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Wyatt-Johnson SK, Kersey HN, Brutkiewicz RR. Enrichment of liver MAIT cells in a mouse model of Alzheimer's disease. J Neuroimmunol 2024; 390:578332. [PMID: 38537322 DOI: 10.1016/j.jneuroim.2024.578332] [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: 01/30/2024] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 05/13/2024]
Abstract
Emerging evidence has supported a role for the immune system and liver in Alzheimer's disease (AD). However, our understanding of how hepatic immune cells are altered in AD is limited. We previously found that brain mucosal-associated invariant T (MAIT) cell numbers are increased in AD. Furthermore, loss of MAIT cells and their antigen-presenting molecule, MR1, reduced amyloid-β accumulation in the brain. MAIT cells are also significantly present in the liver. Therefore, we sought to analyze MAIT and other immune cells in the AD liver. Increased frequency of activated MAIT cells (but not conventional T cells) were found in 8-month-old 5XFAD mouse livers. Therefore, these data raise the possibility that there is a role for peripheral MAIT cells in AD pathology.
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Affiliation(s)
- Season K Wyatt-Johnson
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, United States of America; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, United States of America.
| | - Holly N Kersey
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, United States of America
| | - Randy R Brutkiewicz
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, United States of America; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, United States of America.
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2
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Krix S, Wilczynski E, Falgàs N, Sánchez-Valle R, Yoles E, Nevo U, Baruch K, Fröhlich H. Towards early diagnosis of Alzheimer's disease: advances in immune-related blood biomarkers and computational approaches. Front Immunol 2024; 15:1343900. [PMID: 38720902 PMCID: PMC11078023 DOI: 10.3389/fimmu.2024.1343900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Alzheimer's disease has an increasing prevalence in the population world-wide, yet current diagnostic methods based on recommended biomarkers are only available in specialized clinics. Due to these circumstances, Alzheimer's disease is usually diagnosed late, which contrasts with the currently available treatment options that are only effective for patients at an early stage. Blood-based biomarkers could fill in the gap of easily accessible and low-cost methods for early diagnosis of the disease. In particular, immune-based blood-biomarkers might be a promising option, given the recently discovered cross-talk of immune cells of the central nervous system with those in the peripheral immune system. Here, we give a background on recent advances in research on brain-immune system cross-talk in Alzheimer's disease and review machine learning approaches, which can combine multiple biomarkers with further information (e.g. age, sex, APOE genotype) into predictive models supporting an earlier diagnosis. In addition, mechanistic modeling approaches, such as agent-based modeling open the possibility to model and analyze cell dynamics over time. This review aims to provide an overview of the current state of immune-system related blood-based biomarkers and their potential for the early diagnosis of Alzheimer's disease.
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Affiliation(s)
- Sophia Krix
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
- Bonn-Aachen International Center for Information Technology (b-it), University of Bonn, Bonn, Germany
| | - Ella Wilczynski
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Neus Falgàs
- Alzheimer’s Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FCRB-IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Raquel Sánchez-Valle
- Alzheimer’s Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FCRB-IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Eti Yoles
- ImmunoBrain Checkpoint Ltd., Rechovot, Israel
| | - Uri Nevo
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Kuti Baruch
- ImmunoBrain Checkpoint Ltd., Rechovot, Israel
| | - Holger Fröhlich
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
- Bonn-Aachen International Center for Information Technology (b-it), University of Bonn, Bonn, Germany
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3
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Yang B, Hu S, Jiang Y, Xu L, Shu S, Zhang H. Advancements in Single-Cell RNA Sequencing Research for Neurological Diseases. Mol Neurobiol 2024:10.1007/s12035-024-04126-3. [PMID: 38564138 DOI: 10.1007/s12035-024-04126-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Neurological diseases are a major cause of the global burden of disease. Although the mechanisms of the occurrence and development of neurological diseases are not fully clear, most of them are associated with cells mediating neuroinflammation. Yet medications and other therapeutic options to improve treatment are still very limited. Single-cell RNA sequencing (scRNA-seq), as a delightfully potent breakthrough technology, not only identifies various cell types and response states but also uncovers cell-specific gene expression changes, gene regulatory networks, intercellular communication, and cellular movement trajectories, among others, in different cell types. In this review, we describe the technology of scRNA-seq in detail and discuss and summarize the application of scRNA-seq in exploring neurological diseases, elaborating the corresponding specific mechanisms of the diseases as well as providing a reliable basis for new therapeutic approaches. Finally, we affirm that scRNA-seq promotes the development of the neuroscience field and enables us to have a deeper cellular understanding of neurological diseases in the future, which provides strong support for the treatment of neurological diseases and the improvement of patients' prognosis.
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Affiliation(s)
- Bingjie Yang
- Department of Neurology, The Fourth Clinical School of Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Shuqi Hu
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Neurology, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang, China
| | - Yiru Jiang
- Department of Neurology, The Fourth Clinical School of Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Lei Xu
- Department of Neurology, Zhejiang Rongjun Hospital, Jiaxing, Zhejiang, China
| | - Song Shu
- Department of Neurology, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang, China
| | - Hao Zhang
- Department of Neurology, The Fourth Clinical School of Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
- Department of Neurology, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang, China.
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Marmarelis MG, Littman R, Battaglin F, Niedzwiecki D, Venook A, Ambite JL, Galstyan A, Lenz HJ, Ver Steeg G. q-Diffusion leverages the full dimensionality of gene coexpression in single-cell transcriptomics. Commun Biol 2024; 7:400. [PMID: 38565955 DOI: 10.1038/s42003-024-06104-w] [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: 06/23/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
Unlocking the full dimensionality of single-cell RNA sequencing data (scRNAseq) is the next frontier to a richer, fuller understanding of cell biology. We introduce q-diffusion, a framework for capturing the coexpression structure of an entire library of genes, improving on state-of-the-art analysis tools. The method is demonstrated via three case studies. In the first, q-diffusion helps gain statistical significance for differential effects on patient outcomes when analyzing the CALGB/SWOG 80405 randomized phase III clinical trial, suggesting precision guidance for the treatment of metastatic colorectal cancer. Secondly, q-diffusion is benchmarked against existing scRNAseq classification methods using an in vitro PBMC dataset, in which the proposed method discriminates IFN-γ stimulation more accurately. The same case study demonstrates improvements in unsupervised cell clustering with the recent Tabula Sapiens human atlas. Finally, a local distributional segmentation approach for spatial scRNAseq, driven by q-diffusion, yields interpretable structures of human cortical tissue.
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Affiliation(s)
- Myrl G Marmarelis
- Information Sciences Institute, University of Southern California, 4676 Admiralty Way, Marina del Rey, CA, 90292, USA.
| | - Russell Littman
- University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Francesca Battaglin
- Keck School of Medicine, University of Southern California, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | | | - Alan Venook
- University of California San Francisco, San Francisco, CA, 94143, USA
| | - Jose-Luis Ambite
- Information Sciences Institute, University of Southern California, 4676 Admiralty Way, Marina del Rey, CA, 90292, USA
| | - Aram Galstyan
- Information Sciences Institute, University of Southern California, 4676 Admiralty Way, Marina del Rey, CA, 90292, USA
| | - Heinz-Josef Lenz
- Keck School of Medicine, University of Southern California, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Greg Ver Steeg
- Information Sciences Institute, University of Southern California, 4676 Admiralty Way, Marina del Rey, CA, 90292, USA
- University of California Riverside, Riverside, CA, 92521, USA
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Li J, Zhang Y, You Y, Huang Z, Wu L, Liang C, Weng B, Pan L, Huang Y, Huang Y, Yang M, Lu M, Li R, Yan X, Liu Q, Deng S. Unraveling the mechanisms of NK cell dysfunction in aging and Alzheimer's disease: insights from GWAS and single-cell transcriptomics. Front Immunol 2024; 15:1360687. [PMID: 38464521 PMCID: PMC10920339 DOI: 10.3389/fimmu.2024.1360687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/06/2024] [Indexed: 03/12/2024] Open
Abstract
Background Aging is an important factor in the development of Alzheimer's disease (AD). The senescent cells can be recognized and removed by NK cells. However, NK cell function is gradually inactivated with age. Therefore, this study used senescence as an entry point to investigate how NK cells affect AD. Methods The study validated the correlation between cognition and aging through a prospective cohort of the National Health and Nutrition Examination Survey database. A cellular trajectory analysis of the aging population was performed using single-cell nuclear transcriptome sequencing data from patients with AD and different ages. The genome-wide association study (GWAS) cohort of AD patients was used as the outcome event, and the expression quantitative trait locus was used as an instrumental variable. Causal associations between genes and AD were analyzed by bidirectional Mendelian randomization (MR) and co-localization. Finally, clinical cohorts were constructed to validate the expression of key genes. Results A correlation between cognition and aging was demonstrated using 2,171 older adults over 60 years of age. Gene regulation analysis revealed that most of the highly active transcription factors were concentrated in the NK cell subpopulation of AD. NK cell trajectories were constructed for different age populations. MR and co-localization analyses revealed that CHD6 may be one of the factors influencing AD. Conclusion We explored different levels of AD and aging from population cohorts, single-cell data, and GWAS cohorts and found that there may be some correlations of NK cells between aging and AD. It also provides some basis for potential causation.
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Affiliation(s)
- Jinwei Li
- Department of Neurosurgery, Liuzhou Workers Hospital, Liuzhou, China
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yang Zhang
- Department of Vascular Surgery, Fuwai Yunnan Cardiovascular Hospital, Affiliated Cardiovascular Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yanwei You
- Division of Sports Science and Physical Education, Tsinghua University, Beijing, China
| | - Zhiwei Huang
- Department of Neurosurgery, Liuzhou Workers Hospital, Liuzhou, China
| | - Liya Wu
- Department of Neurology, Liuzhou Workers Hospital, Liuzhou, China
| | - Cong Liang
- Department of Pharmacy, Liuzhou Workers Hospital, Liuzhou, China
| | - Baohui Weng
- Department of Neurology, Liuzhou Workers Hospital, Liuzhou, China
| | - Liya Pan
- Department of Neurology, Liuzhou Workers Hospital, Liuzhou, China
| | - Yan Huang
- Department of Neurology, Liuzhou Workers Hospital, Liuzhou, China
| | - Yushen Huang
- Department of Pharmacy, Liuzhou Workers Hospital, Liuzhou, China
| | - Mengqi Yang
- Department of Neurology, Liuzhou Workers Hospital, Liuzhou, China
| | - Mengting Lu
- Department of Dermatology, Liuzhou Workers Hospital, Liuzhou, China
| | - Rui Li
- Department of Medical Imaging, Liuzhou Workers Hospital, Liuzhou, China
| | - Xianlei Yan
- Department of Neurosurgery, Liuzhou Workers Hospital, Liuzhou, China
| | - Quan Liu
- Department of Neurosurgery, Liuzhou Workers Hospital, Liuzhou, China
| | - Shan Deng
- Department of Neurology, Liuzhou Workers Hospital, Liuzhou, China
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Tan S, Pan S, Wei L, Chen W, Pan B, Kong G, Chen J, Xie Y. Association of peripheral B cells and delirium: combined single-cell sequencing and Mendelian randomization analysis. Front Neurol 2024; 15:1343726. [PMID: 38379709 PMCID: PMC10876872 DOI: 10.3389/fneur.2024.1343726] [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: 11/24/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
Background Delirium seriously affects the prognosis of patients and greatly reduces the ability to work and live. Peripheral inflammatory events may contribute to the development of delirium, the mechanism of which is still unclear. There is a lack of effective diagnostic and treatments for delirium in clinical practice. The study aims to investigate alterations in peripheral immune cell subsets under inflammatory stress and to explore causal associations with delirium. Methods Single-cell transcriptional sequencing data of human peripheral blood mononuclear cells (PBMC) before and after lipopolysaccharide (LPS) intervention were processed by the Seurat package in R software. PBMC subsets and cellular markers were defined after downscaling and clustering by the Harmony algorithm to identify characteristic subsets in the context of inflammatory stress. Subsequently, a two-sample Mendelian randomization (MR) study was used to explore the causal associations of these inflammation-related PBMC subsets and their molecular phenotypes with delirium. Based on publicly available genetic data, the study incorporated 70 PBMC-associated immune traits, including 8 types of circulating immune cells, 33 B cell subsets and molecular phenotypes, 13 T cell subsets, and 16 B cell-associated cytokines. The results were also validated for robustness, heterogeneity, and horizontal pleiotropy. Results Under LPS-induced inflammatory stress, B cells, T cells, monocytes, and dendritic cells in human PBMC showed significant activation and quantitative changes. Of these, only lymphocyte and B cell counts were causally associated with delirium risk. This risk link is also seen in the TNF pathway. Further studies of B cells and their subsets revealed that this association may be related to unswitched memory B cells and CD27 expressed on memory B cells. Annotation of the screened SNPs revealed significant polymorphisms in CD27 and CD40 annotated by rs25680 and rs9883798, respectively. The functions of the key annotated genes may be related to the regulation of immune responses, cell differentiation, proliferation, and intercellular interactions. Conclusion The present study revealed the potential possibility that B cell, memory B cell subset, and TNF-related molecules may be involved in the development of delirium due to peripheral inflammation, which can provide clues for further investigation of delirium prevention and treatment strategies.
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Affiliation(s)
- Siyou Tan
- Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Sining Pan
- Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Lai Wei
- Department of Anesthesiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Wenyan Chen
- Department of Anesthesiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Bingbing Pan
- Department of Anesthesiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Gaoyin Kong
- Department of Anesthesiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Jing Chen
- Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yubo Xie
- Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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He Z, Chen Q, Wang K, Lin J, Peng Y, Zhang J, Yan X, Jie Y. Single-cell transcriptomics analysis of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. Eur J Neurosci 2024; 59:333-357. [PMID: 38221677 DOI: 10.1111/ejn.16242] [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: 05/17/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 01/16/2024]
Abstract
Single-cell transcriptomics analysis is an advanced technology that can describe the intracellular transcriptome in complex tissues. It profiles and analyses datasets by single-cell RNA sequencing. Neurodegenerative diseases are identified by the abnormal apoptosis of neurons in the brain with few or no effective therapy strategies at present, which has been a growing healthcare concern and brought a great burden to society. The transcriptome of individual cells provides deep insights into previously unforeseen cellular heterogeneity and gene expression differences in neurodegenerative disorders. It detects multiple cell subsets and functional changes during pathological progression, which deepens the understanding of the molecular underpinnings and cellular basis of neurodegenerative diseases. Furthermore, the transcriptome analysis of immune cells shows the regulation of immune response. Different subtypes of immune cells and their interaction are found to contribute to disease progression. This finding enables the discovery of novel targets and biomarkers for early diagnosis. In this review, we emphasize the principles of the technology, and its recent progress in the study of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. The application of single-cell transcriptomics analysis in neurodegenerative disorders would help explore the pathogenesis of these diseases and develop novel therapeutic methods.
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Affiliation(s)
- Ziping He
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Qianqian Chen
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Kaiyue Wang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiang Lin
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Yilin Peng
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Jinlong Zhang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
| | - Xisheng Yan
- Department of Cardiovascular Medicine, Wuhan Third Hospital & Tongren Hospital of Wuhan University, Wuhan, China
| | - Yan Jie
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
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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 2024:10.1007/s10072-024-07324-y. [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] [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.
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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
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Wei Z, Chenjun W, Feiyang X, Mingfeng J, Yixuan Z, Qi L, Zhuoxing S, Qi D. scHybridBERT: integrating gene regulation and cell graph for spatiotemporal dynamics in single-cell clustering. Brief Bioinform 2024; 25:bbae018. [PMID: 38517692 PMCID: PMC10959234 DOI: 10.1093/bib/bbae018] [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: 08/14/2023] [Revised: 12/19/2023] [Accepted: 01/09/2024] [Indexed: 03/24/2024] Open
Abstract
Graph learning models have received increasing attention in the computational analysis of single-cell RNA sequencing (scRNA-seq) data. Compared with conventional deep neural networks, graph neural networks and language models have exhibited superior performance by extracting graph-structured data from raw gene count matrices. Established deep neural network-based clustering approaches generally focus on temporal expression patterns while ignoring inherent interactions at gene-level as well as cell-level, which could be regarded as spatial dynamics in single-cell data. Both gene-gene and cell-cell interactions are able to boost the performance of cell type detection, under the framework of multi-view modeling. In this study, spatiotemporal embedding and cell graphs are extracted to capture spatial dynamics at the molecular level. In order to enhance the accuracy of cell type detection, this study proposes the scHybridBERT architecture to conduct multi-view modeling of scRNA-seq data using extracted spatiotemporal patterns. In this scHybridBERT method, graph learning models are employed to deal with cell graphs and the Performer model employs spatiotemporal embeddings. Experimental outcomes about benchmark scRNA-seq datasets indicate that the proposed scHybridBERT method is able to enhance the accuracy of single-cell clustering tasks by integrating spatiotemporal embeddings and cell graphs.
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Affiliation(s)
- Zhang Wei
- Zhejiang Sci-Tech University, 310028, Hangzhou, China
| | - Wu Chenjun
- Zhejiang Sci-Tech University, 310028, Hangzhou, China
| | - Xing Feiyang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | | | - Zhang Yixuan
- Zhejiang Sci-Tech University, 310028, Hangzhou, China
| | - Liu Qi
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Shi Zhuoxing
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China
| | - Dai Qi
- Zhejiang Sci-Tech University, 310028, Hangzhou, China
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Hernández-Contreras KA, Martínez-Díaz JA, Hernández-Aguilar ME, Herrera-Covarrubias D, Rojas-Durán F, Chi-Castañeda LD, García-Hernández LI, Aranda-Abreu GE. Alterations of mRNAs and Non-coding RNAs Associated with Neuroinflammation in Alzheimer's Disease. Mol Neurobiol 2024:10.1007/s12035-023-03908-5. [PMID: 38236345 DOI: 10.1007/s12035-023-03908-5] [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: 04/12/2023] [Accepted: 12/27/2023] [Indexed: 01/19/2024]
Abstract
Alzheimer's disease is a neurodegenerative pathology whose pathognomonic hallmarks are increased generation of β-amyloid (Aβ) peptide, production of hyperphosphorylated (pTau), and neuroinflammation. The last is an alteration closely related to the progression of AD and although it is present in multiple neurodegenerative diseases, the pathophysiological events that characterize neuroinflammatory processes vary depending on the disease. In this article, we focus on mRNA and non-coding RNA alterations as part of the pathophysiological events characteristic of neuroinflammation in AD and the influence of these alterations on the course of the disease through interaction with multiple RNAs related to the generation of Aβ, pTau, and neuroinflammation itself.
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Affiliation(s)
- Karla Aketzalli Hernández-Contreras
- Doctorado en Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Jorge Antonio Martínez-Díaz
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - María Elena Hernández-Aguilar
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Deissy Herrera-Covarrubias
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Fausto Rojas-Durán
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Lizbeth Donají Chi-Castañeda
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Luis Isauro García-Hernández
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Gonzalo Emiliano Aranda-Abreu
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México.
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11
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Wang Y, Tang Y, Liu TH, Shao L, Li C, Wang Y, Tan P. Integrative Multi-omics Analysis to Characterize Herpes Virus Infection Increases the Risk of Alzheimer's Disease. Mol Neurobiol 2024:10.1007/s12035-023-03903-w. [PMID: 38191694 DOI: 10.1007/s12035-023-03903-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/22/2023] [Indexed: 01/10/2024]
Abstract
Evidence suggests that herpes virus infection is associated with an increased risk of Alzheimer's disease (AD), and innate and adaptive immunity plays an important role in the association. Although there have been many studies, the mechanism of the association is still unclear. This study aims to reveal the underlying molecular and immune regulatory network through multi-omics data and provide support for the study of the mechanism of infection and AD in the future. Here, we found that the herpes virus infection significantly increased the risk of AD. Genes associated with the occurrence and development of AD and genetically regulated by herpes virus infection are mainly enrichment in immune-related pathways. The 22 key regulatory genes identified by machine learning are mainly immune genes. They are also significantly related to the infiltration changes of 3 immune cell in AD. Furthermore, many of these genes have previously been reported to be linked, or potentially linked, to the pathological mechanisms of both herpes virus infection and AD. In conclusion, this study contributes to the study of the mechanisms related to herpes virus infection and AD, and indicates that the regulation of innate and adaptive immunity may be an effective strategy for preventing and treating herpes virus infection and AD. Additionally, the identified key regulatory genes, whether previously studied or newly discovered, may serve as valuable targets for prevention and treatment strategies.
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Affiliation(s)
- Yongheng Wang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Yaqin Tang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Tai-Hang Liu
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Lizhen Shao
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Chunying Li
- Chongqing Vocational College of Resources and Environmental Protection, Chongqing, China.
| | - Yingxiong Wang
- Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China.
| | - Pengcheng Tan
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China.
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12
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Liu B, Luo W, Huang L, Wei C, Huang X, Liu J, Tao R, Mo Y, Li X. Migration Inhibition Factor Secreted by Peripheral Blood Memory B Cells Binding to CD74-CD44 Receptor Complex Drives Macrophage Behavior in Alzheimer's Disease. Am J Alzheimers Dis Other Demen 2024; 39:15333175241238577. [PMID: 38491918 PMCID: PMC10944588 DOI: 10.1177/15333175241238577] [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] [Indexed: 03/18/2024]
Abstract
Dysregulation of the peripheral immune system is be involved in the neuroinflammation in Alzheimer disease (AD) and accelerate the disease progression. The contribution of immune cells, particularly B cells, to AD pathogenesis has gained attention in recent research. In this study, we investigated the role of Peripheral Blood Memory B cells (PBMBs) and their secreted Migration Inhibition Factor (MIF) in driving macrophage behavior in AD based on the scRNA-seq technique, immunofluorescence and flow cytometry. We discovered that MIF binds to the CD74-CD44 receptor complex on macrophages, influencing their behavior. The dysregulated macrophage response hampers the clearance of amyloid-beta (Aβ) plaques, exacerbating AD pathology. Targeting the MIF-CD74-CD44 signal pathway may hold therapeutic potential in modulating macrophage activity and mitigating neuroinflammation in AD. This study provides a further understanding of peripheral immune cells dysregulated in AD.
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Affiliation(s)
- Bo Liu
- Department of Neurology, The First Clinical Medical College of Jinan University, Jinan University, Guangzhou, China
- Department of Geriatric Neurology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Wei Luo
- Department of Physical Examination Center, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ling Huang
- Department of Neurology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Chunying Wei
- Department of Geriatric Neurology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xiaorui Huang
- Department of Neurology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jun Liu
- Department of Geriatric Neurology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Ran Tao
- Department of Geriatric Neurology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yingmin Mo
- Department of Geriatric Neurology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xuebin Li
- Department of Neurology, The First Clinical Medical College of Jinan University, Jinan University, Guangzhou, China
- Department of Neurology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Department of Neurology, West Guangxi Key Laboratory for Prevention and Treatment of High-Incidence Diseases, Youjiang Medical University for Nationalities, Baise, China
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13
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Challa K, Paysan D, Leiser D, Sauder N, Weber DC, Shivashankar GV. Imaging and AI based chromatin biomarkers for diagnosis and therapy evaluation from liquid biopsies. NPJ Precis Oncol 2023; 7:135. [PMID: 38092866 PMCID: PMC10719365 DOI: 10.1038/s41698-023-00484-8] [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: 05/28/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023] Open
Abstract
Multiple genomic and proteomic studies have suggested that peripheral blood mononuclear cells (PBMCs) respond to tumor secretomes and thus could provide possible avenues for tumor prognosis and treatment evaluation. We hypothesized that the chromatin organization of PBMCs obtained from liquid biopsies, which integrates secretome signals with gene expression programs, provides efficient biomarkers to characterize tumor signals and the efficacy of proton therapy in tumor patients. Here, we show that chromatin imaging of PBMCs combined with machine learning methods provides such robust and predictive chromatin biomarkers. We show that such chromatin biomarkers enable the classification of 10 healthy and 10 pan-tumor patients. Furthermore, we extended our pipeline to assess the tumor types and states of 30 tumor patients undergoing (proton) radiation therapy. We show that our pipeline can thereby accurately distinguish between three tumor groups with up to 89% accuracy and enables the monitoring of the treatment effects. Collectively, we show the potential of chromatin biomarkers for cancer diagnostics and therapy evaluation.
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Affiliation(s)
- Kiran Challa
- Mechano-Genomic Group, Division of Biology and Chemistry, Paul-Scherrer Institute, Villigen, Switzerland
| | - Daniel Paysan
- Mechano-Genomic Group, Division of Biology and Chemistry, Paul-Scherrer Institute, Villigen, Switzerland
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Dominic Leiser
- Center for Proton Therapy, Paul-Scherrer Institute, Villigen, Switzerland
| | - Nadia Sauder
- Center for Proton Therapy, Paul-Scherrer Institute, Villigen, Switzerland
| | - Damien C Weber
- Center for Proton Therapy, Paul-Scherrer Institute, Villigen, Switzerland.
- Department of Radio-Oncology, University Hospital Zurich, Zurich, Switzerland.
- Department of Radio-Oncology, University of Bern, Bern, Switzerland.
| | - G V Shivashankar
- Mechano-Genomic Group, Division of Biology and Chemistry, Paul-Scherrer Institute, Villigen, Switzerland.
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
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Pozojevic J, Spielmann M. Single-Cell Sequencing in Neurodegenerative Disorders. Mol Diagn Ther 2023; 27:553-561. [PMID: 37552451 PMCID: PMC10435411 DOI: 10.1007/s40291-023-00668-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 08/09/2023]
Abstract
Neurodegenerative disorders are typically characterized by late onset progressive damage to specific (sub)populations of cells of the nervous system that are essential for mobility, coordination, strength, sensation, and cognition. Addressing this selective cellular vulnerability has become feasible with the emergence of single-cell-omics technologies, which now represent the state-of-the-art approach to profile heterogeneity of complex tissues including human post-mortem brain at unprecedented resolution. In this review, we briefly recapitulate the experimental workflow of single-cell RNA sequencing and summarize the recent knowledge acquired with it in the most common neurodegenerative diseases: Parkinson's, Alzheimer's, Huntington's disease, and multiple sclerosis. We also discuss the possibility of applying single-cell approaches in the diagnostics and therapy of neurodegenerative disorders, as well as the limitations. While we are currently at the point of deeply exploring the transcriptomic changes in the affected cells, further technological developments hold a promise of manipulating the affected pathways once we understand them better.
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Affiliation(s)
- Jelena Pozojevic
- Institute of Human Genetics, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, 23562, Lübeck, Germany
| | - Malte Spielmann
- Institute of Human Genetics, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, 23562, Lübeck, Germany.
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, 23562, Lübeck, Germany.
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Lu J, Liang F, Bai P, Liu C, Xu M, Sun Z, Tian W, Dong Y, Zhang Y, Quan Q, Khatri A, Shen Y, Marcantonio E, Crosby G, Culley D, Wang C, Yang G, Xie Z. Blood tau-PT217 contributes to the anesthesia/surgery-induced delirium-like behavior in aged mice. Alzheimers Dement 2023; 19:4110-4126. [PMID: 37249148 PMCID: PMC10524579 DOI: 10.1002/alz.13118] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Blood phosphorylated tau at threonine 217 (tau-PT217) is a newly established biomarker for Alzheimer's disease and postoperative delirium in patients. However, the mechanisms and consequences of acute changes in blood tau-PT217 remain largely unknown. METHODS We investigated the effects of anesthesia/surgery on blood tau-PT217 in aged mice, and evaluated the associated changes in B cell populations, neuronal excitability in anterior cingulate cortex, and delirium-like behavior using positron emission tomography imaging, nanoneedle technology, flow cytometry, electrophysiology, and behavioral tests. RESULTS Anesthesia/surgery induced acute increases in blood tau-PT217 via enhanced generation in the lungs and release from B cells. Tau-PT217 might cross the blood-brain barrier, increasing neuronal excitability and inducing delirium-like behavior. B cell transfer and WS635, a mitochondrial function enhancer, mitigated the anesthesia/surgery-induced changes. DISCUSSION Acute increases in blood tau-PT217 may contribute to brain dysfunction and postoperative delirium. Targeting B cells or mitochondrial function may have therapeutic potential for preventing or treating these conditions.
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Affiliation(s)
- Jing Lu
- Department of Anesthesiology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, 610072, China
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, United States
| | - Feng Liang
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, United States
| | - Ping Bai
- Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, United States
| | - Chenghao Liu
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, United States
- Chinese Academy of Sciences, Institute of Automation, Beijing, 100080, China
| | - Miao Xu
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, United States
- Department of Anesthesiology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510120, China
| | - Zhengwang Sun
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, United States
| | - Wenjie Tian
- Department of Cardiology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, 610072, China
- Cardiovascular Research Center and Cardiology Division of the Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, United States
| | - Yuanlin Dong
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, United States
| | - Yiying Zhang
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, United States
| | - Qimin Quan
- NanoMosaic, Inc., Woburn, MA, 01801, United States
| | - Ashok Khatri
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02129, United States
| | - Yuan Shen
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, United States
- Anesthesia and Brain Research Institute, Tongji University School of Medicine, Shanghai, 200092, China
- Mental Health Center affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Edward Marcantonio
- Divisions of General Medicine and Primary Care and Gerontology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02115, United States
| | - Gregory Crosby
- Department of Anesthesiology, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA, 02115, United States
| | - Deborah Culley
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania Health System, Philadelphia, PA, 19104, United States
| | - Changning Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, United States
| | - Guang Yang
- Department of Anesthesiology, Columbia University Medical Center, New York, NY, 10032, United States
| | - Zhongcong Xie
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, United States
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段 婷, 初 金, 胡 斐. [Identification of Peripheral Blood GZMK + CD8 + T Cells As Biomarkers of Alzheimer's Disease Based on Single-Cell Transcriptome]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2023; 54:863-873. [PMID: 37866940 PMCID: PMC10579064 DOI: 10.12182/20230960107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Indexed: 10/24/2023]
Abstract
Objective Based on single-cell RNA sequencing (scRNA-seq) to explore immune characteristics in the peripheral blood of patients with Alzheimer's disease (AD) as biomarkers. Methods GSE168522, the scRNA-seq dataset of AD peripheral blood immune cells, was downloaded from the Gene Expression Omnibus (GEO) database and was analyzed in the RAD-Blood web server (http://www.bioinform.cn/RAD-Blood/). The changes in blood cell composition in AD patients were analyzed. The abnormal communications between different types of cells in AD patients were investigated by the CellChat R package. Results There were two kinds of CD8 + T cells in the blood of AD patients and healthy individuals, one of which highly expressed granzyme K ( GZMK) (false discovery rate [FDR]<0.05), and the other highly expressed GZMA, GZMB, and GZMH (FDR<0.05). In the blood of AD patients, the content of GZMK + CD8 + T cells was increased by 32.9% ( P=5.15E-21), their interactions with other cell types were increased, and they might be associated with AD through the abnormal signal transduction of major histocompatibility complex class Ⅰ (MHC-Ⅰ). Erythrocyte provided the main ligands, that are, human leukocyte antigen (HLA) class Ⅰ molecules, including HLA- A, HLA- B, HLA- C, and HLA- E, for the abnormal MHC-Ⅰ signaling pathway of GZMK + CD8 + T cells. The RESISTIN signaling pathway was specifically enriched in the blood of AD patients. Conclusion The increased content of peripheral blood GZMK + CD8 + T cells, the increased interaction between GZMK + CD8 + T cells and erythrocytes, and the enhanced RESISTIN pathway are potential blood biomarkers of AD.
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Affiliation(s)
- 婷婷 段
- 武汉科技大学医学院 脑科学先进技术研究院 (武汉 430081)Brain Science and Advanced Technology Institute, School of Medicine, Wuhan University of Science and Technology, Wuhan 430081, China
| | - 金语 初
- 武汉科技大学医学院 脑科学先进技术研究院 (武汉 430081)Brain Science and Advanced Technology Institute, School of Medicine, Wuhan University of Science and Technology, Wuhan 430081, China
| | - 斐斐 胡
- 武汉科技大学医学院 脑科学先进技术研究院 (武汉 430081)Brain Science and Advanced Technology Institute, School of Medicine, Wuhan University of Science and Technology, Wuhan 430081, China
- 武汉科技大学附属亚洲心脏病医院 (武汉 430022)Wuhan Asia Heart Hospital, Wuhan University of Science and Technology, Wuhan 430022, China
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17
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Abdolmaleky HM, Zhou JR. Underlying Mechanisms of Brain Aging and Neurodegenerative Diseases as Potential Targets for Preventive or Therapeutic Strategies Using Phytochemicals. Nutrients 2023; 15:3456. [PMID: 37571393 PMCID: PMC10473240 DOI: 10.3390/nu15153456] [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: 07/01/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
During aging, several tissues and biological systems undergo a progressive decline in function, leading to age-associated diseases such as neurodegenerative, inflammatory, metabolic, and cardiovascular diseases and cancer. In this review, we focus on the molecular underpinning of senescence and neurodegeneration related to age-associated brain diseases, in particular, Alzheimer's and Parkinson's diseases, along with introducing nutrients or phytochemicals that modulate age-associated molecular dysfunctions, potentially offering preventive or therapeutic benefits. Based on current knowledge, the dysregulation of microglia genes and neuroinflammation, telomere attrition, neuronal stem cell degradation, vascular system dysfunction, reactive oxygen species, loss of chromosome X inactivation in females, and gut microbiome dysbiosis have been seen to play pivotal roles in neurodegeneration in an interactive manner. There are several phytochemicals (e.g., curcumin, EGCG, fucoidan, galangin, astin C, apigenin, resveratrol, phytic acid, acacetin, daucosterol, silibinin, sulforaphane, withaferin A, and betulinic acid) that modulate the dysfunction of one or several key genes (e.g., TREM2, C3, C3aR1, TNFA, NF-kb, TGFB1&2, SIRT1&6, HMGB1, and STING) affected in the aged brain. Although phytochemicals have shown promise in slowing down the progression of age-related brain diseases, more studies to identify their efficacy, alone or in combinations, in preclinical systems can help to design novel nutritional strategies for the management of neurodegenerative diseases in humans.
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Affiliation(s)
| | - Jin-Rong Zhou
- Nutrition/Metabolism Laboratory, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA;
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18
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Zheng P, Zhang N, Ren D, Yu C, Zhao B, Bai Q, Zhang Y, Sun W. Integrated single-cell multiomics reveals novel immune candidate markers for post-traumatic coagulopathy. Front Immunol 2023; 13:1095657. [PMID: 36846021 PMCID: PMC9946684 DOI: 10.3389/fimmu.2022.1095657] [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: 11/11/2022] [Accepted: 12/23/2022] [Indexed: 02/10/2023] Open
Abstract
Introduction Post-traumatic coagulopathy (PTC) is a critical pathology in traumatic brain injury (TBI), however, its potential mechanism is not clear. To explore this in peripheral samples, we integrated single cell RNA-sequencing and T cell repertoire (TCR)-sequencing across a cohort of patients with TBI. Methods Clinical samples from patients with more brain severity demonstrated overexpression of T cell receptor-encoding genes and less TCR diversity. Results By mapping TCR clonality, we found patients with PTC have less TCR clones, and the TCR clones are mainly distributed in cytotoxic effector CD8+T cell. In addition, the counts of CD8+ T cell and natural killer (NK) cells are associated with the coagulation parameter by WGCNA, and the granzyme and lectin-like receptor profiles are also decreased in the peripheral blood from TBI patients, suggesting that reduced peripheral CD8+ clonality and cytotoxic profiles may be involved in PTC after TBI. Conclusion Our work systematically revealed the critical immune status in PTC patients at the single-cell level.
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Affiliation(s)
- Ping Zheng
- Department of Neurosurgery, Shanghai Pudong New area People’s Hospital, Shanghai, China,Key Laboratory, Shanghai Pudong New area People’s Hospital, Shanghai, China,*Correspondence: Ping Zheng,
| | - Ning Zhang
- Department of Neurosurgery, Shanghai Fengxian Hospital, Shanghai, China
| | - Dabin Ren
- Department of Neurosurgery, Shanghai Pudong New area People’s Hospital, Shanghai, China
| | - Cong Yu
- Department of Neurosurgery, Shanghai Pudong New area People’s Hospital, Shanghai, China
| | - Bin Zhao
- Department of Neurosurgery, Second Hospital affiliated to Anhui Medical University, Shanghai, China
| | - Qingke Bai
- Department of Neurology, Shanghai Pudong New area People’s Hospital, Shanghai, China
| | - Yisong Zhang
- Department of Neurosurgery, Shanghai Pudong New area People’s Hospital, Shanghai, China
| | - Wanju Sun
- Department of Emergency Medicine, Shanghai Pudong New area People’s Hospital, Shanghai, China
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Feng W, Zhang Y, Ding S, Chen S, Wang T, Wang Z, Zou Y, Sheng C, Chen Y, Pang Y, Marshall C, Shi J, Nedergaard M, Li Q, Xiao M. B lymphocytes ameliorate Alzheimer's disease-like neuropathology via interleukin-35. Brain Behav Immun 2023; 108:16-31. [PMID: 36427805 DOI: 10.1016/j.bbi.2022.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/28/2022] [Accepted: 11/19/2022] [Indexed: 11/26/2022] Open
Abstract
Increasing evidence supports the involvement of the peripheral immune system in the pathogenesis of Alzheimer's disease (AD). In the present study, we found that B lymphocytes could mitigate beta-Amyloid (Aβ) pathology and memory impairments in a transgenic AD mouse model. Specifically, in young 5 × FAD mice, we evidenced increased B cells in the frontal cortex and meningeal tissues; depletion of mature B cells aggravated these mice's Aβ load and memory deficits. The increased B cells produced more interleukin-35 (IL-35) in the front cortex. We further found IL-35 neutralization exacerbated Aβ pathology, while injecting IL-35 mitigated Aβ load and cognitive dysfunction in 5 × FAD mice with or without mature B cell deficiency. Mechanistically, IL-35 inhibited neuronal BACE1 transcription through modulating the SOCS1/STAT1 pathway, and reduced Aβ production accordingly. Reanalysis of the single-cell RNA sequencing data from blood samples of AD patients suggested an increased population of IL-35-producing B cells. Together, the present study revealed a novel effect of B lymphocyte-derived IL-35 on inhibiting Aβ production in the frontal cortex, which may serve as a potential target for future AD treatment.
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Affiliation(s)
- Weixi Feng
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 211166, China; Center for Global Health, Nanjing Medical University, Nanjing 211166, China.
| | - Yanli Zhang
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 211166, China; Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Shixin Ding
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 211166, China; Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Sijia Chen
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 211166, China; Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Tianqi Wang
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 211166, China; Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Ze Wang
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 211166, China; Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Ying Zou
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 211166, China; Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Chengyu Sheng
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 211166, China; Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Yan Chen
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 211166, China; Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Yingting Pang
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 211166, China; Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Charles Marshall
- Department of Physical Therapy, University of Kentucky Center of Excellence in Rural Health, Hazard, KY, USA
| | - Jingping Shi
- Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, Department of Neurosurgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Qian Li
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 211166, China; Center for Global Health, Nanjing Medical University, Nanjing 211166, China.
| | - Ming Xiao
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 211166, China; Center for Global Health, Nanjing Medical University, Nanjing 211166, China; Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing 210029, China.
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20
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Liu Y, Tan Y, Zhang Z, Li H, Yi M, Zhang Z, Hui S, Peng W. Neuroimmune mechanisms underlying Alzheimer's disease: Insights into central and peripheral immune cell crosstalk. Ageing Res Rev 2023; 84:101831. [PMID: 36565960 DOI: 10.1016/j.arr.2022.101831] [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: 08/24/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease (AD) is a highly life-threatening neurodegenerative disease. Dysregulation of the immune system plays a critical role in promoting AD, which has attracted extensive attention recently. Central and peripheral immune responses are involved in the pathogenesis of AD. Immune changes precede Aβ-associated senile plaque formation and tau-related neurofibrillary tangles, which are the recognised pathological features of AD. Therefore, elucidating immune-related mechanisms underlying the development of AD can help to prevent and treat AD at the source by blocking its progression before the development of pathological changes. To understand the specific pathogenesis of AD, it is important to examine the role of central and peripheral immunity in AD. This review summarises immune-related mechanisms underlying the pathogenesis of AD, focusing on the effect of various central and peripheral immune cells, and describes the possible crosstalk between central and peripheral immunity during the development of AD. This review provides novel insights into the treatment of AD and offers a new direction for immune-related research on AD in the future.
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Affiliation(s)
- Yuqing Liu
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, China; National Clinical Research Center for Metabolic Diseases, Changsha 410011, China.
| | - Yejun Tan
- School of Mathematics, University of Minnesota Twin Cities, Minneapolis, MN, USA.
| | - Zheyu Zhang
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, China; National Clinical Research Center for Metabolic Diseases, Changsha 410011, China.
| | - Hongli Li
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, China; National Clinical Research Center for Metabolic Diseases, Changsha 410011, China.
| | - Min Yi
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, China; National Clinical Research Center for Metabolic Diseases, Changsha 410011, China.
| | - Zhen Zhang
- YangSheng College of Traditional Chinese Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, China.
| | - Shan Hui
- Department of Geratology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha 410005, China.
| | - Weijun Peng
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, China; National Clinical Research Center for Metabolic Diseases, Changsha 410011, China.
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21
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Feng W, Zhang Y, Sun P, Xiao M. Acquired immunity and Alzheimer's disease. J Biomed Res 2023; 37:15-29. [PMID: 36165328 PMCID: PMC9898041 DOI: 10.7555/jbr.36.20220083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Alzheimer's disease (AD) is an age-related neurodegenerative disease characterized by progressive cognitive defects. The role of the central immune system dominated by microglia in the progression of AD has been extensively investigated. However, little is known about the peripheral immune system in AD pathogenesis. Recently, with the discovery of the meningeal lymphatic vessels and glymphatic system, the roles of the acquired immunity in the maintenance of central homeostasis and neurodegenerative diseases have attracted an increasing attention. The T cells not only regulate the function of neurons, astrocytes, microglia, oligodendrocytes and brain microvascular endothelial cells, but also participate in the clearance of β-amyloid (Aβ) plaques. Apart from producing antibodies to bind Aβ peptides, the B cells affect Aβ-related cascades via a variety of antibody-independent mechanisms. This review systemically summarizes the recent progress in understanding pathophysiological roles of the T cells and B cells in AD.
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Affiliation(s)
- Weixi Feng
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, Jiangsu 211166, China,Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Chinese Academy of Sciences, Shanghai 200031, China,Weixi Feng, Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, Jiangsu 211166, China. Tel: +86-25-86869338; E-mail:
| | - Yanli Zhang
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, Jiangsu 211166, China,Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Peng Sun
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, Jiangsu 211166, China,Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Ming Xiao
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, Jiangsu 211166, China,Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Chinese Academy of Sciences, Shanghai 200031, China,Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, China
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22
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Sutter PA, Crocker SJ. Glia as antigen-presenting cells in the central nervous system. Curr Opin Neurobiol 2022; 77:102646. [PMID: 36371828 PMCID: PMC10183975 DOI: 10.1016/j.conb.2022.102646] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/22/2022] [Accepted: 10/06/2022] [Indexed: 11/11/2022]
Abstract
The contribution of the cells within the central nervous system (CNS) toward adaptive immune responses is emerging and incompletely understood. Recent findings indicate important functional interactions between T-cells and glial cells within the CNS that may contribute to disease and neuropathology through antigen presentation. Although glia are not classically considered antigen-presenting cell (APC) types, there is growing evidence indicating that glial antigen presentation plays an important role in several neurological diseases. This review discusses these findings which incriminate microglia, astrocytes, and oligodendrocyte lineage cells as CNS-resident APC types with implications for understanding disease.
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Affiliation(s)
- Pearl A Sutter
- Departments of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Stephen J Crocker
- Departments of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA.
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23
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Li J, Zhang Y, Lu T, Liang R, Wu Z, Liu M, Qin L, Chen H, Yan X, Deng S, Zheng J, Liu Q. Identification of diagnostic genes for both Alzheimer's disease and Metabolic syndrome by the machine learning algorithm. Front Immunol 2022; 13:1037318. [PMID: 36405716 PMCID: PMC9667080 DOI: 10.3389/fimmu.2022.1037318] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/23/2022] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Alzheimer's disease is the most common neurodegenerative disease worldwide. Metabolic syndrome is the most common metabolic and endocrine disease in the elderly. Some studies have suggested a possible association between MetS and AD, but few studied genes that have a co-diagnostic role in both diseases. METHODS The microarray data of AD (GSE63060 and GSE63061 were merged after the batch effect was removed) and MetS (GSE98895) in the GEO database were downloaded. The WGCNA was used to identify the co-expression modules related to AD and MetS. RF and LASSO were used to identify the candidate genes. Machine learning XGBoost improves the diagnostic effect of hub gene in AD and MetS. The CIBERSORT algorithm was performed to assess immune cell infiltration MetS and AD samples and to investigate the relationship between biomarkers and infiltrating immune cells. The peripheral blood mononuclear cells (PBMCs) single-cell RNA (scRNA) sequencing data from patients with AD and normal individuals were visualized with the Seurat standard flow dimension reduction clustering the metabolic pathway activity changes each cell with ssGSEA. RESULTS The brown module was identified as the significant module with AD and MetS. GO analysis of shared genes showed that intracellular transport and establishment of localization in cell and organelle organization were enriched in the pathophysiology of AD and MetS. By using RF and Lasso learning methods, we finally obtained eight diagnostic genes, namely ARHGAP4, SNRPG, UQCRB, PSMA3, DPM1, MED6, RPL36AL and RPS27A. Their AUC were all greater than 0.7. Higher immune cell infiltrations expressions were found in the two diseases and were positively linked to the characteristic genes. The scRNA-seq datasets finally obtained seven cell clusters. Seven major cell types including CD8 T cell, monocytes, T cells, NK cell, B cells, dendritic cells and macrophages were clustered according to immune cell markers. The ssGSEA revealed that immune-related gene (SNRPG) was significantly regulated in the glycolysis-metabolic pathway. CONCLUSION We identified genes with common diagnostic effects on both MetS and AD, and found genes involved in multiple metabolic pathways associated with various immune cells.
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Affiliation(s)
- Jinwei Li
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Yang Zhang
- General Surgery, The First Affiliated Hospital of Dali University, Dali, China
| | - Tanli Lu
- Department of Neurology, The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, China
| | - Rui Liang
- College of Bioengineering, Chongqing University, Chongqing, China
| | - Zhikang Wu
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Meimei Liu
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Linyao Qin
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Hongmou Chen
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Xianlei Yan
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Shan Deng
- Department of Neurology, The Fourth Affliated Hospital of Guangxi Medical University, Liuzhou, Guangxi, China
| | - Jiemin Zheng
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Quan Liu
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
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24
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Park JC, Noh J, Jang S, Kim KH, Choi H, Lee D, Kim J, Chung J, Lee DY, Lee Y, Lee H, Yoo DK, Lee AC, Byun MS, Yi D, Han SH, Kwon S, Mook-Jung I. Association of B cell profile and receptor repertoire with the progression of Alzheimer's disease. Cell Rep 2022; 40:111391. [PMID: 36130492 DOI: 10.1016/j.celrep.2022.111391] [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: 02/28/2022] [Revised: 07/04/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Alzheimer's disease (AD) is the most prevalent type of dementia. Reports have revealed that the peripheral immune system is linked to neuropathology; however, little is known about the contribution of B lymphocytes in AD. For this longitudinal study, 133 participants are included at baseline and second-year follow-up. Also, we analyze B cell receptor (BCR) repertoire data generated from a public dataset of three normal and 10 AD samples and perform BCR repertoire profiling and pairwise sharing analysis. As a result, longitudinal increase in B lymphocytes is associated with increased cerebral amyloid deposition and hyperactivates induced pluripotent stem cell-derived microglia with loss-of-function for beta-amyloid clearance. Patients with AD share similar class-switched BCR sequences with identical isotypes, despite the high somatic hypermutation rate. Thus, BCR repertoire profiling can lead to the development of individualized immune-based therapeutics and treatment. We provide evidence of both quantitative and qualitative changes in B lymphocytes during AD pathogenesis.
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Affiliation(s)
- Jong-Chan Park
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; Neuroscience Research Institute, Medical Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Jinsung Noh
- Department of Electrical and Computer Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Sukjin Jang
- Department of Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Ki Hyun Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hayoung Choi
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Dongjoon Lee
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Jieun Kim
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Dong Young Lee
- Institute of Human Behavioral Medicine, Medical Research Center, Seoul National University, Seoul 03080, Republic of Korea; Department of Psychiatry, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; Department of Neuropsychiatry, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Yonghee Lee
- Department of Electrical and Computer Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Duck Kyun Yoo
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Amos Chungwon Lee
- Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Min Soo Byun
- Department of Psychiatry, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; Department of Neuropsychiatry, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Dahyun Yi
- Department of Neuropsychiatry, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Sun-Ho Han
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; Neuroscience Research Institute, Medical Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea.
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea; BK21+ Creative Research Engineer Development for IT, Seoul National University, Seoul 08826, Republic of Korea; Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea; Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea.
| | - Inhee Mook-Jung
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; Neuroscience Research Institute, Medical Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea.
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25
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C. Silva T, Zhang W, Young JI, Gomez L, Schmidt MA, Varma A, Chen XS, Martin ER, Wang L. Distinct sex-specific DNA methylation differences in Alzheimer's disease. Alzheimers Res Ther 2022; 14:133. [PMID: 36109771 PMCID: PMC9479371 DOI: 10.1186/s13195-022-01070-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/30/2022] [Indexed: 01/17/2023]
Abstract
BACKGROUND Sex is increasingly recognized as a significant factor contributing to the biological and clinical heterogeneity in AD. There is also growing evidence for the prominent role of DNA methylation (DNAm) in Alzheimer's disease (AD). METHODS We studied sex-specific DNA methylation differences in the blood samples of AD subjects compared to cognitively normal subjects, by performing sex-specific meta-analyses of two large blood-based epigenome-wide association studies (ADNI and AIBL), which included DNA methylation data for a total of 1284 whole blood samples (632 females and 652 males). Within each dataset, we used two complementary analytical strategies, a sex-stratified analysis that examined methylation to AD associations in male and female samples separately, and a methylation-by-sex interaction analysis that compared the magnitude of these associations between different sexes. After adjusting for age, estimated immune cell type proportions, batch effects, and correcting for inflation, the inverse-variance fixed-effects meta-analysis model was used to identify the most consistent DNAm differences across datasets. In addition, we also evaluated the performance of the sex-specific methylation-based risk prediction models for AD diagnosis using an independent external dataset. RESULTS In the sex-stratified analysis, we identified 2 CpGs, mapped to the PRRC2A and RPS8 genes, significantly associated with AD in females at a 5% false discovery rate, and an additional 25 significant CpGs (21 in females, 4 in males) at P-value < 1×10-5. In methylation-by-sex interaction analysis, we identified 5 significant CpGs at P-value < 10-5. Out-of-sample validations using the AddNeuroMed dataset showed in females, the best logistic prediction model included age, estimated immune cell-type proportions, and methylation risk scores (MRS) computed from 9 of the 23 CpGs identified in AD vs. CN analysis that are also available in AddNeuroMed dataset (AUC = 0.74, 95% CI: 0.65-0.83). In males, the best logistic prediction model included only age and MRS computed from 2 of the 5 CpGs identified in methylation-by-sex interaction analysis that are also available in the AddNeuroMed dataset (AUC = 0.70, 95% CI: 0.56-0.82). CONCLUSIONS Overall, our results show that the DNA methylation differences in AD are largely distinct between males and females. Our best-performing sex-specific methylation-based prediction model in females performed better than that for males and additionally included estimated cell-type proportions. The significant discriminatory classification of AD samples with our methylation-based prediction models demonstrates that sex-specific DNA methylation could be a predictive biomarker for AD. As sex is a strong factor underlying phenotypic variability in AD, the results of our study are particularly relevant for a better understanding of the epigenetic architecture that underlie AD and for promoting precision medicine in AD.
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Affiliation(s)
- Tiago C. Silva
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA
| | - Wei Zhang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA
| | - Juan I. Young
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lissette Gomez
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Michael A. Schmidt
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Achintya Varma
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - X. Steven Chen
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Eden R. Martin
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lily Wang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
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26
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Song L, Yang YT, Guo Q, Zhao XM. Cellular transcriptional alterations of peripheral blood in Alzheimer's disease. BMC Med 2022; 20:266. [PMID: 36031604 PMCID: PMC9422129 DOI: 10.1186/s12916-022-02472-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD), a progressive neurodegenerative disease, is the most common cause of dementia worldwide. Accumulating data support the contributions of the peripheral immune system in AD pathogenesis. However, there is a lack of comprehensive understanding about the molecular characteristics of peripheral immune cells in AD. METHODS To explore the alterations of cellular composition and the alterations of intrinsic expression of individual cell types in peripheral blood, we performed cellular deconvolution in a large-scale bulk blood expression cohort and identified cell-intrinsic differentially expressed genes in individual cell types with adjusting for cellular proportion. RESULTS We detected a significant increase and decrease in the proportion of neutrophils and B lymphocytes in AD blood, respectively, which had a robust replicability across other three AD cohorts, as well as using alternative algorithms. The differentially expressed genes in AD neutrophils were enriched for some AD-associated pathways, such as ATP metabolic process and mitochondrion organization. We also found a significant enrichment of protein-protein interaction network modules of leukocyte cell-cell activation, mitochondrion organization, and cytokine-mediated signaling pathway in neutrophils for AD risk genes including CD33 and IL1B. Both changes in cellular composition and expression levels of specific genes were significantly associated with the clinical and pathological alterations. A similar pattern of perturbations on the cellular proportion and gene expression levels of neutrophils could be also observed in mild cognitive impairment (MCI). Moreover, we noticed an elevation of neutrophil abundance in the AD brains. CONCLUSIONS We revealed the landscape of molecular perturbations at the cellular level for AD. These alterations highlight the putative roles of neutrophils in AD pathobiology.
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Affiliation(s)
- Liting Song
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China
| | - Yucheng T Yang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China.,MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China.,Zhangjiang Fudan International Innovation Center, Shanghai, 200433, China
| | - Qihao Guo
- Department of Gerontology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | | | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China. .,MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China. .,Zhangjiang Fudan International Innovation Center, Shanghai, 200433, China. .,International Human Phenome Institutes (Shanghai), Shanghai, 200433, China.
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27
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Yu G, Lu W, Chen X, Li Y, Long J, Zheng Z, Yin C, Xu D. Single-cell RNA sequencing to explore composition of peripheral blood NK cells in patients with chronic myeloid leukemia in treatment-free remission. Leuk Lymphoma 2022; 63:2604-2615. [PMID: 35695125 DOI: 10.1080/10428194.2022.2086243] [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: 10/18/2022]
Abstract
This study was to explore the role of NK cell subsets and gene expression in maintaining TFR status. We identified six types of NK cells in the PBMCs over both groups (healthy controls and patients with TFR). Gene Oncology analysis showed that up regulated genes were enriched in the categories of "immune response," "reaction to tumor cells," and "cytolysis." In addition, we found that the three NK cell subsets, mature and terminal NK cells, CD56 bright NK cells, and transitional NK cells, contained many significantly up regulated genes in both groups, and that CD56 bright NK cells and transitional NK cells in patients with CML-TFR were in a proliferating and activated state. Through single-cell RNA sequencing analysis, we confirmed that the mature and terminal, CD56 bright, and transitional subsets of NK cells play an indispensable role in maintaining TFR in patients with CML.
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Affiliation(s)
- Guopan Yu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Weixiang Lu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaofan Chen
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanlin Li
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiaxin Long
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhongxin Zheng
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Changxin Yin
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dan Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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