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miRNAs Potentially Involved in Post Lung Transplant-Obliterative Bronchiolitis: The Role of miR-21-5p. Cells 2021; 10:cells10030688. [PMID: 33804639 PMCID: PMC8003603 DOI: 10.3390/cells10030688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022] Open
Abstract
Epigenetic changes, including miRNAs deregulation, have been suggested to play a significant role in development of obliterative bronchiolitis (OB) in transplanted lungs. Many studies have tried to identify ideal candidate miRNAs and the downstream pathways implicated in the bronchiolar fibro-obliterative process. Several candidate miRNAs, previously indicated as possibly being associated with OB, were analyzed by combining the quantitative real time-polymerase chain reaction (qRT-PCR) and in situ hybridization (ISH) of lung tissues of OB affected patients. Disease and OB-lesion-specific expression of miR-21-5p was confirmed and by computational analysis we were able to identify the network of genes most probably associated miR-21-5p in the context of OB fibrogenesis. Among all potentially associated genes, STAT3 had a very high probability score. Immunohistochemistry showed that STAT3/miR-21-5p were co-over expressed in OB lesions, thus, suggesting miR-21-5p could regulate STAT3 expression. However, miR-21-5p inhibition in cultures of bronchiolitis obliterans syndrome (BOS) derived myofibroblasts did not significantly affect STAT3 mRNA and protein expression levels. This study demonstrates the specificity of miR-21-5p over-expression in OB lesions and contributes to existing knowledge on the miR-21-5p downstream pathway. Activation of STAT3 is associated with miR-21-5p upregulation, however, STAT-3 network activation is most likely complex and miR-21-5p is not the sole regulator of STAT3.
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The Regulatory Properties of the Ccr4-Not Complex. Cells 2020; 9:cells9112379. [PMID: 33138308 PMCID: PMC7692201 DOI: 10.3390/cells9112379] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
The mammalian Ccr4–Not complex, carbon catabolite repression 4 (Ccr4)-negative on TATA-less (Not), is a large, highly conserved, multifunctional assembly of proteins that acts at different cellular levels to regulate gene expression. In the nucleus, it is involved in the regulation of the cell cycle, chromatin modification, activation and inhibition of transcription initiation, control of transcription elongation, RNA export, nuclear RNA surveillance, and DNA damage repair. In the cytoplasm, the Ccr4–Not complex plays a central role in mRNA decay and affects protein quality control. Most of our original knowledge of the Ccr4–Not complex is derived, primarily, from studies in yeast. More recent studies have shown that the mammalian complex has a comparable structure and similar properties. In this review, we summarize the evidence for the multiple roles of both the yeast and mammalian Ccr4–Not complexes, highlighting their similarities.
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Huang Y, Chen S, Qin W, Wang Y, Li L, Li Q, Yuan X. A Novel RNA Binding Protein-Related Prognostic Signature for Hepatocellular Carcinoma. Front Oncol 2020; 10:580513. [PMID: 33251144 PMCID: PMC7673432 DOI: 10.3389/fonc.2020.580513] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly malignant and aggressive cancer with high recurrence rates and mortality. Some studies have illustrated that RNA binding proteins (RBPs) were involved in the carcinogenesis and development of multiple cancers, but the roles in HCC were still unclear. We downloaded the RNA-seq and corresponding clinical information of HCC from The Cancer Genome Atlas (TCGA) database, and 330 differentially expressed RBPs were identified between normal and HCC tissues. Through series of the univariate, the least absolute shrinkage selection operator (LASSO), and the stepwise multivariate Cox regression analyses, six prognosis-related key RBPs (CNOT6, UPF3B, MRPL54, ZC3H13, IFIT5, and PPARGC1A) were screened out from DE RBPs, and a six-RBP gene risk score signature was constructed in training set. Survival analysis indicated that HCC patients with high-risk scores had significantly worse overall survival than low-risk patients, and furthermore, the signature can be used as an independent prognostic indicator. The good accuracy of this prognostic signature was confirmed by the ROC curve analysis and was further validated in the International Cancer Genome Consortium (ICGC) HCC cohort. Besides, a nomogram based on six RBP genes was established and internally validated in the TCGA cohort. Gene set enrichment analysis demonstrated some cancer-related phenotypes were significantly gathered in the high-risk group. Overall, our study first identified an RBP-related six-gene prognostic signature, which could serve as a promising prognostic biomarker and provide some potential therapeutic targets for HCC.
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Affiliation(s)
- Yongbiao Huang
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Wan Qin
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Yali Wang
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Long Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Qianxia Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
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Zhao H, Chen C, Chen X, Zhang D, Li J, Yang C, Ren C, Ren X, Fu X, Li Y, He J, Zhao H. Analysis of CNOT Family Gene Expression, Clinicopathological Features, and Prognosis Value in Hepatocellular Carcinoma. DNA Cell Biol 2020; 39:2226-2244. [PMID: 33085544 DOI: 10.1089/dna.2020.5818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The carbon catabolite repressor 4-negative on TATA (CCR4-NOT) complex, abbreviated CNOT, has deadenylation and 3'-5' exonuclease activity, mediates deadenylation in the degradation of RNA, initiates the exonuclease degradation pathway, and participates in tumor gene regulation. CNOT proteins comprise a family of global transcriptional regulators that are evolutionarily conserved in eukaryotic cells. Several subunit types of the CNOT complex have been discovered; however, little is known about the role of different subunits in tumorigenesis and development. We observed overexpression of CNOT1-11 in liver cancer and correlations with clinicopathological characteristics. The expression of some CNOTs subunits was associated with histological grades, lymph node metastasis, and tumor stages in patients with hepatocellular carcinoma (HCC). Our data suggested that some CNOTs can be used as predictors of poor prognosis in HCC patients. At the same time, we conducted an analysis of CNOTs mutations in HCC patients. Moreover, we selected CNOT6, CNOT10, and CNOT11 for protein interaction network analysis and Gene Ontology enrichment analysis to investigate their related biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Finally, the results of western blot and quantitative reverse transcription-PCR (qRT-PCR) experiments were consistent with the database findings. Results of this study suggest that CNOT6, CNOT10, and CNOT11, acting as regulators of transcription, may play an important role in the development of HCC and may serve as biological markers in the diagnosis and prognosis of HCC.
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Affiliation(s)
| | | | | | | | - Jian Li
- Shanxi Medical University, Taiyuan, China
| | - Chuanli Yang
- Department of General Surgery, Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan, China
| | - Chongren Ren
- Department of General Surgery, Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan, China
| | - Xiaojing Ren
- Department of General Surgery, Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan, China
| | - Xifeng Fu
- Department of General Surgery, Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan, China
| | - Yanjun Li
- Department of General Surgery, Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan, China
| | - Jiefeng He
- Department of General Surgery, Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan, China
| | - Haoliang Zhao
- Department of General Surgery, Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan, China
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Wang X, Wu X, Xin J, Li S, Zheng R, Guan D, Gong W, Zhao Q, Wang M, Chu H, Du M, Tao G, Zhang H, Zhang Z. Genetic variants in Ras/Raf/MEK/ERK pathway are associated with gastric cancer risk in Chinese Han population. Arch Toxicol 2020; 94:2683-2690. [DOI: 10.1007/s00204-020-02771-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/04/2020] [Indexed: 12/22/2022]
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6
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Feng Y, Liu H, Duan B, Liu Z, Abbruzzese J, Walsh KM, Zhang X, Wei Q. Potential functional variants in SMC2 and TP53 in the AURORA pathway genes and risk of pancreatic cancer. Carcinogenesis 2020; 40:521-528. [PMID: 30794721 DOI: 10.1093/carcin/bgz029] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 01/02/2019] [Accepted: 02/21/2019] [Indexed: 12/13/2022] Open
Abstract
The AURORA pathway participates in mitosis and cell division, and alterations in mitosis and cell division can lead to carcinogenesis. Therefore, genetic variants in the AURORA pathway genes may be associated with susceptibility to pancreatic cancer. To test this hypothesis, we used three large publically available pancreatic cancer genome-wide association study (GWAS) datasets (PanScan I, II/III and PanC4) to assess the associations of 7168 single nucleotide polymorphisms (SNPs) in a set of 62 genes of this pathway with pancreatic cancer risk in 8477 cases and 6946 controls of European ancestry. We identify 15 significant pancreatic cancer risk-associated SNPs in three genes (SMC2, ARHGEF7 and TP53) after correction for multiple comparisons by a false discovery rate < 0.20. Through further linkage disequilibrium analysis, SNP functional prediction and stepwise logistic regression analysis, we focused on three SNPs: rs3818626 in SMC2, rs79447092 in ARHGEF7 and rs9895829 in TP53. We found that these three SNPs were associated with pancreatic cancer risk [odds ratio (OR) = 1.12, 95% confidence interval (CI) = 1.07-1.17 and P = 2.20E-06 for the rs3818626 C allele; OR = 0.76, CI = 0.66-0.88 and P = 1.46E-04 for the rs79447092 A allele and OR = 0.82, CI = 0.74-0.91 and P = 1.51E-04 for the rs9895829 G allele]. Their joint effect as the number of protective genotypes also showed a significant association with pancreatic cancer risk (trend test P ≤ 0.001). Finally, we performed an expression quantitative trait loci analysis and found that rs3818626 and rs9895829 were significantly associated with SMC2 and TP53 messenger RNA expression levels in 373 lymphoblastoid cell lines, respectively. In conclusion, these three representative SNPs may be potentially susceptibility loci for pancreatic cancer and warrant additional validation.
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Affiliation(s)
- Yun Feng
- Department of Respiration, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Institute of Respiratory Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Bensong Duan
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Department of Gastroenterology, Institute of Digestive Diseases, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhensheng Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - James Abbruzzese
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Kyle M Walsh
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
| | - Xuefeng Zhang
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
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Feng Y, Wang Y, Liu H, Liu Z, Mills C, Owzar K, Xie J, Han Y, Qian DC, Hung Rj RJ, Brhane Y, McLaughlin J, Brennan P, Bickeböller H, Rosenberger A, Houlston RS, Caporaso N, Landi MT, Brüske I, Risch A, Ye Y, Wu X, Christiani DC, Amos CI, Wei Q. Novel genetic variants in the P38MAPK pathway gene ZAK and susceptibility to lung cancer. Mol Carcinog 2018; 57:216-224. [PMID: 29071797 PMCID: PMC6128286 DOI: 10.1002/mc.22748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 07/21/2017] [Accepted: 09/29/2017] [Indexed: 01/18/2023]
Abstract
The P38MAPK pathway participates in regulating cell cycle, inflammation, development, cell death, cell differentiation, and tumorigenesis. Genetic variants of some genes in the P38MAPK pathway are reportedly associated with lung cancer risk. To substantiate this finding, we used six genome-wide association studies (GWASs) to comprehensively investigate the associations of 14 904 single nucleotide polymorphisms (SNPs) in 108 genes of this pathway with lung cancer risk. We identified six significant lung cancer risk-associated SNPs in two genes (CSNK2B and ZAK) after correction for multiple comparisons by a false discovery rate (FDR) <0.20. After removal of three CSNK2B SNPs that are located in the same locus previously reported by GWAS, we performed the LD analysis and found that rs3769201 and rs7604288 were in high LD. We then chose two independent representative SNPs of rs3769201 and rs722864 in ZAK for further analysis. We also expanded the analysis by including these two SNPs from additional GWAS datasets of Harvard University (984 cases and 970 controls) and deCODE (1319 cases and 26 380 controls). The overall effects of these two SNPs were assessed using all eight GWAS datasets (OR = 0.92, 95%CI = 0.89-0.95, and P = 1.03 × 10-5 for rs3769201; OR = 0.91, 95%CI = 0.88-0.95, and P = 2.03 × 10-6 for rs722864). Finally, we performed an expression quantitative trait loci (eQTL) analysis and found that these two SNPs were significantly associated with ZAK mRNA expression levels in lymphoblastoid cell lines. In conclusion, the ZAK rs3769201 and rs722864 may be functional susceptibility loci for lung cancer risk.
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Affiliation(s)
- Yun Feng
- Department of Respiration, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Yanru Wang
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Zhensheng Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Coleman Mills
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Kouros Owzar
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Duke Cancer Institute and Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina
| | - Jichun Xie
- Duke Cancer Institute and Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina
| | - Younghun Han
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
| | - David C Qian
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
| | - Rayjean J Hung Rj
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Irene Brüske
- Helmholtz Centre Munich, German Research Centre for Environmental Health, Institute of Epidemiology I, Neuherberg, Germany
| | - Angela Risch
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David C Christiani
- Massachusetts General Hospital, Boston, Massachusetts
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts
| | - Christopher I Amos
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
- Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
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8
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Liu D, Xu W, Ding X, Yang Y, Su B, Fei K. Polymorphisms of CCNB1 Associated With the Clinical Outcomes of Platinum-Based Chemotherapy in Chinese NSCLC Patients. J Cancer 2017; 8:3785-3794. [PMID: 29151966 PMCID: PMC5688932 DOI: 10.7150/jca.21151] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/15/2017] [Indexed: 12/18/2022] Open
Abstract
As a crucial cell cycle regulator and G2/M phase promotor, CCNB1 played an essential role in progression of chemotherapy related cell death. Platinum-based chemotherapy is still the first-line chemotherapy regimen for most advanced NSCLC patients. We aim to investigate the correlation of CCNB1 polymorphisms to the efficiency of platinum-based chemotherapy in Chinese advanced NSCLC patients. We enrolled 972 patients with advanced NSCLC, and extracted DNA from their peripheral blood for genotyping CCNB1 four tagSNPs which selected from the Hapmap database. We analyzed the association of CCNB1 four tagSNPs with efficiency of platinum-based chemotherapy. We found that rs2069429 and rs2069433 of CCNB1 were associated with the OS of advanced NSCLC patients. Patients with GG genotype of rs2069429 had longer OS than non-GG patients (HR=0.81, 95%CI=0.68-0.95, p=0.009); and patients with AA genotype of rs2069433 had longer OS than non-AA patients (HR=0.78, 95%CI=0.61-0.98, p=0.036). And the haplotype GAAA of CCNB1 was a putative factor in subgroup patients with clinical stage IV. The association of CCNB1 polymorphisms and toxicities after platinum-based chemotherapy was assessed. Rs2069433 and rs350104 were related with gastrointestinal toxicity of platinum-based chemotherapy. The patients with GG genotype of rs2069433 (p=0.013) and/or non-GG genotype of rs350104 (p=0.042) may have a severe gastrointestinal toxicity after chemotherapy, and then clinician may can reduce the dosage of chemotherapy agents to avoid sever toxicities in these patients. In summary, CCNB1 polymorphisms may contribute to the clinical efficiency of platinum-based chemotherapy in advanced NSCLC patients, and it is helpful for the personalized treatment.
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Affiliation(s)
- Di Liu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P.R. China
| | - Wen Xu
- Department of Respirology and Critical Care Medicines, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P.R. China
| | - Xi Ding
- Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P.R. China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiaotong Universtiy, Shanghai, P.R. China
| | - Bo Su
- Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P.R. China
| | - Ke Fei
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P.R. China
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