1
|
Elizaldi SR, Hawes CE, Verma A, Shaan Lakshmanappa Y, Dinasarapu AR, Schlegel BT, Rajasundaram D, Li J, Durbin-Johnson BP, Ma ZM, Pal PB, Beckman D, Ott S, Raeman R, Lifson J, Morrison JH, Iyer SS. Chronic SIV-Induced neuroinflammation disrupts CCR7+ CD4+ T cell immunosurveillance in the rhesus macaque brain. J Clin Invest 2024; 134:e175332. [PMID: 38470479 PMCID: PMC11060742 DOI: 10.1172/jci175332] [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: 09/22/2023] [Accepted: 03/05/2024] [Indexed: 03/13/2024] Open
Abstract
CD4+ T cells survey and maintain immune homeostasis in the brain, yet their differentiation states and functional capabilities remain unclear. Our approach, combining single-cell transcriptomic analysis, ATAC-Seq, spatial transcriptomics, and flow cytometry, revealed a distinct subset of CCR7+ CD4+ T cells resembling lymph node central memory (TCM) cells. We observed chromatin accessibility at the CCR7, CD28, and BCL-6 loci, defining molecular features of TCM. Brain CCR7+ CD4+ T cells exhibited recall proliferation and interleukin-2 production ex vivo, showcasing their functional competence. We identified the skull bone marrow as a local niche for these cells alongside CNS border tissues. Sequestering TCM cells in lymph nodes using FTY720 led to reduced CCR7+ CD4+ T cell frequencies in the cerebrospinal fluid, accompanied by increased monocyte levels and soluble markers indicating immune activation. In macaques chronically infected with SIVCL757 and experiencing viral rebound due to cessation of antiretroviral therapy, a decrease in brain CCR7+ CD4+ T cells was observed, along with increased microglial activation and initiation of neurodegenerative pathways. Our findings highlight a role for CCR7+ CD4+ T cells in CNS immune surveillance, and their decline during chronic SIV highlights their responsiveness to neuroinflammation.
Collapse
Affiliation(s)
| | - Chase E. Hawes
- Graduate Group in Immunology, UCD, Davis, California, USA
| | - Anil Verma
- Department of Pathology, School of Medicine, University of Pittsburgh, Pennsylvania, USA
| | | | - Ashok R. Dinasarapu
- Department of Neurology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Brent T. Schlegel
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jie Li
- Bioinformatics Core, UCD, Davis, California, USA
| | | | - Zhong-Min Ma
- California National Primate Research Center, UCD, Davis, California, USA
| | - Pabitra B. Pal
- Department of Pathology, School of Medicine, University of Pittsburgh, Pennsylvania, USA
| | - Danielle Beckman
- California National Primate Research Center, UCD, Davis, California, USA
| | - Sean Ott
- California National Primate Research Center, UCD, Davis, California, USA
| | - Reben Raeman
- Department of Pathology, School of Medicine, University of Pittsburgh, Pennsylvania, USA
| | - Jeffrey Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
| | - John H. Morrison
- California National Primate Research Center, UCD, Davis, California, USA
- Department of Neurology, School of Medicine, and
| | - Smita S. Iyer
- Department of Pathology, School of Medicine, University of Pittsburgh, Pennsylvania, USA
- California National Primate Research Center, UCD, Davis, California, USA
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, UCD, Davis, California, USA
| |
Collapse
|
2
|
Plaza-Zabala A, Sierra A. Studying Autophagy in Microglia: Overcoming the Obstacles. Methods Mol Biol 2024; 2713:45-70. [PMID: 37639114 DOI: 10.1007/978-1-0716-3437-0_3] [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: 08/29/2023]
Abstract
In this chapter, we provide an overview of the main techniques and experimental approaches that can be used to analyze autophagy flux in microglia, the brain-resident macrophages. For this purpose, we first briefly introduce the main peculiarities of microglial biology, describe the basic mechanisms and functions of autophagy, and summarize the evidence accumulated so far on the role of autophagy in the regulation of microglial survival and functions, mainly phagocytosis and inflammation. Then, we highlight conceptual and technical aspects of autophagic recycling and microglial physiology that need to be taken into account for the accurate evaluation of autophagy flux in microglia. Finally, we describe the main assays that can be used to analyze the complete sequence of autophagosome formation and degradation or autophagy flux, mainly in cultured microglia and in vivo. The main approaches include indirect tracking of autophagosomes by autophagic enzymes such as LC3 by western blot and fluorescence-based confocal microscopy, as well as direct analysis of autophagic vesicles by electron microscopy. We also discuss the advantages and disadvantages of using these methods in specific experimental contexts and highlight the need to complement LC3 and/or electron microscopy data with analysis of other autophagic effectors and lysosomal proteins that participate in the initiation and completion of autophagy flux, respectively. In summary, we provide an experimental guide for the analysis of autophagosome turnover in microglia, emphasizing the need to combine as many markers and complementary approaches as possible to fully characterize the status of autophagy flux in microglia.
Collapse
Affiliation(s)
- Ainhoa Plaza-Zabala
- Achucarro Basque Center for Neuroscience, Leioa, Spain.
- Department of Pharmacology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Amanda Sierra
- Achucarro Basque Center for Neuroscience, Leioa, Spain
- Department of Neurosciences, University of the Basque Country (UPV/EHU), Leioa, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Ikerbasque Foundation, Bilbao, Spain
| |
Collapse
|
3
|
Elizaldi SR, Hawes CE, Verma A, Dinasarapu AR, Lakshmanappa YS, Schlegel BT, Rajasundaram D, Li J, Durbin-Johnson BP, Ma ZM, Beckman D, Ott S, Lifson J, Morrison JH, Iyer SS. CCR7+ CD4 T Cell Immunosurveillance Disrupted in Chronic SIV-Induced Neuroinflammation in Rhesus Brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555037. [PMID: 37693567 PMCID: PMC10491118 DOI: 10.1101/2023.08.28.555037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
CD4 T cells survey and maintain immune homeostasis in the brain, yet their differentiation states and functional capabilities remain unclear. Our approach, combining single-cell transcriptomic analysis, ATAC-seq, spatial transcriptomics, and flow cytometry, revealed a distinct subset of CCR7+ CD4 T cells resembling lymph node central memory (T CM ) cells. We observed chromatin accessibility at the CCR7, CD28, and BCL-6 loci, defining molecular features of T CM . Brain CCR7+ CD4 T cells exhibited recall proliferation and interleukin-2 production ex vivo, showcasing their functional competence. We identified the skull bone marrow as a local niche for these cells alongside other CNS border tissues. Sequestering T CM cells in lymph nodes using FTY720 led to reduced CCR7+ CD4 T cell frequencies in the cerebrospinal fluid, accompanied by increased monocyte levels and soluble markers indicating immune activation. In macaques chronically infected with SIVCL57 and experiencing viral rebound due to cessation of antiretroviral therapy, a decrease in brain CCR7+ CD4 T cells was observed, along with increased microglial activation and initiation of neurodegenerative pathways. Our findings highlight a role for CCR7+ CD4 T cells in CNS immune surveillance and their decline during chronic SIV-induced neuroinflammation highlights their responsiveness to neuroinflammatory processes. GRAPHICAL ABSTRACT In Brief Utilizing single-cell and spatial transcriptomics on adult rhesus brain, we uncover a unique CCR7+ CD4 T cell subset resembling central memory T cells (T CM ) within brain and border tissues, including skull bone marrow. Our findings show decreased frequencies of this subset during SIV- induced chronic neuroinflammation, emphasizing responsiveness of CCR7+ CD4 T cells to CNS disruptions. Highlights CCR7+ CD4 T cells survey border and parenchymal CNS compartments during homeostasis; reduced presence of CCR7+ CD4 T cells in cerebrospinal fluid leads to immune activation, implying a role in neuroimmune homeostasis. CNS CCR7+ CD4 T cells exhibit phenotypic and functional features of central memory T cells (T CM ) including production of interleukin 2 and the capacity for rapid recall proliferation. Furthermore, CCR7+ CD4 T cells reside in the skull bone marrow. CCR7+ CD4 T cells are markedly decreased within the brain parenchyma during chronic viral neuroinflammation.
Collapse
|
4
|
Wang P, Chen Q, Tang Z, Wang L, Gong B, Li M, Li S, Yang M. Uncovering ferroptosis in Parkinson's disease via bioinformatics and machine learning, and reversed deducing potential therapeutic natural products. Front Genet 2023; 14:1231707. [PMID: 37485340 PMCID: PMC10358855 DOI: 10.3389/fgene.2023.1231707] [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: 05/30/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023] Open
Abstract
Objective: Ferroptosis, a novel form of cell death, is closely associated with excessive iron accumulated within the substantia nigra in Parkinson's disease (PD). Despite extensive research, the underlying molecular mechanisms driving ferroptosis in PD remain elusive. Here, we employed a bioinformatics and machine learning approach to predict the genes associated with ferroptosis in PD and investigate the interactions between natural products and their active ingredients with these genes. Methods: We comprehensively analyzed differentially expressed genes (DEGs) for ferroptosis associated with PD (PDFerDEGs) by pairing 3 datasets (GSE7621, GSE20146, and GSE202665) from the NCBI GEO database and the FerrDb V2 database. A machine learning approach was then used to screen PDFerDEGs for signature genes. We mined the interacted natural product components based on screened signature genes. Finally, we mapped a network combined with ingredients and signature genes, then carried out molecular docking validation of core ingredients and targets to uncover potential therapeutic targets and ingredients for PD. Results: We identified 109 PDFerDEGs that were significantly enriched in biological processes and KEGG pathways associated with ferroptosis (including iron ion homeostasis, iron ion transport and ferroptosis, etc.). We obtained 29 overlapping genes and identified 6 hub genes (TLR4, IL6, ADIPOQ, PTGS2, ATG7, and FADS2) by screening with two machine learning algorithms. Based on this, we screened 263 natural product components and subsequently mapped the "Overlapping Genes-Ingredients" network. According to the network, top 5 core active ingredients (quercetin, 17-beta-estradiol, glycerin, trans-resveratrol, and tocopherol) were molecularly docked to hub genes to reveal their potential role in the treatment of ferroptosis in PD. Conclusion: Our findings suggested that PDFerDEGs are associated with ferroptosis and play a role in the progression of PD. Taken together, core ingredients (quercetin, 17-beta-estradiol, glycerin, trans-resveratrol, and tocopherol) bind well to hub genes (TLR4, IL6, ADIPOQ, PTGS2, ATG7, and FADS2), highlighting novel biomarkers for PD.
Collapse
Affiliation(s)
- Peng Wang
- Postgraduate School, Medical School of Chinese PLA, Beijing, China
- Department of Traditional Chinese Medicine, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Qi Chen
- Department of Traditional Chinese Medicine, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhuqian Tang
- School of Pharmacy, Key Laboratory for Modern Research of Traditional Chinese Medicine of Jiangsu, Nanjing University of Chinese Medicine, Nan Jing, Jiangsu, China
| | - Liang Wang
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Bizhen Gong
- Postgraduate School, Medical School of Chinese PLA, Beijing, China
- Department of Traditional Chinese Medicine, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Min Li
- Department of Traditional Chinese Medicine, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Shaodan Li
- Department of Traditional Chinese Medicine, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Minghui Yang
- Department of Traditional Chinese Medicine, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| |
Collapse
|
5
|
Zhang Z, Liu L, Zhang H, Li C, Chen Y, Zhang J, Pan C, Cheng S, Yang X, Meng P, Yao Y, Jia Y, Wen Y, Zhang F. The genetic structure of pain in depression patients: A genome-wide association study and proteome-wide association study. J Psychiatr Res 2022; 156:547-556. [PMID: 36368244 DOI: 10.1016/j.jpsychires.2022.10.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/18/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Comparing with the general population, the pain in depression patients has more complex biological mechanism. We aim to explore the etiological mechanism of pain in depression patients from the perspective of genetics. METHODS Utilizing the UK Biobank samples with self-reported depression status or PHQ score ≥10, we conducted genome-wide association studies (GWAS) of seven pain traits (N = 1,133-58,349). Additionally, we used FUSION pipeline to perform proteome-wide association study (PWAS) and transcriptome-wide association study (TWAS) by integrating GWAS summary data with two different proteome reference weights (ROS/MAP and Banner) and Rnaseq gene expression reference weights, respectively. RESULTS GWAS identified 3 significant genes associated with different pain traits in depression patients, including TRIOBP (PGWAS = 4.48 × 10-8) for stomach or abdominal pain, SLC9A9(PGWAS = 2.77 × 10-8) for multisite chronic pain (MCP) and ADGRF1 (PGWAS = 1.51 × 10-8) for neck or shoulder pain. In addition, PWAS and TWAS analysis also identified multiple candidate genes associated with different pain traits in depression patients, such as TPRG1L (PPWAS-Banner = 3.38 × 10-2) and SIRPA (PPWAS-Banner = 3.65 × 10-2) for MCP, etc. Notably, when comparing the results of PWAS and TWAS analysis, we found overlapping candidate genes in these pain traits, such as GSTM3 (PPWAS-Banner = 3.38 × 10-2, PTWAS = 6.92 × 10-3) in the stomach or abdominal pain phenotype, ATG7 (PPWAS-Rosmap = 3.15 × 10-2, PTWAS = 2.98 × 10-2) in the MCP, etc. CONCLUSIONS: We identified multiple novel candidate genes for pain traits in depression patients from different perspectives of genetics, which provided novel clues for understanding the genetic mechanisms underlying the pain in depression patients.
Collapse
Affiliation(s)
- Zhen Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Huijie Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chun'e Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yujing Chen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jingxi Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chuyu Pan
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Peilin Meng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yao Yao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.
| |
Collapse
|
6
|
Deficient Autophagy in Microglia Aggravates Repeated Social Defeat Stress-Induced Social Avoidance. Neural Plast 2022; 2022:7503553. [PMID: 35222638 PMCID: PMC8866015 DOI: 10.1155/2022/7503553] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/20/2022] [Accepted: 02/02/2022] [Indexed: 01/12/2023] Open
Abstract
Major depressive disorder (MDD) is associated with repeated exposure to environmental stress. Autophagy is activated under various stress conditions that are associated with several diseases in the brain. This study was aimed at elucidating the autophagy signaling changes in the prefrontal cortex (PFC) under repeated social defeat (RSD) to investigate the involvement of microglial autophagy in RSD-induced behavioral changes. We found that RSD stress, an animal model of MDD, significantly induced initial autophagic signals followed by increased transcription of autophagy-related genes (Atg6, Atg7, and Atg12) in the PFC. Similarly, significantly increased transcripts of ATGs (Atg6, Atg7, Atg12, and Atg5) were confirmed in the postmortem PFC of patients with MDD. The protein levels of the prefrontal cortical LC3B were significantly increased, whereas p62 was significantly decreased in the resilient but not in susceptible mice and patients with MDD. This indicates that enhanced autophagic flux may alleviate stress-induced depression. Furthermore, we identified that FKBP5, an early-stage autophagy regulator, was significantly increased in the PFC of resilient mice at the transcript and protein levels. In addition, the resilient mice exhibited enhanced autophagic flux in the prefrontal cortical microglia, and the autophagic deficiency in microglia aggravated RSD-induced social avoidance, indicating that microglial autophagy involves stress-induced behavioral changes.
Collapse
|
7
|
Yuan N, Wang X, Zhang Y, Kong L, Yuan L, Ge Y. Intervention of NF-Κb Signaling Pathway and Preventing Post-Operative Cognitive Dysfunction as Well as Neuronal Apoptosis. IRANIAN JOURNAL OF PUBLIC HEALTH 2022; 51:124-132. [PMID: 35223633 PMCID: PMC8837897 DOI: 10.18502/ijph.v51i1.8303] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/04/2021] [Indexed: 11/25/2022]
Abstract
Background: The Postoperative cognitive dysfunction (POCD) model was constructed by resection of the left hepatic lobe in aged mice to determine the behavioral effects of the POCD model in aged mice and the relationship between NF-κB and POCD in apoptosis and autophagy. Provide a theoretical basis for POCD prevention and treatment. Methods: This study was carried out in Ningbo No. 6 Hospital, Zhejiang, China, from Jun 2019 to Dec 2020. The POCD model was constructed after resection of the left extrahepatic lobe in aged mice and randomly divided into 6 groups: sham operation group, operation group (normal saline control group, solvent group, YC-1 group, PDTC group and 3-MA group). Related indicators of behavioral changes, neuronal inflammatory responses, apoptosis, and autophagy were examined. Results: The escape latency of the aged mice in the surgical group was significantly prolonged at three time points compared with the control group, and the number of insertions decreased significantly. Microglia are activated and the inflammatory response is increased, whereas PDTC has an inhibitory effect. It was demonstrated that apoptosis and necrosis of neurons can be induced by the NF-κb pathway, and autophagy can be promoted, whereas autophagy occurs before apoptosis. Conclusion: Activation of NF-κb pathway in neurons after POCD causes neuronal apoptosis and autophagy, and cognitive impairment occurs. PDTC, a NF-κb pathway inhibitor, can effectively reduce neuronal apoptosis induced by secondary brain injury after POCD. Necrosis, to protect the brain tissue.
Collapse
Affiliation(s)
- Na Yuan
- Department of Anaesthesia, Ningbo NO.6 Hospital, Zhejiang 315040, China
| | - Xiuzhen Wang
- Department of Anaesthesia, Ningbo NO.6 Hospital, Zhejiang 315040, China
| | - Yu Zhang
- Department of Anaesthesia, Ningbo NO.6 Hospital, Zhejiang 315040, China
| | - Lingsi Kong
- Department of Anaesthesia, Ningbo NO.6 Hospital, Zhejiang 315040, China
| | - Liyong Yuan
- Department of Anaesthesia, Ningbo NO.6 Hospital, Zhejiang 315040, China
| | - Yeying Ge
- Department of Anaesthesia, Ningbo NO.6 Hospital, Zhejiang 315040, China
| |
Collapse
|