610000, China
| | - Ding-Yuan Tian
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
- Department of Cardiology, Southwest Hospital, Third Military Medical University, Chongqing, 400042, China
| | - Si-Han Chen
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
- Department of Neurology, Nanchong Central Hospital, The Second Clinical Medical School, North Sichuan Medical College, Nanchong, 637000, China
| | - Wang-Sheng Jin
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
- Chongqing Key Laboratory of Ageing and Brain Diseases, Chongqing, 400042, China
| | - Yuan Cheng
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | - Jia-Yan Xin
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, 637000, China
| | - Wei-Wei Li
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
- Department of Neurology, The General Hospital of Western Theater Command, Chengdu, 610000, China
| | - Gui-Hua Zeng
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
- Chongqing Key Laboratory of Ageing and Brain Diseases, Chongqing, 400042, China
| | - Cheng-Rong Tan
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
- Chongqing Key Laboratory of Ageing and Brain Diseases, Chongqing, 400042, China
| | - Jie-Ming Jian
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | - Dong-Yu Fan
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
- Shigatse Branch, Xinqiao Hospital, Third Military Medical University, Shigatse, 857000, China
| | - Jun-Rong Ren
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | - Yu-Hui Liu
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
- Chongqing Key Laboratory of Ageing and Brain Diseases, Chongqing, 400042, China
| | - Yan-Jiang Wang
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China.
- The Institute of Brain and Intelligence, Third Military Medical University, Chongqing, 400042, China.
- Chongqing Key Laboratory of Ageing and Brain Diseases, Chongqing, 400042, China.
- State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Third Military Medical University, Chongqing, 400042, China.
| | - Fan Zeng
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China.
- Chongqing Key Laboratory of Ageing and Brain Diseases, Chongqing, 400042, China.
| |
Collapse
|
40
|
Chen HY, Zhao Y, Xie YZ. Immunosenescence of brain accelerates Alzheimer's disease progression. Rev Neurosci 2023; 34:85-101. [PMID: 35791032 DOI: 10.1515/revneuro-2022-0021] [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: 02/25/2022] [Accepted: 06/04/2022] [Indexed: 01/07/2023]
Abstract
Most of Alzheimer's disease (AD) cases are sporadic and occur after age 65. With prolonged life expectancy and general population aging, AD is becoming a significant public health concern. The immune system supports brain development, plasticity, and homeostasis, yet it is particularly vulnerable to aging-related changes. Aging of the immune system, called immunosenescence, is the multifaceted remodeling of the immune system during aging. Immunosenescence is a contributing factor to various age-related diseases, including AD. Age-related changes in brain immune cell phenotype and function, crosstalk between immune cells and neural cells, and neuroinflammation work together to promote neurodegeneration and age-related cognitive impairment. Although numerous studies have confirmed the correlation between systemic immune changes and AD, few studies focus on the immune state of brain microenvironment in aging and AD. This review mainly addresses the changes of brain immune microenvironment in aging and AD. Specifically, we delineate how various aspects of the brain immune microenvironment, including immune gateways, immune cells, and molecules, and the interplay between immune cells and neural cells, accelerate AD pathogenesis during aging. We also propose a theoretical framework of therapeutic strategies selectively targeting the different mechanisms to restore brain immune homeostasis.
Collapse
Affiliation(s)
- Hou-Yu Chen
- Department of Abdominal Surgery, Affiliated Cancer Hospital, Institute of Guangzhou Medical University, Guangdong 510095, China
| | - Yan Zhao
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Institute of Aging and Age-related Disease Research, Central South University, Changsha, Hunan 410011, China
| | - Yong-Zhi Xie
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| |
Collapse
|
41
|
Ma J, Qin T, Xiang J. Disease-gene prediction based on preserving structure network embedding. Front Aging Neurosci 2023; 15:1061892. [PMID: 36896421 PMCID: PMC9990751 DOI: 10.3389/fnagi.2023.1061892] [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: 10/05/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Many diseases, such as Alzheimer's disease (AD) and Parkinson's disease (PD), are caused by abnormalities or mutations of related genes. Many computational methods based on the network relationship between diseases and genes have been proposed to predict potential pathogenic genes. However, how to effectively mine the disease-gene relationship network to predict disease genes better is still an open problem. In this paper, a disease-gene-prediction method based on preserving structure network embedding (PSNE) is introduced. In order to predict pathogenic genes more effectively, a heterogeneous network with multiple types of bio-entities was constructed by integrating disease-gene associations, human protein network, and disease-disease associations. Furthermore, the low-dimension features of nodes extracted from the network were used to reconstruct a new disease-gene heterogeneous network. Compared with other advanced methods, the performance of PSNE has been confirmed more effective in disease-gene prediction. Finally, we applied the PSNE method to predict potential pathogenic genes for age-associated diseases such as AD and PD. We verified the effectiveness of these predicted potential genes by literature verification. Overall, this work provides an effective method for disease-gene prediction, and a series of high-confidence potential pathogenic genes of AD and PD which may be helpful for the experimental discovery of disease genes.
Collapse
Affiliation(s)
- Jinlong Ma
- School of Information Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, China
| | - Tian Qin
- School of Information Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, China
| | - Ju Xiang
- School of Computer and Communication Engineering, Changsha University of Science and Technology, Changsha, China.,Department of Basic Medical Sciences, Changsha Medical University, Changsha, China
| |
Collapse
|
42
|
Tatara Y, Yamazaki H, Katsuoka F, Chiba M, Saigusa D, Kasai S, Nakamura T, Inoue J, Aoki Y, Shoji M, Motoike IN, Tamada Y, Hashizume K, Shoji M, Kinoshita K, Murashita K, Nakaji S, Yamamoto M, Itoh K. Multiomics and artificial intelligence enabled peripheral blood-based prediction of amnestic mild cognitive impairment. Curr Res Transl Med 2023; 71:103367. [PMID: 36446162 DOI: 10.1016/j.retram.2022.103367] [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: 03/28/2022] [Revised: 08/03/2022] [Accepted: 10/20/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND Since dementia is preventable with early interventions, biomarkers that assist in diagnosing early stages of dementia, such as mild cognitive impairment (MCI), are urgently needed. METHODS Multiomics analysis of amnestic MCI (aMCI) peripheral blood (n = 25) was performed covering the transcriptome, microRNA, proteome, and metabolome. Validation analysis for microRNAs was conducted in an independent cohort (n = 12). Artificial intelligence was used to identify the most important features for predicting aMCI. FINDINGS We found that hsa-miR-4455 is the best biomarker in all omics analyses. The diagnostic index taking a ratio of hsa-miR-4455 to hsa-let-7b-3p predicted aMCI patients against healthy subjects with 97% overall accuracy. An integrated review of multiomics data suggested that a subset of T cells and the GCN (general control nonderepressible) pathway are associated with aMCI. INTERPRETATION The multiomics approach has enabled aMCI biomarkers with high specificity and illuminated the accompanying changes in peripheral blood. Future large-scale studies are necessary to validate candidate biomarkers for clinical use.
Collapse
Affiliation(s)
- Yota Tatara
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Hiromi Yamazaki
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Mitsuru Chiba
- Department of Bioscience and Laboratory Medicine, Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki, Aomori 036-8564, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Shuya Kasai
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Tomohiro Nakamura
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Division of Personalized Prevention and Epidemiology, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Jin Inoue
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Yuichi Aoki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Miho Shoji
- Human Metabolome Technologies, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Yoshinori Tamada
- Innovation Center for Health Promotion, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Katsuhito Hashizume
- Human Metabolome Technologies, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Mikio Shoji
- Department of Neurology, Gunma University Hospital, 3-39-15 Showamachi, Maebashi, Gunma 371-8511, Japan; Department of Neurology, Dementia Research Center, Geriatrics Research Institute and Hospital, 3-26-8 Ootomo-machi, Maebashi, Gunma 371-0847 Japan; COI Research Initiatives Organization, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8216, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan; Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Koichi Murashita
- COI Research Initiatives Organization, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8216, Japan
| | - Shigeyuki Nakaji
- Department of Social Medicine, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8216, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan; Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Ken Itoh
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan.
| |
Collapse
|
43
|
Sousa JA, Bernardes C, Bernardo-Castro S, Lino M, Albino I, Ferreira L, Brás J, Guerreiro R, Tábuas-Pereira M, Baldeiras I, Santana I, Sargento-Freitas J. Reconsidering the role of blood-brain barrier in Alzheimer's disease: From delivery to target. Front Aging Neurosci 2023; 15:1102809. [PMID: 36875694 PMCID: PMC9978015 DOI: 10.3389/fnagi.2023.1102809] [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: 11/21/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
The existence of a selective blood-brain barrier (BBB) and neurovascular coupling are two unique central nervous system vasculature features that result in an intimate relationship between neurons, glia, and blood vessels. This leads to a significant pathophysiological overlap between neurodegenerative and cerebrovascular diseases. Alzheimer's disease (AD) is the most prevalent neurodegenerative disease whose pathogenesis is still to be unveiled but has mostly been explored under the light of the amyloid-cascade hypothesis. Either as a trigger, bystander, or consequence of neurodegeneration, vascular dysfunction is an early component of the pathological conundrum of AD. The anatomical and functional substrate of this neurovascular degeneration is the BBB, a dynamic and semi-permeable interface between blood and the central nervous system that has consistently been shown to be defective. Several molecular and genetic changes have been demonstrated to mediate vascular dysfunction and BBB disruption in AD. The isoform ε4 of Apolipoprotein E is at the same time the strongest genetic risk factor for AD and a known promoter of BBB dysfunction. Low-density lipoprotein receptor-related protein 1 (LRP-1), P-glycoprotein, and receptor for advanced glycation end products (RAGE) are examples of BBB transporters implicated in its pathogenesis due to their role in the trafficking of amyloid-β. This disease is currently devoid of strategies that change the natural course of this burdening illness. This unsuccess may partly be explained by our misunderstanding of the disease pathogenesis and our inability to develop drugs that are effectively delivered to the brain. BBB may represent a therapeutic opportunity as a target itself or as a therapeutic vehicle. In this review, we aim to explore the role of BBB in the pathogenesis of AD including the genetic background and detail how it can be targeted in future therapeutic research.
Collapse
Affiliation(s)
- João André Sousa
- Department of Neurology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Catarina Bernardes
- Department of Neurology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Sara Bernardo-Castro
- Department of Neurology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Miguel Lino
- Centre for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Inês Albino
- Centre for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Lino Ferreira
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Centre for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - José Brás
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, United States
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, United States
| | - Miguel Tábuas-Pereira
- Department of Neurology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Inês Baldeiras
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Isabel Santana
- Department of Neurology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - João Sargento-Freitas
- Department of Neurology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Centre for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| |
Collapse
|
44
|
Lai Y, Lin H, Chen M, Lin X, Wu L, Zhao Y, Lin F, Lin C. Integration of bulk RNA sequencing and single-cell analysis reveals a global landscape of DNA damage response in the immune environment of Alzheimer's disease. Front Immunol 2023; 14:1115202. [PMID: 36895559 PMCID: PMC9989175 DOI: 10.3389/fimmu.2023.1115202] [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: 12/03/2022] [Accepted: 02/06/2023] [Indexed: 02/23/2023] Open
Abstract
Background We developed a novel system for quantifying DNA damage response (DDR) to help diagnose and predict the risk of Alzheimer's disease (AD). Methods We thoroughly estimated the DDR patterns in AD patients Using 179 DDR regulators. Single-cell techniques were conducted to validate the DDR levels and intercellular communications in cognitively impaired patients. The consensus clustering algorithm was utilized to group 167 AD patients into diverse subgroups after a WGCNA approach was employed to discover DDR-related lncRNAs. The distinctions between the categories in terms of clinical characteristics, DDR levels, biological behaviors, and immunological characteristics were evaluated. For the purpose of choosing distinctive lncRNAs associated with DDR, four machine learning algorithms, including LASSO, SVM-RFE, RF, and XGBoost, were utilized. A risk model was established based on the characteristic lncRNAs. Results The progression of AD was highly correlated with DDR levels. Single-cell studies confirmed that DDR activity was lower in cognitively impaired patients and was mainly enriched in T cells and B cells. DDR-related lncRNAs were discovered based on gene expression, and two different heterogeneous subtypes (C1 and C2) were identified. DDR C1 belonged to the non-immune phenotype, while DDR C2 was regarded as the immune phenotype. Based on various machine learning techniques, four distinctive lncRNAs associated with DDR, including FBXO30-DT, TBX2-AS1, ADAMTS9-AS2, and MEG3 were discovered. The 4-lncRNA based riskScore demonstrated acceptable efficacy in the diagnosis of AD and offered significant clinical advantages to AD patients. The riskScore ultimately divided AD patients into low- and high-risk categories. In comparison to the low-risk group, high-risk patients showed lower DDR activity, accompanied by higher levels of immune infiltration and immunological score. The prospective medications for the treatment of AD patients with low and high risk also included arachidonyltrifluoromethane and TTNPB, respectively. Conclusions In conclusion, immunological microenvironment and disease progression in AD patients were significantly predicted by DDR-associated genes and lncRNAs. A theoretical underpinning for the individualized treatment of AD patients was provided by the suggested genetic subtypes and risk model based on DDR.
Collapse
Affiliation(s)
- Yongxing Lai
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China.,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Han Lin
- Department of Gastroenterology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Manli Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Xin Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China.,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Lijuan Wu
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China.,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Yinan Zhao
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China.,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Fan Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China.,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Chunjin Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China.,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| |
Collapse
|
45
|
Kushwah S, Maurya NS, Kushwaha S, Scotti L, Chawade A, Mani A. Herbal Therapeutics for Alzheimer's Disease: Ancient Indian Medicine System from the Modern Viewpoint. Curr Neuropharmacol 2023; 21:764-776. [PMID: 36797613 PMCID: PMC10227917 DOI: 10.2174/1570159x21666230216094353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/16/2022] [Accepted: 12/29/2022] [Indexed: 02/18/2023] Open
Abstract
Alzheimer's is a chronic neurodegenerative disease where amyloid-beta (Aβ) plaques and neurofibrillary tangles are formed inside the brain. It is also characterized by progressive memory loss, depression, neuroinflammation, and derangement of other neurotransmitters. Due to its complex etiopathology, current drugs have failed to completely cure the disease. Natural compounds have been investigated as an alternative therapy for their ability to treat Alzheimer's disease (AD). Traditional herbs and formulations which are used in the Indian ayurvedic system are rich sources of antioxidant, anti-amyloidogenic, neuroprotective, and anti-inflammatory compounds. They promote quality of life by improving cognitive memory and rejuvenating brain functioning through neurogenesis. A rich knowledge base of traditional herbal plants (Turmeric, Gingko, Ashwagandha, Shankhpushpi, Giloy, Gotu kola, Garlic, Tulsi, Ginger, and Cinnamon) combined with modern science could suggest new functional leads for Alzheimer's drug discovery. In this article Ayurveda, the ancient Indian herbal medicine system based on multiple clinical and experimental, evidence have been reviewed for treating AD and improving brain functioning. This article presents a modern perspective on the herbs available in the ancient Indian medicine system as well as their possible mechanisms of action for AD treatment. The main objective of this research is to provide a systematic review of herbal drugs that are easily accessible and effective for the treatment of AD.
Collapse
Affiliation(s)
- Shikha Kushwah
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, 211004, India
| | - Neha Shree Maurya
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, 211004, India
| | | | - Luciana Scotti
- Federal University of Paraiba, Cidade Universittária, Joao Pessoa, BR 58102100, Brazil
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, 211004, India
| |
Collapse
|
46
|
Lai Y, Lin P, Lin F, Chen M, Lin C, Lin X, Wu L, Zheng M, Chen J. Identification of immune microenvironment subtypes and signature genes for Alzheimer's disease diagnosis and risk prediction based on explainable machine learning. Front Immunol 2022; 13:1046410. [PMID: 36569892 PMCID: PMC9773397 DOI: 10.3389/fimmu.2022.1046410] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Background Using interpretable machine learning, we sought to define the immune microenvironment subtypes and distinctive genes in AD. Methods ssGSEA, LASSO regression, and WGCNA algorithms were used to evaluate immune state in AD patients. To predict the fate of AD and identify distinctive genes, six machine learning algorithms were developed. The output of machine learning models was interpreted using the SHAP and LIME algorithms. For external validation, four separate GEO databases were used. We estimated the subgroups of the immunological microenvironment using unsupervised clustering. Further research was done on the variations in immunological microenvironment, enhanced functions and pathways, and therapeutic medicines between these subtypes. Finally, the expression of characteristic genes was verified using the AlzData and pan-cancer databases and RT-PCR analysis. Results It was determined that AD is connected to changes in the immunological microenvironment. WGCNA revealed 31 potential immune genes, of which the greenyellow and blue modules were shown to be most associated with infiltrated immune cells. In the testing set, the XGBoost algorithm had the best performance with an AUC of 0.86 and a P-R value of 0.83. Following the screening of the testing set by machine learning algorithms and the verification of independent datasets, five genes (CXCR4, PPP3R1, HSP90AB1, CXCL10, and S100A12) that were closely associated with AD pathological biomarkers and allowed for the accurate prediction of AD progression were found to be immune microenvironment-related genes. The feature gene-based nomogram may provide clinical advantages to patients. Two immune microenvironment subgroups for AD patients were identified, subtype2 was linked to a metabolic phenotype, subtype1 belonged to the immune-active kind. MK-866 and arachidonyltrifluoromethane were identified as the top treatment agents for subtypes 1 and 2, respectively. These five distinguishing genes were found to be intimately linked to the development of the disease, according to the Alzdata database, pan-cancer research, and RT-PCR analysis. Conclusion The hub genes associated with the immune microenvironment that are most strongly associated with the progression of pathology in AD are CXCR4, PPP3R1, HSP90AB1, CXCL10, and S100A12. The hypothesized molecular subgroups might offer novel perceptions for individualized AD treatment.
Collapse
Affiliation(s)
- Yongxing Lai
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Peiqiang Lin
- Department of Neurology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Fan Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Manli Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Chunjin Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Xing Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Lijuan Wu
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Mouwei Zheng
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China,*Correspondence: Jianhao Chen, ; Mouwei Zheng,
| | - Jianhao Chen
- Department of Rehabilitation Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,*Correspondence: Jianhao Chen, ; Mouwei Zheng,
| |
Collapse
|
47
|
Cai M, Vesely A, Chen X, Li L, Goeman JJ. NetTDP: permutation-based true discovery proportions for differential co-expression network analysis. Brief Bioinform 2022; 23:6754043. [PMID: 36209415 DOI: 10.1093/bib/bbac417] [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: 05/17/2022] [Revised: 08/23/2022] [Accepted: 08/28/2022] [Indexed: 12/14/2022] Open
Abstract
Existing methods for differential network analysis could only infer whether two networks of interest have differences between two groups of samples, but could not quantify and localize network differences. In this work, a novel method, permutation-based Network True Discovery Proportions (NetTDP), is proposed to quantify the number of edges (correlations) or nodes (genes) for which the co-expression networks are different. In the NetTDP method, we propose an edge-level statistic and a node-level statistic, and detect true discoveries of edges and nodes in the sense of differential co-expression network, respectively, by the permutation-based sumSome method. Furthermore, the NetTDP method could further localize the differences by inferring the TDPs for edge or gene subsets of interest, which can be selected post hoc. Our NetTDP method allows inference on data-driven modules or biology-driven gene sets, and remains valid even when these sub-networks are optimized using the same data. Experimental results on both simulation data sets and five real data sets show the effectiveness of the proposed method in inferring the quantification and localization of differential co-expression networks. The R code is available at https://github.com/LiminLi-xjtu/NetTDP.
Collapse
Affiliation(s)
- Menglan Cai
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xianning West, 710049, Shaanxi, China
| | - Anna Vesely
- Department of Statistical Sciences, University of Padova, Italy
| | - Xu Chen
- Department of Biomedical Data Sciences, Leiden University Medical Center, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Limin Li
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xianning West, 710049, Shaanxi, China
| | - Jelle J Goeman
- Department of Biomedical Data Sciences, Leiden University Medical Center, Postbus 9600, 2300 RC Leiden, The Netherlands
| |
Collapse
|
48
|
Immunosenescence and Aging: Neuroinflammation Is a Prominent Feature of Alzheimer's Disease and Is a Likely Contributor to Neurodegenerative Disease Pathogenesis. J Pers Med 2022; 12:jpm12111817. [PMID: 36579548 PMCID: PMC9698256 DOI: 10.3390/jpm12111817] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022] Open
Abstract
Alzheimer's disease (AD) is a chronic multifactorial and complex neuro-degenerative disorder characterized by memory impairment and the loss of cognitive ability, which is a problem affecting the elderly. The pathological intracellular accumulation of abnormally phosphorylated Tau proteins, forming neurofibrillary tangles, and extracellular amyloid-beta (Aβ) deposition, forming senile plaques, as well as neural disconnection, neural death and synaptic dysfunction in the brain, are hallmark pathologies that characterize AD. The prevalence of the disease continues to increase globally due to the increase in longevity, quality of life, and medical treatment for chronic diseases that decreases the mortality and enhance the survival of elderly. Medical awareness and the accurate diagnosis of the disease also contribute to the high prevalence observed globally. Unfortunately, no definitive treatment exists that can be used to modify the course of AD, and no available treatment is capable of mitigating the cognitive decline or reversing the pathology of the disease as of yet. A plethora of hypotheses, ranging from the cholinergic theory and dominant Aβ cascade hypothesis to the abnormally excessive phosphorylated Tau protein hypothesis, have been reported. Various explanations for the pathogenesis of AD, such as the abnormal excitation of the glutamate system and mitochondrial dysfunction, have also been suggested. Despite the continuous efforts to deliver significant benefits and an effective treatment for this distressing, globally attested aging illness, multipronged approaches and strategies for ameliorating the disease course based on knowledge of the underpinnings of the pathogenesis of AD are urgently needed. Immunosenescence is an immune deficit process that appears with age (inflammaging process) and encompasses the remodeling of the lymphoid organs, leading to alterations in the immune function and neuroinflammation during advanced aging, which is closely linked to the outgrowth of infections, autoimmune diseases, and malignant cancers. It is well known that long-standing inflammation negatively influences the brain over the course of a lifetime due to the senescence of the immune system. Herein, we aim to trace the role of the immune system in the pathogenesis of AD. Thus, we explore alternative avenues, such as neuroimmune involvement in the pathogenesis of AD. We determine the initial triggers of neuroinflammation, which is an early episode in the pre-symptomatic stages of AD and contributes to the advancement of the disease, and the underlying key mechanisms of brain damage that might aid in the development of therapeutic strategies that can be used to combat this devastating disease. In addition, we aim to outline the ways in which different aspects of the immune system, both in the brain and peripherally, behave and thus to contribute to AD.
Collapse
|
49
|
Udagawa C, Nakano MH, Yoshida T, Ohe Y, Kato K, Mushiroda T, Zembutsu H. Association between genetic variants and the risk of nivolumab-induced immune-related adverse events. Pharmacogenomics 2022; 23:887-901. [PMID: 36268685 DOI: 10.2217/pgs-2022-0113] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We sought to identify the variants that could predict the risk of nivolumab-induced immune-related adverse events (irAEs) in patients with cancer. Patients & methods: We enrolled 622 Japanese patients and carried out a genome-wide association study. The associations for 507 single nucleotide polymorphisms (SNPs) showing p < 0.001 were further investigated using an independent cohort. Results: In the combined analysis, possible associations were found for a total of 90 SNPs. Although no SNPs were identified to be significantly associated with nivolumab-induced irAEs, the SNP most strongly associated with nivolumab-induced irAEs was rs469490. Conclusion: This study is an important hypothesis-generating study to guide future studies in larger and/or other ethnic cohorts.
Collapse
Affiliation(s)
- Chihiro Udagawa
- Department of Genetics Medicine & services, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Mari Hara Nakano
- Division of Breast & Endocrine Surgery, Department of Surgery, St. Marianna University School of Medicine, Kawasaki, 216-8511, Japan
| | - Teruhiko Yoshida
- Department of Genetics Medicine & services, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Yuichiro Ohe
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Ken Kato
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Science, Yokohama, 230-0045, Japan
| | - Hitoshi Zembutsu
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| |
Collapse
|
50
|
HSPA1A, HSPA2, and HSPA8 Are Potential Molecular Biomarkers for Prognosis among HSP70 Family in Alzheimer’s Disease. DISEASE MARKERS 2022; 2022:9480398. [PMID: 36246562 PMCID: PMC9553556 DOI: 10.1155/2022/9480398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/24/2022] [Accepted: 09/07/2022] [Indexed: 12/01/2022]
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease, which leads to impairment of cognition and memory. The heat shock protein 70 (HSP70) family plays an important role in the pathogenesis of AD. It is known to regulate protein misfolding in a variety of diseases, including inhibition of Aβ aggregation and NFT formation in AD. As yet, the diagnostic molecular markers of AD remain unclear. Herein, we sought to investigate molecular markers of HSP70 family that can affect diagnosis and treatment in AD through computational analysis. In this study, the intersection between HSP70 family members and immune molecules was taken to screen immune-related HSP70 family genes. Based on the datasets from the NCBI-Gene Expression Omnibus (GEO) database, we found that the expression levels of HSPA1A and HSPA2 were significantly increased in AD samples, while HSPA8 significantly decreased. Surprisingly, the combination of the 3 hub genes had a good diagnosis of AD via receiver operating characteristic curve (ROC). Moreover, the clinical value of the 3 hub genes was further assessed by the Spearman correlation analysis with AD-related genes, β-secretase activity, and γ-secretase activity. In terms of immune cell infiltration, we showed that the distribution of seven immune cell types (macrophages M2, neutrophils, T cells CD4 memory activated, macrophages M0, NK cells activated, plasma cells, and T cells follicular helper) was associated with the occurrence of AD by CIBERSORT. Furthermore, our data suggested that EP300, MYC, TP53, JUN, CREBBP, and ESR1 might be key transcription factors (TFs) for the 3 hub genes. In general, these findings suggest that HSPA1A, HSPA2, and HSPA8 are potential molecular biomarkers for prognosis among HSP70 family in AD, and it provides a new perspective on diagnostic and therapeutic targets for AD.
Collapse
|