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Hu J, Dai C, Ding Z, Pan Y, Lu L, Bao J, Zheng J. IKBIP promotes tumor development via the akt signaling pathway in esophageal squamous cell carcinoma. BMC Cancer 2024; 24:759. [PMID: 38914958 PMCID: PMC11197280 DOI: 10.1186/s12885-024-12510-4] [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: 02/20/2024] [Accepted: 06/12/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers worldwide. Inhibitor of kappa B kinase interacting protein (IKBIP) has been reported to promote glioma progression, but its role in other cancers remains unclear. This study aimed to investigate the role of IKBIP and its underlying molecular mechanisms in ESCC. METHODS The mRNA expression of IKBIP was analyzed using multiple cancer databases. Immunohistochemistry was performed to detect IKBIP protein expression in ESCC tissues and adjacent normal tissues, and Kaplan‒Meier survival and Cox regression analyses were carried out. The effects of IKBIP knockdown (or overexpression) on ESCC cells were detected by cell viability, cell migration, flow cytometry and Western blot assays. LY-294002 was used to validate the activation of the AKT signaling pathway by IKBIP. Finally, the role of IKBIP in ESCC was verified in a xenograft model. RESULTS Both bioinformatics analysis and immunohistochemistry indicated that IKBIP expression in ESCC tissues was significantly increased and was associated with the prognosis of ESCC patients. In vitro experiments revealed that IKBIP knockdown significantly inhibited the proliferation and migration of ESCC cells, and induced cell apoptosis and G1/S phase arrest. Molecular mechanism results showed that the AKT signaling pathway was further activated after IKBIP overexpression, thereby increasing the proliferation and migration abilities of ESCC cells. In vivo study confirmed that IKBIP promoted the initiation and development of ESCC tumors in mice. CONCLUSIONS IKBIP plays a tumor-promoting role in ESCC and may serve as a predictive biomarker and a potential therapeutic target for ESCC.
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Affiliation(s)
- Jiannan Hu
- Department of Public Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, 150 Ximenjie, Linhai, Zhejiang Province, 317000, China
| | - Chuanjing Dai
- Department of Public Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, 150 Ximenjie, Linhai, Zhejiang Province, 317000, China
| | - Zhaoji Ding
- Department of Public Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, 150 Ximenjie, Linhai, Zhejiang Province, 317000, China
| | - Yixiao Pan
- Department of Public Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, 150 Ximenjie, Linhai, Zhejiang Province, 317000, China
| | - Lingxiao Lu
- Department of Public Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, 150 Ximenjie, Linhai, Zhejiang Province, 317000, China
| | - Jiaqian Bao
- Department of Public Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, 150 Ximenjie, Linhai, Zhejiang Province, 317000, China
| | - Jingmin Zheng
- Department of Public Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, 150 Ximenjie, Linhai, Zhejiang Province, 317000, China.
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Zhang Y, Liu B, Zhou Y. A novel disulfidptosis-related gene signature predicts overall survival of glioblastoma patients. Future Sci OA 2024; 10:FSO948. [PMID: 38817361 PMCID: PMC11137853 DOI: 10.2144/fsoa-2023-0136] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/30/2023] [Indexed: 06/01/2024] Open
Abstract
Aim: The aim of this study was to investigate the prognostic relevance of disulfidptosis-related genes in glioblastoma using bioinformatic analysis in The Cancer Genome Atlas Program-Glioblastoma (TCGA-GBM) database and develop a gene signature model for predicting patient prognosis. Methods: We conducted a bioinformatic analysis using the TCGA-GBM database and employed weighted co-expression network analysis to identify disulfidptosis-related genes. Subsequently, we developed a predictive gene signature model based on these genes to stratify glioblastoma patients into high and low-risk groups. Results: Patients categorized into the high-risk group based on the disulfidptosis-related gene signature exhibited a significantly reduced survival rate in comparison to those in the low-risk group. Functional analysis also revealed notable differences in the immune status between the two risk groups. Conclusion: In conclusion, a new disulfidptosis-related gene signature can be utilised to predict prognosis in GBM.
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Affiliation(s)
- Yuxia Zhang
- Intensive Care Unit, Shandong Dongying People's Hospital, Dongying, 257091, China
- Department of Oncology, Shandong Dongying People's Hospital, Dongying, 257091, China
| | - Bing Liu
- Department of Oncology, Shandong Dongying People's Hospital, Dongying, 257091, China
| | - Yuelian Zhou
- Department of Oncology, Shandong Dongying People's Hospital, Dongying, 257091, China
- Department of Social & Medical Work, Shandong Dongying People's Hospital, Dongying, 257091, China
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3
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Li Y, Yang W, Liu C, Zhou S, Liu X, Zhang T, Wu L, Li X, Zhang J, Chang E. SFXN1-mediated immune cell infiltration and tumorigenesis in lung adenocarcinoma: A potential therapeutic target. Int Immunopharmacol 2024; 132:111918. [PMID: 38537539 DOI: 10.1016/j.intimp.2024.111918] [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: 01/29/2024] [Revised: 03/17/2024] [Accepted: 03/20/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND Sideroflexin 1 (SFXN1), a mitochondrial serine transporter implicated in one-carbon metabolism, is a prognostic biomarker in lung adenocarcinoma (LUAD). However, its role in LUAD progression remains elusive. This study aimed to investigate the functional significance of SFXN1 in LUAD and evaluate its potential as a therapeutic target. METHODS We analyzed SFXN1 expression and its diagnostic and prognostic value in LUAD using the Pan-cancer TCGA dataset. In vitro assays (CCK-8, cell cycle, EDU, wound-healing, and transwell) were employed to assess the role of SFXN1, complemented by in vivo experiments. RNA sequencing elucidated SFXN1-mediated cellular functions and potential mechanisms. Bulk RNA-seq and scRNA-seq data from TCGA and GEO were used to investigate the correlation between SFXN1 and the tumor immune microenvironment. RT-qPCR, Western blot, and IHC assays validated SFXN1 expression and its impact on the immune microenvironment in LUAD. RESULTS SFXN1 was upregulated in LUAD tissues and associated with poor prognosis. RNA-seq and scRNA-seq analyses revealed increased SFXN1 expression in tumor cells, accompanied by decreased infiltration of NK and cytotoxic T cells. SFXN1 knockdown significantly reduced cell proliferation and migration, and the inhibition of ERK phosphorylation and CCL20 expression may be the molecular mechanism involved. In vivo, targeting SFXN1 decreased Tregs infiltration and inhibited tumor growth. CONCLUSIONS Our findings suggest that SFXN1 may be a potential therapeutic target for LUAD treatment.
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Affiliation(s)
- Yanjun Li
- Department of Anaesthesiology and Perioperative Medicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, China
| | - Wenke Yang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, China
| | - Chaojun Liu
- Department of Breast Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, China
| | - Shengli Zhou
- Department of Pathology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, China
| | - Xiaozhuan Liu
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, China
| | - Tingting Zhang
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, China
| | - Lingzhi Wu
- Division of Anaesthetics, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Faulty of Medicine, Imperial College London, Chelsea and Westminster Hospital, UK
| | - Xinyi Li
- Division of Anaesthetics, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Faulty of Medicine, Imperial College London, Chelsea and Westminster Hospital, UK
| | - Jiaqiang Zhang
- Department of Anaesthesiology and Perioperative Medicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, China.
| | - Enqiang Chang
- Department of Anaesthesiology and Perioperative Medicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, China; Division of Anaesthetics, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Faulty of Medicine, Imperial College London, Chelsea and Westminster Hospital, UK.
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4
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Lv L, Zhang X, Liu Y, Zhu X, Pan R, Huang L. Three Liquid-Liquid Phase Separation-Related Genes Associated with Prognosis in Glioma. Pharmgenomics Pers Med 2024; 17:171-181. [PMID: 38681062 PMCID: PMC11048218 DOI: 10.2147/pgpm.s442000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/16/2024] [Indexed: 05/01/2024] Open
Abstract
Purpose Dysregulated liquid-liquid phase separation (LLPS) instigates tumorigenesis through biomolecular condensate dysfunction. However, the association between LLPS-associated genes and glioma remains underexplored. Patients and Methods Differentially expressed genes (DEGs) of glioma were obtained from the GSE50161 dataset, including 34 glioma and 13 normal samples. We analyzed differentially expressed LLPS-related genes in glioma from public databases. These genes informed refined molecular subtyping on the TCGA-glioma dataset. CIBERSORT assessed immune cell infiltration across three subclusters. A prognostic model was devised using univariate and lasso Cox regressions on intersecting genes. Prognostic gene expression was validated in glioma cells via RT-qPCR. Results A total of 673 differentially expressed LLPS-associated genes were identified in glioma. Three distinct molecular subtypes (C1, C2, and C3) of glioma were obtained with a marked variance in the expression of immune checkpoint genes PD1 and PDL1. Differences in immune cell infiltration were observed across subtypes. In addition, a tri-gene prognostic signature (TAGLN2, NTNG2, and IGF2BP2) was derived with significant survival differences between high and low-risk groups. The prognostic model displayed impressive AUC values for 1, 3, and 5-year survival in both training and validation sets. Further analysis highlighted a notable correlation between the three prognostic genes and immune cells in glioma samples. Furthermore, we found the upregulation of TAGLN2 and IGF2BP2 and the downregulation of NTNG2 in glioma tumors and cells. Conclusion This study innovatively uncovers the significant role of LLPS-related genes in glioma tumor grading and prognosis. The constructed tri-gene prognostic model holds promise for enhancing personalized prognosis assessments and optimizing immunotherapy strategies for glioma patients.
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Affiliation(s)
- Ling Lv
- Department of Neurosurgery, the First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, People’s Republic of China
| | - Xin Zhang
- Department of Neurosurgery, the First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, People’s Republic of China
| | - Yajun Liu
- Department of Neurosurgery, the First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, People’s Republic of China
| | - Xutong Zhu
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People's Republic of China
| | - Ruihan Pan
- Department of Neurosurgery, the First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, People’s Republic of China
| | - Lifa Huang
- Department of Neurosurgery, the First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, People’s Republic of China
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Shi Y, Yao M, Shen S, Wang L, Yao D. Abnormal expression of Krüppel-like transcription factors and their potential values in lung cancer. Heliyon 2024; 10:e28292. [PMID: 38560274 PMCID: PMC10979174 DOI: 10.1016/j.heliyon.2024.e28292] [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: 07/27/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Lung cancer still is one of the most common malignancy tumors in the world. However, the mechanisms of its occurrence and development have not been fully elucidated. Zinc finger protein family (ZNFs) is the largest transcription factor family in human genome. Recently, the more and more basic and clinical evidences have confirmed that ZNFs/Krüppel-like factors (KLFs) refer to a group of conserved zinc finger-containing transcription factors that are involved in lung cancer progression, with the functions of promotion, inhibition, dual roles and unknown classifications. Based on the recent literature, some of the oncogenic KLFs are promising molecular biomarkers for diagnosis, prognosis or therapeutic targets of lung cancer. Interestingly, a novel computational approach has been proposed by using machine learning on features calculated from primary sequences, the XGBoost-based model with accuracy of 96.4 % is efficient in identifying KLF proteins. This paper reviews the recent some progresses of the oncogenic KLFs with their potential values for diagnosis, prognosis and molecular target in lung cancer.
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Affiliation(s)
- Yang Shi
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University & Department of Medical Immunology, Medical School of Nantong University, Nantong 226001, China
- Department of Thoracic Surgery, First People's Hospital of Yancheng, Yancheng 224001, China
| | - Min Yao
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University & Department of Medical Immunology, Medical School of Nantong University, Nantong 226001, China
| | - Shuijie Shen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University & Department of Medical Immunology, Medical School of Nantong University, Nantong 226001, China
| | - Li Wang
- Research Center for Intelligent Information Technology, Nantong University, Nantong 226019, Jiangsu, China
| | - Dengfu Yao
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University & Department of Medical Immunology, Medical School of Nantong University, Nantong 226001, China
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Zhao Z, Xing N, Guo H, Li J, Sun G. Identification of Lower Grade Glioma Antigens Based on Ferroptosis Status for mRNA Vaccine Development. Pharmgenomics Pers Med 2024; 17:105-123. [PMID: 38623558 PMCID: PMC11018127 DOI: 10.2147/pgpm.s449230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/16/2024] [Indexed: 04/17/2024] Open
Abstract
Purpose mRNA vaccines represent a promising and innovative strategy within the realm of cancer immunotherapy. However, their efficacy in treating lower-grade glioma (LGG) requires evaluation. Ferroptosis exhibits close associations with the initiation, evolution, and suppression of cancer. In this study, we explored the landscape of the ferroptosis-associated tumor microenvironment to facilitate the development of mRNA vaccines for LGG patients. Patients and Methods Genomic and clinical data of the LGG patients was obtained from the Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases. Ferroptosis-related tumor antigens were identified based on differential expression, mutation status, correlation with antigen-presenting cells, and prognosis, relevance to immunogenic cell death (ICD). Antigen expression levels in LGG specimens and cell lines were validated using real time-polymerase chain reaction (RT-PCR). Consensus clustering was employed for patient classification. The immune landscapes of ferroptosis subtypes were further characterized, including immune responses, prognostic ability, tumor microenvironment, and tumor-related signatures. Results Five tumor antigens, namely, HOTAIR, IDO1, KIF20A, NR5A2, and RRM2 were identified in LGG. RT-PCR demonstrated higher expression of these genes in LGG compared to the control. Twelve gene modules and four ferroptosis subtypes (FS1-FS4) of LGG were defined. FS2 and FS4, characterized as "cold" tumors due to their decreased tumor mutation burden (TMB) and immune checkpoint proteins (ICPs), were deemed appropriate candidates for the mRNA vaccine. Conclusion HOTAIR, IDO1, KIF20A, NR5A2, and RRM2 were identified as promising candidate antigens for the development of an LGG mRNA vaccine, particularly offering potential benefits to FS2 and FS4 patients.
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Affiliation(s)
- Zhenxiang Zhao
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Na Xing
- Department of Endocrinology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Hao Guo
- Department of Hepatobiliary Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Jianfeng Li
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Guozhu Sun
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
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Esteves L, Caramelo F, Roda D, Carreira IM, Melo JB, Ribeiro IP. Identification of Novel Molecular and Clinical Biomarkers of Survival in Glioblastoma Multiforme Patients: A Study Based on The Cancer Genome Atlas Data. BIOMED RESEARCH INTERNATIONAL 2024; 2024:5582424. [PMID: 38606198 PMCID: PMC11008977 DOI: 10.1155/2024/5582424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/14/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
Abstract
Glioblastoma multiforme (GBM) is the most prevalent type of brain tumour; although advancements in treatment have been made, the median survival time for GBM patients has persisted at 15 months. This study is aimed at investigating the genetic alterations and clinical features of GBM patients to find predictors of survival. GBM patients' methylation and gene expression data along with clinical information from TCGA were retrieved. The most overrepresented pathways were identified independently for each omics dataset. From the genes found in at least 30% of these pathways, one gene that was identified in both sets was further examined using the Kaplan-Meier method for survival analysis. Additionally, three groups of patients who started radio and chemotherapy at different times were identified, and the influence of these variations in treatment modality on patient survival was evaluated. Four pathways that seemed to negatively impact survival and two with the opposite effect were identified. The methylation status of PRKCB was highlighted as a potential novel biomarker for patient survival. The study also found that treatment with chemotherapy prior to radiotherapy can have a significant impact on patient survival, which could lead to improvements in clinical management and therapeutic approaches for GBM patients.
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Affiliation(s)
- Luísa Esteves
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Francisco Caramelo
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal
- University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB) and Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- Laboratory of Biostatistics and Medical Informatics, iCBR-Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Domingos Roda
- Algarve Radiation Oncology Unit-Joaquim Chaves Saúde (JCS), Faro, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal
- University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB) and Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal
- University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB) and Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
| | - Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal
- University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB) and Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
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Xu W, Tang Y, Yang Y, Wang C, Liu C, Zhang J, Zhao L, Wang G. Depletion of CPNE7 sensitizes colorectal cancer to 5-fluorouracil by downregulating ATG9B expression. J Cell Mol Med 2024; 28:e18261. [PMID: 38526029 PMCID: PMC10962129 DOI: 10.1111/jcmm.18261] [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: 08/23/2023] [Revised: 02/10/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024] Open
Abstract
We aimed to explore the biological function of CPNE7 and determine the impact of CPNE7 on chemotherapy resistance in colorectal cancer (CRC) patients. According to the Gene Expression Profiling Interactive Analysis database and previously published data, CPNE7 was identified as a potential oncogene in CRC. RT-qPCR and Western blotting were performed to verify the expression of CPNE7. Chi-square test was used to evaluate the associations between CPNE7 and clinical features. Cell proliferation, colony formation, cell migration and invasion, cell cycle and apoptosis were assessed to determine the effects of CPNE7. Transcriptome sequencing was used to identify potential downstream regulatory genes, and gene set enrichment analysis was performed to investigate downstream pathways. The effect of CPNE7 on 5-fluorouracil chemosensitivity was verified by half maximal inhibitory concentration (IC50). Subcutaneous tumorigenesis assay was used to examine the role of CPNE7 in sensitivity of CRC to chemotherapy in vivo. Transmission electron microscopy was used to detect autophagosomes. CPNE7 was highly expressed in CRC tissues, and its expression was correlated with T stage and tumour site. Knockdown of CPNE7 inhibited the proliferation and colony formation of CRC cells and promoted apoptosis. Knockdown of CPNE7 suppressed the expression of ATG9B and enhanced the sensitivity of CRC cells to 5-fluorouracil in vitro and in vivo. Knockdown of CPNE7 reversed the induction of the autophagy pathway by rapamycin and reduced the number of autophagosomes. Depletion of CPNE7 attenuated the malignant proliferation of CRC cells and enhanced the chemosensitivity of CRC cells to 5-fluorouracil.
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Affiliation(s)
- Weile Xu
- The Department of General surgeryThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- The Department of General surgeryHebei Chest HospitalShijiazhuangHebeiChina
- The Second Department of SurgeryThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Yujie Tang
- The Department of Gastrointestinal surgeryThe Third Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Yang Yang
- The Department of Gastrointestinal surgeryThe Third Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Changjing Wang
- The Department of Gastrointestinal surgeryThe Third Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Chen Liu
- The Department of Gastrointestinal surgeryThe Third Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Jianqing Zhang
- The Department of Gastrointestinal surgeryThe Third Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Lianmei Zhao
- Scientific Research CenterThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Guiying Wang
- The Department of General surgeryThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- The Second Department of SurgeryThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
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9
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Tong L, Zheng X, Wang T, Gu W, Shen T, Yuan W, Wang S, Xing S, Liu X, Zhang C, Zhang C. Inhibition of UBA52 induces autophagy via EMC6 to suppress hepatocellular carcinoma tumorigenesis and progression. J Cell Mol Med 2024; 28:e18164. [PMID: 38445807 PMCID: PMC10915828 DOI: 10.1111/jcmm.18164] [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: 07/10/2023] [Revised: 01/08/2024] [Accepted: 01/24/2024] [Indexed: 03/07/2024] Open
Abstract
Ubiquitin A-52 residue ribosomal protein fusion product 1 (UBA52) has a role in the occurrence and development of tumours. However, the mechanism by which UBA52 regulates hepatocellular carcinoma (HCC) tumorigenesis and progression remains poorly understood. By using the Cell Counting Kit (CCK-8), colony formation, wound healing and Transwell assays, we assessed the effects of UBA52 knockdown and overexpression on the proliferation and migration of HCC cells in vitro. By establishing subcutaneous and metastatic tumour models in nude mice, we evaluated the effects of UBA52 on HCC cell proliferation and migration in vivo. Through bioinformatic analysis of data from the Gene Expression Profiling Interactive Analysis (GEPIA) and The Cancer Genome Atlas (TCGA) databases, we discovered that UBA52 is associated with autophagy. In addition, we discovered that HCC tissues with high UBA52 expression had a poor prognosis in patients. Moreover, knockdown of UBA52 reduced HCC cell growth and metastasis both in vitro and in vivo. Mechanistically, knockdown of UBA52 induced autophagy through EMC6 in HCC cells. These findings suggest that UBA52 promoted the proliferation and migration of HCC cells through autophagy regulation via EMC6 and imply that UBA52 may be a viable novel treatment target for HCC patients.
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Affiliation(s)
- Li Tong
- Department of General SurgeryThe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Xiaofei Zheng
- Department of General SurgeryThe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Tianqi Wang
- Department of General SurgeryThe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Wang Gu
- Department of General SurgeryThe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Tingting Shen
- Department of PathologyThe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Wenkang Yuan
- Department of General SurgeryThe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Siyu Wang
- Department of General SurgeryThe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Songlin Xing
- Department of General SurgeryThe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Xiaoying Liu
- College of Life Sciences of Anhui Medical UniversityHefeiChina
| | - Chong Zhang
- Department of General SurgeryThe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Chao Zhang
- Department of General SurgeryThe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
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Zhang YH, Liu XS, Gao Y, Yuan LL, Huang ZM, Zhang Y, Liu ZY, Yang Y, Liu XY, Ke CB, Pei ZJ. SFXN1 as a potential diagnostic and prognostic biomarker of LUAD is associated with 18F-FDG metabolic parameters. Lung Cancer 2024; 188:107449. [PMID: 38184958 DOI: 10.1016/j.lungcan.2023.107449] [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: 10/28/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND Sideroflexin 1 (SFXN1) has been discovered as a novel tumor marker for lung adenocarcinoma, but data on its importance in the development of lung adenocarcinoma is still limited. This study evaluated the correlation between SFXN1 and parameters related to 18F-flurodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT), and further explored the role of SFXN1 in the value-added and glycolytic processes of LUAD. METHOD The expression and prognostic value of SFXN1 mRNA in LUAD were analyzed using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) data base. Retrospective analysis of 18F-FDG PET imaging and metabolic parameters in 42 patients to explore the relationship between the expression of SFXN1 and glucose metabolism levels in lung adenocarcinoma and its clinical significance. H1975 cells were selected as the in vitro research object, and the biological effects of SFXN1 on LUAD were further elucidated through Edu proliferation assay, CCK8 activity assay, wound healing experiment, and cell flow cytometry. RESULT SFXN1 is highly expressed in various tumors, including LUAD, and its high expression can serve as an independent predictor of overall survival in lung adenocarcinoma. In addition, the expression of SFXN1 in LUAD was significantly correlated with 18F-FDG PET/CT parameters: maximum and average standardized uptake values (SUVmax and SUVmean), as well as total lesion glycolysis (TLG) (rho = 0.574, 0.589, and 0.338, p < 0.05), which can predict the expression of SFXN1 with an accuracy of 0.934. In vitro functional experiments have shown that knocking down SFXN1 inhibits the proliferation and migration of LUAD cells, promotes cell apoptosis, and may inhibit tumor activity by regulating the expression of glycolytic related genes SLC2A1, HK2, GPI, ALDOA, GAPDH, ENO1, PKM, and LDHA. CONCLUSION The overexpression of SFXN1 is closely related to FDG uptake, and SFXN1, as a promising prognostic biomarker, may mediate the development of LUAD through the glycolytic pathway.
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Affiliation(s)
- Yao-Hua Zhang
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Xu-Sheng Liu
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China; Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Shiyan 442000, Hubei, China
| | - Yan Gao
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Ling-Ling Yuan
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Zhong-Min Huang
- Department of Medical Ultrasound, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Yu Zhang
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Zi-Yue Liu
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Yi Yang
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Xiao-Yu Liu
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Chang-Bin Ke
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China.
| | - Zhi-Jun Pei
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China; Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Shiyan 442000, Hubei, China.
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11
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Liu F, Zhang X, Lu M, Liu C, Zhang X, Chu Q, Chen Y, Zhang P. The association of genomic alterations with PD-L1 expression in Chinese patients with EGFR/ALK wild-type lung adenocarcinoma and potential predictive value of Hippo pathway mutations to immunotherapy. Cancer Med 2024; 13:e7038. [PMID: 38396367 PMCID: PMC10891359 DOI: 10.1002/cam4.7038] [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: 09/11/2023] [Revised: 01/23/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND The study focuses on PD-L1 expression as an essential biomarker for gauging the response of EGFR/ALK wild-type NSCLC patients to FDA-approved immune checkpoint inhibitors (ICIs). It aims to explore clinical, molecular, and immune microenvironment characteristics associated with PD-L1 expression in EGFR/ALK wild-type lung adenocarcinoma patients eligible for ICI therapy. METHODS In this retrospective study, tumor samples from 359 Chinese EGFR/ALK wild-type lung adenocarcinoma patients underwent comprehensive evaluations for PD-L1 expression and NGS-targeted sequencing. The investigation encompassed the analysis and comparison of clinical traits, gene mutations, pathways, and immune signatures between two groups categorized by PD-L1 status: negative (TPS < 1%) and positive (TPS ≥ 1%). Additionally, the study explored the link between genomic changes and outcomes following immunotherapy. RESULTS High tumor mutational burden correlated significantly with PD-L1 positivity in patients with EGFR/ALK wild-type lung adenocarcinoma. Gene alterations, including TP53, KRAS, and others, were more pronounced in the PD-L1 positive group. Pathway analysis highlighted higher frequencies of alterations in pathways like RTK/RAS, p53, and Hippo in PD-L1-positive patients. The Hippo pathway's relevance was confirmed in separate immunotherapy cohorts, associated with better outcomes. In terms of immune cell infiltration, Hippo mutants exhibited higher levels of CD68+ PD-L1+ macrophages, CD8+ T cells, and CD8+ PD-1- T cells. CONCLUSIONS This study offers insights into genomic features of Chinese EGFR/ALK wild-type lung adenocarcinoma patients based on PD-L1 expression. Notably, Hippo pathway alterations were linked to improved immunotherapy outcomes. These findings suggest connections between the Hippo pathway and PD-L1 expression, warranting further clinical and functional investigations. The research advances our understanding of PD-L1 expression's genomic context and immunotherapy response in EGFR/ALK wild-type lung adenocarcinoma.
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Affiliation(s)
- Fangfang Liu
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xuemei Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Mengyao Lu
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Chun Liu
- Genecast Biotechnology Co., LtdWuxiJiangsuChina
| | | | - Qian Chu
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yuan Chen
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Peng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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12
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Qian T, Wenxian T, Anbing H. β-elemene enhances cisplatin sensitivity of non-small cell lung cancer cells via the miR-17-5p/STAT3 axis. Chem Biol Drug Des 2024; 103:e14395. [PMID: 37973414 DOI: 10.1111/cbdd.14395] [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: 08/24/2023] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
In China, β-elemene, a sesquiterpene compound derived from Curcuma wenyujin, is clinically used to treat many human malignancies, including non-small cell lung cancer (NSCLC). Nonetheless, the role of β-elemene in regulating cisplatin sensitivity of NSCLC cells and the related mechanisms are not clear. This study was conducted to investigate the role of β-elemene in sensitizing NSCLC cells to cisplatin. In this work, cisplatin-resistant NSCLC cell lines were constructed. CCK-8, colony formation, and flow cytometry assays were executed to examine cell viability, growth, and apoptosis. MiR-17-5p and STAT3 expression levels in cells were detected by qRT-PCR. Western blot was executed to determine the expression levels of STAT3 and apoptosis-related proteins (Bax and Bcl-2) in the cells. Dual-luciferase reporter gene experiments were performed to verify the targeting relationship between miR-17-5p and STAT3. Herein, we report that, β-elemene inhibits the viability, and induces the apoptosis of cisplatin-resistant NSCLC cells. Additionally, β-elemene induces the upregulation miR-17-5p and downregulation of STAT3. STAT3 is validated to be a target of miR-17-5p in NSCLC cells. Additionally, the role of β-elemene to repress the viability of cisplatin-resistant NSCLC cells is partially counteracted by miR-17-5p inhibitor or STAT3 overexpression. In summary, our study suggests that β-elemene enhances cisplatin sensitivity of NSCLC cells by modulating miR-17-5p/STAT3 axis, and it may be a choice for the complementary treatment of NSCLC patients.
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Affiliation(s)
- Tian Qian
- Department of Oncology, The Fifth Hospital of Wuhan, Wuhan, P.R. China
| | - Tong Wenxian
- Department of Oncology, The Fifth Hospital of Wuhan, Wuhan, P.R. China
| | - He Anbing
- Department of Oncology, The Fifth Hospital of Wuhan, Wuhan, P.R. China
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Lai H, Xiang X, Long X, Chen Z, Liu Y, Huang X. Multi-omics and single-cell sequencing analyses reveal the potential significance of circadian pathways in cancer therapy. Expert Rev Mol Diagn 2024; 24:107-121. [PMID: 38288973 DOI: 10.1080/14737159.2023.2296668] [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: 05/17/2023] [Accepted: 11/24/2023] [Indexed: 02/22/2024]
Abstract
BACKGROUND Circadian rhythm disturbance is an independent risk factor for cancer. However, few studies have been reported on circadian rhythm related genes (CRGs) in cancer, so it is important to further explore the impact of CRGs in pan-cancer. RESEARCH DESIGN AND METHODS The Cancer Genome Atlas database was used to collect cancer-related data such as copy number variation, single nucleotide variants, methylation, and survival differences. Immunohistochemistry (IHC) was used to verify the expression of circadian rhythm hub genes. The circadian pathway scores (CRS) were calculated using single-sample gene enrichment analysis. TIMER and GEPIA databases were used for immune-cell integration and assessment. Single-cell sequencing data was used to evaluate the abundance of CRS in tumor microenvironment cells. RESULTS In this study, we found that the expression of circadian pathway varies between tumors. CSNK1E was significantly up-regulated in most tumors and CRY2 was significantly down-regulated in most tumors. The protein interaction network suggested CRY2 as the core gene and IHC verified its significant low expression in KIRC. In addition, CRGs were found to be protective factors in most tumors and have the potential to act as specific immune markers in different tumors. CRS was significantly lower in abundance in most tumors. CRS was significantly associated with overall survival in tumor patients and associated with the expression of many immune cells in the tumor immune microenvironment. CRS is significantly associated with tumor mutational burden and microsatellite instability scores in most tumors and may serve as a potential immunotherapeutic marker. CONCLUSIONS The circadian rhythm pathway may be a breakthrough point in regulating the tumor microenvironment meanwhile a suitable immunotherapy method in the future.
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Affiliation(s)
- Hao Lai
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, The People's Republic of China
| | - Xiaoyun Xiang
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, The People's Republic of China
| | - Xingqing Long
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, The People's Republic of China
| | - Zuyuan Chen
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, The People's Republic of China
| | - Yanling Liu
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, The People's Republic of China
| | - Xiaoliang Huang
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, The People's Republic of China
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14
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Su F, Liu Y, Zong Y, Gao Z, Zhou G, Deng C, Liu Y, Zeng Y, Ma X, Wang Y, Wu Y, Xu F, Guan L, Liu B. Identification of circulating miRNA as early diagnostic molecular markers in malignant glioblastoma base on decision tree joint scoring algorithm. J Cancer Res Clin Oncol 2023; 149:17823-17836. [PMID: 37943358 DOI: 10.1007/s00432-023-05448-w] [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: 08/09/2023] [Accepted: 09/27/2023] [Indexed: 11/10/2023]
Abstract
PURPOSE The lack of clinical markers prevents early diagnosis of glioblastoma (GBM). Many studies have found that circulating microRNAs (miRNAs) can be used as early diagnostic markers of malignant tumours. Therefore, the identification of novel circulating miRNA biomolecular markers could be beneficial to clinicians in the early diagnosis of GBM. METHODS We developed a decision tree joint scoring algorithm (DTSA), systematically integrating significance analysis of microarray (SAM), Pearson hierarchical clustering, T test, Decision tree and Entropy weight score algorithm, to screen out circulating miRNA molecular markers with high sensitivity and accuracy for early diagnosis of GBM. RESULTS DTSA was developed and applied for GBM datasets and three circulating miRNA molecular markers were identified, namely, hsa-miR-2278, hsa-miR-555 and hsa-miR-892b. We have found that hsa-miR-2278 and hsa-miR-892b regulate the GBM pathway through target genes, promoting the development of GBM and affecting the survival of patients. DTSA has better classification effect in all data sets than other classification algorithms, and identified miRNAs are better than existing markers of GBM. CONCLUSION These results suggest that DTSA can effectively identify circulating miRNA, thus contributing to the early diagnosis and personalised treatment of GBM.
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Affiliation(s)
- Fei Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Yueyang Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yonghua Zong
- Department of Modern Medicine, University of Tibetan Medicine, Lhasa, 850000, China
| | - Ziyu Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
- Department of Anatomy, Harbin Medical University, Harbin, 150081, China
| | - Guiqin Zhou
- Department of Immunology, Harbin Medical University, Harbin, 150081, China
| | - Chao Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
- Department of Anatomy, Harbin Medical University, Harbin, 150081, China
| | - Yuyu Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
- Department of Anatomy, Harbin Medical University, Harbin, 150081, China
| | - Yue Zeng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xiaoyan Ma
- Department of Anatomy, Harbin Medical University, Harbin, 150081, China
| | - Yongxia Wang
- Department of Anatomy, Harbin Medical University, Harbin, 150081, China
| | - Yinwei Wu
- Department of Anatomy, Harbin Medical University, Harbin, 150081, China
| | - Fusheng Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
- Department of Anatomy, Harbin Medical University, Harbin, 150081, China
| | - Lili Guan
- Department of Information Management, Shanghai Lixin University of Accounting and Finance, Shanghai, 200438, China.
| | - Baoquan Liu
- Department of Anatomy, Harbin Medical University, Harbin, 150081, China.
- Department of Modern Medicine and Pharmacy, University of Tibetan Medicine, Lhasa, 850000, China.
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Nassani R, Bokhari Y, Alrfaei BM. Molecular signature to predict quality of life and survival with glioblastoma using Multiview omics model. PLoS One 2023; 18:e0287448. [PMID: 37972206 PMCID: PMC10653472 DOI: 10.1371/journal.pone.0287448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/05/2023] [Indexed: 11/19/2023] Open
Abstract
Glioblastoma multiforme (GBM) patients show a variety of signs and symptoms that affect their quality of life (QOL) and self-dependence. Since most existing studies have examined prognostic factors based only on clinical factors, there is a need to consider the value of integrating multi-omics data including gene expression and proteomics with clinical data in identifying significant biomarkers for GBM prognosis. Our research aimed to isolate significant features that differentiate between short-term (≤ 6 months) and long-term (≥ 2 years) GBM survival, and between high Karnofsky performance scores (KPS ≥ 80) and low (KPS ≤ 60), using the iterative random forest (iRF) algorithm. Using the Cancer Genomic Atlas (TCGA) database, we identified 35 molecular features composed of 19 genes and 16 proteins. Our findings propose molecular signatures for predicting GBM prognosis and will improve clinical decisions, GBM management, and drug development.
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Affiliation(s)
- Rayan Nassani
- Center for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Yahya Bokhari
- Department of AI and Bioinformatics, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
- Department of Health Informatics, College of Public Health and Health Informatics, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Bahauddeen M. Alrfaei
- King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
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Xu Z, Xu H, Chen X, Huang X, Tian J, Zhao J, Liu B, Shi F, Wu J, Pu J. CCDC103 as a Prognostic Biomarker Correlated with Tumor Progression and Immune Infiltration in Glioma. Onco Targets Ther 2023; 16:819-837. [PMID: 37873495 PMCID: PMC10590567 DOI: 10.2147/ott.s429958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023] Open
Abstract
Background The Coiled-coil domain-containing proteins (CCDCs) are expressed in many cancers, but the role of Coiled-coil domain-containing protein 103 (CCDC103) in cancers remains unclear. Further investigations are necessary to ascertain its diagnostic significance and understand its biological function in cancers. This study aims to elucidate the biological functionalities of CCDC103 in glioma and evaluate the correlation between CCDC103 expression with glioma progression. Methods Clinical data on glioma patients were acquired from The Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA), and the Gene Expression Omnibus (GEO). The evaluation encompassed the examination of correlations between CCDC103 expression, pathological characteristics, and clinical outcomes. Furthermore, the analysis included the assessment of the correlations between CCDC103 expression and immune cell infiltration as well as glioma progression. Results Gliomas have higher levels of CCDC103 expression than the para-carcinoma tissues. Poorer prognosis, unfavorable histological characteristics, the absence of IDH gene mutations, and the absence of chromosome 1p and 19q deletions were all associated with higher expression of CCDC103 in gliomas. In addition to patient age, tumor grade, the absence of IDH mutations, and the absence of chromosome 1p and 19q deletions, univariate and multivariate Cox analyses showed that CCDC103 expression was independently prognostic of overall survival, disease-free survival, and progression-free survival in patients with glioma. Furthermore, tumor infiltration of B cells, neutrophils, macrophages, and dendritic cells were all linked with elevated expression of CCDC103. High CCDC103 expression was linked to immune response-related signaling pathways and cell proliferation, according to gene set enrichment analysis (GSEA). Notably, the knockdown of CCDC103 in glioma cell lines resulted in a significant reduction in cell proliferation and migration. Conclusion The correlation between CCDC103 expression and both glioma progression and immune cell infiltration implies that CCDC103 expression holds promise as a valuable prognostic biomarker for glioma.
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Affiliation(s)
- Zhixing Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
- Department of Neurosurgery, The Pu’er People’s Hospital, Pu’er, 665000, People’s Republic of China
| | - Haitao Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
| | - Xi Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
| | - Xiaobing Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
| | - Jintao Tian
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
| | - Jinxi Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
| | - Bohu Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
| | - Fengcai Shi
- Department of Neurosurgery, The Pu’er People’s Hospital, Pu’er, 665000, People’s Republic of China
| | - Jin Wu
- Department of Neurosurgery, The Pu’er People’s Hospital, Pu’er, 665000, People’s Republic of China
| | - Jun Pu
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
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Ge Q, Zhou C, Zang C, Li C, Hong H, Wang K, Chen L, Zhu H, Wang A. MPZL1 suppresses the cancer stem-like properties of lung cancer through β-catenin/TCF4 signaling. Funct Integr Genomics 2023; 23:304. [PMID: 37726580 DOI: 10.1007/s10142-023-01232-8] [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: 07/20/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023]
Abstract
This study was designed to explore the influence of myelin protein zero-like protein 1 (MPZL1) on the stem-like properties of cancer cells and the underlying mechanism in lung adenocarcinoma. Real-time quantitative polymerase chain reaction (RT-qPCR) was utilized to evaluate mRNA expression level. CCK8, wound healing, and transwell assays were applied to assess cell proliferation, migration, and invasion. Tumorsphere-formation assay was utilized to assess cancer stem cell-like properties. LF3 was used to block the β-catenin/Transcription factor 4 (TCF-4) signaling. Xenograft nude mouse model was conducted; tumor weight and volume were recorded. Western blot assay was utilized to detect the expression levels of CD44, CD133, β-catenin, TCF-4, and MPZL1. Following MPZL1 knockdown, the mRNA expression levels of MPZL1, β-catenin, and TCF-4 were inhibited, while the mRNA expression levels of the above genes were increased after the MPZL1 overexpression. MPZL1 knockdown suppressed cell proliferation, migration, and invasion, reduced the tumorsphere-formation capacity, and restrained the expression levels of CD44 and CD133. However, MPZL1 overexpression promoted the cell proliferation, migration, and invasion, enhanced the tumorsphere-formation capacity, and increased the expression levels of CD44 and CD133. Interestingly, LF3 treatment partially revised the effect of MPZL1 overexpression. These findings were further corroborated by in vivo experiments. We concluded that MPZL1 could suppress the lung adenocarcinoma cells' proliferation, migration, invasion, and lung cancer stem cells characteristics. The underlying mechanism is involved in the activation of β-catenin/TCF-4 signaling.
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Affiliation(s)
- Qiao Ge
- Department of Thoracic Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Chao Zhou
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Zang
- Department of Thoracic Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Chao Li
- Department of Thoracic Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Haining Hong
- Department of Thoracic Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Kangwu Wang
- Department of Thoracic Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Liwei Chen
- Department of Thoracic Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Haonan Zhu
- Department of Thoracic Surgery, Fu Yang People's Hospital, Fuyang, Anhui, China.
| | - Ansheng Wang
- Department of Thoracic Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China.
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Tran TO, Lam LHT, Le NQK. Hyper-methylation of ABCG1 as an epigenetics biomarker in non-small cell lung cancer. Funct Integr Genomics 2023; 23:256. [PMID: 37523012 DOI: 10.1007/s10142-023-01185-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/01/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the most prevalent histological type of lung cancer and the leading cause of death globally. Patients with NSCLC have a poor prognosis for various factors, and a late diagnosis is one of them. The DNA methylation of CpG island sequences found in the promoter regions of tumor suppressor genes has recently received attention as a potential biomarker of human cancer. In this study, we report DNA methylation changes of the adenosine triphosphate (ATP)-binding cassette transporter G1 (ABCG1), which belongs to the ATP cassette transporter family in NSCLC patients. Our results demonstrate that ABCG1 is hyper-methylation in NSCLC samples, and these changes are negatively correlated to gene and protein expression. Furthermore, the expression of the ABCG1 gene is significantly associated with the survival time of lung adenocarcinoma (LUAD) patients; however, it did not show a correlation to overall survival (OS) of lung squamous cell carcinoma (LUSC) patients. Notably, we found ABCG1 methylation status at locus cg20214535 is strongly associated with the survival time and consistently observed hyper-methylation in LUAD samples. This novel finding suggests ABCG1 is a potential candidate for targeted therapy in lung cancer via this specific probe. In addition, we illustrate the protein-protein interaction (PPI) of ABCG1 with other proteins and the strong communication of ABCG1 with immune cells.
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Affiliation(s)
- Thi-Oanh Tran
- International Ph.D. Program in Cell Therapy and Regenerative Medicine, College of Medicine, Taipei Medical University, 110, Taipei, Taiwan
- AIBioMed Research Group, Taipei Medical University, Taipei, 110, Taiwan
- Hematology and Blood Transfusion Center, Bach Mai Hospital, No. 78, Giai Phong street, Hanoi, Vietnam
| | - Luu Ho Thanh Lam
- Department of Pediatrics, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Khanh Le
- AIBioMed Research Group, Taipei Medical University, Taipei, 110, Taiwan.
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan.
- Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei, 110, Taiwan.
- Translational Imaging Research Center, Taipei Medical University Hospital, Taipei, 110, Taiwan.
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Dang HH, Ta HDK, Nguyen TTT, Wang CY, Lee KH, Le NQK. Identification of a Novel Eight-Gene Risk Model for Predicting Survival in Glioblastoma: A Comprehensive Bioinformatic Analysis. Cancers (Basel) 2023; 15:3899. [PMID: 37568715 PMCID: PMC10417140 DOI: 10.3390/cancers15153899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Glioblastoma (GBM) is one of the most progressive and prevalent cancers of the central nervous system. Identifying genetic markers is therefore crucial to predict prognosis and enhance treatment effectiveness in GBM. To this end, we obtained gene expression data of GBM from TCGA and GEO datasets and identified differentially expressed genes (DEGs), which were overlapped and used for survival analysis with univariate Cox regression. Next, the genes' biological significance and potential as immunotherapy candidates were examined using functional enrichment and immune infiltration analysis. Eight prognostic-related DEGs in GBM were identified, namely CRNDE, NRXN3, POPDC3, PTPRN, PTPRN2, SLC46A2, TIMP1, and TNFSF9. The derived risk model showed robustness in identifying patient subgroups with significantly poorer overall survival, as well as those with distinct GBM molecular subtypes and MGMT status. Furthermore, several correlations between the expression of the prognostic genes and immune infiltration cells were discovered. Overall, we propose a survival-derived risk score that can provide prognostic significance and guide therapeutic strategies for patients with GBM.
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Affiliation(s)
- Huy-Hoang Dang
- International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan;
| | - Hoang Dang Khoa Ta
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110, Taiwan; (H.D.K.T.); (C.-Y.W.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Truc Tran Thanh Nguyen
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Taiwan University and Academia Sinica, Taipei 115, Taiwan;
| | - Chih-Yang Wang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110, Taiwan; (H.D.K.T.); (C.-Y.W.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Kuen-Haur Lee
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110, Taiwan; (H.D.K.T.); (C.-Y.W.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 110, Taiwan
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- AIBioMed Research Group, Taipei Medical University, Taipei 110, Taiwan
- Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei 110, Taiwan
- Translational Imaging Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
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20
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Hu M, Wei J, Hao J, Jin T, Li B. Impact of TREM1 Variants on the Risk and Prognosis of Glioma in the Chinese Han Population. Pharmgenomics Pers Med 2023; 16:707-715. [PMID: 37426899 PMCID: PMC10327902 DOI: 10.2147/pgpm.s403870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/21/2023] [Indexed: 07/11/2023] Open
Abstract
Background Glioma is the main pathological subtype of brain tumors with high mortality. Objective This study aimed to elucidate the correlation between TREM1 variants and glioma risk in the Chinese Han population. Methods Genotyping of six variants of TREM1 was completed by Agena MassARRAY platform in 1061 subjects (503 controls and 558 glioma patients). The relationship between TREM1 polymorphisms and glioma risk was calculated using the logistic regression model, with odds ratio (OR) and 95% confidence intervals (CIs). A multifactor dimensionality reduction (MDR) method was performed to assess SNP-SNP interactions to predict glioma risk. Results In this research, overall analysis illustrated an association between TREM1 rs9369269 and an increased risk of glioma. Rs9369269 was also related to the risk of glioma in patients aged ≤40 years and females. Subjects with rs9369269 AC genotype were likely to obtain glioma compared to people with CC genotype (patients with astroglioma vs healthy people). Compared to TT genotype carriers, carriers with AT genotype of rs1351835 were significantly associated with overall survival (OS). Conclusion Taken together, the study identified the association between TREM1 variants and glioma risk and TREM1 variants were significantly associated with the prognosis of glioma. In the future, larger samples are needed to verify the results.
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Affiliation(s)
- Mingjun Hu
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Department of Neurosurgery, Xi’an Chang’an District Hospital, Xi’an, Shaanxi Province, People’s Republic of China
| | - Jie Wei
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Jie Hao
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Tianbo Jin
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Bin Li
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
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21
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Dai L, Han Y, Yang Z, Zeng Y, Liang W, Shi Z, Tao Y, Liang X, Liu W, Zhou S, Xing Z, Hu W, Wang X. Identification and validation of SOCS1/2/3/4 as potential prognostic biomarkers and correlate with immune infiltration in glioblastoma. J Cell Mol Med 2023. [PMID: 37315184 PMCID: PMC10399539 DOI: 10.1111/jcmm.17807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/11/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023] Open
Abstract
Suppressor of cytokine signalling (SOCS) 1/2/3/4 are involved in the occurrence and progression of multiple malignancies; however, their prognostic and developmental value in patients with glioblastoma (GBM) remains unclear. The present study used TCGA, ONCOMINE, SangerBox3.0, UALCAN, TIMER2.0, GENEMANIA, TISDB, The Human Protein Atlas (HPA) and other databases to analyse the expression profile, clinical value and prognosis of SOCS1/2/3/4 in GBM, and to explore the potential development mechanism of action of SOCS1/2/3/4 in GBM. The majority of analyses showed that SOCS1/2/3/4 transcription and translation levels in GBM tissues were significantly higher than those in normal tissues. qRT-PCR, western blotting (WB) and immunohistochemical staining were used to verify that SOCS3 was expressed at higher mRNA and protein levels in GBM than in normal tissues or cells. High SOCS1/2/3/4 mRNA expression was associated with poor prognosis in patients with GBM, especially SOCS3. SOCS1/2/3/4 were highly contraindicated, which had few mutations, and were not associated with clinical prognosis. Furthermore, SOCS1/2/3/4 were associated with the infiltration of specific immune cell types. In addition, SOCS3 may affect the prognosis of patients with GBM through JAK/STAT signalling pathway. Analysis of the GBM-specific protein interaction (PPI) network showed that SOCS1/2/3/4 were involved in multiple potential carcinogenic mechanisms of GBM. In addition, colony formation, Transwell, wound healing and western blotting assays revealed that inhibition of SOCS3 decreased the proliferation, migration and invasion of GBM cells. In conclusion, the present study elucidated the expression profile and prognostic value of SOCS1/2/3/4 in GBM, which may provide potential prognostic biomarkers and therapeutic targets for GBM, especially SOCS3.
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Affiliation(s)
- Lirui Dai
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Yongjie Han
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Zhuo Yang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Yuling Zeng
- Department of Blood Transfusion, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wulong Liang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Zimin Shi
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Yiran Tao
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Xianyin Liang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Wanqing Liu
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Shaolong Zhou
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Zhe Xing
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Weihua Hu
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Xinjun Wang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
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22
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Liu C, Wei X. Unraveling the potential of senescence-related genes in guiding clinical therapy of lung adenocarcinoma patients. Funct Integr Genomics 2023; 23:188. [PMID: 37246190 DOI: 10.1007/s10142-023-01073-5] [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: 12/02/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/30/2023]
Abstract
Lung adenocarcinoma (LUAD) is the most common histological type of lung cancer. In recent years, cell senescence emerges as a potential therapeutic target of cancer therapy. However, the role of cell senescence in LUAD has not been comprehensively unveiled. One single cell RNA sequencing (scRNA-seq) dataset (GSE149655) and two bulk RNA-seq datasets (TCGA and GSE31210) of LUAD were included. Seurat R package was used to process scRNA-seq data and identify immune cell subgroups. Single sample gene set enrichment analysis (ssGSEA) was performed to calculate enrichment score of senescence-related pathways. Senescence-based molecular subtyping for LUAD samples was conducted through unsupervised consensus clustering. pRRophetic package was introduced to analysis drug sensitivity. The senescence-associated risk model was established using univariate regression and stepAIC methods. Western blot, RT-qPCR, immunofluorescence assay and CCK-8 were used to explore the effect of CYCS in LUAD cell lines. Malignant immune cells had remarkedly higher enrichment of senescence-related pathways than non-malignant cells. P53 signaling and DNA damage telomere stress induced senescence pathways were found to be significantly activated in LUAD samples compared with normal samples. We identified two clusters (clust1 and clust2) based on senescence-related genes. Clust1 had severe genomic instability, aggravated senescent features, and low immune and stromal infiltration. The senescence-associated risk model including CASP9, CHEK1, CYCS, SERPINE1, SESN2, TP53I3, LMNB1, RAD50 and TERF2IP, was effective to distinguish high- and low-risk groups. Moreover, low-risk group exhibited sensitive responses to immunotherapy and chemotherapeutic drugs. In vitro experiments results showed that CYCS expression was increased and promoted cell viability in LUAD cell lines. This study explored the important role of senescence in LUAD progression, and confirmed the potential of senescence-related genes in predicting LUAD prognosis and response to immunotherapy and chemotherapy.
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Affiliation(s)
- Chuan Liu
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 59, Haier RoadLaoshan DistrictShandong Province, 266001, Qingdao, China
| | - Xiaojuan Wei
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 59, Haier RoadLaoshan DistrictShandong Province, 266001, Qingdao, China.
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23
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Wang P, Wang Y, Wang Y. Ferroptosis patterns modulate immunocyte communication in tumor microenvironments: clinical value and therapeutic guidance of lung adenocarcinoma. Funct Integr Genomics 2023; 23:181. [PMID: 37231311 DOI: 10.1007/s10142-023-01100-5] [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: 03/05/2023] [Revised: 04/12/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023]
Abstract
Lung adenocarcinoma (LUAD) emerges as one of the most aggressive tumor types with a poor prognosis. As a novel form of regulated cell death, ferroptosis promotes the clearance of tumor cells. However, few studies demonstrated whether ferroptosis-related genes can modify the behavior of tumor microenvironment (TME) cells. Resorting to non-negative matrix factorization (NMF) clustering based on the expression of ferroptosis-related genes, we identified multiple LUAD TME cell-type subpopulations. These subtypes of TME cells displayed extensive communication with tumor epithelial cells. ATF3+cancer-associated fibroblasts (CAFs), SLC40A1+CD8+T cells, and ALOX5+CD8+T cells showed distinct biological features compared to non-ferroptosis-related TME cells. Patients with a higher abundance of these ferroptosis-related TME cell subtypes showed a favorable clinical outcome. Our study depicted a detailed landscape of LUAD cell composition with a focus on ferroptosis-related genes, which, hopefully, may provide novel insight into further study of the LAUD immune microenvironment.
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Affiliation(s)
- Peng Wang
- Department of Oncology, First Hospital Affiliated to Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Ye Wang
- Department of Endocrinology, First Hospital Affiliated to Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Yu Wang
- Physical Diagnostics Section, First Hospital Affiliated to Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China.
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24
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Niu N, Zhou L, Zhao J, Ma X, Yang F, Qi W. Sublobar resection versus lobectomy in the treatment of synchronous multiple primary lung cancer. World J Surg Oncol 2023; 21:135. [PMID: 37088839 PMCID: PMC10124016 DOI: 10.1186/s12957-023-02996-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 03/18/2023] [Indexed: 04/25/2023] Open
Abstract
OBJECTIVE Although synchronous multiple primary lung cancers (sMPLCs) are common in clinical practice, the choice of surgical modalities for the main lesion is still at the stage of exploration. This study is designed to analyze the prognosis of sMPLCs and single primary lung cancers with similar tumor stages and to explore whether sublobar resection has a similar prognosis as lobectomy for sMPLCs. METHODS One-hundred forty-one cases of sMPLCs were selected, including the following: 65 cases underwent lobectomy for main lesions, and 76 cases underwent sublobar resection for main lesions. One thousand one hundred forty-four cases of single primary lung cancer were matched at 1:1 by propensity score matching. Then, the patients with sMPLCs were divided into a lobectomy group and a sublobar group according to the first tumor stage. Ninety-eight cases of patients with sMPLCs were matched. The short-term perioperative effect, 5-year disease-free survival (DFS) rate, and 5-year overall survival (OS) rate between the two groups were compared. RESULTS There was no significant difference in OS between sMPLCs and single primary lung cancer after lobectomy (77.1% vs. 77.2%, P = 0.157) and sublobar resection (98.7% vs. 90.7%, P = 0.309). There was no significant difference in OS (86.7% vs. 83.9%, P = 0.482) or DFS (67.6 vs. 87.7%, P = 0.324) between the lobectomy group and sublobar group with sMPLCs. The sublobar resection group obtained a lower incidence of postoperative complications (40.8% vs. 16.3%, P = 0.007) and shorter postoperative hospital stay (11.22 vs. 9.27, P = 0.049). CONCLUSION The prognosis of patients with sMPLCs generally depends on the main tumor state, which has no statistical difference regardless of sublobar resection or lobectomy, and the perioperative period of sublobar resection is safer than that of lobectomy.
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Affiliation(s)
- Niu Niu
- Department of Cardiothoracic Surgery, First Hospital of Jiaxing (Affiliated Hospital of Jiaxing University), Jiaxing, 314000, China
| | - Liang Zhou
- Graduate School of Bengbu Medical College, Bengbu, 233000, China
| | - Junjie Zhao
- Department of Cardiothoracic Surgery, First Hospital of Jiaxing (Affiliated Hospital of Jiaxing University), Jiaxing, 314000, China
| | - Xingjie Ma
- Department of Cardiothoracic Surgery, First Hospital of Jiaxing (Affiliated Hospital of Jiaxing University), Jiaxing, 314000, China
| | - Fan Yang
- Department of Cardiothoracic Surgery, First Hospital of Jiaxing (Affiliated Hospital of Jiaxing University), Jiaxing, 314000, China
| | - Weibo Qi
- Department of Cardiothoracic Surgery, First Hospital of Jiaxing (Affiliated Hospital of Jiaxing University), Jiaxing, 314000, China.
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25
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Zhao N, Xu H. Pan-cancer analysis of aldolase B gene as a novel prognostic biomarker for human cancers. Medicine (Baltimore) 2023; 102:e33577. [PMID: 37083815 PMCID: PMC10118374 DOI: 10.1097/md.0000000000033577] [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: 11/21/2022] [Accepted: 03/30/2023] [Indexed: 04/22/2023] Open
Abstract
Aldolase B (ALDOB) gene is essential for the process of glycolysis and differentially expressed in cancers. The aims of this study were to explore the potential role of ALDOB in pan-cancer, in order to deepen the research on the pathological mechanism of cancer. Hence, we used several online tools (TIMER2, GEPIA2, UALCAN, cBioPortal, and MXPRESS) and R language to identify the correlation between the ALDOB expression and survival analysis, genetic alteration, DNA methylation, and immune cell infiltration based on The Cancer Genome Atlas project. The results showed that ALDOB was lowly expressed in pan-cancer. Survival analysis revealed that low expression of ALDOB was markedly related with poor clinical prognosis, while the genetic alteration within ALDOB changed along with the difference of overall survival (OS) and disease-free survival (DFS) prognosis in several cancers. A possible relationship between DNA methylation and ALDOB expression for several tumors was found. Besides, ALDOB expression was confirmed to be associated with tumor immune cell infiltration, especially in breast invasive carcinoma (BRCA), esophageal carcinoma (ESCA), and testicular germ cell tumors (TGCT) cases. Further, the enrichment analysis demonstrated that metabolic pathway was closely related to ALDOB expression. Our results provide a comprehensive pan-cancer analysis and suggest ALDOB could act as a promising tumor predictive biomarker for human cancer.
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Affiliation(s)
- Nannan Zhao
- School of Food and Biology Engineering, Xuzhou University of Technology, Xuzhou, China
| | - Haixu Xu
- School of Food and Biology Engineering, Xuzhou University of Technology, Xuzhou, China
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26
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Yuan D, Liu J, Sang W, Li Q. Comprehensive analysis of the role of SFXN family in breast cancer. Open Med (Wars) 2023; 18:20230685. [PMID: 37020524 PMCID: PMC10068752 DOI: 10.1515/med-2023-0685] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 03/02/2023] [Accepted: 03/08/2023] [Indexed: 04/04/2023] Open
Abstract
Abstract
The sideroflexin (SFXN) family is a group of mitochondrial membrane proteins. Although the function of the SFXN family in mitochondria has been widely recognized, the expression levels, role, and prognostic value of this family in breast cancer (BC) have not been clearly articulated and systematically analysed. In our research, SFXN1 and SFXN2 were significantly upregulated in BC versus normal samples based on Gene Expression Profiling Interactive Analysis 2 and the Human Protein Atlas databases. We found that high SFXN1 expression was significantly related to poor prognosis in BC patients and that high SFXN2 expression was significantly associated with good prognosis in BC patients. Gene Ontology analysis of the SFXN family was performed based on the STRING database to explore the potential functions of this family, including biological processes, cellular components, and molecular functions. Based on the MethSurv database, we found that two SFXN1 CpG sites (5′-UTR-S_Shelf-cg06573254 and TSS200-Island-cg17647431), two SFXN2 CpG sites (3′-UTR-Open_Sea-cg04774043 and Body-Open_Sea-cg18994254), one SFXN3 CpG site (Body-S_Shelf-cg17858697), and nine SFXN5 CpG sites (1stExon;5′-UTR-Island-cg03856450, Body-Open_Sea-cg04016113, Body-Open_Sea-cg04197631, Body-Open_Sea-cg07558704, Body-Open_Sea-cg08383863, Body-Open_Sea-cg10040131, Body-Open_Sea-cg10588340, Body-Open_Sea-cg17046766, and Body-Open_Sea-cg22830638) were significantly related to the prognosis of BC patients. According to the ENCORI database, four negative regulatory miRNAs for SFXN1 (hsa-miR-22-3p, hsa-miR-140-5p, hsa-miR-532-5p, and hsa-miR-582-3p) and four negative regulatory miRNAs for SFXN2 (hsa-miR-9-5p, hsa-miR-34a-5p, hsa-miR-532-5p, and hsa-miR-885-5p) were related to poor prognosis for BC patients. This study suggests that SFXN1 and SFXN2 are valuable biomarkers and treatment targets for patients with BC.
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Affiliation(s)
- Ding Yuan
- Department of General Surgery, Shouguang City People’s Hospital , Shouguang , 262700 , China
| | - Jialiang Liu
- Department of General Surgery, Shouguang City People’s Hospital , Shouguang , 262700 , China
| | - Wenbo Sang
- Department of General Surgery, Shouguang City People’s Hospital , Shouguang , 262700 , China
| | - Qing Li
- Department of General Surgery, Shouguang City People’s Hospital , Shouguang , 262700 , China
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27
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Liu X, Xie F, Ding J, Li S, Li J. Systematic pan-cancer analysis identifies gasdermin B as an immunological and prognostic biomarker for kidney renal clear cell carcinoma. Front Oncol 2023; 13:1164214. [PMID: 37064151 PMCID: PMC10101337 DOI: 10.3389/fonc.2023.1164214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023] Open
Abstract
Gasdermin (GSDM)-mediated cell lytic death plays an essential role in immunity and tumorigenesis. Despite the association of gasdermin B (GSDMB) with the tumorigenesis of various cancers, whether GSDMB functions as a prognostic biomarker in renal cell carcinoma remains poorly understood. Here, we explored the potential immunological functions and the prognostic value of GSDMB across multiple tumors with The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, including analyzing the relationship between GSDMB expression and prognosis, tumor–immune system interactions, immunomodulators, and immune cell infiltration of different tumors. Importantly, elevated expression of GSDMB is an essential factor for the poor prognosis of kidney renal clear cell carcinoma (KIRC) patients, suggesting that it might be helpful to predict a survival benefit from a clinical therapy regimen. Furthermore, GSDMB expression promoted the level of CD4+ T-cell infiltration of the tumors but is significantly negatively associated with immature dendritic cells (iDCs) in KIRC. Additionally, we identified TNFRSF25 and TNFSF14 as immunostimulators highly correlated with GSDMB expression. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses showed that GSDMB and its interacting proteins might affect tumor growth through the serine metabolism pathway. Our current results demonstrate a promising therapeutic strategy targeting GSDMB and provide new insights into GSDMB as an immunological and prognostic biomarker for KIRC.
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Affiliation(s)
- Xuehe Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai, China
| | - Feiyan Xie
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai, China
| | - Jin Ding
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Suhua Li
- Division of Natural Science, Duke Kunshan University, Jiangsu, China
- *Correspondence: Jixi Li, ; Suhua Li,
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai, China
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
- *Correspondence: Jixi Li, ; Suhua Li,
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28
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Wadapurkar RM, Sivaram A, Vyas R. RNA-Seq Analysis of Clinical Samples from TCGA Reveal Molecular Signatures for Ovarian Cancer. Cancer Invest 2023; 41:394-404. [PMID: 36797673 DOI: 10.1080/07357907.2023.2182123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Identifying differentially expressed genes and co-expression modules lead to novel biomarkers. GO, pathway enrichment, network, and tumor stage analysis of 318 ovarian cancer samples from TCGA, categorised into primary and recurrent, pre-menopause and post-menopause, and early and late stage tumors was performed. Upregulated and downregulated genes in primary vs recurrent, early stage vs late-stage and pre-menopause vs post-menopause tumors were 84 and 62, 84 and 35, and 88 and 14, respectively. IRAK2 and CXCL8 had higher expression in recurrent tumors while REG1A had higher expression in post-menopause samples. In late stage tumors constant expression of IRAK2 and REG1A was observed, while that of CXCL8 and EGF decreased. These genes may be potential biomarkers for the diagnosis of the disease.
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Affiliation(s)
- Rucha M Wadapurkar
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Aruna Sivaram
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Renu Vyas
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
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Dai L, Guo X, Xing Z, Tao Y, Liang W, Shi Z, Hu W, Zhou S, Wang X. Multi-omics analyses of CD276 in pan-cancer reveals its clinical prognostic value in glioblastoma and other major cancer types. BMC Cancer 2023; 23:102. [PMID: 36717836 PMCID: PMC9885708 DOI: 10.1186/s12885-023-10575-1] [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: 10/19/2022] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND CD276 (also known as B7-H3) is one of the most important immune checkpoints of the CD28 and B7 superfamily, and its abnormal expression is closely associated with various types of cancer. It has been shown that CD276 is able to inhibit the function of T cells, and that this gene may potentially be a promising immunotherapy target for different types of cancer. METHODS Since few systematic studies have been published on the role of CD276 in cancer to date, the present study has employed single-cell sequencing and bioinformatics methods to analyze the expression patterns, clinical significance, prognostic value, epigenetic alterations, DNA methylation level, tumor immune cell infiltration and immune functions of CD276 in different types of cancer. In order to analyze the potential underlying mechanism of CD276 in glioblastoma (GBM) to assess its prognostic value, the LinkedOmics database was used to explore the biological function and co-expression pattern of CD276 in GBM, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. In addition, a simple validation of the above analyses was performed using reverse transcription-quantitative (RT-q)PCR assay. RESULTS The results revealed that CD276 was highly expressed, and was often associated with poorer survival and prognosis, in the majority of different types of cancer. In addition, CD276 expression was found to be closely associated with T cell infiltration, immune checkpoint genes and immunoregulatory interactions between lymphoid and a non-lymphoid cell. It was also shown that the CD276 expression network exerts a wide influence on the immune activation of GBM. The expression of CD276 was found to be positively correlated with neutrophil-mediated immunity, although it was negatively correlated with the level of neurotransmitters, neurotransmitter transport and the regulation of neuropeptide signaling pathways in GBM. It is noteworthy that CD276 expression was found to be significantly higher in GBM compared with normal controls according to the RT-qPCR analysis, and the co-expression network, biological function and chemotherapeutic drug sensitivity of CD276 in GBM were further explored. In conclusion, the findings of the present study have revealed that CD276 is strongly expressed and associated with poor prognosis in most types of cancer, including GBM, and its expression is strongly associated with T-cell infiltration, immune checkpoint genes, and immunomodulatory interactions between lymphocytes and non-lymphoid cells. CONCLUSIONS Taken together, based on our systematic analysis, our findings have revealed important roles for CD276 in different types of cancers, especially GBM, and CD276 may potentially serve as a biomarker for cancer.
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Affiliation(s)
- Lirui Dai
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Xuyang Guo
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Zhe Xing
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Yiran Tao
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Wulong Liang
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Zimin Shi
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Weihua Hu
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Shaolong Zhou
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Xinjun Wang
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
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Tran TO, Vo TH, Lam LHT, Le NQK. ALDH2 as a potential stem cell-related biomarker in lung adenocarcinoma: Comprehensive multi-omics analysis. Comput Struct Biotechnol J 2023; 21:1921-1929. [PMID: 36936815 PMCID: PMC10018390 DOI: 10.1016/j.csbj.2023.02.045] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/06/2023] [Accepted: 02/23/2023] [Indexed: 03/09/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most prevalent lung cancer and one of the leading causes of death. Previous research found a link between LUAD and Aldehyde Dehydrogenase 2 (ALDH2), a member of aldehyde dehydrogenase gene (ALDH) superfamily. In this study, we identified additional useful prognostic markers for early LUAD identification and targeting LUAD therapy by analyzing the expression level, epigenetic mechanism, and signaling activities of ALDH2 in LUAD patients. The obtained results demonstrated that ALDH2 gene and protein expression significantly downregulated in LUAD patient samples. Furthermore, The American Joint Committee on Cancer (AJCC) reported that diminished ALDH2 expression was closely linked to worse overall survival (OS) in different stages of LUAD. Considerably, ALDH2 showed aberrant DNA methylation status in LUAD cancer. ALDH2 was found to be downregulated in the proteomic expression profile of several cell biology signaling pathways, particularly stem cell-related pathways. Finally, the relationship of ALDH2 activity with stem cell-related factors and immune system were reported. In conclusion, the downregulation of ALDH2, abnormal DNA methylation, and the consequent deficit of stemness signaling pathways are relevant prognostic and therapeutic markers in LUAD.
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Key Words
- 4-HNE, 4-Hydroxynonenal
- AJCC, American Joint Committee On Cancer
- ALDH, Aldehyde Dehydrogenase
- Aldehyde Dehydrogenase 2
- CGI, Cpg Island
- CPTAC, Clinical Proteomic Tumor Analysis Consortium
- CSCs, Cancer Stem Cells
- Cancer stem cells
- DNA methylation
- Gene expression
- IHC, Immunohistochemical
- LCSCs, Liver Cancer Stem Cells
- LUAD, Lung Adenocarcinoma
- Lung adenocarcinoma
- MAPK, Mitogen-Activated Protein Kinase
- MDA, Malondialdehyde
- NSCLC, Non-Small Cell Lung Cancer
- OS, Overall Survival
- Protein expression
- ROS, Reactive Oxygen Species
- SCLC, Small Cell Lung Cancer
- Survival analysis
- TCGA, The Cancer Genome Atlas
- TMT, Tandem Mass Tags
- TNM, Tumor-Node-Metastasis
- UICC, International Union For Cancer Control
- XRCC1, X-Ray Repair Cross-Complementing Protein 1
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Affiliation(s)
- Thi-Oanh Tran
- International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Hematology and Blood Transfusion Center, Bach Mai Hospital, No.78, Giai Phong street, Hanoi, Viet Nam
| | - Thanh Hoa Vo
- Department of Science, School of Science and Computing, South East Technological University, Waterford X91 K0EK, Ireland
- Pharmaceutical and Molecular Biotechnology Research Center (PMBRC), South East Technological University, Waterford X91 K0EK, Ireland
| | - Luu Ho Thanh Lam
- Department of Pediatrics, Pham Ngoc Thach University of Medicine, Ho Chi Minh city, Viet Nam
- Children’s Hospital 1, Ho Chi Minh city, Viet Nam
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 106, Taiwan
- Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei 106, Taiwan
- Translational Imaging Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
- Corresponding author at: Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 106, Taiwan.
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Development and Validation of Novel Deep-Learning Models Using Multiple Data Types for Lung Cancer Survival. Cancers (Basel) 2022; 14:cancers14225562. [PMID: 36428655 PMCID: PMC9688689 DOI: 10.3390/cancers14225562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
A well-established lung-cancer-survival-prediction model that relies on multiple data types, multiple novel machine-learning algorithms, and external testing is absent in the literature. This study aims to address this gap and determine the critical factors of lung cancer survival. We selected non-small-cell lung cancer patients from a retrospective dataset of the Taipei Medical University Clinical Research Database and Taiwan Cancer Registry between January 2008 and December 2018. All patients were monitored from the index date of cancer diagnosis until the event of death. Variables, including demographics, comorbidities, medications, laboratories, and patient gene tests, were used. Nine machine-learning algorithms with various modes were used. The performance of the algorithms was measured by the area under the receiver operating characteristic curve (AUC). In total, 3714 patients were included. The best performance of the artificial neural network (ANN) model was achieved when integrating all variables with the AUC, accuracy, precision, recall, and F1-score of 0.89, 0.82, 0.91, 0.75, and 0.65, respectively. The most important features were cancer stage, cancer size, age of diagnosis, smoking, drinking status, EGFR gene, and body mass index. Overall, the ANN model improved predictive performance when integrating different data types.
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Cai JS, Qiu MT, Yang F, Wang X. Stage IV non-small cell lung cancer among young individuals: Incidence, presentations, and survival outcomes of conventional therapies. Front Oncol 2022; 12:894780. [PMID: 36439488 PMCID: PMC9691661 DOI: 10.3389/fonc.2022.894780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 10/18/2022] [Indexed: 11/12/2022] Open
Abstract
Background There is a paucity of data published on the clinicopathological features and prognosis of stage IV non-small cell lung cancer (NSCLC) patients aged ≤45 years. Herein, we evaluated a large clinical series in an effort to provide a clearer picture of this population. Methods The least absolute shrinkage and selection operator (LASSO)-penalized Cox regression model was performed to identify prognostic factors for NSCLC among individuals aged ≤45 years. The Kaplan–Meier method with log-rank test was used to compare overall survival (OS) differences between groups. Competing risk analysis with the Fine–Gray test was used to analyze cancer-specific survival (CSS) differences. Propensity score matching (PSM) was used to minimize selection bias. Results Incidence-rate analyses, including 588,680 NSCLC cases (stage IV, 233,881; age ≤ 45 years stage IV, 5,483; and age > 45 years stage IV, 228,398) from 2004 to 2015, showed that the incidence of stage IV NSCLC among young individuals decreased over the years. In comparative analyses of clinical features and survival outcomes, a total of 48,607 eligible stage IV cases (age ≤ 45 years stage IV, 1,390; age > 45 years stage IV, 47,217) were included. The results showed that although patients in the young cohort were more likely to be diagnosed at advanced stages, they were also more likely to receive aggressive treatments. In addition, the survival rates of the young patients were superior to those of the older patients both before and after PSM. Conclusions Stage IV NSCLC patients aged ≤45 years comprise a relatively small but special NSCLC subgroup. Although this population had better survival outcomes than older patients, these patients deserve more attention due to their young age and the significant socioeconomic implications.
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Affiliation(s)
| | | | - Fan Yang
- *Correspondence: Xun Wang, ; Fan Yang,
| | - Xun Wang
- *Correspondence: Xun Wang, ; Fan Yang,
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