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Wang C, He Z. Integrating bulk and single-cell RNA sequencing data reveals epithelial-mesenchymal transition molecular subtype and signature to predict prognosis, immunotherapy efficacy, and drug candidates in low-grade gliomas. Front Pharmacol 2023; 14:1276466. [PMID: 38053842 PMCID: PMC10694300 DOI: 10.3389/fphar.2023.1276466] [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: 08/12/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
Objective: Epithelial-mesenchymal transition (EMT) is a tightly regulated and dynamic process occurring in both embryonic development and tumor progression. Our study aimed to comprehensively explore the molecular subtypes, immune landscape, and prognostic signature based on EMT-related genes in low-grade gliomas (LGG) in order to facilitate treatment decision-making and drug discovery. Methods: We curated EMT-related genes and performed molecular subtyping with consensus clustering algorithm to determine EMT expression patterns in LGG. The infiltration level of diverse immune cell subsets was evaluated by implementing the single-sample gene set enrichment analysis (ssGSEA) and ESTIMATE algorithms. The distinctions in clinical characteristics, mutation landscape, and immune tumor microenvironment (TME) among the subtypes were subjected to further investigation. Gene Set Variation Analysis (GSVA) was performed to explore the biological pathways that were involved in subtypes. The chemo drug sensitivity and immunotherapy of subtypes were estimated through GDSC database and NTP algorithm. To detect EMT subtype-related prognostic gene modules, the analysis of weighted gene co-expression network (WGCNA) was performed. The LASSO algorithm was utilized to construct a prognostic risk model, and its efficacy was verified through an independent CGGA dataset. Finally, the expression of the hub genes from the prognostic model was evaluated through the single-cell dataset and in-vitro experiment. Results: The TCGA-LGG dataset revealed the creation of two molecular subtypes that presented different prognoses, clinical implications, TME, mutation landscapes, chemotherapy, and immunotherapy. A three-gene signature (SLC39A1, CTSA and CLIC1) based on EMT expression pattern were established through WGCNA analysis. Low-risk patients showed a positive outlook, increased immune cell presence, and higher expression of immune checkpoint proteins. In addition, several promising drugs, including birinapant, fluvastatin, clofarabine, dasatinib, tanespimycin, TAK-733, GDC-0152, AZD8330, trametinib and ingenol-mebutate had great potential to the treatment of high risk patients. Finally, CTSA and CLIC1 were highly expressed in monocyte cell through single-cell RNA sequencing analysis. Conclusion: Our research revealed non-negligible role of EMT in the TME diversity and complexity of LGG. A prognostic signature may contribute to the personalized treatment and prognostic determination.
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Affiliation(s)
- Chengcheng Wang
- Department of Pharmacy, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong, China
| | - Zheng He
- Department of Neurosurgery, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong, China
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The basement membrane-related gene signature is associated with immunity and predicts survival accurately in hepatocellular carcinoma. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04549-2. [PMID: 36575345 DOI: 10.1007/s00432-022-04549-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022]
Abstract
AIMS Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. Expression defects and turnover of basement membrane (BM) proteins are key pathogenic factors in cancer. It is still uncertain how the expression of BM-related genes (BMGs) in HCC relates to prognosis. METHODS All of the HCC cohort's RNA-seq and clinical information came from TCGA datasets. The least absolute shrinkage and selection operator (LASSO) regression algorithm was utilized to filter down the candidate genes and construct the prognostic model. Univariate and multivariate Cox analyses were run to examine if the risk score may serve as a standalone prognostic indicator. The single-sample gene set enrichment analysis (ssGSEA) was utilized to analyze examine immune cell infiltration and pathway activity. RESULTS Five genes and their risk coefficients were eventually identified and patients with HCC were classified as either high or low risk based on the median of risk scores. Multivariate Cox regression analysis found a significant correlation between risk score and OS (p < 0.001). Subgroup analysis showed that BMGs signature had good prediction ability for HCC patients in age, gender, T stage, and AJCC stage (all p < 0.05). According to the ssGSEA, the high-risk subgroup showed higher levels of immune cell infiltration and immune-related pathways were more engaged in the high-risk group. CONCLUSIONS Our research systematically built a prognostic model using risk score based on BMGs signature in HCC patients. The immune feature analysis of the BMGs signature indicated a potential regulation between tumor immunity and BM in HCC.
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Zhang M, Huang J, Wang Y, Nie Q, Zhang X, Yang Y, Mao G. Cathepsin a upregulation in glioma: A potential therapeutic target associated with immune infiltration. J Med Biochem 2022; 41:459-465. [PMID: 36381072 PMCID: PMC9618335 DOI: 10.5937/jomb0-35677] [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: 02/23/2022] [Accepted: 04/03/2022] [Indexed: 12/10/2023] Open
Abstract
BACKGROUND Glioma is the result of malignant transformation of glial cells in the white matter of the brain or spinal cord and accounts for approximately 80% of all intracranial malignancies. Cathepsin A (CTSA) is highly expressed in a variety of tumor tissues, but its role in glioma is poorly studied. This study analyses the relationship between CTSA, and glioma based on The Cancer Genome Atlas (TCGA). METHODS Data for glioma patients were collected from TCGA. The expression level of CTSA was compared between paired glioma tissues and normal tissues with Wilcoxon rank-sum test. In addition, the Wilcoxon ranksum test was also applied to analyze the relationship between clinicopathologic features and CTSA expression. Kaplan-Meier Plotter was applied to analyze OS, DSS and PFI. Immuno-infiltration analysis of BLCA was performed by single sample gene set enrichment analysis (ssGSEA) in the "GSVA" R package. RESULTS The CTSA was overexpressed in glioma tissues compared to normal tissues (P<0.001). The high expression of CTSA was significantly related to 1p/19q codeletion, IDH, WHO grade and histological type. Kaplan-Meier survival analysis showed that patients with glioma characterized with high expressed CTSA had a poorer OS (HR=2.16 P<0.001), DSS (HR=2.17 P<0.001) and PFI (HR=1.48 P<0.001) than patients with low CTSA expression. Moreover, High expressed CTSA was associated with immune cell infiltration. CONCLUSIONS CTSA may serve as a candidate prognostic biomarker for determining prognosis associated with immune infiltration in glioma.
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Affiliation(s)
- Ming Zhang
- The Third Medical Centre Chinese PLA (People's Liberation Army) General Hospital, Department of Neurosurgery, Beijing, China
| | - Jun Huang
- The Third Medical Centre Chinese PLA (People's Liberation Army) General Hospital, Department of Neurosurgery, Beijing, China
| | - Yunfei Wang
- The Third Medical Centre Chinese PLA (People's Liberation Army) General Hospital, Department of Neurosurgery, Beijing, China
| | - Qingbin Nie
- The Third Medical Centre Chinese PLA (People's Liberation Army) General Hospital, Department of Neurosurgery, Beijing, China
| | - Xinye Zhang
- The Third Medical Centre Chinese PLA (People's Liberation Army) General Hospital, Department of Neurosurgery, Beijing, China
| | - Yufeng Yang
- The Third Medical Centre Chinese PLA (People's Liberation Army) General Hospital, Department of Neurosurgery, Beijing, China
| | - Gengsheng Mao
- The Third Medical Centre Chinese PLA (People's Liberation Army) General Hospital, Department of Neurosurgery, Beijing, China
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4
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Luo L, Wang X, Wang H, Yang C, Zhang Y, Li X, Xu Z. High cathepsin A protein expression predicts poor prognosis and tumor recurrence of hepatocellular carcinoma patients after curative hepatectomy. Am J Cancer Res 2022; 12:3843-3856. [PMID: 36119821 PMCID: PMC9441997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023] Open
Abstract
Cathepsin A (CTSA) is overexpressed in various types of cancer and is linked to poor clinical outcomes. However, the clinical application of CTSA in HCC has not been explored. In this study, we examined the protein level of CTSA in the archived HCC samples from 161 patients by Immunohistochemistry (IHC). The high protein level of CTSA was significantly correlated to the poor clinicopathological parameters, such as TNM stage, serum AFP level, tumor differentiation, liver cirrhosis, Child-Pugh class, vascular invasion, tumor encapsulation, tumor recurrence, and patient death. In addition, multivariate Cox regression analysis indicated that high CTSA expression was an independent prognostic factor of OS and RFS. We also analyzed the area under the curve (AUC) of the time-dependent receiver operating characteristic (ROC) of CTSA expression for 1-, 3-, and 5-year OS and RFS prediction. Furthermore, we constructed a nomogram that exhibited excellent prediction performance, which was validated by the calibration curve and decision curve analysis. Together, our study demonstrated that CTSA protein level is strongly associated with poor clinical outcome of HCC patients and may be used as a potential diagnostic and prognostic biomarker in HCC.
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Affiliation(s)
- Laibang Luo
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical CollegeNanchang 330006, Jiangxi, China
| | - Xuyang Wang
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical CollegeNanchang 330006, Jiangxi, China
| | - Huaxiang Wang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of MedicineShiyan 442000, Hubei, China
- The Fuzong Clinical Medical College of Fujian Medical UniversityFuzhou 350025, Fujian, China
| | - Chengkai Yang
- The Fuzong Clinical Medical College of Fujian Medical UniversityFuzhou 350025, Fujian, China
| | - Youfu Zhang
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical CollegeNanchang 330006, Jiangxi, China
| | - Xinchang Li
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical CollegeNanchang 330006, Jiangxi, China
| | - Zhidan Xu
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical CollegeNanchang 330006, Jiangxi, China
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Wang H, Xu F, Yang F, Lv L, Jiang Y. Prognostic significance and oncogene function of cathepsin A in hepatocellular carcinoma. Sci Rep 2021; 11:14611. [PMID: 34272452 PMCID: PMC8285409 DOI: 10.1038/s41598-021-93998-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/30/2021] [Indexed: 12/19/2022] Open
Abstract
Cathepsin A (CTSA) is a lysosomal protease that regulates galactoside metabolism. The previous study has shown CTSA is abnormally expressed in various types of cancer. However, rarely the previous study has addressed the role of CTSA in hepatocellular carcinoma (HCC) and its prognostic value. To study the clinical value and potential function of CTSA in HCC, datasets from the Cancer Genome Atlas (TCGA) database and a 136 HCC patient cohort were analyzed. CTSA expression was found to be significantly higher in HCC patients compared with normal liver tissues, which was supported by immunohistochemistry (IHC) validation. Both gene ontology (GO) and The Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses demonstrated that CTSA co-expressed genes were involved in ATP hydrolysis coupled proton transport, carbohydrate metabolic process, lysosome organization, oxidative phosphorylation, other glycan degradation, etc. Survival analysis showed a significant reduction both in overall survival (OS) and recurrence-free survival (RFS) of patients with high CTSA expression from both the TCGA HCC cohort and 136 patients with the HCC cohort. Furthermore, CTSA overexpression has diagnostic value in distinguishing between HCC and normal liver tissue [Area under curve (AUC) = 0.864]. Moreover, Gene set enrichment analysis (GSEA) showed that CTSA expression correlated with the oxidative phosphorylation, proteasome, and lysosome, etc. in HCC tissues. These findings demonstrate that CTSA may as a potential diagnostic and prognostic biomarker in HCC.
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Affiliation(s)
- Huaxiang Wang
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, People's Republic of China
| | - Fengfeng Xu
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, People's Republic of China.,Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, No. 156 The Second West Ring Road, Fuzhou, 350025, Fu Jian Province, People's Republic of China
| | - Fang Yang
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, People's Republic of China.,Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, No. 156 The Second West Ring Road, Fuzhou, 350025, Fu Jian Province, People's Republic of China
| | - Lizhi Lv
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, People's Republic of China.,Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, No. 156 The Second West Ring Road, Fuzhou, 350025, Fu Jian Province, People's Republic of China
| | - Yi Jiang
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, People's Republic of China. .,Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, No. 156 The Second West Ring Road, Fuzhou, 350025, Fu Jian Province, People's Republic of China.
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Zhang Z, Yue P, Lu T, Wang Y, Wei Y, Wei X. Role of lysosomes in physiological activities, diseases, and therapy. J Hematol Oncol 2021; 14:79. [PMID: 33990205 PMCID: PMC8120021 DOI: 10.1186/s13045-021-01087-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/03/2021] [Indexed: 02/07/2023] Open
Abstract
Long known as digestive organelles, lysosomes have now emerged as multifaceted centers responsible for degradation, nutrient sensing, and immunity. Growing evidence also implicates role of lysosome-related mechanisms in pathologic process. In this review, we discuss physiological function of lysosomes and, more importantly, how the homeostasis of lysosomes is disrupted in several diseases, including atherosclerosis, neurodegenerative diseases, autoimmune disorders, pancreatitis, lysosomal storage disorders, and malignant tumors. In atherosclerosis and Gaucher disease, dysfunction of lysosomes changes cytokine secretion from macrophages, partially through inflammasome activation. In neurodegenerative diseases, defect autophagy facilitates accumulation of toxic protein and dysfunctional organelles leading to neuron death. Lysosomal dysfunction has been demonstrated in pathology of pancreatitis. Abnormal autophagy activation or inhibition has been revealed in autoimmune disorders. In tumor microenvironment, malignant phenotypes, including tumorigenesis, growth regulation, invasion, drug resistance, and radiotherapy resistance, of tumor cells and behaviors of tumor-associated macrophages, fibroblasts, dendritic cells, and T cells are also mediated by lysosomes. Based on these findings, a series of therapeutic methods targeting lysosomal proteins and processes have been developed from bench to bedside. In a word, present researches corroborate lysosomes to be pivotal organelles for understanding pathology of atherosclerosis, neurodegenerative diseases, autoimmune disorders, pancreatitis, and lysosomal storage disorders, and malignant tumors and developing novel therapeutic strategies.
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Affiliation(s)
- Ziqi Zhang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, 610041 Sichuan People’s Republic of China
| | - Pengfei Yue
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, 610041 Sichuan People’s Republic of China
| | - Tianqi Lu
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, 610041 Sichuan People’s Republic of China
| | - Yang Wang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, 610041 Sichuan People’s Republic of China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, 610041 Sichuan People’s Republic of China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, 610041 Sichuan People’s Republic of China
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PAR2 Promoter Hypomethylation Regulates PAR2 Gene Expression and Promotes Lung Adenocarcinoma Cell Progression. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:5542485. [PMID: 33968158 PMCID: PMC8081642 DOI: 10.1155/2021/5542485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/11/2021] [Accepted: 03/26/2021] [Indexed: 12/31/2022]
Abstract
Objective Protease-activated receptor-2 (PAR2) also known as F2RL1 is a G protein-coupled receptor that intimately correlates with cancer occurrence. DNA methylation turns out a vital mechanism regulating gene expression, while PAR2 promoter methylation is proven to be involved in cancer development. Hence, this study attempted to clarify the molecular mechanism by which PAR2 mediates lung adenocarcinoma (LUAD) progression, via identifying the effect of PAR2 promoter methylation on LUAD cell progression. Methods Associations of PAR2 promoter methylation with PAR2 gene expression and prognosis of LUAD patients were analyzed via bioinformatics analysis. PAR2 promoter methylation and gene expression at the cellular level were measured using methylation-specific PCR, qRT-PCR, and Western blot assays. DNA methyltransferase inhibitor 5-AzadC was used to treat cells to assess PAR2 gene expression alteration. Cell biological behaviors upon PAR2 overexpression were characterized via MTT, wound healing assay, and Transwell assay. Results Bioinformatics analysis revealed that PAR2 promoter methylation was negatively related to PAR2 gene expression, while PAR2 promoter hypermethylation and low gene expression indicated favorable LUAD prognosis. Besides, it turned out that PAR2 presented upregulated expression and hypomethylated promoter in LUAD cells. Moreover, PAR2 gene expression was elevated in cells treated with 5-AzadC, and the proliferative, migratory, and invasive capabilities of cells with 5-AzadC or high PAR2 gene expression were all enhanced. Conclusion In sum, PAR2 promoter hypomethylation potentiates LUAD cell progression, in turn affecting the prognosis of LUAD patients.
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The Role of Lysosomes in the Cancer Progression: Focus on the Extracellular Matrix Degradation. ACTA BIOMEDICA SCIENTIFICA 2021. [DOI: 10.29413/abs.2020-5.6.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Wu S, Pan Y, Mao Y, Chen Y, He Y. Current progress and mechanisms of bone metastasis in lung cancer: a narrative review. Transl Lung Cancer Res 2021; 10:439-451. [PMID: 33569325 PMCID: PMC7867745 DOI: 10.21037/tlcr-20-835] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lung cancer is a kind of malignant tumor with rapid progression and poor prognosis. Distant metastasis has been the main cause of mortality among lung cancer patients. Bone is one of the most common sites. Among all lung cancer patients with bone metastasis, most of them are osteolytic metastasis. Some serious clinical consequences like bone pain, pathological fractures, spinal instability, spinal cord compression and hypercalcemia occur as well. Since the severity of bone metastasis in lung cancer, it is undoubtedly necessary to know how lung cancer spread to bone, how can we diagnose it and how can we treat it. Here, we reviewed the process, possible mechanisms, diagnosis methods and current treatment of bone metastasis in lung cancer. We divided the process of bone metastasis in lung cancer into three steps: tumor invasion, tumor cell migration and invasion in bone tissue. It may be influenced by genetic factors, microenvironment and other adhesion-related factors. Imaging examination, laboratory examination, and pathological examination are used to diagnose lung cancer metastasis to bone. Surgery, radiotherapy, targeted therapy, bisphosphonate, radiation therapy and chemotherapy are the common clinical treatment methods currently. We also found some problems remained to be solved. For example, drugs for skeletal related events mainly target on osteoclasts at present, which increase the ratio of patients in osteoporosis and fractures in the long term. In all, this review provides the direction for future research on bone metastasis in lung cancer.
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Affiliation(s)
- Shengyu Wu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China.,Medical School, Tongji University, Shanghai, China
| | - Yue Pan
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China.,Medical School, Tongji University, Shanghai, China
| | - Yanyu Mao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China.,Medical School, Tongji University, Shanghai, China
| | - Yu Chen
- Spine Center, Orthopedic department, Shanghai Changzheng Hospital, Shanghai, China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
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