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Yan M, Wu R, Fu H, Hu C, Hao Y, Zeng J, Chen T, Wang Y, Wang Y, Hu J, Jin A. Integrated analysis of single-cell and bulk RNA sequencing data reveals the association between hypoxic tumor cells and exhausted T cells in predicting immune therapy response. Comput Biol Med 2024; 171:108179. [PMID: 38394803 DOI: 10.1016/j.compbiomed.2024.108179] [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: 11/19/2023] [Revised: 01/30/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024]
Abstract
Continuous stimulation of tumor neoantigens and various cytokines in the tumor microenvironment leads to T cell dysfunction, but the specific mechanisms by which these key factors are distributed among different cell subpopulations and how they affect patient outcomes and treatment response are incompletely characterized. By integrating single-cell and bulk sequencing data of non-small cell lung cancer patients, we constructed a clinical outcome-associated T cell exhaustion signature. We discovered a significant association between the T cell exhaustion state and tumor cell hypoxia. Hypoxic malignant cells were significantly correlated with the proportion of exhausted T cells, and they co-occurred in patients at advanced stage. By analyzing the ligand-receptor interactions between these two cell states, we observed that T cells were recruited towards tumor cells through production of chemokines such as CXCL16-CXCR6 axis and CCL3/CCL4/CCL5-CCR5 axis. Based on 15 immune checkpoint blockade (ICB)-treatment cohorts, we constructed an interaction signature that can be used to predict the response to immune checkpoint blockade therapy. Among genes composed of the signature, CXCR6 alone has similarly high prediction efficacy (Area Under Curve (AUC) = 1, 0.89 and 0.73 for GSE126044, GSE135222 and GSE93157, respectively) with the signature and thus could serve as a potential biomarker for predicting immunotherapy response. Together, we have discovered and validated a significant association between exhausted T cells and hypoxic malignant cells, elucidating key interaction factors that significantly associated with response to immunotherapy.
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Affiliation(s)
- Min Yan
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China; Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, 400010, China
| | - Ruixin Wu
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
| | - Han Fu
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
| | - Chao Hu
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
| | - Yanan Hao
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
| | - Jie Zeng
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
| | - Tong Chen
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
| | - Yingming Wang
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
| | - Yingying Wang
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
| | - Jing Hu
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Aishun Jin
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China; Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, 400010, China.
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Chen Y, Zheng S, Zhao X, Zhang Y, Yu S, Wei J. Unveiling the protective effects of BMSCs/anti-miR-124-3p exosomes on LPS-induced endometrial injury. Funct Integr Genomics 2024; 24:32. [PMID: 38363406 DOI: 10.1007/s10142-024-01303-4] [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: 09/30/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/17/2024]
Abstract
Researchers have reported that miR-124-3p is highly expressed in patients with chronic endometritis. However, the underlying mechanism of miR-124-3p in the development of endometritis remains unclear. This study constructed an in vitro endometrial cell injury model by treating HEECs with 2 μg/mL LPS for 48 h. Then, 1 mg/kg LPS was injected into both sides of the mouse uterus to construct an in vivo endometrial injury model. The expression of miR-124-3p in human endometrial epithelial cells (HEECs) was assessed using RT‒qPCR. Exosomes were separated from bone marrow-derived mesenchymal stem cells (BMSCs) and cocultured with HEECs. A dual-luciferase reporter assay was performed to confirm the relationship between miR-124-3p and DUSP6. The results indicated that LPS inhibited HEEC viability in a time- and dose-dependent manner. The miR-124-3p inhibitor reversed the LPS-induced apoptosis and inhibition of HEEC viability. In addition, miR-124-3p could be transferred from BMSCs to HEECs by exosomes. Exosomes were derived from BMSCs treated with an NC inhibitor (BMSCs/NC Exo) or miR-124-3p inhibitor (BMSCs/anti-miR-124-3p Exo). In addition, BMSCs/anti-miR-124-3p Exo abolished the LPS-induced inhibition of HEEC viability and proliferation by inducing HEEC apoptosis. Moreover, BMSCs/anti-miR-124-3p Exo alleviated the LPS-induced inflammation of HEECs by upregulating DUSP6 and downregulating p-p65 and p-ERK. Furthermore, in an LPS-induced in vivo endometrial injury model, BMSCs/anti-miR-124-3p Exo increased the expression level of DUSP6 and decreased the expression levels of p-p65 and p-ERK. BMSCs/anti-miR-124-3p Exo protected against LPS-induced endometrial damage in vitro and in vivo by upregulating DUSP6 and downregulating p-p65 and p-ERK1/2. This study showed that BMSCs/anti-miR-124-3p Exo might be a potential alternative for the treatment of endometritis.
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Grants
- 2020J01986, 2021J1236, 2022J01689 Natural Science Foundation of Fujian Province
- 2020J01986, 2021J1236, 2022J01689 Natural Science Foundation of Fujian Province
- 2020J01986, 2021J1236, 2022J01689 Natural Science Foundation of Fujian Province
- 2020J01986, 2021J1236, 2022J01689 Natural Science Foundation of Fujian Province
- 2020J01986, 2021J1236, 2022J01689 Natural Science Foundation of Fujian Province
- 2020J01986, 2021J1236, 2022J01689 Natural Science Foundation of Fujian Province
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Affiliation(s)
- Yihong Chen
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Fujian Medical University, No. 20 Chazhong Road, Taijiang District, Fuzhou, 350005, Fujian, China
| | - Shan Zheng
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Fujian Medical University, No. 20 Chazhong Road, Taijiang District, Fuzhou, 350005, Fujian, China
| | - Xiumei Zhao
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Fujian Medical University, No. 20 Chazhong Road, Taijiang District, Fuzhou, 350005, Fujian, China
| | - Yi Zhang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Fujian Medical University, No. 20 Chazhong Road, Taijiang District, Fuzhou, 350005, Fujian, China
| | - Suchai Yu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Fujian Medical University, No. 20 Chazhong Road, Taijiang District, Fuzhou, 350005, Fujian, China
| | - Juanbing Wei
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Fujian Medical University, No. 20 Chazhong Road, Taijiang District, Fuzhou, 350005, Fujian, China.
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Patysheva MR, Prostakishina EA, Budnitskaya AA, Bragina OD, Kzhyshkowska JG. Dual-Specificity Phosphatases in Regulation of Tumor-Associated Macrophage Activity. Int J Mol Sci 2023; 24:17542. [PMID: 38139370 PMCID: PMC10743672 DOI: 10.3390/ijms242417542] [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: 11/22/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
The regulation of protein kinases by dephosphorylation is a key mechanism that defines the activity of immune cells. A balanced process of the phosphorylation/dephosphorylation of key protein kinases by dual-specificity phosphatases is required for the realization of the antitumor immune response. The family of dual-specificity phosphatases is represented by several isoforms found in both resting and activated macrophages. The main substrate of dual-specificity phosphatases are three components of mitogen-activated kinase signaling cascades: the extracellular signal-regulated kinase ERK1/2, p38, and Janus kinase family. The results of the study of model tumor-associated macrophages supported the assumption of the crucial role of dual-specificity phosphatases in the formation and determination of the outcome of the immune response against tumor cells through the selective suppression of mitogen-activated kinase signaling cascades. Since mitogen-activated kinases mostly activate the production of pro-inflammatory mediators and the antitumor function of macrophages, the excess activity of dual-specificity phosphatases suppresses the ability of tumor-associated macrophages to activate the antitumor immune response. Nowadays, the fundamental research in tumor immunology is focused on the search for novel molecular targets to activate the antitumor immune response. However, to date, dual-specificity phosphatases received limited discussion as key targets of the immune system to activate the antitumor immune response. This review discusses the importance of dual-specificity phosphatases as key regulators of the tumor-associated macrophage function.
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Affiliation(s)
- Marina R. Patysheva
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, 634050 Tomsk, Russia; (M.R.P.); (E.A.P.); (A.A.B.)
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia;
| | - Elizaveta A. Prostakishina
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, 634050 Tomsk, Russia; (M.R.P.); (E.A.P.); (A.A.B.)
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia;
| | - Arina A. Budnitskaya
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, 634050 Tomsk, Russia; (M.R.P.); (E.A.P.); (A.A.B.)
- Laboratory of Genetic Technologies, Siberian State Medical University, 634050 Tomsk, Russia
| | - Olga D. Bragina
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia;
| | - Julia G. Kzhyshkowska
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, 634050 Tomsk, Russia; (M.R.P.); (E.A.P.); (A.A.B.)
- Laboratory of Genetic Technologies, Siberian State Medical University, 634050 Tomsk, Russia
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Mannheim Institute of Innate Immunosciences (MI3), University of Heidelberg, 68167 Mannheim, Germany
- German Red Cross Blood Service Baden-Württemberg—Hessen, 69117 Mannheim, Germany
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