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He H, Yang Y, Wang L, Guo Z, Ye L, Ou-Yang W, Yang M. Combined analysis of single-cell and bulk RNA sequencing reveals the expression patterns of circadian rhythm disruption in the immune microenvironment of Alzheimer's disease. Front Immunol 2023; 14:1182307. [PMID: 37251379 PMCID: PMC10213546 DOI: 10.3389/fimmu.2023.1182307] [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: 03/08/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
Background Circadian rhythm disruption (CRD) represents a critical contributor to the pathogenesis of Alzheimer's disease (AD). Nonetheless, how CRD functions within the AD immune microenvironment remains to be illustrated. Methods Circadian rhythm score (CRscore) was utilized to quantify the microenvironment status of circadian disruption in a single-cell RNA sequencing dataset derived from AD. Bulk transcriptome datasets from public repository were employed to validate the effectiveness and robustness of CRscore. A machine learning-based integrative model was applied for constructing a characteristic CRD signature, and RT-PCR analysis was employed to validate their expression levels. Results We depicted the heterogeneity in B cells, CD4+ T cells, and CD8+ T cells based on the CRscore. Furthermore, we discovered that CRD might be strongly linked to the immunological and biological features of AD, as well as the pseudotime trajectories of major immune cell subtypes. Additionally, cell-cell interactions revealed that CRD was critical in the alternation of ligand-receptor pairs. Bulk sequencing analysis indicated that the CRscore was found to be a reliable predictive biomarker in AD patients. The characteristic CRD signature, which included 9 circadian-related genes (CRGs), was an independent risk factor that accurately predicted the onset of AD. Meanwhile, abnormal expression of several characteristic CRGs, including GLRX, MEF2C, PSMA5, NR4A1, SEC61G, RGS1, and CEBPB, was detected in neurons treated with Aβ1-42 oligomer. Conclusion Our study revealed CRD-based cell subtypes in the AD microenvironment at single-cell level and proposed a robust and promising CRD signature for AD diagnosis. A deeper knowledge of these mechanisms may provide novel possibilities for incorporating "circadian rhythm-based anti-dementia therapies" into the treatment protocols of individualized medicine.
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Duan X, Pan T, Wang Z, Pu Y, Li Q, Pang Y, Xu Y, Gou M. Molecular characterization and expression analysis of a novel cold-inducible RNA-binding protein (CIRBP) gene in lamprey (Lethenteron reissneri). Dev Genes Evol 2023:10.1007/s00427-022-00700-8. [PMID: 36658408 DOI: 10.1007/s00427-022-00700-8] [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: 03/23/2022] [Accepted: 12/15/2022] [Indexed: 01/20/2023]
Abstract
Cold-inducible RNA-binding protein (CIRBP) responds to a wide array of cellular stresses such as cold shock, hypoxia, and inflammatory responses. However, functional studies of CIRBP in jawless vertebrates are limited. In this study, a CIRBP homolog from the jawless vertebrate lamprey (Lethenteron reissneri) was cloned and characterized (named Lr-CIRBP). The cDNA fragment of Lr-CIRBP has a 516 bp open reading frame (ORF) that encodes 171 amino acids, comprising a glycine-rich region at the C-terminal, similar to higher vertebrates but slightly shorter, and an RNA recognition motif (RRM) domain at the N-terminus. The predicted Lr-CIRBP sequence had 51.4 ~ 70.6% similarity with CIRBPs from other vertebrates. Further phylogenetic analysis revealed that Lr-CIRBP is located in the outgroup of vertebrates and is the ancestor of vertebrates. Based on real-time quantitative PCR experimental analysis, Lr-CIRBP expression was highest in leukocytes and increased significantly after multi-stimulation, peaking at 12 h. RNA interference showed that Lr-CIRBP knockdown can down-regulate the expression of inflammatory factors in Lethenteron reissneri. In conclusion, our study successfully clarifies the ancestral features and functions of CIRBP, while revealing valuable insight into how the protein is involved in the immune responses of a jawless vertebrate.
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Affiliation(s)
- Xuyuan Duan
- College of Life Science, Liaoning Normal University, Dalian, 116081, China.,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Tong Pan
- College of Life Science, Liaoning Normal University, Dalian, 116081, China
| | - Zhuoying Wang
- College of Life Science, Liaoning Normal University, Dalian, 116081, China
| | - Yunhong Pu
- College of Life Science, Liaoning Normal University, Dalian, 116081, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, 116081, China.,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, 116081, China.,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Yang Xu
- College of Life Science, Liaoning Normal University, Dalian, 116081, China. .,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China. .,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.
| | - Meng Gou
- College of Life Science, Liaoning Normal University, Dalian, 116081, China. .,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China. .,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.
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Rao M, Ke D, Cheng G, Hu S, Wu Y, Wang Y, Zhou F, Liu H, Zhu C, Xia W. The regulation of CIRBP by transforming growth factor beta during heat shock-induced testicular injury. Andrology 2018; 7:244-250. [PMID: 30461215 DOI: 10.1111/andr.12566] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 09/26/2018] [Accepted: 10/29/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Cold-inducible RNA-binding protein (CIRBP) is associated with cell stress. However, its upstream regulatory factors are still largely unknown. OBJECTIVES This study investigated whether CIRBP expression was regulated by transforming growth factor beta (TGF-β) during the process of heat-induced testicular damage. MATERIALS AND METHODS Ten male adult ICR mice were allocated to heat treatment (scrotal hyperthermia at 43 °C for 30 min, n = 5) and control group (n = 5); CIRBP and TGF-β1, TGF-β2, and TGF-β3 expression levels in the testis in mRNA and protein were analyzed. Then, we conducted in vivo and in vitro studies to investigate the regulatory effects of TGF-β on CIRBP. In the in vivo study, male adult ICR mice were subjected to testicular hyperthermia followed by a local testicular injection of TGF-β antagonist (non-selective TGF-β I/II receptor inhibitor, 5 μg or 10 μg). In the in vitro study, GC2-spd cells were cultured under 43 °C for 30 min or with different TGF-β isoforms (10 ng/mL), and CIRBP expression levels in the testis and GC2-spd cells were analyzed 24 and 48 h, respectively, after treatment. RESULTS As a result, heat treatment significantly downregulated the relative CIRBP mRNA and protein expression (p = 0.006 and 0.011), and significantly upregulated TGF-β2 and TGF-β3 expression levels (p = 0.022 and 0.04, for mRNA, and p = 0.001 for both protein levels). Local testicular injection of 10 μg TGF-β antagonist significantly attenuated heat-induced histological damage to the testes and CIRBP downregulation (p = 0.038). Furthermore, TGF-β2 and TGF-β3 significantly downregulated CIRBP mRNA and protein expression in GC2-spd cells (all p < 0.01), exerting a similar effect to heat treatment. DISCUSSION AND CONCLUSION Our in vivo and in vitro experiments demonstrated that heat-induced CIRBP downregulation in the testes was mediated by the upregulation of TGF-β. Further studies are needed to clarify the molecular mechanisms underlying these processes.
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Affiliation(s)
- M Rao
- Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Reproduction and Genetics, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - D Ke
- Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - G Cheng
- Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - S Hu
- Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Y Wu
- Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Y Wang
- Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - F Zhou
- Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - H Liu
- Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - C Zhu
- Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Reproductive Medicine Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - W Xia
- Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Reproductive Medicine Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Lujan DA, Ochoa JL, Hartley RS. Cold-inducible RNA binding protein in cancer and inflammation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9. [PMID: 29322631 DOI: 10.1002/wrna.1462] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/17/2017] [Accepted: 11/29/2017] [Indexed: 12/17/2022]
Abstract
RNA binding proteins (RBPs) play key roles in RNA dynamics, including subcellular localization, translational efficiency and metabolism. Cold-inducible RNA binding protein (CIRP) is a stress-induced protein that was initially described as a DNA damage-induced transcript (A18 hnRNP), as well as a cold-shock domain containing cold-stress response protein (CIRBP) that alters the translational efficiency of its target messenger RNAs (mRNAs). This review summarizes recent work on the roles of CIRP in the context of inflammation and cancer. The function of CIRP in cancer appeared to be solely driven though its functions as an RBP that targeted cancer-associated mRNAs, but it is increasingly clear that CIRP also modulates inflammation. Several recent studies highlight roles for CIRP in immune responses, ranging from sepsis to wound healing and tumor-promoting inflammation. While modulating inflammation is an established role for RBPs that target cytokine mRNAs, CIRP appears to modulate inflammation by several different mechanisms. CIRP has been found in serum, where it binds the TLR4-MD2 complex, acting as a Damage-associated molecular pattern (DAMP). CIRP activates the NF-κB pathway, increasing phosphorylation of Iκκ and IκBα, and stabilizes mRNAs encoding pro-inflammatory cytokines. While CIRP promotes higher levels of pro-inflammatory cytokines in certain cancers, it also decreases inflammation to accelerate wound healing. This dichotomy suggests that the influence of CIRP on inflammation is context dependent and highlights the importance of detailing the mechanisms by which CIRP modulates inflammation. WIREs RNA 2018, 9:e1462. doi: 10.1002/wrna.1462 This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Daniel A Lujan
- Department of Cell Biology and Physiology, University of New Mexico School of Medicine and University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico
| | - Joey L Ochoa
- Department of Cell Biology and Physiology, University of New Mexico School of Medicine and University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico
| | - Rebecca S Hartley
- Department of Cell Biology and Physiology, University of New Mexico School of Medicine and University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico
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