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Zhang M, Zeng Y, Wang F, Feng H, Liu Q, Li F, Zhao S, Zhao J, Liu Z, Zheng F, Liu H. Effects of the Nonstructural Protein-Nucleolar and Coiled-Body Phosphoprotein 1 Protein Interaction on rRNA Synthesis Through Telomeric Repeat-Binding Factor 2 Regulation Under Nucleolar Stress. AIDS Res Hum Retroviruses 2024; 40:408-416. [PMID: 38062753 DOI: 10.1089/aid.2023.0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024] Open
Abstract
To investigate the effects and underlying molecular mechanisms of the interaction between the non-structural protein 1 (NS1) and nucleolar and coiled-body phosphoprotein 1 (NOLC1) on rRNA synthesis through nucleolar telomeric repeat-binding factor 2 (TRF2) under nucleolar stress in avian influenza A virus infection. The analysis of TRF2 ties into the exploration of ribosomal protein L11 (RPL11) and mouse double minute 2 (MDM2) because TRF2 has been found to interact with NOLC1, and the RPL11-MDM2 pathway plays an important role in nucleolar regulation and cellular processes. Both human embryonic kidney 293T cells and human lung adenocarcinoma A549 cells were transfected with the plasmids pCAGGS-HA and pCAGGS-HA-NS1, respectively. In addition, A549 cells were transfected with the plasmids pEGFP-N1, pEGFP-N1-NS1, and pDsRed2-N1-TRF2. The cell cycle was detected by flow cytometry, and coimmunoprecipitation was applied to examine the interactions between different proteins. The effect of NS1 on TRF2 was detected by immunoprecipitation, and the colocalization of NOLC1 and TRF2 or NS1 and TRF2 was visualized by immunofluorescence. Quantitative real-time PCR was conducted to detect the expression of the TRF2 and p21. There is a strong interaction between NOLC1 and TRF2, and the colocalization of NOLC1 and TRF2 in the nucleus. The protein expression of NOLC1 in A549-HA-NS1 cells was lower than that in A549-HA cells, which was accompanied by the upregulated protein expression of p53 in A549-HA-NS1 cells (all p < .05). TRF2 was scattered throughout the nucleus without clear nucleolar aggregation. RPL11 specifically interacted with MDM2 in the NS1 group, and expression of the p21 gene was significantly increased in the HA-NS1 group compared with the HA group (p < .01). NS1 protein can lead to the reduced aggregation of TRF2 in the nucleolus, inhibition of rRNA expression, and cell cycle blockade by interfering with the NOLC1 protein and generating nucleolar stress.
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Affiliation(s)
- Man Zhang
- School of Life Science, Liaoning University, Shenyang, China
| | - Yingyue Zeng
- School of Life Science, Liaoning University, Shenyang, China
- Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules of Liaoning, Shenyang, China
- Shenyang Key Laboratory of Computational Simulation and Information Processing of Biological Macromolecules, Shenyang, China
| | - Fengchao Wang
- School of Life Science, Liaoning University, Shenyang, China
| | - Huawei Feng
- Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules of Liaoning, Shenyang, China
- Shenyang Key Laboratory of Computational Simulation and Information Processing of Biological Macromolecules, Shenyang, China
- School of Pharmacy, Liaoning University, Shenyang, China
- Liaoning Provincial Engineering Laboratory of Molecular Modeling and Design for Drug, Shenyang, China
| | - Qingqing Liu
- School of Life Science, Liaoning University, Shenyang, China
| | - Feng Li
- School of Life Science, Liaoning University, Shenyang, China
| | - Shan Zhao
- School of Life Science, Liaoning University, Shenyang, China
| | - Jian Zhao
- School of Life Science, Liaoning University, Shenyang, China
- Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules of Liaoning, Shenyang, China
- Shenyang Key Laboratory of Computational Simulation and Information Processing of Biological Macromolecules, Shenyang, China
- School of Pharmacy, Liaoning University, Shenyang, China
- Liaoning Provincial Engineering Laboratory of Molecular Modeling and Design for Drug, Shenyang, China
| | - Zhikui Liu
- Liaoning Huikang Testing and Evaluation Technology Co., Shenyang, China
| | - Fangliang Zheng
- School of Life Science, Liaoning University, Shenyang, China
| | - Hongsheng Liu
- Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules of Liaoning, Shenyang, China
- Shenyang Key Laboratory of Computational Simulation and Information Processing of Biological Macromolecules, Shenyang, China
- School of Pharmacy, Liaoning University, Shenyang, China
- Liaoning Provincial Engineering Laboratory of Molecular Modeling and Design for Drug, Shenyang, China
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Zhou Y, Liu S, Zheng Y, Wang Y, Zhou Y. The role of THBS1 and PDGFD in the immune microenvironment of Helicobacter pylori-associated gastric cancer. Arab J Gastroenterol 2024; 25:194-204. [PMID: 38705811 DOI: 10.1016/j.ajg.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/28/2023] [Accepted: 02/09/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND AND STUDY AIMS Immunotherapy has emerged as a hot topic in cancer treatment in recent years and has also shown potential in the treatment of Helicobacter pylori-associated gastric cancer. However, there is still a need to identify potential immunotherapy targets. MATERIAL AND METHODS We used the GSE116312 dataset of Helicobacter pylori-associated gastric cancer to identify differentially expressed genes, which were then overlapped with immune genes from the ImmPort database. The identified immune genes were used to classify gastric cancer samples and evaluate the relationship between classification and tumor mutations, as well as immune infiltration. An immune gene-based prognostic model was constructed, and the expression levels of the genes involved in constructing the model were explored in the tumor immune microenvironment. RESULTS We successfully identified 60 immune genes and classified gastric cancer samples into two subtypes, which showed differences in prognosis, tumor mutations, immune checkpoint expression, and immune cell infiltration. Subsequently, we constructed an immune prognostic model consisting of THBS1 and PDGFD, which showed significant associations with macrophages and fibroblasts. CONCLUSION We identified abnormal expression of THBS1 and PDGFD in cancer-associated fibroblasts (CAFs) within the tumor immune microenvironment, suggesting their potential as therapeutic targets.
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Affiliation(s)
- Yun Zhou
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou 730000, China; Department of Geriatrics Gerontology, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Shixiong Liu
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou 730000, China; Department of Geriatrics Gerontology, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Ya Zheng
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou 730000, China; Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Yuping Wang
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou 730000, China; Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou 730000, China.
| | - Yongning Zhou
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou 730000, China; Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou 730000, China.
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Jiang C, Chao CC, Li J, Ge X, Shen A, Jucaud V, Cheng C, Shen X. Tissue-resident memory T cell signatures from single-cell analysis associated with better melanoma prognosis. iScience 2024; 27:109277. [PMID: 38455971 PMCID: PMC10918229 DOI: 10.1016/j.isci.2024.109277] [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: 08/28/2023] [Revised: 01/05/2024] [Accepted: 02/15/2024] [Indexed: 03/09/2024] Open
Abstract
Tissue-resident memory T cells (TRM) are a specialized T cell population residing in peripheral tissues. The presence and potential impact of TRM in the tumor immune microenvironment (TIME) remain to be elucidated. Here, we systematically investigated the relationship between TRM and melanoma TIME based on multiple clinical single-cell RNA-seq datasets and developed signatures indicative of TRM infiltration. TRM infiltration is associated with longer overall survival and abundance of T cells, NK cells, M1 macrophages, and memory B cells in the TIME. A 22-gene TRM-derived risk score was further developed to effectively classify patients into low- and high-risk categories, distinguishing overall survival and immune activation, particularly in T cell-mediated responses. Altogether, our analysis suggests that TRM abundance is associated with melanoma TIME activation and patient survival, and the TRM-based machine learning model can potentially predict prognosis in melanoma patients.
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Affiliation(s)
- Chongming Jiang
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Cheng-Chi Chao
- Department of Pipeline Development, Biomap, Inc, San Francisco, CA, USA
| | - Jianrong Li
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Xin Ge
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA
| | - Aidan Shen
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA
| | - Vadim Jucaud
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA
| | - Chao Cheng
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Xiling Shen
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA
- Xilis, Inc., Durham, NC 27713, USA
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Zhang M, Liang Y, Song P. COL3A1-positive endothelial cells influence LUAD prognosis and regulate LUAD carcinogenesis by NCL-PI3K-AKT axis. J Gene Med 2024; 26:e3573. [PMID: 37547956 DOI: 10.1002/jgm.3573] [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: 04/27/2023] [Revised: 06/24/2023] [Accepted: 07/04/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD), as the most common type of lung cancer, poses a significant threat to public health. Tumor heterogeneity plays a crucial role in carcinogenesis, which could be largely deciphered by next-generation sequencing (NGS). METHODS We obtained and screened single-cell RNA sequencing (scRNA-seq) data from 16 LUAD samples, and endothelial cells (ECs) were grouped into three clusters. The origin of EC differentiation was explored by pseudo-time analysis. CellChat analysis was used to detect potential communication between ECs and malignant cells, and gene regulatory network analysis was used to identify changes in transcription factor activity. We explored the prognosis of specific ECs clusters and their effects on the tumor microenvironment (TME) at the bulk transcriptome level. 5-Ethynyl-2'- deoxyuridine (EdU) and Ki-67 staining were conducted to study the proliferative phenotype of LUAD cell lines. Western blotting targeting the phosphorylation of PI3K-AKT proteins was utilized for determination of the downstream pathway of NCL. RESULTS COL3A1-positive ECs showed the highest crosstalk interaction with malignant cells, indicating that they have important effects on driving LUAD carcinogenesis. Vascular endothelial growth factor (VEGF) signaling pathway was identified as the main signaling pathway, mediating signal transduction from malignant cells. The TME-related genes of COL3A1-positive ECs were significantly more highly expressed. COL3A1-positive ECs showed unique metabolic and immune characteristics, as well as highly activated metabolic signaling pathways and inflammatory responses. Importantly, LUAD patients with low COL3A1-positive ECs scores displayed an inferior prognosis outcome and a higher risk of metastasis. The key target gene NCL, which is involved in the interaction between epithelial cells and cancer cells, has been identified through screening. Flow cytometry showed that knockdown of NCL prompted the apoptosis of A549 and NCI-H1299. Western blotting showed that knockdown of NCL decreased the phosphorylation of AKT and PI3K, which identified the downstream pathway of NCL. CONCLUSIONS COL3A1-positive ECs have important effects on the development of LUAD and the formation of an immune microenvironment. Furthermore, we identified a key target gene, NCL, which is involved in the interaction between endothelial cells and cancer cells. NCL also affected the apoptosis and proliferation in LUAD through the PI3K-AKT pathway.
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Affiliation(s)
- Moyan Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yicheng Liang
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Peng Song
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Ali M, Coit P, Sawalha AH. Sex-based comparison of CD4+ T cell DNA methylation in lupus reveals proinflammatory epigenetic changes in men. Clin Immunol 2022; 243:109116. [PMID: 36075396 PMCID: PMC10236946 DOI: 10.1016/j.clim.2022.109116] [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: 06/28/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 11/15/2022]
Abstract
Systemic lupus erythematosus (SLE) is more common in women than men, but the disease is more severe when it affects men. Lupus CD4+ T cells demonstrate dysregulated DNA methylation patterns. The purpose of this study was to investigate genome-wide CD4+ T cell differential DNA methylation between men (n = 12) and women (n = 10) with SLE. DNA methylation was evaluated using the Infinium MethylationEPIC array, and differences between male versus female SLE patients were calculated with probe-wise linear regressions with adjustment for age and disease activity. We identified 198 hypomethylated and 108 hypermethylated CpG sites in CD4+ T cells isolated from male compared to female SLE patients, annotated to 201 and 102 genes, respectively. A great proportion of these genes were related to apoptosis and immune functions. Among differentially methylated genes, CASP10, which is involved in the extrinsic apoptotic pathway, and multiple genes involved in T cell function and differentiation such as ELAVL1, UHRF1, and SMAD2, were hypomethylated in men compared to women with SLE. Importantly, network analysis of differentially methylated genes revealed a pattern consistent with increased activation of ROCK, PP2A, PI3K, and ERK1/ERK2 in men compared to women with SLE. These data provide epigenetic evidence suggesting activation of key T cell pathways in men compared to women with SLE and shed new light into possible mechanisms underlying increased SLE disease severity in men.
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Affiliation(s)
- Mustafa Ali
- University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Patrick Coit
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA; Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, PA, USA; Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA.
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