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Camblor-Perujo S, Ozer Yildiz E, Küpper H, Overhoff M, Rastogi S, Bazzi H, Kononenko NL. The AP-2 complex interacts with γ-TuRC and regulates the proliferative capacity of neural progenitors. Life Sci Alliance 2024; 7:e202302029. [PMID: 38086550 PMCID: PMC10716017 DOI: 10.26508/lsa.202302029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Centrosomes are organelles that nucleate microtubules via the activity of gamma-tubulin ring complexes (γ-TuRC). In the developing brain, centrosome integrity is central to the progression of the neural progenitor cell cycle, and its loss leads to microcephaly. We show that NPCs maintain centrosome integrity via the endocytic adaptor protein complex-2 (AP-2). NPCs lacking AP-2 exhibit defects in centrosome formation and mitotic progression, accompanied by DNA damage and accumulation of p53. This function of AP-2 in regulating the proliferative capacity of NPCs is independent of its role in clathrin-mediated endocytosis and is coupled to its association with the GCP2, GCP3, and GCP4 components of γ-TuRC. We find that AP-2 maintains γ-TuRC organization and regulates centrosome function at the level of MT nucleation. Taken together, our data reveal a novel, noncanonical function of AP-2 in regulating the proliferative capacity of NPCs and open new avenues for the identification of novel therapeutic strategies for the treatment of neurodevelopmental and neurodegenerative disorders with AP-2 complex dysfunction.
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Affiliation(s)
| | - Ebru Ozer Yildiz
- CECAD Excellence Center, University of Cologne, Cologne, Germany
| | - Hanna Küpper
- CECAD Excellence Center, University of Cologne, Cologne, Germany
| | - Melina Overhoff
- CECAD Excellence Center, University of Cologne, Cologne, Germany
- Center for Physiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Saumya Rastogi
- CECAD Excellence Center, University of Cologne, Cologne, Germany
| | - Hisham Bazzi
- CECAD Excellence Center, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Dermatology and Venereology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Natalia L Kononenko
- CECAD Excellence Center, University of Cologne, Cologne, Germany
- Center for Physiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Institute of Genetics, Natural Faculty, University of Cologne, Cologne, Germany
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2
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Banushi B, Joseph SR, Lum B, Lee JJ, Simpson F. Endocytosis in cancer and cancer therapy. Nat Rev Cancer 2023:10.1038/s41568-023-00574-6. [PMID: 37217781 DOI: 10.1038/s41568-023-00574-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/24/2023]
Abstract
Endocytosis is a complex process whereby cell surface proteins, lipids and fluid from the extracellular environment are packaged, sorted and internalized into cells. Endocytosis is also a mechanism of drug internalization into cells. There are multiple routes of endocytosis that determine the fate of molecules, from degradation in the lysosomes to recycling back to the plasma membrane. The overall rates of endocytosis and temporal regulation of molecules transiting through endocytic pathways are also intricately linked with signalling outcomes. This process relies on an array of factors, such as intrinsic amino acid motifs and post-translational modifications. Endocytosis is frequently disrupted in cancer. These disruptions lead to inappropriate retention of receptor tyrosine kinases on the tumour cell membrane, changes in the recycling of oncogenic molecules, defective signalling feedback loops and loss of cell polarity. In the past decade, endocytosis has emerged as a pivotal regulator of nutrient scavenging, response to and regulation of immune surveillance and tumour immune evasion, tumour metastasis and therapeutic drug delivery. This Review summarizes and integrates these advances into the understanding of endocytosis in cancer. The potential to regulate these pathways in the clinic to improve cancer therapy is also discussed.
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Affiliation(s)
- Blerida Banushi
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Shannon R Joseph
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Benedict Lum
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Jason J Lee
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Fiona Simpson
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia.
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3
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The Impact of YRNAs on HNSCC and HPV Infection. Biomedicines 2023; 11:biomedicines11030681. [PMID: 36979661 PMCID: PMC10045647 DOI: 10.3390/biomedicines11030681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/20/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023] Open
Abstract
HPV infection is one of the most important risk factors for head and neck squamous cell carcinoma among younger patients. YRNAs are short non-coding RNAs involved in DNA replication. YRNAs have been found to be dysregulated in many cancers, including head and neck squamous cell carcinoma (HNSCC). In this study, we investigated the role of YRNAs in HPV-positive HNSCC using publicly available gene expression datasets from HNSCC tissue, where expression patterns of YRNAs in HPV(+) and HPV(−) HNSCC samples significantly differed. Additionally, HNSCC cell lines were treated with YRNA1-overexpressing plasmid and RNA derived from these cell lines was used to perform a NGS analysis. Additionally, a deconvolution analysis was performed to determine YRNA1’s impact on immune cells. YRNA expression levels varied according to cancer pathological and clinical stages, and correlated with more aggressive subtypes. YRNAs were mostly associated with more advanced cancer stages in the HPV(+) group, and YRNA3 and YRNA1 expression levels were found to be correlated with more advanced clinical stages despite HPV infection status, showing that they may function as potential biomarkers of more advanced stages of the disease. YRNA5 was associated with less-advanced cancer stages in the HPV(−) group. Overall survival and progression-free survival analyses showed opposite results between the HPV groups. The expression of YRNAs, especially YRNA1, correlated with a vast number of proteins and cellular processes associated with viral infections and immunologic responses to viruses. HNSCC-derived cell lines overexpressing YRNA1 were then used to determine the correlation of YRNA1 and the expression of genes associated with HPV infections. Taken together, our results highlight the potential of YRNAs as possible HNSCC biomarkers and new molecular targets.
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4
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Huang C, Li Y, Ling Q, Wei C, Fang B, Mao X, Yang R, Zhang L, Huang S, Cheng J, Liao N, Wang F, Mo L, Mo Z, Li L. Establishment of a risk score model for bladder urothelial carcinoma based on energy metabolism-related genes and their relationships with immune infiltration. FEBS Open Bio 2023; 13:736-750. [PMID: 36814419 PMCID: PMC10068335 DOI: 10.1002/2211-5463.13580] [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: 10/20/2022] [Revised: 01/28/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
Bladder urothelial carcinoma (BLCA) is a common malignant tumor of the human urinary system, and a large proportion of BLCA patients have a poor prognosis. Therefore, there is an urgent need to find more efficient and sensitive biomarkers for the prognosis of BLCA patients in clinical practice. RNA sequencing (RNA-seq) data and clinical information were obtained from The Cancer Genome Atlas, and 584 energy metabolism-related genes (EMRGs) were obtained from the Reactome pathway database. Cox regression analysis and least absolute shrinkage and selection operator analysis were applied to assess prognostic genes and build a risk score model. The estimate and cibersort algorithms were used to explore the immune microenvironment, immune infiltration, and checkpoints in BLCA patients. Furthermore, we used the Human Protein Atlas database and our single-cell RNA-seq datasets of BLCA patients to verify the expression of 13 EMRGs at the protein and single-cell levels. We constructed a risk score model; the area under the curve of the model at 5 years was 0.792. The risk score was significantly correlated with the immune markers M0 macrophages, M2 macrophages, CD8 T cells, follicular helper T cells, regulatory T cells, and dendritic activating cells. Furthermore, eight immune checkpoint genes were significantly upregulated in the high-risk group. The risk score model can accurately predict the prognosis of BLCA patients and has clinical application value. In addition, according to the differences in immune infiltration and checkpoints, BLCA patients with the most significant benefit can be selected for immune checkpoint inhibitor therapy.
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Affiliation(s)
- Caihong Huang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, Institute of Urology and Nephrology, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yexin Li
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, Institute of Urology and Nephrology, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qiang Ling
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Chunmeng Wei
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, Institute of Urology and Nephrology, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Bo Fang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Xingning Mao
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Rirong Yang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - LuLu Zhang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Shengzhu Huang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, Institute of Urology and Nephrology, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiwen Cheng
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Naikai Liao
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Fubo Wang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Linjian Mo
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, Institute of Urology and Nephrology, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, Institute of Urology and Nephrology, First Affiliated Hospital of Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Longman Li
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, Institute of Urology and Nephrology, First Affiliated Hospital of Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
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5
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Liu X, Zhao X, Yang J, Wang H, Piao Y, Wang L. High expression of AP2M1 correlates with worse prognosis by regulating immune microenvironment and drug resistance to R-CHOP in diffuse large B cell lymphoma. Eur J Haematol 2023; 110:198-208. [PMID: 36335584 DOI: 10.1111/ejh.13895] [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: 09/27/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND First-line treatment with R-CHOP has cured 50%-60% patients of diffuse large B cell lymphoma (DLBCL), and more than one-third patients will eventually progressed to relapsed/refractory disease with dismal outcomes. Adaptor Related Protein Complex 2 Subunit Mu 1 (AP2M1) is required for the activity of a vacuolar ATPase and may also play an important role in regulating the intracellular trafficking and function of CTLA-4 protein. Herein, using both public databases and our own tumor samples, we aimed to demonstrate the prognostic role of AP2M1 and the potential tumor-promoting mechanisms in DLBCL. METHOD Using public datasets of DLBCL from both GEO and TCGA databases, we analyzed the role of AP2M1 in mediating chemoresistance to R-CHOP and its correlation with various clinical parameters and prognosis. By using various R packages, we evaluated the role of AP2M1 on regulating tumor immune microenvironment. Moreover, tumor samples of DLBCL from Beijing TongRen Hospital were used to validate our findings by immunohistochemistry staining. RESULT Expression of AP2M1 was significantly increased in DLBCL, which was correlated with poor prognosis and a variety of clinical indicators. On the basis of enrichment analysis, it was found that AP2M1 may be related to intracellular receptor signaling pathway. Through immune analysis and drug prediction, we found that the expression of AP2M1 affected the immune environment and drug response of DLBCL, which further revealed the important role of AP2M1 in DLBCL. By analyzing 61 patients treated uniformly with R-CHOP regimen in our center, we validated the above findings that high expression of AP2M1 correlated with inferior survival outcomes and affected sensitivity to R-CHOP treatment. CONCLUSION Expression of AP2M1 may affect the prognosis of DLBCL patients probably by affecting the immune environment and the responses to many drugs in treating DLBCL, indicating AP2M1 as a potential therapy target in DLBCL.
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Affiliation(s)
- Xindi Liu
- Department of Hematology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Xiaoli Zhao
- Department of Pathology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Head and Neck Molecular Diagnostic Pathology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Jing Yang
- Department of Hematology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Henan Wang
- Department of Hematology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Yingshi Piao
- Department of Pathology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Head and Neck Molecular Diagnostic Pathology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Liang Wang
- Department of Hematology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
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6
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Zhang X, Liu X, Xiong R, An HX. Identification and validation of ubiquitin-proteasome system related genes as a prognostic signature for papillary renal cell carcinoma. Aging (Albany NY) 2022; 14:9599-9616. [PMID: 36385010 PMCID: PMC9792205 DOI: 10.18632/aging.204383] [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: 07/30/2022] [Accepted: 10/21/2022] [Indexed: 11/18/2022]
Abstract
Dysregulation of the ubiquitin-proteasome system (UPS) pathway greatly affects uncontrolled proliferation, genomic instability, and carcinogenesis, particularly in those with renal papillary cell carcinoma (PRCC). However, there is little information at the molecular level about the full link between changes in the genes involved in ubiquitin-mediated proteolysis and PRCC. METHODS The Cancer Genome Atlas (TCGA) and GeneCards databases were utilized to find the clinical data and gene expression patterns of patients with PRCC. Univariate Cox regression analysis and absolute shrinkage and selection operator (LASSO) analyses identified a risk signature formed by ten optimal UPS genes. The predictive value of the risk signature in TCGA-PRCC cohorts was evaluated using Kaplan-Meier analysis and receiver operating characteristic (ROC) curves. By utilizing GO enrichment and the KEGG pathway, the interactions of differentially expressed genes connected to ubiquitin-mediated proteolysis were functionally examined. The protein expression of the hub genes was affirmed using the Human Protein Atlas (HPA) database. The effectiveness of particular CDC20 and UBE2C in vitro was confirmed by experimental research. RESULTS Ten of the best ubiquitin-mediated proteolysis genes (UBE2C, DDB2, CBLC, BIRC3, PRKN, UBE2O, SIAH1, SKP2, UBC, and CDC20) were detected to create a risk signature. The high-risk score group stratified was associated with advanced tumor status and poor survival of PRCC patients. 10 genes were also found to be associated with the cell cycle pathway and ubiquitin-mediated proteolysis to GO and KEGG analysis. Of these 10 genes, CDC20 and UBE2C are highly expressed in tumor tissue and correlated with cancer immunity founded on the analyses of the expression of human protein atlas and TISIDB. The downregulation of UBE2C facilitated tumor inhibition and the anti-immune effect was confirmed by in vitro experiments. CONCLUSION Our results indicate that the risk model created from the ubiquitin-mediated proteolysis genes can be reliably and accurately predict the prognosis of PRCC patients, highlighting its targeted value for PRCC treatment. Particularly, the expression of UBE2C may be crucial for the prognosis and immunological treatment of renal cancer.
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Affiliation(s)
- Xin Zhang
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Fujian 361005, China,Xiamen Key Laboratory of Endocrine-Related Cancer Precision Medicine, Fujian 361102, China
| | - Xinli Liu
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Fujian 361005, China
| | - Renhua Xiong
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Fujian 361005, China,Xiamen Key Laboratory of Endocrine-Related Cancer Precision Medicine, Fujian 361102, China
| | - Han-Xiang An
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Fujian 361005, China,Xiamen Key Laboratory of Endocrine-Related Cancer Precision Medicine, Fujian 361102, China
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7
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Cai Z, Tang B, Chen L, Lei W. Mast cell marker gene signature in head and neck squamous cell carcinoma. BMC Cancer 2022; 22:577. [PMID: 35610596 PMCID: PMC9128261 DOI: 10.1186/s12885-022-09673-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/17/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Mast cells can reshape the tumour immune microenvironment and greatly affect tumour occurrence and development. However, mast cell gene prognostic and predictive value in head and neck squamous cell carcinoma (HNSCC) remains unclear. This study was conducted to identify and establish a prognostic mast cell gene signature (MCS) for assessing the prognosis and immunotherapy response of patients with HNSCC. METHODS Mast cell marker genes in HNSCC were identified using single-cell RNA sequencing analysis. A dataset from The Cancer Genome Atlas was divided into a training cohort to construct the MCS model and a testing cohort to validate the model. Fluorescence in-situ hybridisation was used to evaluate the MCS model gene expression in tissue sections from patients with HNSCC who had been treated with programmed cell death-1 inhibitors and further validate the MCS. RESULTS A prognostic MCS comprising nine genes (KIT, RAB32, CATSPER1, SMYD3, LINC00996, SOCS1, AP2M1, LAT, and HSP90B1) was generated by comprehensively analysing clinical features and 47 mast cell-related genes. The MCS effectively distinguished survival outcomes across the training, testing, and entire cohorts as an independent prognostic factor. Furthermore, we identified patients with favourable immune cell infiltration status and immunotherapy responses. Fluorescence in-situ hybridisation supported the MCS immunotherapy response of patients with HNSCC prediction, showing increased high-risk gene expression and reduced low-risk gene expression in immunotherapy-insensitive patients. CONCLUSIONS Our MCS provides insight into the roles of mast cells in HNSCC prognosis and may have applications as an immunotherapy response predictive indicator in patients with HNSCC and a reference for immunotherapy decision-making.
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Affiliation(s)
- Zhimou Cai
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, No. 58 Zhongshan Er Road, Guangzhou, 510080, China
| | - Bingjie Tang
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, No. 58 Zhongshan Er Road, Guangzhou, 510080, China
| | - Lin Chen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, No. 58 Zhongshan Er Road, Guangzhou, 510080, China.
| | - Wenbin Lei
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, No. 58 Zhongshan Er Road, Guangzhou, 510080, China.
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8
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Systematic Construction and Validation of an Immune-Related Gene-Based Model to Predict Prognosis for Ovarian Cancer. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7356992. [PMID: 35496047 PMCID: PMC9050317 DOI: 10.1155/2022/7356992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/14/2022] [Indexed: 11/25/2022]
Abstract
Ovarian cancer (OC) is a malignancy with poor prognosis, stubborn resistance, and frequent recurrence. Recently, it has been widely recognized that immune-related genes (IRGs) have demonstrated their indispensable importance in the occurrence and progression of OC. Given this, this study aimed to identify IRGs with predictive value and build a prognostic model for a more accurate assessment. First, we obtained transcriptome and clinical information of ovarian samples from both TCGA and GTEx databases. After integration, we figured out 10 genes as immune-related prognostic genes (IRPGs) by performing the univariate Cox regression analysis. Subsequently, we established a TF-associated network to investigate its internal mechanism. The prognosis model consisting of 5 IRPGs was constructed later by lasso regression analysis. The comparison of the score with the clinical factors validated its independence and superiority in OC's prognosis. Moreover, the association between the signature and immune cell infiltration demonstrated its ability to image the immune situation of the tumor microenvironment. Finally, the reliability of the risk model was confirmed by the GEO cohort. Together, our study has constructed an independent prognostic model for OC, which may deepen the understanding of the immune microenvironment and help present novel biomarkers or ideas for targeted therapy.
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9
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Prognostic value and underlying mechanism of autophagy-related genes in bladder cancer. Sci Rep 2022; 12:2219. [PMID: 35140317 PMCID: PMC8828781 DOI: 10.1038/s41598-022-06334-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/20/2022] [Indexed: 12/29/2022] Open
Abstract
Bladder cancer (BLCA) is the most common malignancy whose early diagnosis can ensure a better prognosis. However, the predictive accuracy of commonly used predictors, including patients’ general condition, histological grade, and pathological stage, is insufficient to identify the patients who need invasive treatment. Autophagy is regarded as a vital factor in maintaining mitochondrial function and energy homeostasis in cancer cells. Whether autophagy-related genes (ARGs) can predict the prognosis of BLCA patients deserves to be investigated. Based on BLCA data retrieved from the Cancer Genome Atlas and ARGs list obtained from the Human Autophagy Database website, we identified prognosis-related differentially expressed ARGs (PDEARGs) through Wilcox text and constructed a PDEARGs-based prognostic model through multivariate Cox regression analysis. The predictive accuracy, independent forecasting capability, and the correlation between present model and clinical variables or tumor microenvironment were evaluated through R software. Enrichment analysis of PDEARGs was performed to explore the underlying mechanism, and a systematic prognostic signature with nomogram was constructed by integrating clinical variables and the aforementioned PDEARGs-based model. We found that the risk score generated by PDEARGs-based model could effectively reflect deteriorated clinical variables and tumor-promoting microenvironment. Additionally, several immune-related gene ontology terms were significantly enriched by PDEARGs, which might provide insights for present model and propose potential therapeutic targets for BLCA patients. Finally, a systematic prognostic signature with promoted clinical utility and predictive accuracy was constructed to assist clinician decision. PDEARGs are valuable prognostic predictors and potential therapeutic targets for BLCA patients.
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10
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Shin J, Nile A, Oh JW. Role of adaptin protein complexes in intracellular trafficking and their impact on diseases. Bioengineered 2021; 12:8259-8278. [PMID: 34565296 PMCID: PMC8806629 DOI: 10.1080/21655979.2021.1982846] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023] Open
Abstract
Adaptin proteins (APs) play a crucial role in intracellular cell trafficking. The 'classical' role of APs is carried out by AP1‒3, which bind to clathrin, cargo, and accessory proteins. Accordingly, AP1-3 are crucial for both vesicle formation and sorting. All APs consist of four subunits that are indispensable for their functions. In fact, based on studies using cells, model organism knockdown/knock-out, and human variants, each subunit plays crucial roles and contributes to the specificity of each AP. These studies also revealed that the sorting and intracellular trafficking function of AP can exert varying effects on pathology by controlling features such as cell development, signal transduction related to the apoptosis and proliferation pathways in cancer cells, organelle integrity, receptor presentation, and viral infection. Although the roles and functions of AP1‒3 are relatively well studied, the functions of the less abundant and more recently identified APs, AP4 and AP5, are still to be investigated. Further studies on these APs may enable a better understanding and targeting of specific diseases.APs known or suggested locations and functions.
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Affiliation(s)
- Juhyun Shin
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
| | - Arti Nile
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
| | - Jae-Wook Oh
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
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11
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Miao F, Lou Z, Ji S, Wang D, Sun Y, Liu H, Yang C. Downregulated Expression of CLEC9A as Novel Biomarkers for Lung Adenocarcinoma. Front Oncol 2021; 11:682814. [PMID: 34616670 PMCID: PMC8489846 DOI: 10.3389/fonc.2021.682814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022] Open
Abstract
Purpose Abnormal CLEC9A expression is concerned with carcinogenesis. However, the role of CLEC9A in lung adenocarcinoma (LUAD) remains unknown. The goal of this study was to reveal the role of CLEC9A in LUAD based on bioinformatics and cellular functional experiments. Materials and methods Data available from The Cancer Genome Atlas (TCGA) were employed to study CLEC9A expression and mutations in LUAD. Expression and alterations of CLEC9A were analyzed using UALCAN and cBioPortal, respectively. Kaplan-Meier analysis was used to analyze the effect of CLEC9A on the survival of LUAD. Protein-protein interaction (PPI) network was built using GeneMANIA analysis. The similar genes of CLEC9A were obtained using GEPIA analysis, while co-expression genes correlated with CLEC9A were identified using LinkedOmics analysis. The effects of CLEC9A expression on immune cell infiltration was assessed. The effect of CLEC9A on the proliferation, apoptosis, cell cycle distribution, and invasion of human LUAD cells was detected in the LUAD cell line. Results CLEC9A was downregulated and the CLEC9A gene was often altered in LUAD. The survival of LUAD patients was correlated with the expression level of CLEC9A. The similar genes of CLEC9A were linked to functional networks involving positive regulation of interleukin-12 production, plasma membrane and CD40 receptor binding, primary immunodeficiency, intestinal immune network for IgA production, and cell adhesion molecules pathways. Cell cycle, apoptosis, EMT, and RAS/MAPK were significantly enriched pathways in positive and negative correlation genes with CLEC9A. A difference in the immune infiltration level of immune cell between the high and low CLEC9A expression groups was observed. Somatic cell copy number alternations (CNAs) of the CLEC9A, including arm-level gain and arm-level deletion, observably changed the infiltration levels of B cells, CD4+ T cells, macrophages, and neutrophils in LUAD. Except for LAG3, the expression of CD274, CTLA4, PDCD1, and TIGIT was positively correlated with the expression level of CLEC9A. After transfection, overexpression and knockdown of CLEC9A could affect the proliferation, apoptosis, cell cycle distribution, and invasion of LUAD cells. Conclusion CLEC9A is associated with prognosis and tumor immune microenvironment of LUAD, suggesting that CLEC9A may be considered as a novel biomarker for LUAD.
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Affiliation(s)
- Fang Miao
- School of Basic Medical Sciences, Shandong First Medical University, Jinan, China
| | - Zhiguo Lou
- Department of General Education, Shandong First Medical University, Jinan, China
| | - Shuhua Ji
- Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD, Beijing, China
| | - Dan Wang
- Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD, Beijing, China
| | - Yaolan Sun
- Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD, Beijing, China
| | - Huan Liu
- Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD, Beijing, China
| | - Chenggang Yang
- Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD, Beijing, China.,Department of Research and Development, Gu'an Bojian Bio-Technology Co., LTD, Langfang, China
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12
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Fu M, Wang Q, Wang H, Dai Y, Wang J, Kang W, Cui Z, Jin X. Immune-Related Genes Are Prognostic Markers for Prostate Cancer Recurrence. Front Genet 2021; 12:639642. [PMID: 34490029 PMCID: PMC8417385 DOI: 10.3389/fgene.2021.639642] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 07/30/2021] [Indexed: 12/24/2022] Open
Abstract
Background Prostate cancer (PCa) is an immune-responsive disease. The current study sought to explore a robust immune-related prognostic gene signature for PCa. Methods Data were retrieved from the tumor Genome Atlas (TCGA) database and GSE46602 database for performing the least absolute shrinkage and selection operator (LASSO) cox regression model analysis. Immune related genes (IRGs) data were retrieved from ImmPort database. Results The weighted gene co-expression network analysis (WGCNA) showed that nine functional modules are correlated with the biochemical recurrence of PCa, including 259 IRGs. Univariate regression analysis and survival analysis identified 35 IRGs correlated with the prognosis of PCa. LASSO Cox regression model analysis was used to construct a risk prognosis model comprising 18 IRGs. Multivariate regression analysis showed that risk score was an independent predictor of the prognosis of PCa. A nomogram comprising a combination of this model and other clinical features showed good prediction accuracy in predicting the prognosis of PCa. Further analysis showed that different risk groups harbored different gene mutations, differential transcriptome expression and different immune infiltration levels. Patients in the high-risk group exhibited more gene mutations compared with those in the low-risk group. Patients in the high-risk groups showed high-frequency mutations in TP53. Immune infiltration analysis showed that M2 macrophages were significantly enriched in the high-risk group implying that it affected prognosis of PCa patients. In addition, immunostimulatory genes were differentially expressed in the high-risk group compared with the low-risk group. BIRC5, as an immune-related gene in the prediction model, was up-regulated in 87.5% of prostate cancer tissues. Knockdown of BIRC5 can inhibit cell proliferation and migration. Conclusion In summary, a risk prognosis model based on IGRs was developed. A nomogram comprising a combination of this model and other clinical features showed good accuracy in predicting the prognosis of PCa. This model provides a basis for personalized treatment of PCa and can help clinicians in making effective treatment decisions.
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Affiliation(s)
- Min Fu
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qiang Wang
- Department of Human Resources, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Hanbo Wang
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Human Resources, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yun Dai
- Department of Ultrasound, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Ultrasound, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jin Wang
- Department of Urology, The First Affiliated Hospital of Shandong First Medical University, Jinan, China.,Department of Urology, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Weiting Kang
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zilian Cui
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xunbo Jin
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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13
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Chen J, Zhan Y, Zhang R, Chen B, Huang J, Li C, Zhang W, Wang Y, Gao Y, Zheng J, Li Y. A New Prognostic Risk Signature of Eight Ferroptosis-Related Genes in the Clear Cell Renal Cell Carcinoma. Front Oncol 2021; 11:700084. [PMID: 34249761 PMCID: PMC8267866 DOI: 10.3389/fonc.2021.700084] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/10/2021] [Indexed: 01/03/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common renal cell carcinoma and has poor prognosis in the locally advanced stage. Ferroptosis, a relatively new type of cell death, has gained significant attention in recent years. This study aimed to explore the prognostic value of ferroptosis-related genes (FRGs) in ccRCC. In this study, 50 differentially expressed FRGs between ccRCC and adjacent normal kidney tissues were identified, 26 of them correlated with overall survival (OS) (P <0.05). Eight optimal FRGs were selected by Lasso regression and multivariate Cox regression analysis, and used to construct a new prognostic risk signature to predict the prognosis of ccRCC patients. In addition, the signature passed the validation of prognostic survival analyses by a significant margin, and the risk score was identified as an independent prognostic marker via Cox regression analyses. Further studies indicated that the signature was significantly correlated with immune cell infiltration. Moreover, the levels of eight FRGs were examined in ccRCC. Collectively, the 8-FRG prognostic risk signature helps the clinicians predict the prognosis and OS of the patients, and standardize prognostic assessments.
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Affiliation(s)
- Ji Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yating Zhan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Rongrong Zhang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bo Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Junting Huang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chunxue Li
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenjie Zhang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yajing Wang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuxiang Gao
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianjian Zheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yeping Li
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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14
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Panagopoulou M, Karaglani M, Manolopoulos VG, Iliopoulos I, Tsamardinos I, Chatzaki E. Deciphering the Methylation Landscape in Breast Cancer: Diagnostic and Prognostic Biosignatures through Automated Machine Learning. Cancers (Basel) 2021; 13:1677. [PMID: 33918195 PMCID: PMC8037759 DOI: 10.3390/cancers13071677] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/23/2021] [Accepted: 03/31/2021] [Indexed: 12/24/2022] Open
Abstract
DNA methylation plays an important role in breast cancer (BrCa) pathogenesis and could contribute to driving its personalized management. We performed a complete bioinformatic analysis in BrCa whole methylome datasets, analyzed using the Illumina methylation 450 bead-chip array. Differential methylation analysis vs. clinical end-points resulted in 11,176 to 27,786 differentially methylated genes (DMGs). Innovative automated machine learning (AutoML) was employed to construct signatures with translational value. Three highly performing and low-feature-number signatures were built: (1) A 5-gene signature discriminating BrCa patients from healthy individuals (area under the curve (AUC): 0.994 (0.982-1.000)). (2) A 3-gene signature identifying BrCa metastatic disease (AUC: 0.986 (0.921-1.000)). (3) Six equivalent 5-gene signatures diagnosing early disease (AUC: 0.973 (0.920-1.000)). Validation in independent patient groups verified performance. Bioinformatic tools for functional analysis and protein interaction prediction were also employed. All protein encoding features included in the signatures were associated with BrCa-related pathways. Functional analysis of DMGs highlighted the regulation of transcription as the main biological process, the nucleus as the main cellular component and transcription factor activity and sequence-specific DNA binding as the main molecular functions. Overall, three high-performance diagnostic/prognostic signatures were built and are readily available for improving BrCa precision management upon prospective clinical validation. Revisiting archived methylomes through novel bioinformatic approaches revealed significant clarifying knowledge for the contribution of gene methylation events in breast carcinogenesis.
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Affiliation(s)
- Maria Panagopoulou
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece; (M.P.); (M.K.); (V.G.M.)
| | - Makrina Karaglani
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece; (M.P.); (M.K.); (V.G.M.)
| | - Vangelis G. Manolopoulos
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece; (M.P.); (M.K.); (V.G.M.)
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, GR-71003 Heraklion, Greece;
| | - Ioannis Tsamardinos
- JADBio, Gnosis Data Analysis PC, Science and Technology Park of Crete, GR-70013 Heraklion, Greece;
- Department of Computer Science, University of Crete, GR-70013 Heraklion, Greece
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology–Hellas, GR-70013 Heraklion, Greece
| | - Ekaterini Chatzaki
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece; (M.P.); (M.K.); (V.G.M.)
- Institute of Agri-Food and Life Sciences, Hellenic Mediterranean University Research Centre, GR-71410 Heraklion, Greece
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15
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Zhang K, Xu C, Liu S, Jiang Y, Zhao X, Ma S, Li Y, Yang F, Wang Y, Meng P, Shi C, Han D, Wen W, Qin W. The Diagnostic and Immunotherapeutic Value of CD248 in Renal Cell Carcinoma. Front Oncol 2021; 11:644612. [PMID: 33791227 PMCID: PMC8006336 DOI: 10.3389/fonc.2021.644612] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
Background: Renal cell carcinoma (RCC) is the most common malignancy in the urinary system. Despite substantial improvements in available treatment options, the survival outcome of advanced RCC is unsatisfactory. Identifying novel biomarkers to assist in early diagnosis and to screen patients who are sensitive to immunotherapy would be beneficial. CD248 is a promising candidate that deserves to be investigated. Methods: The Cancer Genome Atlas (TCGA) data set and clinical specimens were adopted to analyze the expression of CD248 between normal and tumor tissues. Univariate and multivariate Cox regression analyses were employed to identify independent prognostic factors and construct a CD248-based prognostic signature. The correlation among the present signature, tumor-infiltrating immune cells (TIICs), the tumor mutation burden (TMB), and immunomodulatory molecules was evaluated. The weighted gene co-expression network analysis (WGCNA), the enrichment analysis, and the miRNA correlation analysis were performed to explore the underlying mechanism of CD248 in the progression of RCC. Results: The overexpression of CD248 in RCC was related to a poor prognosis, and a CD248-based prognostic signature could precisely stratify patients with RCC with different survival outcomes regardless of the training or testing cohort. The present signature could reflect the immunosuppressive landscape of RCC (i.e., increased infiltration of regulatory T cells and upregulated immune checkpoints), accompanied by deteriorated clinicopathologic indexes. The TMB and immunostimulatory molecules expression also increased with the risk score generated from the present signature. CD248 co-expressed gene sets were identified through the WGCNA algorithm, and several immunosuppressive Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly enriched. The result of CD248-correlated miRNA further emphasized the importance of CD248 in RCC. Conclusion: CD248 is a valuable biomarker to improve the diagnostic and therapeutic efficiency of RCC. The immunosuppressive effect of CD248 co-expressed genes may provide insight for the present study, and miRNA would help to reveal the mechanism of the expressive regulation of CD248.
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Affiliation(s)
- Keying Zhang
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Chao Xu
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Shaojie Liu
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yao Jiang
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiaolong Zhao
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Shanjin Ma
- Department of Urology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Yu Li
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Fa Yang
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yan Wang
- Department of Emergency, 987th Hospital of the Chinese People's Liberation Army, Baoji, China
| | - Ping Meng
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Changhong Shi
- Laboratory Animal Center, Fourth Military Medical University, Xi'an, China
| | - Donghui Han
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Weihong Wen
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China
| | - Weijun Qin
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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16
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Yu DH, Chen C, Liu XP, Yao J, Li S, Ruan XL. Dysregulation of miR-138-5p/RPS6KA1-AP2M1 Is Associated With Poor Prognosis in AML. Front Cell Dev Biol 2021; 9:641629. [PMID: 33732707 PMCID: PMC7959750 DOI: 10.3389/fcell.2021.641629] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/28/2021] [Indexed: 12/22/2022] Open
Abstract
Acute myeloid leukemia (AML) is a malignant disease of hematopoietic stem/progenitor cells, and most AML patients are in a severe state. Internal tandem duplication mutations in FLT3 gene (FLT3-ITD) detected in AML stem cells account for 20–30 percent of AML patients. In this study, we attempted to study the impact of the interaction of FLT3-ITD mutation and the CXCL12/CXCR4 axis in AML, and the possible mechanisms caused by the impact by bioinformatics. Gene set variation analysis (GSVA) revealed that the PI3K-Akt-mTOR pathway positively correlated with the status of FLT3-ITD mutation. Multiple survival analyses were performed on TCGA-AML to screen the prognostic-related genes, and RPS6KA1 and AP2M1 are powerful prognostic candidates for overall survival in AML. WGCNA, KEGG/GO analysis, and the functional roles of RPS6KA1 and AP2M1 in AML were clarified by correlation analysis. We found that the expression levels of RPS6KA1 and AP2M1 were significantly associated with chemoresistance of AML, and the CXCL12/CXCR4 axis would regulate RPS6KA1/AP2M1 expression. Besides, miR-138-5p, regulated by the CXCL12/CXCR4 axis, was the common miRNA target of RPS6KA1 and AP2M1. Taken together, the interaction of FLT3-ITD mutation and the CXCL12/CXCR4 axis activated the PI3K-Akt-mTOR pathway, and the increased expression of RPS6KA1 and AP2M1 caused by hsa-miR-138-5p downregulation regulates the multi-resistance gene expression leading to drug indications.
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Affiliation(s)
- Dong-Hu Yu
- Department of Biological Repositories, Human Genetics Resource Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, China.,The Second Clinical College, Wuhan University, Wuhan, China
| | - Chen Chen
- Department of Biological Repositories, Human Genetics Resource Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiao-Ping Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jie Yao
- Department of Biological Repositories, Human Genetics Resource Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Sheng Li
- Department of Biological Repositories, Human Genetics Resource Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiao-Lan Ruan
- Department of Hematology, Renmin Hospital of Wuhan University, Wuhan, China
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17
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Jiang A, Liu N, Bai S, Wang J, Gao H, Zheng X, Fu X, Ren M, Zhang X, Tian T, Ruan Z, Liang X, Yao Y. Identification and validation of an autophagy-related long non-coding RNA signature as a prognostic biomarker for patients with lung adenocarcinoma. J Thorac Dis 2021; 13:720-734. [PMID: 33717544 PMCID: PMC7947511 DOI: 10.21037/jtd-20-2803] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Background Lung adenocarcinoma (LUAD) is the most predominant pathological subtype of lung cancer, accounting for 40–70% of all lung cancer cases. Although significant improvements have been made in the screening, diagnosis, and precise management in recent years, the prognosis of LUAD remains bleak. This study aimed to investigate the prognostic significance of autophagy-related long non-coding RNAs (lncRNAs) and construct an autophagy-related lncRNA prognostic model in LUAD. Methods The gene expression data of LUAD patients were obtained from The Cancer Genome Atlas (TCGA) database. All autophagy-related genes were downloaded from the Human Autophagy Database (HADb). Spearman’s correlation test was exploited to identify potential autophagy-related lncRNAs. The multivariate Cox regression analysis was used to construct the prognostic signature, which divided LUAD patients into high-risk and low-risk groups. Subsequently, the receiver operating characteristic (ROC) curves were generated to assess the predictive ability of this prognostic model for overall survival (OS) in these individuals. Then, the Gene set enrichment analysis (GSEA) was conducted to execute pathway enrichment analysis. Finally, a multidimensional validation was exploited to verify our findings. Results A total of 1,144 autophagy-related lncRNAs were identified to construct the co-expression network via Spearman’s correlation test (|R2| >0.4 and P≤0.001). Ultimately, a 16 autophagy-related lncRNAs prognostic model was constructed, and the area under the ROC curve (AUC) was 0.775. The results of GSEA enrichment analysis showed that the genes in the high-risk group were mainly enriched in cell cycle and p53 signaling pathways. The results of the multidimensional database validation indicated that the expression level of BIRC5 was significantly correlated with the expression level of TMPO-AS1. Furthermore, both TMPO-AS1 and BIRC5 had a higher expression level in LUAD samples. LUAD patients with high expression levels of TMPO-AS1 and BIRC5 were correlated with advanced disease stage and poor OS. Conclusions In summary, our results suggested that the prognostic signature of the 16 autophagy-related lncRNAs has significant prognostic value for LUAD patients. Furthermore, TMPO-AS1 and BIRC5 are potential predictors and therapeutic targets in these individuals.
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Affiliation(s)
- Aimin Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Liu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shuheng Bai
- Department of Radiotherapy Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jingjing Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huan Gao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoqiang Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiao Fu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Mengdi Ren
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoni Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Tao Tian
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhiping Ruan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xuan Liang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yu Yao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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18
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Jiang A, Liu N, Bai S, Wang J, Gao H, Zheng X, Fu X, Ren M, Zhang X, Tian T, Ruan Z, Yao Y, Liang X. The Construction and Analysis of Tumor-Infiltrating Immune Cells and ceRNA Networks in Bladder Cancer. Front Genet 2021; 11:605767. [PMID: 33391354 PMCID: PMC7775311 DOI: 10.3389/fgene.2020.605767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
Background Bladder cancer (BLCA) is the 11th most common malignancy worldwide. Although significant improvements have been made in screening, diagnosis, and precise management in recent years, the prognosis of BLCA remains bleak. Objectives This study aimed to investigate the prognostic significance of tumor-infiltrating immune cells and construct ceRNA networks in BLCA patients. Methods The expression data of BLCA patients were obtained from The Cancer Genome Atlas (TCGA) database. A competing endogenous RNA (ceRNA) network was constructed to identify the hub genes involved in the prognosis of BLCA. The CIBERSORT algorithm was utilized to investigate the infiltration levels of 22 subsets of immune cells. Ultimately, the nomogram was generated to visualize the survival probability of each patient, with the calibration curve being performed to assess its performance. Furthermore, the Pearson correlation test was used to explore the correlation between the identified hub genes in the ceRNA network and the prognostic-related immune cells. Results A total of eight elements in the ceRNA network were considered as key members and correlated with the prognosis of BLCA, including ELN, SREBF1, DSC2, TTLL7, DIP2C, SATB1, hsa-miR-20a-5p, and hsa-miR-29c-3p. T cells CD8, T cells follicular helper (Tfh), and neutrophils were identified as independent prognostic factors in BLCA. The co-expression analysis showed that there was a significant correlation between the identified hub genes and immune cells. Conclusion Our results suggest that the mechanism of hsa-miR-29c-3p regulates the expression of ELN and DSC2, and the infiltration of Tfh and neutrophils might play pivotal roles in the progression of BLCA.
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Affiliation(s)
- Aimin Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Liu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shuheng Bai
- Department of Radiotherapy Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jingjing Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huan Gao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoqiang Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiao Fu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Mengdi Ren
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoni Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Tao Tian
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhiping Ruan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yu Yao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xuan Liang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Jiang AM, Ren MD, Liu N, Gao H, Wang JJ, Zheng XQ, Fu X, Liang X, Ruan ZP, Tian T, Yao Y. Tumor Mutation Burden, Immune Cell Infiltration, and Construction of Immune-Related Genes Prognostic Model in Head and Neck Cancer. Int J Med Sci 2021; 18:226-238. [PMID: 33390791 PMCID: PMC7738958 DOI: 10.7150/ijms.51064] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide, and the prognosis of HNSCC remains bleak. Numerous studies revealed that the tumor mutation burden (TMB) could predict the survival outcomes of a variety of tumors. Objectives: This study aimed to investigate the TMB and immune cell infiltration in these patients and construct an immune-related genes (IRGs) prognostic model. Methods: The expression data of 546 HNSCC patients were obtained from The Cancer Genome Atlas (TCGA) database. All patients were divided into high- and low- TMB groups, and the relationship between TMB and clinical relevance was further analyzed. The differentially expressed genes (DEGs) were identified using the R software package, limma. Functional enrichment analyses were conducted to identify the significantly enriched pathways between two groups. CIBERSORT algorithm was adopted to calculate the abundance of 22 leukocyte subtypes. The IRGs prognostic model was constructed via the multivariate Cox regression analysis. Results: Missense mutation and single nucleotide variants (SNV) were the most predominant mutation types in HNSCC. TP53, TTN, and FAT1 were the most frequently mutated genes. Patients with high TMB were observed with worse survival outcomes. The functional analysis of TMB associated DEGs showed that the identified DEGs mainly involved in spliceosome, RNA degradation, proteasome, and RNA polymerase pathways. We observed that macrophages, T cells CD8, and T cells CD4 memory were the most commonly infiltrated subtypes of immune cells in HNSCC. Finally, an IRGs prognostic model was constructed, and the AUC of the ROC curve was 0.635. Conclusions: Our results suggest that high TMB is associated with poor prognosis in HNSCC patients. The constructed model has potential prognostic value for the prognosis of these individuals, and it needs to be further validated in large-scale and prospective studies.
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Affiliation(s)
- Ai-Min Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Meng-Di Ren
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Na Liu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Huan Gao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Jing-Jing Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Xiao-Qiang Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Xiao Fu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Xuan Liang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Zhi-Ping Ruan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Tao Tian
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Yu Yao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
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20
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Zuo H, Chen L, Li N, Song Q. Identification of a Ubiquitination-Related Gene Risk Model for Predicting Survival in Patients With Pancreatic Cancer. Front Genet 2020; 11:612196. [PMID: 33414811 PMCID: PMC7782244 DOI: 10.3389/fgene.2020.612196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
Pancreatic cancer is known as "the king of cancer," and ubiquitination/deubiquitination-related genes are key contributors to its development. Our study aimed to identify ubiquitination/deubiquitination-related genes associated with the prognosis of pancreatic cancer patients by the bioinformatics method and then construct a risk model. In this study, the gene expression profiles and clinical data of pancreatic cancer patients were downloaded from The Cancer Genome Atlas (TCGA) database and the Genotype-tissue Expression (GTEx) database. Ubiquitination/deubiquitination-related genes were obtained from the gene set enrichment analysis (GSEA). Univariate Cox regression analysis was used to identify differentially expressed ubiquitination-related genes selected from GSEA which were associated with the prognosis of pancreatic cancer patients. Using multivariate Cox regression analysis, we detected eight optimal ubiquitination-related genes (RNF7, NPEPPS, NCCRP1, BRCA1, TRIM37, RNF25, CDC27, and UBE2H) and then used them to construct a risk model to predict the prognosis of pancreatic cancer patients. Finally, the eight risk genes were validated by the Human Protein Atlas (HPA) database, the results showed that the protein expression level of the eight genes was generally consistent with those at the transcriptional level. Our findings suggest the risk model constructed from these eight ubiquitination-related genes can accurately and reliably predict the prognosis of pancreatic cancer patients. These eight genes have the potential to be further studied as new biomarkers or therapeutic targets for pancreatic cancer.
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Affiliation(s)
- Hao Zuo
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China.,Hubei Provincial Research Center for Precision Medicine of Cancer, Wuhan, China
| | - Luojun Chen
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China.,Hubei Provincial Research Center for Precision Medicine of Cancer, Wuhan, China
| | - Na Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China.,Hubei Provincial Research Center for Precision Medicine of Cancer, Wuhan, China
| | - Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China.,Hubei Provincial Research Center for Precision Medicine of Cancer, Wuhan, China
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21
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Wu L, Quan W, Luo Q, Pan Y, Peng D, Zhang G. Identification of an Immune-Related Prognostic Predictor in Hepatocellular Carcinoma. Front Mol Biosci 2020; 7:567950. [PMID: 33195412 PMCID: PMC7542239 DOI: 10.3389/fmolb.2020.567950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/27/2020] [Indexed: 12/13/2022] Open
Abstract
Liver hepatocellular carcinoma (LIHC) is the most prevalent primary cancer of the liver, and immune-related genes (IRGs) regulate its development. So far, there is still no precise biomarker that predicts response to immunotherapy in LIHC. Therefore, this research seeks to identify immunogenic prognostic biomarkers and explore potential predictors for the efficacy of anti-PD-1/PD-L1 therapies in LIHC. The clinical data and gene expression profiles of patients diagnosed with LIHC were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Moreover, IRGs were obtained from the ImmPort database. We discovered 35 IRGs that were differentially expressed between LIHC tissues and corresponding normal tissues. Through univariate Cox regression analysis, eight prognostic differentially expressed IRGs (PDEIRGs) were identified. Further, three optimal PDEIRGs (BIRC5, LPA, and ROBO1) were identified and used to construct a prognostic risk signature of LIHC patients via multivariate Cox regression analysis. The signature was validated by ROC curves. Subsequently, based on gene set enrichment analysis (GSEA) analysis, two out of the three optimal PDEIRGs (BIRC5 and LPA) were significantly enriched in the mismatch repair (MMR) pathway. Moreover, the two PDEIRGs (BIRC5 and LPA) were significantly correlated with the expression of genes related to mismatch repair (MLH1, MSH2, MSH6, and PMS2). Furthermore, correlations between the two PDEIRGs (BIRC5 and LPA) and immune checkpoints of cancer treatment (such as CTLA4, PD-1, and PD-L1) were demonstrated. Hyperprogressive disease (HPD) is a novel pattern of tumor progression which has a close relationship with immune checkpoint inhibitors (ICIs) utilization. MDM2 family amplification might promote the HPD phenomenon. Finally, we found a positive regulatory relationship between HPD related gene (MDM2) and BIRC5. Notably, MDM2 can either interact directly with BIRC5 or indirectly via downstream transcription factors of BIRC5. Overall, our study uncovered a novel 3-immune-related prognostic genes in LIHC.
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Affiliation(s)
- Lei Wu
- Department of Oncology, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Wen Quan
- Department of Oncology, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Qiong Luo
- Department of Oncology, Affiliated Zhuhai Hospital, Southern Medical University, Zhuhai, China
| | - Ying Pan
- Department of Oncology, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Dongxu Peng
- Department of Oncology, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Guihai Zhang
- Department of Oncology, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
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Alantolactone inhibits cell autophagy and promotes apoptosis via AP2M1 in acute lymphoblastic leukemia. Cancer Cell Int 2020; 20:442. [PMID: 32943990 PMCID: PMC7488238 DOI: 10.1186/s12935-020-01537-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Background Acute lymphoblastic leukemia (ALL) is an aggressive hematopoietic malignancy that is most commonly observed in children. Alantolactone (ALT) has been reported to exhibit anti-tumor activity in different types of cancer. The aim of the present study was to investigate the anti-tumor activity and molecular mechanism of ALT in ALL. Methods ALL cell lines were treated with 1, 5 and 10 μM ALT, and cell viability was assessed using an MTT assay and RNA sequencing. Flow cytometry, JC-1 staining and immunofluorescence staining assays were used to measure cell apoptosis and autophagy. Additionally, western blot analysis was used to detect expression of apoptosis and autophagy related proteins. Finally, the effects of ALT on tumor growth were assessed in a BV173 xenograft nude mouse model. Results ALT inhibited the proliferation of ALL cells in a dose-dependent manner. Additionally, it was demonstrated that ALT inhibited cell proliferation, colony formation, autophagy, induced apoptosis and reduced tumor growth in vivo through upregulating the expression of adaptor related protein complex 2 subunit mu 1 (AP2M1). Moreover, the autophagy activator rapamycin, attenuated the pro-apoptotic effects of ALT on BV173 and NALM6 cell lines. Overexpression of AP2M1 decreased the expression of Beclin1 and the LC3-II/LC3-1 ratio, and increased p62 expression. Knockdown of Beclin1 increased the levels of bax, cleaved caspase 3 and cytochrome C, and decreased bcl-2 expression. Conclusions The present study demonstrated that ALT exerts anti-tumor activity through inducing apoptosis and inhibiting autophagy by upregulating AP2M1 in ALL, highlighting a potential therapeutic strategy for treatment of ALL.
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23
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Wu C, Li H, Xiao Y, Deng W, Sun Z. Expression levels of SIX1, ME2, and AP2M1 in adenoid cystic carcinoma and mucoepidermoid carcinoma. Oral Dis 2020; 26:1687-1695. [PMID: 32564485 DOI: 10.1111/odi.13506] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/20/2020] [Accepted: 06/10/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Cong‐Cong Wu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) & Key Laboratory of Oral Biomedicine Ministry of Education School & Hospital of Stomatology Wuhan University Wuhan China
| | - Hao Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) & Key Laboratory of Oral Biomedicine Ministry of Education School & Hospital of Stomatology Wuhan University Wuhan China
| | - Yao Xiao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) & Key Laboratory of Oral Biomedicine Ministry of Education School & Hospital of Stomatology Wuhan University Wuhan China
| | - Wei‐Wei Deng
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) & Key Laboratory of Oral Biomedicine Ministry of Education School & Hospital of Stomatology Wuhan University Wuhan China
| | - Zhi‐Jun Sun
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) & Key Laboratory of Oral Biomedicine Ministry of Education School & Hospital of Stomatology Wuhan University Wuhan China
- Department of Oral and Maxillofacial‐Head Neck Surgery School & Hospital of Stomatology Wuhan University Wuhan China
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24
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Quan X, Zhang N, Chen Y, Zeng H, Deng J. Development of an immune-related prognostic model for pediatric acute lymphoblastic leukemia patients. Mol Genet Genomic Med 2020; 8:e1404. [PMID: 32666718 PMCID: PMC7507390 DOI: 10.1002/mgg3.1404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/19/2020] [Accepted: 06/29/2020] [Indexed: 01/12/2023] Open
Abstract
Background Acute lymphoblastic leukemia (ALL) is the most common hematological malignancy in pediatrics, and immune‐related genes (IRGs) play crucial role in its development. Our study aimed to identify prognostic immune biomarkers of pediatric ALL and construct a risk assessment model. Methods Pediatric ALL patients’ gene expression data were downloaded from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. We screened differentially expressed IRGs (DEIRGs) between the relapse and non‐relapse groups. Cox regression analysis was used to identify optimal prognostic genes, then, a risk model was constructed, and its accuracy was verified in different cohorts. Results We screened 130 DEIRGs from 251 pediatric ALL samples. The top three pathways that DEIRGs may influence tumor progression are NABA matrisome‐associated, chemotaxis, and antimicrobial humoral response. A set of 84 prognostic DEIRGs was identified by using univariate Cox analysis. Then, Lasso regression and multivariate Cox regression analysis screened four optimal genes (PRDX2, S100A10, RORB, and SDC1), which were used to construct the prognostic risk model. The risk score was calculated and the survival analysis results showed that high‐risk score was associated with poor overall survival (OS) (p = 3.195 × 10−7). The time‐dependent survival receiver operating characteristic curves showed good prediction accuracy (Area Under Curves for 3‐year, 5‐year OS were 0.892 and 0.89, respectively). And the predictive performance of our risk model was successfully verified in testing cohort and entire cohort. Conclusions Our prognostic risk model can effectively divide pediatric ALL patients into high‐risk and low‐risk groups, which may help predict clinical prognosis and optimize individualized treatment.
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Affiliation(s)
- Xi Quan
- Department of Hematology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Nan Zhang
- Department of Hematology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Ying Chen
- Department of Hematology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Hanqing Zeng
- Department of Hematology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Jianchuan Deng
- Department of Hematology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
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25
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Chen G, Cai Z, Dong X, Zhao J, Lin S, Hu X, Liu FE, Liu X, Zhang H. Genomic and Transcriptomic Landscape of Tumor Clonal Evolution in Cholangiocarcinoma. Front Genet 2020; 11:195. [PMID: 32231683 PMCID: PMC7083074 DOI: 10.3389/fgene.2020.00195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
Cholangiocarcinoma remained a severe threat to human health. Deciphering the genomic and/or transcriptomic profiles of tumor has been proved to be a promising strategy for exploring the mechanism of tumorigenesis and development, which could also provide valuable insights into Cholangiocarcinoma. However, little knowledge has been obtained regarding to how the alteration among different omics levels is connected. Here, using whole exome sequencing and transcriptome sequencing, we performed a thorough evaluation for the landscape of genome and transcriptome in cholangiocarcinoma and illustrate the alteration of tumor on different biological levels. Meanwhile, we also identified the clonal structure of each included tumor sample and discovered different clonal evolution patterns related to patients’ survival. Furthermore, we extracted subnetworks that were greatly influenced by tumor clonal/subclonal mutations or transcriptome change. The topology relationship between genes affected by genomic/transcriptomic changes in biological interaction networks revealed that alteration of genome and transcriptome was highly correlated, and somatic mutations located on important genes might affect the expression of numerous genes in close range.
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Affiliation(s)
- Geng Chen
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Zhixiong Cai
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xiuqing Dong
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Jing Zhao
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Song Lin
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xi Hu
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Fang-E Liu
- Department of Nursing, School of Medicine, Xi'an Peihua University, Xi'an, China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Huqing Zhang
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
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26
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Ha M, Kim J, Park SM, Hong CM, Han ME, Song P, Kang CD, Lee D, Kim YH, Hur J, Oh SO. Prognostic Role of Zinc Finger Homeobox 4 in Ovarian Serous Cystadenocarcinoma. Genet Test Mol Biomarkers 2020; 24:145-149. [PMID: 32105524 DOI: 10.1089/gtmb.2019.0185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Introduction: The zinc finger homeobox 4 (ZFHX4) protein is a crucial molecular regulator of tumor-initiating stem cell-like functions. Objective: This study aimed to determine the role of ZFHX4 in the progression of ovarian serous cystadenocarcinoma (OSC). Methods: Differential gene expression ZFHX4 among low-stage (stages I and II), high-stage (stages III and IV), low-grade (grades I and II), and high-grade (grades III and IV) OSC patients was identified using four independent cohorts from the Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO). We compared ZFHX4 expression as a prognostic factor using Kaplan-Meier survival curves, multivariate analysis, the time-dependent area under the curve (AUC) of Uno's C-index, and the AUC of the receiver operating characteristics at 4 years post diagnosis. Results: ZFHX4 gene expression in high-stage tumors is significantly higher than in low-stage tumors (TCGA, p = 0.007; GSE9891, p = 0.001). A Kaplan-Meier analysis revealed that elevated expression of ZFHX4 was associated with a poor prognosis in OSC patients for all cohorts, regardless of stage and grade (TCGA, p = 1e-04; GSE9891, p = 0.0044; GSE13876, p = 0.00078; GSE26712, p = 0.039). Analysis of C-indices and the area under the receiver operating characteristic curve further supported this result (C-index: TCGA, 0.599; GSE9891, 0.642; GSE13876, 0.585; GSE26712, 0.597). Moreover, univariate and multivariate Cox hazards analyses confirmed the prognostic significance of ZFHX4 levels. Conclusion: Collectively, these findings suggest that ZFHX4 is a prognostic factor for OSC.
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Affiliation(s)
- Mihyang Ha
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Jayoung Kim
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Su Min Park
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Chae Mi Hong
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Myoung-Eun Han
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Parkyong Song
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Chi-Dug Kang
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea.,Department of Biochemistry, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Dongjun Lee
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Yun Hak Kim
- Department of Anatomy, Biomedical Research Institute, Pusan National University School of Medicine, Yangsan, Republic of Korea.,Department of Biomedical Informatics, Biomedical Research Institute, Pusan National University School of Medicine, Yangsan, Republic of Korea.,Biomedical Research Institute, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Jin Hur
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Sae-Ock Oh
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Republic of Korea
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27
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Wan B, Liu B, Huang Y, Yu G, Lv C. Prognostic value of immune-related genes in clear cell renal cell carcinoma. Aging (Albany NY) 2019; 11:11474-11489. [PMID: 31821170 PMCID: PMC6932908 DOI: 10.18632/aging.102548] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/19/2019] [Indexed: 12/23/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common pathological subtype of renal cell carcinoma, and immune-related genes (IRGs) are key contributors to its development. In this study, the gene expression profiles and clinical data of ccRCC patients were downloaded from The Cancer Genome Atlas database and the cBioPortal database, respectively. IRGs were obtained from the ImmPort database. We analyzed the expression of IRGs in ccRCC, and discovered 681 that were differentially expressed between ccRCC and normal kidney tissues. Univariate Cox regression analysis was used to identify prognostic differentially expressed IRGs (PDEIRGs). Using Lasso regression and multivariate Cox regression analyses, we detected seven optimal PDEIRGs (PLAU, ISG15, IRF9, ARG2, RNASE2, SEMA3G and UCN) and used them to construct a risk model to predict the prognosis of ccRCC patients. This model accurately stratified patients with different survival outcomes and precisely identified patients with different mutation burdens. Our findings suggest the seven PDEIRGs identified in this study are valuable prognostic predictors in ccRCC patients. These genes could be used to investigate the developmental mechanisms of ccRCC and to design individualized treatments for ccRCC patients.
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Affiliation(s)
- Bangbei Wan
- Department of Urology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan 570208, China
| | - Bo Liu
- Laboratory of Developmental Cell Biology and Disease, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325003, China
| | - Yuan Huang
- Department of Neurology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan 570208, China
| | - Gang Yu
- Department of Urology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan 570208, China
| | - Cai Lv
- Department of Urology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan 570208, China
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28
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Liu J, Li W, Zhao H. CFHR3 is a potential novel biomarker for hepatocellular carcinoma. J Cell Biochem 2019; 121:2970-2980. [PMID: 31709629 DOI: 10.1002/jcb.29551] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/10/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Jun Liu
- Department of Clinical LaboratoryYue Bei People's Hospital Shaoguan Guangdong China
| | - Wenli Li
- Reproductive Medicine CenterYue Bei People's Hospital Shaoguan Guangdong China
| | - Hetong Zhao
- Department of Traditional Chinese Medicine, Changhai HospitalNaval Military Medical University Shanghai China
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29
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Lee D, Ha M, Hong CM, Kim J, Park SM, Park D, Sohn DH, Shin HJ, Yu HS, Kim CD, Kang CD, Han ME, Oh SO, Kim YH. GABRQ expression is a potential prognostic marker for patients with clear cell renal cell carcinoma. Oncol Lett 2019; 18:5731-5738. [PMID: 31788046 PMCID: PMC6865077 DOI: 10.3892/ol.2019.10960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 06/27/2019] [Indexed: 01/08/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer. Novel biomarkers of ccRCC may provide crucial information on tumor features and prognosis. The present study aimed to determine whether the expression of γ-aminobutyric acid (GABA) A receptor subunit θ (GABRQ) could serve as a novel prognostic marker of ccRCC. GABA is the main inhibitory neurotransmitter in the brain that activates the receptor GABAA, which is comprised of three subunit isoforms: GABRA3, GABRB3 and GABRQ. A recent study reported that GABRQ is involved in the initiation and progression of hepatocellular carcinoma; however, the role of GABRQ in ccRCC remains unknown. In the present study, clinical and transcriptomic data were obtained from cohorts of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). Differential GABRQ expression levels among early (TI and II), late (TIII and IV), nonmetastatic (M0) and metastatic (M1, primary tumor) stages of ccRCC samples were then identified. Furthermore, the use of GABRQ as a prognostic gene was analyzed using Uno's C-index based on the time-dependent area under the curve (AUC), the AUC of the receiver operating characteristic curve at 5 years, the Kaplan-Meier survival curve and multivariate analysis. The survival curve analysis revealed that low GABRQ mRNA expression was significantly associated with a poor prognosis of ccRCC (P<0.001 and P=0.0012 for TCGA and ICGC data, respectively). In addition, analyses of the C-index and AUC values further supported this discriminatory power. Furthermore, the prognostic value of GABRQ mRNA expression was confirmed by multivariate Cox regression analysis. Taken together, these results suggested that GABRQ mRNA expression may be considered as a novel prognostic biomarker of ccRCC.
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Affiliation(s)
- Dongjun Lee
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea
| | - Mihyang Ha
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea
| | - Chae Mi Hong
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea
| | - Jayoung Kim
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea
| | - Su Min Park
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea
| | - Dongsu Park
- Department of Molecular Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA.,Center for Skeletal Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dong Hyun Sohn
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea
| | - Ho Jin Shin
- Department of Hematology-Oncology, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea
| | - Hak-Sun Yu
- Department of Parasitology, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea
| | - Chi Dae Kim
- Department of Pharmacology, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea
| | - Chi-Dug Kang
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea.,Department of Biochemistry, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea
| | - Myoung-Eun Han
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea
| | - Sae-Ock Oh
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea
| | - Yun Hak Kim
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea.,Department of Biomedical Informatics, Pusan National University School of Medicine, Yangsan, Gyeongsangnam-do 50612, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan 49241, Republic of Korea
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Ha M, Kim DW, Kim J, Hong CM, Park SM, Woo IA, Kim MY, Koo H, Namkoong J, Kim J, Han ME, Song P, Hur J, Kang CD, Kim YH, Lee D, Oh SO. Prognostic role of the beta-2 adrenergic receptor in clear cell renal cell carcinoma. Anim Cells Syst (Seoul) 2019; 23:365-369. [PMID: 31700702 PMCID: PMC6830282 DOI: 10.1080/19768354.2019.1658638] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/31/2019] [Accepted: 08/14/2019] [Indexed: 12/18/2022] Open
Abstract
The beta-2 adrenergic receptor (ADRB2) regulates the proliferation, apoptosis, angiogenesis, migration, and metastasis of cancer cells. However, its function in the progression of clear cell renal cell carcinoma (ccRCC) is unknown. Here, we report that ADRB2 can be a novel prognostic factor for patients with ccRCC. The differential expression of ADRB2 in low-stage (stages I and II), high-stage (stages III and IV), low-grade (grades I and II), and high-grade (grades III and IV) ccRCC was identified in cohorts of patients from The Cancer Genome Atlas and the International Cancer Genome Consortium. We evaluated ADRB2 expression as a prognostic factor using the Kaplan-Meier survival curve, multivariate analysis, time-dependent area under the curve (AUC) of Uno’s C-index, and AUC of the receiver operating characteristics (ROC) at five years. Kaplan-Meier analysis revealed that reduced ADRB2 expression is associated with poor prognosis in ccRCC patients. Analysis of C-indices and AUC-ROC further confirmed this result. Moreover, multivariate analysis confirmed the prognostic significance of ADRB2 expression. Collectively, these findings suggest that ADRB2 is a potential prognostic factor for ccRCC.
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Affiliation(s)
- Mihyang Ha
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Dong Woo Kim
- Department of Premedicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Jayoung Kim
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Chae Mi Hong
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Su Min Park
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - In Ae Woo
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Min Yong Kim
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Hyunjun Koo
- Department of Premedicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Jin Namkoong
- Department of Premedicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Jaehyun Kim
- Department of Premedicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Myoung-Eun Han
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Parkyong Song
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Jin Hur
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Chi-Dug Kang
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Yun Hak Kim
- Department of Anatomy, Department of Biomedical Informatics, and Biomedical Research Institute, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Dongjun Lee
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Sae-Ock Oh
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Republic of Korea
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31
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Ha M, Jeong H, Roh JS, Lee B, Han ME, Oh SO, Sohn DH, Kim YH. DYSF expression in clear cell renal cell carcinoma: A retrospective study of 2 independent cohorts. Urol Oncol 2019; 37:735-741. [PMID: 31377166 DOI: 10.1016/j.urolonc.2019.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/28/2019] [Accepted: 07/11/2019] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Renal cell carcinoma (RCC) is the most typical type of kidney cancer in adults. Hypercalcemia is a well known paraneoplastic syndrome associated with RCC and recent studies have reported that hypercalcemia is closely related to the poor prognosis of RCC patients. Clear cell RCC (ccRCC) is the most common and aggressive subtype of RCC. Although the histological classification of RCC is important for determination of appropriate treatment strategies, effective biomarkers for predicting prognosis of ccRCC have not yet been identified. Since calcium levels affect the prognosis of RCC patients, we evaluated whether the calcium-sensing genes on the plasma membrane, including those encoding calcium channels, CaSR, GPRC6a, and DYSF, could be used as biomarkers to predict the prognosis of ccRCC patients. METHODS Information from 537 patients from The Cancer Genome Atlas (TCGA; n = 446) and International Cancer Genome Consortium (ICGC; n = 91) was used in this study. Among these genes, DYSF was the only gene whose expression correlated with overall survival of both TGCA and ICGC patients. RESULTS Although DYSF gene expression was higher in ccRCC tissue than in normal kidney tissue, Kaplan-Meier curves showed that the survival rate of ccRCC patients with high DYSF expression was significantly higher than that of patients with low DYSF expression (TCGA, P < 0.0001; ICGC, P = 0.0011). We also validated the potential of DYSF as a prognostic biomarker for ccRCC by conducting a time-dependent area under the curve (AUC) analysis and 5-years receiver operating characteristic curve analysis. Finally, multivariate regression analysis revealed that the expression of DYSF is independent of other prognostic parameters (TCGA, P = 0.017; ICGC, P = 0.006). CONCLUSIONS These results suggested that DYSF may play a suppressive role in the progression of ccRCC and could act as a promising prognostic biomarker for predicting the survival of ccRCC patients.
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Affiliation(s)
- Mihyang Ha
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Hoim Jeong
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Jong Seong Roh
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Beomgu Lee
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Myoung-Eun Han
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Sae-Ock Oh
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Dong Hyun Sohn
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan, Republic of Korea.
| | - Yun Hak Kim
- Department of Anatomy and Department of Biomedical Informatics, Pusan National University School of Medicine, Yangsan, Republic of Korea; Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea.
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32
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Li B, Pu K, Wu X. Identifying novel biomarkers in hepatocellular carcinoma by weighted gene co-expression network analysis. J Cell Biochem 2019; 120:11418-11431. [PMID: 30746803 DOI: 10.1002/jcb.28420] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 12/04/2018] [Indexed: 01/24/2023]
Abstract
Hepatocellular carcinoma (HCC) is a highly malignant tumor found in the bile duct epithelial cells, and the second most common tumor of the liver. However, the pivotal roles of most molecules of tumorigenesis in HCC are still unclear. Hence, it is essential to detect the tumorigenic mechanism and develop novel prognostic biomarkers for clinical application. The data of HCC mRNA-seq and clinical information from The Cancer Genome Atlas (TCGA) database were analyzed by weighted gene co-expression network analysis (WGCNA). Co-expression modules and clinical traits were constructed by the Pearson correlation analysis, interesting modules were selected and gene ontology and pathway enrichment analysis were performed. Intramodule analysis and protein-protein interaction construction of selected modules were conducted to screen hub genes. In addition, upstream transcription factors and microRNAs of hub genes were predicted by miRecords and NetworkAnalyst database. Afterward, a high connectivity degree of hub genes from two networks was picked out to perform the differential expression validation in the Gene Expression Profiling Interactive Analysis database and Human Protein Atlas database and survival analysis in Kaplan-Meier plotter online tool. By utilizing WGCNA, several hub genes that regulate the mechanism of tumorigenesis in HCC were identified, which was associated with clinical traits including the pathological stage, histological grade, and liver function. Surprisingly, ZWINT, CENPA, RACGAP1, PLK1, NCAPG, OIP5, CDCA8, PRC1, and CDK1 were identified statistically as hub genes in the blue module, which were closely implicated in pathological T stage and histologic grade of HCC. Moreover, these genes also were strongly associated with the HCC cell growth and division. Network and survival analyses found that nine hub genes may be considered theoretically as indicators to predict the prognosis of patients with HCC or clinical treatment target, it will be necessary for basic experiments and large-scale cohort studies to validate further.
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Affiliation(s)
- Boxuan Li
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China.,Department of Pharmacy, The First Hospital of Lanzhou University, Lanzhou, China
| | - Ke Pu
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Key Laboratory for Gastrointestinal Diseases of Gansu Province, Lanzhou University, Lanzhou, China
| | - Xinan Wu
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China.,Department of Pharmacy, The First Hospital of Lanzhou University, Lanzhou, China
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Ha M, Moon H, Choi D, Kang W, Kim JH, Lee KJ, Park D, Kang CD, Oh SO, Han ME, Kim YH, Lee D. Prognostic Role of TMED3 in Clear Cell Renal Cell Carcinoma: A Retrospective Multi-Cohort Analysis. Front Genet 2019; 10:355. [PMID: 31057605 PMCID: PMC6478656 DOI: 10.3389/fgene.2019.00355] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/02/2019] [Indexed: 12/02/2022] Open
Abstract
Transmembrane p24 trafficking protein 3 (TMED3) is a metastatic suppressor in colon cancer and hepatocellular carcinoma. However, its function in the progression of clear cell renal cell carcinoma (ccRCC) is unknown. Here, we report that TMED3 could be a new prognostic marker for ccRCC. Patient data were extracted from cohorts in the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Differential expression of TMED3 was observed between the low stage (Stage I and II) and high stage (Stage III and IV) patients in the TCGA and ICGC cohorts and between the low grade (Grade I and II) and high grade (Grade III and IV) patients in the TCGA cohort. Further, we evaluated TMED3 expression as a prognostic gene using Kaplan-Meier survival analysis, multivariate analysis, the time-dependent area under the curve (AUC) of Uno’s C-index, and the AUC of the receiver operating characteristics at 5 years. The Kaplan-Meier analysis revealed that TMED3 overexpression was associated with poor prognosis for ccRCC patients. Analysis of the C-indices and area under the receiver operating characteristic curve further supported this. Multivariate analysis confirmed the prognostic significance of TMED3 expression levels (P = 0.005 and 0.006 for TCGA and ICGC, respectively). Taken together, these findings demonstrate that TMED3 is a potential prognostic factor for ccRCC.
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Affiliation(s)
- Mihyang Ha
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, South Korea
| | - Hwan Moon
- Department of Premedicine, School of Medicine, Pusan National University, Yangsan, South Korea
| | - Dongwook Choi
- Division of Drug Process Development, New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, South Korea
| | - Wonmo Kang
- Division of Drug Process Development, New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, South Korea
| | - Ji-Hong Kim
- Division of Drug Process Development, New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, South Korea
| | - Keon Jin Lee
- Division of Drug Process Development, New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, South Korea
| | - Dongsu Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States.,Center for Skeletal Medicine and Biology, Baylor College of Medicine, Houston, TX, United States
| | - Chi-Dug Kang
- Department of Biochemistry, Pusan National University School of Medicine, Yangsan, South Korea.,Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, South Korea
| | - Sae-Ock Oh
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, South Korea
| | - Myoung-Eun Han
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, South Korea
| | - Yun Hak Kim
- Department of Anatomy, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, South Korea.,Department of Biomedical Informatics, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, South Korea
| | - Dongjun Lee
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, South Korea
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Goh TS, Ha M, Lee JS, Jeong DC, Jung ES, Han ME, Kim YH, Oh SO. Prognostic significance of EIF4G1 in patients with pancreatic ductal adenocarcinoma. Onco Targets Ther 2019; 12:2853-2859. [PMID: 31043796 PMCID: PMC6472433 DOI: 10.2147/ott.s202101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background Advances in genomics have greatly improved the survival rate in cancer patients. However, due to genetic heterogeneity, pancreatic ductal adenocarcinoma (PDAC) is still difficult to diagnose early, and its survival rate is extremely low. Therefore, we identified biomarkers that predict the prognosis of PDAC patients using independent cohort data. Materials and methods To develop a novel prognostic biomarker, we used the gene expression and clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Kaplan-Meier survival curve using median values of genes as cutoff showed that EIF4G1 was the only statistically significant gene in the 3 cohorts. We analyzed the prognostic significance of EIF4G1 using the time-dependent area under the curve (AUC) of Uno's C-index, the AUC value of the receiver operating characteristics (ROC) at 3 years, and multivariate Cox analysis. We also compared EIF4G1 levels between tumors and matched non-tumor tissues. Results EIF4G1 is the only prognostic gene in patients with PDAC, which was selected by Kaplan-Meier survival analysis. The survival curve showed that high expression of EIF4G1 was associated with poor prognosis of PDAC with a good discriminative ability in 3 independent cohorts. The risk stratifying ability of EIF4G1 was demonstrated by analyzing C-indices and AUC values. Multivariate Cox regression confirmed its prognostic significance. EIF4G1 expression was significantly higher in PDAC tissues than in the matched normal tissues. Conclusion EIF4G1 could be used as a novel prognostic marker for PDAC and to determine suitable treatment options.
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Affiliation(s)
- Tae Sik Goh
- Department of Orthopaedic Surgery and Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Mihyang Ha
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea,
| | - Jung Sub Lee
- Department of Orthopaedic Surgery and Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Dae Cheon Jeong
- Deloitte Analytics Group, Deloitte Consulting LLC, Seoul, Republic of Korea
| | - Eun Sang Jung
- Department of Bioenvironmental Energy, College of Life & Resources Science, Pusan National University, Miryang, Republic of Korea
| | - Myoung-Eun Han
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea,
| | - Yun Hak Kim
- Department of Anatomy and Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea, .,Biomedical Research Institute, Pusan National University, Busan, Republic of Korea,
| | - Sae-Ock Oh
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea,
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35
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Jeon YH, Ha M, Kim SW, Kim MJ, Lee CS, Oh CK, Han ME, Oh SO, Kim YH. Evaluation of the prognostic significances of γ-secretase genes in pancreatic cancer. Oncol Lett 2019; 17:4614-4620. [PMID: 30944650 PMCID: PMC6444455 DOI: 10.3892/ol.2019.10113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/19/2019] [Indexed: 12/19/2022] Open
Abstract
With the growing requirement for novel prognostic biomarkers for pancreatic cancer, many studies have focused on clinical and/or genomic variables. Although many studies have been performed, carbohydrate antigen 19-9 is the only biomarker in clinical use. Therefore, the present study examined whether γ-secretase genes, including presenilin (PSEN), nicastrin (NCSTN), presenilin enhancer protein 2 (PSENEN), and anterior pharynx-defective 1 (APH1-), could serve as prognostic factors for pancreatic cancer. The cohorts selected included >100 pancreatic cancer patients. Patient data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GSE21501). The prognostic roles of the γ-secretase genes were analyzed by several survival analysis methods. Among the γ-secretase genes, the prognosis tended to be worse in the 2 cohorts with increasing expression of PSEN1, APH1A, and PSENEN, while the remaining genes were the opposite in the 2 cohorts. Notably, although the patient characteristics were quite different, APH1A was statistically significantly associated with prognosis in the 2 cohorts. The hazard ratio of APH1A for overall survival was 1.598 (TCGA) and 2.724 (GSE21501). These results contribute to the study of γ-secretase in pancreatic cancer. We believe that γ-secretase, particularly APH1A, will be a new prognostic biomarker for pancreatic cancer.
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Affiliation(s)
- Yun Ho Jeon
- Department of Pediatrics, Busan St. Mary's Hospital, Busan 48575, Republic of Korea
| | - Mihyang Ha
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
| | - Sung Won Kim
- Department of Pediatrics, Busan St. Mary's Hospital, Busan 48575, Republic of Korea
| | - Mun Ju Kim
- Department of Pediatrics, Busan St. Mary's Hospital, Busan 48575, Republic of Korea
| | - Chi-Seung Lee
- Biomedical Research Institute, Pusan National University Hospital, Busan 49241, Republic of Korea
| | - Chang-Kyu Oh
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Myoung-Eun Han
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
| | - Sae-Ock Oh
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
| | - Yun Hak Kim
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan 49241, Republic of Korea.,Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
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36
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Ha M, Jeong H, Roh JS, Lee B, Lee D, Han ME, Oh SO, Sohn DH, Kim YH. VNN3 is a potential novel biomarker for predicting prognosis in clear cell renal cell carcinoma. Anim Cells Syst (Seoul) 2019; 23:112-117. [PMID: 30949398 PMCID: PMC6440501 DOI: 10.1080/19768354.2019.1583126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/13/2019] [Accepted: 02/10/2019] [Indexed: 02/07/2023] Open
Abstract
Although pathological observations provide approximate prognoses, it is difficult to achieve prognosis in patients with existing prognostic factors. Therefore, it is very important to find appropriate biomarkers to achieve accurate cancer prognosis. Renal cell carcinoma (RCC) has several subtypes, the discrimination of which is crucial for proper treatment. Here, we present a novel biomarker, VNN3, which is used to prognose clear cell renal cell carcinoma (ccRCC), the most common and aggressive subtype of kidney cancer. Patient information analyzed in our study was extracted from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) cohorts. VNN3 expression was considerably higher in stages III and IV than in stages I and II. Moreover, Kaplan–Meier curves associated high VNN3 expression with poor prognoses (TCGA, p < .0001; ICGC, p = .00076), confirming that ccRCC prognosis can be predicted via VNN3 expression patterns. Consistent with all patient results, the prognosis of patients with higher VNN3 expression was worse in both low stage (I and II) and high stage (III and IV) (TCGA, p < 0.0001 in stage I and II; ICGC, p = 0.028 in stage I and II; TCGA, p = 0.005 in stage III and IV). Area under the curve and receiver operating characteristic curves supported our results that highlighted VNN3 expression as a suitable ccRCC biomarker. Multivariate analysis also verified the prognostic performance of VNN3 expression (TCGA, p < .001; ICGC, p = .017). Altogether, we suggest that VNN3 is applicable as a new biomarker to establish prognosis in patients with ccRCC.
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Affiliation(s)
- Mihyang Ha
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Hoim Jeong
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Jong Seong Roh
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Beomgu Lee
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Dongjun Lee
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Myoung-Eun Han
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Sae-Ock Oh
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Dong Hyun Sohn
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Yun Hak Kim
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Republic of Korea.,Department of Biomedical Informatics, Pusan National University School of Medicine, Yangsan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
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