1
|
Gautam P, Gupta S, Sachan M. Comprehensive DNA methylation profiling by MeDIP-NGS identifies potential genes and pathways for epithelial ovarian cancer. J Ovarian Res 2024; 17:83. [PMID: 38627856 PMCID: PMC11022481 DOI: 10.1186/s13048-024-01395-3] [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: 12/27/2023] [Accepted: 03/16/2024] [Indexed: 04/19/2024] Open
Abstract
Ovarian cancer, among all gynecologic malignancies, exhibits the highest incidence and mortality rate, primarily because it is often presents with non-specific or no symptoms during its early stages. For the advancement of Ovarian Cancer Diagnosis, it is crucial to identify the potential molecular signatures that could significantly differentiate between healthy and ovarian cancerous tissues and can be used further as a diagnostic biomarker for detecting ovarian cancer. In this study, we investigated the genome-wide methylation patterns in ovarian cancer patients using Methylated DNA Immunoprecipitation (MeDIP-Seq) followed by NGS. Identified differentially methylated regions (DMRs) were further validated by targeted bisulfite sequencing for CpG site-specific methylation profiles. Furthermore, expression validation of six genes by Quantitative Reverse Transcriptase-PCR was also performed. Out of total 120 differentially methylated genes (DMGs), 68 genes were hypermethylated, and 52 were hypomethylated in their promoter region. After analysis, we identified the top 6 hub genes, namely POLR3B, PLXND1, GIGYF2, STK4, BMP2 and CRKL. Interestingly we observed Non-CpG site methylation in the case of POLR3B and CRKL which was statistically significant in discriminating ovarian cancer samples from normal controls. The most significant pathways identified were focal adhesion, the MAPK signaling pathway, and the Ras signaling pathway. Expression analysis of hypermethylated genes was correlated with the downregulation of the genes. POLR3B and GIGYF2 turned out to be the novel genes associated with the carcinogenesis of EOC. Our study demonstrated that methylation profiling through MeDIP-sequencing has effectively identified six potential hub genes and pathways that might exacerbate our understanding of underlying molecular mechanisms of ovarian carcinogenesis.
Collapse
Affiliation(s)
- Priyanka Gautam
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Prayagraj, 211004, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Prayagraj, 211004, India.
| |
Collapse
|
2
|
Cheng L, Xu J, Yuan H, Zhao Q, Yue W, Ma S, Lu W. An aptamer and Au/Si CCA based SERS sensor for ultra-sensitive detection of Vimentin during EMT in gastric cancer. Front Bioeng Biotechnol 2023; 11:1310258. [PMID: 38130825 PMCID: PMC10733448 DOI: 10.3389/fbioe.2023.1310258] [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: 10/09/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction: In this study, a surface-enhanced Raman scattering (SERS) sensor based on a functionalized Au/Si cap-cone array (Au/Si CCA) was constructed using the identity-release strategy to detect Vimentin changes during epithelial-mesenchymal transition (EMT) in gastric cancer (GC). Methods: The periodic structure of Au/Si CCA, which can form "hot spots" with high density and regular arrangement, is a substrate with excellent performance. Au/Si CCA was functionalized with aptamers as the capture substrate, and Au nanocubes (AuNCs) were modified with 5-carboxyfluorescein (5-FAM) labelled complementary strand as SERS probe. The capture substrate and SERS probe were assembled by hybridization, and the SERS signal intensity of 5-FAM was greatly enhanced. The binding of Vimentin to the aptamer resulted in a broken connection between the SERS sensor Au/Si CCA array and AuNCs, which resulted in a decrease in the signal intensity of 5-FAM. The identity-release strategy requires only a simple step of reaction to achieve rapid detection of target proteins, which has clinical practicability. Results: Using this protocol, the concentration of Vimentin in GES-1 cells could be successfully detected, and the detection limit was as low as 4.92 pg/mL. Biological experiments of Vincristine, Oncovin (VCR)-treated GES-1 cells effectively mimicked the EMT process, and Vimentin changes during EMT could be accurately detected by this method. Discussion: This study provides a selective, ultra-sensitive and accurate assay for Vimentin detection, which may provide a means for the future detection of EMT process in GC.
Collapse
Affiliation(s)
- Lingling Cheng
- Department of Oncology, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng, Jiangsu, China
| | - Jianlin Xu
- Department of Oncology, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng, Jiangsu, China
| | - Hua Yuan
- Pharmacy Department, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng, Jiangsu, China
| | - Qihao Zhao
- Department of Laboratory Medicine, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng, Jiangsu, China
| | - Wei Yue
- Department of Oncology, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng, Jiangsu, China
| | - Shuang Ma
- Department of Oncology, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng, Jiangsu, China
| | - Weimin Lu
- General Internal Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, China
| |
Collapse
|
3
|
Kondo S, Okabe A, Nakagawa T, Matsusaka K, Fukuyo M, Rahmutulla B, Dochi H, Mizokami H, Kitagawa Y, Kurokawa T, Mima M, Endo K, Sugimoto H, Wakisaka N, Misawa K, Yoshizaki T, Kaneda A. Repression of DERL3 via DNA methylation by Epstein-Barr virus latent membrane protein 1 in nasopharyngeal carcinoma. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166598. [PMID: 36372158 DOI: 10.1016/j.bbadis.2022.166598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 08/05/2022] [Accepted: 10/22/2022] [Indexed: 11/13/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is Epstein-Barr virus (EBV)-associated invasive malignancy. Increasing evidence indicates that epigenetic abnormalities, including DNA methylation, play important roles in the development of NPC. In particular, the EBV principal oncogene, latent membrane protein 1 (LMP1), is considered a key factor in inducing aberrant DNA methylation of several tumour suppressor genes in NPC, although the mechanism remains unclear. Herein, we comprehensively analysed the methylome data of Infinium BeadArray from 51 NPC and 52 normal nasopharyngeal tissues to identify LMP1-inducible methylation genes. Using hierarchical clustering analysis, we classified NPC into the high-methylation, low-methylation, and normal-like subgroups. We defined high-methylation genes as those that were methylated in the high-methylation subgroup only and common methylation genes as those that were methylated in both high- and low-methylation subgroups. Subsequently, we identified 715 LMP1-inducible methylation genes by observing the methylome data of the nasopharyngeal epithelial cell line with or without LMP1 expression. Because high-methylation genes were enriched with LMP1-inducible methylation genes, we extracted 95 high-methylation genes that overlapped with the LMP1-inducible methylation genes. Among them, we identified DERL3 as the most significantly methylated gene affected by LMP1 expression. DERL3 knockdown in cell lines resulted in significantly increased cell proliferation, migration, and invasion. Lower DERL3 expression was more frequently detected in the advanced T-stage NPC than in early T-stage NPC. These results indicate that DERL3 repression by DNA methylation contributes to NPC tumour progression.
Collapse
Affiliation(s)
- Satoru Kondo
- Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan; Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-0856, Japan
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-0856, Japan
| | - Takuya Nakagawa
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-0856, Japan; Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-2856, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-0856, Japan; Department of Pathology, Chiba University Hospital, Chiba, Chiba 260-2856, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-0856, Japan; Department of Genome Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-0856, Japan
| | - Hirotomo Dochi
- Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan
| | - Harue Mizokami
- Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan; Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-0856, Japan
| | - Yuki Kitagawa
- Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan
| | - Tomoya Kurokawa
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-0856, Japan; Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-2856, Japan
| | - Masato Mima
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-0856, Japan; Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Kazuhira Endo
- Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan
| | - Hisashi Sugimoto
- Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan
| | - Naohiro Wakisaka
- Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan
| | - Kiyoshi Misawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Tomokazu Yoshizaki
- Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-0856, Japan.
| |
Collapse
|
4
|
Li F, Niu Y, Zhao W, Yan C, Qi Y. Construction and validation of a prognostic model for lung adenocarcinoma based on endoplasmic reticulum stress-related genes. Sci Rep 2022; 12:19857. [PMID: 36400857 PMCID: PMC9674626 DOI: 10.1038/s41598-022-23852-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the most universal types of cancer all over the world and its morbidity continues to rise year by year. Growing evidence has demonstrated that endoplasmic reticulum stress is highly activated in cancer cells and plays a key role in regulating the fate of cancer cells. However, the role and mechanism of endoplasmic reticulum stress in lung adenocarcinoma genesis and development remains unclear. In this research, we developed a prognostic model to predict the overall survival of patients with LUAD utilizing endoplasmic reticulum stress-related genes and screened out potential small molecular compounds, which could assist the clinician in making accurate decisions and better treat LUAD patients. Firstly, we downloaded 419 endoplasmic reticulum stress-related genes (ERSRGs) from Molecular Signatures Database (MSigDB). Secondly, we obtained information about the transcriptome profiling and corresponding clinical data of 59 normal samples and 535 lung adenocarcinoma samples from The Cancer Genome Atlas (TCGA) database. Next, we used the DESeq2 package to identify differentially expressed genes related to endoplasmic reticulum stress. We performed univariate Cox, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analysis to establish a prognostic model for LUAD patients based on ERSRGs. Then, we carried out univariate and multivariate independent prognostic analysis of endoplasmic reticulum stress-related gene (ERSRG) score and some clinical traits of lung adenocarcinoma. Additionally, we developed a clinically applicable nomogram for predicting survival for LUAD patients over one, three, and five years. Moreover, we carried out a drug sensitivity analysis to identify novel small molecule compounds for LUAD treatment. Finally, we examined the tumor microenvironment (TME) and immune cell infiltrating analysis to explore the interactions between immune and cancer cells. 142 differentially expressed ERSRGs were identified by using the DESeq2 package. A prognostic model was built based on 7 differentially expressed ERSRGs after performing univariate Cox regression, LASSO regression, and multivariate Cox regression analysis. According to the results of univariate and multivariate independent prognostic analysis, we found ERSRG score can be used as an independent prognostic maker. Using the Kaplan-Meier curves, we found low-risk patients had higher survival probability than high-risk patients in both training set and test set. A nomogram was drawn to predict 1-, 3-, and 5-year survival probability. The calibration curves explained good performance of the model for the prediction of survival. Phenformin, OSU-03012, GSK-650394 and KIN001-135 were identified as the drugs most likely to provide important information to clinicians about the treatment of LUAD patients. A prognostic prediction model was established based on 7 differentially expressed ERSRGs (PDX1, IGFBP1, DDIT4, PPP1R3G, CFTR, DERL3 and NUPR1), which could effectively predict the prognosis of LUAD patients and give a reference for clinical doctors to help LUAD patients to make better treatment tactics. Based on the 4 small molecule compounds (Phenformin, OSU-03012, GSK-650394 and KIN001-135) we discovered, targeting endoplasmic reticulum stress-related genes may also be a therapeutic approach for LUAD patients.
Collapse
Affiliation(s)
- Feng Li
- grid.495434.b0000 0004 1797 4346School of Pharmacy, Key Laboratory of Nano-Carbon Modified Film Technology of Henan Province, Diagnostic Laboratory of Animal Diseases, Xinxiang University, Xinxiang, China
| | - Yandie Niu
- grid.495434.b0000 0004 1797 4346School of Pharmacy, Key Laboratory of Nano-Carbon Modified Film Technology of Henan Province, Diagnostic Laboratory of Animal Diseases, Xinxiang University, Xinxiang, China
| | - Wei Zhao
- grid.495434.b0000 0004 1797 4346School of Pharmacy, Key Laboratory of Nano-Carbon Modified Film Technology of Henan Province, Diagnostic Laboratory of Animal Diseases, Xinxiang University, Xinxiang, China
| | - Cheng Yan
- grid.495434.b0000 0004 1797 4346School of Pharmacy, Key Laboratory of Nano-Carbon Modified Film Technology of Henan Province, Diagnostic Laboratory of Animal Diseases, Xinxiang University, Xinxiang, China
| | - Yonghua Qi
- grid.495434.b0000 0004 1797 4346School of Pharmacy, Key Laboratory of Nano-Carbon Modified Film Technology of Henan Province, Diagnostic Laboratory of Animal Diseases, Xinxiang University, Xinxiang, China
| |
Collapse
|
5
|
Lin L, Lin G, Lin H, Chen L, Chen X, Lin Q, Xu Y, Zeng Y. Integrated profiling of endoplasmic reticulum stress-related DERL3 in the prognostic and immune features of lung adenocarcinoma. Front Immunol 2022; 13:906420. [PMID: 36275646 PMCID: PMC9585215 DOI: 10.3389/fimmu.2022.906420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022] Open
Abstract
Background DERL3 has been implicated as an essential element in the degradation of misfolded lumenal glycoproteins induced by endoplasmic reticulum (ER) stress. However, the correlation of DERL3 expression with the malignant phenotype of lung adenocarcinoma (LUAD) cells is unclear and remains to be elucidated. Herein, we investigated the interaction between the DERL3 and LUAD pathological process. Methods The Cancer Genome Atlas (TCGA) database was utilized to determine the genetic alteration of DERL3 in stage I LUAD. Clinical LUAD samples including carcinoma and adjacent tissues were obtained and were further extracted to detect DERL3 mRNA expression via RT-qPCR. Immunohistochemistry was performed to evaluate the protein expression of DERL3 in LUAD tissues. The GEPIA and TIMER website were used to evaluate the correlation between DERL3 and immune cell infiltration. We further used the t-SNE map to visualize the distribution of DERL3 in various clusters at the single-cell level via TISCH database. The potential mechanisms of the biological process mediated by DERL3 in LUAD were conducted via KEGG and GSEA. Results It was indicated that DERL3 was predominantly elevated in carcinoma compared with adjacent tissues in multiple kinds of tumors from the TCGA database, especially in LUAD. Immunohistochemistry validated that DERL3 was also upregulated in LUAD tissues compared with adjacent tissues from individuals. DERL3 was preliminarily found to be associated with immune infiltration via the TIMER database. Further, the t-SNE map revealed that DERL3 was predominantly enriched in plasma cells of the B cell population. It was demonstrated that DERL3 high-expressed patients presented significantly worse response to chemotherapy and immunotherapy. GSEA and KEGG results indicated that DERL3 was positively correlated with B cell activation and unfolded protein response (UPR). Conclusion Our findings indicated that DERL3 might play an essential role in the endoplasmic reticulum-associated degradation (ERAD) process in LUAD. Moreover, DERL3 may act as a promising immune biomarker, which could predict the efficacy of immunotherapy in LUAD.
Collapse
Affiliation(s)
- Lanlan Lin
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Respiratory Medicine Center of Fujian Province, Quanzhou, China
- The Second Clinical College, Fujian Medical University, Quanzhou, China
| | - Guofu Lin
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Respiratory Medicine Center of Fujian Province, Quanzhou, China
- The Second Clinical College, Fujian Medical University, Quanzhou, China
| | - Hai Lin
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Respiratory Medicine Center of Fujian Province, Quanzhou, China
- The Second Clinical College, Fujian Medical University, Quanzhou, China
| | - Luyang Chen
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Respiratory Medicine Center of Fujian Province, Quanzhou, China
- The Second Clinical College, Fujian Medical University, Quanzhou, China
| | - Xiaohui Chen
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Respiratory Medicine Center of Fujian Province, Quanzhou, China
- The Second Clinical College, Fujian Medical University, Quanzhou, China
| | - Qinhui Lin
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Respiratory Medicine Center of Fujian Province, Quanzhou, China
| | - Yuan Xu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Respiratory Medicine Center of Fujian Province, Quanzhou, China
- Clinical Research Unit, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- *Correspondence: Yiming Zeng, ; Yuan Xu,
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Respiratory Medicine Center of Fujian Province, Quanzhou, China
- Clinical Research Unit, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- *Correspondence: Yiming Zeng, ; Yuan Xu,
| |
Collapse
|
6
|
Shu L, Liu S, Tao Y. Development and validation of a prognosis prediction model based on 18 endoplasmic reticulum stress-related genes for patients with lung adenocarcinoma. Front Oncol 2022; 12:902353. [PMID: 36110953 PMCID: PMC9469654 DOI: 10.3389/fonc.2022.902353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/12/2022] [Indexed: 11/25/2022] Open
Abstract
Background Endoplasmic reticulum (ER) stress had a crucial impact on cell survival, proliferation, and metastasis in various cancers. However, the role of ER stress in lung adenocarcinoma remains unclear. Method Gene expression and clinical data of lung adenocarcinoma (LUAD) samples were extracted from The Cancer Genome Atlas (TCGA) and three Gene Expression Omnibus (GEO) datasets. ER stress score (ERSS) was constructed based on hub genes selected from 799 ER stress-related genes by least absolute shrinkage and selection operator (LASSO) regression. A Cox regression model, integrating ERSS and the TNM stage, was developed to predict overall survival (OS) in TCGA cohort and was validated in GEO cohorts. Gene set enrichment analysis (GSEA), single-sample GSEA (ssGSEA), and gene mutation analyses were performed to further understand the molecular features of ERSS. The tumor immune infiltration was evaluated by ESTIMATE, CIBERSORT, and xCell algorithms. The receiver operating characteristic (ROC) curves were used to evaluate the predictive value of the risk model. p< 0.05 was considered statistically significant. Results One hundred fifty-seven differentially expressed genes (DEGs) were identified between tumor and para-carcinoma tissues, and 45 of them significantly correlated with OS. Next, we identified 18 hub genes and constructed ERSS by LASSO regression. Multivariate analysis demonstrated that higher ERSS (p< 0.0001, hazard ratio (HR) = 3.8, 95%CI: 2.8–5.2) and TNM stage (p< 0.0001, HR = 1.55, 95%CI: 1.34–1.8) were independent predictors for worse OS. The prediction model integrating ERSS and TNM stage performed well in TCGA cohort (area under the curve (AUC) at five years = 0.748) and three GEO cohorts (AUC at 5 years = 0.658, 0.717, and 0.739). Pathway enrichment analysis showed that ERSS significantly correlated with unfolded protein response. Meanwhile, pathways associated with the cell cycle, growth, and metabolism were significantly enriched in the high ERSS group. Patients with SMARCA4, TP53, and EGFR mutations showed significantly higher ERSS (p = 4e−04, 0.0027, and 0.035, respectively). Tissues with high ERSS exhibited significantly higher infiltration of M1 macrophages, activated dendritic cells, and lower infiltration of CD8+ T cells and B cells, which indicate an activated tumor antigen-presenting but suppressive immune response status. Conclusion We developed and validated an ER stress-related risk model that exhibited great predictive value for OS in patients with LUAD. Our work also expanded the understanding of the role of ER stress in LUAD.
Collapse
Affiliation(s)
- Long Shu
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute School of Basic Medicine, Central South University, Changsha, China
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yongguang Tao, ; Shuang Liu,
| | - Yongguang Tao
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute School of Basic Medicine, Central South University, Changsha, China
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, School of Basic Medicine, Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yongguang Tao, ; Shuang Liu,
| |
Collapse
|
7
|
Yang Z, Liu E, Wang SM, Xiao YF, Zeng S, Yang SM, Zhao XY, Huang Y. Development of a long noncoding RNA BC032469-dependent gold nanoparticle molecular beacon for the detection of gastric cancer cells. Nanomedicine (Lond) 2021; 16:2255-2267. [PMID: 34569291 DOI: 10.2217/nnm-2021-0249] [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] [Indexed: 01/29/2023] Open
Abstract
Aim: Long noncoding RNA (lncRNA) BC032469-dependent gold nanoparticle molecular beacons (AuNP-MB) were constructed for the detection of gastric cancer cells. Materials & methods: The AuNP-MBs were prepared according to well-established procedures based on the Au-S interaction between the gold lattice and thiol functionalized oligonucleotides. More importantly, the stability and targeting ability of AuNP-MB were verified by a series of in vitro and in vivo experiments. Results: The lncRNA-dependent probes were successfully utilized for AuNP-MB-based intracellular imaging, with fluorescence effectively emitted in GC cells, but not in normal cells. Notably, such fluorescent emission was positively correlated with lncRNA BC032469 expression. Conclusion: The authors developed an effective fluorescent imaging probe for the recognition of gastric cancer cells.
Collapse
Affiliation(s)
- Zhuo Yang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, No. 83, Xinqiao Street, Shapingba District, Chongqing, 400037, China
| | - En Liu
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, No. 83, Xinqiao Street, Shapingba District, Chongqing, 400037, China
| | - Su Min Wang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, No. 83, Xinqiao Street, Shapingba District, Chongqing, 400037, China
| | - Yu Feng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, No. 83, Xinqiao Street, Shapingba District, Chongqing, 400037, China
| | - Shuo Zeng
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, No. 83, Xinqiao Street, Shapingba District, Chongqing, 400037, China
| | - Shi Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, No. 83, Xinqiao Street, Shapingba District, Chongqing, 400037, China
| | - Xiao Yan Zhao
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, No. 83, Xinqiao Street, Shapingba District, Chongqing, 400037, China
| | - Yu Huang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, No. 83, Xinqiao Street, Shapingba District, Chongqing, 400037, China
| |
Collapse
|
8
|
Jin XS, Ji TT, Shi ZC, Zhang QQ, Ye FP, Yu WL, Li RZ. Knockdown of ZNF479 inhibits proliferation and glycolysis of gastric cancer cells through regulating β-catenin/c-Myc signaling pathway. Kaohsiung J Med Sci 2021; 37:759-767. [PMID: 34042257 DOI: 10.1002/kjm2.12399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/12/2021] [Accepted: 04/20/2021] [Indexed: 12/09/2022] Open
Abstract
Gastric cancer is the fifth most common malignancy and the third most deadly tumor in the world. Zinc finger protein 479 (ZNF479) has been demonstrated to play crucial roles in hepatocellular carcinoma. However, the function of ZNF479 in gastric cancer remains to be clarified. The current study aimed to investigate the role of ZNF479 in gastric cancer progression and elucidate the potential molecular mechanism. In this study, Cell Count Kit-8 and colony formation assays demonstrated that knockdown of ZNF479 inhibited cell proliferation in AGS and SGC-7901 cells. Of note, knockdown of ZNF479 hinders tumor growth of xenograft tumor mice. What is more, knockdown of ZNF479 inhibited glucose uptake, lactate production, adenosine triphosphate level, and extracellular acidification ratio; increased oxygen consumption ratio in gastric cancer cells; and decreased the expression of glycolytic proteins both in vitro and in vivo. Furthermore, analysis mechanism suggests that ZNF479 participated in the regulation of gastric cancer progression through affecting the β-catenin/c-Myc signaling pathway. Collectively, ZNF479 plays a role as an oncogene through modulating β-catenin/c-Myc signaling pathway in the development of gastric cancer, which provides a new research target for future studies.
Collapse
Affiliation(s)
- Xiao-Sheng Jin
- Department of Gastroenterology, Ruian people's hospital, Rui'an City, China
| | - Ting-Ting Ji
- Department of Gastroenterology, Ruian people's hospital, Rui'an City, China
| | - Zheng-Chao Shi
- Department of Gastroenterology, Ruian people's hospital, Rui'an City, China
| | - Qing-Qing Zhang
- Department of Gastroenterology, Ruian people's hospital, Rui'an City, China
| | - Fang-Peng Ye
- Department of Gastroenterology, Ruian people's hospital, Rui'an City, China
| | - Wei-Lai Yu
- Department of Gastroenterology, Ruian people's hospital, Rui'an City, China
| | - Rong-Zhou Li
- Department of Gastroenterology, Ruian people's hospital, Rui'an City, China
| |
Collapse
|
9
|
Geng M, Xu K, Meng L, Xu J, Jiang C, Guo Y, Ren X, Li X, Peng Y, Wang S, Huang F, Zhang J, Wang X, Zhu W, Lu S. Up-regulated DERL3 in fibroblast-like synoviocytes exacerbates inflammation of rheumatoid arthritis. Clin Immunol 2020; 220:108579. [PMID: 32866644 DOI: 10.1016/j.clim.2020.108579] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 08/26/2020] [Indexed: 12/23/2022]
Abstract
Endoplasmic reticulum (ER) stress associated proteins contribute to the pathogenesis of rheumatoid arthritis (RA) through affecting synoviocyte proliferation and proinflammatory cytokine production. The role of DERL3, an ER-associated degradation component, in joint inflammation of RA was explored. Synovial tissues from RA and osteoarthritis (OA) patients were collected, and in RA synovial tissue, DERL3 showed up-regulation and significantly positive correlation with the expression of tumor necrosis factor alpha (TNF-α), interleukin (IL)-6 and matrix metalloproteinase (MMP)-1. Immunofluorescence result suggested DERL3 was located in fibroblast-like synoviocytes (FLS). Among different inflammatory stimuli, DERL3 could be up-regulated by TNF-α stimulation in FLS. Under TNF-α stimulation, knocking down DERL3, the expression of IL-6, IL-8, MMP-1, MMP-13 was reduced and the activation of nuclear factor kappa B (NF-κB) signaling pathway was inhibited. In pristane-induced arthritis (PIA) rat model, Derl3 was up-regulated in synovial tissue and disease was attenuated after intraarticular injection of siDerl3. Overall, we conclude that TNF-α inducing DERL3 expression promotes the inflammation of FLS through activation of NF-κB signaling pathway, suggesting DERL3 plays important roles in the pathogenesis of RA and is a promising therapeutic target.
Collapse
Affiliation(s)
- Manman Geng
- Institute of Molecular and Translational Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, China
| | - Ke Xu
- Xi'an Hong Hui Hospital, the Affiliated Hospital of Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Liesu Meng
- Institute of Molecular and Translational Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, China
| | - Jing Xu
- Institute of Molecular and Translational Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Congshan Jiang
- Institute of Molecular and Translational Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yuanxu Guo
- Institute of Molecular and Translational Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiaoyu Ren
- Xi'an Hong Hui Hospital, the Affiliated Hospital of Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiaowei Li
- Institute of Molecular and Translational Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yizhao Peng
- Institute of Molecular and Translational Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Si Wang
- Institute of Molecular and Translational Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Fumeng Huang
- Institute of Molecular and Translational Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Jing Zhang
- Institute of Molecular and Translational Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xipeng Wang
- Institute of Molecular and Translational Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wenhua Zhu
- Institute of Molecular and Translational Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, China.
| | - Shemin Lu
- Institute of Molecular and Translational Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, China.
| |
Collapse
|
10
|
Derlin-3 Is Required for Changes in ERAD Complex Formation under ER Stress. Int J Mol Sci 2020; 21:ijms21176146. [PMID: 32858914 PMCID: PMC7504720 DOI: 10.3390/ijms21176146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 12/17/2022] Open
Abstract
Endoplasmic reticulum (ER)-associated protein degradation (ERAD) is a quality control system that induces the degradation of ER terminally misfolded proteins. The ERAD system consists of complexes of multiple ER membrane-associated and luminal proteins that function cooperatively. We aimed to reveal the role of Derlin-3 in the ERAD system using the liver, pancreas, and kidney obtained from different mouse genotypes. We performed coimmunoprecipitation and sucrose density gradient centrifugation to unravel the dynamic nature of ERAD complexes. We observed that Derlin-3 is exclusively expressed in the pancreas, and its deficiency leads to the destabilization of Herp and accumulation of ERAD substrates. Under normal conditions, Complex-1a predominantly contains Herp, Derlin-2, HRD1, and SEL1L, and under ER stress, Complex-1b contains Herp, Derlin-3 (instead of Derlin-2), HRD1, and SEL1L. Complex-2 is upregulated under ER stress and contains Derlin-1, Derlin-2, p97, and VIMP. Derlin-3 deficiency suppresses the transition of Derlin-2 from Complex-1a to Complex-2 under ER stress. In the pancreas, Derlin-3 deficiency blocks Derlin-2 transition. In conclusion, the composition of ERAD complexes is tissue-specific and changes in response to ER stress in a Derlin-3-dependent manner. Derlin-3 may play a key role in changing ERAD complex compositions to overcome ER stress.
Collapse
|