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Lin Z, Zhang J, Chen Q, Zhang X, Zhang D, Lin J, Lin D. Transcriptome analysis of the adenoma-carcinoma sequences identifies novel biomarkers associated with development of canine colorectal cancer. Front Vet Sci 2023; 10:1192525. [PMID: 38098990 PMCID: PMC10720982 DOI: 10.3389/fvets.2023.1192525] [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: 03/23/2023] [Accepted: 10/11/2023] [Indexed: 12/17/2023] Open
Abstract
The concept of adenoma-to-cancer transformation in human colorectal cancer (CRC) is widely accepted. However, the relationship between transcriptome features and adenoma to carcinoma transformation in canines is not clear. We collected transcriptome data from 8 normal colon tissues, 4 adenoma tissues, and 15 cancer tissues. Differential analysis was unable to determine the dynamic changes of genes but revealed that PFKFB3 may play a key role in this process. Enrichment analysis explained metabolic dysregulation, immunosuppression, and typical cancer pathways in canine colorectal tumors. MFuzz generated specific dynamic expression patterns of five differentially expressed genes (DEGs). Weighted correlation network analysis showed that DEGs in cluster 3 were associated with malignant tissues, revealing the key role of inflammatory and immune pathways in canine CRC, and the S100A protein family was also found to be involved in the malignant transformation of canine colorectal tumors. By comparing strategies between humans and dogs, we found five novel markers that may be drivers of CRC. Among them, GTBP4 showed excellent diagnostic and prognostic ability. This study was the first systematic exploration of transformation in canine CRC, complemented the molecular characteristics of the development and progression of canine CRC, and provided new potential biomarkers and comparative oncologic evidence for biomarker studies in human colorectal cancer.
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Affiliation(s)
- Zixiang Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Jiatong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qi Chen
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaohu Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Di Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiahao Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Degui Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Wu J, Chen G, Wang W, Yang Y, Yuan Y, Shang A, Quan W, Wang L. GTPBP4: A New Therapeutic Target Gene Promotes Tumor Progression in Non-Small Cell Lung Cancer via EMT. JOURNAL OF ONCOLOGY 2022; 2022:2164897. [PMID: 36405249 PMCID: PMC9674418 DOI: 10.1155/2022/2164897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/05/2022] [Accepted: 09/27/2022] [Indexed: 09/03/2023]
Abstract
Lung cancer has a complex etiology involving multiple regulatory systems. Uncertainty about the biology and evolution of lung cancer has made it difficult to improve its poor prognosis. To create efficient therapeutic targets and optimal molecular screening tools for lung cancer, the most important task seems to be to understand how it develops and progresses. The expression and regulation of GTPBP4 in non-small cell lung cancer (NSCLC) are not well understood. Using methods such as knocking down GTPBP4 in lung cancer cells and establishing a mouse lung cancer model, we found that the expression of GTPBP4 was upregulated in human lung adenocarcinoma cells and tissues, and that knocking down the expression of the GTPBP4 gene in A549 and Calu-1 lung adenocarcinoma cells can inhibit the proliferation of lung adenocarcinoma cells and reduce their invasion ability. The results of the mouse lung cancer model showed that the lung weight and the number of lung surface nodules decreased significantly in the LLC-GTPBP4 KO group. The mechanism by which GTPBP4 regulation affects the progression of lung adenocarcinoma may be related to the regulation of EMT. From this study, new research ideas emerge to explore GTPBP4 as a biomarker and therapeutic target for early diagnosis and treatment of lung cancer.
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Affiliation(s)
- Junlu Wu
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China
- Center for Laboratory Medicine and School of Clinical Medicine, General Hospital of Ningxia Medical University, Yinchuan 750003, Ningxia, China
| | - Guofei Chen
- Department of Laboratory Medicine, Suzhou Hospital of Integrated Traditional Chinese and Western Medicine, Suzhou 215101, China
| | - Weiwei Wang
- Department of Pathology, Tinghu People's Hospital of Yancheng City, Yancheng 224001, Jiangsu, China
| | - Yang Yang
- Department of Radiology, Luodian Hospital, Baoshan District, Shanghai 201908, China
| | - Yi Yuan
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China
| | - Anquan Shang
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China
| | - Wenqiang Quan
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China
| | - Lixin Wang
- Center for Laboratory Medicine and School of Clinical Medicine, General Hospital of Ningxia Medical University, Yinchuan 750003, Ningxia, China
- Center for Laboratory Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
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Zhu J, Han T, Zhao S, Zhu Y, Ma S, Xu F, Bai T, Tang Y, Xu Y, Liu L. Computational Characterizing Necroptosis Reveals Implications for Immune Infiltration and Immunotherapy of Hepatocellular Carcinoma. Front Oncol 2022; 12:933210. [PMID: 35875102 PMCID: PMC9301124 DOI: 10.3389/fonc.2022.933210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/06/2022] [Indexed: 12/24/2022] Open
Abstract
Necroptosis is a programmed form of necrotic cell death in regulating cancer ontogenesis, progression, and tumor microenvironment (TME) and could drive tumor-infiltrating cells to release pro-inflammatory cytokines, incurring strong immune responses. Nowadays, there are few identified biomarkers applied in clinical immunotherapy, and it is increasingly recognized that high levels of tumor necroptosis could enhance the response to immunotherapy. However, comprehensive characterization of necroptosis associated with TME and immunotherapy in Hepatocellular carcinoma (HCC) remains unexplored. Here, we computationally characterized necroptosis landscape in HCC samples from TCGA and ICGA cohorts and stratified them into two necroptosis clusters (A or B) with significantly different characteristics in clinical prognosis, immune cell function, and TME-landscapes. Additionally, to further evaluate the necroptosis levels of each sample, we established a novel necroptosis-related gene score (NRGscore). We further investigated the TME, tumor mutational burden (TMB), clinical response to immunotherapy, and chemotherapeutic drug sensitivity of HCC subgroups stratified by the necroptosis landscapes. The NRGscore is robust and highly predictive of HCC clinical outcomes. Further analysis indicated that the high NRGscore group resembles the immune-inflamed phenotype while the low score group is analogous to the immune-exclusion or metabolism phenotype. Additionally, the high NRGscore group is more sensitive to immune checkpoint blockade-based immunotherapy, which was further validated using an external HCC cohort, metastatic melanoma cohort, and advanced urothelial cancer cohort. Besides, the NRGscore was demonstrated as a potential biomarker for chemotherapy, wherein the high NRGscore patients with more tumor stem cell composition could be more sensitive to Cisplatin, Doxorubicin, Paclitaxel-based chemotherapy, and Sorafenib therapy. Collectively, a comprehensive characterization of the necroptosis in HCC suggested its implications for predicting immune infiltration and response to immunotherapy of HCC, providing promising strategies for treatment.
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Affiliation(s)
- Jun Zhu
- Department of Gastroenterology, Daping Hospital, Army Medical University, Chongqing, China
- Department of General Surgery, The Southern Theater Air Force Hospital, Guangzhou, China
| | - Tenghui Han
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Shoujie Zhao
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, China
| | - Yejing Zhu
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, China
| | - Shouzheng Ma
- Department of Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, China
| | - Fenghua Xu
- Department of Gastroenterology, Daping Hospital, Army Medical University, Chongqing, China
| | - Tingting Bai
- Department of Gastroenterology, Daping Hospital, Army Medical University, Chongqing, China
| | - Yuxin Tang
- Department of Gastroenterology, Daping Hospital, Army Medical University, Chongqing, China
| | - Yungang Xu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Centre for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Centre at Houston, Houston, TX, United States
- *Correspondence: Lei Liu, ; Yungang Xu,
| | - Lei Liu
- Department of Gastroenterology, Daping Hospital, Army Medical University, Chongqing, China
- *Correspondence: Lei Liu, ; Yungang Xu,
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Xin S, Sun X, Jin L, Li W, Liu X, Zhou L, Ye L. The Prognostic Signature and Therapeutic Value of Phagocytic Regulatory Factors in Prostate Adenocarcinoma (PRAD). Front Genet 2022; 13:877278. [PMID: 35706452 PMCID: PMC9190300 DOI: 10.3389/fgene.2022.877278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/19/2022] [Indexed: 01/03/2023] Open
Abstract
There is growing evidence that phagocytosis regulatory factors (PRFs) play important roles in tumor progression, and therefore, identifying and characterizing these factors is crucial for understanding the mechanisms of cellular phagocytosis in tumorigenesis. Our research aimed to comprehensively characterize PRFs in prostate adenocarcinoma (PRAD) and to screen and determine important PRFs in PRAD which may help to inform tumor prognostic and therapeutic signatures based on these key PRFs. Here, we first systematically described the expression of PRFs in PRAD and evaluated their expression patterns and their prognostic value. We then analyzed prognostic phagocytic factors by Cox and Lasso analysis and constructed a phagocytic factor-mediated risk score. We then divided the samples into two groups with significant differences in overall survival (OS) based on the risk score. Then, we performed correlation analysis between the risk score and clinical features, immune infiltration levels, immune characteristics, immune checkpoint expression, IC50 of several classical sensitive drugs, and immunotherapy efficacy. Finally, the Human Protein Atlas (HPA) database was used to determine the protein expression of 18 PRF characteristic genes. The aforementioned results confirmed that multilayer alterations of PRFs were associated with the prognosis of patients with PRAD and the degree of macrophage infiltration. These findings may provide us with potential new therapies for PRAD.
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Affiliation(s)
- Shiyong Xin
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xianchao Sun
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Liang Jin
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Weiyi Li
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiang Liu
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Liqing Zhou
- Department of Rheumatology and Immunology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Lin Ye
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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Hu Y, Xie J, Chen L, Tang Q, Wei W, Lin W, Du W, Xiang T, Yin L, Ji J. Integrated Analysis of Genomic and Transcriptomic Profiles Identified the Role of GTP Binding Protein-4 (GTPBP4) in Breast Cancer. Front Pharmacol 2022; 13:880445. [PMID: 35784753 PMCID: PMC9243593 DOI: 10.3389/fphar.2022.880445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: To explore the significance of GTP-binding protein 4 (GTPBP4) in breast cancer. Methods: Firstly, GTPBP4 expression analysis was performed in TIMER and UALCAN databases. Subsequently, the TCGA cohort and multiple Gene Expression Omnibus Cohorts were used as validation for GTPBP4 expression. Besides, we also evaluated the diagnostic value of GTPBP4 in TCGA Cohort and multiple GEO Cohorts. The predictive effect of GTPBP4 in breast cancer was then assessed using survival analysis. Then we look at the role of GTPBP4 in the immune milieu and create a Nomogram to help patients with breast cancer understand their prognosis. Finally, in vitro tests were carried out to look at GTPBP4 expression and function in breast cancer cell lines. Results: GTPBP4 is an independent breast cancer prognostic factor that is upregulated in the disease (p < 0.05). Enrichment analysis showed that GTPBP4 was associated with multiple functions and pathways. In addition, GTPBP4 is associated with a variety of immune cell types (p < 0.05). PCR assay showed that GTPBP4 expression was up-regulated in breast cancer cell lines. The activity, migration, and proliferation of breast cancer cells were considerably reduced after GTPBP4 knockdown in the CCK-8, Transwell, and Scratch assays. Conclusions: Our research discovered a new breast cancer biomarker that can be used as a guide for breast cancer diagnosis and treatment.
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Affiliation(s)
- Yiming Hu
- College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Jiaheng Xie
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liang Chen
- Department of General Surgery, Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, China
| | - Qikai Tang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Wei Wei
- Department of General Surgery, Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, China
| | - Wenfeng Lin
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wang Du
- Department of General Surgery, Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, China
| | - Tinghong Xiang
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lu Yin
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Ji
- College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
- *Correspondence: Jing Ji,
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Mutai H, Momozawa Y, Kamatani Y, Nakano A, Sakamoto H, Takiguchi T, Nara K, Kubo M, Matsunaga T. Whole exome analysis of patients in Japan with hearing loss reveals high heterogeneity among responsible and novel candidate genes. Orphanet J Rare Dis 2022; 17:114. [PMID: 35248088 PMCID: PMC8898489 DOI: 10.1186/s13023-022-02262-4] [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: 09/10/2021] [Accepted: 02/20/2022] [Indexed: 11/16/2022] Open
Abstract
Background Heterogeneous genetic loci contribute to hereditary hearing loss; more than 100 deafness genes have been identified, and the number is increasing. To detect pathogenic variants in multiple deafness genes, in addition to novel candidate genes associated with hearing loss, whole exome sequencing (WES), followed by analysis prioritizing genes categorized in four tiers, were applied.
Results Trios from families with non-syndromic or syndromic hearing loss (n = 72) were subjected to WES. After segregation analysis and interpretation according to American College of Medical Genetics and Genomics guidelines, candidate pathogenic variants in 11 previously reported deafness genes (STRC, MYO15A, CDH23, PDZD7, PTPN11, SOX10, EYA1, MYO6, OTOF, OTOG, and ZNF335) were identified in 21 families. Discrepancy between pedigree inheritance and genetic inheritance was present in one family. In addition, eight genes (SLC12A2, BAIAP2L2, HKDC1, SVEP1, CACNG1, GTPBP4, PCNX2, and TBC1D8) were screened as single candidate genes in 10 families. Conclusions Our findings demonstrate that four-tier assessment of WES data is efficient and can detect novel candidate genes associated with hearing loss, in addition to pathogenic variants of known deafness genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02262-4.
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Zhang N, Shen H, Huang S, Wang F, Liu H, Xie F, Jiang L, Chen X. LncRNA FGD5-AS1 functions as an oncogene to upregulate GTPBP4 expression by sponging miR-873-5p in hepatocellular carcinoma. Eur J Histochem 2021; 65. [PMID: 34783233 PMCID: PMC8611415 DOI: 10.4081/ejh.2021.3300] [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: 07/02/2021] [Accepted: 10/11/2021] [Indexed: 11/28/2022] Open
Abstract
The long non-coding FGD5-AS1 (LncFGD5-AS1) has been reported to be a novel carcinogenic gene and participant in regulating tumor progression by sponging microRNAs (miRNAs). However, the pattern of expression and the biological role of FGD5-AS1 in hepatocellular carcinoma (HCC) remains largely unknown. The expression level of FGD5-AS1 in tumor tissues and cell lines was measured by RT-qPCR. CCK-8, EdU, flow cytometry, wound healing and transwell chamber assays were performed to investigate the role of FGD5-AS1 in cell proliferation, apoptosis, migration, and invasion in HCC. Dual luciferase reporter, and RNA pull-down assays were performed to identify the regulatory interactions among FGD5-AS1, miR-873-5p and GTP-binding protein 4 (GTPBP4). We found that the expression of FGD5-AS1 was upregulated in HCC tissues and cell lines. Moreover, the knockdown of FGD5-AS1 suppressed cell proliferation, migration and invasion, and induced apoptosis in HCC cells. Further studies demonstrated that FGD5-AS1 could function as a competitive RNA by sponging miR-873-5p in HCC cells. Moreover, GTPBP4 was identified as direct downstream target of miR-873-5p in HCC cells and FGD5-AS1mediated the effects of GTPBP4 by competitively binding with miR-873-5p. Taken together, this study demonstrated the regulatory role of FGD5-AS1 in the progression of HCC and identified the miR-873-5p/GTPBP4 axis as the direct downstream pathway. It represents a promising novel therapeutic strategy for HCC patients.
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Affiliation(s)
- Nuobei Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang.
| | - Hao Shen
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang.
| | - Shenan Huang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang.
| | - Fenfen Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang.
| | - Huifang Liu
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang.
| | - Fen Xie
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang.
| | - Lei Jiang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang.
| | - Xin Chen
- Department of Nuclear Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang.
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Chen J, Zhang J, Zhang Z. Upregulation of GTPBP4 Promotes the Proliferation of Liver Cancer Cells. JOURNAL OF ONCOLOGY 2021; 2021:1049104. [PMID: 34712323 PMCID: PMC8548153 DOI: 10.1155/2021/1049104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/16/2021] [Accepted: 08/26/2021] [Indexed: 01/21/2023]
Abstract
RESULTS The GTPBP4 has upregulated expression in liver cancer patients (P < 0.01), but there was no difference in its expression in patients with different clinicopathological stages. The expression of GTPBP4 increased with the increase of cancer metastasis in lymph nodes (P < 0.01). Liver cancer patients with upregulated expression of GTPBP4 showed a shorter overall survival rate (P=0.02). GTPBP4 is closely related to genes such as NIFK, WDR12, and RPF2, and these genes are involved in life processes such as GTP binding and rRNA processing. The upregulated expression of GTPBP4 promotes the proliferation of liver cancer cells and promotes the growth of tumors in mice, while the downregulated expression of GTPBP4 inhibits the proliferation of liver cancer cells and inhibits the growth of tumors in mice. CONCLUSION The expression of GTPBP4 is upregulated in liver cancer patients and affects the overall survival rate of patients. The upregulated expression of GTPBP4 promotes the proliferation of liver cancer cells and the growth of tumors.
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Affiliation(s)
- Jia Chen
- Cancer Research Institute of Hengyang Medical College, University of South China, Hengyang, China
- Physical Examination Center, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Jie Zhang
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Zhiwei Zhang
- Cancer Research Institute of Hengyang Medical College, University of South China, Hengyang, China
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Integrated bioinformatic analysis of RNA binding proteins in hepatocellular carcinoma. Aging (Albany NY) 2020; 13:2480-2505. [PMID: 33411682 PMCID: PMC7880356 DOI: 10.18632/aging.202281] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022]
Abstract
RNA binding proteins (RBPs) are aberrantly expressed in a tissue-specific manner across many tumors. These proteins, which play a vital role in post-transcriptional gene regulation, are involved in RNA splicing, maturation, transport, stability, degradation, and translation. We set out to establish an accurate risk score model based on RBPs to estimate prognosis in hepatocellular carcinoma (HCC). RNA-sequencing data, proteomic data and corresponding clinical information were acquired from the Cancer Genome Atlas database and the Clinical Proteomic Tumor Analysis Consortium database respectively. We identified 406 differentially expressed RBPs between HCC tumor and normal tissues at the transcriptional and protein level. Overall, 11 RBPs (BRIX1, DYNC1H1, GTPBP4, PRKDC, RAN, RBM19, SF3B4, SMG5, SPATS2, TAF9, and THOC5) were selected to establish a risk score model. We divided HCC patients into low-risk and high-risk groups based on the median of risk score values. The survival analysis indicated that patients in the high-risk group had poorer overall survival compared to patients in the low-risk group. Our study demonstrated that 11 RBPs were associated with the overall survival of HCC patients. These RBPs may represent potential drug targets and can help optimize future clinical treatment.
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Determining the Clinical Value and Critical Pathway of GTPBP4 in Lung Adenocarcinoma Using a Bioinformatics Strategy: A Study Based on Datasets from The Cancer Genome Atlas. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5171242. [PMID: 33134380 PMCID: PMC7593728 DOI: 10.1155/2020/5171242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 01/16/2023]
Abstract
Lung cancer is the leading cause of cancer-related death worldwide, and the most common histologic subtype is lung adenocarcinoma (LUAD). Due to the significant mortality and morbidity rates among patients with LUAD, the identification of novel biomarkers to guide diagnosis, prognosis, and therapy is urgent. Guanosine triphosphate-binding protein 4 (GTPBP4) has been found to be associated with tumorigenesis in recent years, but the underlying molecular mechanism remains to be elucidated. In the present study, we demonstrate that GTPBP4 is significantly overexpressed in LUAD primary tumors. A total of 55 genes were identified as potential targets of GTPBP4. GO enrichment analysis identified the top 25 pathways among these target genes, among which, ribosome biogenesis was shown to be the most central. Each target gene demonstrated strong and complex interactions with other genes. Of the potential target genes, 12 abnormally expressed candidates were associated with survival probability and correlated with GTPBP4 expression. These findings suggest that GTPBP4 is associated with LUAD progression. Finally, we highlight the importance of the role of GTPBP4 in LUAD in vitro. GTPBP4 knockdown in LUAD cells inhibited proliferation and metastasis, promoted apoptosis, and enhanced sensitivity to TP. Overall, we conclude that GTPBP4 may be considered as a potential biomarker of LUAD.
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11
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Hu F, Wang Q, Yang Z, Zhang Z, Liu X. Network-based identification of biomarkers for colon adenocarcinoma. BMC Cancer 2020; 20:668. [PMID: 32680494 PMCID: PMC7367377 DOI: 10.1186/s12885-020-07157-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 07/09/2020] [Indexed: 12/15/2022] Open
Abstract
Background As one of the most common cancers with high mortality in the world, we are still facing a huge challenge in the prevention and treatment of colon cancer. With the rapid development of high throughput technologies, new biomarkers identification for colon cancer has been confronted with the new opportunities and challenges. Methods We firstly constructed functional networks for each sample of colon adenocarcinoma (COAD) by using a sample-specific network (SSN) method which can construct individual-specific networks based on gene expression profiles of a single sample. The functional genes and interactions were identified from the functional networks, respectively. Results Classification and subtyping were used to test the function of the functional genes and interactions. The results of classification showed that the functional genes could be used as diagnostic biomarkers. The subtypes displayed different mechanisms, which were shown by the functional and pathway enrichment analysis for the representative genes of each subtype. Besides, subtype-specific molecular patterns were also detected, such as subtype-specific clinical and mutation features. Finally, 12 functional genes and 13 functional edges could serve as prognosis biomarkers since they were associated with the survival rate of COAD. Conclusions In conclusion, the functional genes and interactions in the constructed functional network could be used as new biomarkers for COAD.
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Affiliation(s)
- Fuyan Hu
- Department of Statistics, School of Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, China
| | - Qing Wang
- Department of Traditional Chinese Medicine of Wuhan Puren Hospital, Affiliated Hospital of Wuhan University of Science and Technology, Benxi Street 1#, Qingshan District, Wuhan, Hubei, P.R. China
| | - Zhiyuan Yang
- College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou, People's Republic of China
| | - Zeng Zhang
- Department of Statistics, School of Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, China
| | - Xiaoping Liu
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China.
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12
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Yan K, Yang Y, Zhang Y, Zhao W, Liao L. Normalization Method Utilizing Endogenous Proteins for Quantitative Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1380-1388. [PMID: 32268065 DOI: 10.1021/jasms.0c00012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We developed a normalization method utilizing the expression levels of a panel of endogenous proteins as normalization standards (EPNS herein). We tested the validity of the method using two sets of tandem mass tag (TMT)-labeled data and found that this normalization method effectively reduced global intensity bias at the protein level. The coefficient of variation (CV) of the overall median was reduced by 55% and 82% on average, compared to the reduction by 72% and 86% after normalization using the upper quartile. Furthermore, we used differential protein expression analysis and statistical learning to identify biomarkers for colorectal cancer from a CPTAC data set. The expression changes of a panel of proteins, including NUP205, GTPBP4, CNN2, GNL3, and S100A11, all of which highly correlate with colorectal cancer. Applying these five proteins as model features, random forest modeling obtained prediction results with the maximum AUC of 0.9998 using EPNS-normalized data, comparing favorably to the AUC of 0.9739 using the raw data. Thus, the normalization method based on EPNS reduced the global intensity bias and is applicable for quantitative proteomic analysis.
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Affiliation(s)
- Kai Yan
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yueying Yang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yunpeng Zhang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wanbing Zhao
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
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PBX3 Promotes Tumor Growth and Angiogenesis via Activation of AT1R/VEGFR2 Pathway in Papillary Thyroid Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8954513. [PMID: 32047817 PMCID: PMC7007751 DOI: 10.1155/2020/8954513] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/20/2019] [Accepted: 07/29/2019] [Indexed: 11/17/2022]
Abstract
PBX3 (Pre-B-cell leukemia homeobox 3) had been considered to be a multifunctional oncogene which involved in tumor growth, invasion, and metastasis in leukemia and some solid tumors. However, the contribution of PBX3 to papillary thyroid carcinoma (PTC) remains unclear. In this study, we found that PBX3 expression was significantly upregulated in PTC tissues compared to adjacent normal tissues, and high levels of PBX3 were correlated with tumor size, lymphatic metastasis, TMN stage, and poor prognosis of PTC patients. Overexpression of PBX3 in PTC cell lines promoted cell proliferation. Consistently, knockdown of PBX3 by shRNA induced cell cycle arrest at G0/G1 phase, and inhibited angiogenesis and tumor growth in vitro and in vivo. Furthermore, PBX3 promoted PTC cell proliferation and angiogenesis through activation of AT1R/VEGFR2 pathway while overexpression of AT1R and treatment with VEGFA reversed PBX3-shRNA-induced decreased phosphorylation of VEGFR2 and its downstream (ERK1/2, AKT and Src). It demonstrated that PBX3 could be used as a potential prognostic biomarker and therapeutic target for PTC.
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Park KM, Lee HJ, Koo KT, Ben Amara H, Leesungbok R, Noh K, Lee SC, Lee SW. Oral Soft Tissue Regeneration Using Nano Controlled System Inducing Sequential Release of Trichloroacetic Acid and Epidermal Growth Factor. Tissue Eng Regen Med 2020; 17:91-103. [PMID: 31970697 DOI: 10.1007/s13770-019-00232-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/23/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The effect of nano controlled sequential release of trichloroacetic acid (TCA) and epidermal growth factor (EGF) on the oral soft tissue regeneration was determined. METHODS Hydrophobically modified glycol chitosan (HGC) nano controlled system was developed for the sequential release of TCA and EGF, and the release pattern was identified. The HGC-based nano controlled release system was injected into the critical-sized defects created in beagles' palatal soft tissues. The palatal impression and its scanned body was obtained on various time points post-injection, and the volumetric amount of soft tissue regeneration was compared among the three groups: CON (natural regeneration control group), EXP1 (TCA-loaded nano controlled release system group), EXP2 (TCA and EGF individually loaded nano controlled release system). DNA microarray analysis was performed and various soft tissue regeneration parameters in histopathological specimens were measured. RESULTS TCA release was highest at Day 1 whereas EGF release was highest at Day 2 and remained high until Day 3. In the volumetric measurements of impression body scans, no significant difference in soft tissue regeneration between the three groups was shown in two-way ANOVA. However, in the one-way ANOVA at Day 14, EXP2 showed a significant increase in soft tissue regeneration compared to CON. High correlation was determined between the histopathological results of each group. DNA microarray showed up-regulation of various genes and related cell signaling pathways in EXP2 compared to CON. CONCLUSION HGC-based nano controlled release system for sequential release of TCA and EGF can promote regeneration of oral soft tissue defects.
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Affiliation(s)
- Kwang Man Park
- Department of Dentistry, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Hong Jae Lee
- Department of Maxillofacial Biomedical Engineering and Institute of Oral Biology, School of Dentistry, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Ki-Tae Koo
- Department of Periodontology and Dental Research Institute Translational Research Laboratory for Tissue Engineering (TTE), School of Dentistry, Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Heithem Ben Amara
- Department of Periodontology and Dental Research Institute Translational Research Laboratory for Tissue Engineering (TTE), School of Dentistry, Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Richard Leesungbok
- Department of Biomaterials and Prosthodontics, Kyung Hee University Hospital at Gangdong Institute of Oral Biology, School of Dentistry, Kyung Hee University, 892 Dongnam-ro, Gangdong-gu, Seoul, 05278, Republic of Korea
| | - Kwantae Noh
- Department of Prosthodontics, School of Dentistry, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Sang Cheon Lee
- Department of Maxillofacial Biomedical Engineering and Institute of Oral Biology, School of Dentistry, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea.
| | - Suk Won Lee
- Department of Biomaterials and Prosthodontics, Kyung Hee University Hospital at Gangdong Institute of Oral Biology, School of Dentistry, Kyung Hee University, 892 Dongnam-ro, Gangdong-gu, Seoul, 05278, Republic of Korea.
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15
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Qi M, Li L, Lu Y, Chen H, Zhang M, Wang M, Ge L, Yang J, Shi N, Chen T, Tang X. Proteome profiling to identify peroxiredoxin 1 interacting protein partners in nicotine-associated oral leukoplakia. Arch Oral Biol 2019; 108:104537. [PMID: 31525533 DOI: 10.1016/j.archoralbio.2019.104537] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/31/2019] [Accepted: 08/21/2019] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Tobacco smoking is one of the main risk factors for oral squamous cell carcinoma (OSCC) and can induce generation of reactive oxygen species (ROS). In our previous studies, we demonstrated that nicotine, the major ingredient in tobacco, can upregulate an important antioxidant enzyme Peroxiredoxin 1 (Prx1), in oral leukoplakia (OLK), an oral precancerous lesion. The underlying regulatory mechanisms, however, remain unclear. This study aims to identify regulatory mechanisms of nicotine and identify Prx1 interacting proteins in nicotine-associated OLK. DESIGN Liquid chromatography-tandem mass spectrometry (LC-MS/MS) combined with bioinformatics analysis was conducted to profile Prx1 binding proteins in human dysplastic oral keratinocyte (DOK) cells. Candidate interaction proteins were further verified using Co-immunoprecipitation (Co-IP), Western blot or Duolink assay in 4-nitro-quinoline-1-oxide (4NQO)-induced OLK in mice and human OLK tissues. RESULTS We identified Thioredoxin (Trx), Nucleolar GTP-binding protein 1 (GTPBP4), GTP-binding protein Di-Ras2 (DIRAS2) and apoptosis signal-regulating kinase 1 (ASK1) as key Prx1 interacting proteins regulated by nicotine. Our data showed that nicotine upregulated Trx, GTPBP4, DIRAS2, and downregulated ASK1 in 4NQO-induced OLK in mice, at least in part dependent on Prx1. The modulations of Trx, GTPBP4, DIRAS2 and ASK1 by nicotine were also found in OLK smokers compared to OLK non-smokers. The in-situ interaction of Trx, GTPBP4, DIRAS2 and ASK1 with Prx1 were validated in human OLK tissues. CONCLUSION Nicotine may promote OLK development via regulating Prx1 binding proteins Trx, GTPBP4, DIRAS2 and ASK1. The results of this study will help to develop therapeutic approaches for OLK in humans targeting Prx1 interacting protein network.
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Affiliation(s)
- Moci Qi
- Division of Oral Pathology, Beijing Institute of Dental Research, Beijing Key Laboratory, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, No. 4 TiantanXili, Dongcheng District, Beijing 100050, China
| | - Lingyu Li
- Division of Oral Pathology, Beijing Institute of Dental Research, Beijing Key Laboratory, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, No. 4 TiantanXili, Dongcheng District, Beijing 100050, China
| | - Yunping Lu
- Division of Oral Pathology, Beijing Institute of Dental Research, Beijing Key Laboratory, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, No. 4 TiantanXili, Dongcheng District, Beijing 100050, China
| | - Hui Chen
- Division of Oral Pathology, Beijing Institute of Dental Research, Beijing Key Laboratory, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, No. 4 TiantanXili, Dongcheng District, Beijing 100050, China
| | - Min Zhang
- Division of Oral Pathology, Beijing Institute of Dental Research, Beijing Key Laboratory, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, No. 4 TiantanXili, Dongcheng District, Beijing 100050, China
| | - Min Wang
- Division of Oral Pathology, Beijing Institute of Dental Research, Beijing Key Laboratory, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, No. 4 TiantanXili, Dongcheng District, Beijing 100050, China
| | - Lihua Ge
- Division of Oral Pathology, Beijing Institute of Dental Research, Beijing Key Laboratory, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, No. 4 TiantanXili, Dongcheng District, Beijing 100050, China
| | - Jing Yang
- Division of Oral Pathology, Beijing Institute of Dental Research, Beijing Key Laboratory, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, No. 4 TiantanXili, Dongcheng District, Beijing 100050, China
| | - Ni Shi
- Division of Medical Oncology, Department of Internal Medicine, The Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Tong Chen
- Division of Medical Oncology, Department of Internal Medicine, The Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH 43210, USA.
| | - Xiaofei Tang
- Division of Oral Pathology, Beijing Institute of Dental Research, Beijing Key Laboratory, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, No. 4 TiantanXili, Dongcheng District, Beijing 100050, China.
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Liu WB, Jia WD, Ma JL, Xu GL, Zhou HC, Peng Y, Wang W. Knockdown of GTPBP4 inhibits cell growth and survival in human hepatocellular carcinoma and its prognostic significance. Oncotarget 2017; 8:93984-93997. [PMID: 29212203 PMCID: PMC5706849 DOI: 10.18632/oncotarget.21500] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 09/08/2017] [Indexed: 01/08/2023] Open
Abstract
GTP-binding protein 4 (GTPBP4), as a novel member of GTPases involved in the synthesis of 60S subunit and maturation, is closely related to cell proliferation and growth. Till now, a small number of existing studies have found a contradictory dual role of GTPBP4 in cancer. Whether the expression level of GTPBP4 in hepatocellular carcinoma (HCC) is associated with the patients' prognosis or its function and underlying molecular mechanisms still remains unclear. In the present study, the above issues were explored for the first time. Our results showed that GTPBP4 was overexpressed in HCC and knockdown of GTPBP4 delayed cell proliferation, impaired colony formation ability, induced cell cycle arrest in G2/M period and promoted apoptosis in HCC cell lines. Besides, in vivo xenograft nude mice model revealed that GTPBP4 knockdown could significantly suppress HCC tumorigenesis. Gene microarray and further pathway enrichment analyses indicated that ERBB signaling pathway was the most significantly changed one. More importantly, high GTPBP4 expression level significantly correlated to the poor prognosis of HCC patients. Taken together, all these findings suggest that GTPBP4 serves as an oncogene and plays a pivotal role in HCC development, which will be a potential therapeutic target or a biomarker for HCC.
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Affiliation(s)
- Wen-Bin Liu
- Department of Hepatic Surgery, Anhui Provincial Hospital, Anhui Medical University, Hefei 230001, P.R. China.,Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Hefei 230001, P.R. China
| | - Wei-Dong Jia
- Department of Hepatic Surgery, Anhui Provincial Hospital, Anhui Medical University, Hefei 230001, P.R. China.,Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Hefei 230001, P.R. China
| | - Jin-Liang Ma
- Department of Hepatic Surgery, Anhui Provincial Hospital, Anhui Medical University, Hefei 230001, P.R. China.,Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Hefei 230001, P.R. China
| | - Ge-Liang Xu
- Department of Hepatic Surgery, Anhui Provincial Hospital, Anhui Medical University, Hefei 230001, P.R. China.,Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Hefei 230001, P.R. China
| | - Hang-Cheng Zhou
- Department of Pathology, Anhui Provincial Hospital, Anhui Medical University, Hefei 230001, P.R. China
| | - Yan Peng
- Department of Pathology, Anhui Provincial Hospital, Anhui Medical University, Hefei 230001, P.R. China
| | - Wei Wang
- Department of Medical Oncology, Anhui Provincial Hospital, Anhui Medical University, Hefei 230001, P.R. China
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