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Zhu L, Sun L, Zhang Y, Liu X, Li X, Zhou Z, Cui Y, Zhou CX, Li TJ. PON3::LCN1 and HTN3::MSANTD3 Gene Fusions With NR4A3/NR4A2 Expression in Salivary Acinic Cell Carcinoma. Am J Surg Pathol 2024; 48:681-690. [PMID: 38682454 DOI: 10.1097/pas.0000000000002219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Acinic cell carcinoma of the salivary gland (AciCC) is a low-grade carcinoma characterized by the overexpression of the transcription factor nuclear receptor subfamily 4 group A member 3 (NR4A3). AciCC has been the subject of a few molecular research projects. This study delves into AciCC's molecular landscape to identify additional alterations and explore their clinical implications. RNA sequencing and immunohistochemical staining for markers NR4A3/NR4A2, DOG-1, S100, and mammaglobin were utilized on 41 AciCCs and 11 secretory carcinoma (SC) samples. NR4A3 was evident in 35 AciCCs, while the residual 6 were NR4A3-negative and NR4A2-positive; SC samples were consistently NR4A3-negative. A novel fusion, PON3 exon 1- LCN1 exon 5, was detected in 9/41 (21.9%) AciCCs, exhibiting a classical histologic pattern with serous cell components growing in solid sheets alongside the intercalated duct-like component. Clinical follow-up of 39 patients over a median of 59 months revealed diverse prognostic outcomes: 34 patients exhibited no disease evidence, whereas the remaining 5 experienced poorer prognosis, involving local recurrence, lymph node, and distant metastasis, and disease-associated death, 4 of which harbored the PON3::LCN1 fusion. In addition, the HTN3::MSANTD3 fusion was recurrently identified in 7/41 AciCC cases. SC patients lacked both fusions. Immunohistochemistry uncovered differential expression of DOG-1, S100, and mammaglobin across samples, providing nuanced insights into their roles in AciCC. This study accentuates PON3::LCN1 and HTN3::MSANTD3 fusions as recurrent molecular events in AciCC, offering potential diagnostic and prognostic utility and propelling further research into targeted therapeutic strategies.
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MESH Headings
- Humans
- Male
- Carcinoma, Acinar Cell/genetics
- Carcinoma, Acinar Cell/pathology
- Female
- Salivary Gland Neoplasms/genetics
- Salivary Gland Neoplasms/pathology
- Salivary Gland Neoplasms/mortality
- Salivary Gland Neoplasms/metabolism
- Salivary Gland Neoplasms/chemistry
- Middle Aged
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/analysis
- Adult
- Aged
- Nuclear Receptor Subfamily 4, Group A, Member 2/genetics
- Nuclear Receptor Subfamily 4, Group A, Member 2/analysis
- Receptors, Steroid/genetics
- Receptors, Steroid/metabolism
- Receptors, Thyroid Hormone/genetics
- Receptors, Thyroid Hormone/analysis
- Receptors, Thyroid Hormone/metabolism
- Young Adult
- Gene Fusion
- Aged, 80 and over
- DNA-Binding Proteins/genetics
- Oncogene Proteins, Fusion/genetics
- Immunohistochemistry
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Affiliation(s)
- Lijing Zhu
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, Beijing, China
- National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China
| | - Lisha Sun
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ye Zhang
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, Beijing, China
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoxiao Liu
- Central laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - XueFen Li
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China
| | - Zheng Zhou
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, Beijing, China
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yajuan Cui
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, Beijing, China
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chuan-Xiang Zhou
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, Beijing, China
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tie-Jun Li
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, Beijing, China
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Reduced Expression of SFRP1 is Associated with Poor Prognosis and Promotes Cell Proliferation in Breast Cancer: An Integrated Bioinformatics Approach. INDIAN JOURNAL OF GYNECOLOGIC ONCOLOGY 2022. [DOI: 10.1007/s40944-022-00650-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Ding Q, Li H, Xu Z, Hu K, Ye Q. Identification of CFHR4 associated with poor prognosis of hepatocellular carcinoma. Front Oncol 2022; 12:812663. [PMID: 36338737 PMCID: PMC9632743 DOI: 10.3389/fonc.2022.812663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most leading causes of cancer death worldwide. The 5-year survival rate of HCC patients remains low due to the lack of early-stage symptoms. Human complement factor H-related protein 4 (CFHR4) is a critical gene that belongs to the factor H family of plasma glycoproteins, which has not been linked to HCC development. The correlations between CFHR4 and prognosis and tumor-infiltrating lymphocytes in HCC are yet unknown. The present study demonstrated the involvement of CFHR4 in HCC via data mining approaches. Results A total of 18 upregulated and 67 down-regulated differentially expressed genes (DEGs) were identified. Importantly, CFHR4, which was screened from DEGs, was shown to express at a lower level in HCC tumor tissue than normal tissues. Western blotting (WB), immunohistochemical (IHC) and quantitative reverse transcription PCR (qRT-PCR) experiments of clinical samples further validated CFHR4 was aberrantly expressed in HCC patients; Data from TCGA showed that CFHR4 was inversely correlated with a cancer family history, histological grade, tumor node metastasis (TNM) stage, and serum AFP level of HCC patients; Univariate and multivariate analyses revealed that low expression of CFHR4 was an independent predictive marker in patients with HCC; Kaplan-Meier analysis showed that the lower expression of CFHR4 was significantly associated with the progression of HCC and poor prognosis rates. Furthermore, TIMER analysis indicated that CFHR4 expression levels had correlations with infiltrating levels of immune cells in HCC. Conclusion CFHR4 expression was low in HCC and was significantly related to the poor prognosis of HCC and the level of immune infiltration. CFHR4 played important roles in regulating the initiation and progression of HCC and could be a potential biomarker for the diagnosis and prognosis of HCC. Methods The expression of CFHR4 was analyzed by GEO and TCGA-LIHC database and verified by WB and IHC assay. The biological function of CFHR4 was performed by GO and KEGG enrichment analysis, and the genomic alteration of CFHR4 was investigated by cBioPortal database.The correlation between CFHR4 expression and clinical relevance was evaluated through Cox proportional hazards model, and the correlation between CFHR4 expression and tumor immune infiltrates were studied by TIMER database.
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Affiliation(s)
- Qinglin Ding
- Sino-German Biomedical Center, National Center for Cellular Regulation and Molecular Pharmaceutics, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan, China
| | - Hanluo Li
- Sino-German Biomedical Center, National Center for Cellular Regulation and Molecular Pharmaceutics, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan, China
| | - Zhigao Xu
- Institute of Hepatobiliary Diseases of Wuhan University, National Quality Control Center for Donated Organ Procurement, Hubei Key Laboratory of Medical Technology on Transplantation, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kanghong Hu
- Sino-German Biomedical Center, National Center for Cellular Regulation and Molecular Pharmaceutics, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan, China
| | - Qifa Ye
- Institute of Hepatobiliary Diseases of Wuhan University, National Quality Control Center for Donated Organ Procurement, Hubei Key Laboratory of Medical Technology on Transplantation, Zhongnan Hospital of Wuhan University, Wuhan, China
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Targeted proteomics using parallel reaction monitoring confirms salivary proteins indicative of metastatic triple-negative breast cancer. J Proteomics 2022; 267:104701. [PMID: 35995384 DOI: 10.1016/j.jprot.2022.104701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/28/2022] [Accepted: 08/04/2022] [Indexed: 12/11/2022]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype due to the absence of hormonal receptors. Our study aimed to identify and determine the effectiveness of salivary proteins as candidate markers for metastatic TNBC subtype using parallel reaction monitoring mass spectrometry (PRM-MS). Three salivary proteins (lipocalin-1, SMR3B, and plastin-2) that showed significant differential expression in label-free quantitation (LFQ) between TNBC (N = 6) and health subjects (HS; N = 6) were selected for further validation. The developed PRM assay was used to quantify peptides GLST and NNLE (lipocalin-1), VYAL and MINL (Plastin-2) and GPYP, and IPPP (SMR3B) on a different cohort of TNBC patients (N = 20) and HS (N = 20) for evaluating their discriminating performances. Quantitative validation using PRM correlated well with the LFQ results, and 5 peptides from three proteins showed a similar up-or down-regulation. Subsequently, these proteins were validated by Western blot analysis. Compared to one protein's performance as an individual marker, the five-signature panel with salivary GLST, VYAL, MINL, GPYP, and IPPP achieved better performance in differentiating aggressive TNBC and HS with sensitivity (80%) and specificity (95%). Targeted proteomic analysis of the prioritized proteins highlights a peptide-based signature in saliva as the potential predictor to distinguish between TNBC and HS. SIGNIFICANCE OF THE STUDY: This study was designed to identify and quantify potential markers in saliva from the triple-negative breast cancer (TNBC) patients using parallel reaction monitoring assay. Three salivary proteins, Lipocalin-1 (LCN-1), Submaxillary androgen-regulated protein 3B (SMR3B), and Plastin-2 (LCP-1) selected in the discovery-phase were further quantified by targeted proteomics and Western blots. The salivary proteins successfully differentiated TNBC patients from healthy subjects with a sensitivity (80%) and specificity (95%).
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5
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He Y, Song H, Jiang Y, Ren W. Identification of Immune-Related Prognostic Markers in Gastric Cancer. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:7897274. [PMID: 35299682 PMCID: PMC8923768 DOI: 10.1155/2022/7897274] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/11/2022] [Indexed: 01/09/2023]
Abstract
Gastric cancer (GC) is a malignant tumor with a high fatality rate. Poor prognosis is the main cause of death caused by GC. In this study, the gene expression difference between GC and the control group was analyzed. Differentially expressed genes (DEGs) related to immunity were screened for enrichment analysis. The differences in immune cell infiltration and immune function between GC and normal were identified. Cox regression analysis and survival analysis were used to determine the prognostic genes of GC in TCGA and GSE62254. The potential prognostic role of genes was further evaluated by risk score. Difference genes in GC were analyzed in TCGA. Candidate genes in TCGA and GSE62254 are analyzed, and prognostic genes are determined. The potential prognostic role of genes was further evaluated by risk score. The immune-related prognostic markers in GC were determined. FABP4, LBP, LCN1, CMA1, INHBA, ANGPTL1, ACKR1, GHR, and OGN may be used as markers for monitoring the prognosis of GC in the future.
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Affiliation(s)
- Yanxin He
- Department of Gastroenterology, Provincial Hospital Affiliated to Shandong University, Jinan 266042, Shandong, China
- Department of Gastroenterology, The Affiliated Qingdao Central Hospital of Qingdao University, Qingdao 266000, Shandong, China
| | - Haiping Song
- Department of Oncology, The Affiliated Qingdao Central Hospital of Qingdao University, Qingdao 266000, Shandong, China
| | - Yanfang Jiang
- Department of Gastroenterology, The Affiliated Qingdao Central Hospital of Qingdao University, Qingdao 266000, Shandong, China
| | - Wanhua Ren
- Department of Gastroenterology, Provincial Hospital Affiliated to Shandong University, Jinan 266042, Shandong, China
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6
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Cao C, Yu R, Gong W, Liu D, Zhang X, Fang Y, Xia Y, Zhang W, Gao Q. Genomic mutation features identify distinct BRCA-associated mutation characteristics in endometrioid carcinoma and endometrioid ovarian carcinoma. Aging (Albany NY) 2021; 13:24686-24709. [PMID: 34837690 PMCID: PMC8660599 DOI: 10.18632/aging.203710] [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: 06/11/2021] [Accepted: 10/25/2021] [Indexed: 01/19/2023]
Abstract
Although endometrioid carcinoma (EC) and endometrioid ovarian carcinoma (EnOC) display similar pathological features, their molecular characteristics remain to be determined. Somatic mutation data from 2777 EC, 423 EnOC, and 57 endometriosis patients from the Catalogue of Somatic Mutations in Cancer (COSMIC) dataset were analyzed and showed similar profiles with different mutation frequencies among them. By using 275 overlapping mutated genes, EC was clustered into two groups with different disease outcomes and different clinical characteristics. Although BRCA-associated mutation characteristics were identified in both EC and EnOC, the mutation frequencies of BRCA1 (P=0.0146), BRCA2 (P=0.0321), ATR (P=3.25E-11), RAD51 (P=3.95E-08), RAD1 (P=0.0003), TP53 (P=6.11E-33), and BRIP1 (P=2.90E-09) were higher in EnOC. Further analysis showed that EnOC cell lines with BRCA-associated mutation characteristics were more sensitive to poly ADP-ribose polymerase (PARP) inhibitors than EC cell lines, including olaparib, talazoparib, rucaparib, and veliparib. Moreover, based on BRCA-associated mutational and transcriptomic profiles, EC with BRCA-associated mutational burdens shows lower levels of immune cell infiltration, higher expression of immunosuppressive checkpoint molecules and worse prognosis than EC without BRCA mutation. Our study comprehensively analyzed the genome mutation features of EC and EnOC and provide insights into the molecular characteristics of EC and EnOC.
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Affiliation(s)
- Canhui Cao
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ruidi Yu
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wenjian Gong
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dan Liu
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoxue Zhang
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yong Fang
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yu Xia
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Zhang
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qinglei Gao
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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7
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Glasgow BJ. Tear Lipocalin and Lipocalin-Interacting Membrane Receptor. Front Physiol 2021; 12:684211. [PMID: 34489718 PMCID: PMC8417070 DOI: 10.3389/fphys.2021.684211] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/13/2021] [Indexed: 11/24/2022] Open
Abstract
Tear lipocalin is a primate protein that was recognized as a lipocalin from the homology of the primary sequence. The protein is most concentrated in tears and produced by lacrimal glands. Tear lipocalin is also produced in the tongue, pituitary, prostate, and the tracheobronchial tree. Tear lipocalin has been assigned a multitude of functions. The functions of tear lipocalin are inexorably linked to structural characteristics that are often shared by the lipocalin family. These characteristics result in the binding and or transport of a wide range of small hydrophobic molecules. The cavity of tear lipocalin is formed by eight strands (A-H) that are arranged in a β-barrel and are joined by loops between the β-strands. Recently, studies of the solution structure of tear lipocalin have unveiled new structural features such as cation-π interactions, which are extant throughout the lipocalin family. Lipocalin has many unique features that affect ligand specificity. These include a capacious and a flexible cavity with mobile and short overhanging loops. Specific features that confer promiscuity for ligand binding in tear lipocalin will be analyzed. The functions of tear lipocalin include the following: antimicrobial activities, scavenger of toxic and tear disruptive compounds, endonuclease activity, and inhibition of cysteine proteases. In addition, tear lipocalin binds and may modulate lipids in the tears. Such actions support roles as an acceptor for phospholipid transfer protein, heteropolymer formation to alter viscosity, and tear surface interactions. The promiscuous lipid-binding properties of tear lipocalin have created opportunities for its use as a drug carrier. Mutant analogs have been created to bind other molecules such as vascular endothelial growth factor for medicinal use. Tear lipocalin has been touted as a useful biomarker for several diseases including breast cancer, chronic obstructive pulmonary disease, diabetic retinopathy, and keratoconus. The functional possibilities of tear lipocalin dramatically expanded when a putative receptor, lipocalin-interacting membrane receptor was identified. However, opposing studies claim that lipocalin-interacting membrane receptor is not specific for lipocalin. A recent study even suggests a different function for the membrane protein. This controversy will be reviewed in light of gene expression data, which suggest that tear lipocalin has a different tissue distribution than the putative receptor. But the data show lipocalin-interacting membrane receptor is expressed on ocular surface epithelium and that a receptor function here would be rational.
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Affiliation(s)
- Ben J. Glasgow
- Departments of Ophthalmology, Pathology and Laboratory Medicine, Jules Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
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Deng Y, Zhao H, Ye L, Hu Z, Fang K, Wang J. Correlations Between the Characteristics of Alternative Splicing Events, Prognosis, and the Immune Microenvironment in Breast Cancer. Front Genet 2021; 12:686298. [PMID: 34194482 PMCID: PMC8236959 DOI: 10.3389/fgene.2021.686298] [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: 03/26/2021] [Accepted: 05/17/2021] [Indexed: 12/28/2022] Open
Abstract
Objective Alternative splicing (AS) is the mechanism by which a few genes encode numerous proteins, and it redefines the concept of gene expression regulation. Recent studies showed that dysregulation of AS was an important cause of tumorigenesis and microenvironment formation. Therefore, we performed a systematic analysis to examine the role of AS in breast cancer (Breast Cancer, BrCa) progression. Methods The present study included 993 BrCa patients from The Cancer Genome Atlas (TCGA) database in the genome-wide analysis of AS events. We used differential and prognostic analyses and found differentially expressed alternative splicing (DEAS) events and independent prognostic factors related to patients' overall survival (OS) and disease-free survival (DFS). We divided the patients into two groups based on these AS events and analyzed their clinical features, molecular subtyping and immune characteristics. We also constructed a splicing factor (SF) regulation network for key AS events and verified the existence of AS events in tissue samples using real-time quantitative PCR. Results A total of 678 AS events were identified as differentially expressed, of which 13 and 10 AS events were independent prognostic factors of patients' OS and DFS, respectively. Unsupervised clustering analysis based on these prognostic factors indicated that the Cluster 1 group had a better prognosis and more immune cell infiltration. SFs were significantly related to the expression of AS events, and AA-RPS21 was significantly upregulated in tumors. Conclusion Alternative splicing expands the mechanism of breast cancer progression from a new perspective. Notably, alternative splicing may affect the patient's prognosis by affecting the infiltration of immune cells. Our research provides important guidance for subsequent studies of AS in breast cancer.
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Affiliation(s)
- Youyuan Deng
- Department of General Surgery, Xiangtan Central Hospital, Xiangtan, China
| | - Hongjun Zhao
- Department of General Surgery, Xiangtan Central Hospital, Xiangtan, China
| | - Lifen Ye
- Department of General Surgery, Xiangtan Central Hospital, Xiangtan, China
| | - Zhiya Hu
- Department of Pharmacy, Third Hospital of Changsha, Changsha, China
| | - Kun Fang
- Department of Surgery, Yinchuan Maternal and Child Health Hospital, Yinchuan, China
| | - Jianguo Wang
- Department of General Surgery, Xiangtan Central Hospital, Xiangtan, China
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Huo L, Tan Y, Wang S, Geng C, Li Y, Ma X, Wang B, He Y, Yao C, Ouyang T. Machine Learning Models to Improve the Differentiation Between Benign and Malignant Breast Lesions on Ultrasound: A Multicenter External Validation Study. Cancer Manag Res 2021; 13:3367-3379. [PMID: 33889025 PMCID: PMC8057795 DOI: 10.2147/cmar.s297794] [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: 12/23/2020] [Accepted: 03/23/2021] [Indexed: 12/24/2022] Open
Abstract
Purpose This study aimed to establish and evaluate the usefulness of a simple, practical, and easy-to-promote machine learning model based on ultrasound imaging features for diagnosing breast cancer (BC). Materials and Methods Logistic regression, random forest, extra trees, support vector, multilayer perceptron, and XG Boost models were developed. The modeling data set of 1345 cases was from a tertiary class A hospital in China. The external validation data set of 1965 cases were from 3 tertiary class A hospitals and 2 primary hospitals. The area under the receiver operating characteristic curve (AUC) was used as the main evaluation index, and pathological biopsy was used as the gold standard for evaluating each model. Diagnostic capability was also compared with that of clinicians. Results Among the six models, the logistic model showed superior diagnostic efficiency, with an AUC of 0.771 and 0.906 and Brier scores of 0.181 and 0.165 in the test and validation sets, respectively. The AUCs of the clinician diagnosis and the logistic model were 0.913 and 0.906. Their AUCs in the tertiary class A hospitals were 0.915 and 0.915, respectively, and were 0.894 and 0.873 in primary hospitals, respectively. Conclusion The externally validated logical model can be used to distinguish between malignant and benign breast lesions in ultrasound images. Compared with clinician diagnosis, the logistic model has better diagnostic efficiency, making it potentially useful to assist in screening, particularly in lower level medical institutions. Trial Registration http://www.clinicaltrials.gov. ClinicalTrials.gov ID: NCT03080623.
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Affiliation(s)
- Ling Huo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Yao Tan
- Department of Biostatistics, Peking University First Hospital, Beijing, People's Republic of China
| | - Shu Wang
- Department of Breast Center, Peking University People's Hospital, Beijing, People's Republic of China
| | - Cuizhi Geng
- The Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Yi Li
- Shunyi District Health Care Hospital for Women and Children of Beijing, Beijing, People's Republic of China
| | - XiangJun Ma
- Haidian Maternal and Child Health Hospital, Beijing, People's Republic of China
| | - Bin Wang
- Department of Biostatistics, Peking University First Hospital, Beijing, People's Republic of China
| | - YingJian He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Chen Yao
- Department of Biostatistics, Peking University First Hospital, Beijing, People's Republic of China.,Peking University Clinical Research Institute, Peking University Health Science Center, Beijing, People's Republic of China
| | - Tao Ouyang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
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Zhang C, Wang L, Liu H, Deng G, Xu P, Tan Y, Xu Y, Liu B, Chen Q, Tian D. ADPRH is a prognosis-related biomarker and correlates with immune infiltrates in low grade glioma. J Cancer 2021; 12:2912-2920. [PMID: 33854592 PMCID: PMC8040889 DOI: 10.7150/jca.51643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 03/03/2021] [Indexed: 12/12/2022] Open
Abstract
Background: ADPRH is a modulator of CD8+ T cell functions, and dysregulation of ADPRH has been identified to involve in carcinogenesis of cancers. However, the association of ADPRH with low grade glioma (LGG) remains unclear. Methods: The expression of ADPRH in LGG was first analyzed in GLIOVIS and GEPIA databases and then validated by real-time PCR (rt-PCR), immunochemistry and human protein atlas (HPA). Univariate and multivariate Cox analysis and Kaplan-Meier plots were designed to assess the prognostic value of ADPRH in LGG. The correlation of ADPRH and immune infiltration was evaluated by data in TIMER and ESTIMATE databases. Gene set enrichment analysis was conducted to detect biological processes associated with ADPRH. Results: ADPRH was significantly upregulated in LGG in comparison to non-tumor brain samples in transcriptomic and proteomic levels. The high ADPRH expression indicated unfavorable overall survival (OS) and progression-free survival (PFS) in patients with LGG using Kaplan-Meier plots. And multivariate Cox analysis demonstrated the expression level of ADPRH was an independent prognosis-predicting index for OS and PFS of LGG patients in all cohorts separately. Gene Set Enrichment Analysis (GSEA) indicated that high expression of ADPRH was involved in the upregulation of P53 signaling pathway, KRAS signaling pathway, IL6/JAK-STAT3 signaling and TNF-beta signaling pathways. By TIMER and ESTIMATE databases, we identified ADPRH expression had strong correlation with tumor immune infiltrating cells (TIICs). Conclusions: In summary, our findings demonstrated that ADPRH might be a potential prognostic biomarker and correlated with TIICs in LGG.
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Affiliation(s)
- Chunyu Zhang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R.C
| | - Long Wang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R.C
| | - Haitao Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Jiaxing University, Jiaxing, 314001, Zhejiang Province, P.R.C
| | - Gang Deng
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R.C
| | - Pengfei Xu
- Sun Yat-sen University, The Seventh Affiliated Hospital, Shenzhen, 518000, Guangdong Province, P.R.C
| | - Yinqiu Tan
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R.C
| | - Yang Xu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R.C
| | - Baohui Liu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R.C
| | - Qianxue Chen
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R.C
| | - Daofeng Tian
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R.C
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11
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A five-immune-related genes-based prognostic signature for colorectal cancer. Int Immunopharmacol 2020; 88:106866. [DOI: 10.1016/j.intimp.2020.106866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/06/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
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12
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Characterization of the expression and prognostic value of 14-3-3 isoforms in breast cancer. Aging (Albany NY) 2020; 12:19597-19617. [PMID: 33052135 PMCID: PMC7732302 DOI: 10.18632/aging.103919] [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: 01/12/2020] [Accepted: 07/25/2020] [Indexed: 01/24/2023]
Abstract
The tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation proteins (14-3-3) participate in the tumorigenesis and progression of numerous malignances, but their precise prognostic values in breast cancer (BrCa) remain unknown. Here, we investigated the expression profiles and prognostic roles of 14-3-3 isoforms by employing multiple online databases. The transcriptional levels of most 14-3-3 isoforms in BrCa tissues were significantly higher than those in normal tissues. High mRNA expression of 14-3-3 beta/sigma/theta/zeta was significantly associated with poor overall survival (OS) in BrCa patients, while high mRNA expression of 14-3-3 epsilon was notably related to favorable OS. High mRNA expression of 14-3-3 beta/gamma/sigma/theta/zeta was significantly associated with poor relapse-free survival (RFS) in BrCa patients. A high mutation rate of 14-3-3 was determined to be associated with poor clinical outcomes. In addition, 14-3-3 expression was correlated with the infiltration of specific immune cells types. Analysis of the breast-specific protein-protein interaction (PPI) network suggested that 14-3-3 proteins were involved in several potential oncogenic mechanisms in BrCa. Finally, we performed experimentally validated their oncogenic roles in BrCa. Overall, our findings systematically elucidate the expression and distinct prognostic value of 14-3-3 isoforms in BrCa, which may provide potential therapeutic targets and prognostic biomarkers for BrCa.
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13
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Chen Y, Li L, Zhang J. Cell migration inducing hyaluronidase 1 (CEMIP) activates STAT3 pathway to facilitate cell proliferation and migration in breast cancer. J Recept Signal Transduct Res 2020; 41:145-152. [PMID: 32757700 DOI: 10.1080/10799893.2020.1800732] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yu Chen
- Department of Breast Surgery, The Affiliated Hospital of Putian University, Putian City, Fujian Province, China
| | - Lihong Li
- Department of Breast Surgery, The Affiliated Hospital of Putian University, Putian City, Fujian Province, China
| | - Jinfan Zhang
- Department of Breast Surgery, The Affiliated Hospital of Putian University, Putian City, Fujian Province, China
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14
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Amjad E, Asnaashari S, Sokouti B, Dastmalchi S. Systems biology comprehensive analysis on breast cancer for identification of key gene modules and genes associated with TNM-based clinical stages. Sci Rep 2020; 10:10816. [PMID: 32616754 PMCID: PMC7331704 DOI: 10.1038/s41598-020-67643-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
Breast cancer (BC), as one of the leading causes of death among women, comprises several subtypes with controversial and poor prognosis. Considering the TNM (tumor, lymph node, metastasis) based classification for staging of breast cancer, it is essential to diagnose the disease at early stages. The present study aims to take advantage of the systems biology approach on genome wide gene expression profiling datasets to identify the potential biomarkers involved at stage I, stage II, stage III, and stage IV as well as in the integrated group. Three HER2-negative breast cancer microarray datasets were retrieved from the GEO database, including normal, stage I, stage II, stage III, and stage IV samples. Additionally, one dataset was also extracted to test the developed predictive models trained on the three datasets. The analysis of gene expression profiles to identify differentially expressed genes (DEGs) was performed after preprocessing and normalization of data. Then, statistically significant prioritized DEGs were used to construct protein-protein interaction networks for the stages for module analysis and biomarker identification. Furthermore, the prioritized DEGs were used to determine the involved GO enrichment and KEGG signaling pathways at various stages of the breast cancer. The recurrence survival rate analysis of the identified gene biomarkers was conducted based on Kaplan-Meier methodology. Furthermore, the identified genes were validated not only by using several classification models but also through screening the experimental literature reports on the target genes. Fourteen (21 genes), nine (17 genes), eight (10 genes), four (7 genes), and six (8 genes) gene modules (total of 53 unique genes out of 63 genes with involving those with the same connectivity degree) were identified for stage I, stage II, stage III, stage IV, and the integrated group. Moreover, SMC4, FN1, FOS, JUN, and KIF11 and RACGAP1 genes with the highest connectivity degrees were in module 1 for abovementioned stages, respectively. The biological processes, cellular components, and molecular functions were demonstrated for outcomes of GO analysis and KEGG pathway assessment. Additionally, the Kaplan-Meier analysis revealed that 33 genes were found to be significant while considering the recurrence-free survival rate as an alternative to overall survival rate. Furthermore, the machine learning calcification models show good performance on the determined biomarkers. Moreover, the literature reports have confirmed all of the identified gene biomarkers for breast cancer. According to the literature evidence, the identified hub genes are highly correlated with HER2-negative breast cancer. The 53-mRNA signature might be a potential gene set for TNM based stages as well as possible therapeutics with potentially good performance in predicting and managing recurrence-free survival rates at stages I, II, III, and IV as well as in the integrated group. Moreover, the identified genes for the TNM-based stages can also be used as mRNA profile signatures to determine the current stage of the breast cancer.
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Affiliation(s)
- Elham Amjad
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Solmaz Asnaashari
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Babak Sokouti
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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15
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Chen Y, Wang H, Jiang Y, Zhang X, Wang Q. Transcriptional profiling to identify the key genes and pathways of pterygium. PeerJ 2020; 8:e9056. [PMID: 32411530 PMCID: PMC7204871 DOI: 10.7717/peerj.9056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/03/2020] [Indexed: 12/21/2022] Open
Abstract
Purpose Pterygium results from a variety of biological pathways that are involved in the formation of ocular surface diseases. However, the exact pathogenesis of pterygium is still unclear. Our study focused on gene expression profiles to better understand the potential mechanisms of pterygium. Methods RNA sequencing experiments were performed on clinical pterygium tissues and normal conjunctival tissues. To identify the hub genes for the development of pterygium, we further conducted weighted gene co-expression network analysis (WGCNA). qRT-PCR was utilized to validate the dysregulation of the most significant differentially expressed genes (DEGs) and key hub genes in the independent subjects. Results A total of 339 DEGs (P-adjusted < 0.05 and log2 fold change [log2FC] ≥ 1.0) were obtained that reached statistical significance with p-values < 0.05. Among them, 200 DEGs were upregulated; these genes were mainly associated with the extracellular matrix and with cell adhesion or migration. In contrast, the 139 downregulated genes were enriched for endocrine and inflammation pathways. With regard to WGCNA, five modules were assigned based on the DEG profiles, and the biological functions of each module were verified with previously published GO terms. The functions included ECM-receptor interactions, the PI3K-Akt signalling pathway and an endoplasmic reticulum (ER)-related pathway. The five hub genes with the highest connectivity in each module and the five most significant DEGs showed dysregulated expression in the independent cohort samples. Conclusions RNA sequencing and WGCNA provided novel insights into the potential regulatory mechanisms of pterygium. The identified DEGs and hub genes, which were classified into two groups according to different functions or signalings, may provide important references for further research on the molecular biology of pterygium.
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Affiliation(s)
- Yihui Chen
- Department of Ophthalmology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Haoyu Wang
- Department of Dermatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yaping Jiang
- Department of Ophthalmology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoyan Zhang
- Department of Ophthalmology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qingzhong Wang
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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16
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Gao Y, Liu M, Shi S, Sun Y, Li M, Zhang M, Sheng Z, Zhang J, Tian J. Diagnostic value of seven biomarkers for breast cancer: an overview with evidence mapping and indirect comparisons of diagnostic test accuracy. Clin Exp Med 2020; 20:97-108. [PMID: 31894424 DOI: 10.1007/s10238-019-00598-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/03/2019] [Indexed: 02/06/2023]
Abstract
Several meta-analyses have evaluated the value of biomarkers in diagnosing breast cancer, but which biomarker has the optimal diagnostic value remains unclear. This overview aimed to compare the accuracy of different biomarkers in diagnosing breast cancer. PubMed, Embase.com, the Cochrane Library of Systematic Reviews, and Web of Science were searched. The assessment of multiple systematic reviews-2 (AMSTAR-2) was used to assess the methodological quality and preferred reporting items for a systematic review and meta-analysis of diagnostic test accuracy (PRISMA-DTA) for reporting quality. Pairwise meta-analyses were performed to estimate the pooled results for each biomarker, and indirect comparisons were conducted to compare diagnostic accuracy between biomarkers. Eleven systematic reviews (SRs) involving 218 original studies were included. All SRs were of critically low methodological quality, 3 SRs had minimal reporting flaws and 8 SRs had minor flaws. The pooled sensitivity and specificity were 0.77 and 0.87 for miRNA, 0.70 and 0.87 for circulating cell-free DNA, 0.29 and 0.96 for APC gene promoter methylation, 0.69 and 0.99 for 14-3-3σ promoter methylation, 0.63 and 0.82 for CA153, 0.58 and 0.87 for CEA, and 0.73 and 0.56 for PSA. Compared with CA153 and PSA, miRNA had a higher sensitivity and specificity. The sensitivity of miRNA was higher than circulating cell-free DNA and CEA, although they had the same specificities. APC gene promoter methylation and 14-3-3σ promoter methylation were more specific than miRNA, but they had unacceptably low sensitivity. In conclusion, miRNA had better diagnostic accuracy than the other six biomarkers. But due to the low quality of included SRs, the results need to be interpreted with caution. Further study should investigate the diagnostic accuracy of different biomarkers in direct comparisons and focus on the value of combined biomarkers.
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Affiliation(s)
- Ya Gao
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Lanzhou City, 730000, Gansu Province, China
| | - Ming Liu
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Lanzhou City, 730000, Gansu Province, China
| | - Shuzhen Shi
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Lanzhou City, 730000, Gansu Province, China
| | - Yue Sun
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Lanzhou City, 730000, Gansu Province, China
| | - Muyang Li
- The Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Mei Zhang
- Department of Radiology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Zhijuan Sheng
- Department of Galactophore, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Junhua Zhang
- Evidence-Based Medicine Center, Tianjin University of Traditional Chinese Medicine, No. 312 Anshanxi Street, Nankai District, Tianjin, 300193, China.
| | - Jinhui Tian
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.
- Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Lanzhou City, 730000, Gansu Province, China.
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