1
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Liu G, Zhang T, Gui D, Liu Q. Clinical significance and immune landscape of angiogenesis-related genes in bladder cancer. Aging (Albany NY) 2023; 15:13118-13133. [PMID: 37988196 DOI: 10.18632/aging.205222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/17/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Angiogenesis is a major promotor of tumor progression and metastasis. Nevertheless, it is undetermined how angiogenesis-related genes (ARGs) influence bladder cancer. METHODS The profiles of bladder cancer gene expression were collected from the TCGA-BLCA cohort. The LASSO regression analysis was used to build an angiogenesis-related signature (ARG_score) with the prognostic ARGs. Verification analyses were conducted across the GSE48075 dataset to demonstrate the robustness of the signature. Differences between the two risk groups based on clinical outcomes, immune landscape, mutation status, chemotherapeutic effectiveness for anticancer drugs, and immunotherapy efficacy were analyzed. A nomogram was developed to improve the clinical efficacy of this predictive tool. The expression levels of model genes in normal bladder epithelial cell lines (SV-HUC-1) and bladder cancer cell lines (T24 and 5637) were detected by qRT-PCR assay. RESULTS Four angiogenesis-associated gene signature was constructed based on the LASSO regression algorithm. The signature showed independent risk factors of overall survival for bladder cancer, validated using two external survival datasets. Additionally, we built a prognostic nomogram to improve the practicality of the ARG_score. High-risk individuals showed stronger immunocyte infiltration, immune-related functions, elevated expression of immune checkpoints, reduced TIDE score, and higher combined IPS-PD-1 and IPS-CTLA4 scores, suggesting a heightened responsiveness to immune checkpoint inhibitors. Furthermore, patients with low and high risk showed distinct responsiveness to anticancer drugs. The expression levels of 5 model genes (COL5A2, JAG1, MSX1, OLR1, and STC) were significantly increased in bladder cancer cell lines (T24 and 5637) compared with the normal bladder epithelial cell line SV-HUC-1. CONCLUSIONS The model constructed based on ARGs may have wide application in predicting outcomes and therapeutic responses.
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Affiliation(s)
- Gang Liu
- Department of Urology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei, People’s Republic of China
| | - Tingting Zhang
- Department of Clinical Laboratory, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei, People’s Republic of China
| | - Dingwen Gui
- Department of Urology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei, People’s Republic of China
| | - Qin Liu
- Department of Breast Surgery, Thyroid Surgery, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei, People’s Republic of China
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2
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Broeders M, van Rooij J, Oussoren E, van Gestel T, Smith C, Kimber S, Verdijk R, Wagenmakers M, van den Hout J, van der Ploeg A, Narcisi R, Pijnappel W. Modeling cartilage pathology in mucopolysaccharidosis VI using iPSCs reveals early dysregulation of chondrogenic and metabolic gene expression. Front Bioeng Biotechnol 2022; 10:949063. [PMID: 36561048 PMCID: PMC9763729 DOI: 10.3389/fbioe.2022.949063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Mucopolysaccharidosis type VI (MPS VI) is a metabolic disorder caused by disease-associated variants in the Arylsulfatase B (ARSB) gene, resulting in ARSB enzyme deficiency, lysosomal glycosaminoglycan accumulation, and cartilage and bone pathology. The molecular response to MPS VI that results in cartilage pathology in human patients is largely unknown. Here, we generated a disease model to study the early stages of cartilage pathology in MPS VI. We generated iPSCs from four patients and isogenic controls by inserting the ARSB cDNA in the AAVS1 safe harbor locus using CRISPR/Cas9. Using an optimized chondrogenic differentiation protocol, we found Periodic acid-Schiff positive inclusions in hiPSC-derived chondrogenic cells with MPS VI. Genome-wide mRNA expression analysis showed that hiPSC-derived chondrogenic cells with MPS VI downregulated expression of genes involved in TGF-β/BMP signalling, and upregulated expression of inhibitors of the Wnt/β-catenin signalling pathway. Expression of genes involved in apoptosis and growth was upregulated, while expression of genes involved in glycosaminoglycan metabolism was dysregulated in hiPSC-derived chondrogenic cells with MPS VI. These results suggest that human ARSB deficiency in MPS VI causes changes in the transcriptional program underlying the early stages of chondrogenic differentiation and metabolism.
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Affiliation(s)
- M. Broeders
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Jgj van Rooij
- Department of Internal Medicine, Erasmus MC Medical Center, Rotterdam, Netherlands
| | - E. Oussoren
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Tjm van Gestel
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Ca Smith
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Sj Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Rm Verdijk
- Department of Pathology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Maem Wagenmakers
- Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, Erasmus MC Medical Center, Rotterdam, Netherlands
| | - Jmp van den Hout
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - At van der Ploeg
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - R. Narcisi
- Department of Orthopaedics and Sports Medicine, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Wwmp Pijnappel
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
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3
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Mori T, Ueno K, Tokunaga K, Kawai Y, Matsuda K, Nishida N, Komine K, Saito S, Nagasaki M. A single-nucleotide-polymorphism in the 5′-flanking region of MSX1 gene as a predictive marker candidate for platinum-based therapy of esophageal carcinoma. Ther Adv Med Oncol 2022; 14:17588359221080580. [PMID: 35251318 PMCID: PMC8891864 DOI: 10.1177/17588359221080580] [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: 08/19/2021] [Accepted: 01/28/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Platinum derivatives are important treatment options for patients with esophageal carcinoma (EC), and a predictive marker for platinum-based therapy is needed for precision medicine. Patients and methods: This study contained two cohorts consisting of EC patients treated using platinum-based chemoradiation therapy (CRT) as the first-line and another external cohort of nationwide clinicogenomic data from the BioBank Japan (BBJ). Results: Genome-wide association study (GWAS) of therapeutic outcomes, refractory disease or not, following platinum-based CRT as first-line in 94 patients in the first cohort suggested the association of 89 SNPs using p < 0.0001. The top 10 SNPs selected from each chromosomal region by odds ratio were evaluated for progression-free survival (PFS) and overall survival (OS) hazard ratios in the first cohort, resulting in four candidates (p < 0.0025). The four selected candidates were re-evaluated in another cohort of 24 EC patients, which included patients prospectively enrolled in this study to fulfill the sample size statistically suggested by the results of the first cohort, and of the four, only rs3815544 was replicated (p < 0.0125). Furthermore, this candidate genotype of rs3815544 proceeded to the re-evaluation study in an external cohort consisting of EC patients treated with platinum derivatives and/or by radiation therapy as the first-line treatment in BBJ, which confirmed that the alternative allele (G) of rs3815544 was statistically associated with non-response (SD or PD) to platinum-based therapy in EC patients (odds ratio = 1.801, p = 0.048). The methylation QTL database as well as online clinicogenomic databases suggested that the region including rs3815544 may regulate MSX1 expression through CpG methylation, and this down-regulation was statistically associated with poor prognosis after platinum-based therapies for EC. Conclusion: rs3815544 is a novel candidate predictive marker for platinum-based EC therapy.
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Affiliation(s)
- Takahiro Mori
- Departments of Clinical Oncology and Gastroenterological Surgery, National Hospital Organization Sagamihara National Hospital, 18-1 Sakuradai, Minami-ku, Sagamihara 252-0392, Kanagawa, Japan
- Laboratory of Tumor Immunology, Clinical Research Center, National Hospital Organization Sagamihara National Hospital, Sagamihara, Japan
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Keigo Komine
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Japan
| | - Sakae Saito
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masao Nagasaki
- Center for the Promotion of Interdisciplinary Education and Research, and nd Center for Genomic Midicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Li H, Chen L, Ke ZB, Chen SH, Xue XY, Zheng QS, Wei Y, Zeng K, Xu N. Angiogenesis-Related Molecular Subtypes and a Novel Prognostic Signature in Clear Cell Renal Cell Carcinoma Patients. Int J Gen Med 2021; 14:6325-6342. [PMID: 34629897 PMCID: PMC8497487 DOI: 10.2147/ijgm.s332732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/09/2021] [Indexed: 11/26/2022] Open
Abstract
Background This study aimed to develop and validate a novel angiogenesis-related gene (ARG) signature and molecular subtypes by bioinformatics analysis. Materials and Methods The transcriptome data and clinical data were obtained from TCGA and ICGC database. We performed consensus clustering analysis to identify angiogenesis molecular subtypes for ccRCC. Univariate and multivariate Cox regression analyses were used to develop a novel ARG-related signature as a prognostic biomarker for ccRCC. Internal and external validation were then performed in TCGA and ICGC cohort, respectively. Results We identified a total of two angiogenesis molecular subtypes of ccRCC. The overall survival (OS) of subtype 1 ccRCC was significantly decreased compared with that of subtype 2 ccRCC (P=0.001). These two molecular subtypes have significantly different tumor microenvironment and immune checkpoint inhibitor sensitivities (P<0.05). Besides, we developed a novel signature based on three ARGs (including MSX1, TIMP1 and JAG2) for subtype 1 ccRCC. The difference in OS between high- and low-risk group was statistically significant in training cohort (P=0.009), test cohort (P=0.024), the whole type 1 cohort (P<0.001), and validation cohort (P=0.041). The AUC for one-year OS prediction was 0.732, 0.710, 0.725, and 0.645 in training cohort, test cohort, the whole type 1 cohort, and validation cohort, respectively. Independent prognostic analysis showed that this signature was an independent predictor for OS of subtype 1 ccRCC (P=0.028914). The power of this prognostic signature was superior to other signatures reported in previous studies. Conclusion We developed and successfully validated a novel ARG signature for predicting prognosis of subtype 1 ccRCC, which was superior to several previous signatures.
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Affiliation(s)
- Hao Li
- Department of Anesthesiology, Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China.,Department of Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Lu Chen
- Department of Anesthesiology, Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China.,Department of Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Zhi-Bin Ke
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Shao-Hao Chen
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Xue-Yi Xue
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Qing-Shui Zheng
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Yong Wei
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Kai Zeng
- Department of Anesthesiology, Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China.,Department of Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Ning Xu
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China.,Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
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5
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West J, Rathinasabapathy A, Chen X, Shay S, Gladson S, Talati M. Overexpression of Msx1 in Mouse Lung Leads to Loss of Pulmonary Vessels Following Vascular Hypoxic Injury. Cells 2021; 10:cells10092306. [PMID: 34571956 PMCID: PMC8471093 DOI: 10.3390/cells10092306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/11/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a progressive lung disease caused by thickening of the pulmonary arterial wall and luminal obliteration of the small peripheral arteries leading to increase in vascular resistance which elevates pulmonary artery pressure that eventually causes right heart failure and death. We have previously shown that transcription factor Msx1 (mainly expressed during embryogenesis) is strongly upregulated in transformed lymphocytes obtained from PAH patients, especially IPAH. Under pathological conditions, Msx1 overexpression can cause cell dedifferentiation or cell apoptosis. We hypothesized that Msx1 overexpression contributes to loss of small pulmonary vessels in PAH. In IPAH lung, MSX1 protein localization was strikingly increased in muscularized remodeled pulmonary vessels, whereas it was undetectable in control pulmonary arteries. We developed a transgenic mouse model overexpressing MSX1 (MSX1OE) by about 4-fold and exposed these mice to normoxic, sugen hypoxic (3 weeks) or hyperoxic (100% 02 for 3 weeks) conditions. Under normoxic conditions, compared to controls, MSX1OE mice demonstrated a 30-fold and 2-fold increase in lung Msx1 mRNA and protein expression, respectively. There was a significant retinal capillary dropout (p < 0.01) in MSX1OE mice, which was increased further (p < 0.03) with sugen hypoxia. At baseline, the number of pulmonary vessels in MSX1OE mice was similar to controls. In sugen-hypoxia-treated MSX1OE mice, the number of small (0-25 uM) and medium (25-50 uM) size muscularized vessels increased approximately 2-fold (p < 0.01) compared to baseline controls; however, they were strikingly lower (p < 0.001) in number than in sugen-hypoxia-treated control mice. In MSX1OE mouse lung, 104 genes were upregulated and 67 genes were downregulated compared to controls. Similarly, in PVECs, 156 genes were upregulated and 320 genes were downregulated from siRNA to MSX1OE, and in PVSMCs, 65 genes were upregulated and 321 genes were downregulated from siRNA to MSX1OE (with control in the middle). Many of the statistically significant GO groups associated with MSX1 expression in lung, PVECs, and PVSMCs were similar, and were involved in cell cycle, cytoskeletal and macromolecule organization, and programmed cell death. Overexpression of MSX1 suppresses many cell-cycle-related genes in PVSMCs but induces them in PVECs. In conclusion, overexpression of Msx1 leads to loss of pulmonary vessels, which is exacerbated by sugen hypoxia, and functional consequences of Msx1 overexpression are cell-dependent.
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Affiliation(s)
| | | | | | | | | | - Megha Talati
- Correspondence: ; Tel.: +1-615-322-8095; Fax: +1-615-343-7448
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6
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Liu C, Huang M, Han C, Li H, Wang J, Huang Y, Chen Y, Zhu J, Fu G, Yu H, Lei Z, Chu X. A narrative review of the roles of muscle segment homeobox transcription factor family in cancer. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:810. [PMID: 34268423 PMCID: PMC8246185 DOI: 10.21037/atm-21-220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/05/2021] [Indexed: 11/23/2022]
Abstract
Deregulation of many homeobox genes has been observed in various cancers and has caused functional implications in the tumor progression. In this review, we will focus on the roles of the human muscle segment homeobox (MSX) transcription factor family in the process of tumorigenesis. The MSX transcription factors, through complex downstream regulation mechanisms, are promoters or inhibitors of diverse cancers by participating in cell proliferation, cell invasion, cell metastasis, cell apoptosis, cell differentiation, drug resistance of tumors, maintenance of tumor stemness, and tumor angiogenesis. Moreover, their upstream regulatory mechanisms in cancers may include: gene mutation and chromosome aberration; DNA methylation and chromatin modification; regulation by non-coding RNAs; regulation by other transcription factors and post-translational modification. These mechanisms may provide a better understanding of why MSX transcription factors are abnormally expressed in tumors. Notably, intermolecular interactions and post-translational modification can regulate the transcriptional activity of MSX transcription factors. It is also crucial to know what affects the transcriptional activity of MSX transcription factors in tumors for possible interventions in them in the future. This systematic summary of the regulatory patterns of the MSX transcription factor family may help to further understand the mechanisms involved in transcriptional regulation and also provide new therapeutic approaches for tumor progression.
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Affiliation(s)
- Chao Liu
- Department of Medical Oncology, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Mengxi Huang
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Chao Han
- Department of Medical Oncology, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Huiyu Li
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Jing Wang
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Yadi Huang
- Department of Medical Oncology, Jinling Hospital, First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Yanyan Chen
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Jialong Zhu
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Gongbo Fu
- Department of Medical Oncology, Jinling Hospital, Nanjing Medical University, Nanjing, China.,Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Hanqing Yu
- Department of Clinical Laboratory, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Zengjie Lei
- Department of Medical Oncology, Jinling Hospital, Nanjing Medical University, Nanjing, China.,Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Xiaoyuan Chu
- Department of Medical Oncology, Jinling Hospital, Nanjing Medical University, Nanjing, China
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7
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Sun R, Du C, Li J, Zhou Y, Xiong W, Xiang J, Liu J, Xiao Z, Fang L, Li Z. Systematic Investigation of DNA Methylation Associated With Platinum Chemotherapy Resistance Across 13 Cancer Types. Front Pharmacol 2021; 12:616529. [PMID: 33995018 PMCID: PMC8117351 DOI: 10.3389/fphar.2021.616529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Platinum resistance poses a significant problem for oncology clinicians. As a result, the role of epigenetics and DNA methylation in platinum-based chemoresistance has gained increasing attention from researchers in recent years. A systematic investigation of aberrant methylation patterns related to platinum resistance across various cancer types is urgently needed. Methods: We analyzed the platinum chemotherapy response-related methylation patterns from different perspectives of 618 patients across 13 cancer types and integrated transcriptional and clinical data. Spearman’s test was used to evaluate the correlation between methylation and gene expression. Cox analysis, the Kaplan-Meier method, and log-rank tests were performed to identify potential risk biomarkers based on differentially methylated positions (DMPs) and compare survival based on DMP values. Support vector machines and receiver operating characteristic curves were used to identify the platinum-response predictive DMPs. Results: A total of 3,703 DMPs (p value < 0.001 and absolute delta beta >0.10) were identified, and the DMP numbers of each cancer type varied. A total of 39.83% of DMPs were hypermethylated and 60.17% were hypomethylated in platinum-resistant patients. Among them, 405 DMPs (Benjamini and Hochberg adjusted p value < 0.05) were found to be associated with prognosis in tumor patients treated with platinum-based regimens, and 664 DMPs displayed the potential to predict platinum chemotherapy response. In addition, we defined six DNA DMPs consisting of four gene members (mesothelin, protein kinase cAMP-dependent type II regulatory subunit beta, msh homeobox 1, and par-6 family cell polarity regulator alpha) that may have favorable prognostic and predictive values for platinum chemotherapy. Conclusion: The methylation-transcription axis exists and participates in the complex biological mechanism of platinum resistance in various cancers. Six DMPs and four associated genes may have the potential to serve as promising epigenetic biomarkers for platinum-based chemotherapy and guide clinical selection of optimal treatment.
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Affiliation(s)
- Ruizheng Sun
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Chao Du
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Jiaxin Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Yanhong Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Juanjuan Xiang
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Jiheng Liu
- Department of Hematology and Oncology, The First Hospital of Changsha, Changsha, China
| | - Zhigang Xiao
- Department of General Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Li Fang
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Zheng Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
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8
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Yang X, Cheng Y, Li X, Zhou J, Dong Y, Shen B, Zhao L, Wang J. A Novel Transcription Factor-Based Prognostic Signature in Endometrial Cancer: Establishment and Validation. Onco Targets Ther 2021; 14:2579-2598. [PMID: 33880037 PMCID: PMC8053499 DOI: 10.2147/ott.s293085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/18/2021] [Indexed: 12/24/2022] Open
Abstract
Background Endometrial cancer (EC) is a common malignancy of the female reproductive system worldwide. Increasing evidence has suggested that many transcription factors are aberrantly expressed in various cancers. This study aimed to develop a transcription factor-based prognostic signature for EC. Methods Gene expression data and clinical data of EC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Univariate Cox regression and Multivariate Cox regression analysis was used to construct a prognostic signature. Then, the efficacy of the prognostic signature was validated in a training cohort, testing cohort and then the entire cohort. Correlations between clinical features and the model were also analyzed, and a nomogram based on the multivariate Cox analysis was developed. Furthermore, we verified the effect of a key transcription factor, E2F1, on biological functions of EC in vitro. Results We developed a nine-transcription factor (MSX1, HOXB9, E2F1, DLX4, BNC2, DLX2, PDX1, POU3F2, and FOXP3) prognostic signature. Compared with those in the low-risk group, patients in the high-risk group had worse clinical outcomes. The area under the curve (AUC) of this prognostic signature for 5-year survival was 0.806 in the training cohort, 0.710 in the testing cohort and 0.761 in the entire cohort. Gene set enrichment analysis (GSEA) revealed a correlation between the prognostic signature and various cancer signaling pathways, and a hub transcription factor regulatory network was constructed. The prognostic signature was confirmed to have independent predictive value. Finally, a nomogram based on the prognostic signature and clinical independent prognostic factors was also established and performed well according to the calibration curves. Further, knockdown of E2F1 inhibited invasion and metastasis of EC cells. Conclusion Our study developed and validated a transcription factor-based prognostic signature that accurately predicts prognosis of EC patients. Moreover, E2F1 may represent a potential target for the treatment of EC.
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Affiliation(s)
- Xiao Yang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, People's Republic of China
| | - Yuan Cheng
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, People's Republic of China
| | - Xingchen Li
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, People's Republic of China
| | - Jingyi Zhou
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, People's Republic of China
| | - Yangyang Dong
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, People's Republic of China
| | - Boqiang Shen
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, People's Republic of China
| | - Lijun Zhao
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, People's Republic of China
| | - Jianliu Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, People's Republic of China
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Zhang Q, Zhao K, Song L, Ji C, Cong R, Luan J, Zhou X, Xia J, Song N. A Novel Apoptosis-Related Gene Signature Predicts Biochemical Recurrence of Localized Prostate Cancer After Radical Prostatectomy. Front Genet 2020; 11:586376. [PMID: 33329725 PMCID: PMC7734189 DOI: 10.3389/fgene.2020.586376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/29/2020] [Indexed: 01/21/2023] Open
Abstract
Background: Nowadays, predictions of biochemical recurrence (BCR) in localized prostate cancer (PCa) patients after radical prostatectomy (RP) are mainly based on clinical parameters with a low predictive accuracy. Given the critical role of apoptosis in PCa occurrence and progression, we aimed to establish a novel predictive model based on apoptosis-related gene signature and clinicopathological parameters that can improve risk stratification for BCR and assist in clinical decision-making. Methods: Expression data and corresponding clinical information were obtained from four public cohorts, one from The Cancer Genome Atlas (TCGA) dataset and three from the Gene Expression Omnibus (GEO) dataset. Weighted gene co-expression network analysis (WGCNA) was performed to identify candidate modules closely correlated to BCR, and univariate and multivariate Cox regression analyses were utilized to build the gene signature. Time-dependent receiver operating curve (ROC) and Kaplan-Meier (KM) survival analysis were used to assess the prognostic value. Finally, we analyzed the expression of genes in the signature and validated the results using quantitative real-time PCR (qRT-PCR). Results: The novel gene signature we established exhibited a high prognostic value and was able to act as an independent risk factor for BCR [Training set: P < 0.001, hazard ratio (HR) = 7.826; Validation set I: P = 0.006, HR = 2.655; Validation set II: P = 0.003, HR = 4.175; Validation set III: P < 0.001, HR = 3.008]. Nomogram based on the gene signature and clinical parameters was capable of distinguishing high-risk BCR patients. Additionally, functional enrichment analysis showed several enriched pathways and biological processes, which might help reveal the underlying mechanism. The expression results of qRT-PCR were consistent with TCGA results. Conclusion: The apoptosis-related gene signature could serve as a powerful predictor and risk factor for BCR in localized PCa patients after RP.
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Affiliation(s)
- Qijie Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kai Zhao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lebin Song
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chengjian Ji
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rong Cong
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiaochen Luan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiang Zhou
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiadong Xia
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ninghong Song
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,The Affiliated Kezhou People's Hospital of Nanjing Medical University, Xinjiang, China
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Yang L, Cui Y, Huang T, Sun X, Wang Y. Identification and Validation of MSX1 as a Key Candidate for Progestin Resistance in Endometrial Cancer. Onco Targets Ther 2020; 13:11669-11688. [PMID: 33235459 PMCID: PMC7679365 DOI: 10.2147/ott.s271494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022] Open
Abstract
Purpose Progestin resistance is a critical obstacle for endometrial conservative therapy. Therefore, studies to acquire a more comprehensive understanding of the mechanisms are urgent. However, the pivotal molecules are still unexplored. Materials and Methods We downloaded GSE121367 from the GEO database. The “limma” R language package was applied to identify differentially expressed genes (DEGs). We conducted Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA). Protein–protein interaction was constructed by STRING and visualized in Cytoscape. The tumor immune microenvironment was explored by the TISIDB database. Methylation validation and overall survival analysis were conducted by the TCGA database. In addition, the upstream modulators of hub genes were predicted by miRTarBase and Network Analyst databases. The expression levels of candidate genes were validated by quantitative real-time PCR (qRT-PCR), Western blot, and immunohistochemical assay (IHC). Cell growth, clone formation, migration, invasion, and wound healing assays were studied to explore the role of MSX1 in progestin resistance in vitro. Results A total of 3,282 DEGs were identified and they were mostly enriched in the cell adhesion pathway. We screened out ten hub genes whose genomic alteration rates were low based on the current endometrial carcinoma sample sets. Has-miR-335-5p, has-miR-124-3p, MAZ, and TFDP1 were the most prominent upstream regulators. The methylation status of CDH1, JAG1, EPCAM, and MSX1 was decreased, corresponding to their high protein expression, which also predicted better overall survival. The homeobox protein of MSX1 showed significant tissue specificity and better prognostic value and its knockdown inhibited epithelial–mesenchymal transitions (EMT) and enhanced progesterone efficacy. Conclusion Our study identified that the gene of MSX1 promised to be the specific indicator and therapeutic target for progestin resistance. This would shed new light on the underlying biological mechanism to overcome progestin resistance of endometrial cancer.
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Affiliation(s)
- Linlin Yang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,Shanghai Municipal Key Clinical Specialty, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, People's Republic of China
| | - Yunxia Cui
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,Shanghai Municipal Key Clinical Specialty, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, People's Republic of China
| | - Ting Huang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,Shanghai Municipal Key Clinical Specialty, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, People's Republic of China
| | - Xiao Sun
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,Shanghai Municipal Key Clinical Specialty, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, People's Republic of China
| | - Yudong Wang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,Shanghai Municipal Key Clinical Specialty, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, People's Republic of China
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11
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Eppich S, Kuhn C, Schmoeckel E, Mayr D, Mahner S, Jeschke U, Gallwas J, Heidegger HH. MSX1-A Potential Marker for Uterus-Preserving Therapy of Endometrial Carcinomas. Int J Mol Sci 2020; 21:ijms21124529. [PMID: 32630554 PMCID: PMC7350265 DOI: 10.3390/ijms21124529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/17/2020] [Accepted: 06/22/2020] [Indexed: 12/28/2022] Open
Abstract
Prognostic factors are of great interest in patients with endometrial cancer. One potential factor could be the protein MSX1, a transcription repressor, that has an inhibitory effect on the cell cycle. For this study, endometrioid endometrial carcinomas (n = 53), clear cell endometrial carcinomas (n = 6), endometrioid ovarian carcinomas (n = 19), and clear cell ovarian carcinomas (n = 11) were immunochemically stained for the protein MSX1 and evaluated using the immunoreactive score (IRS). A significant stronger expression of MSX1 was found in endometrioid endometrial carcinomas (p < 0.001), in grading 2 (moderate differentiation) (p = 0.001), and in tumor material of patients with no involvement of lymph nodes (p = 0.031). Correlations were found between MSX1 expression and the expression of β-Catenin, p21, p53, and the steroid receptors ERα, ERβ, PRα, and PRβ. A significant (p = 0.023) better survival for patients with an MSX1 expression in more than 10% of the tumor cells was observed for endometrioid endometrial carcinomas (21.3 years median survival (MSX1-positive) versus 17.3 years (MSX1-negative)). Although there is evidence that MSX1 expression correlates with improved long-term survival, further studies are necessary to evaluate if MSX1 can be used as a prognostic marker.
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Affiliation(s)
- Simon Eppich
- Department of Obstetrics and Gynecology, University Hospital, Ludwig Maximilians University (LMU), Marchioninistraße 15, 81377 Munich, Germany; (S.E.); (C.K.); (S.M.); (J.G.); (H.H.H.)
| | - Christina Kuhn
- Department of Obstetrics and Gynecology, University Hospital, Ludwig Maximilians University (LMU), Marchioninistraße 15, 81377 Munich, Germany; (S.E.); (C.K.); (S.M.); (J.G.); (H.H.H.)
| | - Elisa Schmoeckel
- Department of Pathology, LMU Munich, Thalkirchner Str. 56, 80337 Munich, Germany; (E.S.); (D.M.)
| | - Doris Mayr
- Department of Pathology, LMU Munich, Thalkirchner Str. 56, 80337 Munich, Germany; (E.S.); (D.M.)
| | - Sven Mahner
- Department of Obstetrics and Gynecology, University Hospital, Ludwig Maximilians University (LMU), Marchioninistraße 15, 81377 Munich, Germany; (S.E.); (C.K.); (S.M.); (J.G.); (H.H.H.)
| | - Udo Jeschke
- Department of Obstetrics and Gynecology, University Hospital, Ludwig Maximilians University (LMU), Marchioninistraße 15, 81377 Munich, Germany; (S.E.); (C.K.); (S.M.); (J.G.); (H.H.H.)
- Department of Obstetrics and Gynecology, University Hospital Augsburg, Stenglinstr. 2, 86156 Augsburg, Germany
- Correspondence: ; Tel.: +49-89-4400-54240
| | - Julia Gallwas
- Department of Obstetrics and Gynecology, University Hospital, Ludwig Maximilians University (LMU), Marchioninistraße 15, 81377 Munich, Germany; (S.E.); (C.K.); (S.M.); (J.G.); (H.H.H.)
- Department of Gynecology and Obstetrics, Georg August University Goettingen, University Medicine, 37075 Goettingen, Germany
| | - Helene Hildegard Heidegger
- Department of Obstetrics and Gynecology, University Hospital, Ludwig Maximilians University (LMU), Marchioninistraße 15, 81377 Munich, Germany; (S.E.); (C.K.); (S.M.); (J.G.); (H.H.H.)
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12
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Han G, Zhang X, Liu P, Yu Q, Li Z, Yu Q, Wei X. Knockdown of anti-silencing function 1B histone chaperone induces cell apoptosis via repressing PI3K/Akt pathway in prostate cancer. Int J Oncol 2018; 53:2056-2066. [PMID: 30132513 PMCID: PMC6192734 DOI: 10.3892/ijo.2018.4526] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/09/2018] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer (PCa) is one of the most common malignancies among males worldwide. Anti-silencing function 1B histone chaperone (ASF1B) has been reported to be involved in PCa. The present study aimed to investigate the role and molecular mechanism of ASF1B in PCa. Data of genes were obtained from The Cancer Genome Atlas data- base. The core gene was identified using the DAVID website. Cell viability and colony formation were detected using a cell counting kit-8 assay and crystal violet staining, respectively. Cell cycle distribution and apoptosis were assessed using flow cytometry analysis. The corresponding factors were analyzed by reverse transcription-quantitative polymerase chain reaction and western blotting. It was demonstrated that ASF1B was highly expressed in the PCa tissues and cells compared with the non-PCa tissues and cells, respectively. While siRNA-ASF1B significantly reduced the viability and colony formation, it promoted apoptosis, G1 phase cell cycle arrest of LNCap as well as C4-2 cells. siRNA-ASF1B was revealed to significantly reduce the level of B-cell lymphoma-2 and cyclin D1, and enhance the expression levels of p53, caspase-3 and Bcl-2 associated X protein. Furthermore, the phosphorylation levels of phosphatidylinositol 3 kinase (PI3K) and protein kinase B (Akt) were significantly decreased in the siRNA-ASF1B group compared with the mock group. In summary, the present study demonstrated that silencing of ASF1B suppressed the proliferation, and promoted apoptosis and cell cycle arrest of PCa cells. Inhibition of the PI3K/Akt signaling pathway was pertinent to the role of si-ASF1B. This phenomenon suggests that the downregulation of ASF1B may aid in inhibiting the progression of PCa.
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Affiliation(s)
- Guangye Han
- The Second Ward of Urology Department, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453100, P.R. China
| | - Xinjun Zhang
- The First Ward of Urology Department, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453100, P.R. China
| | - Pei Liu
- The Second Ward of Urology Department, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453100, P.R. China
| | - Quanfeng Yu
- The Second Ward of Urology Department, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453100, P.R. China
| | - Zeyu Li
- The Second Ward of Urology Department, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453100, P.R. China
| | - Qinnan Yu
- The First Ward of Urology Department, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453100, P.R. China
| | - Xiaoxia Wei
- The Second Ward of Infection Department, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453100, P.R. China
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