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Alghamdi MA, AL-Eitan LN, Tarkhan AH. Integrative analysis of gene expression and DNA methylation to identify biomarkers of non-genital warts induced by low-risk human papillomaviruses infection. Heliyon 2023; 9:e16101. [PMID: 37215908 PMCID: PMC10196596 DOI: 10.1016/j.heliyon.2023.e16101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
Background Human papillomaviruses have been shown to dysregulate the gene expression and DNA methylation profiles of their host cells over the course of infection. However, there is a lack of information on the impact of low-risk HPV infection and wart formation on host cell's expression and methylation patterns. Therefore, the objective of this study is to analyse the genome and methylome of common warts using an integrative approach. Methods In the present study, gene expression (GSE136347) and methylation (GSE213888) datasets of common warts were obtained from the GEO database. Identification of the differentially expressed and differentially methylated genes was carried out using the RnBeads R package and the edgeR Bioconductor package. Next, functional annotation of the identified genes was obtained using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Network construction and analyses of the gene-gene, protein-protein, and signaling interactions of the differentially expressed and differentially methylated genes was performed using the GeneMANIA web interface, the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and the Signaling Network Open Resource 2.0 (SIGNOR 2.0), respectively. Lastly, significant hub genes were identified using the Cytoscape application CytoHubba. Results A total of 276 genes were identified as differentially expressed and differentially methylated in common warts, with 52% being upregulated and hypermethylated. Functional enrichment analysis identified extracellular components as the most enriched annotations, while network analyses identified ELN, ITGB1, TIMP1, MMP2, LGALS3, COL1A1 and ANPEP as significant hub genes. Conclusions To the best knowledge of the authors, this is the first integrative study to be carried out on non-genital warts induced by low-risk HPV types. Future studies are required to re-validate the findings in larger populations using alternative approaches.
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Affiliation(s)
- Mansour A. Alghamdi
- Department of Anatomy, College of Medicine, King Khalid University, Abha, 61421, Saudi Arabia
- Genomics and Personalized Medicine Unit, College of Medicine, King Khalid University, Abha, 61421, Saudi Arabia
| | - Laith N. AL-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Amneh H. Tarkhan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
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Shen X, Shen H, Wu D, Feng M, Hu J, Liu J, Yang Y, Yang M, Li Y, Shi L, Chen K, Li X. Scalable batch-correction approach for integrating large-scale single-cell transcriptomes. Brief Bioinform 2022; 23:6659742. [PMID: 35947966 DOI: 10.1093/bib/bbac327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/26/2022] [Accepted: 07/19/2022] [Indexed: 11/14/2022] Open
Abstract
Integration of accumulative large-scale single-cell transcriptomes requires scalable batch-correction approaches. Here we propose Fugue, a simple and efficient batch-correction method that is scalable for integrating super large-scale single-cell transcriptomes from diverse sources. The core idea of the method is to encode batch information as trainable parameters and add it to single-cell expression profile; subsequently, a contrastive learning approach is used to learn feature representation of the additive expression profile. We demonstrate the scalability of Fugue by integrating all single cells obtained from the Human Cell Atlas. We benchmark Fugue against current state-of-the-art methods and show that Fugue consistently achieves improved performance in terms of data alignment and clustering preservation. Our study will facilitate the integration of single-cell transcriptomes at increasingly large scale.
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Affiliation(s)
- Xilin Shen
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Hongru Shen
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Dan Wu
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Mengyao Feng
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jiani Hu
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jilei Liu
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yichen Yang
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Meng Yang
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yang Li
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Lei Shi
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiangchun Li
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
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Puetkasichonpasutha J, Namwat N, Sa-Ngiamwibool P, Titapun A, Suthiphongchai T. Evaluation of p53 and Its Target Gene Expression as Potential Biomarkers of Cholangiocarcinoma in Thai Patients. Asian Pac J Cancer Prev 2020; 21:791-798. [PMID: 32212809 PMCID: PMC7437311 DOI: 10.31557/apjcp.2020.21.3.791] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/04/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA), a common cancer in northeastern Thailand, is a severe disease with poor prognosis and short survival time following diagnosis. DNA damage in CCA is believed to be caused by liver fluke infection in combination with exposure to carcinogens. p53, a tumor suppressor, is the most mutated gene in human cancers including liver fluke-associated CCA. Hence, expression patterns of p53 and its target genes may be useful for diagnosis and/or prognosis of CCA patients. METHODS Differential mRNA expression of p53 and its target genes, namely, FUCA1, ICAM2 MDM2, p21, PAI-1, S100A9, and WIP1 in CCA tissue samples (n = 30) relative to matched adjacent non-tumor tissues was determined by quantitative RT-PCR and compared to clinicopathological features. Level of p53 protein was determined by immunohistochemistry and correlated with the expression of its target genes. RESULTS Immunohistochemistry showed elevation of p53 protein level in 77% of the cases, while RT-PCR showed downregulation of p53 mRNA and its seven target genes in 23% and 47-97% of the samples. PAI-1 was down-regulated in almost all CCA samples, thus highlighting it as a potential diagnostic marker for CCA. However, no significant clinical associations were found except for down-regulation of WIP1 that was significantly correlated with non-papillary type tissue (p-value = 0.001) and with high p53 protein level (p-value = 0.007). CONCLUSION Our results demonstrated statistically significant association between down-regulation of WIP1 with non-papillary type and with high p53 protein level, and PAI-1 was down-regulated in almost all CCA. Therefore, expression level of WIP1 and PAI-1 may be useful for predicting p53 functional status and as a potential diagnostic marker of CCA, respectively.
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Affiliation(s)
| | - Nisana Namwat
- Department of Biochemistry,
- Department of Pathology,
| | | | - Attapol Titapun
- Department of Pathology,
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.
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Li Y, Kong F, Jin C, Hu E, Shao Q, Liu J, He D, Xiao X. The expression of S100A8/S100A9 is inducible and regulated by the Hippo/YAP pathway in squamous cell carcinomas. BMC Cancer 2019; 19:597. [PMID: 31208368 PMCID: PMC6580480 DOI: 10.1186/s12885-019-5784-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 05/31/2019] [Indexed: 12/15/2022] Open
Abstract
Background S100A8 and S100A9, two heterodimer-forming members of the S100 family, aberrantly express in a variety of cancer types. However, little is known about the mechanism that regulates S100A8/S100A9 co-expression in cancer cells. Methods The expression level of S100A8/S100A9 measured in three squamous cell carcinomas (SCC) cell lines and their corresponding xenografts, as well as in 257 SCC tissues. The correlation between S100A8/S100A9, Hippo pathway and F-actin cytoskeleton were evaluated using western blot, qPCR, ChIP and Immunofluorescence staining tests. IncuCyte ZOOM long time live cell image monitoring system, qPCR and Flow Cytometry measured the effects of S100A8/S100A9 and YAP on cell proliferation, cell differentiation and apoptosis. Results Here, we report that through activation of the Hippo pathway, suspension and dense culture significantly induce S100A8/S100A9 co-expression and co-localization in SCC cells. Furthermore, these expressional characteristics of S100A8/S100A9 also observed in the xenografts derived from the corresponding SCC cells. Importantly, Co-expression of S100A8/S100A9 detected in 257 SCC specimens derived from five types of SCC tissues. Activation of the Hippo pathway by overexpression of Lats1, knockdown of YAP, as well as disruption of F-actin indeed obviously results in S100A8/S100A9 co-expression in attached SCC cells. Conversely, inhibition of the Hippo pathway leads to S100A8/S100A9 co-expression in a manner opposite of cell suspension and dense. In addition, we found that TEAD1 is required for YAP-induced S100A8/S100A9-expressions. The functional studies provide evidence that knockdown of S100A8/S100A9 together significantly inhibit cell proliferation but promote squamous differentiation and apoptosis. Conclusions Our findings demonstrate for the first time that the expression of S100A8/S100A9 is inducible by changes of cell shape and density through activation of the Hippo pathway in SCC cells. Induced S100A8/S100A9 promoted cell proliferation, inhibit cell differentiation and apoptosis. Electronic supplementary material The online version of this article (10.1186/s12885-019-5784-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunguang Li
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, 19th, Beijing, 100875, China
| | - Fei Kong
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, 19th, Beijing, 100875, China
| | - Chang Jin
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, 19th, Beijing, 100875, China
| | - Enze Hu
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, 19th, Beijing, 100875, China
| | - Qirui Shao
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, 19th, Beijing, 100875, China
| | - Jin Liu
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, 19th, Beijing, 100875, China
| | - Dacheng He
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, 19th, Beijing, 100875, China
| | - Xueyuan Xiao
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, 19th, Beijing, 100875, China.
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Cao H, Zhang L, Chen H, Zhang W, Zhang Q, Liang X, Guo Y, Tang P. Hub genes and gene functions associated with postmenopausal osteoporosis predicted by an integrated method. Exp Ther Med 2019; 17:1262-1267. [PMID: 30680001 PMCID: PMC6327640 DOI: 10.3892/etm.2018.7095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/21/2018] [Indexed: 11/06/2022] Open
Abstract
Postmenopausal osteoporosis (PO) imposes great burden on individuals and society. This study predicted hub genes and gene functions for PO by an integration of the convergent evidence (CE) method, rank product (RP) algorithm and the combing of P-values. Using the gene expression data, genes were ranked by the CE method, RP algorithm and combing P-values, respectively. Subsequently, the top 100 genes were selected from each of the three gene lists, and then the common genes for two or three methods were denoted as informative genes of PO. A mutual information network (MIN) was constructed for the informative genes utilizing the context likelihood of relatedness algorithm. Topological centrality (degree) analysis was conducted on the MIN to investigate hub genes. Then we performed Gene Ontology (GO) enrichment analysis dependent upon the Biological Networks Gene Ontology tool (BiNGO) plugin of Cytoscape to investigate hub gene functions for PO patients. Consequently, a total of 82 informative genes were obtained by integrating the results of the three methods. There were 82 nodes and 1,741 edges in the MIN, of which 8 hub genes were identified, such as PFN1, EEF2 and S100A9. The result of GO enrichment analysis showed that 49 GO terms with P<0.001 were detected, especially the top 5 gene sets were defined as hub gene functions of PO, for instance, translational elongation, translation and cellular macromolecule biosynthetic process. In conclusion, we have predicted 8 hub genes and 5 hub gene functions associated with PO patients. The findings might help understand the molecular mechanism underlying PO.
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Affiliation(s)
- Honghai Cao
- Department of Orthopedics, Chinese PLA Hong Kong Hospital, Shenzhen, Guangdong 518048, P.R. China
| | - Lihai Zhang
- Department of Orthopedics, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Hua Chen
- Department of Orthopedics, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Wei Zhang
- Department of Orthopedics, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Qun Zhang
- Department of Orthopedics, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Xiangdang Liang
- Department of Orthopedics, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Yizhu Guo
- Department of Orthopedics, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Peifu Tang
- Department of Orthopedics, Chinese PLA General Hospital, Beijing 100853, P.R. China
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Bhunia S, Gupta S, Shrivastava BR, Tiwari PK. Identification of S100 calcium binding protein A9 as a prognostic biomarker in gallbladder cancer. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Chen YC, Lin MC, Hsiao CC, Zheng YX, Chen KD, Sung MT, Chen CJ, Wang TY, Lin YY, Chang HC, Chen YM, Chang JC. Increased S100A15 expression and decreased DNA methylation of its gene promoter are involved in high metastasis potential and poor outcome of lung adenocarcinoma. Oncotarget 2017; 8:45710-24. [PMID: 28498804 DOI: 10.18632/oncotarget.17391] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/10/2017] [Indexed: 01/02/2023] Open
Abstract
Purpose This study aims to determine the functional role of S100A15 and its promoter DNA methylation patterns in lung cancer progression. Experimental Design We analyzed 178 formalin-fixed paraffin embedded specimens from lung cancer patients, including 24 early stage and 91 advanced stage adenocarcinoma. S100A15 protein expression was evaluated by immunohistochemistry stain, and its DNA methylation levels were measured by pyrosequencing. Results S100A15 nuclear staining was increased in lung adenocarcinoma patients with distant metastasis versus those without distant metastasis. There was reduced one/three-year overall survival in adenocarcinoma patients receiving first line target therapy and harboring high nuclear expressions of S100A15. Both DNA methylation levels over -423 and -248 CpG sites of the S100A15 gene promoter were decreased in adenocarcinoma patients with distant metastasis, and the former was associated with lower one-year overall survival. The highly invasive CL1-5 cell lines display decreased DNA methylation over −412/−248/−56 CpG sites of the S100A15 gene promoter and increased S100A15 gene/protein expressions as compared with the less invasive CL1-0 cell lines. Knockdown of S100A15 in CL1-5 cell line inhibited cell proliferation, migration, and invasion, while over-expression of S100A15 in CL1-0 cell line promoted cell proliferation, migration, and invasion. RNA sequencing analysis revealed potential biological effects of S100A15 over-expression and knock-down with CTNNB1, ZEB1, CDC42, HSP90AA1, BST2, and PCNA being the pivotal down-stream mediators. Conclusions Increased S100A15 expression and decreased DNA methylation of its gene promoter region were associated with high metastasis potential and poor outcome in lung adenocarcinoma, probably through triggering CTNNB1 -centered pathways.
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Dai Y, Wang Q, Gonzalez Lopez A, Anders M, Malfertheiner P, Vieth M, Kemmner W. Genome-Wide Analysis of Barrett's Adenocarcinoma. A First Step Towards Identifying Patients at Risk and Developing Therapeutic Paths. Transl Oncol 2017; 11:116-124. [PMID: 29223109 PMCID: PMC6002392 DOI: 10.1016/j.tranon.2017.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/12/2017] [Accepted: 10/23/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND: Barrett's esophagus metaplasia is the key precursor lesion of esophageal adenocarcinoma. The aim of this study was to find a subset of markers that may allow the identification of patients at risk for esophageal adenocarcinoma, and to determine genes differentially expressed in esophageal squamous cell carcinoma. METHODS: Laser capture microdissection technique was applied to procure cells from defined regions. Genome-wide RNA profiling was performed on esophageal adenocarcinoma (n = 21), Barrett's esophagus (n = 20), esophageal squamous carcinoma (n = 9) and healthy esophageal biopsies (n = 18) using the Affymetrix Human Genome U133plus 2.0 array. Microarray results were validated by quantitative real-time polymerase chain reaction in a second and independent cohort and by immunohistochemistry of two putative markers in a third independent cohort. RESULTS: Through unsupervised hierarchical clustering and principal component analysis, samples were separated into four distinct groups that match perfectly with histology. Many genes down-regulated in esophageal cancers belong to the epidermal differentiation complex or the related GO-group “cornified envelope” of terminally differentiated keratinocytes. Similarly, retinol metabolism was strongly down-regulated. Genes showing strong overexpression in esophageal carcinomas belong to the GO groups extracellular region /matrix such as MMP1, CTHRC1, and INHBA. According to an analysis of genes strongly up-regulated in both esophageal adenocarcinoma and Barrett's esophagus, REG4 might be of particular interest as an early marker for esophageal adenocarcinoma. CONCLUSIONS: Our study provides high quality data, which could serve for identification of potential biomarkers of Barrett's esophagus at risk of esophageal adenocarcinoma progression.
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Affiliation(s)
- Yiyang Dai
- Translational Oncology, Experimental Clinical Research Center (ECRC), Charité Campus Buch, 13125 Berlin, Germany
| | - Qing Wang
- Translational Oncology, Experimental Clinical Research Center (ECRC), Charité Campus Buch, 13125 Berlin, Germany
| | - Adrian Gonzalez Lopez
- Department of Anesthesiology and Operative Intensive Care Medicine, Charité Campus Virchow-Klinikum, 13353 Berlin, Germany
| | - Mario Anders
- Gastroenterologie und Interdisziplinäre Endoskopie, Vivantes Wenckebach-Klinikum, 12099 Berlin, Germany
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Magdeburg, 39120 Magdeburg, Germany
| | - Michael Vieth
- Institute of Pathology, Klinikum Bayreuth, 95445 Bayreuth, Germany
| | - Wolfgang Kemmner
- Translational Oncology, Experimental Clinical Research Center (ECRC), Charité Campus Buch, 13125 Berlin, Germany.
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