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Li Y, Cai Y, Ji L, Wang B, Shi D, Li X. Machine learning and bioinformatics analysis of diagnostic biomarkers associated with the occurrence and development of lung adenocarcinoma. PeerJ 2024; 12:e17746. [PMID: 39071134 PMCID: PMC11276766 DOI: 10.7717/peerj.17746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/24/2024] [Indexed: 07/30/2024] Open
Abstract
Objective Lung adenocarcinoma poses a major global health challenge and is a leading cause of cancer-related deaths worldwide. This study is a review of three molecular biomarkers screened by machine learning that are not only important in the occurrence and progression of lung adenocarcinoma but also have the potential to serve as biomarkers for clinical diagnosis, prognosis evaluation and treatment guidance. Methods Differentially expressed genes (DEGs) were identified using comprehensive GSE1987 and GSE18842 gene expression databases. A comprehensive bioinformatics analysis of these DEGs was conducted to explore enriched functions and pathways, relative expression levels, and interaction networks. Random Forest and LASSO regression analysis techniques were used to identify the three most significant target genes. The TCGA database and quantitative polymerase chain reaction (qPCR) experiments were used to verify the expression levels and receiver operating characteristic (ROC) curves of these three target genes. Furthermore, immune invasiveness, pan-cancer, and mRNA-miRNA interaction network analyses were performed. Results Eighty-nine genes showed increased expression and 190 genes showed decreased expression. Notably, the upregulated DEGs were predominantly associated with organelle fission and nuclear division, whereas the downregulated DEGs were mainly associated with genitourinary system development and cell-substrate adhesion. The construction of the DEG protein-protein interaction network revealed 32 and 19 hub genes with the highest moderate values among the upregulated and downregulated genes, respectively. Using random forest and LASSO regression analyses, the hub genes were employed to identify three most significant target genes.TCGA database and qPCR experiments were used to verify the expression levels and ROC curves of these three target genes, and immunoinvasive analysis, pan-cancer analysis and mRNA-miRNA interaction network analysis were performed. Conclusion Three target genes identified by machine learning: BUB1B, CENPF, and PLK1 play key roles in LUAD development of lung adenocarcinoma.
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Affiliation(s)
- Yong Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Huzhou University, The First People’s Hospital of Huzhou City, Zhejiang Province, China
- School of Medical Technology and Information Engineering, Zhejiang University of Traditional Chinese Medicine, Zhejiang Province, China
| | - Yunxiang Cai
- Department of Clinical Laboratory, The First Affiliated Hospital of Huzhou University, The First People’s Hospital of Huzhou City, Zhejiang Province, China
| | - Longfei Ji
- Department of Clinical Laboratory, The First Affiliated Hospital of Huzhou University, The First People’s Hospital of Huzhou City, Zhejiang Province, China
| | - Binyu Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Huzhou University, The First People’s Hospital of Huzhou City, Zhejiang Province, China
| | - Danfei Shi
- Department of Pathology, The First Affiliated Hospital of Huzhou University, The First People’s Hospital of Huzhou City, Zhejiang Province, China
| | - Xinmin Li
- Department of Clinical Laboratory, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
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Zafra J, Onieva JL, Oliver J, Garrido-Barros M, González-Hernández A, Martínez-Gálvez B, Román A, Ordóñez-Marmolejo R, Pérez-Ruiz E, Benítez JC, Mesas A, Vera A, Chicas-Sett R, Rueda-Domínguez A, Barragán I. Novel Blood Biomarkers for Response Prediction and Monitoring of Stereotactic Ablative Radiotherapy and Immunotherapy in Metastatic Oligoprogressive Lung Cancer. Int J Mol Sci 2024; 25:4533. [PMID: 38674117 PMCID: PMC11050102 DOI: 10.3390/ijms25084533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Up to 80% of patients under immune checkpoint inhibitors (ICI) face resistance. In this context, stereotactic ablative radiotherapy (SABR) can induce an immune or abscopal response. However, its molecular determinants remain unknown. We present early results of a translational study assessing biomarkers of response to combined ICI and SABR (I-SABR) in liquid biopsy from oligoprogressive patients in a prospective observational multicenter study. Cohort A includes metastatic patients in oligoprogression to ICI maintaining the same ICI due to clinical benefit and who receive concomitant SABR. B is a comparative group of oligometastatic patients receiving only SABR. Blood samples are extracted at baseline (T1), after the first (T2) and last (T3) fraction, two months post-SABR (T4) and at further progression (TP). Response is evaluated by iRECIST and defined by the objective response rate (ORR)-complete and partial responses. We assess peripheral blood mononuclear cells (PBMCs), circulating cell-free DNA (cfDNA) and small RNA from extracellular vesicles. Twenty-seven patients could be analyzed (cohort A: n = 19; B: n = 8). Most were males with non-small cell lung cancer and one progressing lesion. With a median follow-up of 6 months, the last ORR was 63% (26% complete and 37% partial response). A decrease in cfDNA from T2 to T3 correlated with a good response. At T2, CD8+PD1+ and CD8+PDL1+ cells were increased in non-responders and responders, respectively. At T2, 27 microRNAs were differentially expressed. These are potential biomarkers of response to I-SABR in oligoprogressive disease.
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Affiliation(s)
- Juan Zafra
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Department of Radiation Oncology, Virgen de la Victoria University Hospital, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain;
- Faculty of Medicine, University of Malaga (UMA), 29071 Málaga, Spain; (J.L.O.); (M.G.-B.); (A.G.-H.)
| | - Juan Luis Onieva
- Faculty of Medicine, University of Malaga (UMA), 29071 Málaga, Spain; (J.L.O.); (M.G.-B.); (A.G.-H.)
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - Javier Oliver
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - María Garrido-Barros
- Faculty of Medicine, University of Malaga (UMA), 29071 Málaga, Spain; (J.L.O.); (M.G.-B.); (A.G.-H.)
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - Andrea González-Hernández
- Faculty of Medicine, University of Malaga (UMA), 29071 Málaga, Spain; (J.L.O.); (M.G.-B.); (A.G.-H.)
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - Beatriz Martínez-Gálvez
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - Alicia Román
- Department of Radiation Oncology, Virgen de la Victoria University Hospital, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (A.R.); (R.O.-M.)
| | - Rafael Ordóñez-Marmolejo
- Department of Radiation Oncology, Virgen de la Victoria University Hospital, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (A.R.); (R.O.-M.)
| | - Elisabeth Pérez-Ruiz
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - José Carlos Benítez
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - Andrés Mesas
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, 29010 Málaga, Spain;
| | - Andrés Vera
- Department of Radiation Oncology, Dr Negrín University Hospital, 35010 Las Palmas de Gran Canaria, Spain;
| | - Rodolfo Chicas-Sett
- Department of Radiation Oncology, La Fe University Hospital, 46026 Valencia, Spain;
- Group of Clinical and Translational Cancer Research, Le Fe Health Research Institute, 46026 Valencia, Spain
| | - Antonio Rueda-Domínguez
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - Isabel Barragán
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
- Group of Pharmacoepigenetics, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
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Li C, Cai Q. Two ferroptosis-specific expressed genes NOX4 and PARP14 are considered as potential biomarkers for the diagnosis and treatment of diabetic retinopathy and atherosclerosis. Diabetol Metab Syndr 2024; 16:61. [PMID: 38443950 PMCID: PMC10913658 DOI: 10.1186/s13098-024-01301-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
OBJECTIVES Both Diabetic retinopathy (DR) and Atherosclerosis (AS) are common complications in patients with diabetes, and they share major pathophysiological similarities and have a common pathogenesis. Studies performed to date have demonstrated that ferroptosis plays a vital part in the occurrence and development of DR and AS, but its mechanism in the two diseases remains poorly understood. METHODS DR Chip data (GSE60436 and GSE102485) and AS chip data (GSE100927 and GSE57691) were obtained from the Gene Expression Omnibus (GEO) database. The screening of the differential expression genes (DEGs) was analyzed using the limma package, and the genes related to ferroptosis were obtained from the FerrDb V2 database. Two key genes (NOX4 and PARP14) were identified through external datasets validation and receiver operating characteristic (ROC) curve analysis. Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA) were used to conduct a functional enrichment analysis, and miRNA-mRNA networks were established. The CIBERSORT algorithm was applied to identify the immune cell infiltration between the disease group and control group. Next, the correlations between key genes and infiltrating immune cells were investigated by the Spearman method. Finally, the correlation between 2 key genes and ferroptosis markers was confirmed. RESULTS Nine ferroptosis differentially expressed genes (DE-FRGs) between DR and AS were identified in this study. NOX4 and PARP14 were selected as key genes for further analysis by external datasets and ROC curve analysis. The key genes NOX4, PARP14 and their correlated genes (such as CYBA, NOX1, NOX3, CYBB, PARP9, PARP10, and PARP15) are mainly enriched in oxidoreductase activity, protein ADP-ribosylation, superoxide metabolic process, reactive oxygen species metabolic process, PID pathway, and VEGFA-VEGFR2 pathway. A miRNA-mRNA network was constructed, and we got 12 miRNAs correlated with the target gene NOX4, 38 miRNAs correlated with the target gene PARP14. Three common miRNAs (hsa-miR-1-3p, hsa-miR-129-2-3p, and hsa-miR-155-5p) were observed in the network. Immune infiltration analysis displayed that activated B cell, MDSC, and Type 17 T helper cell are the common immune cells involved in the immune infiltration process of DR and AS. The results revealed that there are significant correlations between two key genes and most ferroptosis marker genes no matter in DR or AS. CONCLUSION Ferroptosis-related genes NOX4 and PARP14 may be common biomarkers of DR and AS. Both were associated with immune infiltration in patients with DR and AS. Our data provide a theoretical basis for the early diagnosis and immunotherapy of the two diseases.
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Affiliation(s)
- Chen Li
- Department of Ophthalmology, The First Affiliated Hospital of Soochow University, Shizi Street 188, Suzhou, 21006, Jiangsu, China
| | - QinHua Cai
- Department of Ophthalmology, The First Affiliated Hospital of Soochow University, Shizi Street 188, Suzhou, 21006, Jiangsu, China.
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Sun Z, Zhang L, Wang R, Wang Z, Liang X, Gao J. Identification of shared pathogenetic mechanisms between COVID-19 and IC through bioinformatics and system biology. Sci Rep 2024; 14:2114. [PMID: 38267482 PMCID: PMC10808107 DOI: 10.1038/s41598-024-52625-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024] Open
Abstract
COVID-19 increased global mortality in 2019. Cystitis became a contributing factor in SARS-CoV-2 and COVID-19 complications. The complex molecular links between cystitis and COVID-19 are unclear. This study investigates COVID-19-associated cystitis (CAC) molecular mechanisms and drug candidates using bioinformatics and systems biology. Obtain the gene expression profiles of IC (GSE11783) and COVID-19 (GSE147507) from the Gene Expression Omnibus (GEO) database. Identified the common differentially expressed genes (DEGs) in both IC and COVID-19, and extracted a number of key genes from this group. Subsequently, conduct Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis on the DEGs. Additionally, design a protein-protein interaction (PPI) network, a transcription factor gene regulatory network, a TF miRNA regulatory network, and a gene disease association network using the DEGs. Identify and extract hub genes from the PPI network. Then construct Nomogram diagnostic prediction models based on the hub genes. The DSigDB database was used to forecast many potential molecular medicines that are associated with common DEGs. Assess the precision of hub genes and Nomogram models in diagnosing IC and COVID-19 by employing Receiver Operating Characteristic (ROC) curves. The IC dataset (GSE57560) and the COVID-19 dataset (GSE171110) were selected to validate the models' diagnostic accuracy. A grand total of 198 DEGs that overlapped were found and chosen for further research. FCER1G, ITGAM, LCP2, LILRB2, MNDA, SPI1, and TYROBP were screened as the hub genes. The Nomogram model, built using the seven hub genes, demonstrates significant utility as a diagnostic prediction model for both IC and COVID-19. Multiple potential molecular medicines associated with common DEGs have been discovered. These pathways, hub genes, and models may provide new perspectives for future research into mechanisms and guide personalised and effective therapeutics for IC patients infected with COVID-19.
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Affiliation(s)
- Zhenpeng Sun
- Department of Urology, Qingdao Municipal Hospital, No.5, Donghai Middle Road, Shinan District, Qingdao, 266001, Shandong, China
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Li Zhang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Ruihong Wang
- Department of Outpatient, Qingdao Central Hospital, Qingdao University, Qingdao, China
| | - Zheng Wang
- Zhucheng People's Hospital, Zhucheng, China
| | - Xin Liang
- Department of Urology, Qingdao Municipal Hospital, No.5, Donghai Middle Road, Shinan District, Qingdao, 266001, Shandong, China
| | - Jiangang Gao
- Department of Urology, Qingdao Municipal Hospital, No.5, Donghai Middle Road, Shinan District, Qingdao, 266001, Shandong, China.
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Dai S, Li F, Xu S, Hu J, Gao L. The important role of miR-1-3p in cancers. J Transl Med 2023; 21:769. [PMID: 37907984 PMCID: PMC10617136 DOI: 10.1186/s12967-023-04649-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/22/2023] [Indexed: 11/02/2023] Open
Abstract
Cancer is a malignant tumor that seriously threatens human life and health. At present, the main treatment methods include surgical resection, chemotherapy, radiotherapy, and immunotherapy. However, the mechanism of tumor occurrence and development is complex, and it produces resistance to some traditional treatment methods, leading to treatment failure and a high mortality rate for patients. Therefore, exploring the molecular mechanisms of tumor occurrence, development, and drug resistance is a very important task. MiRNAs are a type of non-coding small RNA that regulate a series of biological effects by binding to the 3'-UTR of the target mRNA, degrading the mRNA, or inhibiting its translation. MiR-1-3p is an important member of them, which is abnormally expressed in various tumors and closely related to the occurrence and development of tumors. This article introduces miR-1-3p from multiple aspects, including its production and regulation, role in tumor occurrence and development, clinical significance, role in drug resistance, and approaches for targeting miR-1-3p. Intended to provide readers with a comprehensive understanding of the important role of miR-1-3p in tumors.
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Affiliation(s)
- Shangming Dai
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Fengjiao Li
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Shuoguo Xu
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Jinda Hu
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Lichen Gao
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China.
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China.
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Huo A, Xiong X. PAICS as a potential target for cancer therapy linking purine biosynthesis to cancer progression. Life Sci 2023; 331:122070. [PMID: 37673296 DOI: 10.1016/j.lfs.2023.122070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/02/2023] [Accepted: 09/02/2023] [Indexed: 09/08/2023]
Abstract
Tumor cells are required to undergo metabolic reprogramming for rapid development and progression, and one of the metabolic characteristics of cancer cells is the excessive synthesis and utilization of nucleotides. Abnormally increased nucleotides and their metabolites not only directly accelerate tumor cell progression but also indirectly act on stromal cells in the tumor microenvironment (TME) via a paracrine manner to regulate tumor progression. Purine nucleotides are mainly produced via de novo nucleotide synthesis in tumor cells; therefore, intervening in their synthesis has emerged as a promising strategy in anti-tumor therapy. De novo purine synthesis is a 10-step reaction catalyzed by six enzymes to synthesize inosine 5-monophosphate (IMP) and subsequently synthesize AMP and GMP. Phosphoribosylaminoimidazole carboxylase/phosphori-bosylaminoimidazole succinocarboxamide synthetase (PAICS) is a bifunctional enzyme that catalyzes de novo purine synthesis. Aberrantly elevated PAICS expression in various tumors is associated with poor prognosis. Evidence suggests that PAICS and its catalytic product, N-succinylcarboxamide-5-aminoimidazole ribonucleotide (SAICAR), could inhibit tumor cell apoptosis and promote the growth, epithelial-mesenchymal transition (EMT), invasion, and metastasis by regulating signaling pathways such as pyruvate kinase M2 (PKM2), extracellular signal-related kinases 1 and 2 (ERK1/2), focal adhesion kinase (FAK) and so on. This review summarizes the structure, biological functions and the molecular mechanisms of PAICS in cancer development and discusses its potential to be a target for tumor therapy.
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Affiliation(s)
- Anqi Huo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi 330006, China; The First Clinical Medical College, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Xiangyang Xiong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi 330006, China; Province Key Laboratory of Tumor Pathogens and Molecular Pathology, Nanchang University, Nanchang, Jiangxi 330006, China.
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