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Chai GS, Gong J, Mao YM, Wu JJ, Bi SG, Wang F, Zhang YQ, Shen MT, Lei ZY, Nie YJ, Yu H. H3K4 Trimethylation Mediate Hyperhomocysteinemia Induced Neurodegeneration via Suppressing Histone Acetylation by ANP32A. Mol Neurobiol 2024; 61:6788-6804. [PMID: 38351418 DOI: 10.1007/s12035-024-03995-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/29/2024] [Indexed: 08/22/2024]
Abstract
Homocysteine (Hcy) is an independent and serious risk factor for dementia, including Alzheimer's disease (AD), but the precise mechanisms are still poorly understood. In the current study, we observed that the permissive histone mark trimethyl histone H3 lysine 4 (H3K4me3) and its methyltransferase KMT2B were significantly elevated in hyperhomocysteinemia (HHcy) rats, with impairment of synaptic plasticity and cognitive function. Further research found that histone methylation inhibited synapse-associated protein expression, by suppressing histone acetylation. Inhibiting H3K4me3 by downregulating KMT2B could effectively restore Hcy-inhibited H3K14ace in N2a cells. Moreover, chromatin immunoprecipitation revealed that Hcy-induced H3K4me3 resulted in ANP32A mRNA and protein overexpression in the hippocampus, which was regulated by increased transcription Factor c-fos and inhibited histone acetylation and synapse-associated protein expression, and downregulating ANP32A could reverse these changes in Hcy-treated N2a cells. Additionally, the knockdown of KMT2B restored histone acetylation and synapse-associated proteins in Hcy-treated primary hippocampal neurons. These data have revealed a novel crosstalk mechanism between KMT2B-H3K4me3-ANP32A-H3K14ace, shedding light on its role in Hcy-related neurogenerative disorders.
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Affiliation(s)
- Gao-Shang Chai
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China.
| | - Juan Gong
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Yu-Ming Mao
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Jia-Jun Wu
- Department of Electrophysiology, Wuhan Children's Hospital (Wuhan Maternal and Children's Healthcare Center), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430010, People's Republic of China
| | - Shu-Guang Bi
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Fangzhou Wang
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Yu-Qi Zhang
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Meng-Ting Shen
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Zhuo-Ya Lei
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Yun-Juan Nie
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Haitao Yu
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China.
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Martá-Ariza M, Leitner DF, Kanshin E, Suazo J, Pedrosa AG, Thierry M, Lee EB, Devinsky O, Drummond E, Fortea J, Lleó A, Ueberheide B, Wisniewski T. Comparison of the Amyloid Plaque Proteome in Down Syndrome, Early-Onset Alzheimer's Disease and Late-Onset Alzheimer's Disease. RESEARCH SQUARE 2024:rs.3.rs-4469045. [PMID: 39070643 PMCID: PMC11275979 DOI: 10.21203/rs.3.rs-4469045/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Background Down syndrome (DS) is strongly associated with Alzheimer's disease (AD), attributable to APP overexpression. DS exhibits Amyloid-β (Aβ) and Tau pathology similar to early-onset AD (EOAD) and late-onset AD (LOAD). The study aimed to evaluate the Aβ plaque proteome of DS, EOAD and LOAD. Methods Using unbiased localized proteomics, we analyzed amyloid plaques and adjacent plaque-devoid tissue ('non-plaque') from post-mortem paraffin-embedded tissues in four cohorts (n = 20/group): DS (59.8 ± 4.99 y/o), EOAD (63 ± 4.07 y/o), LOAD (82.1 ± 6.37 y/o) and controls (66.4 ± 13.04). We assessed functional associations using Gene Ontology (GO) enrichment and protein interaction networks. Results We identified differentially abundant Aβ plaque proteins vs. non-plaques (FDR < 5%, fold-change > 1.5) in DS (n = 132), EOAD (n = 192) and in LOAD (n = 128); there were 43 plaque-associated proteins shared between all groups. Positive correlations (p < 0.0001) were observed between plaque-associated proteins in DS and EOAD (R2 = 0.77), DS and LOAD (R2 = 0.73), and EOAD vs. LOAD (R2 = 0.67). Top Biological process (BP) GO terms (p < 0.0001) included lysosomal transport for DS, immune system regulation for EOAD, and lysosome organization for LOAD. Protein networks revealed a plaque enriched signature across all cohorts involving APP metabolism, immune response, and lysosomal functions. In DS, EOAD and LOAD non-plaque vs. control tissue, we identified 263, 269, and 301 differentially abundant proteins, including 65 altered non-plaque proteins across all cohorts. Differentially abundant non-plaque proteins in DS showed a significant (p < 0.0001) but weaker positive correlation with EOAD (R2 = 0.59) and LOAD (R2 = 0.33) compared to the stronger correlation between EOAD and LOAD (R2 = 0.79). The top BP GO term for all groups was chromatin remodeling (DS p = 0.0013, EOAD p = 5.79×10- 9, and LOAD p = 1.69×10- 10). Additional GO terms for DS included extracellular matrix (p = 0.0068), while EOAD and LOAD were associated with protein-DNA complexes and gene expression regulation (p < 0.0001). Conclusions We found strong similarities among the Aβ plaque proteomes in individuals with DS, EOAD and LOAD, and a robust association between the plaque proteomes and lysosomal and immune-related pathways. Further, non-plaque proteomes highlighted altered pathways related to chromatin structure and extracellular matrix (ECM), the latter particularly associated with DS. We identified novel Aβ plaque proteins, which may serve as biomarkers or therapeutic targets.
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Affiliation(s)
| | | | | | | | | | | | - Edward B Lee
- University of Pennsylvania Perelman School of Medicine
| | | | | | - Juan Fortea
- Universitat Autònoma de Barcelona: Universitat Autonoma de Barcelona
| | - Alberto Lleó
- Universitat Autònoma de Barcelona: Universitat Autonoma de Barcelona
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3
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Cui Y, Zhang X, Liu J, Hou Y, Song Q, Cao M, Zhang J, Wang X, Liu C, Wang P, Wang Y. Myeloid ectopic viral integration site 2 accelerates the progression of Alzheimer's disease. Aging Cell 2024:e14260. [PMID: 38994634 DOI: 10.1111/acel.14260] [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: 02/28/2024] [Revised: 05/29/2024] [Accepted: 06/11/2024] [Indexed: 07/13/2024] Open
Abstract
Amyloid plaques, a major pathological hallmark of Alzheimer's disease (AD), are caused by an imbalance between the amyloidogenic and non-amyloidogenic pathways of amyloid precursor protein (APP). BACE1 cleavage of APP is the rate-limiting step for amyloid-β production and plaque formation in AD. Although the alteration of BACE1 expression in AD has been investigated, the underlying mechanisms remain unknown. In this study, we determined MEIS2 was notably elevated in AD models and AD patients. Alterations in the expression of MEIS2 can modulate the levels of BACE1. MEIS2 downregulation improved the learning and memory retention of AD mice and decreased the number of amyloid plaques. MEIS2 binds to the BACE1 promoter, positively regulates BACE1 expression, and accelerates APP amyloid degradation in vitro. Therefore, our findings suggest that MEIS2 might be a critical transcription factor in AD, since it regulates BACE1 expression and accelerates BACE1-mediated APP amyloidogenic cleavage. MEIS2 is a promising early intervention target for AD treatment.
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Affiliation(s)
- Yuting Cui
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Xiaomin Zhang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Jing Liu
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Yuli Hou
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Qiao Song
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Min Cao
- Department of Clinical Laboratory, Beijing Huairou Hospital, Beijing, People's Republic of China
| | - Jingjing Zhang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Xiaoling Wang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Congcong Liu
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Peichang Wang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Yaqi Wang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, People's Republic of China
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4
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Wang J, Zhen Y, Yang J, Yang S, Zhu G. Recognizing Alzheimer's disease from perspective of oligodendrocytes: Phenomena or pathogenesis? CNS Neurosci Ther 2024; 30:e14688. [PMID: 38516808 PMCID: PMC10958408 DOI: 10.1111/cns.14688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/11/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Accumulation of amyloid beta, tau hyperphosphorylation, and microglia activation are the three highly acknowledged pathological factors of Alzheimer's disease (AD). However, oligodendrocytes (OLs) were also widely investigated in the pathogenesis and treatment for AD. AIMS We aimed to update the regulatory targets of the differentiation and maturation of OLs, and emphasized the key role of OLs in the occurrence and treatment of AD. METHODS This review first concluded the targets of OL differentiation and maturation with AD pathogenesis, and then advanced the key role of OLs in the pathogenesis of AD based on both clinic and basic experiments. Later, we extensively discussed the possible application of the current progress in the diagnosis and treatment of this complex disease. RESULTS Molecules involving in OLs' differentiation or maturation, including various transcriptional factors, cholesterol homeostasis regulators, and microRNAs could also participate in the pathogenesis of AD. Clinical data point towards the impairment of OLs in AD patients. Basic research further supports the central role of OLs in the regulation of AD pathologies. Additionally, classic drugs, including donepezil, edaravone, fluoxetine, and clemastine demonstrate their potential in remedying OL impairment in AD models, and new therapeutics from the perspective of OLs is constantly being developed. CONCLUSIONS We believe that OL dysfunction is one important pathogenesis of AD. Factors regulating OLs might be biomarkers for early diagnosis and agents stimulating OLs warrant the development of anti-AD drugs.
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Affiliation(s)
- Jingji Wang
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, and Key Laboratory of Molecular Biology (Brain Diseases)Anhui University of Chinese MedicineHefeiChina
- Acupuncture and Moxibustion Clinical Medical Research Center of Anhui ProvinceThe Second Affiliation Hospital of Anhui University of Chinese MedicineHefeiChina
| | - Yilan Zhen
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, and Key Laboratory of Molecular Biology (Brain Diseases)Anhui University of Chinese MedicineHefeiChina
| | - Jun Yang
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, and Key Laboratory of Molecular Biology (Brain Diseases)Anhui University of Chinese MedicineHefeiChina
- The First Affiliation Hospital of Anhui University of Chinese MedicineHefeiChina
| | - Shaojie Yang
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, and Key Laboratory of Molecular Biology (Brain Diseases)Anhui University of Chinese MedicineHefeiChina
| | - Guoqi Zhu
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, and Key Laboratory of Molecular Biology (Brain Diseases)Anhui University of Chinese MedicineHefeiChina
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Tang S, Cui X, Wang R, Li S, Li S, Huang X, Chen S. scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data. Nat Commun 2024; 15:1629. [PMID: 38388573 PMCID: PMC10884038 DOI: 10.1038/s41467-024-46045-w] [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: 09/21/2023] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Single-cell chromatin accessibility sequencing (scCAS) has emerged as a valuable tool for interrogating and elucidating epigenomic heterogeneity and gene regulation. However, scCAS data inherently suffers from limitations such as high sparsity and dimensionality, which pose significant challenges for downstream analyses. Although several methods are proposed to enhance scCAS data, there are still challenges and limitations that hinder the effectiveness of these methods. Here, we propose scCASE, a scCAS data enhancement method based on non-negative matrix factorization which incorporates an iteratively updating cell-to-cell similarity matrix. Through comprehensive experiments on multiple datasets, we demonstrate the advantages of scCASE over existing methods for scCAS data enhancement. The interpretable cell type-specific peaks identified by scCASE can provide valuable biological insights into cell subpopulations. Moreover, to leverage the large compendia of available omics data as a reference, we further expand scCASE to scCASER, which enables the incorporation of external reference data to improve enhancement performance.
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Affiliation(s)
- Songming Tang
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, China
| | - Xuejian Cui
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Rongxiang Wang
- Department of Computer Science, University of Virginia, Charlottesville, VA, 22903, USA
| | - Sijie Li
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, China
| | - Siyu Li
- School of Statistics and Data Science, Nankai University, Tianjin, 300071, China
| | - Xin Huang
- Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, 100850, Beijing, China
| | - Shengquan Chen
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, China.
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Chen XY, Feng SN, Bao Y, Zhou YX, Ba F. Identification of Clec7a as the therapeutic target of rTMS in alleviating Parkinson's disease: targeting neuroinflammation. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166814. [PMID: 37495085 DOI: 10.1016/j.bbadis.2023.166814] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/25/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disease. Repetitive transcranial magnetic stimulation (rTMS) is a therapeutic tool in PD. High-throughput sequencing was performed to screen potential therapeutic targets in unilaterally 6-hydroxydopamine (6-OHDA)-lesioned rats. The candidate gene, Clec7a, was screened out and validated. Clec7a is a pattern recognition receptor involved in neuroinflammation. The higher expression of Clec7a was observed in the substantia nigra (SN) and striatum of PD rats with dopaminergic neurons damage and was mainly localized in the microglial. Adeno-associated virus (AAV)-mediated specific knockdown of Clec7a in microglial alleviated 6-OHDA induced motor deficits and nigrostriatal dopaminergic neuron damage of rats, as evidenced by the increase of tyrosine hydroxylase (TH) -positive neurons in SN, as well as dopaminergic nerve fibers in the striatum. Clec7a knockdown restrained the neuroinflammation by suppressing inflammatory factors (IFN-γ, TNF-α, IL-1β, IL-18, and IL-6) release in SN, which might result from enhanced Arg-1 expression (M2 polarization) and defective inducible nitric oxide synthase (iNOS) expression (M1 polarization). The same phenomena were also observed in the LPS inflammatory rat model of PD. In vitro, α-synuclein fibrils induced upregulation of Clec7a expression and microglia polarization to a pro-inflammatory state of BV2 cells, leading to increased release of cytokines. However, Clec7a knockdown reversed those changes and induced a shift to an anti-inflammatory phenotype in BV2 cells. In conclusion, our study suggested that Clec7a was involved in PD pathogenesis, and its inhibition might protect rats from PD by depressing neuroinflammation through microglial polarization.
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Affiliation(s)
- Xue-Yun Chen
- Department of Rehabilitation, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, China
| | - Si-Ning Feng
- Department of Rehabilitation, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, China
| | - Yin Bao
- Department of Rehabilitation, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, China
| | - Yu-Xin Zhou
- Department of Rehabilitation, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, China
| | - Fang Ba
- Department of Rehabilitation, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, China.
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7
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Wang H, Guo B, Guo X. Histone demethylases in neurodevelopment and neurodegenerative diseases. Int J Neurosci 2023:1-11. [PMID: 37902510 DOI: 10.1080/00207454.2023.2276656] [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: 06/21/2023] [Accepted: 10/23/2023] [Indexed: 10/31/2023]
Abstract
Neurodevelopment can be precisely regulated by epigenetic mechanisms, including DNA methylations, noncoding RNAs, and histone modifications. Histone methylation was a reversible modification, catalyzed by histone methyltransferases and demethylases. So far, dozens of histone lysine demethylases (KDMs) have been discovered, and they (members from KDM1 to KDM7 family) are important for neurodevelopment by regulating cellular processes, such as chromatin structure and gene transcription. The role of KDM5C and KDM7B in neural development is particularly important, and mutations in both genes are frequently found in human X-linked mental retardation (XLMR). Functional disorders of specific KDMs, such as KDM1A can lead to the development of neurodegenerative diseases, including Alzheimer's disease (AD) and Parkinson's disease (PD). Several KDMs can serve as potential therapeutic targets in the treatment of neurodegenerative diseases. At present, the function of KDMs in neurodegenerative diseases is not fully understood, so more comprehensive and profound studies are needed. Here, the role and mechanism of histone demethylases were summarized in neurodevelopment, and the potential of them was introduced in the treatment of neurodegenerative diseases.
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Affiliation(s)
- Haiying Wang
- Department of Sports Human Sciences, Hebei Social Science Foundation Project Research Group, Hebei Sport University, Shijiazhuang, Hebei, China
| | - Beiyi Guo
- School of Sports Medicine and Rehabilitation, Beijing Sport University, Beijing, China
| | - Xiaoqiang Guo
- Department of Sports Human Sciences, Hebei Social Science Foundation Project Research Group, Hebei Sport University, Shijiazhuang, Hebei, China
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8
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Jin J, Guang M, Li S, Liu Y, Zhang L, Zhang B, Cheng M, Schmalz G, Huang X. Immune-related signature of periodontitis and Alzheimer's disease linkage. Front Genet 2023; 14:1230245. [PMID: 37849501 PMCID: PMC10577303 DOI: 10.3389/fgene.2023.1230245] [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: 06/27/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023] Open
Abstract
Background: Periodontits (PD) and Alzheimer's disease (AD) are both associated with ageing and clinical studies increasingly evidence their association. However, specific mechanisms underlying this association remain undeciphered, and immune-related processes are purported to play a signifcant role. The accrual of publicly available transcriptomic datasets permits secondary analysis and the application of data-mining and bioinformatic tools for biological discovery. Aim: The present study aimed to leverage publicly available transcriptomic datasets and databases, and apply a series of bioinformatic analysis to identify a robust signature of immune-related signature of PD and AD linkage. Methods: We downloaded gene-expresssion data pertaining PD and AD and identified crosstalk genes. We constructed a protein-protein network analysis, applied immune cell enrichment analysis, and predicted crosstalk immune-related genes and infiltrating immune cells. Next, we applied consisent cluster analysis and performed immune cell bias analysis, followed by LASSO regression to select biomarker immune-related genes. Results: The results showed a 3 gene set comprising of DUSP14, F13A1 and SELE as a robust immune-related signature. Macrophages M2 and NKT, B-cells, CD4+ memory T-cells and CD8+ naive T-cells emerged as key immune cells linking PD with AD. Conclusion: Candidate immune-related biomarker genes and immune cells central to the assocation of PD with AD were identified, and merit investigation in experimental and clinical research.
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Affiliation(s)
- Jieqi Jin
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Mengkai Guang
- Department of Stomatology, China-Japan Friendship Hospital, Beijing, China
| | - Simin Li
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Yong Liu
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Liwei Zhang
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Bo Zhang
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Menglin Cheng
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Gerhard Schmalz
- Department of Cariology, Endodontology and Periodontology, Leipzig University, Leipzig, Germany
| | - Xiaofeng Huang
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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9
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Hashemi KS, Aliabadi MK, Mehrara A, Talebi E, Hemmati AA, Rezaeiye RD, Ghanbary MJ, Motealleh M, Dayeri B, Alashti SK. A meta-analysis of microarray datasets to identify biological regulatory networks in Alzheimer's disease. Front Genet 2023; 14:1225196. [PMID: 37705610 PMCID: PMC10497115 DOI: 10.3389/fgene.2023.1225196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023] Open
Abstract
Background: Alzheimer's Disease (AD) is an age-related progressive neurodegenerative disorder characterized by mental deterioration, memory deficit, and multiple cognitive abnormalities, with an overall prevalence of ∼2% among industrialized countries. Although a proper diagnosis is not yet available, identification of miRNAs and mRNAs could offer valuable insights into the molecular pathways underlying AD's prognosis. Method: This study aims to utilize microarray bioinformatic analysis to identify potential biomarkers of AD, by analyzing six microarray datasets (GSE4757, GSE5281, GSE16759, GSE28146, GSE12685, and GSE1297) of AD patients, and control groups. Furthermore, this study conducted gene ontology, pathways analysis, and protein-protein interaction network to reveal major pathways linked to probable biological events. The datasets were meta-analyzed using bioinformatics tools, to identify significant differentially expressed genes (DEGs) and hub genes and their targeted miRNAs'. Results: According to the findings, CXCR4, TGFB1, ITGB1, MYH11, and SELE genes were identified as hub genes in this study. The analysis of DEGs using GO (gene ontology) revealed that these genes were significantly enriched in actin cytoskeleton regulation, ECM-receptor interaction, and hypertrophic cardiomyopathy. Eventually, hsa-mir-122-5p, hsa-mir-106a-5p, hsa-mir-27a-3p, hsa-mir16-5p, hsa-mir-145-5p, hsa-mir-12-5p, hsa-mir-128-3p, hsa-mir 3200-3p, hsa-mir-103a-3p, and hsa-mir-9-3p exhibited significant interactions with most of the hub genes. Conclusion: Overall, these genes can be considered as pivotal biomarkers for diagnosing the pathogenesis and molecular functions of AD.
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Affiliation(s)
- Kimia Sadat Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohadese Koohi Aliabadi
- Faculty of Interdisciplinary Science and Technology, Tarbiat Modares University, Tehran, Iran
| | - Arian Mehrara
- School of Pharmacy, Ramsar International Campus, Mazandaran University of Medical Sciences, Ramsar, Iran
| | - Elham Talebi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ali Akbar Hemmati
- Department of Biology and Biotechnology, Molecular Biology, and Genetics, Pavia University, Lombardi, Italy
| | | | | | - Maryam Motealleh
- Department of System Biology Lab, University of Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Behnaz Dayeri
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Biotechnology, University of Milan, Milan, Italy
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10
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Powell J, Talenti A, Fisch A, Hemmink JD, Paxton E, Toye P, Santos I, Ferreira BR, Connelley TK, Morrison LJ, Prendergast JGD. Profiling the immune epigenome across global cattle breeds. Genome Biol 2023; 24:127. [PMID: 37218021 DOI: 10.1186/s13059-023-02964-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 05/08/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Understanding the variation between well and poorly adapted cattle breeds to local environments and pathogens is essential for breeding cattle with improved climate and disease-resistant phenotypes. Although considerable progress has been made towards identifying genetic differences between breeds, variation at the epigenetic and chromatin levels remains poorly characterized. Here, we generate, sequence and analyse over 150 libraries at base-pair resolution to explore the dynamics of DNA methylation and chromatin accessibility of the bovine immune system across three distinct cattle lineages. RESULTS We find extensive epigenetic divergence between the taurine and indicine cattle breeds across immune cell types, which is linked to the levels of local DNA sequence divergence between the two cattle sub-species. The unique cell type profiles enable the deconvolution of complex cellular mixtures using digital cytometry approaches. Finally, we show distinct sub-categories of CpG islands based on their chromatin and methylation profiles that discriminate between classes of distal and gene proximal islands linked to discrete transcriptional states. CONCLUSIONS Our study provides a comprehensive resource of DNA methylation, chromatin accessibility and RNA expression profiles of three diverse cattle populations. The findings have important implications, from understanding how genetic editing across breeds, and consequently regulatory backgrounds, may have distinct impacts to designing effective cattle epigenome-wide association studies in non-European breeds.
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Affiliation(s)
- Jessica Powell
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
| | - Andrea Talenti
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Andressa Fisch
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Johanneke D Hemmink
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
- The International Livestock Research Institute, PO Box 30709, Nairobi, 00100, Kenya
| | - Edith Paxton
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Philip Toye
- The International Livestock Research Institute, PO Box 30709, Nairobi, 00100, Kenya
- Centre for Tropical Livestock Genetics and Health, ILRI Kenya, PO Box 30709, Nairobi, 00100, Kenya
| | - Isabel Santos
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Beatriz R Ferreira
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Tim K Connelley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Liam J Morrison
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
| | - James G D Prendergast
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
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11
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Tautou M, Descamps F, Larchanché PE, Buée L, El Bakali J, Melnyk P, Sergeant N. A Polyaminobiaryl-Based β-secretase Modulator Alleviates Cognitive Impairments, Amyloid Load, Astrogliosis, and Neuroinflammation in APPSwe/PSEN1ΔE9 Mice Model of Amyloid Pathology. Int J Mol Sci 2023; 24:ijms24065285. [PMID: 36982363 PMCID: PMC10048993 DOI: 10.3390/ijms24065285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/03/2023] [Accepted: 02/15/2023] [Indexed: 03/12/2023] Open
Abstract
The progress in Alzheimer’s disease (AD) treatment suggests a combined therapeutic approach targeting the two lesional processes of AD, which include amyloid plaques made of toxic Aβ species and neurofibrillary tangles formed of aggregates of abnormally modified Tau proteins. A pharmacophoric design, novel drug synthesis, and structure-activity relationship enabled the selection of a polyamino biaryl PEL24-199 compound. The pharmacologic activity consists of a non-competitive β-secretase (BACE1) modulatory activity in cells. Curative treatment of the Thy-Tau22 model of Tau pathology restores short-term spatial memory, decreases neurofibrillary degeneration, and alleviates astrogliosis and neuroinflammatory reactions. Modulatory effects of PEL24-199 towards APP catalytic byproducts are described in vitro, but whether PEL24-199 can alleviate the Aβ plaque load and associated inflammatory counterparts in vivo remains to be elucidated. We investigated short- and long-term spatial memory, Aβ plaque load, and inflammatory processes in APPSwe/PSEN1ΔE9 PEL24-199 treated transgenic model of amyloid pathology to achieve this objective. PEL24-199 curative treatment induced the recovery of spatial memory and decreased the amyloid plaque load in association with decreased astrogliosis and neuroinflammation. The present results underline the synthesis and selection of a promising polyaminobiaryl-based drug that modulates both Tau and, in this case, APP pathology in vivo via a neuroinflammatory-dependent process.
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Affiliation(s)
- Marie Tautou
- Univ. Lille, Inserm, CHU Lille, UMRS1172—LilNCog—Lille Neuroscience & Cognition, 59000 Lille, France
| | - Florian Descamps
- Univ. Lille, Inserm, CHU Lille, UMRS1172—LilNCog—Lille Neuroscience & Cognition, 59000 Lille, France
| | - Paul-Emmanuel Larchanché
- Univ. Lille, Inserm, CHU Lille, UMRS1172—LilNCog—Lille Neuroscience & Cognition, 59000 Lille, France
| | - Luc Buée
- Univ. Lille, Inserm, CHU Lille, UMRS1172—LilNCog—Lille Neuroscience & Cognition, 59000 Lille, France
- Alzheimer & Tauopathies, LabEx DISTALZ, 59045 Lille, France
| | - Jamal El Bakali
- Univ. Lille, Inserm, CHU Lille, UMRS1172—LilNCog—Lille Neuroscience & Cognition, 59000 Lille, France
| | - Patricia Melnyk
- Univ. Lille, Inserm, CHU Lille, UMRS1172—LilNCog—Lille Neuroscience & Cognition, 59000 Lille, France
- Correspondence: (P.M.); (N.S.); Tel.: +33-663101728 (N.S.)
| | - Nicolas Sergeant
- Univ. Lille, Inserm, CHU Lille, UMRS1172—LilNCog—Lille Neuroscience & Cognition, 59000 Lille, France
- Alzheimer & Tauopathies, LabEx DISTALZ, 59045 Lille, France
- Correspondence: (P.M.); (N.S.); Tel.: +33-663101728 (N.S.)
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12
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Zhao J, Huai J. Role of primary aging hallmarks in Alzheimer´s disease. Theranostics 2023; 13:197-230. [PMID: 36593969 PMCID: PMC9800733 DOI: 10.7150/thno.79535] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease, which severely threatens the health of the elderly and causes significant economic and social burdens. The causes of AD are complex and include heritable but mostly aging-related factors. The primary aging hallmarks include genomic instability, telomere wear, epigenetic changes, and loss of protein stability, which play a dominant role in the aging process. Although AD is closely associated with the aging process, the underlying mechanisms involved in AD pathogenesis have not been well characterized. This review summarizes the available literature about primary aging hallmarks and their roles in AD pathogenesis. By analyzing published literature, we attempted to uncover the possible mechanisms of aberrant epigenetic markers with related enzymes, transcription factors, and loss of proteostasis in AD. In particular, the importance of oxidative stress-induced DNA methylation and DNA methylation-directed histone modifications and proteostasis are highlighted. A molecular network of gene regulatory elements that undergoes a dynamic change with age may underlie age-dependent AD pathogenesis, and can be used as a new drug target to treat AD.
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13
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Wang M, Ji C, Zhang Y, Zhang Z, Zhang Y, Guo H, Qiao N, Zhou X, Cao X, Ye Z, Yu Y, Melnikov V, Gong W, He M, Zhang Z, Zhao Y, Wang X, Wei G, Ye Z. Global changes in chromatin accessibility and transcription in growth hormone-secreting pituitary adenoma. Endocrine 2022; 78:329-342. [PMID: 35947334 PMCID: PMC9584994 DOI: 10.1007/s12020-022-03155-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE Growth hormone-secreting pituitary adenoma (GHPA) is an insidious disease with persistent hypersecretion of growth hormone and insulin-like growth factor 1, causing increased morbidity and mortality. Previous studies have investigated the transcription of GHPA. However, the gene regulatory landscape has not been fully characterized. The objective of our study was to unravel the changes in chromatin accessibility and transcription in GHPA. METHODS Six patients diagnosed with GHPA in the Department of Neurosurgery at Huashan Hospital were enrolled in our study. Primary pituitary adenoma tissues and adjacent normal pituitary specimens with no morphologic abnormalities from these six patients were obtained at surgery. RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) were applied to investigate the underlying relationship between gene expression and chromatin accessibility changes in GHPA. RESULTS Totally, 1528 differential expression genes (DEGs) were identified by transcriptomics analyses, including 725 up-regulated and 803 down-regulated. Further, we obtained 64 significantly DEGs including 10 DEGs were elevated and 54 DEGs were negligibly expressed in tumors tissues. The up-regulated DEGs were mainly involved in terms related to synapse formation, nervous system development and secretory pathway. In parallel, 3916 increased and 2895 decreased chromatin-accessible regions were mapped by ATAC-seq. Additionally, the chromatin accessible changes were frequently located adjacent to transcription factor CTCF and Rfx2 binding site. CONCLUSIONS Our results are the first to demonstrate the landscape of chromatin accessibility in GHPA, which may contribute to illustrate the underlying transcriptional regulation mechanism of this disease.
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Affiliation(s)
- Meng Wang
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chenxing Ji
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, National Center for Neurological Disorders, Shanghai, China
| | - Yichao Zhang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, National Center for Neurological Disorders, Shanghai, China
| | - Zhiqiang Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Huiping Guo
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Nidan Qiao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, National Center for Neurological Disorders, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
| | - Xiang Zhou
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, National Center for Neurological Disorders, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
| | - Xiaoyun Cao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, National Center for Neurological Disorders, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
| | - Zhen Ye
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, National Center for Neurological Disorders, Shanghai, China
| | - Yifei Yu
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Vladimir Melnikov
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Gong
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Min He
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhaoyun Zhang
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yao Zhao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, National Center for Neurological Disorders, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- Sate Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
- Neurosurgical Institute of Fudan University, Fudan University, Shanghai, China
| | - Xuelong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Zhao Ye
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, National Center for Neurological Disorders, Shanghai, China.
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China.
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14
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Song Q, Hou Y, Zhang Y, Liu J, Wang Y, Fu J, Zhang C, Cao M, Cui Y, Zhang X, Wang X, Zhang J, Liu C, Zhang Y, Wang P. Integrated multi-omics approach revealed cellular senescence landscape. Nucleic Acids Res 2022; 50:10947-10963. [PMID: 36243980 PMCID: PMC9638896 DOI: 10.1093/nar/gkac885] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/27/2022] [Accepted: 10/01/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular senescence is a complex multifactorial biological phenomenon that plays essential roles in aging, and aging-related diseases. During this process, the senescent cells undergo gene expression altering and chromatin structure remodeling. However, studies on the epigenetic landscape of senescence using integrated multi-omics approaches are limited. In this research, we performed ATAC-seq, RNA-seq and ChIP-seq on different senescent types to reveal the landscape of senescence and identify the prime regulatory elements. We also obtained 34 key genes and deduced that NAT1, PBX1 and RRM2, which interacted with each other, could be the potential markers of aging and aging-related diseases. In summary, our work provides the landscape to study accessibility dynamics and transcriptional regulations in cellular senescence. The application of this technique in different types of senescence allows us to identify the regulatory elements responsible for the substantial regulation of transcription, providing the insights into molecular mechanisms of senescence.
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Affiliation(s)
- Qiao Song
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yuli Hou
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yiyin Zhang
- Shanghai Jiayin Biotechnology, Shanghai 200092, PR China
| | - Jing Liu
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yaqi Wang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Jingxuan Fu
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Chi Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Min Cao
- Department of Clinical Laboratory, Beijing Huairou Hospital, Beijing 101400, PR China
| | - Yuting Cui
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Xiaomin Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Xiaoling Wang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Jingjing Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Congcong Liu
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yingzhen Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Peichang Wang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
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15
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Tan J, Xu T, Gou Y, Wang H, Liang Z, Cao Y, Wang H, Yu Y, Jiao N, Zhang Z. CCL20/CCR6 axis mediates macrophages to promote proliferation and migration of ESCs by blocking autophagic flux in endometriosis. Stem Cell Res Ther 2022; 13:294. [PMID: 35841069 PMCID: PMC9284876 DOI: 10.1186/s13287-022-02981-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/23/2022] [Indexed: 11/18/2022] Open
Abstract
Background Endometriosis (EMs) is a common benign gynecological disease that affects approximately 10% of females of reproductive age. Endometriosis ectopic lesions could recruit macrophages, which in turn facilitates endometriosis progression. Several studies have indicated that CCL20 derived from macrophages activates the expression of CCR6 in several cells and induces cell proliferation and migration. However, the function of the CCL20/CCR6 axis in the interactions between macrophages and endometriotic stromal cells (ESCs) in EMs has yet to be elucidated. Methods Ectopic and normal endometrial tissues were collected from 35 ovarian endometriosis patients and 21 control participants for immunohistochemical staining. It was confirmed that macrophages secreted CCL20 to promote CCR6 activation of ESCs during co-culture by ELISA, qRT-PCR and western blot analysis. CCK8 and Edu assays were used to detect cell proliferation, and wound healing and Transwell assay were used to detect cell migration. Autophagic flux was detected by measuring the protein expression levels of LC3 and P62by western blot and analyzing the red/yellow puncta after ESCs were transfected with mRFP-GFP-LC3 double fluorescence adenovirus (Ad‐LC3). Lysosomal function was tested by quantifying the fluorescent intensities of Lyso-tracker and Gal3 and activity of acid phosphatase. In addition, co-IP experiments verified the binding relationship between CCR6 and TFEB. Finally, the suppressive effect of CCL20-NAb on endometriosis lesions in vivo was demonstrated in mice models. Results We demonstrated that macrophages secreted CCL20 to promote CCR6 activation of ESCs during co-culture, which further induced the proliferation and migration of ESCs. We observed that the CCL20/CCR6 axis impaired lysosomal function and then blocked the autolysosome degradation process of autophagic flux in ESCs. The combination of CCR6 and TFEB to inhibit TFEB nuclear translocation mediates the role of the CCL20/CCR6 axis in the above process. We also found that co-culture with ESCs upregulated the production and secretion of CCL20 by macrophages. The suppression effect of CCL20-NAb on endometriosis lesions in vivo was demonstrated in mice models. Conclusions Our data indicate that macrophages block TFEB-mediated autolysosome degradation process of autophagic flux in ESCs via the CCL20/CCR6 axis, thereby promoting ESC proliferation and migration. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02981-2.
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Affiliation(s)
- Jiahuan Tan
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Harbin Medical University, 148 Baojian Road, Harbin, 150086, China
| | - Tenghan Xu
- Department of Obstetrics and Gynecology, Luohe Central Hospital, Luohe, China
| | - Yanling Gou
- Department of Obstetrics and Gynecology, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Honglin Wang
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Harbin Medical University, 148 Baojian Road, Harbin, 150086, China
| | - Zongwen Liang
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Harbin Medical University, 148 Baojian Road, Harbin, 150086, China
| | - Yingying Cao
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Harbin Medical University, 148 Baojian Road, Harbin, 150086, China
| | - Han Wang
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Harbin Medical University, 148 Baojian Road, Harbin, 150086, China
| | - Yangyang Yu
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Harbin Medical University, 148 Baojian Road, Harbin, 150086, China
| | - Na Jiao
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Harbin Medical University, 148 Baojian Road, Harbin, 150086, China
| | - Zongfeng Zhang
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Harbin Medical University, 148 Baojian Road, Harbin, 150086, China.
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16
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Park J, Lee K, Kim K, Yi SJ. The role of histone modifications: from neurodevelopment to neurodiseases. Signal Transduct Target Ther 2022; 7:217. [PMID: 35794091 PMCID: PMC9259618 DOI: 10.1038/s41392-022-01078-9] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/11/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022] Open
Abstract
Epigenetic regulatory mechanisms, including DNA methylation, histone modification, chromatin remodeling, and microRNA expression, play critical roles in cell differentiation and organ development through spatial and temporal gene regulation. Neurogenesis is a sophisticated and complex process by which neural stem cells differentiate into specialized brain cell types at specific times and regions of the brain. A growing body of evidence suggests that epigenetic mechanisms, such as histone modifications, allow the fine-tuning and coordination of spatiotemporal gene expressions during neurogenesis. Aberrant histone modifications contribute to the development of neurodegenerative and neuropsychiatric diseases. Herein, recent progress in understanding histone modifications in regulating embryonic and adult neurogenesis is comprehensively reviewed. The histone modifications implicated in neurodegenerative and neuropsychiatric diseases are also covered, and future directions in this area are provided.
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Affiliation(s)
- Jisu Park
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Kyubin Lee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Kyunghwan Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
| | - Sun-Ju Yi
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
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17
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Massimini M, Bachetti B, Dalle Vedove E, Benvenga A, Di Pierro F, Bernabò N. A Set of Dysregulated Target Genes to Reduce Neuroinflammation at Molecular Level. Int J Mol Sci 2022; 23:ijms23137175. [PMID: 35806178 PMCID: PMC9266409 DOI: 10.3390/ijms23137175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 01/27/2023] Open
Abstract
Increasing evidence links chronic neurodegenerative diseases with neuroinflammation; it is known that neuroprotective agents are capable of modulating the inflammatory processes, that occur with the onset of neurodegeneration pathologies. Here, with the intention of providing a means for active compounds’ screening, a dysregulation of neuronal inflammatory marker genes was induced and subjected to neuroprotective active principles, with the aim of selecting a set of inflammatory marker genes linked to neurodegenerative diseases. Considering the important role of microglia in neurodegeneration, a murine co-culture of hippocampal cells and inflamed microglia cells was set up. The evaluation of differentially expressed genes and subsequent in silico analysis showed the main dysregulated genes in both cells and the principal inflammatory processes involved in the model. Among the identified genes, a well-defined set was chosen, selecting those in which a role in human neurodegenerative progression in vivo was already defined in literature, matched with the rate of prediction derived from the Principal Component Analysis (PCA) of in vitro treatment-affected genes variation. The obtained panel of dysregulated target genes, including Cxcl9 (Chemokine (C-X-C motif) ligand 9), C4b (Complement Component 4B), Stc1 (Stanniocalcin 1), Abcb1a (ATP Binding Cassette Subfamily B Member 1), Hp (Haptoglobin) and Adm (Adrenomedullin), can be considered an in vitro tool to select old and new active compounds directed to neuroinflammation.
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Affiliation(s)
- Marcella Massimini
- Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy
- Correspondence:
| | - Benedetta Bachetti
- R&D Division, C.I.A.M. Srl, 63100 Ascoli Piceno, Italy; (B.B.); (E.D.V.); (A.B.)
| | - Elena Dalle Vedove
- R&D Division, C.I.A.M. Srl, 63100 Ascoli Piceno, Italy; (B.B.); (E.D.V.); (A.B.)
| | - Alessia Benvenga
- R&D Division, C.I.A.M. Srl, 63100 Ascoli Piceno, Italy; (B.B.); (E.D.V.); (A.B.)
| | - Francesco Di Pierro
- Velleja Research, 20125 Milan, Italy;
- Digestive Endoscopy Unit and Gastroenterology, Fondazione Poliambulanza, 25124 Brescia, Italy
| | - Nicola Bernabò
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy;
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18
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Sahinyan K, Blackburn DM, Simon MM, Lazure F, Kwan T, Bourque G, Soleimani VD. Application of ATAC-Seq for genome-wide analysis of the chromatin state at single myofiber resolution. eLife 2022; 11:72792. [PMID: 35188098 PMCID: PMC8901173 DOI: 10.7554/elife.72792] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/09/2022] [Indexed: 12/11/2022] Open
Abstract
Myofibers are the main components of skeletal muscle, which is the largest tissue in the body. Myofibers are highly adaptive and can be altered under different biological and disease conditions. Therefore, transcriptional and epigenetic studies on myofibers are crucial to discover how chromatin alterations occur in the skeletal muscle under different conditions. However, due to the heterogenous nature of skeletal muscle, studying myofibers in isolation proves to be a challenging task. Single-cell sequencing has permitted the study of the epigenome of isolated myonuclei. While this provides sequencing with high dimensionality, the sequencing depth is lacking, which makes comparisons between different biological conditions difficult. Here, we report the first implementation of single myofiber ATAC-Seq, which allows for the sequencing of an individual myofiber at a depth sufficient for peak calling and for comparative analysis of chromatin accessibility under various physiological and disease conditions. Application of this technique revealed significant differences in chromatin accessibility between resting and regenerating myofibers, as well as between myofibers from a mouse model of Duchenne Muscular Dystrophy (mdx) and wild-type (WT) counterparts. This technique can lead to a wide application in the identification of chromatin regulatory elements and epigenetic mechanisms in muscle fibers during development and in muscle-wasting diseases.
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Affiliation(s)
- Korin Sahinyan
- Department of Human Genetics, McGill University, Montreal, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Darren M Blackburn
- Department of Human Genetics, McGill University, Montreal, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Marie-Michelle Simon
- Department of Human Genetics, McGill University, Montreal, Canada.,McGill Genome Centre, Montreal, Canada
| | - Felicia Lazure
- Department of Human Genetics, McGill University, Montreal, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University, Montreal, Canada.,McGill Genome Centre, Montreal, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Canada.,McGill Genome Centre, Montreal, Canada.,Canadian Centre for Computational Genomics, Montreal, Canada
| | - Vahab D Soleimani
- Department of Human Genetics, McGill University, Montreal, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
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19
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Fletcher A, Zhao R, Enciso G. Non-cooperative mechanism for bounded and ultrasensitive chromatin remodeling. J Theor Biol 2022; 534:110946. [PMID: 34717936 DOI: 10.1016/j.jtbi.2021.110946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022]
Abstract
Chromatin remodeling is an essential form of gene regulation that is involved in a variety of biological processes. We develop a theoretical model that takes advantage of percolation effects at the level of nucleosome interactions, which allows for ultrasensitive chromatin expansion. This model is non-cooperative and readily provides spatial bounds to the expansion region, preventing uncontrolled remodeling events. We explore different chromatin architectures and the ultrasensitivity of the chromatin density as a function of transcription factor concentration. We also compare our model with experimental data involving an inhibitor of nucleosome acetylation. These results suggest a novel mechanism for spatially-bounded chromatin remodeling and they provide means for quantitative comparisons between proposed models of chromatin architecture.
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Affiliation(s)
- Alvaro Fletcher
- Mathematical, Computational, and Systems Biology program, University of California, Irvine, Irvine, CA, USA
| | - Ruonan Zhao
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
| | - German Enciso
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA.
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20
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Zhang Z, Liu L, Shen Y, Meng Z, Chen M, Lu Z, Zhang X. Characterization of chromatin accessibility in psoriasis. Front Med 2021; 16:483-495. [PMID: 34669155 DOI: 10.1007/s11684-021-0872-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/29/2021] [Indexed: 12/13/2022]
Abstract
The pathological hallmarks of psoriasis involve alterations in T cell genes associated with transcriptional levels, which are determined by chromatin accessibility. However, to what extent these alterations in T cell transcriptional levels recapitulate the epigenetic features of psoriasis remains unknown. Here, we systematically profiled chromatin accessibility on Th1, Th2, Th1-17, Th17, and Treg cells and found that chromatin remodeling contributes significantly to the pathogenesis of the disease. The chromatin remodeling tendency of different subtypes of Th cells were relatively consistent. Next, we profiled chromatin accessibility and transcriptional dynamics on memory Th/Treg cells. In the memory Th cells, 803 increased and 545 decreased chromatin-accessible regions were identified. In the memory Treg cells, 713 increased and 1206 decreased chromatin-accessible regions were identified. A total of 54 and 53 genes were differentially expressed in the peaks associated with the memory Th and Treg cells. FOSL1, SPI1, ATF3, NFKB1, RUNX, ETV4, ERG, FLI1, and ETC1 were identified as regulators in the development of psoriasis. The transcriptional regulatory network showed that NFKB1 and RELA were highly connected and central to the network. NFKB1 regulated the genes of CCL3, CXCL2, and IL1RN. Our results provided candidate transcription factors and a foundational framework of the regulomes of the disease.
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Affiliation(s)
- Zheng Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Lu Liu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China
| | - Yanyun Shen
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Ziyuan Meng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China
| | - Min Chen
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China.,Department of Dermatology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215123, China
| | - Zhong Lu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Xuejun Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China. .,Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China. .,Department of Dermatology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215123, China.
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21
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Fan H, Ren Z, Xu C, Wang H, Wu Z, Rehman ZU, Wu S, Sun MA, Bao W. Chromatin Accessibility and Transcriptomic Alterations in Murine Ovarian Granulosa Cells upon Deoxynivalenol Exposure. Cells 2021; 10:2818. [PMID: 34831041 PMCID: PMC8616273 DOI: 10.3390/cells10112818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 11/26/2022] Open
Abstract
Deoxynivalenol (DON) is a common environmental toxin that is secreted by fusarium fungi that frequently contaminates feedstuff and food. While the detrimental effects of DON on human and animal reproductive systems have been well recognized, the underlying mechanism remains poorly understood. Ovarian granulosa cells (GCs), which surround oocytes, are crucial for regulating oocyte development, mainly through the secretion of hormones such as estrogen and progesterone. Using an in vitro model of murine GCs, we characterized the cytotoxic effects of DON and profiled genome-wide chromatin accessibility and transcriptomic alterations after DON exposure. Our results suggest that DON can induce decreased viability and growth, increased apoptosis rate, and disrupted hormone secretion. In total, 2533 differentially accessible loci and 2675 differentially expressed genes were identified that were associated with Hippo, Wnt, steroid biosynthesis, sulfur metabolism, and inflammation-related pathways. DON-induced genes usually have a concurrently increased occupancy of active histone modifications H3K4me3 and H3K27ac in their promoters. Integrative analyses identified 35 putative directly affected genes including Adrb2 and Fshr, which are key regulators of follicular growth, and revealed that regions with increased chromatin accessibility are enriched with the binding motifs for NR5A1 and NR5A2, which are important for GCs. Moreover, DON-induced inflammatory response is due to the activation of the NF-κB and MAPK signaling pathways. Overall, our results provide novel insights into the regulatory elements, genes, and key pathways underlying the response of ovarian GCs to DON cytotoxicity.
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Affiliation(s)
- Hairui Fan
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
| | - Zhanshi Ren
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
| | - Chao Xu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
| | - Haifei Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Zhengchang Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
| | - Zia ur Rehman
- Faculty of Animal Husbandry and Veterinary Sciences, College of Veterinary Sciences, The University of Agriculture Peshawar, Peshawar 25000, Pakistan;
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Ming-an Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.F.); (Z.R.); (C.X.); (H.W.); (Z.W.); (S.W.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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22
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Deerhake ME, Shinohara ML. Emerging roles of Dectin-1 in noninfectious settings and in the CNS. Trends Immunol 2021; 42:891-903. [PMID: 34489167 DOI: 10.1016/j.it.2021.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 12/15/2022]
Abstract
Dectin-1 is a C-type lectin receptor (CLR) expressed on the surface of various mammalian myeloid cells. Dectin-1 recognizes β-glucans and elicits antifungal proinflammatory immune responses. Recent studies have begun to examine the biology of Dectin-1 in previously less explored settings, such as homeostasis, sterile inflammation, and in the central nervous system. Indeed, in certain contexts, Dectin-1 is now known to promote tolerance, and anti-inflammatory and neuroprotective responses. In this review, we provide an overview of the current understanding of the roles of Dectin-1 in immunology beyond the context of fungal infections, mainly focusing on in vivo neuroimmunology studies, which could reveal new therapeutic approaches to modify innate immune responses in neurologic disorders.
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Affiliation(s)
- M Elizabeth Deerhake
- Department of Immunology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Mari L Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, NC 27705, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27705, USA.
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23
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Senjor E, Perišić Nanut M, Breznik B, Mitrović A, Mlakar J, Rotter A, Porčnik A, Lah Turnšek T, Kos J. Cystatin F acts as a mediator of immune suppression in glioblastoma. Cell Oncol (Dordr) 2021; 44:1051-1063. [PMID: 34189679 DOI: 10.1007/s13402-021-00618-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2021] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Glioblastoma, the most aggressive type of brain cancer, is composed of heterogeneous populations of differentiated cells, cancer stem cells and immune cells. Cystatin F, an endogenous inhibitor of lysosomal cysteine peptidases, regulates the function of cytotoxic immune cells. The aim of this study was to determine which type of cells expresses cystatin F in glioblastoma and to determine the role of cystatin F during disease progression. METHODS RT-qPCR and immunohistochemistry were used to determine cystatin F mRNA and protein levels in glioblastoma tissue samples. The internalization of cystatin F was analyzed by Western blotting. Enzyme kinetics, real time invasion and calcein release cytotoxicity assays were used to assess the role of internalized cystatin F. RESULTS We found that cystatin F was not expressed in non-cancer brain tissues, but that its expression increased with glioma progression. In tumor tissues, extensive staining was observed in cancer stem-like cells and microglia/monocytes, which secrete cystatin F into their microenvironment. In trans activity of cystatin F was confirmed using an in vitro glioblastoma cell model. Internalized cystatin F affected cathepsin L activity in glioblastoma cells and decreased their invasiveness. In addition, we found that cystatin F decreased the susceptibility of glioblastoma cells to the cytotoxic activity of natural killer (NK) cells. CONCLUSIONS Our data implicate cystatin F as a mediator of immune suppression in glioblastoma. Increased cystatin F mRNA and protein levels in immune, glioblastoma and glioblastoma stem-like cells or trans internalized cystatin F may have an impact on decreased susceptibility of glioblastoma cells to NK cytotoxicity.
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Affiliation(s)
- Emanuela Senjor
- Department of Biotechnology, Jožef Stefan Institute, Jamova cesta 39, SI-1000, Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000, Ljubljana, Slovenia
| | - Milica Perišić Nanut
- Department of Biotechnology, Jožef Stefan Institute, Jamova cesta 39, SI-1000, Ljubljana, Slovenia
| | - Barbara Breznik
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
| | - Ana Mitrović
- Department of Biotechnology, Jožef Stefan Institute, Jamova cesta 39, SI-1000, Ljubljana, Slovenia
| | - Jernej Mlakar
- Institute of Pathology, Medical Faculty, University of Ljubljana, Korytkova 2, SI-1000, Ljubljana, Slovenia
| | - Ana Rotter
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
| | - Andrej Porčnik
- Department of Neurosurgery, University Clinical Centre Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Tamara Lah Turnšek
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
| | - Janko Kos
- Department of Biotechnology, Jožef Stefan Institute, Jamova cesta 39, SI-1000, Ljubljana, Slovenia. .,Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000, Ljubljana, Slovenia.
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24
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Li N, Xiao H, Shen J, Qiao X, Zhang F, Zhang W, Gao Y, Liu YD. SELE gene as a characteristic prognostic biomarker of colorectal cancer. J Int Med Res 2021; 49:3000605211004386. [PMID: 33845603 PMCID: PMC8047093 DOI: 10.1177/03000605211004386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE To investigate the expression and clinical value of the E-selectin gene (SELE) in colorectal cancer (CRC). METHODS Using gene expression profiles and clinicopathological data for patients with CRC from The Cancer Genome Atlas, and tumor and adjacent normal tissues from 31 patients with CRC from Xianyang Central Hospital, we studied the correlation between SELE gene expression and clinical parameters using Kaplan-Meier and Cox proportional hazards regression analyses. RESULTS Higher expression of SELE was significantly associated with a poorer prognosis and shorter survival in patients with CRC. The median expression level of SELE was significantly higher in CRC tissues compared with healthy adjacent tissue. Cox regression analysis showed that the prognosis of CRC was significantly correlated with the expression of SELE. Immunohistochemical analysis also showed that positive expression of E-selectin increased significantly in line with increasing TNM stage.Conclusion: This study confirmed that SELE gene expression is an independent prognostic factor in patients with CRC.
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Affiliation(s)
- Na Li
- Department of Anorectal Surgery, Xianyang Central Hospital, Xianyang, China.,Third Clinical College, Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Honghe Xiao
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Jiangli Shen
- Department of Anorectal Surgery, Xianyang Central Hospital, Xianyang, China
| | - Ximin Qiao
- Dean's Office, Xianyang Central Hospital, Xianyang, China
| | - Fenjuan Zhang
- Pathology Department, Xianyang Central Hospital, Xianyang, China
| | - Weibo Zhang
- Pathology Department, Xianyang Central Hospital, Xianyang, China
| | - Yuan Gao
- Surgery Department, Xianyang Central Hospital, Xianyang, China
| | - Yue Dong Liu
- Dean's Office, The Third Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, China
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