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Wei Y, Lan C, Wang X, Zhou X, Liao X, Huang H, Wei Z, Li T, Peng T, Zhu G. RAD51AP1 as an Immune-Related Prognostic Biomarker and Therapeutic Response Predictor in Hepatocellular Carcinoma. Int J Gen Med 2023; 16:4377-4392. [PMID: 37789880 PMCID: PMC10543100 DOI: 10.2147/ijgm.s431206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
Background RAD51 associated protein 1 (RAD51AP1) is shown to regulate cell proliferation and cancer progression. However, the immune-infiltrating correlation and the therapeutics guidance of RAD51AP1 in hepatocellular carcinoma (HCC) still need further investigation. Methods In this study, comprehensive bioinformatic analysis of RAD51AP1 on differential expression, clinicopathologic correlation, prognostic value, and function enrichment were performed in The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO; GSE14520 and GSE76427), and International Cancer Genome Consortium (ICGC) datasets. Besides, the Guangxi cohort containing 50 pairs HCC and adjacent non-cancerous samples from First Affiliated Hospital of Guangxi Medical University was served as validation cohort. Moreover, we explored the predictive value of RAD51AP1 to therapeutics response and its underlying correlation with HCC immunoinfiltration. Results RAD51AP1 was significantly overexpressed in HCC tissues and had a high diagnostic value of HCC. The shorter survival time and poorer clinical features were showed when RAD51AP1 upregulated, and then a nomogram featuring RAD51AP1 expression and other clinicopathologic factors was established to predict prognosis. In CIBERSORT analysis, higher T cells follicular helper but lower T cells CD4+ memory resting infiltration levels were exhibited when RAD51AP1 upregulated. The ssGSEA analysis demonstrated that high-RAD51AP1 expression subgroup had higher macrophages, Th2 and Treg cells infiltration levels, but lower type II IFN response function. Furthermore, high-RAD51AP1 expression subgroup exhibited the upregulated expression levels of immune-related checkpoint genes, but lower IPS and TIDE scores which suggested a possibly better immunotherapy response. The drug sensitivity analysis showed the high-expression subgroup may be more susceptible to Bexarotene, Doxorubicin, Gemcitabine and Tipifarnib. Conclusion Taken together, RAD51AP1 is a potential diagnostic and prognostic biomarker. It may be related to the immunosuppressive microenvironment and could be an underlying HCC treatment strategy. However, the conclusions still require further validation studies.
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Affiliation(s)
- Yongguang Wei
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Nanning, 530021, People’s Republic of China
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, 530021, People’s Republic of China
| | - Chenlu Lan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Nanning, 530021, People’s Republic of China
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, 530021, People’s Republic of China
| | - Xiangkun Wang
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Xin Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Nanning, 530021, People’s Republic of China
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, 530021, People’s Republic of China
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Nanning, 530021, People’s Republic of China
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, 530021, People’s Republic of China
| | - Huasheng Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Nanning, 530021, People’s Republic of China
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, 530021, People’s Republic of China
| | - Zhongliu Wei
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Nanning, 530021, People’s Republic of China
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, 530021, People’s Republic of China
| | - Tianman Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Nanning, 530021, People’s Republic of China
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, 530021, People’s Republic of China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Nanning, 530021, People’s Republic of China
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, 530021, People’s Republic of China
| | - Guangzhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Nanning, 530021, People’s Republic of China
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, 530021, People’s Republic of China
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LIU R, LI M, HU Z, SONG Z, CHEN J. [Research Advances of RAD51AP1 in Tumor Progression and Drug Resistance]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2023; 26:701-708. [PMID: 37985156 PMCID: PMC10600754 DOI: 10.3779/j.issn.1009-3419.2023.102.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Indexed: 11/22/2023]
Abstract
The genomic instability may lead to an initiation of cancer in many organisms. Homologous recombination repair (HRR) is vital in maintaining cellular genomic stability. RAD51 associated protein 1 (RAD51AP1), which plays a crucial role in HRR and primarily participates in forming D-loop, was reported as an essential protein for maintaining cellular genomic stability. However, recent studies showed that RAD51AP1 was significantly overexpressed in various cancer types and correlated with poor prognosis. These results suggested that RAD51AP1 may play a significant pro-cancer effect in multiple cancers. The underlying mechanism is still unclear. Cancer stemness-maintaining effects of RAD51AP1 might be considered as the most reliable mechanism. Meanwhile, RAD51AP1 also promoted resistance to radiation therapy and chemotherapy in many cancers. Thus, researches focused on RAD51AP1, and its regulatory molecules may provide new targets for overcoming cancer progression and treatment resistance. Here, we reviewed the latest research on RAD51AP1 in cancers and summarized its differential expression and prognostic implications. In this review, we also outlined the potential mechanisms of its pro-cancer and drug resistance-promoting effects to provide several potential directions for further research.
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Torres-Montaner A. Interactions between the DNA Damage Response and the Telomere Complex in Carcinogenesis: A Hypothesis. Curr Issues Mol Biol 2023; 45:7582-7616. [PMID: 37754262 PMCID: PMC10527771 DOI: 10.3390/cimb45090478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Contrary to what was once thought, direct cancer originating from normal stem cells seems to be extremely rare. This is consistent with a preneoplastic period of telomere length reduction/damage in committed cells that becomes stabilized in transformation. Multiple observations suggest that telomere damage is an obligatory step preceding its stabilization. During tissue turnover, the telomeres of cells undergoing differentiation can be damaged as a consequence of defective DNA repair caused by endogenous or exogenous agents. This may result in the emergence of new mechanism of telomere maintenance which is the final outcome of DNA damage and the initial signal that triggers malignant transformation. Instead, transformation of stem cells is directly induced by primary derangement of telomere maintenance mechanisms. The newly modified telomere complex may promote survival of cancer stem cells, independently of telomere maintenance. An inherent resistance of stem cells to transformation may be linked to specific, robust mechanisms that help maintain telomere integrity.
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Affiliation(s)
- Antonio Torres-Montaner
- Department of Pathology, Queen’s Hospital, Rom Valley Way, Romford, London RM7 OAG, UK;
- Departamento de Bioquímica y Biologia Molecular, Universidad de Cadiz, Puerto Real, 11510 Cadiz, Spain
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4
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Liu R, Zhu G, Li M, Cao P, Li X, Zhang X, Huang H, Song Z, Chen J. Systematic pan-cancer analysis showed that RAD51AP1 was associated with immune microenvironment, tumor stemness, and prognosis. Front Genet 2022; 13:971033. [PMID: 36468013 PMCID: PMC9708706 DOI: 10.3389/fgene.2022.971033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/01/2022] [Indexed: 12/02/2023] Open
Abstract
Although RAD51 associated protein 1 (RAD51AP1) is crucial in genome stability maintenance, it also promotes cancer development with an unclear mechanism. In this study, we collected intact expression data of RAD51AP1 from the public database, and verified it was significantly over-expressed in 33 cancer types and correlated with poor prognosis in 13 cancer types, including glioma, adrenocortical carcinoma, lung adenocarcinoma. We further authenticated that RAD51AP1 is up-regulated in several typical cancer cell lines and promotes cancer cell proliferation in vitro. Moreover, we also demonstrated that RAD51AP1 was significantly positively related to cancer stemness score mRNAsi in 27 cancer types and broadly correlated to tumor-infiltrating immune cells in various cancers in a diverse manner. It was also negatively associated with immunophenoscore (IPS) and Estimation of STromal and Immune cells in MAlignant Tumours using Expression data (ESTIMATE) scores and positively correlated with mutant-allele tumor heterogeneity (MATH), tumor mutational burden (TMB), microsatellite instability (MSI), and PD-L1 expression in multiple cancers. The tumor stemness enhancing and tumor immune microenvironment affecting functions of RAD51AP1 might compose its carcinogenesis mechanism. Further investigations beyond the bioinformatics level should confirm these findings in each specific cancer.
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Affiliation(s)
- Renwang Liu
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumour Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Guangsheng Zhu
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumour Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Mingbiao Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumour Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Peijun Cao
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumour Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Xuanguang Li
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumour Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiuwen Zhang
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumour Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Hua Huang
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumour Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Zuoqing Song
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumour Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Jun Chen
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumour Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
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5
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Hu YY, Ma CC, Ai KX. Knockdown of RAD51AP1 suppressed cell proliferation and invasion in esophageal squamous cell carcinoma. Discov Oncol 2022; 13:101. [PMID: 36197550 PMCID: PMC9535060 DOI: 10.1007/s12672-022-00566-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Esophageal cancer is a common malignant tumor of digestive tract with esophageal squamous cell carcinoma (ESCC) being the main histological subtype. This study aimed to identify potential hub gene associated with the pathophysiology of ESCC through bioinformatics analysis and experiment validation. METHODS Three microarray datasets were obtained from the Gene Expression Omnibus (GEO) database. The overlapping differentially expressed genes (DEGs) were analyzed by GEO2R tool. Gene Ontology (GO) and Kyoto Encyclopedia of Genes (KEGG) pathway analyses were performed to predict the potential functions of DEGs. Nine hub genes were identified using protein-protein interaction (PPI) network and Cytoscape software. We selected RAD51-associated protein 1 (RAD51AP1) for further research because of its poor prognosis and it has not been sufficiently studied in ESCC. The effects of RAD51AP1 on proliferation, apoptosis, migration and invasion of ESCC cells were determined by in vitro functional assays. RESULTS RAD51AP1 expression was significantly upregulated in ESCC tissues compared with normal tissues by using The Cancer Genome Atlas (TCGA) database. High expression of RAD51AP1 was associated with worse survival in ESCC patients. RAD51AP1 expression was positively associated with the enrichment of Th2 cells and T helper cells. Furthermore, CCK-8 and colony formation assays showed knockdown of RAD51AP1 inhibited the proliferation of ESCC cells. Flow cytometry analysis indicated knockdown of RAD51AP1 induced cell cycle arrest and apoptosis in ESCC cells. Transwell assay revealed knockdown of RAD51AP1 suppressed the migration and invasion of ESCC cells. CONCLUSIONS Finally, our results demonstrated that RAD51AP1 silencing significantly inhibited cell proliferation and invasion in ESCC, thereby highlighting its potential as a novel target for ESCC treatment.
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Affiliation(s)
- Yang-Yang Hu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, No.507, Zhengmin Road, Shanghai, 200433, China
| | - Chen-Chao Ma
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, No.507, Zhengmin Road, Shanghai, 200433, China
| | - Kai-Xing Ai
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, No.507, Zhengmin Road, Shanghai, 200433, China.
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6
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Loo SK, Yates ME, Yang S, Oesterreich S, Lee AV, Wang X. Fusion-Associated Carcinomas of the Breast: Diagnostic, Prognostic, and Therapeutic Significance. Genes Chromosomes Cancer 2022; 61:261-273. [PMID: 35106856 DOI: 10.1002/gcc.23029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/11/2022] Open
Abstract
Recurrent gene fusions comprise a class of viable genetic targets in solid tumors that have culminated several recent break-through cancer therapies. Their role in breast cancer, however, remains largely underappreciated due to the complexity of genomic rearrangements in breast malignancy. Just recently, we and others have identified several recurrent gene fusions in breast cancer with important clinical and biological implications. Examples of the most significant recurrent gene fusions to date include 1) ESR1-CCDC170 gene fusions in luminal B and endocrine resistant breast cancer that exert oncogenic function via modulating the HER2/HER3/SRC complex, 2) ESR1 exon 6 fusions in metastatic disease that drive estrogen-independent ER transcriptional activity, 3) BCL2L14-ETV6 fusions in a more aggressive form of the triple negative subtype that prime epithelial-mesenchymal transition and endow paclitaxel resistance, 4) the ETV6-NTRK3 fusion in secretory breast carcinoma that constitutively activates NTRK3 kinase, 5) the oncogenic MYB-NFIB fusion as a genetic driver underpinning adenoid cystic carcinomas of the breast that activates MYB pathway, and 6) the NOTCH/MAST kinase gene fusions that activate NOTCH and MAST signaling. Importantly, these fusions are enriched in more aggressive and lethal breast cancer presentations and appear to confer therapeutic resistance. Thus, these gene fusions could be utilized as genetic biomarkers to identify patients that require more intensive treatment and surveillance. In addition, kinase fusions are currently being evaluated in breast cancer clinical trials and on-going mechanistic investigation is exposing therapeutic vulnerabilities in patients with fusion positive disease. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Suet Kee Loo
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Megan E Yates
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA.,Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sichun Yang
- Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Steffi Oesterreich
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaosong Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
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7
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Wu Z, Zhu L, Mai J, Shen H, Xu R. Rad51 Silencing with siRNA Delivered by Porous Silicon-Based Microparticle Enhances the Anti-Cancer Effect of Doxorubicin in Triple-Negative Breast Cancer. J Biomed Nanotechnol 2021; 17:2351-2363. [PMID: 34974858 DOI: 10.1166/jbn.2021.3198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Due to its high heterogeneity and aggressiveness, cytotoxic chemotherapy is still a mainstay treatment for triple negative breast cancer. Unfortunately, the above mentioned has not significantly ameliorated TNBC patients and induces drug resistance. Exploring the mechanisms underlying the chemotherapy sensitivity of TNBC and developing novel sensitization strategies are promising approaches for improving the prognosis of patients. Rad51, a key regulator of DNA damage response pathway, repairs DNA damage caused by genotoxic agents through "homologous recombination repair." Therefore, Rad51 inhibition may increase TNBC cell sensitivity to anticancer agents. Based on these findings, we first designed Rad51 siRNA to inhibit the Rad51 protein expression in vitro and evaluated the sensitivity of TNBC cells to doxorubicin. Subsequently, we constructed discoidal porous silicon microparticles (pSi) and encapsulated discoidal 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) liposomes/siRad51 (PS-DOPC/siRad51) to explore the synergistic antitumor effects of siRad51 and doxorubicin on two mouse models of TNBC in vivo. Our in vitro studies indicated that siRad51 enhanced the efficacy of DOX chemotherapy and significantly suppressed TNBC cell proliferation and metastasis. This effect was related to apoptosis induction and epithelial to mesenchymal transition (EMT) inhibition. siRad51 altered the expression of apoptosis- and EMT-related proteins. In orthotopic and lung metastasis xenograft models, the administration of PS-DOPC/siRad51 in combination with DOX significantly alleviated the primary tumor burden and lung metastasis, respectively. Our current studies present an efficient strategy to surmount chemotherapy resistance in TNBC through microvector delivery of siRad51.
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Affiliation(s)
- Zeliang Wu
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Lin Zhu
- Department of Pharmacy, Wuhan Wuchang Hospital, Wuhan University of Science and Technology, Wuhan 430061, People's Republic of China
| | - Junhua Mai
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston 77030, USA
| | - Haifa Shen
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston 77030, USA
| | - Rong Xu
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
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Liu L, Xu K, Zhou Y. Development of a novel embryonic germline gene-related prognostic model of lung adenocarcinoma. PeerJ 2021; 9:e12257. [PMID: 34721973 PMCID: PMC8542372 DOI: 10.7717/peerj.12257] [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: 06/04/2021] [Accepted: 09/15/2021] [Indexed: 11/20/2022] Open
Abstract
Background Emerging evidence implicates the correlation of embryonic germline genes with the tumor progress and patient's outcome. However, the prognostic value of these genes in lung adenocarcinoma (LUAD) has not been fully studied. Here we systematically evaluated this issue, and constructed a novel signature and a nomogram associated with embryonic germline genes for predicting the outcomes of lung adenocarcinoma. Methods The LUAD cohorts retrieved from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database were used as training set and testing set, respectively. The embryonic germline genes were downloaded from the website https://venn.lodder.dev. Then, the differentially expressed embryonic germline genes (DEGGs) between the tumor and normal samples were identified by limma package. The functional enrichment and pathway analyses were also performed by clusterProfiler package. The prognostic model was constructed by the least absolute shrinkage and selection operator (LASSO)-Cox regression method. Survival and Receiver Operating Characteristic (ROC) analyses were performed to validate the model using training set and four testing GEO datasets. Finally, a prognostic nomogram based on the signature genes was constructed using multivariate regression method. Results Among the identified 269 DEGGs, 249 were up-regulated and 20 were down-regulated. GO and KEGG analyses revealed that these DEGGs were mainly enriched in the process of cell proliferation and DNA damage repair. Then, 103 DEGGs with prognostic value were identified by univariate Cox regression and further filtered by LASSO method. The resulting sixteen DEGGs were included in step multivariate Cox regression and an eleven embryonic germline gene related signature (EGRS) was constructed. The model could robustly stratify the LUAD patients into high-risk and low-risk groups in both training and testing sets, and low-risk patients had much better outcomes. The multi-ROC analysis also showed that the EGRS model had the best predictive efficacy compared with other common clinicopathological factors. The EGRS model also showed robust predictive ability in four independent external datasets, and the area under curve (AUC) was 0.726 (GSE30219), 0.764 (GSE50081), 0.657 (GSE37745) and 0.668 (GSE72094). More importantly, the expression level of some genes in EGRS has a significant correlation with the progression of LUAD clinicopathology, suggesting these genes might play an important role in the progression of LUAD. Finally, based on EGRS genes, we built and calibrated a nomogram for conveniently evaluating patients' outcomes.
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Affiliation(s)
- Linjun Liu
- Department of Biotechnology, College of Life Science & Chemistry, Beijing University of Technology, Chaoyang, Beijing, China
| | - Ke Xu
- NHC Key Laboratory of Biosafety, China CDC, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Yubai Zhou
- Department of Biotechnology, College of Life Science & Chemistry, Beijing University of Technology, Chaoyang, Beijing, China
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Lee K, Yu H, Shouse S, Kong B, Lee J, Lee SH, Ko KS. RNA-Seq Reveals Different Gene Expression in Liver-Specific Prohibitin 1 Knock-Out Mice. Front Physiol 2021; 12:717911. [PMID: 34539442 PMCID: PMC8446661 DOI: 10.3389/fphys.2021.717911] [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: 05/31/2021] [Accepted: 07/27/2021] [Indexed: 12/24/2022] Open
Abstract
Prohibitin 1 (PHB1) is an evolutionarily conserved and ubiquitously expressed protein that stabilizes mitochondrial chaperone. Our previous studies showed that liver-specific Phb1 deficiency induced liver injuries and aggravated lipopolysaccharide (LPS)-induced innate immune responses. In this study, we performed RNA-sequencing (RNA-seq) analysis with liver tissues to investigate global gene expression among liver-specific Phb1−/−, Phb1+/−, and WT mice, focusing on the differentially expressed (DE) genes between Phb1+/− and WT. When 78 DE genes were analyzed for biological functions, using ingenuity pathway analysis (IPA) tool, lipid metabolism-related genes, including insulin receptor (Insr), sterol regulatory element-binding transcription factor 1 (Srebf1), Srebf2, and SREBP cleavage-activating protein (Scap) appeared to be downregulated in liver-specific Phb1+/− compared with WT. Diseases and biofunctions analyses conducted by IPA verified that hepatic system diseases, including liver fibrosis, liver hyperplasia/hyperproliferation, and liver necrosis/cell death, which may be caused by hepatotoxicity, were highly associated with liver-specific Phb1 deficiency in mice. Interestingly, of liver disease-related 5 DE genes between Phb1+/− and WT, the mRNA expressions of forkhead box M1 (Foxm1) and TIMP inhibitor of metalloproteinase (Timp1) were matched with validation for RNA-seq in liver tissues and AML12 cells transfected with Phb1 siRNA. The results in this study provide additional insights into molecular mechanisms responsible for increasing susceptibility of liver injuries associated with hepatic Phb1.
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Affiliation(s)
- Kyuwon Lee
- Department of Nutritional Science and Food Management, College of Science and Industry Convergence, Ewha Womans University, Seoul, South Korea
| | - Hyeonju Yu
- Department of Nutritional Science and Food Management, College of Science and Industry Convergence, Ewha Womans University, Seoul, South Korea
| | - Stephanie Shouse
- Center of Excellence for Poultry Science, University of Arkansas System Division of Agriculture, Fayetteville, AR, United States
| | - Byungwhi Kong
- Center of Excellence for Poultry Science, University of Arkansas System Division of Agriculture, Fayetteville, AR, United States
| | - Jihye Lee
- Department of Nutrition and Food Science, College of Agriculture and Natural Resources, University of Maryland, College Park, MD, United States
| | - Seong-Ho Lee
- Department of Nutrition and Food Science, College of Agriculture and Natural Resources, University of Maryland, College Park, MD, United States
| | - Kwang Suk Ko
- Department of Nutritional Science and Food Management, College of Science and Industry Convergence, Ewha Womans University, Seoul, South Korea.,Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Beverly Hills, CA, United States
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10
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Wang H, Dong H, Qiao L, Wu Y, Wu B, Jin X. ZEB1 induces non-small cell lung cancer development by targeting microRNA-320a to increase the expression of RAD51AP1. Exp Cell Res 2021; 405:112687. [PMID: 34097859 DOI: 10.1016/j.yexcr.2021.112687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 05/06/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023]
Abstract
Lung cancer is the most prevalent cancer worldwide, with its mortality rate reported to be in millions annually; one of the two subtypes is non-small cell lung cancer (NSCLC). In this study, we investigated the interactions and expressions of zinc finger E-box binding homeobox 1 (ZEB1), microRNA-320a (miR-320a) and RAD51-associated protein 1 (RAD51AP1) in NSCLC tissues to determine the roles of ZEB1 in regulation of miR-320a and RAD51AP1 in the development and metastasis of NSCLC. First, the expression levels of miR-320a and ZEB1 were quantified in NSCLC tissues and cells. Transfection assay was conducted to identify the effects of miR-320a on the progression of NSCLC cells. The interaction of miR-320a with ZEB1 and RAD51AP1 was predicted and verified using dual-luciferase reporter gene assay and chromatin immunoprecipitation assay. Finally, subcutaneous xenograft tumors of 6-week mice and metastatic model tumors of 8-week mice were established to further explore the in vivo effect of miR-320a/ZEB1/RAD51AP1 on NSCLC. The findings revealed a lower expression of miR-320a in NSCLC tissues and cells, while this result was reversed regarding ZEB1 expression. ZEB1 suppressed miR-320a expression and upregulation of miR-320a resulted in the reduction of proliferation, invasion and metastasis rate of NSCLC cells, and promoted NSCLC cell apoptosis. ZEB1 promoted the expression of RAD51AP1 via inhibition of miR-320a, promoting tumor growth in vivo. ZEB1 transcriptionally inhibited the expression of miR-320a and upregulated the expression of RAD51AP1, thereby promoting metastasis in NSCLC.
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Affiliation(s)
- Huifeng Wang
- The First Department of Oncology, General Hospital of Ningxia Medical University, Yinchuan, 750004, PR China
| | - Hui Dong
- Management Center of Scientific Research Equipment, General Hospital of Ningxia Medical University, Yinchuan, 750004, PR China
| | - Lijiao Qiao
- The Second Department of Oncology, General Hospital of Ningxia Medical University, Yinchuan, 750004, PR China
| | - Yuanyuan Wu
- The First Department of Oncology, General Hospital of Ningxia Medical University, Yinchuan, 750004, PR China
| | - Bo Wu
- The Second Department of Oncology, General Hospital of Ningxia Medical University, Yinchuan, 750004, PR China
| | - Xiangming Jin
- The First Department of Oncology, General Hospital of Ningxia Medical University, Yinchuan, 750004, PR China.
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Guo E, Wu C, Ming J, Zhang W, Zhang L, Hu G. The Clinical Significance of DNA Damage Repair Signatures in Clear Cell Renal Cell Carcinoma. Front Genet 2021; 11:593039. [PMID: 33488669 PMCID: PMC7820869 DOI: 10.3389/fgene.2020.593039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/04/2020] [Indexed: 12/16/2022] Open
Abstract
DNA damage repair plays an important role in cancer’s initiation and progression, and in therapeutic resistance. The prognostic potential of damage repair indicators was studied in the case of clear cell renal cell carcinoma (ccRCC). Gene expression profiles of the disease were downloaded from cancer genome databases and gene ontology was applied to the DNA repair-related genes. Twenty-six differentially expressed DNA repair genes were identified, and regression analysis was used to identify those with prognostic potential and to construct a risk model. The model accurately predicted patient outcomes and distinguished among patients with different expression levels of immune evasion genes. The data indicate that DNA repair genes can be valuable for predicting the progression of clear cell renal cell carcinoma and the clinical benefits of immunotherapy.
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Affiliation(s)
- Ergang Guo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Cheng Wu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Jun Ming
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Wei Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Linli Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Guoqing Hu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
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12
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Zhao H, Gao Y, Chen Q, Li J, Ren M, Zhao X, Yue W. RAD51AP1 promotes progression of ovarian cancer via TGF-β/Smad signalling pathway. J Cell Mol Med 2020; 25:1927-1938. [PMID: 33314567 PMCID: PMC7882964 DOI: 10.1111/jcmm.15877] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 08/13/2020] [Accepted: 08/26/2020] [Indexed: 01/12/2023] Open
Abstract
Ovarian cancer (OC) is one of the leading causes of female deaths. However, the molecular pathogenesis of OC has still remained elusive. This study aimed to explore the potential genes associated with the progression of OC. In the current study, 3 data sets of OC were downloaded from the GEO database to identify hub gene. Somatic mutation data obtained from TCGA were used to analyse the mutation. Immune cells were used to estimate effect of the hub gene to the tumour microenvironment. RNA‐seq and clinical data of OC patients retrieved from TCGA were used to investigate the diagnostic and prognostic values of hub gene. A series of in vitro assays were performed to indicate the function of hub gene and its possible mechanisms in OC. As a result, RAD51AP1 was found as a hub gene, which expression higher was mainly associated with poor survival in OC patients. Up‐regulation of RAD51AP1 was closely associated with mutations. RAD51AP1 up‐regulation accompanied by accumulated Th2 cells, but reduced CD4 + T cells and CD8 + T cells. Nomogram demonstrated RAD51AP1 increased the accuracy of the model. Down‐regulation of RAD51AP1 suppressed proliferation, migration and invasion capabilities of OC cells in vitro. Additionally, scatter plots showed that RAD51AP1 was positively correlated with genes in TGF‐β/Smad pathway. The above‐mentioned results were validated by RT‐qPCR and Western blotting. In conclusion, up‐regulation of RAD51AP1 was closely associated with mutations in OC. RAD51AP1 might represent an indicator for predicting OS of OC patients. Besides, RAD51AP1 might accelerate progression of OC by TGF‐β/Smad signalling pathway.
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Affiliation(s)
- Hongyu Zhao
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital Capital Medical University, Capital Medical University, Beijing, China
| | - Yan Gao
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital Capital Medical University, Capital Medical University, Beijing, China
| | - Qi Chen
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital Capital Medical University, Capital Medical University, Beijing, China
| | - Jie Li
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital Capital Medical University, Capital Medical University, Beijing, China
| | - Meng Ren
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital Capital Medical University, Capital Medical University, Beijing, China
| | - Xiaoting Zhao
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital Capital Medical University, Capital Medical University, Beijing, China
| | - Wentao Yue
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital Capital Medical University, Capital Medical University, Beijing, China
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13
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Bradfield A, Button L, Drury J, Green DC, Hill CJ, Hapangama DK. Investigating the Role of Telomere and Telomerase Associated Genes and Proteins in Endometrial Cancer. Methods Protoc 2020; 3:E63. [PMID: 32899298 PMCID: PMC7565490 DOI: 10.3390/mps3030063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/24/2020] [Accepted: 08/30/2020] [Indexed: 12/16/2022] Open
Abstract
Endometrial cancer (EC) is the commonest gynaecological malignancy. Current prognostic markers are inadequate to accurately predict patient survival, necessitating novel prognostic markers, to improve treatment strategies. Telomerase has a unique role within the endometrium, whilst aberrant telomerase activity is a hallmark of many cancers. The aim of the current in silico study is to investigate the role of telomere and telomerase associated genes and proteins (TTAGPs) in EC to identify potential prognostic markers and therapeutic targets. Analysis of RNA-seq data from The Cancer Genome Atlas identified differentially expressed genes (DEGs) in EC (568 TTAGPs out of 3467) and ascertained DEGs associated with histological subtypes, higher grade endometrioid tumours and late stage EC. Functional analysis demonstrated that DEGs were predominantly involved in cell cycle regulation, while the survival analysis identified 69 DEGs associated with prognosis. The protein-protein interaction network constructed facilitated the identification of hub genes, enriched transcription factor binding sites and drugs that may target the network. Thus, our in silico methods distinguished many critical genes associated with telomere maintenance that were previously unknown to contribute to EC carcinogenesis and prognosis, including NOP56, WFS1, ANAPC4 and TUBB4A. Probing the prognostic and therapeutic utility of these novel TTAGP markers will form an exciting basis for future research.
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Affiliation(s)
- Alice Bradfield
- Department of Women’s and Children’s Health, University of Liverpool, Crown St, Liverpool L69 7ZX, UK; (A.B.); (J.D.); (C.J.H.)
| | - Lucy Button
- Faculty of Health and Life Sciences, University of Liverpool, Brownlow Hill, Liverpool L69 7ZX, UK;
| | - Josephine Drury
- Department of Women’s and Children’s Health, University of Liverpool, Crown St, Liverpool L69 7ZX, UK; (A.B.); (J.D.); (C.J.H.)
| | - Daniel C. Green
- Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L7 8TX, UK;
| | - Christopher J. Hill
- Department of Women’s and Children’s Health, University of Liverpool, Crown St, Liverpool L69 7ZX, UK; (A.B.); (J.D.); (C.J.H.)
| | - Dharani K. Hapangama
- Department of Women’s and Children’s Health, University of Liverpool, Crown St, Liverpool L69 7ZX, UK; (A.B.); (J.D.); (C.J.H.)
- Liverpool Women’s NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK
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14
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Zhuang L, Zhang Y, Meng Z, Yang Z. Oncogenic Roles of RAD51AP1 in Tumor Tissues Related to Overall Survival and Disease-Free Survival in Hepatocellular Carcinoma. Cancer Control 2020; 27:1073274820977149. [PMID: 33269607 PMCID: PMC8480365 DOI: 10.1177/1073274820977149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE This study aimed to investigate the associations between RAD51AP1 and the outcomes of hepatocellular carcinoma (HCC). METHODS RAD51AP1 expression levels were compared in Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets. The Liver Hepatocellular Carcinoma (TCGA, Provisional) and GSE36376 datasets were used for survival analysis. RAD51AP1 associations with clinicopathological features were determined with the GSE36376 dataset. RESULTS RAD51AP1 mRNA expression was significantly upregulated in advanced liver fibrosis samples (S3-4 vs. S0-2 and G3-4 vs. G0-2) from hepatitis B virus (HBV)-related liver fibrosis patients and in tumor tissues and peripheral blood mononuclear cells (PBMCs) from HCC patients (all P < 0.05). HCC patients with high RAD51AP1 expression had significantly worse overall survival (OS) and disease-free survival (DFS) than those with low RAD51AP1 expression (P = 0.0034 and P = 0.0012, respectively) in the TCGA dataset, and these findings were validated with the GSE36376 dataset (P = 0.0074 and P = 0.0003, respectively). A Cox regression model indicated that RAD51AP1 was a risk factor for OS and DFS in HCC patients in GSE36376 (HR = 1.54, 95% CI = 1.02-2.32, P = 0.04 and HR = 1.71, 95% CI = 1.22-2.39, P = 0.002, respectively). Moreover, RAD51AP1 mRNA expression increased gradually with increasing tumor stage, including stratification by American Joint Committee on Cancer (AJCC) stages, Barcelona Clinic Liver Cancer (BCLC) stages and Edmondson grades. In addition, RAD51AP1 was overexpressed in HCC patients with intrahepatic metastasis, major portal vein invasion, vascular invasion and/or an alpha-fetoprotein (AFP) level > 300 ng/ml. CONCLUSIONS Contributing to an advanced tumor stage, intrahepatic metastasis, vascular invasion and AFP level elevation, RAD51AP1 upregulation was significantly associated with OS and DFS in HCC patients.
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Affiliation(s)
- Liping Zhuang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yuan Zhang
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhiqiang Meng
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Zhiqiang Meng, Fudan University Shanghai Cancer Center, Shanghai 200032, China.
| | - Zongguo Yang
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Zongguo Yang, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
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