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Yanaizu M, Adachi H, Araki M, Kontani K, Kino Y. Translational regulation and protein-coding capacity of the 5' untranslated region of human TREM2. Commun Biol 2023; 6:616. [PMID: 37291187 PMCID: PMC10250343 DOI: 10.1038/s42003-023-04998-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
TREM2 is a transmembrane receptor expressed in microglia and macrophages. Elevated TREM2 levels in these cells are associated with age-related pathological conditions, including Alzheimer's disease. However, the regulatory mechanism underlying the protein expression of TREM2 remains unclear. In this study, we uncover the role of the 5' untranslated region (5'-UTR) of human TREM2 in translation. An upstream start codon (uAUG) in the 5'-UTR of TREM2 is specific to some primates, including humans. The expression of the conventional TREM2 protein, starting from the downstream AUG (dTREM2), is repressed by the 5'-UTR in a uAUG-mediated manner. We also detect a TREM2 protein isoform starting from uAUG (uTREM2) that is largely degraded by proteasomes. Finally, the 5'-UTR is essential for the downregulation of dTREM2 expression in response to amino acid starvation. Collectively, our study identifies a species-specific regulatory role of the 5'-UTR in TREM2 translation.
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Affiliation(s)
- Motoaki Yanaizu
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
- Department of RNA Pathobiology and Therapeutics, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Haruka Adachi
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Makoto Araki
- Department of Biochemistry, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Kenji Kontani
- Department of Biochemistry, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Yoshihiro Kino
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan.
- Department of RNA Pathobiology and Therapeutics, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan.
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2
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Zhang E, Dai F, Chen T, Liu S, Xiao C, Shen X. Diagnostic models and predictive drugs associated with cuproptosis hub genes in Alzheimer's disease. Front Neurol 2023; 13:1064639. [PMID: 36776574 PMCID: PMC9909238 DOI: 10.3389/fneur.2022.1064639] [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: 10/08/2022] [Accepted: 12/29/2022] [Indexed: 01/27/2023] Open
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease, and its underlying genes and treatments are unclear. Abnormalities in copper metabolism can prevent the clearance of β-amyloid peptides and promote the progression of AD pathogenesis. Therefore, the present study used a bioinformatics approach to perform an integrated analysis of the hub gene based on cuproptosis that can influence the diagnosis and treatment of AD. The gene expression profiles were obtained from the Gene Expression Omnibus database, including non-demented (ND) and AD samples. A total of 2,977 cuproptosis genes were retrieved from published articles. The seven hub genes associated with cuproptosis and AD were obtained from the differentially expressed genes and WGCNA in brain tissue from GSE33000. The GO analysis demonstrated that these genes were involved in phosphoribosyl pyrophosphate, lipid, and glucose metabolism. By stepwise regression and logistic regression analysis, we screened four of the seven cuproptosis genes to construct a diagnostic model for AD, which was validated by GES15222, GS48350, and GSE5281. In addition, immune cell infiltration of samples was investigated for correlation with these hub genes. We identified six drugs targeting these seven cuproptosis genes in DrugBank. Hence, these cuproptosis gene signatures may be an important prognostic indicator for AD and may offer new insights into treatment options.
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Affiliation(s)
- Erdong Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou, China,Key Laboratory of Optimal Utilization of Natural Medicinal Resources, Guizhou Medical University, Guiyang, Guizhou, China,*Correspondence: Erdong Zhang ✉
| | - Fengqiu Dai
- Department of Anatomy, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Tingting Chen
- Guiyang Maternal and Child Health-Care Hospital, Guiyang, Guizhou, China
| | - Shanhui Liu
- Key Laboratory of Urological Diseases in Gansu Province, Gansu Nephro-Urological Clinical Center, Institute of Urology, Lanzhou University Second Hospital, Lanzhou, Gansu, China
| | - Chaolun Xiao
- Department of Anatomy, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Xiangchun Shen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou, China,Key Laboratory of Optimal Utilization of Natural Medicinal Resources, Guizhou Medical University, Guiyang, Guizhou, China,Xiangchun Shen ✉
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3
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Chai K, Zhang X, Chen S, Gu H, Tang H, Cao P, Wang G, Ye W, Wan F, Liang J, Shen D. Application of weighted co-expression network analysis and machine learning to identify the pathological mechanism of Alzheimer's disease. Front Aging Neurosci 2022; 14:837770. [PMID: 35912089 PMCID: PMC9326231 DOI: 10.3389/fnagi.2022.837770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Aberrant deposits of neurofibrillary tangles (NFT), the main characteristic of Alzheimer's disease (AD), are highly related to cognitive impairment. However, the pathological mechanism of NFT formation is still unclear. This study explored differences in gene expression patterns in multiple brain regions [entorhinal, temporal, and frontal cortex (EC, TC, FC)] with distinct Braak stages (0- VI), and identified the hub genes via weighted gene co-expression network analysis (WGCNA) and machine learning. For WGCNA, consensus modules were detected and correlated with the single sample gene set enrichment analysis (ssGSEA) scores. Overlapping the differentially expressed genes (DEGs, Braak stages 0 vs. I-VI) with that in the interest module, metascape analysis, and Random Forest were conducted to explore the function of overlapping genes and obtain the most significant genes. We found that the three brain regions have high similarities in the gene expression pattern and that oxidative damage plays a vital role in NFT formation via machine learning. Through further filtering of genes from interested modules by Random Forest, we screened out key genes, such as LYN, LAPTM5, and IFI30. These key genes, including LYN, LAPTM5, and ARHGDIB, may play an important role in the development of AD through the inflammatory response pathway mediated by microglia.
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Affiliation(s)
- Keping Chai
- Department of Pediatrics, Zhejiang Hospital, Hangzhou, China
- *Correspondence: Keping Chai
| | - Xiaolin Zhang
- Department of Neurological Surgery, Tongji Hospital, Tongji Medical College, Huazhong University Science and Technology, Wuhan, China
| | - Shufang Chen
- Department of Pediatrics, Zhejiang Hospital, Hangzhou, China
| | - Huaqian Gu
- Department of Pediatrics, Zhejiang Hospital, Hangzhou, China
| | - Huitao Tang
- Department of Pediatrics, Zhejiang Hospital, Hangzhou, China
| | - Panlong Cao
- Department of Pediatrics, Zhejiang Hospital, Hangzhou, China
| | - Gangqiang Wang
- Department of Pediatrics, Zhejiang Hospital, Hangzhou, China
| | - Weiping Ye
- Department of Pediatrics, Zhejiang Hospital, Hangzhou, China
| | - Feng Wan
- Department of Neurological Surgery, Tongji Hospital, Tongji Medical College, Huazhong University Science and Technology, Wuhan, China
- Feng Wan
| | - Jiawei Liang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Jiawei Liang
| | - Daojiang Shen
- Department of Pediatrics, Zhejiang Hospital, Hangzhou, China
- Daojiang Shen
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Puy L, Perbet R, Figeac M, Duchêne B, Deramecourt V, Cordonnier C, Bérézowski V. Brain Peri-Hematomal Area, a Strategic Interface for Blood Clearance: A Human Neuropathological and Transcriptomic Study. Stroke 2022; 53:2026-2035. [DOI: 10.1161/strokeaha.121.037751] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
Enhancing the blood clearance process is a promising therapeutic strategy for intracerebral hemorrhage (ICH). We aimed to investigate the kinetic of this process after ICH in human brain tissue through the monocyte-macrophage scavenger receptor (CD163)/HO-1 (hemoxygenase-1) pathway.
Methods:
We led a cross-sectional post-mortem study including 22 consecutive ICH cases (2005–2019) from the Lille Neurobank. Cases were grouped according to the time of death: ≤72 hours, 4 to 7 days, 8 to 15 days, 16 to 90 days, and >90 days after ICH onset. Paraffin-embedded tissue was extracted from 4 strategic areas, including hematoma core and peri-hematomal area to perform histological investigations. Additionally, we extracted RNA from the peri-hematomal area of 6 cases to perform transcriptomic analysis.
Results:
We included 19 ICH cases (median age: 79 [71–89] years; median delay ICH-death: 13 [5–41] days). The peri-hematomal area concentrated most of reactive microglia, CD163/HO-1 and iron deposits as compared with other brain areas. We found a surge in the blood clearance process from day 8 to day 15 after ICH onset. Transcriptomic analysis showed that HO-1 was the most upregulated gene (2.81±0.39, adjusted
P
=1.11×10
–10
) and CD163 the sixth (1.49±0.29, adjusted
P
=1.68×10
–
5
). We also identified several upregulated genes that exert a beneficial role in terminating inflammation and enhancing tissue repair.
Conclusions:
We provide histological and transcriptomic-based evidence in humans for the key role of peri-hematomal area in endogenous blood clearance process through the CD163/HO-1 pathway, especially from day 8 after ICH and favored by an anti-inflammatory environment. Our findings contribute to identify innovative therapeutic strategies for ICH.
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Affiliation(s)
- Laurent Puy
- Univ. Lille, Inserm, CHU-Lille, Lille Neuroscience & Cognition research Center UMR-S1172, Degenerative and Vascular Cognitive Disorders, France (L.P., R.P., V.D., C.C., V.B.)
| | - Romain Perbet
- Univ. Lille, Inserm, CHU-Lille, Lille Neuroscience & Cognition research Center UMR-S1172, Degenerative and Vascular Cognitive Disorders, France (L.P., R.P., V.D., C.C., V.B.)
- Alzheimer Research Unit, Department of Neurology, Massachusetts General Hospital, Charlestown (R.P.)
- Harvard Medical School, Boston, MA (R.P.)
| | - Martin Figeac
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, France (M.F.)
| | - Bélinda Duchêne
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, France (B.D.)
| | - Vincent Deramecourt
- Univ. Lille, Inserm, CHU-Lille, Lille Neuroscience & Cognition research Center UMR-S1172, Degenerative and Vascular Cognitive Disorders, France (L.P., R.P., V.D., C.C., V.B.)
- Université d’Artois, Lens, France (V.B.)
| | - Charlotte Cordonnier
- Univ. Lille, Inserm, CHU-Lille, Lille Neuroscience & Cognition research Center UMR-S1172, Degenerative and Vascular Cognitive Disorders, France (L.P., R.P., V.D., C.C., V.B.)
| | - Vincent Bérézowski
- Univ. Lille, Inserm, CHU-Lille, Lille Neuroscience & Cognition research Center UMR-S1172, Degenerative and Vascular Cognitive Disorders, France (L.P., R.P., V.D., C.C., V.B.)
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Wang S, Huang Y, Guan X. Fluorescent Probes for Live Cell Thiol Detection. Molecules 2021; 26:3575. [PMID: 34208153 PMCID: PMC8230801 DOI: 10.3390/molecules26123575] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 11/24/2022] Open
Abstract
Thiols play vital and irreplaceable roles in the biological system. Abnormality of thiol levels has been linked with various diseases and biological disorders. Thiols are known to distribute unevenly and change dynamically in the biological system. Methods that can determine thiols' concentration and distribution in live cells are in high demand. In the last two decades, fluorescent probes have emerged as a powerful tool for achieving that goal for the simplicity, high sensitivity, and capability of visualizing the analytes in live cells in a non-invasive way. They also enable the determination of intracellular distribution and dynamitic movement of thiols in the intact native environments. This review focuses on some of the major strategies/mechanisms being used for detecting GSH, Cys/Hcy, and other thiols in live cells via fluorescent probes, and how they are applied at the cellular and subcellular levels. The sensing mechanisms (for GSH and Cys/Hcy) and bio-applications of the probes are illustrated followed by a summary of probes for selectively detecting cellular and subcellular thiols.
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Affiliation(s)
| | | | - Xiangming Guan
- Department of Pharmaceutical Sciences, College of Pharmacy and Allied Health Professions, South Dakota State University, Box 2202C, Brookings, SD 57007, USA; (S.W.); (Y.H.)
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