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Du W, Xia X, Gou Q, Xie Y, Gao L. Comprehensive review regarding the association of E2Fs with the prognosis and immune infiltrates in human head and neck squamous cell carcinoma. Asian J Surg 2024; 47:2106-2121. [PMID: 38320907 DOI: 10.1016/j.asjsur.2024.01.130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 12/14/2023] [Accepted: 01/19/2024] [Indexed: 02/08/2024] Open
Abstract
E2F transcription factors (E2Fs) are a group of genes that encode a family of transcription factors. They have been identified as being involved in the tumor progression of various cancer types. However, little is known about the expression level, genetic variation, molecular mechanism, and prognostic value and immune infiltration of different E2Fs in HNSCC.In this study, we utilized multiple databases to investigate the mRNA expression level, genetic alteration, and biological function of E2Fs in HNSCC patients. Then, the relationship between E2Fs expression and its association with the occurrence, progress, prognosis, and immune cell infiltration in patients with HNSCC was evaluated. We found that all eight E2Fs were higher expressed in HNSCC tissues than in normal tissues, and the expression levels of E2F1/2/3/4/5/6/8 were also associated with the stage and grade of HNSCC. The abnormal expression of E2F1/2/4/8 in HNSCC patients is related to the clinical outcome. The expression of E2Fs was statistically correlated with the immune cell infiltration in HNSCC and the infiltration of B cells and CD8+ T cells were positively associated with better OS in HNSCC patients. Furthermore, we verified the E2F2 at the tissue level in the validation experiment. Our study may provide novel insights into the choice of immunotherapy targets and potential prognostic biomarkers in HNSCC patients.
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Affiliation(s)
- Wei Du
- Department of Targetting Therapy & Immunology, Cancer Cencer, West China Hospital, Sichuan University, Chengdu, China
| | - Xueming Xia
- Division of Head & Neck Tumor Multimodaligy Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qiheng Gou
- Division of Head & Neck Tumor Multimodaligy Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxin Xie
- Division of Head & Neck Tumor Multimodaligy Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lanyang Gao
- Academician (Expert) Workstation of Sichuan Province, Metabolic Hepatobiliary and Pancreatic Diseases Key Laboratory of Luzhou City, The Affiliated Hospital of Southwest Medical University, Sichuan, China.
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2
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Li F, Yan J, Leng J, Yu T, Zhou H, Liu C, Huang W, Sun Q, Zhao W. Expression patterns of E2Fs identify tumor microenvironment features in human gastric cancer. PeerJ 2024; 12:e16911. [PMID: 38371373 PMCID: PMC10870925 DOI: 10.7717/peerj.16911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024] Open
Abstract
Objective E2F transcription factors are associated with tumor development, but their underlying mechanisms in gastric cancer (GC) remain unclear. This study explored whether E2Fs determine the prognosis or immune and therapy responses of GC patients. Methods E2F regulation patterns from The Cancer Genome Atlas (TCGA) were systematically investigated and E2F patterns were correlated with the characteristics of cellular infiltration in the tumor microenvironment (TME). A principal component analysis was used to construct an E2F scoring model based on prognosis-related differential genes to quantify the E2F regulation of a single tumor. This scoring model was then tested in patient cohorts to predict effects of immunotherapy. Results Based on the expression profiles of E2F transcription factors in GC, two different regulatory patterns of E2F were identified. TME and survival differences emerged between the two clusters. Lower survival rates in the Cluster2 group were attributed to limited immune function due to stromal activation. The E2F scoring model was then constructed based on the E2F-related prognostic genes. Evidence supported the E2F score as an independent and effective prognostic factor and predictor of immunotherapy response. A gene-set analysis correlated E2F score with the characteristics of immune cell infiltration within the TME. The immunotherapy cohort database showed that patients with a higher E2F score demonstrated better survival and immune responses. Conclusions This study found that differences in GC prognosis might be related to the E2F patterns in the TME. The E2F scoring system developed in this study has practical value as a predictor of survival and treatment response in GC patients.
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Affiliation(s)
- Fanni Li
- Department of Talent Highland, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jun Yan
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jing Leng
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Tianyu Yu
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Huayou Zhou
- Department of General Surgery, Hanzhong Central Hospital, Hanzhong, China
| | - Chang Liu
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Wenbo Huang
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Qi Sun
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Wei Zhao
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
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Zheng J, Tang H, Yang Y, Yang K. Comprehensive analysis of the prognosis and biological significance of ROR β in head and neck squamous cell carcinoma. ENVIRONMENTAL TOXICOLOGY 2024; 39:487-508. [PMID: 37278231 DOI: 10.1002/tox.23859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/10/2023] [Accepted: 05/29/2023] [Indexed: 06/07/2023]
Abstract
Recent studies have shown that abnormal expression of the core circadian clock gene, retinoic acid-related orphan receptor β (RORβ ), is closely associated with the occurrence and progression of various malignant tumors. However, the expression and function of RORβ in head and neck squamous cell carcinoma (HNSCC) remains unclear. Here, we comprehensively investigated the altered expression, clinical significance, prognostic value, and biological functions of RORβ in HNSC, as well as its correlation with changes in the tumor immune microenvironment. We found that RORβ expression was decreased in HNSC and 19 other cancers. Low RORβ expression was significantly associated with tumor size, clinical stage, and survival time in HNSC patients, indicating that it may have diagnostic and prognostic value in HNSCC. Epigenetic analysis showed that the promoter methylation level of RORβ was significantly higher in HNSCC compared to adjacent noncancerous tissues. Furthermore, RORβ hypermethylation was significantly associated with low expression levels of RORβ and poor prognosis in HNSCC patients (p < 0.05). Enrichment analysis found that RORβ was involved in immune system regulation and T-cell activation, as well as the PI3K/AKT and ECM receptors interaction pathways. In vitro assays revealed that RORβ regulated the proliferation, migration and invasion ability of HNSCC cells. Additionally, we found that RORβ expression was significantly correlated with changes in the tumor immune microenvironment, suggesting it may affect prognosis by regulating immune infiltration in HNSC patients. Therefore, RORβ may serve as a potential prognostic biomarker and therapeutic target for HNSCC patients.
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Affiliation(s)
- Jiawen Zheng
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Tang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yixin Yang
- Xiangya School of Stomatology, Xiangya Stomatological Hospital, Central South University, Changsha, China
| | - Kai Yang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Li J, Huang Y, Xu J, Zuo H, Tang Y, Huang HY, Chen J, Lin YCD, Huang HD. Mechanism of Sophorae Flavescentis Radix (Kushen) in treating NSCLC: Insights from miRNA-mRNA network analysis. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117232. [PMID: 37757992 DOI: 10.1016/j.jep.2023.117232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 09/14/2023] [Accepted: 09/24/2023] [Indexed: 09/29/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Sophorae Flavescentis Radix (Kushen) is the primary herb component of Compound Kushen Injection (CKI), an approved clinical treatment for tumors. Despite CKI's widespread use, the underlying mechanisms of Kushen regarding microRNA-target and pathway remain unclear in non-small cell lung cancer (NSCLC). AIM OF THE STUDY This study aimed to elucidate the crucial miRNAs-targets and pathways responsible for the Kushen's impact on NSCLC. MATERIALS AND METHODS CCK8, colony formation, and apoptosis assays were performed to assess the effects of Kushen on NSCLC cells. Subsequently, we treated the A549 cell line with varying concentrations of Kushen to obtain mRNA and miRNA expression profiles. A DE (differentially expressed) miRNAs-DEGs network was then constructed to identify the critical miRNA-mRNA interaction influenced by Kushen. Furthermore, we performed clinical significance and prognosis analyses of hub genes to narrow down key genes and their corresponding miRNAs. Finally, the effects of Kushen on critical miRNA-mRNA interaction and related pathway were verified by in vitro and in vivo experiments. RESULTS In this study, we initially demonstrated that Kushen significantly inhibited cell proliferation, suppressed colony formation, and induced apoptosis in the A549 cells, PC9 cells, and the A549 zebrafish xenograft model. Through expression profile analysis, a DE miRs-DEGs network was constructed with 16 DE miRs and 68 DEGs. Through the network analysis and expression validation, we found Kushen could significantly down-regulate miR-183-5p expression and up-regulate EGR1 expression. Additionally, Kushen affected the PTEN/Akt pathway, increasing PTEN expression and decreasing pAkt expression. Finally, matrine, the essential active compound of Kushen, also inhibited cell growth, induced apoptosis, and regulated miR-183-5p/EGR1 and PTEN/AKT pathway. CONCLUSIONS Altogether, these findings supported the critical role of miR-183-5p/EGR1 and the PTEN/AKT pathway in the beneficial effects of Kushen on NSCLC, highlighting the therapeutic potential of Kushen in NSCLC treatment.
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Affiliation(s)
- Jing Li
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China; Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China.
| | - Yixian Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China; Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China.
| | - Jiatong Xu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China; Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China.
| | - Huali Zuo
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China; Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China.
| | - Yun Tang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China; Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China.
| | - Hsi-Yuan Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China; Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China.
| | - Jihang Chen
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China.
| | - Yang-Chi-Dung Lin
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China; Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China.
| | - Hsien-Da Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China; Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, PR China.
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Shao D, Zhou H, Yu H, Zhu X. CX3CR1 is a potential biomarker of immune microenvironment and prognosis in epithelial ovarian cancer. Medicine (Baltimore) 2024; 103:e36891. [PMID: 38241595 PMCID: PMC10798769 DOI: 10.1097/md.0000000000036891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
Immunotherapy is less efficient for epithelial ovarian cancer and lacks ideal biomarkers to select the best beneficiaries for immunotherapy. CX3CR1 as chemokine receptor mainly expressed on immune cell membranes, and combined with its unique ligand CX3CL1, mediates tissue chemotaxis and adhesion of immune cells. However, the immune functional and prognostic value of CX3CR1 in epithelial ovarian cancer has not been clarified. A comprehensive retrospective analysis was performed by using the online database to identify the underlying immunological mechanisms and prognostic value of CX3CR1. The Human Protein Atlas, gene expression profiling interactive analysis, and TISIDB (an integrated repository portal for tumor-immune system interactions) database showed that CX3CR1 expressed higher in epithelial ovarian cancer than that in normal ovarian tissue. Four hundred twenty-two cases from Gene Expression Profiling Interactive Analysis and 1656 cases from Kaplan-Meier plotter database showed higher expression of CX3CR1 (above median) was associated with unfavorable overall survival. TIMER, UALCAN, and TISIDB database were applied to validate CX3CR1 negative impact on overall survival. In addition, correlation analysis showed that the expression level of CX3CR1 was positive association with infiltrating levels of B cells (R = 0.31, P = 3.10e-12), CD8+ T cells (R = 0.26, P = 7.93e-09), CD4+ T cells (R = 0.11, P = 1.41e-02), macrophages (R = 0.32, P = 4.29e-13), dendritic cells (R = 0.27, P = 2.98e-09), and neutrophil (R = 0.25, P = 3.25e-08) in epithelial ovarian cancer. Therefore, CX3CR1 involved in reshaping the immune microenvironment for epithelial ovarian cancer and maybe a potential immunotherapy target and prognostic marker for ovarian cancer.
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Affiliation(s)
- Danfeng Shao
- Department of Gynecology, Hangzhou Fuyang First People’s Hospital, Hangzhou, China
| | - Honger Zhou
- Department of Gynecology, Hangzhou Fuyang First People’s Hospital, Hangzhou, China
| | - Huaiying Yu
- Department of Gynecology, Hangzhou Fuyang First People’s Hospital, Hangzhou, China
| | - Xiaoqing Zhu
- Department of Gynecology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Lin S, Yu X, Yan H, Xu Y, Ma K, Wang X, Liu Y, Xie A, Yu Z. E2F7 serves as a potential prognostic biomarker for lung adenocarcinoma. Medicine (Baltimore) 2024; 103:e34342. [PMID: 38241554 PMCID: PMC10798722 DOI: 10.1097/md.0000000000034342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/23/2023] [Indexed: 01/21/2024] Open
Abstract
E2F transcription factors (E2Fs) are a family of transcription factors critical regulators of the cell cycle, apoptosis, and differentiation, thus influencing tumorigenesis. However, the specific roles of E2Fs in lung adenocarcinoma (LUAD) remain unclear. Data from The Cancer Genome Atlas (TCGA) were used. R version. 4.0.3 and multiple databases (TIMER, cBioportal, gene expression profile interaction analysis [GEPIA], LinkedOmics, and CancerSEA) were utilized to investigate mRNA expression, mutational analysis, prognosis, clinical correlations, co-expressed gene, pathway and network, and single-cell analyses. Immunohistochemistry (IHC) confirmed that E2F transcription factor 7 (E2F7) correlated with LUAD. Among the E2Fs, E2F7 was identified by constructing a prognostic model most significantly associated with overall survival (OS) in LUAD patients. The univariate and multivariate Cox regression analyses showed that E2F7, p-T stage, and p-TNM stage were closely related to OS and progression-free survival (PFS) (P < .05) in LUAD. E2F 7/8 were also identified as significantly associated with tumor stage in the GEPIA database. Compared with paracancerous tissues, E2F7 was up-regulated in LUAD by IHC, and E2F7 might be positively correlated with larger tumors and higher TNM stages. E2F7 may primarily regulate DNA repair, damage, and cell cycle processes and thus affect LUAD tumorigenesis, invasion, and metastasis by LinkedOmics and CancerSEA. E2F7 serves as a potential prognostic biomarker for LUAD.
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Affiliation(s)
- Shengcheng Lin
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Xiangyang Yu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Haojie Yan
- Translational Medicine Collaborative Innovation Center, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affifiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Basic Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | - Yafei Xu
- Department of Anesthesiology, Shunde Hospital of Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan, China
| | - Kai Ma
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Xiaoliang Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Yeqing Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Ahuan Xie
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Zhentao Yu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
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Gan Z, Abudurexiti A, Hu X, Chen W, Zhang N, Sang W. E2F3/5/8 serve as potential prognostic biomarkers and new therapeutic direction for human bladder cancer. Medicine (Baltimore) 2024; 103:e35722. [PMID: 38215110 PMCID: PMC10783276 DOI: 10.1097/md.0000000000035722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/29/2023] [Indexed: 01/14/2024] Open
Abstract
OBJECTS Human bladder cancer (BC) is the most common urogenital system malignancy. E2F transcription factors (E2Fs) have been reported to be involved in the growth of various cancers. However, the expression patterns, prognostic value and immune infiltration in the tumor microenvironment of the 8 E2Fs in BC have yet fully to be explored. METHODS AND STRATEGY We investigated the differential expression of E2Fs in BC patients, the prognostic value and correlation with immune infiltration by analyzing a range of databases. RESULTS We found that the mRNA expression levels of E2F1/2/3/4/5/7/8 were significantly higher in BC patients than that of control tissues. And the increased mRNA expression levels of all E2Fs were associated with tumor stage of BC. The survival analysis revealed that the elevated mRNA expression levels of E2F3/5/8 were significantly correlated with the overall survival (OS) of BC patients. And the genetic changes of E2Fs in BC patients were associated with shorter overall survival (OS) and progression-free survival (PFS). In addition, we revealed that the E2F3/5/8 expressions were closely correlated with tumor-infiltrating lymphocytes (TILs). CONCLUSIONS E2F3/5/8 might serve as promising prognostic biomarkers and new therapeutic direction for BC patients.
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Affiliation(s)
- Zhilu Gan
- Surgery Department of Urology, The Third People’s Hospital of Xinjiang Uyghur Autonomous Region, Urumqi, P.R. China
| | - Alimujiang Abudurexiti
- Surgery Department of Urology, The Third People’s Hospital of Xinjiang Uyghur Autonomous Region, Urumqi, P.R. China
| | - Xiaogang Hu
- Surgery Department of Urology, The Third People’s Hospital of Xinjiang Uyghur Autonomous Region, Urumqi, P.R. China
| | - Wenxin Chen
- Surgery Department of Urology, The Third People’s Hospital of Xinjiang Uyghur Autonomous Region, Urumqi, P.R. China
| | - Ning Zhang
- Surgery Department of Urology, The Third People’s Hospital of Xinjiang Uyghur Autonomous Region, Urumqi, P.R. China
| | - Wei Sang
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, P.R. China
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, P.R. China
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Yazdan M, Naghib SM, Mozafari MR. Liposomal Nano-Based Drug Delivery Systems for Breast Cancer Therapy: Recent Advances and Progresses. Anticancer Agents Med Chem 2024; 24:896-915. [PMID: 38529608 DOI: 10.2174/0118715206293653240322041047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 03/27/2024]
Abstract
Breast cancer is a highly prevalent disease on a global scale, with a 30% incidence rate among women and a 14% mortality rate. Developing countries bear a disproportionate share of the disease burden, while countries with greater technological advancements exhibit a higher incidence. A mere 7% of women under the age of 40 are diagnosed with breast cancer, and the prevalence of this ailment is significantly diminished among those aged 35 and younger. Chemotherapy, radiation therapy, and surgical intervention comprise the treatment protocol. However, the ongoing quest for a definitive cure for breast cancer continues. The propensity for cancer stem cells to metastasize and resistance to treatment constitute their Achilles' heel. The advancement of drug delivery techniques that target cancer cells specifically holds significant promise in terms of facilitating timely detection and effective intervention. Novel approaches to pharmaceutical delivery, including nanostructures and liposomes, may bring about substantial changes in the way breast cancer is managed. These systems offer a multitude of advantages, such as heightened bioavailability, enhanced solubility, targeted tumor destruction, and diminished adverse effects. The application of nano-drug delivery systems to administer anti-breast cancer medications is a significant subject of research. This article delves into the domain of breast cancer, conventional treatment methods, the incorporation of nanotechnology into managerial tactics, and strategic approaches aimed at tackling the disease at its core.
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Affiliation(s)
- Mostafa Yazdan
- Department of Nanotechnology, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran, 1684613114, Iran
| | - Seyed Morteza Naghib
- Department of Nanotechnology, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran, 1684613114, Iran
| | - M R Mozafari
- Australasian Nanoscience and Nanotechnology Initiative (ANNI), Monash University LPO, Clayton, VIC 3168, Australia
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9
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Lv Z, Ma G, Zhong Z, Xie X, Li B, Long D. O-GlcNAcylation of RAB10 promotes hepatocellular carcinoma progression. Carcinogenesis 2023; 44:785-794. [PMID: 37218374 DOI: 10.1093/carcin/bgad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 05/10/2023] [Accepted: 05/22/2023] [Indexed: 05/24/2023] Open
Abstract
Ras-related protein Rab-10 (RAB10) is involved in tumorigenesis and progression of hepatocellular carcinoma (HCC). Here, we found RAB10, O-GlcNAc transferase (OGT), and O-GlcNAcylation were upregulated in HCC. In addition, RAB10 protein level was prominently positively correlated with the expression of OGT. O-GlcNAcylation modification of RAB10 was then investigated. Here we showed that RAB10 interacts directly with OGT in HCC cell lines, Meanwhile, O-GlcNAcylation enhanced RAB10 protein stability. Furthermore, knockdown of OGT suppressed aggressive behaviors of HCC in vitro and in vivo, while elevated RAB10 reversed these. Taken together, these results indicated that OGT mediated O-GlcNAcylation stabilized RAB10, thus accelerating HCC progression.
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Affiliation(s)
- Zhuo Lv
- Department of Oncology, Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, China
| | - Guolu Ma
- Cancer Center, Integrated Hospital of Traditional Chinese and Western Medicine, Southern Medical University, Guangzhou, China
| | - Zhuo Zhong
- Department of Oncology, Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, China
| | - Xiong Xie
- Department of Oncology, Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, China
| | - Bin Li
- Li Bin's Clinic of Traditional Chinese Medicine, Guangzhou, China
| | - De Long
- Department of Oncology, Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, China
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10
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Lima BM, de Azevedo ALK, Giner IS, Gomig THB, Ribeiro EMDSF, Cavalli IJ. Biomarker potential of the LEF1/TCF family members in breast cancer: Bioinformatic investigation on expression and clinical significance. Genet Mol Biol 2023; 46:e20220346. [PMID: 38100720 PMCID: PMC10723634 DOI: 10.1590/1678-4685-gmb-2022-0346] [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: 11/11/2022] [Accepted: 10/18/2023] [Indexed: 12/17/2023] Open
Abstract
The LEF1/TCF transcription factor family is related to the development of diverse tissue types, including the mammary tissue, and dysregulation of its expression and function has been described to favor breast tumorigenesis. However, the clinical and biological relevance of this gene family in breast cancer is still poorly understood. Here, we used bioinformatics approaches aiming to reduce this gap. We investigated its expression patterns in molecular and immune breast cancer subtypes; its correlation with immune cell infiltration, and its prognostic values in predicting outcomes. Also, through regulons construction, we determined the genes whose expression is influenced by these transcription factors, and the pathways in which they are involved. We found that LEF1 and TCF3 are over-expressed in breast tumors regarding non-tumor samples, while TCF4 and TCF7 are down-expressed, with the gene's methylation status being associated with its expression dysregulation. All four transcription factors presented significance at the diagnostic and prognostic levels. LEF1, TCF4, and TCF7 presented a significant correlation with immune cell infiltration, being associated with the immune subtypes of less favorable outcomes. Altogether, this research contributes to a more accurate understanding of the expression and clinical and biomarker significance of the LEF1/TCF transcription factors in breast cancer.
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Affiliation(s)
- Beatriz Miotto Lima
- Universidade Federal do Paraná, Departamento de Genética,
Curitiba, Paraná, Brasil
| | | | - Igor Samesima Giner
- Universidade Federal do Paraná, Departamento de Genética,
Curitiba, Paraná, Brasil
| | | | | | - Iglenir João Cavalli
- Universidade Federal do Paraná, Departamento de Genética,
Curitiba, Paraná, Brasil
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11
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Hamelin B, Obradović MMS, Sethi A, Kloc M, Münst S, Beisel C, Eschbach K, Kohler H, Soysal S, Vetter M, Weber WP, Stadler MB, Bentires-Alj M. Single-cell Analysis Reveals Inter- and Intratumour Heterogeneity in Metastatic Breast Cancer. J Mammary Gland Biol Neoplasia 2023; 28:26. [PMID: 38066300 PMCID: PMC10709262 DOI: 10.1007/s10911-023-09551-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Metastasis is the leading cause of cancer-related deaths of breast cancer patients. Some cancer cells in a tumour go through successive steps, referred to as the metastatic cascade, and give rise to metastases at a distant site. We know that the plasticity and heterogeneity of cancer cells play critical roles in metastasis but the precise underlying molecular mechanisms remain elusive. Here we aimed to identify molecular mechanisms of metastasis during colonization, one of the most important yet poorly understood steps of the cascade. We performed single-cell RNA-Seq (scRNA-Seq) on tumours and matched lung macrometastases of patient-derived xenografts of breast cancer. After correcting for confounding factors such as the cell cycle and the percentage of detected genes (PDG), we identified cells in three states in both tumours and metastases. Gene-set enrichment analysis revealed biological processes specific to proliferation and invasion in two states. Our findings suggest that these states are a balance between epithelial-to-mesenchymal (EMT) and mesenchymal-to-epithelial transitions (MET) traits that results in so-called partial EMT phenotypes. Analysis of the top differentially expressed genes (DEGs) between these cell states revealed a common set of partial EMT transcription factors (TFs) controlling gene expression, including ZNF750, OVOL2, TP63, TFAP2C and HEY2. Our data suggest that the TFs related to EMT delineate different cell states in tumours and metastases. The results highlight the marked interpatient heterogeneity of breast cancer but identify common features of single cells from five models of metastatic breast cancer.
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Affiliation(s)
- Baptiste Hamelin
- Department of Biomedicine, Department of Surgery, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Milan M S Obradović
- Department of Biomedicine, Department of Surgery, University Hospital Basel, University of Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- , Roche, Basel, Switzerland
| | - Atul Sethi
- Department of Biomedicine, Department of Surgery, University Hospital Basel, University of Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- , Roche, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michal Kloc
- Department of Biomedicine, Department of Surgery, University Hospital Basel, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Simone Münst
- Institute of Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Katja Eschbach
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Savas Soysal
- Department of Biomedicine, Department of Surgery, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Marcus Vetter
- Department of Biomedicine, Department of Surgery, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Walter P Weber
- Breast Center, Department of Surgery, University Hospital Basel, Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mohamed Bentires-Alj
- Department of Biomedicine, Department of Surgery, University Hospital Basel, University of Basel, Basel, Switzerland.
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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12
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Guan Y, Han J, Chen D, Zhan Y, Chen J. Aquaporin 1 overexpression may enhance glioma tumorigenesis by interacting with the transcriptional regulation networks of Foxo4, Maz, and E2F families. Chin Neurosurg J 2023; 9:34. [PMID: 38057925 DOI: 10.1186/s41016-023-00342-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/06/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND The glioblastoma has served as a valuable experimental model system for investigating the growth and invasive properties of glioblastoma. Aquaporin-1 (AQP1) in facilitating cell migration and potentially contributing to tumor progression. In this study, we analyzed the role of AQP1 overexpression in glioblastoma and elucidated the main mechanisms involved. METHODS AQP1 overexpression recombinant vector was introduced into C6 rat glioma cells to construct an AQP1 overexpression C6 cell line, and its effect on cell viability and migration ability was detected by MTT and Transwell. RNA was extracted by Trizol method for gene sequencing and transcriptomics analysis, and the differentially expressed genes (DEGs) were enriched for up- and downregulated genes by Principal component analysis (PCA), and the molecular mechanism of AQP1 overexpression was analyzed in comparison with the control group using the NCBI GEO database. Statistical analysis was performed using Mann-Whitney paired two tailed t test. RESULTS The cell viability of AQP1-transfected cell lines increased by 23% and the mean distance traveled increased by 67% compared with the control group. Quantitative analysis of gene expression showed that there were 12,121 genes with an average transcripts per million (TPM) value greater than 1. DEGs accounted for 13% of the genes expressed, with the highest correlation with upregulated genes being FOXO4 and MAZ, and the highest with downregulated genes being E2F TFs. CONCLUSIONS AQP1 may be implicated in glioma formation by interacting with the transcriptional regulation networks involving the FOXO4, MAZ, and E2F1/2. These findings shed light on the potential significance of AQP1 in glioma pathogenesis and warrant further investigations to unravel the underlying molecular mechanisms.
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Affiliation(s)
- Ying Guan
- Department of Ultrasound, The First Affiliated Hospital of Hainan Medical College, Haikou City, 570102, Hainan Province, China
| | - Jinhua Han
- Department of Radiology, The First Affiliated Hospital of Hainan Medical College, Haikou City, 570102, Hainan Province, China
| | - Die Chen
- Department of Ultrasound, The First Affiliated Hospital of Hainan Medical College, Haikou City, 570102, Hainan Province, China
| | - Yuefu Zhan
- Department of Radiology, Hainan Children's Hospital, Haikou City, 571103, Hainan Province, China
| | - Jianqiang Chen
- Department of Radiology, The First Affiliated Hospital of Hainan Medical College, Haikou City, 570102, Hainan Province, China.
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Shao G, Fan X, Zhang P, Liu X, Huang L, Ji S. Circ_0004676 exacerbates triple-negative breast cancer progression through regulation of the miR-377-3p/E2F6/PNO1 axis. Cell Biol Toxicol 2023; 39:2183-2205. [PMID: 35870038 DOI: 10.1007/s10565-022-09704-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/23/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND The significant roles of circular RNAs (circRNAs) in different cancers and diseases have been reported. We now focused on the possible role of a newly recognized circRNA, circ_0004674 in triple-negative breast cancer (TNBC), and the related downstream mechanism. METHODS The expression of circ_0004674 in TNBC tissues and cells was determined followed by analysis of the correlation between circ_0004674 and TNBC patients' prognosis. The interaction between circ_0004674, miR-377-3p, E2F6, and PNO1 was then identified using bioinformatics analysis combined with FISH, RIP, RNA pull-down, RT-qPCR, and Western blot analysis. Using gain-of-function and loss-of-function methods, we analyzed the effect of circ_0004674, miR-377-3p, E2F6, and PNO1 on TNBC in vivo and in vitro. RESULTS Increased circ_0004674 and E2F6 but decreased miR-377-3p were observed in TNBC tissues and MDA-MB-231 TNBC cells, all of which findings were associated with poor prognosis in patients with TNBC. Silencing of circ_0004676 remarkably suppressed the proliferation, cell cycle progression, and migration of TNBC cells in vitro, as well as inhibiting tumorigenesis and metastasis in vivo. Additionally, circ_0004676 served as a sponge of miR-377-3p which bound to the transcription factor E2F6. In the presence of overexpression of circ_0004676, E2F6 expression and its target PNO1 expression were elevated, while miR-377-3p expression was decreased. Interestingly, overexpression of E2F6 could reverse the inhibitory effect on tumor growth caused by downregulation of circ_0004676. CONCLUSION Our study highlighted the carcinogenic effect of circ_0004676 on TNBC through regulation of the miR-377-3p/E2F6/PNO1 axis. 1. Circ_0004674 is highly expressed in TNBC tissues and cells. 2. Circ_0004674 upregulates the expression of E2F6 by sponging miR-377-3p. 3. E2F6 upregulates PNO1 by binding to the PNO1 promoter. 4. Circ_0004674 favors TNBC progression by regulating the miR-377-3p/E2F6/PNO1 axis. 5. This study provides a new target for the treatment of TNBC.
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Affiliation(s)
- Guoli Shao
- Special Medical Service Center, Zhujiang Hospital of Southern Medical University, No. 253, Middle Gongye Road, Haizhu District, Guangzhou, 510282, People's Republic of China
| | - Xulong Fan
- Department of Breast Surgery, Maternity and Children's Healthcare Hospital of Foshan, Foshan, 528000, People's Republic of China
| | - Pusheng Zhang
- Department of General Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Xuewen Liu
- Special Medical Service Center, Zhujiang Hospital of Southern Medical University, No. 253, Middle Gongye Road, Haizhu District, Guangzhou, 510282, People's Republic of China
| | - Lei Huang
- Department of General Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Shufeng Ji
- Special Medical Service Center, Zhujiang Hospital of Southern Medical University, No. 253, Middle Gongye Road, Haizhu District, Guangzhou, 510282, People's Republic of China.
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14
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Han X, Chen Y, Xie J, Wang Y. Characteristics of m 6A-related LncRNAs in breast cancer as prognostic biomarkers and immunotherapy. J Cancer 2023; 14:2919-2930. [PMID: 37781080 PMCID: PMC10539557 DOI: 10.7150/jca.87079] [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: 06/12/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
N6-methyladenosine (m6A) is a common RNA modification in coding and non-coding RNAs and plays an important role in the occurrence and development of breast cancer (BC). However, the role of m6A-related lncRNAs in breast cancer prognosis is unclear. This study aimed to help verify the biological function of m6A-related lncRNAs in breast cancer prognosis through bio-informatics techniques. First, we screened 18 m6A-related lncRNAs from the TCGA database: AL137847.1, AC137932.2, OTUD6B-AS1, MORF4L2-AS1, AC078846.1, AC012442.1, AL118556.1, AL138955.1, AC009754.1, AC024257.4, AL391095.1, AC024270.3, AC087392.1, LINC02649, AC090948.2, AL158212.1, ITGA6-AS1, AL133243.2 and constructed a risk-prognosis model based on this. Based on the model's median risk score, BC patients were divided into high-risk and low-risk groups. Then, the predictive value of the model was verified by Cox regression, Lasso regression, Kaplan-Meier curve and ROC curve analysis, and biological differences between the two groups were verified by GO enrichment analysis, tumor mutation burden, immune indications and in vitro tests. Importantly, the risk score of this prognostic model is an excellent independent prognostic factor, and m6A regulators are differentially expressed in patients with different risks. In addition, based on patients' different sensitivities to drugs, some drug candidates for different risk populations are screened to provide targets for breast cancer treatment. The difference in immune function between high-risk and low-risk patients also affected the sensitivity to immunotherapy. In the validation of clinical samples, we analyzed the expression of relevant lncRNAs in different risk groups and speculated the possible impact on the prognosis of breast cancer patients. The risk assessment tool built based on the full analysis of these m6A-related genes and m6A-related lncRNA libraries, as well as the m6A-related lncRNAs, has a high prognostic prediction ability, which may provide a supplementary screening method for accurately judging the prognosis of BC and a new perspective for personalized treatment of breast cancer patients.
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Affiliation(s)
- Xinwei Han
- Tai Zhou Central Hospital (Taizhou University Hospital), No.999 Donghai Road, Jiaojiang District, Taizhou, Zhejiang, 318000, China
- Cytotherapy Laboratory, Shenzhen People's Hospital, 1017, Dongmen North Road, Luohu, Shenzhen, 518020, China
| | - Yu Chen
- Tai Zhou Central Hospital (Taizhou University Hospital), No.999 Donghai Road, Jiaojiang District, Taizhou, Zhejiang, 318000, China
| | - Jiaogui Xie
- Tai Zhou Central Hospital (Taizhou University Hospital), No.999 Donghai Road, Jiaojiang District, Taizhou, Zhejiang, 318000, China
| | - Yichao Wang
- Tai Zhou Central Hospital (Taizhou University Hospital), No.999 Donghai Road, Jiaojiang District, Taizhou, Zhejiang, 318000, China
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15
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Lin SH, Chien CH, Chang KP, Lu MF, Chen YT, Chu YW. SaBrcada: Survival Intervals Prediction for Breast Cancer Patients by Dimension Raising and Age Stratification. Cancers (Basel) 2023; 15:3690. [PMID: 37509351 PMCID: PMC10378351 DOI: 10.3390/cancers15143690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/03/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
(1) Background: Breast cancer is the second leading cause of cancer death among women. The accurate prediction of survival intervals will help physicians make informed decisions about treatment strategies or the use of palliative care. (2) Methods: Gene expression is predictive and correlates to patient prognosis. To establish a reliable prediction tool, we collected a total of 1187 RNA-seq data points from breast cancer patients (median age 58 years) in Fragments Per Kilobase Million (FPKM) format from the TCGA database. Among them, we selected 144 patients with date of death information to establish the SaBrcada-AD dataset. We first normalized the SaBrcada-AD dataset to TPM to build the survival prediction model SaBrcada. After normalization and dimension raising, we used the differential gene expression data to test eight different deep learning architectures. Considering the effect of age on prognosis, we also performed a stratified random sampling test on all ages between the lower and upper quartiles of patient age, 48 and 69 years; (3) Results: Stratifying by age 61, the performance of SaBrcada built by GoogLeNet was improved to a highest accuracy of 0.798. We also built a free website tool to provide five predicted survival periods: within six months, six months to one year, one to three years, three to five years, or over five years, for clinician reference. (4) Conclusions: We built the prediction model, SaBrcada, and the website tool of the same name for breast cancer survival analysis. Through these models and tools, clinicians will be provided with survival interval information as a basis for formulating precision medicine.
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Affiliation(s)
- Shih-Huan Lin
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ching-Hsuan Chien
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Kai-Po Chang
- Department of Pathology, China Medical University Hospital, Taichung 404327, Taiwan
| | - Min-Fang Lu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yu-Ting Chen
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yen-Wei Chu
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan
- Smart Sustainable New Agriculture Research Center (SMARTer), Taichung 40227, Taiwan
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16
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Zhuang X, Zhang G, Bao M, Jiang G, Wang H, Li S, Wang Z, Sun X. Development of a novel immune infiltration-related diagnostic model for Alzheimer's disease using bioinformatic strategies. Front Immunol 2023; 14:1147501. [PMID: 37545529 PMCID: PMC10400274 DOI: 10.3389/fimmu.2023.1147501] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Background The pathogenesis of Alzheimer's disease (AD) is complex and multi-factorial. Increasing evidence has shown the important role of immune infiltration in AD. Thus the current study was designed to identify immune infiltration-related genes and to explore their diagnostic value in AD. Methods The expression data of AD patients were downloaded from the GEO database. The limma R package identified differentially expressed genes (DEGs) between AD and controls. The CIBERSORT algorithm identified differentially infiltrated immune cells (DIICs) between AD and controls. DIIC-correlated DEGs were obtained by Pearson correlation analysis. WGCNA was employed to identify DIIC-related modules. Next, LASSO, RFE, and RF machine learning methods were applied to screen robust DIIC-related gene signatures in AD, followed by the construction and validation of a diagnostic nomogram. Detection of the expression of related genes in the peripheral blood of Alzheimer's disease and healthy volunteers by RT-PCR. In addition, the CTD database predicted chemicals targeting DIIC-related gene signatures in the treatment of AD. Results NK cells, M0 macrophages, activated myeloid dendritic cells, resting mast cells, CD8+ T cells, resting memory CD4+ T cells, gamma delta T cells, and M2 macrophages were differentially infiltrated between AD and controls. Pearson analysis identified a total of 277 DIIC-correlated DEGs between AD and controls. Thereafter, 177 DIIC-related genes were further obtained by WGCNA analysis. By LASSO, RFE and RF algorithms, CMTM2, DDIT4, LDHB, NDUFA1, NDUFB2, NDUFS5, RPL17, RPL21, RPL26 and NDUFAF2 were identified as robust gene signature in AD. The results of RT-PCR detection of peripheral blood samples from Alzheimer's disease and healthy volunteers showed that the expression trend of ten genes screened was consistent with the detection results; among them, the expression levels of CMTM2, DDIT4, LDHB, NDUFS5, and RPL21 are significantly different among groups. Thus, a diagnostic nomogram based on a DIIC-related signature was constructed and validated. Moreover, candidate chemicals targeting those biomarkers in the treatment of AD, such as 4-hydroxy-2-nonenal, rosiglitazone, and resveratrol, were identified in the CTD database. Conclusion For the first time, we identified 10 immune infiltration-related biomarkers in AD, which may be helpful for the diagnosis of AD and provide guidance in the treatment of AD.
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Affiliation(s)
- Xianbo Zhuang
- Department of Neurology, Liaocheng People’s Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, China
| | - Guifeng Zhang
- Department of Neurology, Liaocheng People’s Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, China
| | - Mengxin Bao
- Department of Neurology, Liaocheng People’s Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, China
| | - Guisheng Jiang
- Department of Neurology, Liaocheng People’s Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, China
| | - Huiting Wang
- Department of Neurology, Liaocheng People’s Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, China
| | - Shanshan Li
- Clinical Laboratory, Liaocheng Veterans Hospital, Liaocheng, China
| | - Zheng Wang
- Department of Neurosurgery, Liaocheng Traditional Chinese Medicine Hospital, Liaocheng, China
| | - Xiujuan Sun
- Department of Neurology, Liaocheng People’s Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, China
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17
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Yuan Y, Xie B, Guo D, Liu C, Jiang G, Lai G, Zhang Y, Hu X, Wu Z, Zheng R, Huang L. Identification of ALG3 as a potential prognostic biomarker in lung adenocarcinoma. Heliyon 2023; 9:e18065. [PMID: 37539167 PMCID: PMC10395363 DOI: 10.1016/j.heliyon.2023.e18065] [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: 02/23/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
Background The abnormal expression of Alpha-1,3-mannosyltransferase (ALG3) has been implicated in tumor promotion. However, the clinical significance of ALG3 in Lung Adenocarcinoma (LUAD) remains poorly understood. Therefore, we aimed to assess the prognostic value of ALG3 and its association with immune infiltrates in LUAD. Methods The transcriptional expression profiles of ALG3 were obtained from the Cancer Genome Atlas (TCGA), comparing lung adenocarcinoma tissue with normal tissues. To determine the prognostic significance of AGL3, Kaplan-Meier plotter, and Cox regression analysis were employed. Logistic regression was utilized to analyze the association between ALG3 expression and clinical characteristics. Additionally, a receiver operating characteristic (ROC) curve and a nomogram were constructed. To explore the underlying mechanisms, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and gene set enrichment analysis (GSEA) was conducted. The relationship between AGL3A mRNA expression and immune infiltrates was investigated using the tumor immune estimation resource (TIMER) and tumor-immune system interaction database (TISIDB). Furthermore, an in vitro experiment was performed to assess the impact of ALG3 mRNA on lung cancer stemness abilities and examine key signaling pathway proteins. Results Our results revealed the ALG3 mRNA and protein expression in patients with LUAD was much higher than that in adjacent normal tissues. High expression of ALG3 was significantly associated with N stage (N0, HR = 1.98, P = 0.002), pathological stage (stage I, HR = 2.09, P = 0.003), and the number of pack years (<40, HR = 2.58, P = 0.001). Kaplan-Meier survival analysis showed that high expression of ALG3 was associated with poor overall survival (P < 0.001), disease-free survival (P < 0.001), and progression-free interval (P = 0.007). Through multivariate analysis, it was determined that elevated ALG3 expression independently impacted overall survival (HR = 1.325, P = 0.04). The Tumor Immune Estimation Resource discovered a link between ALG3 expression and tumor-infiltrating immune cells in LUAD. Additionally, ROC analysis proved that ALG3 is a reliable diagnostic marker for LUAD (AUC:0.923). Functional pathways analysis identified that ALG3 is negatively correlated with FAT4. We performed qRT-PCR to assess that knockdown ALG3 expression significantly upregulated FAT4 expression. Spheroid assay and flow cytometry analysis results showed that downregulated of ALG3 inhibited H1975 cell line stemness. Western blot analysis revealed that decreased ALG3 inhibited the YAP/TAZ signal pathway. Conclusion High expression of ALG3 is strongly associated with poor prognosis and immune infiltrates in LUAD.
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Affiliation(s)
- Yinjiao Yuan
- The First School of Chinical Medicine, Southern Medical University, Guangzhou, 510510, China
- Department of Oncology, Dongguan Institute of Clinical Cancer Research, Dongguan Key Laboratory of Precision Diagnosis and Treatment for Tumors, The Tenth Affiliated Hospital of Southern Medical University (Dongguan people's hospital), Dongguan, 523059, China
| | - BaoCheng Xie
- Department of Pharmacy, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Dongbo Guo
- State Key Laboratory of Marine Resource Utilization in South China Sea, Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, China
| | - Caixiang Liu
- Department of Oncology, Dongguan Institute of Clinical Cancer Research, Dongguan Key Laboratory of Precision Diagnosis and Treatment for Tumors, The Tenth Affiliated Hospital of Southern Medical University (Dongguan people's hospital), Dongguan, 523059, China
| | - Guanming Jiang
- Department of Oncology, Dongguan Institute of Clinical Cancer Research, Dongguan Key Laboratory of Precision Diagnosis and Treatment for Tumors, The Tenth Affiliated Hospital of Southern Medical University (Dongguan people's hospital), Dongguan, 523059, China
| | - Guowei Lai
- Department of General Surgery, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
- General Hospital of Third Division, Xinjiang Production and Construction Corps, Tumushuker, China
| | - Yu Zhang
- The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiarong Hu
- Department of General Surgery, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Zhiming Wu
- Department of General Surgery, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Ruinian Zheng
- Department of Oncology, Dongguan Institute of Clinical Cancer Research, Dongguan Key Laboratory of Precision Diagnosis and Treatment for Tumors, The Tenth Affiliated Hospital of Southern Medical University (Dongguan people's hospital), Dongguan, 523059, China
| | - Linxuan Huang
- Department of Oncology, Dongguan Institute of Clinical Cancer Research, Dongguan Key Laboratory of Precision Diagnosis and Treatment for Tumors, The Tenth Affiliated Hospital of Southern Medical University (Dongguan people's hospital), Dongguan, 523059, China
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18
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Chen X, Li Z, Liang M, Zhang Z, Zhu D, Lin B, Zhou R, Lu Y. Identification of DDIT4 as a potential prognostic marker associated with chemotherapeutic and immunotherapeutic response in triple-negative breast cancer. World J Surg Oncol 2023; 21:194. [PMID: 37391802 DOI: 10.1186/s12957-023-03078-7] [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: 10/17/2022] [Accepted: 06/14/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is the most heterogenous and aggressive subtype of breast cancer. Chemotherapy remains the standard treatment option for patients with TNBC owing to the unavailability of acceptable targets and biomarkers in clinical practice. Novel biomarkers and targets for patient stratification and treatment of TNBC are urgently needed. It has been reported that the overexpression of DNA damage-inducible transcript 4 gene (DDIT4) is associated with resistance to neoadjuvant chemotherapy and poor prognosis in patients with TNBC. In this study, we aimed to identify novel biomarkers and therapeutic targets using RNA sequencing (RNA-seq) and data mining using data from public databases. METHODS RNA sequencing (RNA-Seq) was performed to detect the different gene expression patterns in the human TNBC cell line HS578T treated with docetaxel or doxorubicin. Sequencing data were further analyzed by the R package "edgeR" and "clusterProfiler" to identify the profile of differentially expressed genes (DEGs) and annotate gene functions. The prognostic and predictive value of DDIT4 expression in patients with TNBC was further validated by published online data resources, including TIMER, UALCAN, Kaplan-Meier plotter, and LinkedOmics, and GeneMANIA and GSCALite were used to investigate the functional networks and hub genes related to DDIT4, respectively. RESULTS Through the integrative analyses of RNA-Seq data and public datasets, we observed the overexpression of DDIT4 in TNBC tissues and found that patients with DDIT4 overexpression showed poor survival outcomes. Notably, immune infiltration analysis showed that the levels of DDIT4 expression correlated negatively with the abundance of tumor-infiltrating immune cells and immune biomarker expression, but correlated positively with immune checkpoint molecules. Furthermore, DDIT4 and its hub genes (ADM, ENO1, PLOD1, and CEBPB) involved in the activation of apoptosis, cell cycle, and EMT pathways. Eventually, we found ADM, ENO1, PLOD1, and CEBPB showed poor overall survival in BC patients. CONCLUSION In this study, we found that DDIT4 expression is associated with the progression, therapeutic efficacy, and immune microenvironment of patients with TNBC, and DDIT4 would be as a potential prognostic biomarker and therapeutic target. These findings will help to identify potential molecular targets and improve therapeutic strategies against TNBC.
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Affiliation(s)
- Xuanzhao Chen
- The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Zeyan Li
- Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Meihua Liang
- The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Ziyang Zhang
- Guangzhou Huayin Medical Laboratory Center, Ltd., Guangzhou, China
| | - Di Zhu
- Department of Clinical Pathology, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Biyun Lin
- The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Renyu Zhou
- School of Medicine, Jinan University, Guangzhou, China
| | - Yuanzhi Lu
- The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.
- Department of Clinical Pathology, First Affiliated Hospital of Jinan University, Guangzhou, China.
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Zeng Y, Du W, Huang Z, Wu S, Ou X, Zhang J, Peng C, Sun X, Tang H. Hsa_circ_0060467 promotes breast cancer liver metastasis by complexing with eIF4A3 and sponging miR-1205. Cell Death Discov 2023; 9:153. [PMID: 37160894 PMCID: PMC10169853 DOI: 10.1038/s41420-023-01448-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/11/2023] Open
Abstract
Breast cancer (BC) is the most common cancer and the top cause of female mortality worldwide. The prognosis for patients with breast cancer liver metastasis (BCLM) remains poor. Emerging studies suggest that circular RNAs (circRNAs) are associated with the progression of BC. Exploration of circRNAs presents a promising avenue for identifying metastasis-targeting agents and improving the prognosis of patients with BCLM. Microarray and bioinformatic analyses were used to analyze differentially expressed circRNAs between three pairs of BCLM and primary BC. The roles of hsa_circ_0060467 (circMYBL2) and its target gene E2F1 in BC cells were explored by multiple functional experiments. And xenograft mouse models and hepatic metastases of BC hemi-spleen models were used to illustrate the function of circMYBL2 in vivo. The intrinsic molecular mechanism involving circMYBL2 was confirmed by bioinformatics analyses, RIP assays, CHIRP assays, luciferase reporter assays, and rescue experiments. CircMYBL2 was overexpressed in BCLM tissues and BC cells. Functionally, circMYBL2 can facilitate the proliferation and liver metastasis of BC. Mechanistically, circMYBL2 upregulated the transcription factor E2F1 by sponging miR-1205 and complexing with eukaryotic translation initiation factor 4A3 (eIF4A3) and then facilitated the epithelial-mesenchymal transition (EMT) process in BC cells. Our findings showed that circMYBL2 promoted the tumorigenesis and aggressiveness of BC through the circMYBL2/miR-1205/E2F1 and circMYBL2/eIF4A3/E2F1 axes, which may provide a novel targeted therapy for patients with BCLM.
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Affiliation(s)
- Yan Zeng
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Wei Du
- Department of Pathology, the First People's Hospital of Changde City, Changde, Hunan, China
| | - Zhongying Huang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Song Wu
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xueqi Ou
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Jinhui Zhang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.
| | - Xiaoqing Sun
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
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20
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Huang J, Zhao Y. E2F Transcription Factor 1 Activates FKBP Prolyl Isomerase 4 to Promote Angiogenesis in Cervical Squamous Cell Carcinoma Via the PI3K/AKT Signaling Pathway. Reprod Sci 2023; 30:1229-1240. [PMID: 35849266 DOI: 10.1007/s43032-022-01034-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/04/2022] [Indexed: 12/24/2022]
Abstract
Angiogenesis, namely the formation of blood vessels, is crucial for tumor growth, metastasis and development. E2F transcription factor 1 (E2F1) has been linked to tumorigenesis in several human cancers. This work examines the role of E2F1 and its downstream targets in angiogenesis in cervical squamous cell carcinoma (CSCC). E2F1 was predicted as a candidate oncogene in CSCC using a GSE63514 dataset. Increased E2F1 expression was detected in CSCC tumor samples and cell lines by RT-qPCR, immunohistochemistry, and western blot assays. E2F1 downregulation reduced the angiogenesis activity of HUVECs and the invasiveness of CSCC cells. In vivo, E2F1 knockdown also reduced the xenograft tumor growth and promoted tumor necrosis in mice. FKBP prolyl isomerase 4 (FKBP4) was identified as a target of E2F1. E2F1 bound to FKBP4 promoter for transcriptional activation. Further upregulation of FKBP4 blocked the tumor-suppressive role of E2F1 silencing. FKBP4 was enriched in the PI3K/AKT signaling. In cells and xenograft tumors, the E2F1/FKBP4 axis promoted PI3K and AKT phosphorylation. Activation of the PI3K/AKT signaling restored the angiogenesis activity in cells blocked by E2F1 silencing. In summary, this work demonstrates that E2F1 promotes FKBP4 transcription to activate the PI3K/AKT pathway, which augments the angiogenesis and invasiveness of CSCC.
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Affiliation(s)
- Jiazhen Huang
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Dalian Medical University, No. 467, Zhongshan Road, Shahekou District, Dalian, 116023, Liaoning, People's Republic of China
| | - Ying Zhao
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Dalian Medical University, No. 467, Zhongshan Road, Shahekou District, Dalian, 116023, Liaoning, People's Republic of China.
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21
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Li Y, Huang Y, Li B, Yang K. Roles of E2F family members in the diagnosis and prognosis of head and neck squamous cell carcinoma. BMC Med Genomics 2023; 16:38. [PMID: 36855110 PMCID: PMC9976507 DOI: 10.1186/s12920-023-01470-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer worldwide. E2Fs are a group of transcription factors involved in the carcinogenesis and progression of various cancers. However, the exact roles of each member of E2F family in the development and progression of HNSCC are still unknown. METHODS RNASeq and clinical follow-up information were extracted from The Cancer Genome Atlas (TCGA). The expressions of E2Fs and their roles in HNSCC progression were explored using the R software and the cBioPortal database. RESULTS Our results showed that the mRNA levels of E2Fs were significantly higher in HNSCC tumors than in normal tissues. E2F1, E2F3, E2F4, E2F6, and E2F7 were identified as reliable diagnostic markers. E2Fs (except for E2F3) expressions were closely related to the clinical features (excluding metastasis) of HNSCC. High E2F6 mRNA expression was an independent risk factor for the OS of female HNSCC patients. In addition, high E2F4 expression could lead to poor prognosis in HNSCC in both males and females, high expressions of E2F5, E2F6, and E2F7 were associated with poor OS of female HNSCC patients, while high E2F2 and E2F8 expressions were positively correlated with the OS of male HNSCC patients. Interestingly, E2Fs expressions had stronger associations with immune cell infiltrations in male HNSCC patients than in female HNSCC patients. CONCLUSION The expressions of E2Fs were found to be correlated with the progression of HNSCC. E2F1, E2F3, E2F4, E2F6, and E2F7 could be good diagnostic molecules for HNSCC. In addition, E2F6 was an independent risk factor for the prognosis of female HNSCC patients.
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Affiliation(s)
- Yaoxu Li
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, 400016, Chongqing, China
| | - Yinpei Huang
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Bing Li
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China.
| | - Kai Yang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, 400016, Chongqing, China.
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22
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Zhang F, Yan Y, Liang Q, Liu Y, Wu G, Xu Z, Yang K. A combined analysis of bulk and single-cell sequencing data reveals metabolic enzyme, pyruvate dehydrogenase E1 subunit beta (PDHB), as a prediction biomarker for the tumor immune response and immunotherapy. Heliyon 2023; 9:e13456. [PMID: 36816316 PMCID: PMC9929299 DOI: 10.1016/j.heliyon.2023.e13456] [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: 10/18/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
Pyruvate dehydrogenase E1 subunit beta (PDHB) is located in mitochondria and catalyzes the conversion of glucose-derived acetyl-CoA. The detailed roles of PDHB in human cancers is unclear. Here, through comprehensive bioinformatics analysis, we found that PDHB was aberrantly expressed in multiple human cancers and is associated with patients' clinical stage. The abnormal expression of PDHB was related to the prognostic values of cancers, such as kidney renal clear cell carcinoma (KIRC) and kidney renal papillary cell carcinoma (KIRP). The Wanderer database with clinical data from Cancer Genome Atlas (TCGA) showed a significant correlation between PDHB expression and the pathologic stage of KIRP patients. We also evaluated the mutation profiles of PDHB in pan-cancer, and showed its roles on the patients' prognosis. At last, from several immunity algorithms, we demonstrated that the expression of PDHB was correlated with the infiltration of various immune cells in pan-cancer. Moreover, the aberrant PDHB had effects on the response to immune checkpoint inhibitors in cancer patients, such as anti-PD-1. Taken together, our study demonstrated the prognostic values of PDHB in pan-cancers. PDHB may be a potential molecular marker to predicting the immune response in cancer patients.
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Affiliation(s)
- Fan Zhang
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China,Department of Physiology, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yuanhong Liu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Geting Wu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China,Corresponding author. Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Keda Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China,Corresponding author. National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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23
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Zhao YX, Xu BW, Wang FQ, Jiang FY, Xu JW, Yu DX. nc-RNA-mediated high expression of CDK6 correlates with poor prognosis and immune infiltration in pancreatic cancer. Cancer Med 2023; 12:5110-5123. [PMID: 36457244 PMCID: PMC9972169 DOI: 10.1002/cam4.5260] [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: 03/30/2022] [Revised: 08/25/2022] [Accepted: 09/08/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Emerging evidence manifests that cyclin-dependent kinase 6 (CDK6) plays an essential part in the initiation and progression of several types of human cancer, and its descending expression is correlated with an adverse prognosis. However, the precise role of CDK6 in Pancreatic cancer (PC) remains obscure. AIMS To identify the potential ceRNA regulatory axis of CDK6 in PC and explore its relationship with immune cells and immune checkpoints. MATERIALS & METHODS Using The Cancer Genome Atlas TCGA and GTEx data analyze the expression and survival of CDK6 in patients in pan-cancer, and cellular experiments were performed to verify the effect of CDK6 on cell function. Using GEPIA and STARBASE databases to analyze prognosis, expression and survival, and identify non coding RNA (ncRNA) that mediates CDK6 overexpression. The TIMER 2.0 database was used for immune correlation analysis. RESULTS We revealed CDK6 might be an oncogene in PC, and the HOXA11-AS /NR2F1-AS1- miR-454-3p axis was identified as the possible upstream ncRNA-associated pathway of CDK6 in PC. In addition, CDK6 show significant association with three immune checkpoints (PD-L1, PD-L2, and HAVCR2), the infiltration level of immune cells, and immunity biomarkers. DISCUSSION We discussed some applications of CDK6 in breast cancer, melanoma, and hemorrhagic malignancies. The role of miR-15a-5p, HOXA11-AS and NR2F1-AS1 in tumor development was also discussed based on existing studies. The potential mechanism of CDK6 affecting immune cells in pancreatic cancer was discussed. CONCLUSIONS Overall, these results established that nc-RNA-mediated high expression of CDK6 is associated with patient outcomes and immune invasion in pancreatic cancer.
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Affiliation(s)
- Yu-Xuan Zhao
- Department of Radiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bo-Wen Xu
- Department of Hepatobiliary Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fang-Qing Wang
- Department of Radiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Feng-Yang Jiang
- Department of Radiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jian-Wei Xu
- Department of Pancreatic Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - De-Xin Yu
- Department of Radiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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24
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Dai L, Guo X, Xing Z, Tao Y, Liang W, Shi Z, Hu W, Zhou S, Wang X. Multi-omics analyses of CD276 in pan-cancer reveals its clinical prognostic value in glioblastoma and other major cancer types. BMC Cancer 2023; 23:102. [PMID: 36717836 PMCID: PMC9885708 DOI: 10.1186/s12885-023-10575-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND CD276 (also known as B7-H3) is one of the most important immune checkpoints of the CD28 and B7 superfamily, and its abnormal expression is closely associated with various types of cancer. It has been shown that CD276 is able to inhibit the function of T cells, and that this gene may potentially be a promising immunotherapy target for different types of cancer. METHODS Since few systematic studies have been published on the role of CD276 in cancer to date, the present study has employed single-cell sequencing and bioinformatics methods to analyze the expression patterns, clinical significance, prognostic value, epigenetic alterations, DNA methylation level, tumor immune cell infiltration and immune functions of CD276 in different types of cancer. In order to analyze the potential underlying mechanism of CD276 in glioblastoma (GBM) to assess its prognostic value, the LinkedOmics database was used to explore the biological function and co-expression pattern of CD276 in GBM, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. In addition, a simple validation of the above analyses was performed using reverse transcription-quantitative (RT-q)PCR assay. RESULTS The results revealed that CD276 was highly expressed, and was often associated with poorer survival and prognosis, in the majority of different types of cancer. In addition, CD276 expression was found to be closely associated with T cell infiltration, immune checkpoint genes and immunoregulatory interactions between lymphoid and a non-lymphoid cell. It was also shown that the CD276 expression network exerts a wide influence on the immune activation of GBM. The expression of CD276 was found to be positively correlated with neutrophil-mediated immunity, although it was negatively correlated with the level of neurotransmitters, neurotransmitter transport and the regulation of neuropeptide signaling pathways in GBM. It is noteworthy that CD276 expression was found to be significantly higher in GBM compared with normal controls according to the RT-qPCR analysis, and the co-expression network, biological function and chemotherapeutic drug sensitivity of CD276 in GBM were further explored. In conclusion, the findings of the present study have revealed that CD276 is strongly expressed and associated with poor prognosis in most types of cancer, including GBM, and its expression is strongly associated with T-cell infiltration, immune checkpoint genes, and immunomodulatory interactions between lymphocytes and non-lymphoid cells. CONCLUSIONS Taken together, based on our systematic analysis, our findings have revealed important roles for CD276 in different types of cancers, especially GBM, and CD276 may potentially serve as a biomarker for cancer.
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Affiliation(s)
- Lirui Dai
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Xuyang Guo
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Zhe Xing
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Yiran Tao
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Wulong Liang
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Zimin Shi
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Weihua Hu
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Shaolong Zhou
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Xinjun Wang
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
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Dutta D, Sen A, Satagopan J. Sparse canonical correlation to identify breast cancer related genes regulated by copy number aberrations. PLoS One 2022; 17:e0276886. [PMID: 36584096 PMCID: PMC9803132 DOI: 10.1371/journal.pone.0276886] [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: 06/16/2022] [Accepted: 10/16/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Copy number aberrations (CNAs) in cancer affect disease outcomes by regulating molecular phenotypes, such as gene expressions, that drive important biological processes. To gain comprehensive insights into molecular biomarkers for cancer, it is critical to identify key groups of CNAs, the associated gene modules, regulatory modules, and their downstream effect on outcomes. METHODS In this paper, we demonstrate an innovative use of sparse canonical correlation analysis (sCCA) to effectively identify the ensemble of CNAs, and gene modules in the context of binary and censored disease endpoints. Our approach detects potentially orthogonal gene expression modules which are highly correlated with sets of CNA and then identifies the genes within these modules that are associated with the outcome. RESULTS Analyzing clinical and genomic data on 1,904 breast cancer patients from the METABRIC study, we found 14 gene modules to be regulated by groups of proximally located CNA sites. We validated this finding using an independent set of 1,077 breast invasive carcinoma samples from The Cancer Genome Atlas (TCGA). Our analysis of 7 clinical endpoints identified several novel and interpretable regulatory associations, highlighting the role of CNAs in key biological pathways and processes for breast cancer. Genes significantly associated with the outcomes were enriched for early estrogen response pathway, DNA repair pathways as well as targets of transcription factors such as E2F4, MYC, and ETS1 that have recognized roles in tumor characteristics and survival. Subsequent meta-analysis across the endpoints further identified several genes through the aggregation of weaker associations. CONCLUSIONS Our findings suggest that sCCA analysis can aggregate weaker associations to identify interpretable and important genes, modules, and clinically consequential pathways.
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Affiliation(s)
- Diptavo Dutta
- Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, United States of America
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail: ,
| | - Ananda Sen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, United States of America
- Department of Family Medicine, University of Michigan, Ann Arbor, MI, United States of America
| | - Jaya Satagopan
- Department of Biostatistics and Epidemiology, Rutgers University, New Brunswick, NJ, United States of America
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RBCK1 regulates the progression of ER-positive breast cancer through the HIF1α signaling. Cell Death Dis 2022; 13:1023. [PMID: 36473847 PMCID: PMC9726878 DOI: 10.1038/s41419-022-05473-6] [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: 09/01/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
Breast cancer is the most common malignancy in women on a global scale. It can generally be divided into four main categories, of which estrogen receptor ER-positive breast cancer accounts for most breast cancer cases. RBCK1 protein is an E3 ubiquitin ligase containing the UBL, NZF, and RBR domains. It is well known to exhibit abnormal expression in breast tumors, making it a valuable diagnostic marker and drug target. Additionally, studies have confirmed that in breast cancer, about 25 to 40% of tumors appear as visible hypoxic regions, while in hypoxia, tumor cells can activate the hypoxia-inducing factor HIF1 pathway and widely activate the expression of downstream genes. Previous studies have confirmed that in the hypoxic environment of tumors, HIF1α promotes the remodeling of extracellular matrix, induces the recruitment of tumor-associated macrophages (TAM) and immunosuppression of allogeneic tumors, thereby influencing tumor recurrence and metastasis. This research aims to identify RBCK1 as an important regulator of HIF1α signaling pathway. Targeted therapy with RBCK1 could be a promising treatment strategy for ER-positive breast cancer.
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Liu TT, Yang H, Zhuo FF, Yang Z, Zhao MM, Guo Q, Liu Y, Liu D, Zeng KW, Tu PF. Atypical E3 ligase ZFP91 promotes small-molecule-induced E2F2 transcription factor degradation for cancer therapy. EBioMedicine 2022; 86:104353. [PMID: 36375317 PMCID: PMC9667253 DOI: 10.1016/j.ebiom.2022.104353] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The E2F family of transcription factors play a crucial role in the development of various cancers. However, E2F members lack targetable binding pockets and are typically considered "undruggable". Unlike canonical small-molecule therapeutics, molecular glues mediate new E3 ligase-protein interactions to induce selective proteasomal degradation, which represents an attractive option to overcome these limitations. METHODS Human proteome microarray was utilized to identify a natural product-derived molecular glue for targeting E2F2 degradation. Co-IP analysis with stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative proteomics was carried out to further explore the E3 ligase for E2F2 degradation. FINDINGS In this study, we identified a molecular glue bufalin, which significantly promoted E2F2 degradation. Unexpectedly, E2F2 underwent ubiquitination and proteasomal degradation via a previously undisclosed atypical E3 ligase, zinc finger protein 91 (ZFP91). In particular, we observed that bufalin markedly promoted E2F2-ZFP91 complex formation, thereby leading to E2F2 polyubiquitination via K48-linked ubiquitin chains for degradation. E2F2 degradation subsequently caused transcriptional suppression of multiple oncogenes including c-Myc, CCNE1, CCNE2, MCM5 and CDK1, and inhibited hepatocellular carcinoma growth in vitro and in vivo. INTERPRETATION Collectively, our findings open up a new direction for transcription factors degradation by targeting atypical E3 ligase ZFP91. Meanwhile, the chemical knockdown strategy with molecular glue may promote innovative transcription factor degrader development in cancer therapy. FUNDING This work was financially supported by the National Key Research and Development Project of China (2022YFC3501601), National Natural Sciences Foundation of China (81973505, 82174008, 82030114), and China Postdoctoral Science Foundation (2019M650396), the Fundamental Research Funds for the Central Universities.
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Affiliation(s)
- Ting-Ting Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Heng Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Fang-Fang Zhuo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhuo Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Mei-Mei Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qiang Guo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yang Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Dan Liu
- Proteomics Laboratory, Medical and Healthy Analytical Center, Peking University Health Science Center, Beijing 100191, China
| | - Ke-Wu Zeng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China,Corresponding author.
| | - Peng-Fei Tu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China,Corresponding author.
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EL-Naidany SS, Eltorgman AE, Elmadbouh I, Naguib AM, Assar MFA. Association of circadian BMAL1 gene expression and its polymorphism and risk of breast cancer in females. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Ku SC, Liu HL, Su CY, Yeh IJ, Yen MC, Anuraga G, Ta HDK, Chiao CC, Xuan DTM, Prayugo FB, Wang WJ, Wang CY. Comprehensive analysis of prognostic significance of cadherin (CDH) gene family in breast cancer. Aging (Albany NY) 2022; 14:8498-8567. [PMID: 36315446 PMCID: PMC9648792 DOI: 10.18632/aging.204357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
Breast cancer is one of the leading deaths in all kinds of malignancies; therefore, it is important for early detection. At the primary tumor site, tumor cells could take on mesenchymal properties, termed the epithelial-to-mesenchymal transition (EMT). This process is partly regulated by members of the cadherin (CDH) family of genes, and it is an essential step in the formation of metastases. There has been a lot of study of the roles of some of the CDH family genes in cancer; however, a holistic approach examining the roles of distinct CDH family genes in the development of breast cancer remains largely unexplored. In the present study, we used a bioinformatics approach to examine expression profiles of CDH family genes using the Oncomine, Gene Expression Profiling Interactive Analysis 2 (GEPIA2), cBioPortal, MetaCore, and Tumor IMmune Estimation Resource (TIMER) platforms. We revealed that CDH1/2/4/11/12/13 messenger (m)RNA levels are overexpressed in breast cancer cells compared to normal cells and were correlated with poor prognoses in breast cancer patients’ distant metastasis-free survival. An enrichment analysis showed that high expressions of CDH1/2/4/11/12/13 were significantly correlated with cell adhesion, the extracellular matrix remodeling process, the EMT, WNT/beta-catenin, and interleukin-mediated immune responses. Collectively, CDH1/2/4/11/12/13 are thought to be potential biomarkers for breast cancer progression and metastasis.
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Affiliation(s)
- Su-Chi Ku
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Department of General Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Hsin-Liang Liu
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Che-Yu Su
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - I-Jeng Yeh
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Meng-Chi Yen
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Gangga Anuraga
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia
| | - Hoang Dang Khoa Ta
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Chung-Chieh Chiao
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Fidelia Berenice Prayugo
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- International Master/PhD Program in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Wei-Jan Wang
- Department of Biological Science and Technology, Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 40676, Taiwan
| | - Chih-Yang Wang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
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Molecular Analysis of Prognosis and Immune Infiltration of Ovarian Cancer Based on Homeobox D Genes. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:3268386. [PMID: 36213580 PMCID: PMC9537619 DOI: 10.1155/2022/3268386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 12/24/2022]
Abstract
Background Homeobox D (HOXD) genes were associated with cancer pathogenesis. However, the role of HOXD genes in ovarian cancer (OC) and the possible mechanisms involved are unclear. In this study, we analyzed the function and regulatory mechanisms and functions of HOXD genes in OC based on comprehensive bioinformatics analysis. Methods Expression of HOXD1/3/4/8/9/10/11/12/13 mRNA was analyzed between OC tissue and normal tissue using ONCOMINE, GEO, and TCGA databases. The relationship between HOXD expression and clinical stage was studied by GEPIA. The Kaplan-Meier plotter was used to analyze prognosis. cBioPortal was used to analyze the mutation and coexpression of HOXDs. GO and KEGG analyses were performed by the DAVID software to predict the function of HOXD coexpression genes. Immune infiltration analysis was used to evaluate the relationship between the expression of HOXD genes and 24 immune infiltrating cells. Results The expression of HOXD3/4/8/9/10/11 was significantly lower in OC tissues than in normal ovarian tissues, while the expression of HOXD1/12/13 was significantly higher in OC tissues. The expression of HOXD genes was associated with FIGO stage, primary therapy outcome, tumor status, anatomic neoplasm subdivision, and age. The expression levels of HOXD1/3/4/8/9/10 correlated with tumor stage. HOXD1/8/9 could be served as ideal biomarkers to distinguish OC from normal tissue. Low HOXD9 expression was associated with shorter overall survival (OS) (HR: 0.75; 95% CI: 0.58–0.98; P = 0.034) and progression-free survival (PFS) (HR: 0.69; 95% CI: 0.54–0.87; P = 0.002). The HOXD coexpression genes were associated with pathways including cell cycle, TGF-beta signaling pathway, cellular senescence, and Hippo signaling pathway. HOXD genes were significantly associated with immune infiltration. Conclusion The expression of HOXD genes is associated with clinical characteristics. HOXD9 is a new biomarker of prognosis in OC, and HOXD1/4/8/9/10 may be potential therapeutic targets. The members of the HOXD genes may be the response to immunotherapy for OC.
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Mao W, Wang S, Chen R, He Y, Lu R, Zheng M. lncRNA NORAD promotes lung cancer progression by competitively binding to miR-28-3p with E2F2. Open Med (Wars) 2022; 17:1538-1549. [PMID: 36245705 PMCID: PMC9520332 DOI: 10.1515/med-2022-0538] [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: 04/24/2022] [Revised: 07/06/2022] [Accepted: 07/18/2022] [Indexed: 01/21/2023] Open
Abstract
Lung cancer (LC) is a prevailing primary tumor in the lung. lncRNA non-coding RNA activated by DNA damage (NORAD) is a popular target in human cancers. This experiment is designed to probe the mechanism of lncRNA in LC progression. NORAD expression in normal lung epithelial cells and LC cells was examined and then silenced to assess its effect on LC cell proliferation, invasion, and migration. Subcellular localization of NORAD was analyzed through online databases and then corroborated by fractionation of nuclear and cytoplasmic RNA assay. The target binding relations between NORAD and miR-28-3p and between miR-28-3p and E2F2 were verified. Eventually, LC cells with NORAD silencing were transfected with miR-28-3p inhibitor or pcDNA3.1-E2F2 to measure LC cell proliferation, invasion, and migration. NORAD was overexpressed in LC cells and NORAD knockout led to suppressed LC cell proliferation, invasion, and migration. Besides, NORAD targeted miR-28-3p and miR-28-3p targeted E2F2 transcription. Inhibiting miR-28-3p or overexpressing E2F2 could both annul the inhibitory role of si-NORAD in LC cell proliferation, invasion, and migration. Generally, our findings demonstrated that NORAD competitively bound to miR-28-3p with E2F2, to promote LC cell progression.
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Affiliation(s)
- Wenjun Mao
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Shengfei Wang
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Ruo Chen
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Yijun He
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Rongguo Lu
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Mingfeng Zheng
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, No. 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
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Wang F, Wang X, Liu L, Deng S, Ji W, Liu Y, Wang X, Wang R, Zhao X, Gao E. Comprehensive analysis of PTPN gene family revealing PTPN7 as a novel biomarker for immuno-hot tumors in breast cancer. Front Genet 2022; 13:981603. [PMID: 36226189 PMCID: PMC9548886 DOI: 10.3389/fgene.2022.981603] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/26/2022] [Indexed: 11/23/2022] Open
Abstract
Background: The non-receptor protein tyrosine phosphatase (PTPN) gene family has been considered to be involved in the oncogenesis and development of multiple cancers. However, its prognostic utility and immunological relevance in breast cancer (BrCa) have not been clarified. Methods: A transcriptional level interpretation of the expressions and prognostic values was analyzed using the data from The Cancer Genome Atlas (TCGA) cohort. In addition, GO and DAVID pinpoint the functional enrichment of PTPNs. Moreover, the immune correlations of PTPN7 in BrCa and pan-cancer were further investigated based on the TCGA cohort and were testified using the in-house and the Gene Expression Omnibus (GEO) cohorts. Results: For systematic analysis of the PTPN family, we found that the expression levels of PTPN1, PTPN6, PTPN7, PTPN18, PTPN20, and PTPN22 was promoted in tumor tissues while comparing with paraneoplastic tissues during our study. We further investigated their functions and protein-protein interactions (PPI), and these results strongly suggested that PTPN family was associated with protein dephosphorylation. Next, we performed an immunological relevance analysis and found that PTPN7 was correlated with immune infiltration, suggesting a stronger association of PTPN7 with immuno-hot tumors in BrCa. In addition, results from the in-house cohort confirmed the positive correlation between PTPN7 and PD-L1. The pan-cancer analysis revealed that PTPN7 was related to PD-L1 and CTLA-4 expression in almost all cancer types. Finally, the predictive value of PTPN7 for immunotherapy was significant in two independent GEO cohorts. Conclusion: In conclusion, this is the first extensive research on the correlation between PTPN family expression and immune characterization in BrCa. As results, PTPN7 expression is associated with immuno-hot tumors and could be a promising predictive biomarker for immunotherapy in not only BrCa but multiple cancers.
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Affiliation(s)
- Fengxu Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Xuehai Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Lei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Siyuan Deng
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Wenqian Ji
- College of International Studies, Southwest University, Chongqing, China
| | - Yang Liu
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Xiangdong Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Rui Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Xinyuan Zhao
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
- *Correspondence: Xinyuan Zhao, ; Erli Gao,
| | - Erli Gao
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Xinyuan Zhao, ; Erli Gao,
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Systems Network Pharmacology-Based Prediction and Analysis of Potential Targets and Pharmacological Mechanism of Actinidia chinensis Planch. Root Extract for Application in Hepatocellular Carcinoma. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:2116006. [PMID: 36193154 PMCID: PMC9526650 DOI: 10.1155/2022/2116006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 06/07/2022] [Accepted: 07/27/2022] [Indexed: 12/02/2022]
Abstract
Purpose Traditional Chinese medicine (TCM) sometimes plays a crucial role in advanced cancer treatment. Despite the significant therapeutic efficacy in hepatocellular carcinoma (HCC) that Actinidia chinensis Planch root extract (acRoots) has proven, its complex composition and underlying mechanism have not been fully elucidated. Therefore, this study analyzed the multiple chemical compounds in acRoots and their targets via network pharmacology and bioinformatics analysis, with the overarching goal of revealing the potential mechanisms of the anti-HCC effect. Methods The main ingredients contained in acRoots were initially screened from the traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), and the candidate bioactive ingredient targets were identified using DrugBank and the UniProt public databases. Second, the biological processes of the targets of active molecules filtered from the ingredients of acRoots were evaluated using gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Third, weighted gene coexpression network analysis (WGCNA) was performed to identify gene coexpression modules associated with HCC. The hub genes of acRoots in HCC were defined via contrasting the above module eigengenes with candidate target genes of acRoots. Furthermore, the target-pathway network was analyzed to explore the mechanism for anti-HCC effect of hub genes. Kaplan–Meier plotter database analysis was performed to validate the hub genes of acRoots correlation with prognostic values in HCC. In order to verify the results of the network pharmacological analysis, we performed a molecular docking approach on the active ingredients and key targets using the Discovery Studio software. The viability of SMMC-7721 and HL-7702 cells was determined by Cell counting kit-8 (CCK-8) after being treated with different concentrations of (+)-catechin (0, 50, 100, 150, 200, and 250 g/ml) for 24, 48, and 72 hours, respectively. Finally, qRT-PCR and Western blot involving human hepatocarcinoma cells were utilized to verify the impact of (+)-catechin on the hub genes associated with prognosis. Results 6 out of 26 active ingredients extracted from TCMSP were deemed as the core ingredients of acRoots. 175 bioactive-ingredient targets of acRoots were obtained and a bioactive-ingredient targets network was established correspondingly. The biological processes (BP) of target genes mainly involved processes, such as toxic substance and wounding. The results of KEGG pathways indicated that the target genes were mainly enriched in pathways in cancer, AGE-RAGE signaling pathway in diabetic complications, IL-17 signaling pathway, and other pathways. Also, the two hub genes (i.e., ESR1 and CAT) were closely associated with the prognosis of HCC patients. As a consequence, we predicated a series of signaling pathways, including estrogen signaling pathway and longevity regulation pathway, through which acRoots could facilitate the treatment for HCC. The molecular docking experiment ascertained that ESR1 and CAT had an effective binding force with (+)-catechin, one of the core ingredients of acRoots. Furthermore, (+)-catechin inhibited SMMC-7721 cell growth in a dose-dependent manner and a time-dependent manner. Finally, we suggest that the expression level of ESR1 and CAT is positively related to the (+)-catechin concentrations in in-vitro experiments. Conclusion The bioactive ingredients of acRoots, including quercetin, (+)-catechin, beta-sitosterol, and aloe-emodin, have synergistic interactions in reinforcing the anticancer effect in HCC. Evidently, acRoots took effect by regulating multitargets and multipathways through its active ingredients. Further, (+)-catechin, the possible paramount anti-HCC active ingredient in acRoots, helped improve the prognosis of HCC patients by increasing the expression of ESR1 and CAT. Additionally, the findings yielded provide a conceptual guidance for the clinical treatment of HCC and the methods adopted are potentially applicable in the future comprehensive analysis of the underlying mechanisms of TCMs.
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Hu T, Wang X, Xia Y, Wu L, Ma Y, Zhou R, Zhao Y. Comprehensive analysis identifies as a critical prognostic prediction gene in breast cancer. Chin Med J (Engl) 2022; 135:2218-2231. [PMID: 36113844 PMCID: PMC9771277 DOI: 10.1097/cm9.0000000000002025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Aurora kinases (AURKs) family plays a vital role not only in cell division but also in tumorigenesis. However, there are still rare systematic analyses of the diverse expression patterns and prognostic value of the AURKs family in breast cancer (BC). Systematic bioinformatics analysis was conducted to explore the biological role, prognostic value, and immunologic function of AURKs family in BC. METHODS The expression, prognostic value, and clinical functions of AURKs family in BC were evaluated with several bioinformatics web portals: ONCOMINE Gene Expression Profiling Interactive Analysis, Kaplan-Meier plotter, cBioPortal, Metascape, GeneMANIA, and LinkedOmics; and the result was verified using human tissues. RESULTS The expression of AURKA and AURKB were upregulated in BC in subgroup analyses based on tumor stage (all P < 0.05). BC patients with high AURKA and AURKB expression had a worse overall survival, relapse-free survival, and distant metastasis-free survival (all P < 0.05). Verification experiment revealed that AURKA and AURKB were upregulated in BC ( P < 0.05). AURKA and AURKB were specifically associated with several tumor-associated kinases (polo-like kinase 1 and cyclin-dependent kinase 1), miRNAs (miR-507 and miR-381), and E2F transcription factor 1. Moreover, AURKA and AURKB were correlated with immune cell infiltration. Functional enrichment analysis revealed that AURKA and AURKB were involved in the cell cycle signaling pathway, platinum drug resistance signaling pathway, ErbB signaling pathway, Hippo signaling pathway, and nucleotide-binding and oligomerization domain-like receptor signaling pathway. CONCLUSIONS Aurora kinases AURKA and AURKB could be employed as novel prognostic biomarkers or promising therapeutic targets for BC.
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Affiliation(s)
- Ting Hu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Xu Wang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Yun Xia
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Lu Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Yuxi Ma
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Rui Zhou
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Yanxia Zhao
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
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Overexpression of CDCP1 is Associated with Poor Prognosis and Enhanced Immune Checkpoints Expressions in Breast Cancer. JOURNAL OF ONCOLOGY 2022; 2022:1469354. [PMID: 36090897 PMCID: PMC9452972 DOI: 10.1155/2022/1469354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022]
Abstract
CUB-domain containing protein 1 (CDCP1) is a transmembrane protein acting as an effector of SRC family kinases, which play an oncogenic role in multiple human cancers. However, its clinical and immune correlations in breast cancer (BrCa) have not been explored. To define the expression, prognostic value, and potential molecular role of CDCP1 in BrCa, multiple public datasets, and an in-house cohort were used. Compared with paratumor tissue, CDCP1 was remarkably upregulated in the tumor tissues at both mRNA and protein levels. In the in-house cohort, CDCP1 protein expression was related to several clinicopathological parameters, including age, ER status, PR status, molecular type, and survival status. Kaplan–Meier analysis and Cox regression analysis exhibited that CDCP1 was an important prognostic biomarker in BrCa. In addition, enrichment analysis uncovered that CDCP1 was not only involved in multiple oncogenic pathways, but correlated with overexpression of immune checkpoints. Overall, we reported that increased expression of CDCP1 is a favorable prognostic factor in patients with BrCa. In addition, the correlations between CDCP1 and immune checkpoints provide a novel insight into the adjuvant treatment for immune checkpoint blockade via targeting CDCP1.
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Fu J, Sun H, Xu F, Chen R, Wang X, Ding Q, Xia T. RUNX regulated immune-associated genes predicts prognosis in breast cancer. Front Genet 2022; 13:960489. [PMID: 36092942 PMCID: PMC9459239 DOI: 10.3389/fgene.2022.960489] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/25/2022] [Indexed: 12/03/2022] Open
Abstract
Background: Breast cancer is the most common malignant tumor in women. RUNX family has been involved in the regulation of different carcinogenic processes and signaling pathways with cancer, which is closely related to immunity and prognosis of various tumors, and also plays an important role in the development and prognosis of breast cancer. Methods: We discovered the expression of RUNX family through GEPIA Dataset and then evaluated the relationship between RUNX family and immune-related genes and the prognosis of breast cancer through analyzing TCGA database. A prognostic model was established and verified via cox proportional hazards regression model using R packages. We evaluated the accuracy of the prognostic model by Kaplan-Meier curves and receiver operating characteristic (ROC) curves. Additionally, we obtained the relationship between the RUNX family and immune infiltration by TIMER database. Finally, the dual luciferase reporter assay was used to verify the regulation of RUNX3 on potential target genes ULBP2 and TRDV1, and the effects of ULBP2 and TRDV1 on the growth of breast cancer cells were explored by CCK-8, colony formation and wound healing assays. Results: We screened out RUNX family-regulated immune-related genes associated with the prognosis of breast cancer. These predictors included PSME2, ULBP2, IL-18, TSLP, NPR3, TRDV1. Then a prognosis-related risk score model was built using the independent risk factors to provide a clinically appropriate method predicting the overall survival (OS) probability of the patients with breast cancer. In addition, a further research was made on the functions of high risk immune gene ULBP2 and low risk immune gene TRDV1 which regulated by RUNX3, the results showed that down-regulation of ULBP2 suppressed breast cancer cell proliferation and TRDV1 had the opposite functions. The prognostic model we constructed could promote the development of prognostic, and was associated with lower immune infiltration. Conclusion: The expression of RUNX family was closely related to the prognosis of breast cancer. At the same time, RUNX family could modulate the functions of immune-related genes, and affect the development and prognosis of breast cancer. These immune-related genes regulated by RUNX family could be promising prognostic biomarkers and therapeutic targets in breast cancer.
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Affiliation(s)
| | | | | | | | | | - Qiang Ding
- *Correspondence: Tiansong Xia, ; Qiang Ding,
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Zhou C, Chen Z, Xiao B, Xiang C, Li A, Zhao Z, Li H. Comprehensive analysis of GINS subunits prognostic value and ceRNA network in sarcoma. Front Cell Dev Biol 2022; 10:951363. [PMID: 36092720 PMCID: PMC9462653 DOI: 10.3389/fcell.2022.951363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The GINS complex, composed of GINS1/2/3/4 subunits, is an essential structure of Cdc45-MCM-GINS (CMG) helicase and plays a vital role in establishing the DNA replication fork and chromosome replication. Meanwhile, GINS genes have been associated with the poor prognosis of various malignancies. However, the abnormal expression of GINS genes and their diagnostic and prognostic value in sarcomas (SARC) remain unclear. Methods: Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier Plotter, Cancer cell line encyclopedia (CCLE), The University of Alabama at Birmingham Cancer Data Analysis Portal (UALCAN), R studio, and Tumor Immune Estimation Resource (TIMER) were used to analyze the expression profiles, prognostic value, biological function, ceRNA, and immune infiltration associated with GINS genes in sarcomas. Results: We found that GINS1/2/3/4 genes exhibited significantly upregulated transcription levels in SARC samples compared to non-tumor tissues and exhibited high expression levels in sarcoma cell lines. In addition, SARC patients with increased expression levels of GINS1/2/3/4 showed poorer survival rates. Immune infiltration analysis showed that GINS subunits were closely associated with the infiltration of immune cells in sarcomas. Conclusion: Our research identified GINS subunits as potential diagnostic and prognostic biological targets in SARC and elucidated their underlying effects in the genesis and progression of SARC. These results may provide new opportunities and research directions for targeted sarcoma therapy.
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Affiliation(s)
- Chuqiao Zhou
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
| | - Zhuoyuan Chen
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
| | - Bo Xiao
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
| | - Cheng Xiang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
| | - Aoyu Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
| | - Ziyue Zhao
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
| | - Hui Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
- *Correspondence: Hui Li,
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Liu ZG, Su J, Liu H, Yang XJ, Yang X, Wei Y, Zhu XY, Song Y, Zhao XC, Guo HL. Comprehensive bioinformatics analysis of the E2F family in human clear cell renal cell carcinoma. Oncol Lett 2022; 24:351. [PMID: 36168311 PMCID: PMC9478613 DOI: 10.3892/ol.2022.13471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 06/21/2022] [Indexed: 12/03/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) originates from renal tubular epithelial cells and is the most common pathological renal cell carcinoma type with the worst prognosis. The relationship between the expression, prognosis and mechanism of ccRCC and the E2F family remains challenging. In the present study, RNA sequencing and clinical data of ccRCC from The Cancer Genome Atlas and two datasets, GSE36895 and GSE53757, from the Gene Expression Omnibus were used to identify the role of the E2F family in ccRCC. A total of 10 groups of tumor tissues and paired-normal tissues from patients with ccRCC were verified by reverse transcription-quantitative PCR. the expression, tumor grade and stage, prognosis and regulatory mechanism of the E2F family in ccRCC were analyzed. It was found that the expression levels of E2F1 to 4 and 6 to 8 were higher in ccRCC tissues than in normal tissues, whereas the expression level of E2F5 was lower in the former than in the latter. The expression levels of E2F1 to 8 were correlated with tumor stage and grade. Low expression of E2F1 to 5 and 7 to 8 was significantly associated with longer overall survival, disease-specific survival and progression-free survival times. The data revealed that the E2F family rarely has genetic mutations. The expression of E2F1, E2F2, E2F5, E2F7 and E2F8 was significantly correlated with DNA methylation, and E2F1 to E2F7 were significantly correlated with copy number and the data showed that the expression of E2Fs was significantly correlated with the cell cycle. The results of the present study suggested that E2F family genes may be potential targets for ccRCC molecular diagnosis and targeted therapy.
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Affiliation(s)
- Zhi-Guo Liu
- Department of Hospital Pharmacy, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, Jiangsu 223800, P.R. China
| | - Jing Su
- Department of Hematology, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, Jiangsu 223800, P.R. China
| | - Hao Liu
- Department of Urinary Surgery, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, Jiangsu 223800, P.R. China
| | - Xue-Jian Yang
- Department of Urinary Surgery, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, Jiangsu 223800, P.R. China
| | - Xue Yang
- Department of Cardiology, The Affiliated Suqian First People's Hospital of Nanjing Medical University, Suqian, Jiangsu 223800, P.R. China
| | - Ye Wei
- First Clinical Medical College, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Xin-Yao Zhu
- First Clinical Medical College, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Yong Song
- Institute of Preventive Medicine Information, Inspection and Protection, Hubei Provincial Center for Disease Control and Prevention, Wuhan, Hubei 430070, P.R. China
| | - Xian-Cheng Zhao
- Department of Urinary Surgery, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, Jiangsu 223800, P.R. China
| | - Hong-Lin Guo
- School of Public Administration, South Central University for Nationalities, Wuhan, Hubei 430074, P.R. China
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You Q, Wang J, Yu Y, Li F, Meng L, Chen M, Yang Q, Xu Z, Sun J, Zhuo W, Chen Z. The histone deacetylase SIRT6 promotes glycolysis through the HIF-1α/HK2 signaling axis and induces erlotinib resistance in non-small cell lung cancer. Apoptosis 2022; 27:883-898. [PMID: 35915188 PMCID: PMC9617843 DOI: 10.1007/s10495-022-01751-y] [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] [Accepted: 07/01/2022] [Indexed: 12/01/2022]
Abstract
Erlotinib is a first-generation epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI). Overcoming erlotinib resistance is crucial to improve the survival of advanced non-small cell lung cancer (NSCLC) patients with sensitive EGFR mutations. It is also an important clinical problem that urgently needs a solution. In this study, we explored strategies to overcome erlotinib resistance from the perspective of energy metabolism. SIRT6 is a histone deacetylase. Here, we found that high expression of SIRT6 is associated with poor prognosis of lung adenocarcinoma, especially in EGFR-mutated NSCLC patients. The next cell experiment found that SIRT6 expression increased in erlotinib-resistant cells, and SIRT6 expression was negatively correlated with the sensitivity of NSCLC to erlotinib. Inhibition of SIRT6 promoted erlotinib-induced apoptosis in erlotinib-resistant cells, and glycolysis in drug-resistant cells was also inhibited. Functional studies have shown that SIRT6 increases glycolysis through the HIF-1α/HK2 signaling axis in drug-resistant cells and inhibits the sensitivity of NSCLC cells to erlotinib. In addition, the HIF-1α blocker PX478-2HCL attenuated the glycolysis and erlotinib resistance induced by SIRT6. More importantly, we confirmed the antitumor effect of SIRT6 inhibition combined with erlotinib in NSCLC-bearing mice. Our findings indicate that the cancer metabolic pathway regulated by SIRT6 may be a new target for attenuating NSCLC erlotinib resistance and has potential as a biomarker or therapeutic target to improve outcomes in NSCLC patients.
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Affiliation(s)
- Qiai You
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Jianmin Wang
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Yongxin Yu
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Feng Li
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Lingxin Meng
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Mingjing Chen
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Qiao Yang
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Zihan Xu
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Jianguo Sun
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Wenlei Zhuo
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.
| | - Zhengtang Chen
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.
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E2F4 transcription factor is a prognostic biomarker related to immune infiltration of head and neck squamous cell carcinoma. Sci Rep 2022; 12:12132. [PMID: 35840663 PMCID: PMC9287548 DOI: 10.1038/s41598-022-16541-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
To investigate the relationship between the transcription factor, E2F4, and head and neck squamous cell carcinoma (HNSCC), and to preliminarily explore the signaling pathways and immunological role of E2F4. The mRNA expression of E2F4 in HNSCC was evaluated by searching Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets. E2F4 protein expression was analyzed by immunohistochemistry using the CMU1h-ENT database. The association between E2F4 expression and tumor infiltration of immune cells was analyzed. Intracellular signaling by E2F4 was explored using KEGG and GO analysis. The correlation of E2F4 expression with clinical characteristics and its prognostic role were validated and analyzed in TCGA database. From the analysis of GEO and TCGA data, E2F4 expression was found to be up-regulated in HNSCC tumor tissues, and its level was associated with T, Grade, and M staging. Kaplan–Meier curve and Cox analyses indicated that the high expression of E2F4 was related to a poor prognosis. Thus, E2F4 was considered a potential prognostic factor for HNSCC. Immunohistochemical staining showed that E2F4 was mainly localized in the cell nucleus; it was highly expressed in HNSCC tissues, with a significant difference noted from that in pericancerous mucosa tissues. A correlation was observed between the differential expression of E2F4 and the immune infiltration of HNSCC. As revealed by KEGG and GO analysis, differential enrichment was found in the cell cycle, spliceosome, meiosis, microbial polysaccharide synthesis, and WNT signaling pathway, as well as in cyclic adenosine monophosphate, ERBB2, VEGF, GCNP and MYC pathways. E2F4 plays an important role in tumor progression and may be a critical biological prognostic factor for HNSCC. In addition, it functions in the nucleus as a transcription factor, regulates immune cells, and could be a promising molecular target for the diagnosis and treatment of HNSCC.
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Yi D, Zhang D, Zeng Z, Zhang S, Li M, Zhang Y. MicroRNA-144-3p Represses the Growth and EMT of Thyroid Cancer via the E2F2/TNIK Axis in Cells and Male BALB/c Nude Mice. Endocrinology 2022; 163:6586857. [PMID: 35579981 DOI: 10.1210/endocr/bqac071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Indexed: 11/19/2022]
Abstract
CONTEXT microRNA (miR/miRNA)-144-3p has been implicated in thyroid cancer (TC) progression with poorly identified mechanisms. Furthermore, E2F2 has been documented to assume a role in the development of various cancers. OBJECTIVE This research sought to ascertain the role of miR-144-3p in growth and epithelial-mesenchymal transition (EMT) in TC in cells and male BALB/c nude mice. METHODS In the obtained TC cells, miR-144-3p expression was detected by quantitative reverse transcription polymerase chain reaction, and E2F2 and TNIK expression by Western blot analysis. After gain- and loss-of-function assays, cell viability, clone formation, migration, and invasion were assessed by cell counting kit-8, clone formation, scratch, and Transwell assays. The expression of EMT-related proteins (Snail, Vimentin, N-cadherin, and E-cadherin) was tested by Western blot analysis. The targeting relationship between miR-144-3p and E2F2 was evaluated by dual-luciferase reporter and radioimmunoprecipitation assays, and the binding relationship between E2F2 and TNIK by dual-luciferase reporter and chromatin immunoprecipitation assays. TC cell growth in vivo was determined by subcutaneous tumorigenesis assays in nude mice. RESULTS miR-144-3p was downregulated, whereas E2F2 and TNIK were upregulated in TC cells. Mechanistically, miR-144-3p inversely targeted E2F2, which increased TNIK expression by binding to TNIK promoter in TC cells. Overexpression of miR-144-3p reduced proliferation, migration, invasion, and EMT of FRO and KTC3 cells, which was nullified by overexpressing E2F2 or TNIK expression. Upregulation of miR-144-3p diminished FRO cell growth and EMT in nude mice, which was abrogated by overexpressing TNIK. CONCLUSION miR-144-3p inhibits cell growth and EMT in TC through E2F2/TNIK axis inactivation in cells and male BALB/c nude mice.
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Affiliation(s)
- Dan Yi
- Department of Nuclear Medicine, Hunan Provincial People's Hospital (the First Affiliated Hospital of Hunan Normal University), Changsha, Hunan 410005, P. R. China
| | - Dongxin Zhang
- Department of Nuclear Medicine, Hunan Provincial People's Hospital (the First Affiliated Hospital of Hunan Normal University), Changsha, Hunan 410005, P. R. China
| | - Zhaohui Zeng
- Department of Nuclear Medicine, Hunan Provincial People's Hospital (the First Affiliated Hospital of Hunan Normal University), Changsha, Hunan 410005, P. R. China
| | - Shu Zhang
- Department of Nuclear Medicine, Hunan Provincial People's Hospital (the First Affiliated Hospital of Hunan Normal University), Changsha, Hunan 410005, P. R. China
| | - Min Li
- Department of Nuclear Medicine, Hunan Provincial People's Hospital (the First Affiliated Hospital of Hunan Normal University), Changsha, Hunan 410005, P. R. China
| | - Yu Zhang
- Department of Anesthesiology and Pain Management Center, Hunan Provincial People's Hospital (the First Affiliated Hospital of Hunan Normal University), Changsha, Hunan 410005, P. R. China
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Yang Y, Liu X, Wang X, Zhang J, Li S, Ma X. Comprehensive Analysis of ABCA Family Members in Lung Adenocarcinoma with Prognostic Values. Mol Biotechnol 2022; 64:1441-1453. [PMID: 35759117 DOI: 10.1007/s12033-022-00506-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/02/2022] [Indexed: 11/27/2022]
Abstract
ATP-binding cassette subfamily A (ABCA) has received wide recognition because it possesses the capacity to translocate its derivatives, xenobiotics, vitamins, and cholesterol across biological membranes. Some ABCA members have causative relevance to inborn diseases, and a number of studies have explored their functions in cancer progression and metastasis. Here, we explored the interrelation between ABCA genes and lung adenocarcinoma (LUAD). We specified the expression and functions of ABCA members in LUAD using the GEPIA, GEO, Human Protein Atlas, UALCAN, TIMER, and Kaplan-Meier Plotter databases. ABCA5, ABCA6, ABCA8, ABCA9, and ABCA10 were found to be significantly less expressed in LUAD and correlated with TP53 mutation in patients with LUAD. Furthermore, ABCA5, ABCA6, and ABCA8 were relevant to overall survival of patients with LUAD. In conclusion, this study showed that ABCA members may be related to the TP53 mutation of LUAD. Moreover, it may serve as a potential marker for the prognosis of LUAD.
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Affiliation(s)
- Yanxia Yang
- Department of Respiratory and Critical Care Medicine, Second People's Hospital of Gansu Province, Lanzhou, 730000, Gansu, China.,Affiliated Hospital of Northwest University for Nationalities, Lanzhou, 730000, Gansu, China
| | - Xiaoping Liu
- Department of Respiratory and Critical Care Medicine, Second People's Hospital of Gansu Province, Lanzhou, 730000, Gansu, China.,Affiliated Hospital of Northwest University for Nationalities, Lanzhou, 730000, Gansu, China
| | - Xin Wang
- Department of Respiratory and Critical Care Medicine, Second People's Hospital of Gansu Province, Lanzhou, 730000, Gansu, China.,Affiliated Hospital of Northwest University for Nationalities, Lanzhou, 730000, Gansu, China
| | - Jie Zhang
- Department of Respiratory and Critical Care Medicine, Second People's Hospital of Gansu Province, Lanzhou, 730000, Gansu, China.,Affiliated Hospital of Northwest University for Nationalities, Lanzhou, 730000, Gansu, China
| | - Shuhua Li
- Department of Respiratory and Critical Care Medicine, Second People's Hospital of Gansu Province, Lanzhou, 730000, Gansu, China.,Affiliated Hospital of Northwest University for Nationalities, Lanzhou, 730000, Gansu, China
| | - Xueping Ma
- Department of Respiratory and Critical Care Medicine, Second People's Hospital of Gansu Province, Lanzhou, 730000, Gansu, China. .,Affiliated Hospital of Northwest University for Nationalities, Lanzhou, 730000, Gansu, China.
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Samling BA, Assim Z, Tong WY, Leong CR, Rashid SA, Nik Mohamed Kamal NNS, Muhamad M, Tan WN. Cynometra cauliflora essential oils loaded-chitosan nanoparticles: Evaluations of their antioxidant, antimicrobial and cytotoxic activities. Int J Biol Macromol 2022; 210:742-751. [PMID: 35513100 DOI: 10.1016/j.ijbiomac.2022.04.230] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/16/2022] [Accepted: 04/29/2022] [Indexed: 12/11/2022]
Abstract
Nanoencapsulation has appeared as an alternative approach to protect the bioactive constituents of essential oils (EOs) and to improve their properties. In this study, Cynometra cauliflora essential oils (CCEOs) were nanoencapsulated in chitosan nanoparticles (CSNPs) using an emulsion-ionic gelation technique. Transmission electron microscopy (TEM) images illustrated a well dispersion and spherical shape of C. cauliflora EOs-loaded chitosan nanoparticles (CCEOs-CSNPs) with an average size of less than 100 nm. In addition to that, Fourier transform infrared (FTIR) spectroscopy, dynamic light scattering (DLS) and X-ray diffraction (XRD) analyses revealed the success of CCEOs nanoencapsulation. The encapsulation efficiency (EE) was in the range of 38.83% to 44.16% while the loading capacity (LC) reached 32.55% to 33.73%. The antioxidant activity (IC50) of CCEOs-CSNPs was ranged from 21.65 to 259.13 μg/mL when assessed using DPPH radical scavenging assay. CCEOs-CSNPs showed an appreciable antimicrobial effects on diabetic wound microorganisms. Notably, cytotoxic effects against human breast cancer MCF-7 and MDA-MB-231 cells recorded IC50 of 3.72-17.81 μg/mL and 16.24-17.65 μg/mL, respectively, after 72 h treatment. Interestingly, no cytotoxicity against human breast normal MCF-10A cells was observed. Thus, nanoencapsulation using CSNPs could improve the properties of CCEOs in biomedical related applications.
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Affiliation(s)
- Benedict Anak Samling
- Chemistry Section, School of Distance Education, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia; Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Zaini Assim
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Woei-Yenn Tong
- Universiti Kuala Lumpur, Branch Campus Institute of Medical Science Technology, 43000 Kajang, Selangor, Malaysia
| | - Chean-Ring Leong
- Universiti Kuala Lumpur, Branch Campus Malaysian Institute of Chemical and Bioengineering Technology, Alor Gajah, 78000 Melaka, Malaysia
| | - Syarifah Ab Rashid
- Universiti Kuala Lumpur, Branch Campus Malaysian Institute of Chemical and Bioengineering Technology, Alor Gajah, 78000 Melaka, Malaysia
| | - Nik Nur Syazni Nik Mohamed Kamal
- Cluster of Integrative Medicine, Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Kepala Batas, Penang, Malaysia
| | - Musthahimah Muhamad
- Cluster of Integrative Medicine, Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Kepala Batas, Penang, Malaysia
| | - Wen-Nee Tan
- Chemistry Section, School of Distance Education, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia.
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Prognostic and tumor immunity implication of inflammatory bowel disease-associated genes in colorectal cancer. Eur J Med Res 2022; 27:91. [PMID: 35698180 PMCID: PMC9190109 DOI: 10.1186/s40001-022-00720-0] [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: 04/13/2022] [Accepted: 05/31/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epidemiologic studies continue to emphasize that increasing patients with inflammatory bowel disease (IBD) develop to colorectal cancer (CRC). Although the function and mechanisms of IBD-associated genes (IBDGs) in CRC tumorigenesis have been extensively researched, the implications of IBDGs in the prognosis value and tumor immunity of CRC remain unclear. RESULTS In this study, the expression, pathological stages and prognostic value of IBDGs in CRC were systematically analyzed, and 7 prognostic genes including CDH1, CCL11, HLA-DRA, NOS2, NAT2, TIMP1 and TP53 were screened through LASSO-Cox regression analysis. Then, a prognostic signature was established based on the 7 prognostic genes, and the model exhibited a good ability in risk stratification of CRC patients. Subsequent results showed that the genetic alterations of the 7 prognostic genes exhibited more significant and extensive influence on immune cells infiltration in colon adenocarcinoma than that in rectal adenocarcinoma. Meanwhile, immune cells infiltration also showed a significant difference between low-risk group and high-risk group. What's more, 7 prognostic genes-based risk stratification was associated with microsatellite instability, and its prognostic characteristics were significantly negatively correlated with mismatch repair genes. CONCLUSIONS This study provided a promising insight that the 7 IBDGs could be used as valuable biomarkers for prognostic diagnosis and personalized immunotherapy of CRC patients.
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Lan C, Yamashita YI, Hayashi H, Nakagawa S, Imai K, Mima K, Kaida T, Matsumoto T, Maruno M, Liu Z, Wu X, Wei F, Baba H. High Expression of Bloom Syndrome Helicase is a Key Factor for Poor Prognosis and Advanced Malignancy in Patients with Pancreatic Cancer: A Retrospective Study. Ann Surg Oncol 2022; 29:3551-3564. [PMID: 35419757 DOI: 10.1245/s10434-022-11500-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/18/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND Bloom syndrome helicase (BLM) is overexpressed in multiple types of cancers and its overexpression may induce genomic instability. This study aimed to determine the function of BLM expression in pancreatic cancer. METHODS BLM messenger RNA (mRNA) expression was analyzed using public datasets to determine its relationship with pancreatic cancer prognosis. Overall, 182 patients with pancreatic cancer who underwent radical resection at our institution were enrolled. BLM expression was evaluated by immunohistochemistry (IHC). We explored the effect of BLM on the proliferation, invasion, migration, and chemoresistance of pancreatic cancer cells via small-interfering RNAs and performed pathway analysis using gene set enrichment analysis. RESULTS BLM mRNA expression was higher in tumor tissue than in normal tissue and had a prognostic effect on overall survival (OS) and recurrence-free survival. The same results were validated by IHC. Multivariate analysis showed that high BLM expression was an independent poor prognostic factor for OS (hazard ratio [HR] 1.678, p = 0.029). In subgroup analysis, the effect of high BLM expression was more significant on OS in patients with younger age (HR 2.27, p = 0.006), male sex (HR 2.39, p = 0.002), high cancer antigen 19-9 level (HR 2.44, p = 0.001), advanced tumor stage (HR 2.25, p = 0.001), lymph node metastasis (HR 2.51, p = 0.001), nerve invasion (HR 2.07, p = 0.002), and adjuvant chemotherapy (HR 2.66, p < 0.001). In vitro, BLM suppression resulted in reduced tumor proliferation, invasion, migration, and chemoresistance. Mechanistically, BLM expression may be associated with E2F1 and E2F2. CONCLUSION BLM expression is a prognostic factor for patients with pancreatic cancer, especially in those with advanced malignancies and receiving chemotherapy.
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Affiliation(s)
- Chuan Lan
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
- Department of Hepatobiliary Surgery and Center of Severe Acute Pancreatitis, The Affiliated Hospital of North Sichuan Medical College, Nanchong, People's Republic of China
| | - Yo-Ichi Yamashita
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiromitsu Hayashi
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Shigeki Nakagawa
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Katsunori Imai
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kosuke Mima
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takayoshi Kaida
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takashi Matsumoto
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Masataka Maruno
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Zhao Liu
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Xiyu Wu
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Feng Wei
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan.
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Yang Y, Liu HL, Liu YJ. A Novel Five-Gene Signature Related to Clinical Outcome and Immune Microenvironment in Breast Cancer. Front Genet 2022; 13:912125. [PMID: 35646102 PMCID: PMC9136328 DOI: 10.3389/fgene.2022.912125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022] Open
Abstract
Breast cancer (BC) is the most frequent cancer in women and the main cause of cancer-related deaths in the globe, according to the World Health Organization. The need for biomarkers that can help predict survival or guide treatment decisions in BC patients is critical in order to provide each patient with an individualized treatment plan due to the wide range of prognoses and therapeutic responses. A reliable prognostic model is essential for determining the best course of treatment for patients. Patients’ clinical and pathological data, as well as their mRNA expression levels at level 3, were gleaned from the TCGA databases. Differentially expressed genes (DEGs) between BC and non-tumor specimens were identified. Tumor immunity analyses have been utilized in order to decipher molecular pathways and their relationship to the immune system. The expressions of KIF4A in BC cells were determined by RT-PCR. To evaluate the involvement of KIF4A in BC cell proliferation, CCK-8 tests were used. In this study, utilizing FC > 4 and p < 0.05, we identified 140 upregulated genes and 513 down-regulated genes. A five-gene signature comprising SFRP1, SAA1, RBP4, KIF4A and COL11A1 was developed for the prediction of overall survivals of BC. Overall survival was distinctly worse for patients in the high-risk group than those in the low-risk group. Cancerous and aggressiveness-related pathways and decreased B cell, T cell CD4+, T cell CD8+, Neutrophil and Myeloid dendritic cells levels were seen in the high-risk group. In addition, we found that KIF4A was highly expressed in BC and its silence resulted in the suppression of the proliferation of BC cells. Taken together, as a possible prognostic factor for BC, the five-gene profile created and verified in this investigation could guide the immunotherapy selection.
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Transcription Factor E2F1 Exacerbates Papillary Thyroid Carcinoma Cell Growth and Invasion via Upregulation of LINC00152. Anal Cell Pathol (Amst) 2022; 2022:7081611. [PMID: 35592867 PMCID: PMC9113902 DOI: 10.1155/2022/7081611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/07/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
Background Papillary thyroid carcinoma (PTC) is the most common thyroid neoplasm, whereas transcription factor E2F1 has been previously implicated in PTC progression. The current study sought to elucidate the underlying mechanism of E2F1 in PTC cell biological activities via regulation of long intergenic noncoding RNA 152 (LINC00152). Methods Firstly, the expression patterns of LINC00152 and E2F1 in PTC were determined. Besides, TPC-1 and IHH-4 cells were adopted to carry out a series of experiments. Cell proliferation was detected by means of a cell counting kit-8 assay and colony formation assay, while cell migration and invasion abilities were assessed using a Transwell assay. Next, the interaction between E2F1 and LINC00152 was certified. Lastly, xenograft transplantation was carried out to validate the effects of E2F1 depletion on PTC. Results Both LINC00152 and E2F1 were highly expressed in PTC cells. Knockdown of LINC00152 led to reduced cell activity, while LINC00152 overexpression brought about the opposing trends. Likewise, E2F1 knockdown quenched cell proliferation, migration, and invasion. However, the combination of E2F1 knockdown and LINC00152 overexpression resulted in augmented cell growth. In addition, E2F1 induced LINC00152 overexpression, which accelerated cell proliferation, migration, and invasion by activating the PI3K/AKT axis, whereas the administration of LY294002, the inhibitor of PI3K, led to reversal of the same. Finally, xenograft transplantation validated that E2F1 inhibition could suppress LY294002, thereby discouraging tumor growth. Conclusion Our findings highlighted that E2F1 augmented PTC cell proliferation and invasion by upregulating LINC00152 and the PI3K/AKT axis. Our discovery provides therapeutic implications for PTC alleviation.
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Yang Y, Li Z, Zhong Q, Zhao L, Wang Y, Chi H. Identification and validation of a novel prognostic signature based on transcription factors in breast cancer by bioinformatics analysis. Gland Surg 2022; 11:892-912. [PMID: 35694087 PMCID: PMC9177273 DOI: 10.21037/gs-22-267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/18/2022] [Indexed: 08/20/2023]
Abstract
BACKGROUND Breast cancer (BRCA) is the leading cause of cancer mortality among women, and it is associated with many tumor suppressors and oncogenes. There is increasing evidence that transcription factors (TFs) play vital roles in human malignancies, but TFs-based biomarkers for BRCA prognosis were still rare and necessary. This study sought to develop and validate a prognostic model based on TFs for BRCA patients. METHODS Differentially expressed TFs were screened from 1,109 BRCA and 113 non-tumor samples downloaded from The Cancer Genome Atlas (TCGA). Univariate Cox regression analysis was used to identify TFs associated with overall survival (OS) of BRCA, and multivariate Cox regression analysis was performed to establish the optimal risk model. The predictive value of the TF model was established using TCGA database and validated using a Gene Expression Omnibus (GEO) data set (GSE20685). A gene set enrichment analysis was conducted to identify the enriched signaling pathways in high-risk and low-risk BRCA patients. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the TF target genes were also conducted separately. RESULTS A total of 394 differentially expressed TFs were screened. A 9-TF prognostic model, comprising PAX7, POU3F2, ZIC2, WT1, ALX4, FOXJ1, SPIB, LEF1 and NFE2, was constructed and validated. Compared to those in the low-risk group, patients in the high-risk group had worse clinical outcomes (P<0.001). The areas under the curve of the prognostic model for 5-year OS were 0.722 in the training cohort and 0.651 in the testing cohort. Additionally, the risk score was an independent prediction indicator for BRCA patients both in the training cohort (HR =1.757, P<0.001) and testing cohort (HR =1.401, P=0.001). It was associated with various cancer signaling pathways. Ultimately, 9 overlapping target genes were predicted by 3 prediction nomograms. The GO and KEGG enrichment analyses of these target genes suggested that the TFs in the model may regulate the activation of some classical tumor signaling pathways to control the progression of BRCA through these target genes. CONCLUSIONS Our study developed and validated a novel prognostic TF model that can effectively predict 5-year OS for BRCA patients.
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Affiliation(s)
- Yingmei Yang
- Department of Clinical Laboratory Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Zhaoyun Li
- Department of Clinical Laboratory Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Qianyi Zhong
- Department of Clinical Laboratory Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Lei Zhao
- Department of Clinical Laboratory Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Yichao Wang
- Department of Clinical Laboratory Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Hongbo Chi
- Department of Clinical Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
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Xu Z, Qu H, Ren Y, Gong Z, Ri HJ, Zhang F, Shao S, Chen X, Chen X. Systematic Analysis of E2F Expression and Its Relation in Colorectal Cancer Prognosis. Int J Gen Med 2022; 15:4849-4870. [PMID: 35585998 PMCID: PMC9109810 DOI: 10.2147/ijgm.s352141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/22/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
- ZhaoHui Xu
- Department of Hernia and Colorectal Surgery, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
- Graduate School of Dalian Medical University, Dalian, People’s Republic of China
| | - Hui Qu
- Department of Hernia and Colorectal Surgery, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
- Graduate School of Dalian Medical University, Dalian, People’s Republic of China
| | - YanYing Ren
- Department of Hernia and Colorectal Surgery, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
| | - ZeZhong Gong
- Department of Hernia and Colorectal Surgery, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
- Graduate School of Dalian Medical University, Dalian, People’s Republic of China
| | - Hyok Ju Ri
- Department of Hernia and Colorectal Surgery, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
- Graduate School of Dalian Medical University, Dalian, People’s Republic of China
| | - Fan Zhang
- Department of Hernia and Colorectal Surgery, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
| | - Shuai Shao
- Department of Hernia and Colorectal Surgery, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
| | - XiaoLiang Chen
- Department of Hernia and Colorectal Surgery, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
| | - Xin Chen
- Department of Hernia and Colorectal Surgery, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
- Correspondence: Xin Chen, Tel +86 17709872266, Email
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Wei C, Wang B, Peng D, Zhang X, Li Z, Luo L, He Y, Liang H, Du X, Li S, Zhang S, Zhang Z, Han L, Zhang J. Pan-Cancer Analysis Shows That ALKBH5 Is a Potential Prognostic and Immunotherapeutic Biomarker for Multiple Cancer Types Including Gliomas. Front Immunol 2022; 13:849592. [PMID: 35444654 PMCID: PMC9013910 DOI: 10.3389/fimmu.2022.849592] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/11/2022] [Indexed: 12/18/2022] Open
Abstract
Background AlkB homolog 5 (ALKBH5) is a N6-methyladenosine (m6A) demethylase associated with the development, growth, and progression of multiple cancer types. However, the biological role of ALKBH5 has not been investigated in pan-cancer datasets. Therefore, in this study, comprehensive bioinformatics analysis of pan-cancer datasets was performed to determine the mechanisms through which ALKBH5 regulates tumorigenesis. Methods Online websites and databases such as NCBI, UCSC, CCLE, HPA, TIMER2, GEPIA2, cBioPortal, UALCAN, STRING, SangerBox, ImmuCellAl, xCell, and GenePattern were used to extract data of ALKBH5 in multiple cancers. The pan-cancer patient datasets were analyzed to determine the relationship between ALKBH5 expression, genetic alterations, methylation status, and tumor immunity. Targetscan, miRWalk, miRDB, miRabel, LncBase databases and Cytoscape tool were used to identify microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) that regulate expression of ALKBH5 and construct the lncRNA-miRNA-ALKBH5 network. In vitro CCK-8, wound healing, Transwell and M2 macrophage infiltration assays as well as in vivo xenograft animal experiments were performed to determine the biological functions of ALKBH5 in glioma cells. Results The pan-cancer analysis showed that ALKBH5 was upregulated in several solid tumors. ALKBH5 expression significantly correlated with the prognosis of cancer patients. Genetic alterations including duplications and deep mutations of the ALKBH5 gene were identified in several cancer types. Alterations in the ALKBH5 gene correlated with tumor prognosis. GO and KEGG enrichment analyses showed that ALKBH5-related genes were enriched in the inflammatory, metabolic, and immune signaling pathways in glioma. ALKBH5 expression correlated with the expression of immune checkpoint (ICP) genes, and influenced sensitivity to immunotherapy. We constructed a lncRNA-miRNA network that regulates ALKBH5 expression in tumor development and progression. In vitro and in vivo experiments showed that ALKBH5 promoted proliferation, migration, and invasion of glioma cells and recruited the M2 macrophage to glioma cells. Conclusions ALKBH5 was overexpressed in multiple cancer types and promoted the development and progression of cancers through several mechanisms including regulation of the tumor-infiltration of immune cells. Our study shows that ALKBH5 is a promising prognostic and immunotherapeutic biomarker in some malignant tumors.
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Affiliation(s)
- Cheng Wei
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Bo Wang
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Dazhao Peng
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaoyang Zhang
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Zesheng Li
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Lin Luo
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingjie He
- Department of Hepatopancreatobiliary Surgery, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Hao Liang
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Xuezhi Du
- Department of Hepatopancreatobiliary Surgery, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Shenghui Li
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Shu Zhang
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhenyu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Han
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Jianning Zhang
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
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