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Lan W, Liao H, Chen Q, Zhu L, Pan Y, Chen YPP. DeepKEGG: a multi-omics data integration framework with biological insights for cancer recurrence prediction and biomarker discovery. Brief Bioinform 2024; 25:bbae185. [PMID: 38678587 PMCID: PMC11056029 DOI: 10.1093/bib/bbae185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/07/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024] Open
Abstract
Deep learning-based multi-omics data integration methods have the capability to reveal the mechanisms of cancer development, discover cancer biomarkers and identify pathogenic targets. However, current methods ignore the potential correlations between samples in integrating multi-omics data. In addition, providing accurate biological explanations still poses significant challenges due to the complexity of deep learning models. Therefore, there is an urgent need for a deep learning-based multi-omics integration method to explore the potential correlations between samples and provide model interpretability. Herein, we propose a novel interpretable multi-omics data integration method (DeepKEGG) for cancer recurrence prediction and biomarker discovery. In DeepKEGG, a biological hierarchical module is designed for local connections of neuron nodes and model interpretability based on the biological relationship between genes/miRNAs and pathways. In addition, a pathway self-attention module is constructed to explore the correlation between different samples and generate the potential pathway feature representation for enhancing the prediction performance of the model. Lastly, an attribution-based feature importance calculation method is utilized to discover biomarkers related to cancer recurrence and provide a biological interpretation of the model. Experimental results demonstrate that DeepKEGG outperforms other state-of-the-art methods in 5-fold cross validation. Furthermore, case studies also indicate that DeepKEGG serves as an effective tool for biomarker discovery. The code is available at https://github.com/lanbiolab/DeepKEGG.
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Affiliation(s)
- Wei Lan
- Guangxi Key Laboratory of Multimedia Communications and Network Technology, School of Computer, Electronic and Information, Guangxi University, No. 100 Daxue Road, Xixiangtang District, Nanning 530004, China
| | - Haibo Liao
- Guangxi Key Laboratory of Multimedia Communications and Network Technology, School of Computer, Electronic and Information, Guangxi University, No. 100 Daxue Road, Xixiangtang District, Nanning 530004, China
| | - Qingfeng Chen
- Guangxi Key Laboratory of Multimedia Communications and Network Technology, School of Computer, Electronic and Information, Guangxi University, No. 100 Daxue Road, Xixiangtang District, Nanning 530004, China
| | - Lingzhi Zhu
- School of Computer and Information Science, Hunan Institute of Technology, No. 18 Henghua Road, Zhuhui District, Hengyang 421002, China
| | - Yi Pan
- School of Computer Science and Control Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, No. 1068 Xueyuan Avenue, Shenzhen University Town, Nanshan District, Shenzhen 518055, China
| | - Yi-Ping Phoebe Chen
- Department of Computer Science and Information Technology, La Trobe University, Plenty Rd, Bundoora, Melbourne, Victoria 3086, Australia
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Amore G, Calì E, Spanò M, Ceravolo G, Mangano GD, Scorrano G, Efthymiou S, Salpietro V, Houlden H, Di Rosa G. ATP6V1B2-related disorders featuring Lennox-Gastaut-syndrome: A case-based overview. Brain Dev 2023; 45:588-596. [PMID: 37633739 DOI: 10.1016/j.braindev.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 06/15/2023] [Accepted: 07/21/2023] [Indexed: 08/28/2023]
Abstract
BACKGROUND ATP6V1B2 (ATPase, H+ transporting, lysosomal VI subunit B, isoform 2) encodes for a subunit of a ubiquitous transmembrane lysosomal proton pump, implicated in the acidification of intracellular organelles and in several additional cellular functions. Variants in ATP6V1B2 have been related to a heterogeneous group of multisystemic disorders sometimes associated with variable neurological involvement. However, our knowledge of genotype-phenotype correlations and the neurological spectrum of ATP6V1B2-related disorders remain limited due to the few numbers of reported cases. CASE STUDY We hereby report the case of an 18-year-old male Sicilian patient affected by a global developmental delay, skeletal abnormalities, and epileptic encephalopathy featuring Lennox-Gastaut syndrome (LGS), in which exome sequencing led to the identification of a novel de novo variant in ATP6V1B2 (NM_001693.4: c.973G > C, p.Gly325Arg). CONCLUSIONS Our report provides new insights on the inclusion of developmental epileptic encephalopathies (DEEs) within the continuum group of ATP6V1B2-related disorders, expanding the phenotypic and molecular spectrum associated with these conditions.
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Affiliation(s)
- Greta Amore
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom; Unit of Child Neurology and Psychiatry, Department of Human Pathology of the Adult and Developmental Age "Gaetano Barresi", University of Messina, Via C. Valeria 1, 98125 Messina, Italy
| | - Elisa Calì
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Maria Spanò
- Unit of Child Neurology and Psychiatry, Department of Human Pathology of the Adult and Developmental Age "Gaetano Barresi", University of Messina, Via C. Valeria 1, 98125 Messina, Italy
| | - Giorgia Ceravolo
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom; Unit of Emergency Pediatrics, Department of Human Pathology and Evolutive Age "Gaetano Barresi", University of Messina, Via C. Valeria 1, 98125 Messina, Italy
| | - Giuseppe Donato Mangano
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BiND), Human Anatomy Section, Via del Vespro 129, 90127 Palermo, Italy
| | - Giovanna Scorrano
- Department of Pediatrics "G. D'Annunzio", University of Chieti-Pescara, Chieti, Italy
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom; Department of Pediatrics, University of L'Aquila, 67100 L'Aquila, Italy
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Gabriella Di Rosa
- Unit of Child Neurology and Psychiatry, Department of Human Pathology of the Adult and Developmental Age "Gaetano Barresi", University of Messina, Via C. Valeria 1, 98125 Messina, Italy.
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Peskar D, Kuret T, Lakota K, Erman A. Molecular Profiling of Inflammatory Processes in a Mouse Model of IC/BPS: From the Complete Transcriptome to Major Sex-Related Histological Features of the Urinary Bladder. Int J Mol Sci 2023; 24:ijms24065758. [PMID: 36982831 PMCID: PMC10058956 DOI: 10.3390/ijms24065758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Animal models are invaluable in the research of the pathophysiology of interstitial cystitis/bladder pain syndrome (IC/BPS), a chronic aseptic urinary bladder disease of unknown etiology that primarily affects women. Here, a mouse model of IC/BPS was induced with multiple low-dose cyclophosphamide (CYP) applications and thoroughly characterized by RNA sequencing, qPCR, Western blot, and immunolabeling to elucidate key inflammatory processes and sex-dependent differences in the bladder inflammatory response. CYP treatment resulted in the upregulation of inflammatory transcripts such as Ccl8, Eda2r, and Vegfd, which are predominantly involved in innate immunity pathways, recapitulating the crucial findings in the bladder transcriptome of IC/BPS patients. The JAK/STAT signaling pathway was analyzed in detail, and the JAK3/STAT3 interaction was found to be most activated in cells of the bladder urothelium and lamina propria. Sex-based data analysis revealed that cell proliferation was more pronounced in male bladders, while innate immunity and tissue remodeling processes were the most distinctive responses of female bladders to CYP treatment. These processes were also reflected in prominent histological changes in the bladder. The study provides an invaluable reference dataset for preclinical research on IC/BPS and an insight into the sex-specific mechanisms involved in the development of IC/BPS pathology, which may explain the more frequent occurrence of this disease in women.
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Affiliation(s)
- Dominika Peskar
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadeja Kuret
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Katja Lakota
- Department of Rheumatology, University Medical Center Ljubljana, 1000 Ljubljana, Slovenia
| | - Andreja Erman
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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Stevens C, Hightower A, Buxbaum SG, Falzarano SM, Rhie SK. Genomic, epigenomic, and transcriptomic signatures of prostate cancer between African American and European American patients. Front Oncol 2023; 13:1079037. [PMID: 36937425 PMCID: PMC10018228 DOI: 10.3389/fonc.2023.1079037] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
Prostate cancer is the second most common cancer in men in the United States, and racial disparities are greatly observed in the disease. Specifically, African American (AA) patients have 60% higher incidence and mortality rates, in addition to higher grade and stage prostate tumors, than European American (EA) patients. In order to narrow the gap between clinical outcomes for these two populations, genetic and molecular signatures contributing to this disparity have been characterized. Over the past decade, profiles of prostate tumor samples from different ethnic groups have been developed using molecular and functional assays coupled with next generation sequencing or microarrays. Comparative genome-wide analyses of genomic, epigenomic, and transcriptomic profiles from prostate tumor samples have uncovered potential race-specific mutations, copy number alterations, DNA methylation, and gene expression patterns. In this study, we reviewed over 20 published studies that examined the aforementioned molecular contributions to racial disparities in AA and EA prostate cancer patients. The reviewed genomic studies revealed mutations, deletions, amplifications, duplications, or fusion genes differentially enriched in AA patients relative to EA patients. Commonly reported genomic alterations included mutations or copy number alterations of FOXA1, KMT2D, SPOP, MYC, PTEN, TP53, ZFHX3, and the TMPRSS2-ERG fusion. The reviewed epigenomic studies identified that CpG sites near the promoters of PMEPA1, RARB, SNRPN, and TIMP3 genes were differentially methylated between AA and EA patients. Lastly, the reviewed transcriptomic studies identified genes (e.g. CCL4, CHRM3, CRYBB2, CXCR4, GALR1, GSTM3, SPINK1) and signaling pathways dysregulated between AA and EA patients. The most frequently found dysregulated pathways were involved in immune and inflammatory responses and neuroactive ligand signaling. Overall, we observed that the genomic, epigenomic, and transcriptomic alterations evaluated between AA and EA prostate cancer patients varied between studies, highlighting the impact of using different methods and sample sizes. The reported genomic, epigenomic, and transcriptomic alterations do not only uncover molecular mechanisms of tumorigenesis but also provide researchers and clinicians valuable resources to identify novel biomarkers and treatment modalities to improve the disparity of clinical outcomes between AA and EA patients.
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Affiliation(s)
- Claire Stevens
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
| | - Alexandria Hightower
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
| | - Sarah G. Buxbaum
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
- Department of Epidemiology and Biostatistics, College of Pharmacy and Pharmaceutical Sciences, Institute of Public Health, Florida A&M University, Tallahassee, FL, United States
| | - Sara M. Falzarano
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Suhn K. Rhie
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
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Guneri-Sozeri PY, Özden-Yılmaz G, Kisim A, Cakiroglu E, Eray A, Uzuner H, Karakülah G, Pesen-Okvur D, Senturk S, Erkek-Ozhan S. FLI1 and FRA1 transcription factors drive the transcriptional regulatory networks characterizing muscle invasive bladder cancer. Commun Biol 2023; 6:199. [PMID: 36805539 PMCID: PMC9941102 DOI: 10.1038/s42003-023-04561-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/07/2023] [Indexed: 02/22/2023] Open
Abstract
Bladder cancer is mostly present in the form of urothelium carcinoma, causing over 150,000 deaths each year. Its histopathological classification as muscle invasive (MIBC) and non-muscle invasive (NMIBC) is the most prominent aspect, affecting the prognosis and progression of this disease. In this study, we defined the active regulatory landscape of MIBC and NMIBC cell lines using H3K27ac ChIP-seq and used an integrative approach to combine our findings with existing data. Our analysis revealed FRA1 and FLI1 as two critical transcription factors differentially regulating MIBC regulatory landscape. We show that FRA1 and FLI1 regulate the genes involved in epithelial cell migration and cell junction organization. Knock-down of FRA1 and FLI1 in MIBC revealed the downregulation of several EMT-related genes such as MAP4K4 and FLOT1. Further, ChIP-SICAP performed for FRA1 and FLI1 enabled us to infer chromatin binding partners of these transcription factors and link this information with their target genes. Finally, we show that knock-down of FRA1 and FLI1 result in significant reduction of invasion capacity of MIBC cells towards muscle microenvironment using IC-CHIP assays. Our results collectively highlight the role of these transcription factors in selection and design of targeted options for treatment of MIBC.
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Affiliation(s)
- Perihan Yagmur Guneri-Sozeri
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey ,grid.21200.310000 0001 2183 9022Dokuz Eylül University Izmir International Biomedicine and Genome Institute, Inciralti, 35340 Izmir, Turkey
| | - Gülden Özden-Yılmaz
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey
| | - Asli Kisim
- grid.419609.30000 0000 9261 240XIzmir Institute of Technology, Urla, 35430 Izmir, Turkey
| | - Ece Cakiroglu
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey ,grid.21200.310000 0001 2183 9022Dokuz Eylül University Izmir International Biomedicine and Genome Institute, Inciralti, 35340 Izmir, Turkey
| | - Aleyna Eray
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey ,grid.21200.310000 0001 2183 9022Dokuz Eylül University Izmir International Biomedicine and Genome Institute, Inciralti, 35340 Izmir, Turkey
| | - Hamdiye Uzuner
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey ,grid.21200.310000 0001 2183 9022Dokuz Eylül University Izmir International Biomedicine and Genome Institute, Inciralti, 35340 Izmir, Turkey
| | - Gökhan Karakülah
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey ,grid.21200.310000 0001 2183 9022Dokuz Eylül University Izmir International Biomedicine and Genome Institute, Inciralti, 35340 Izmir, Turkey
| | - Devrim Pesen-Okvur
- grid.419609.30000 0000 9261 240XIzmir Institute of Technology, Urla, 35430 Izmir, Turkey
| | - Serif Senturk
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey ,grid.21200.310000 0001 2183 9022Dokuz Eylül University Izmir International Biomedicine and Genome Institute, Inciralti, 35340 Izmir, Turkey
| | - Serap Erkek-Ozhan
- Izmir Biomedicine and Genome Center, Inciralti, 35340, Izmir, Turkey.
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Chen B, Chakrobortty N, Saha AK, Shang X. Identifying colon cancer stage related genes and their cellular pathways. Front Genet 2023; 14:1120185. [PMID: 36741325 PMCID: PMC9893497 DOI: 10.3389/fgene.2023.1120185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
In the world, colon cancer is regarded as one of the most common deadly cancer. Due to the lack of a better understanding of its prognosis system, this prevailing cancer has the second-highest morbidity and mortality rate compared with other cancers. A variety of genes are responsible to participate in colon cancer and the molecular mechanism is almost unsure. In addition, various studies have been done to identify the differentially expressed genes to investigate the dysfunctions of the genes but most of them did it individually. In this study, we constructed a functional interaction network for identifying the group of genes that conduct cellular functions and Protein-Protein Interaction network, which aims to better understanding protein functions and their biological relationships. A functional evolution network was also generated to analyze the dysfunctions from initial stage to later stage of colon cancer by investigating the gene modules and their molecular functions. The results show that the proposed evolution network is able to detect the significant cellular functions, which can be used to explore the evolution process of colon cancer. Moreover, a total of 10 core genes associated with colon cancer were identified, which were INS, SNAP25, GRIA2, SST, GCG, PVALB, SLC17A7, SLC32A1, SLC17A6, and NPY, respectively. The responsible candidate genes and corresponding pathways presented in this study could be used to develop new tumor indicators and novel therapeutic targets for the prevention and treatment of colon cancer.
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Affiliation(s)
- Bolin Chen
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China,MIIT Key Laboratory of Big Data Storage and Management, Northwestern Polytechnical University, Xi’an, Shaanxi, China,National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Nandita Chakrobortty
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Apu Kumar Saha
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China,MIIT Key Laboratory of Big Data Storage and Management, Northwestern Polytechnical University, Xi’an, Shaanxi, China,National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology, Northwestern Polytechnical University, Xi’an, Shaanxi, China,*Correspondence: Xuequn Shang,
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Tu H, Liu H, Zhang L, Tan Z, Wang H, Jiang Y, Xia Z, Guo L, Xia X, Gu P, Liu X. A novel prognostic model based on three integrin subunit genes-related signature for bladder cancer. Front Oncol 2022; 12:970576. [PMID: 36267977 PMCID: PMC9577111 DOI: 10.3389/fonc.2022.970576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/14/2022] [Indexed: 11/25/2022] Open
Abstract
Background Presently, a comprehensive analysis of integrin subunit genes (ITGs) in bladder cancer (BLCA) is absent. This study endeavored to thoroughly analyze the utility of ITGs in BLCA through computer algorithm-based bioinformatics. Methods BLCA-related materials were sourced from reputable databases, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). R software-based bioinformatics analyses included limma-differential expression analysis, survival-Cox analysis, glmnet-Least absolute shrinkage and selection operator (LASSO), clusterProfiler-functional annotation, and gsva-estimate-immune landscape analysis. The expression difference of key genes was verified by quantitative real-time polymerase chain reaction (qRT-PCR). Results Among the 11 ITGs that were abnormally expressed in BLCA, ITGA7, ITGA5, and ITGB6 were categorized as the optimal variables for structuring the risk model. The high-risk subcategories were typified by brief survival, abysmal prognosis, prominent immune and stromal markers, and depressed tumor purity. The risk model was also an isolated indicator of the impact of clinical outcomes in BLCA patients. Moreover, the risk model, specifically the high-risk subcategory with inferior prognosis, became heavily interlinked with the immune-inflammatory response and smooth muscle contraction and relaxation. Conclusion This study determined three ITGs with prognostic values (ITGA7, ITGA5, and ITGB6), composed a novel (ITG-associated) prognostic gene signature, and preliminarily probed the latent molecular mechanisms of the model.
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Affiliation(s)
- Hongtao Tu
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
- The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming, China
| | - Haolin Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Longfei Zhang
- Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Zhiyong Tan
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Hai Wang
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
- The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming, China
| | - Yongming Jiang
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
- The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming, China
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zhongyou Xia
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
- The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming, China
| | - Liwei Guo
- Department of Urology, The Dazhu County People’s Hospital, Dazhou, China
| | - Xiaodong Xia
- Department of Urology, The Dazhu County People’s Hospital, Dazhou, China
| | - Peng Gu
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
- The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming, China
- *Correspondence: Xiaodong Liu, ; Peng Gu,
| | - Xiaodong Liu
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
- The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Chronic Kidney Disease, Kunming, China
- *Correspondence: Xiaodong Liu, ; Peng Gu,
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Screening and Biological Function Analysis of miRNA and mRNA Related to Lung Adenocarcinoma Based on Bioinformatics Technology. JOURNAL OF ONCOLOGY 2022; 2022:4339391. [PMID: 36090902 PMCID: PMC9452934 DOI: 10.1155/2022/4339391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 11/17/2022]
Abstract
Objective. To screen the differentially expressed miRNAs (DEMs) and the differentially expressed gene mRNAs (DEGs) in lung adenocarcinoma (LUAD) from the TCGA database and to explore the relationship between miRNAs and the prognosis of lung adenocarcinoma and their biological functions. Methods. The RNA-seq and miRNA-seq data of lung adenocarcinoma samples were downloaded from the TCGA database for analysis, and the R program was used to screen for differentially expressed miRNAs and mRNAs. Then, the molecular functions, biological processes, cellular components, and signaling pathways involved in the occurrence and development of LUAD were analyzed using the functional accumulation analysis software of GSEA. The relationship between the integrated differentially expressed RNAs was analyzed by miRcode, TargetScan, and miRTarbase databases, and the miRNA-mRNA network was constructed. Result. A total of 516 differentially expressed miRNAs and 5464 differentially expressed mRNAs were identified in LUAD. The GSEA enrichment analysis showed that miRNAs and mRNAs were mainly enriched in extracellular structure organization, external encapsulating structure organization, extracellular matrix organization, and gated channel activity. They were mainly involved in neuroactive ligand-receptor interaction signaling pathway. Some miRNAs and mRNAs in clustering modules were found to be associated with the prognosis of LUAD. Four targeting networks consisting of 22 miRNAs and 531 mRNAs were constructed. Conclusion. The miRNA and mRNA related to the prognosis of LUAD were screened out, which provided a valuable preliminary basis for the follow-upin-depth clinical research and basic experimental research of LUAD.
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Mao W, Zhou J, Hu J, Zhao K, Fu Z, Wang J, Mao K. A pan-cancer analysis of FAT atypical cadherin 4 (FAT4) in human tumors. Front Public Health 2022; 10:969070. [PMID: 36051999 PMCID: PMC9424548 DOI: 10.3389/fpubh.2022.969070] [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: 06/14/2022] [Accepted: 07/28/2022] [Indexed: 01/25/2023] Open
Abstract
Objective We performed a pan-cancer analysis to explore the potential mechanisms of FAT4 in 33 different tumors. Methods In this study, we selected 33 types of cancers based on the datasets of TCGA (the cancer genome atlas). We analyzed the expression of FAT4 in tumor and normal tissues. Meanwhile, we analyzed the expression levels of FAT4 in tissues from tumors of different stages. Kaplan-Meier survival analysis, Tumor Mutational Burden (TMB), Microsatellite Instability (MSI), immune infiltration analysis, Gene set enrichment analysis (GSEA), and FAT4-related gene enrichment analysis were performed. Results FAT4 expression in most tumor tissues was lower than in corresponding control tissues. FAT4 expression was different in different stages of bladder cancer (BLCA), kidney clear cell carcinoma (KIRC), and breast cancer (BRCA). In addition, the expression level of FAT4 in different types of tumors has an important impact on the prognosis of patients. FAT4 might influence the efficacy of immunotherapy via tumor burden and microsatellite instability. We observed a statistically positive correlation between cancer-associated fibroblasts and FAT4 expression in most tumors. GSEA of BLCA indicated that low FAT4 expression groups were mainly enriched in calcium signaling pathway and chemokine signaling pathway. GSEA analysis of KIRC suggested low FAT4 expression groups were mainly involved in olfactory transduction and oxidative phosphorylation. Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that the role of FAT4 in the pathogenesis of cancer may be related to human papillomavirus infection, Hippo signaling pathway, PI3K-Akt signaling pathway, etc. Gene Ontology (GO) enrichment analysis further showed that most of these genes were related to the pathways or cell biology, such as peptidyl-tyrosine phosphorylation, cell junction assembly, protein tyrosine kinase activity, etc. Conclusion Our study summarized and analyzed the antitumor effect of FAT4 in different tumors comprehensively, which aided in understanding the role of FAT4 in tumorigenesis from the perspective of clinical tumor samples. Pan-cancer analysis showed that FAT4 to be novel biomarkers for various cancers prognosis.
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Affiliation(s)
- Weili Mao
- Department of Pharmacy, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Jiajing Zhou
- Department of Oncology, Yantai Hospital of Traditional Chinese Medicine, Yantai, China
| | - Jie Hu
- Department of Pharmacy, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Kui Zhao
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhenling Fu
- Department of Pharmacy, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Jun Wang
- Department of Pharmacy, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China,*Correspondence: Jun Wang
| | - Kaili Mao
- Department of Pharmacy, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China,Kaili Mao
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Rao X, Cao H, Yu Q, Ou X, Deng R, Huang J. NEAT1/MALAT1/XIST/PKD--Hsa-Mir-101-3p--DLGAP5 Axis as a Novel Diagnostic and Prognostic Biomarker Associated With Immune Cell Infiltration in Bladder Cancer. Front Genet 2022; 13:892535. [PMID: 35873473 PMCID: PMC9305813 DOI: 10.3389/fgene.2022.892535] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/16/2022] [Indexed: 12/24/2022] Open
Abstract
Background: The clinical value of the biomarkers of bladder cancer (BC) is limited due to their low sensitivity or specificity. As a biomarker, DLG associated protein 5 (DLGAP5) is a potential cell cycle regulator in cancer cell carcinogenesis. However, its functional part in BC remains unclear. Therefore, this study aims to identify DLGAP5 expression in BC and its potential diagnostic and prognostic values. Eventually, it predicts the possible RNA regulatory pathways of BC.Methods: Data on DLGAP5 expression levels in BC and normal bladder tissues were obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. The receiver operating characteristic (ROC), Kaplan–Meier survival curves, and the univariate and multivariate Cox regression analysis determined the diagnostic and prognostic values of DLGAP5 in BC patients. Finally, the StarBase predicted the target RNAs and constructed networks using Cytoscape.Results: DLGAP5 expression was significantly upregulated in BC tissue, verified by the TCGA (p < 0.001), GSE3167, GSE7476, and GSE65635 datasets (p < 0.01). BC patients with increased DLGAP5 had poor overall survival (OS) (p = 0.01), disease specific survival (DSS) (p = 0.006) and progress free interval (DFI) (p = 0.007). The area under the ROC curve (AUC) was 0.913. The multivariate Cox analysis identified that lymphovascular invasion (p = 0.007) and DLGAP5 (p = 0.002) were independent prognostic factors.Conclusion: Increased DLGAP5 expression was closely associated with a poor prognosis in BC patients. In this case, DLGAP5 might be a diagnostic and prognostic biomarker for BC. DLGAP5 expression might be regulated by NEAT1/MALAT1/XIST/PKD--Hsa-mir-101-3p pathways.
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Affiliation(s)
- Xiaosheng Rao
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haiyan Cao
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin, China
| | - Qingfeng Yu
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiuyu Ou
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ruiqi Deng
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jinkun Huang
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Jinkun Huang,
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Hernández-Gómez C, Hernández-Lemus E, Espinal-Enríquez J. The Role of Copy Number Variants in Gene Co-Expression Patterns for Luminal B Breast Tumors. Front Genet 2022; 13:806607. [PMID: 35432489 PMCID: PMC9010943 DOI: 10.3389/fgene.2022.806607] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/03/2022] [Indexed: 12/20/2022] Open
Abstract
Gene co-expression networks have become a usual approach to integrate the vast amounts of information coming from gene expression studies in cancer cohorts. The reprogramming of the gene regulatory control and the molecular pathways depending on such control are central to the characterization of the disease, aiming to unveil the consequences for cancer prognosis and therapeutics. There is, however, a multitude of factors which have been associated with anomalous control of gene expression in cancer. In the particular case of co-expression patterns, we have previously documented a phenomenon of loss of long distance co-expression in several cancer types, including breast cancer. Of the many potential factors that may contribute to this phenomenology, copy number variants (CNVs) have been often discussed. However, no systematic assessment of the role that CNVs may play in shaping gene co-expression patterns in breast cancer has been performed to date. For this reason we have decided to develop such analysis. In this study, we focus on using probabilistic modeling techniques to evaluate to what extent CNVs affect the phenomenon of long/short range co-expression in Luminal B breast tumors. We analyzed the co-expression patterns in chromosome 8, since it is known to be affected by amplifications/deletions during cancer development. We found that the CNVs pattern in chromosome 8 of Luminal B network does not alter the co-expression patterns significantly, which means that the co-expression program in this cancer phenotype is not determined by CNV structure. Additionally, we found that region 8q24.3 is highly dense in interactions, as well as region p21.3. The most connected genes in this network belong to those cytobands and are associated with several manifestations of cancer in different tissues. Interestingly, among the most connected genes, we found MAF1 and POLR3D, which may constitute an axis of regulation of gene transcription, in particular for non-coding RNA species. We believe that by advancing on our knowledge of the molecular mechanisms behind gene regulation in cancer, we will be better equipped, not only to understand tumor biology, but also to broaden the scope of diagnostic, prognostic and therapeutic interventions to ultimately benefit oncologic patients.
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Affiliation(s)
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Jesús Espinal-Enríquez, ; Enrique Hernández-Lemus,
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Jesús Espinal-Enríquez, ; Enrique Hernández-Lemus,
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12
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Li H, Sun L, Zhuang Y, Tian C, Yan F, Zhang Z, Hu Y, Liu P. Molecular mechanisms and differences in lynch syndrome developing into colorectal cancer and endometrial cancer based on gene expression, methylation, and mutation analysis. Cancer Causes Control 2022; 33:489-501. [PMID: 35149954 PMCID: PMC8904372 DOI: 10.1007/s10552-021-01543-w] [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: 03/11/2021] [Accepted: 12/14/2021] [Indexed: 11/29/2022]
Abstract
Purpose The aim of this study was to screen biomarkers specific to Lynch syndrome (LS) with colorectal cancer (CRC) or endometrial cancer (EC) to explore the mechanisms by which LS develops into CRC and EC and their differences. Methods Differentially expressed or differentially methylated genes and differential mutations were identified in 10 LS, 50 CRC, and 50 EC patients from TCGA, and genes overlapping between LS and CRC or EC (named SGs-LCs and SGs-LEs, respectively) were identified. Afterward, we annotated the enriched GO terms and pathways and constructed a protein–protein interaction (PPI) network. Finally, samples from 10 clinical cases with MSI-H/MSS CRC and EC were collected to verify the mutations and their correlations with five LS pathogenic genes in the SGs-LCs and SGs-LEs. Results A total of 494 SGs-LCs and 104 SGs-LEs were identified and enriched in 106 and 14 GO terms, respectively. There were great differences in the gene count and enriched terms between SGs-LCs and SGs-LEs. In the PPI network, SST, GCG, SNAP25, and NPY had the highest degree of connection among the SGs-LCs, and KIF20A and NUF2 had the highest degree of connection among the SGs-LE. In the SGs-LCs and SGs-LEs, the genes whose expression levels affected the survival of LS, CRC or EC patients were quite different. Conclusions COL11A1 was found to be mutated in MSS CRC patients, similar to the mutations of MSH6. SST, GCG, SNAP25, and NPY may be biomarkers for the development of LS into CRC, and KIF20A and NUF2 may be markers of LS developing into EC. Supplementary Information The online version contains supplementary material available at 10.1007/s10552-021-01543-w.
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Affiliation(s)
- Hongfeng Li
- Department of Clinical Laboratory, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, 300120, China
| | - Liwei Sun
- Department of Interventional Oncology, Tianjin Huanhu Hospital, Tianjin, 300350, China
| | - Yan Zhuang
- Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Department of Colorectal Oncology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Caijuan Tian
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co., Ltd, Tianjin, 300381, China
| | - Fang Yan
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co., Ltd, Tianjin, 300381, China
| | - Zhenzhen Zhang
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co., Ltd, Tianjin, 300381, China
| | - Yuanjing Hu
- Department of Gynecological Oncology, Tianjin Central Hospital of Gynecology & Obstetrics, No. 156 Nankaisan Road, Nankai District, Tianjin, 300100, China.
| | - Pengfei Liu
- Department of Oncology, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, No. 354 Beima Road, Hongqiao District, Tianjin, 300120, China.
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13
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Zhang Y, Chen Q, Gong M, Zeng Y, Gao D. Gene regulatory networks analysis of muscle-invasive bladder cancer subtypes using differential graphical model. BMC Genomics 2021; 22:863. [PMID: 34852762 PMCID: PMC8638098 DOI: 10.1186/s12864-021-08113-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Recently, erdafitinib (Balversa), the first targeted therapy drug for genetic alteration, was approved to metastatic urothelial carcinoma. Cancer genomics research has been greatly encouraged. Currently, a large number of gene regulatory networks between different states have been constructed, which can reveal the difference states of genes. However, they have not been applied to the subtypes of Muscle-invasive bladder cancer (MIBC). RESULTS In this paper, we propose a method that construct gene regulatory networks under different molecular subtypes of MIBC, and analyse the regulatory differences between different molecular subtypes. Through differential expression analysis and the differential network analysis of the top 100 differential genes in the network, we find that SERPINI1, NOTUM, FGFR1 and other genes have significant differences in expression and regulatory relationship between MIBC subtypes. CONCLUSIONS Furthermore, pathway enrichment analysis and differential network analysis demonstrate that Neuroactive ligand-receptor interaction and Cytokine-cytokine receptor interaction are significantly enriched pathways, and the genes contained in them are significant diversity in the subtypes of bladder cancer.
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Affiliation(s)
- Yongqing Zhang
- School of Computer Science, Chengdu University of Information Technology, Chengdu, 610225, China
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Qingyuan Chen
- School of Computer Science, Chengdu University of Information Technology, Chengdu, 610225, China
| | - Meiqin Gong
- West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuanqi Zeng
- School of Computer Science, Chengdu University of Information Technology, Chengdu, 610225, China
| | - Dongrui Gao
- School of Computer Science, Chengdu University of Information Technology, Chengdu, 610225, China.
- School of life Science and technology, center for information in medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China.
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14
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Nagaya N, Rosenfeld J, Lee GT, Kim IY. RNA-seq profile of African American men with a clinically localized prostate cancer. Prostate Int 2021; 9:125-131. [PMID: 34692584 PMCID: PMC8498718 DOI: 10.1016/j.prnil.2020.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/12/2020] [Accepted: 11/01/2020] [Indexed: 12/12/2022] Open
Abstract
Background Prostate cancer in African American (AA) men has a poor prognosis. This study aimed to identify potential genetic risk factors for prostate cancer in AA men. Methods We used prostate cancer tissue from 61 patients who underwent radical prostatectomy. We compared somatic gene expression in Caucasian (CA) and AA men using RNA sequencing. Results By comparing the RNA-seq data obtained from prostate cancer tissue between AA and CA men, this study showed a significant difference in expression levels of 45 genes. Pathway analysis of 45 genes using Kyoto Encyclopedia of Genes and Genomesenrichment analysis revealed a neuroactive ligand–receptor interaction signal. In addition, the results of the Ingenuity Pathway Analysis showed pathways involved sphingosine-1-phosphate signaling. Furthermore, validating 45 genes in the The Cancer Genome Atlas (TCGA) Provisional cohort, cholinergic receptor muscarinic 3 expression level was significantly lower in AA than in CA men, and the results showed a significantly higher rate of biochemical recurrence in patients with low expression. Conclusions We identified genetic differences of clinically localized prostate cancer in AAs and CAs by RNA sequencing.
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Affiliation(s)
- Naoya Nagaya
- Section of Urologic Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Jeffrey Rosenfeld
- Pathology and Laboratory Medicine, Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Geun Taek Lee
- Section of Urologic Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Isaac Yi Kim
- Section of Urologic Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
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15
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A Systems Approach to Interrogate Gene Expression Patterns in African American Men Presenting with Clinically Localized Prostate Cancer. Cancers (Basel) 2021; 13:cancers13205143. [PMID: 34680291 PMCID: PMC8533960 DOI: 10.3390/cancers13205143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Men of African origin have a 2–3 times greater chance of developing prostate cancer than those of European origin, and of patients that are diagnosed with the disease, men of African descent are 2 times more likely to die compared to white men. Men of African origin are still greatly underrepresented in genetic studies and clinical trials. This, unfortunately, means that new discoveries in cancer treatment are missing key information on the group with a greater chance of mortality. The objective of this study was to increase our knowledge of prostate cancer in men undergoing a prostate biopsy. We carried out RNA sequencing of biopsy specimens and examined racial differences in prostate gene expression. A gene expression signature was uncovered which separated the men based on their race. Furthermore, within men of African descent this signature separated men with the most severe clinical characteristics. Abstract An emerging theory about racial differences in cancer risk and outcomes is that psychological and social stressors influence cellular stress responses; however, limited empirical data are available on racial differences in cellular stress responses among men who are at risk for adverse prostate cancer outcomes. In this study, we undertook a systems approach to examine molecular profiles and cellular stress responses in an important segment of African American (AA) and European American (EA) men: men undergoing prostate biopsy. We assessed the prostate transcriptome with a single biopsy core via high throughput RNA sequencing (RNA-Seq). Transcriptomic analyses uncovered impacted biological pathways including PI3K-Akt signaling pathway, Neuroactive ligand-receptor interaction pathway, and ECM-receptor interaction. Additionally, 187 genes mapping to the Gene Ontology (GO) terms RNA binding, structural constituent of ribosome, SRP-dependent co-translational protein targeting to membrane and the biological pathways, translation, L13a-mediated translational silencing of Ceruloplasmin expression were differentially expressed (DE) between EA and AA. This signature allowed separation of AA and EA patients, and AA patients with the most severe clinical characteristics. AA patients with elevated expression levels of this genomic signature presented with higher Gleason scores, a greater number of positive core biopsies, elevated dehydroepiandrosterone sulfate levels and serum vitamin D deficiency. Protein-protein interaction (PPI) network analysis revealed a high degree of connectivity between these 187 proteins.
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16
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Zarei Ghobadi M, Emamzadeh R, Teymoori-Rad M, Mozhgani SH. Decoding pathogenesis factors involved in the progression of ATLL or HAM/TSP after infection by HTLV-1 through a systems virology study. Virol J 2021; 18:175. [PMID: 34446027 PMCID: PMC8393454 DOI: 10.1186/s12985-021-01643-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022] Open
Abstract
Background Human T-cell Leukemia Virus type-1 (HTLV-1) is a retrovirus that causes two diseases including Adult T-cell Leukemia/Lymphoma (ATLL cancer) and HTLV-1 Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP, a neurodegenerative disease) after a long latency period as an asymptomatic carrier (AC). There are no obvious explanations about how each of the mentioned diseases develops in the AC carriers. Finding the discriminative molecular factors and pathways may clarify the destiny of the infection. Methods To shed light on the involved molecular players and activated pathways in each state, differentially co-expressed modules (DiffCoEx) algorithm was employed to identify the highly correlated genes which were co-expressed differently between normal and ACs, ACs and ATLL, as well as ACs and HAM/TSP samples. Through differential pathway analysis, the dysregulated pathways and the specific disease-genes-pathways were figured out. Moreover, the common genes between the member of DiffCoEx and differentially expressed genes were found and the specific genes in ATLL and HAM/TSP were introduced as possible biomarkers. Results The dysregulated genes in the ATLL were mostly enriched in immune and cancer-related pathways while the ones in the HAM/TSP were enriched in immune, inflammation, and neurological pathways. The differential pathway analysis clarified the differences between the gene players in the common activated pathways. Eventually, the final analysis revealed the involvement of specific dysregulated genes including KIRREL2, RAB36, and KANK1 in HAM/TSP as well as LTB4R2, HCN4, FZD9, GRIK5, CREB3L4, TACR2, FRMD1, LHB, FGF3, TEAD3, GRIN2D, GNRH2, PRLH, GPR156, and CRHR2 in ATLL. Conclusion The identified potential prognostic biomarkers and therapeutic targets are proposed as the most important platers in developing ATLL or HAM/TSP. Moreover, the proposed signaling network clarifies the differences between the functional players in the activated pathways in ACs, ATLL, and HAM/TSP. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01643-8.
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Affiliation(s)
- Mohadeseh Zarei Ghobadi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Rahman Emamzadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Majid Teymoori-Rad
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Sayed-Hamidreza Mozhgani
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.,Non‑Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
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17
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Proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer. Sci Rep 2021; 11:7595. [PMID: 33828141 PMCID: PMC8027873 DOI: 10.1038/s41598-021-87003-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 03/22/2021] [Indexed: 11/08/2022] Open
Abstract
Samples in biobanks are generally preserved by formalin-fixation and paraffin-embedding (FFPE) and/or optimal cutting temperature compound (OCT)-embedding and subsequently frozen. Mass spectrometry (MS)-based analysis of these samples is now available via developed protocols, however, the differences in results with respect to preservation methods needs further investigation. Here we use bladder urothelial carcinoma tissue of two different tumor stages (Ta/T1-non-muscle invasive bladder cancer (NMIBC), and T2/T3-muscle invasive bladder cancer (MIBC)) which, upon sampling, were divided and preserved by FFPE and OCT. Samples were parallel processed from the two methods and proteins were analyzed with label-free quantitative MS. Over 700 and 1200 proteins were quantified in FFPE and OCT samples, respectively. Multivariate analysis indicates that the preservation method is the main source of variation, but also tumors of different stages could be differentiated. Proteins involved in mitochondrial function were overrepresented in OCT data but missing in the FFPE data, indicating that these proteins are not well preserved by FFPE. Concordant results for proteins such as HMGCS2 (uniquely quantified in Ta/T1 tumors), and LGALS1, ANXA5 and plastin (upregulated in T2/T3 tumors) were observed in both FFPE and OCT data, which supports the use of MS technology for biobank samples and encourages the further evaluation of these proteins as biomarkers.
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Liu S, Shi J, Liu Y, Wang L, Zhang J, Huang Y, Chen Z, Yang J. Analysis of mRNA expression differences in bladder cancer metastasis based on TCGA datasets. J Int Med Res 2021; 49:300060521996929. [PMID: 33787386 PMCID: PMC8020247 DOI: 10.1177/0300060521996929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE To investigate the metastatic mechanism of muscle invasive bladder cancer (MIBC), which accounts for approximately 30% of all bladder cancer cases, and is a considerable medical problem with high metastatic and mortality rates. METHODS The mRNA levels of patients with metastatic MIBC and nonmetastatic MIBC from The Cancer Genome Atlas dataset were compared. An integrated bioinformatics analysis was performed of the differentially expressed genes (DEGs), and analyses of Gene Ontology, Kyoto Encyclopaedia of Genes and Genomes pathway, protein-protein interaction, and survival were performed to investigate differences between metastatic and nonmetastatic MIBC. RESULTS Data from 264 patients were included (131 with, and 133 without, metastasis). A total of 385 significantly DEGs were identified, including 209 upregulated genes and 176 downregulated genes. Based on results using the STRING database and the MCODE plugin of Cytoscape software, two clusters were obtained. Moreover, two genes were identified that may be valuable for prognostic analysis: Keratin 38, type I (KRT38) and Histone cluster 1, H3f (HIST1H3F). CONCLUSION The KRT38 and HIST1H3F genes may be important in metastasis of MIBC.
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Affiliation(s)
- Sha Liu
- Department of Cell Biology, Third Military Medical University, Chongqing, China.,Department of Urology, Chinese People's Armed Police Force Tibet Corps Hospital, Lhasa, Tibet, China
| | - Jiazhong Shi
- Department of Cell Biology, Third Military Medical University, Chongqing, China
| | - Yuting Liu
- Department of Cell Biology, Third Military Medical University, Chongqing, China
| | - Liwei Wang
- Department of Urology, the First Affiliated Hospital of the Third Military Medical University, Chongqing, China
| | - Jingqi Zhang
- Department of Urology, the First Affiliated Hospital of the Third Military Medical University, Chongqing, China
| | - Yaqin Huang
- Department of Cell Biology, Third Military Medical University, Chongqing, China
| | - Zhiwen Chen
- Department of Cell Biology, Third Military Medical University, Chongqing, China
| | - Jin Yang
- Department of Urology, the First Affiliated Hospital of the Third Military Medical University, Chongqing, China
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Deregulation of extracellular matrix modeling with molecular prognostic markers revealed by transcriptome sequencing and validations in Oral Tongue squamous cell carcinoma. Sci Rep 2021; 11:250. [PMID: 33420101 PMCID: PMC7794513 DOI: 10.1038/s41598-020-78624-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Oral Tongue Squamous Cell Carcinoma (OTSCC), a distinct sub-group of head and neck cancers, is characteristically aggressive in nature with a higher incidence of recurrence and metastasis. Recent advances in therapeutics have not improved patient survival. The phenomenon of occult node metastasis, even among the purportedly good prognosis group of early-stage and node-negative tongue tumors, leads to a high incidence of locoregional failure in OTSCC which needs to be addressed. In the current study, transcriptome analysis of OTSCC patients identified the key genes and deregulated pathways. A panel of 26 marker genes was shortlisted and validated using real-time PCR in a prospective cohort of 100 patients. The gene expression was correlated with clinicopathological features including occult node metastasis, survival, and therapeutic outcome. The up-regulation of a panel of 6 genes namely, matrix metalloproteinase 9 (MMP9), Laminin subunit Gamma 2 (LAMC2), Desmoglein 2 (DSG2), Plasminogen Activator Urokinase (PLAU), Forkhead Box M1 (FOXM1), and Myosin 1B (MYO1B) was associated with failure of treatment in the early stage (T1, T2). Up-regulation of Tenacin C (TNC) and Podoplanin (PDPN) was significantly correlated with occult node positivity. Immunohistochemical analysis of LAMC2, MMP9, and E-Cadherin (ECAD) confirmed these markers to be indicators of poor prognosis. We propose this panel of valuable prognostic markers can be clinically useful to identify poor prognosis and occult node metastasis in OTSCC patients.
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Krishnan R, Murugiah M, Lakshmi NP, Mahalingam S. Guanine nucleotide binding protein like-1 (GNL1) promotes cancer cell proliferation and survival through AKT/p21 CIP1 signaling cascade. Mol Biol Cell 2020; 31:2904-2919. [PMID: 33147101 PMCID: PMC7927199 DOI: 10.1091/mbc.e20-04-0267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Human guanine nucleotide binding protein like 1 (GNL1) is an evolutionary conserved putative nucleolar GTPase belonging to the HSR1_MMR1 subfamily of GTPases. GNL1 was found to be highly up-regulated in various cancers. Here, we report for the first time that GNL1 inhibits apoptosis by modulating the expression of Bcl2 family of proteins and the cleavage of caspases 7 and 8. Furthermore, GNL1 protects colon cancer cells from chemo-drug-induced apoptosis. Interestingly, GNL1 up-regulates the expression of p53 and its transcriptional target, p21 but the up-regulation of p21 was found to be p53 dependent as well as independent mechanisms. Our results further demonstrate that GNL1 promotes cell growth and survival by inducing cytoplasmic retention and stabilization of p21 through AKT-mediated phosphorylation. In addition, GNL1 failed to inhibit apoptosis under p21 knockdown conditions which suggests the critical role of p21 in GNL1-mediated cell survival. Finally, an inverse correlation of GNL1, p21, and AKT expression in primary colon and breast cancer with patient survival suggests their critical role in tumorigenesis. Collectively, our study reveals that GNL1 executes its antiapoptotic function by a novel mechanism and suggests that it may function as a regulatory component of the PI3K/AKT/p21 signaling network to promote cell proliferation and survival in cancers.
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Affiliation(s)
- Rehna Krishnan
- Laboratory of Molecular Cell Biology, National Cancer Tissue Biobank, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai 600 036, India
| | - Mariappan Murugiah
- Laboratory of Molecular Cell Biology, National Cancer Tissue Biobank, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai 600 036, India
| | - Naga Padma Lakshmi
- Laboratory of Molecular Cell Biology, National Cancer Tissue Biobank, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai 600 036, India
| | - Sundarasamy Mahalingam
- Laboratory of Molecular Cell Biology, National Cancer Tissue Biobank, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai 600 036, India
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Choi SY, Kim TH, Hong MW, Park TS, Lee H, Lee SJ. Transcriptomic alterations induced by aflatoxin B1 and ochratoxin A in LMH cell line. Poult Sci 2020; 99:5265-5274. [PMID: 33142442 PMCID: PMC7647754 DOI: 10.1016/j.psj.2020.05.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/09/2020] [Accepted: 05/22/2020] [Indexed: 12/23/2022] Open
Abstract
Aflatoxin B1 (AFB1) and ochratoxin A (OTA), which are toxic metabolites of ubiquitously occurring molds, show diverse toxicological effects such as hepatotoxicity, genotoxicity, and immunotoxicity in human and animals. Despite poultry show sensitivity to AFB1 and OTA, the mechanism of these mycotoxins in chickens has not been fully investigated. Here, we aimed to elucidate the molecular mechanism induced by AFB1 and/or OTA in chicken hepatic cells using transcriptomic analysis. Aflatoxin B1 and OTA induced cytotoxic effects in a dose-dependent manner at 48 h after exposure. Furthermore, correlation effect indicated an antagonism between the 2 toxins. The mRNA sequencing of AFB1-treated or OTA-treated chicken hepatocarcinoma and functional analysis revealed the pathways that were commonly regulated by both mycotoxins, especially PPAR signaling, focal adhesion, and MAPK signaling. Based on these findings, a possible hypothesis is that AFB1 and OTA have similar toxic mechanisms and compete for some steps in the chicken liver, and it is expected that the mycotoxins would have antagonistic effects. In addition, genes identified through transcriptome analysis provide candidates for further study of AFB1 and OTA toxicity and targets for efforts to improve the health of chickens exposed to mycotoxins.
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Affiliation(s)
- So-Young Choi
- Department of Animal Life Science, Kangwon National University, Chuncheon-si, Gangwon-do 24341, Korea
| | - Tae Hyun Kim
- Department of Animal Science, University of California, Davis, Davis, CA 95616, USA
| | - Min-Wook Hong
- Department of Animal Life Science, Kangwon National University, Chuncheon-si, Gangwon-do 24341, Korea
| | - Tae Sub Park
- Graduate School of International Agricultural Technology and Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang-gun, Gangwon-do 25354, Korea
| | - Hyojeong Lee
- Department of Animal Life Science, Kangwon National University, Chuncheon-si, Gangwon-do 24341, Korea
| | - Sung-Jin Lee
- Department of Animal Life Science, Kangwon National University, Chuncheon-si, Gangwon-do 24341, Korea.
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22
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Liang X, Gao J, Wang Q, Hou S, Wu C. ECRG4 Represses Cell Proliferation and Invasiveness via NFIC/OGN/NF-κB Signaling Pathway in Bladder Cancer. Front Genet 2020; 11:846. [PMID: 32922434 PMCID: PMC7456849 DOI: 10.3389/fgene.2020.00846] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/13/2020] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BCa) is a malignant tumor in the urinary system with high cancer-related mortality worldwide. However, the molecular mechanisms of many genes dysregulated in BCa are still unclear. Herein, we showed that esophageal cancer-related gene-4 (ECRG4), which is downregulated in BCa tissues and cell lines, has a positive correlation with osteoglycin (OGN). Further functional experimental studies suggested that both ECRG4 and OGN inhibit cell proliferation, migration, and invasion in BCa cells. Moreover, ECRG4 acts as a tumor repressor and promotes the expression of OGN via the upregulation of nuclear factor 1 C-type (NFIC), which can bind to the promoter region of OGN and regulate its transcription. Bioinformatics analysis revealed that NFIC is downregulated in BCa tissues and has a positive correlation with ECRG4 or OGN. Esophageal cancer-related gene-4 could positively regulate the protein levels of NFIC in BCa cells. In addition, we demonstrated for the first time that ECRG4 inhibits the nuclear factor (NF)-κB signaling pathway via the upregulation of OGN in BCa cells. Overall, these findings provide evidence that both ECRG4 and OGN function as tumor repressors and that overexpression of ECRG4 inhibits the NF-κB signaling pathway by promoting NFIC/OGN signaling in BCa cells. Our results reveal the molecular regulatory mechanisms of the ECRG4-mediated repression of the NFIC/OGN/NF-κB signaling pathway in BCa and provide potential biomarkers or therapeutic targets for BCa.
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Affiliation(s)
- Xin Liang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China.,Department of Urology, Qingdao Municipal Hospital, Qingdao, China
| | - Jiangang Gao
- Department of Urology, Qingdao Municipal Hospital, Qingdao, China
| | - Quan Wang
- Department of Anesthesiology, Qingdao Municipal Hospital, Qingdao, China
| | - Sichuan Hou
- Department of Urology, Qingdao Municipal Hospital, Qingdao, China
| | - Changli Wu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
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23
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Wong AHH, Shin EM, Tergaonkar V, Chng WJ. Targeting NF-κB Signaling for Multiple Myeloma. Cancers (Basel) 2020; 12:cancers12082203. [PMID: 32781681 PMCID: PMC7463546 DOI: 10.3390/cancers12082203] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 07/30/2020] [Accepted: 08/01/2020] [Indexed: 12/11/2022] Open
Abstract
Multiple myeloma (MM) is the second most common hematologic malignancy in the world. Even though survival rates have significantly risen over the past years, MM remains incurable, and is also far from reaching the point of being managed as a chronic disease. This paper reviews the evolution of MM therapies, focusing on anti-MM drugs that target the molecular mechanisms of nuclear factor kappa B (NF-κB) signaling. We also provide our perspectives on contemporary research findings and insights for future drug development.
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Affiliation(s)
- Ada Hang-Heng Wong
- Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore; (E.M.S.); (V.T.)
- AW Medical Company Limited, Macau, China
- Correspondence: (A.H.-H.W.); (W.-J.C.); Tel.: +65-6586-9709 (A.H.-H.W.); +65-6772-4612 (W.-J.C.)
| | - Eun Myoung Shin
- Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore; (E.M.S.); (V.T.)
| | - Vinay Tergaonkar
- Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore; (E.M.S.); (V.T.)
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore
- Department of Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Department of Hematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore 119074, Singapore
- Correspondence: (A.H.-H.W.); (W.-J.C.); Tel.: +65-6586-9709 (A.H.-H.W.); +65-6772-4612 (W.-J.C.)
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24
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Rusinek D, Pfeifer A, Cieslicka M, Kowalska M, Pawlaczek A, Krajewska J, Szpak-Ulczok S, Tyszkiewicz T, Halczok M, Czarniecka A, Zembala-Nozynska E, Chekan M, Lamch R, Handkiewicz-Junak D, Ledwon A, Paliczka-Cieslik E, Kropinska A, Jarzab B, Oczko-Wojciechowska M. TERT Promoter Mutations and Their Impact on Gene Expression Profile in Papillary Thyroid Carcinoma. Cancers (Basel) 2020; 12:E1597. [PMID: 32560331 PMCID: PMC7352936 DOI: 10.3390/cancers12061597] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Telomerase reverse transcriptase promoter (TERTp) mutations are related to a worse prognosis in various malignancies, including papillary thyroid carcinoma (PTC). Since mechanisms responsible for the poorer outcome of TERTp(+) patients are still unknown, searching for molecular consequences of TERTp mutations in PTC was the aim of our study. METHODS The studied cohort consisted of 54 PTCs, among them 24 cases with distant metastases. BRAF V600E, RAS, and TERTp mutational status was evaluated in all cases. Differences in gene expression profile between TERTp(+) and TERTp(-) PTCs were examined using microarrays. The evaluation of signaling pathways and gene ontology was based on the Gene Set Enrichment Analysis. RESULTS Fifty-nine percent (32/54) of analyzed PTCs were positive for at least one mutation: 27 were BRAF(+), among them eight were TERTp(+), and 1 NRAS(+), whereas five other samples harbored RAS mutations. Expression of four genes significantly differed in BRAF(+)TERTp(+) and BRAF(+)TERTp(-) PTCs. Deregulation of pathways involved in key cell processes was observed. CONCLUSIONS TERTp mutations are related to higher PTC aggressiveness. CRABP2 gene was validated as associated with TERTp mutations. However, its potential use in diagnostics or risk stratification in PTC patients needs further studies.
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Affiliation(s)
- Dagmara Rusinek
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Aleksandra Pfeifer
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Marta Cieslicka
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Malgorzata Kowalska
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Agnieszka Pawlaczek
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Jolanta Krajewska
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Sylwia Szpak-Ulczok
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Tomasz Tyszkiewicz
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Monika Halczok
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Agnieszka Czarniecka
- Department of Oncological and Reconstructive Surgery, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland;
| | - Ewa Zembala-Nozynska
- Tumor Pathology Department, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (E.Z.-N.); (M.C.); (R.L.)
| | - Mykola Chekan
- Tumor Pathology Department, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (E.Z.-N.); (M.C.); (R.L.)
| | - Roman Lamch
- Tumor Pathology Department, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (E.Z.-N.); (M.C.); (R.L.)
| | - Daria Handkiewicz-Junak
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Aleksandra Ledwon
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Ewa Paliczka-Cieslik
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Aleksandra Kropinska
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Barbara Jarzab
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Malgorzata Oczko-Wojciechowska
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
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25
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Zhou DN, Ye CS, Yang QQ, Deng YF. Integrated analysis of transcriptome profiling predicts potential lncRNA and circRNA targets in human nasopharyngeal carcinoma. Oncol Lett 2020; 19:3123-3136. [PMID: 32218863 PMCID: PMC7068695 DOI: 10.3892/ol.2020.11412] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 11/08/2019] [Indexed: 01/08/2023] Open
Abstract
Non-coding RNAs (ncRNAs) regulate numerous genes and influence the progression of various human diseases, including cancer. The role of regulatory ncRNAs implicated in nasopharyngeal carcinoma (NPC), as well as their target genes, remains unclear. The present study aimed to investigate specific long non-coding (lnc)RNAs, circular RNAs (circRNAs) and mRNAs associated with the molecular pathogenesis of NPC, and to predict the underlying target genes of specific lncRNAs and circRNAs. The expression levels of lncRNAs, circRNAs and mRNAs in NPC and chronic nasopharyngitis tissues were detected and analyzed using microarray and bioinformatics techniques. A total of 2.80% lncRNAs (425 upregulated and 431 downregulated) were significantly differentially expressed (DE) between the two tissue types. Additionally, 0.96% circRNAs (18 upregulated and 13 downregulated) were significantly DE, while 2.94% mRNAs (426 upregulated and 341 downregulated) were significantly DE between the two tissue types. In total, 420 NPC-associated nearby encoding genes (196 up- and 224 downregulated) of the DE lncRNAs were identified. Overlap analysis identified 23 DE circRNAs and their corresponding target genes, with 37 microRNAs and 50 mRNAs, from which 14 interaction networks were constructed. Subsequent pathway analysis revealed 221 DE target genes corresponding to 31 key signaling pathways associated with NPC, 14 of which may represent hub genes associated with NPC pathophysiology. Thus, certain lncRNAs, circRNAs and mRNAs are aberrantly expressed in NPC tissues, and partially specific lncRNAs, circRNAs and their target genes may influence the tumorigenesis and progression of NPC. Target prediction and regulatory network identification may help to determine the pathogenic mechanisms of NPC.
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Affiliation(s)
- Dong-Ni Zhou
- Department of Pathology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Chun-Sheng Ye
- Department of Otolaryngology-Head and Neck Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Qing-Qing Yang
- Department of Otolaryngology-Head and Neck Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Yan-Fei Deng
- Department of Otolaryngology-Head and Neck Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, P.R. China.,Department of Otolaryngology-Head and Neck Surgery, Union School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
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26
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Xu H, Sun Y, Ma Z, Xu X, Qin L, Luo B. LOC134466 methylation promotes oncogenesis of endometrial carcinoma through LOC134466/hsa-miR-196a-5p/TAC1 axis. Aging (Albany NY) 2019; 10:3353-3370. [PMID: 30485833 PMCID: PMC6286819 DOI: 10.18632/aging.101644] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/04/2018] [Indexed: 12/20/2022]
Abstract
To investigate possible mechanism of abnormal methylation of long non-coding RNA (lncRNA) on endometrial carcinoma (EC) progression, we detected the genome methylation profiling of endometrial carcinoma by bioinformatic analysis. Accordingly, gene LOC134466 was chosen for the further research. We also found that TAC1 was the target gene of LOC134466 and miRNA, hsa-miR-196a-5p, might form a connection between LOC134466 and TAC1. The relationship was further proved by dual-luciferase reporter assay. In vitro studies, DNA methylation and expression were determined by MSP and qRT-PCR respectively. Cell proliferation, apoptosis and cell cycle were demonstrated by colony formation assay, Annexin V/PI double staining and flow cytometry. Besides, the function of LOC134466 and TAC1 in EC was further confirmed by Tumor Xenograft. Our results indicated that EC progression was promoted by hypermethylated LOC134466 and TAC1. Moreover, TAC1 transcription was regulated by LOC134466 via hsa-miR-196a-5p binding. LOC134466 and TAC1 demethylation by 5-Aza-2-Deoxycytidine inhibited EC cells proliferation and accelerated cell apoptosis. Furthermore, the expression of TACR1, TACR2 and TACR3 was remarkably decreased through LOC134466 and TAC1 treatments. Our findings establish a novel regulatory axis, LOC134466/hsa-miR-196a-5p/TAC1. Downregulation of the axis promoted EC development through TACR3, which further activated neuroactive ligand-receptor interaction.
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Affiliation(s)
- Hai Xu
- Department of Obstetrics and Gynecology, Huangjiahu Hospital of Hubei University of Chinese Medicine, Wuhan 430065, Hubei, China
| | - Yuan Sun
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, Hubei, China
| | - Zhen Ma
- Department of Dermatology, Hubei University of Chinese Medicine, Wuhan 430065, Hubei, China
| | - Xin Xu
- Department of Obstetrics and Gynecology, Hubei Provincial Hospital of TCM, Wuhan 430065, Hubei, China
| | - Lili Qin
- Department of Oncology, The First Clinic College of Hubei University of Chinese Medicine, Wuhan 430065, Hubei, China
| | - Baoping Luo
- Department of Oncology, The First Clinic College of Hubei University of Chinese Medicine, Wuhan 430065, Hubei, China.,Department of Oncology, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430065, Hubei, China
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27
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Shaikh I, Ansari A, Ayachit G, Gandhi M, Sharma P, Bhairappanavar S, Joshi CG, Das J. Differential gene expression analysis of HNSCC tumors deciphered tobacco dependent and independent molecular signatures. Oncotarget 2019; 10:6168-6183. [PMID: 31692905 PMCID: PMC6817442 DOI: 10.18632/oncotarget.27249] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022] Open
Abstract
Head and neck cancer is the sixth most common cancer worldwide, with tobacco as the leading cause. However, it is increasing in non-tobacco users also, hence limiting our understanding of its underlying molecular mechanisms. RNA-seq analysis of cancers has proven as effective tool in understanding disease etiology. In the present study, RNA-Seq of 86 matched Tumor/Normal pairs, of tobacco smoking (TOB) and non-smokers (N-TOB) HNSCC samples analyzed, followed by validation on 375 similar datasets. Total 2194 and 2073 differentially expressed genes were identified in TOB and N-TOB tumors, respectively. GO analysis found muscle contraction as the most enriched biological process in both TOB and N-TOB tumors. Pathway analysis identified muscle contraction and salivary secretion pathways enriched in both categories, whereas calcium signaling and neuroactive ligand-receptor pathway was more enriched in TOB and N-TOB tumors respectively. Network analysis identified muscle development related genes as hub node i. e. ACTN2, MYL2 and TTN in both TOB and N-TOB tumors, whereas EGFR and MYH6, depicts specific role in TOB and N-TOB tumors. Additionally, we found enriched gene networks possibly be regulated by tumor suppressor miRNAs such as hsa-miR-29/a/b/c, hsa-miR-26b-5p etc., suggestive to be key riboswitches in regulatory cascade of HNSCC. Interestingly, three genes PKLR, CST1 and C17orf77 found to show opposite regulation in each category, hence suggested to be key genes in separating TOB from N-TOB tumors. Our investigation identified key genes involved in important pathways implicated in tobacco dependent and independent carcinogenesis hence may help in designing precise HNSCC diagnostics and therapeutics strategies.
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Affiliation(s)
- Inayatullah Shaikh
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Afzal Ansari
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Garima Ayachit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Monika Gandhi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Priyanka Sharma
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Shivarudrappa Bhairappanavar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Jayashankar Das
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
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28
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Li J, Wang X, Zheng K, Liu Y, Li J, Wang S, Liu K, Song X, Li N, Xie S, Wang S. The clinical significance of collagen family gene expression in esophageal squamous cell carcinoma. PeerJ 2019; 7:e7705. [PMID: 31598423 PMCID: PMC6779144 DOI: 10.7717/peerj.7705] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/19/2019] [Indexed: 12/24/2022] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is a subtype of esophageal cancer with high incidence and mortality. Due to the poor 5-year survival rates of patients with ESCC, exploring novel diagnostic markers for early ESCC is emergent. Collagen, the abundant constituent of extracellular matrix, plays a critical role in tumor growth and epithelial-mesenchymal transition. However, the clinical significance of collagen genes in ESCC has been rarely studied. In this work, we systematically analyzed the gene expression of whole collagen family in ESCC, aiming to search for ideal biomarkers. Methods Clinical data and gene expression profiles of ESCC patients were collected from The Cancer Genome Atlas and the gene expression omnibus databases. Bioinformatics methods, including differential expression analysis, survival analysis, gene sets enrichment analysis (GSEA) and co-expression network analysis, were performed to investigate the correlation between the expression patterns of 44 collagen family genes and the development of ESCC. Results A total of 22 genes of collagen family were identified as differentially expressed genes in both the two datasets. Among them, COL1A1, COL10A1 and COL11A1 were particularly up-regulated in ESCC tissues compared to normal controls, while COL4A4, COL6A5 and COL14A1 were notably down-regulated. Besides, patients with low COL6A5 expression or high COL18A1 expression showed poor survival. In addition, a 7-gene prediction model was established based on collagen gene expression to predict patient survival, which had better predictive accuracy than the tumor-node-metastasis staging based model. Finally, GSEA results suggested that collagen genes might be tightly associated with PI3K/Akt/mTOR pathway, p53 pathway, apoptosis, cell cycle, etc. Conclusion Several collagen genes could be potential diagnostic and prognostic biomarkers for ESCC. Moreover, a novel 7-gene prediction model is probably useful for predicting survival outcomes of ESCC patients. These findings may facilitate early detection of ESCC and help improves prognosis of the patients.
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Affiliation(s)
- Jieling Li
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Xiao Wang
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Kai Zheng
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Ying Liu
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Junjun Li
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Shaoqi Wang
- Department of Oncology, Hubei Provincial Corps Hospital, Chinese People Armed Police Forces, Wuhan, China
| | - Kaisheng Liu
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Xun Song
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Nan Li
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Shouxia Xie
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Shaoxiang Wang
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
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Gong YZ, Ruan GT, Liao XW, Wang XK, Liao C, Wang S, Gao F. Diagnostic and prognostic values of integrin α subfamily mRNA expression in colon adenocarcinoma. Oncol Rep 2019; 42:923-936. [PMID: 31322253 PMCID: PMC6667841 DOI: 10.3892/or.2019.7216] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/26/2019] [Indexed: 12/24/2022] Open
Abstract
The integrin α (ITGA) subfamily genes play a fundamental role in various cancers. However, the potential mechanism and application values of ITGA genes in colon adenocarcinoma (COAD) remain elusive. The present study investigated the significance of the expression of ITGA genes in COAD from the perspective of diagnosis and prognosis. A COAD RNA-sequencing dataset was obtained from The Cancer Genome Atlas. The present study investigated the biological function of the ITGA subfamily genes through bioinformatics analysis. Reverse transcription-quantitative polymerase chain reaction was applied to investigate the distribution of integrin α8 (ITGA8) expression in COAD tumors and adjacent normal tissues. Bioinformatics analysis indicated that ITGA genes were noticeably enriched in cell adhesion and the integrin-mediated signaling pathway, and co-expressed with each other. It was also revealed through observation that the majority of gene expression was significantly low in tumor tissues (P<0.05), and diagnostic receiver operating characteristic curves revealed that most of the genes could serve as significant diagnostic markers in COAD (P<0.05), especially ITGA8 which had a high diagnostic value with an area under curve (AUC) of 0.989 [95% confidence interval (CI) 0.980–0.997] in COAD (P<0.0001). In addition, ITGA8 expression was verified in clinical samples and it was revealed that it was higher in adjacent normal tissues (P=0.041) compared to COAD tissues, and the AUC was 0.704 (95% CI, 0.577–0.831; P<0.0085). Multivariate survival analysis indicated that integrin α (ITGA5) may be an independent prognostic indicator for COAD overall survival. Gene set enrichment analysis indicated that ITGA5 may participate in multiple biological processes and pathways. The present study revealed that ITGA genes were associated with the diagnosis and prognosis of COAD. The mRNA expression of ITGA8 may be a potential diagnosis biomarker and ITGA5 may serve as an independent prognosis indicator for COAD.
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Affiliation(s)
- Yi-Zhen Gong
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Guo-Tian Ruan
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Xi-Wen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Xiang-Kun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Cun Liao
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Shuai Wang
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Feng Gao
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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30
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Hao S, Lv J, Yang Q, Wang A, Li Z, Guo Y, Zhang G. Identification of Key Genes and Circular RNAs in Human Gastric Cancer. Med Sci Monit 2019; 25:2488-2504. [PMID: 30948703 PMCID: PMC6463957 DOI: 10.12659/msm.915382] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Globally, gastric cancer (GC) is the third most common source of cancer-associated mortality. The aim of this study was to identify key genes and circular RNAs (circRNAs) in GC diagnosis, prognosis, and therapy and to further explore the potential molecular mechanisms of GC. Material/Methods Differentially expressed genes (DEGs) and circRNAs (DE circRNAs) between GC tissues and adjacent non-tumor tissues were identified from 3 mRNA and 3 circRNA expression profiles. Functional analyses were performed, and protein–protein interaction (PPI) networks were constructed. The significant modules and key genes in the PPI networks were identified. Kaplan-Meier analysis was performed to evaluate the prognostic value of these key genes. Potential miRNA-binding sites of the DE circRNAs and target genes of these miRNAs were predicted and used to construct DE circRNA–miRNA–mRNA networks. Results A total of 196 upregulated and 311 downregulated genes were identified in GC. The results of functional analysis showed that these DEGs were significantly enriched in a variety of functions and pathways, including extracellular matrix-related pathways. Ten hub genes (COL1A1, COL3A1, COL1A2, COL5A2, FN1, THBS1, COL5A1, SPARC, COL18A1, and COL11A1) were identified via PPI network analysis. Kaplan-Meier analysis revealed that 7 of these were associated with a poor overall survival in GC patients. Furthermore, we identified 2 DE circRNAs, hsa_circ_0000332 and hsa_circ_0021087. To reveal the potential molecular mechanisms of circRNAs in GC, DE circRNA–microRNA–mRNA networks were constructed. Conclusions Key candidate genes and circRNAs were identified, and novel PPI and circRNA–microRNA–mRNA networks in GC were constructed. These may provide useful information for the exploration of potential biomarkers and targets for the diagnosis, prognosis, and therapy of GC.
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Affiliation(s)
- Shuhong Hao
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Junfeng Lv
- Department of Radiology, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Qiwei Yang
- Medical Research Center, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Ao Wang
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Zhaoyan Li
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Yuchen Guo
- Department of Gastrointestinal Surgery, The First Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Guizhen Zhang
- Medical Research Center, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland).,Department of Orthopedics, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
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Interplay between human nucleolar GNL1 and RPS20 is critical to modulate cell proliferation. Sci Rep 2018; 8:11421. [PMID: 30061673 PMCID: PMC6065441 DOI: 10.1038/s41598-018-29802-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/13/2018] [Indexed: 12/29/2022] Open
Abstract
Human Guanine nucleotide binding protein like 1 (GNL1) belongs to HSR1_MMR1 subfamily of nucleolar GTPases. Here, we report for the first time that GNL1 promotes cell cycle and proliferation by inducing hyperphosphorylation of retinoblastoma protein. Using yeast two-hybrid screening, Ribosomal protein S20 (RPS20) was identified as a functional interacting partner of GNL1. Results from GST pull-down and co-immunoprecipitation assays confirmed that interaction between GNL1 and RPS20 was specific. Further, GNL1 induced cell proliferation was altered upon knockdown of RPS20 suggesting its critical role in GNL1 function. Interestingly, cell proliferation was significantly impaired upon expression of RPS20 interaction deficient GNL1 mutant suggest that GNL1 interaction with RPS20 is critical for cell growth. Finally, the inverse correlation of GNL1 and RPS20 expression in primary colon and gastric cancers with patient survival strengthen their critical importance during tumorigenesis. Collectively, our data provided evidence that cross-talk between GNL1 and RPS20 is critical to promote cell proliferation.
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32
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Flentje A, Kober KM, Carrico AW, Neilands TB, Flowers E, Heck NC, Aouizerat BE. Minority stress and leukocyte gene expression in sexual minority men living with treated HIV infection. Brain Behav Immun 2018; 70:335-345. [PMID: 29548994 PMCID: PMC5953835 DOI: 10.1016/j.bbi.2018.03.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/20/2018] [Accepted: 03/12/2018] [Indexed: 12/17/2022] Open
Abstract
Sexual minority (i.e., non-heterosexual) individuals experience poorer mental and physical health, accounted for in part by the additional burden of sexual minority stress occurring from being situated in a culture favoring heteronormativity. Informed by previous research, the purpose of this study was to identify the relationship between sexual minority stress and leukocyte gene expression related to inflammation, cancer, immune function, and cardiovascular function. Sexual minority men living with HIV who were on anti-retroviral medication, had viral load < 200 copies/mL, and had biologically confirmed, recent methamphetamine use completed minority stress measures and submitted blood samples for RNA sequencing on leukocytes. Differential gene expression and pathway analyses were conducted comparing those with clinically elevated minority stress (n = 18) and those who did not meet the clinical cutoff (n = 20), covarying reactive urine toxicology results for very recent stimulant use. In total, 90 differentially expressed genes and 138 gene set pathways evidencing 2-directional perturbation were observed at false discovery rate (FDR) < 0.10. Of these, 41 of the differentially expressed genes and 35 of the 2-directionally perturbed pathways were identified as functionally related to hypothesized mechanisms of inflammation, cancer, immune function, and cardiovascular function. The neuroactive-ligand receptor pathway (implicated in cancer development) was identified using signaling pathway impact analysis. Our results suggest several potential biological pathways for future work investigating the relationship between sexual minority stress and health.
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Affiliation(s)
- Annesa Flentje
- Community Health Systems, School of Nursing, University of California, San Francisco, United States.
| | - Kord M Kober
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, United States; Institute for Computational Health Sciences, University of California, San Francisco, United States
| | | | - Torsten B Neilands
- Center for AIDS Prevention Studies, Department of Medicine, University of California, San Francisco, United States
| | - Elena Flowers
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, United States; Institute for Human Genetics, University of California, San Francisco, United States
| | - Nicholas C Heck
- Department of Psychology, Marquette University, United States
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, College of Dentistry, New York University, United States
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33
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Holfeld A, Valdés A, Malmström PU, Segersten U, Lind SB. Parallel Proteomic Workflow for Mass Spectrometric Analysis of Tissue Samples Preserved by Different Methods. Anal Chem 2018; 90:5841-5849. [PMID: 29624047 DOI: 10.1021/acs.analchem.8b00379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Formalin-fixed and paraffin-embedded (FFPE) and optimal cutting temperature (OCT)-embedded and frozen tissue specimens in biobanks are highly valuable in clinical studies but proteomic and post-translational modification (PTM) studies using mass spectrometry (MS) have been limited due to structural arrangement of proteins and contaminations from embedding material. This study aims to develop a parallel proteomic workflow for FFPE and OCT/frozen samples that allows for large-scale, quick, reproducible, qualitative, and quantitative high-resolution MS analysis. The optimized protocol gives details on removal of embedding material, protein extraction, and multienzyme digestion using filter-aided sample preparation method. The method was evaluated by investigating the protein expression levels in nonmuscle-invasive and muscle-invasive bladder cancer samples in two cohorts and MS spectra were carefully reviewed for contaminations. More than 2000 and 3000 proteins in FFPE and OCT/frozen samples, respectively, were identified, and samples could be clustered in different tumor stages based on their protein expression. Furthermore, more than 250 and 400 phosphopeptides could be identified from specific patient samples of FFPE and OCT/frozen, respectively, using titanium dioxide enrichment. The paper presents unique data describing the similarities and differences observed in FFPE and OCT/frozen samples and shows the feasibility to detect proteins and site-specific phosphorylation even after long-term storage of clinical samples.
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34
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Zhang H, Liu J, Fu X, Yang A. Identification of Key Genes and Pathways in Tongue Squamous Cell Carcinoma Using Bioinformatics Analysis. Med Sci Monit 2017; 23:5924-5932. [PMID: 29240723 PMCID: PMC5738838 DOI: 10.12659/msm.905035] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Tongue squamous cell carcinoma (TSCC) is a major type of oral cancers and has remained an intractable cancer over the past decades. The aim of this study was to identify differentially expressed genes (DEGs) during TSCC and reveal their potential mechanisms. MATERIAL AND METHODS The gene expression profiles of GSE13601 were downloaded from the GEO database. The GSE13601 dataset contains 57 samples, including 31 tongue SCC samples and 26 matched normal mucosa samples. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed; Cytoscape software was used for the protein-protein interaction (PPI) network and module analysis of the DEGs. RESULTS We identified a total of 1,050 upregulated DEGs (uDEGs) and 702 downregulated DEGs (dDEGs) of TSCC. The GO analysis results showed that uDEGs were significantly enriched in the following biological processes (BP): signal transduction, positive or negative regulation of cell proliferation, and negative regulation of cell proliferation. The dDEGs were significantly enriched in the following biological processes: signal transduction, cell adhesion, and apoptotic process. The KEGG pathway analysis showed that uDEGs were enriched in metabolic pathways, pathways in cancer, and PI3K-Akt signaling pathway, while the dDEGs were enriched in focal adhesion and ECM-receptor interaction. The top centrality hub genes RAC1, APP, EGFR, KNG1, AGT, and HRAS were identified from the PPI network. Module analysis revealed that TSCC was associated with significant pathways, including neuroactive ligand-receptor interaction, calcium signaling pathway, and chemokine signaling pathway. CONCLUSIONS The present study identified key genes and signal pathways, which deepen our understanding of the molecular mechanisms of carcinogenesis and development of the disease, and might be used as diagnostic and therapeutic molecular biomarkers for TSCC.
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Affiliation(s)
- Huayong Zhang
- Department of Head and Neck Surgery, Sun Yan-sen University Cancer Centre, Guangzhou, Guangdong, China (mainland).,Department of Cardiothoracic Surgery, The Fifth Affiliated Hospital of Sun Yan-sen University, Zhuhai, Guangdong, China (mainland)
| | - Jianmin Liu
- Department of Otorhinolaryngology and Head and Neck Surgery, People's Hospital of Deyang City, Deyang, Sichuan, China (mainland)
| | - Xiaoyan Fu
- Department of Head and Neck Surgery, Sun Yan-sen University Cancer Centre, Guangzhou, Guangdong, China (mainland)
| | - Ankui Yang
- Department of Head and Neck Surgery, Sun Yan-sen University Cancer Centre, Guangzhou, Guangdong, China (mainland)
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35
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Wang X, Xu T, Gao F, He H, Zhu Y, Shen Z. Targeting of CCN2 suppresses tumor progression and improves chemo-sensitivity in urothelial bladder cancer. Oncotarget 2017; 8:66316-66327. [PMID: 29029514 PMCID: PMC5630414 DOI: 10.18632/oncotarget.19987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 07/19/2017] [Indexed: 11/25/2022] Open
Abstract
Urothelial bladder cancer (UBC) is the most common urinary neoplasm in China. CCN family protein 2 (CCN2), a cysteine-rich matricellular protein, is abnormally expressed in several cancer types and involved in tumor progression or chemo-resistance. However, detailed expression patterns and effects of CCN2 in UBC still remain unknown. We found that down-regulation of CCN2 suppressed proliferation, migration and invasion of UBC cells in vitro and targeting of CCN2 decelerated xenograft growth in vivo. When treated with mitomycin C (MMC), CCN2-scilencing UBC cells showed lower survival and higher apoptotic rates and these effects were probably mediated via inactivation of Akt and Erk pathways. We also demonstrated the clinical significance of CCN2 expression, which was higher in UBC tissues and associated with advanced tumor stage and high pathologic grade. Taken together, our data suggest that CCN2 is an oncogene in UBC and might serve as a matricellular target for improving chemotherapeutic efficacy.
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Affiliation(s)
- Xiaojing Wang
- Department of Urology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Tianyuan Xu
- Department of Urology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Fengbin Gao
- Department of Urology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Hongchao He
- Department of Urology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yu Zhu
- Department of Urology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Zhoujun Shen
- Department of Urology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
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36
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Schmucker HS, Park JP, Coissieux MM, Bentires-Alj M, Feltus FA, Booth BW. RNA Expression Profiling Reveals Differentially Regulated Growth Factor and Receptor Expression in Redirected Cancer Cells. Stem Cells Dev 2017; 26:646-655. [DOI: 10.1089/scd.2016.0340] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Hannah S. Schmucker
- Department of Biological Sciences, Clemson University, Clemson, South Carolina
| | - Jang Pyo Park
- Institute for Biological Interfaces of Engineering, Clemson University, Clemson, South Carolina
| | - Marie-May Coissieux
- Friedrich-Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Biomedicine, University of Basel, University Hospital Basel, Basel, Switzerland
| | - Mohamed Bentires-Alj
- Friedrich-Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Biomedicine, University of Basel, University Hospital Basel, Basel, Switzerland
| | - F. Alex Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina
| | - Brian W. Booth
- Institute for Biological Interfaces of Engineering, Clemson University, Clemson, South Carolina
- Department of Bioengineering, Clemson University, Clemson, South Carolina
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37
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Hussain SA, Palmer DH, Syn WK, Sacco JJ, Greensmith RMD, Elmetwali T, Aachi V, Lloyd BH, Jithesh PV, Arrand J, Barton D, Ansari J, Sibson DR, James ND. Gene expression profiling in bladder cancer identifies potential therapeutic targets. Int J Oncol 2017; 50:1147-1159. [PMID: 28259975 PMCID: PMC5363876 DOI: 10.3892/ijo.2017.3893] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/27/2017] [Indexed: 01/08/2023] Open
Abstract
Despite advances in management, bladder cancer remains a major cause of cancer related complications. Characterisation of gene expression patterns in bladder cancer allows the identification of pathways involved in its pathogenesis, and may stimulate the development of novel therapies targeting these pathways. Between 2004 and 2005, cystoscopic bladder biopsies were obtained from 19 patients and 11 controls. These were subjected to whole transcript-based microarray analysis. Unsupervised hierarchical clustering was used to identify samples with similar expression profiles. Hypergeometric analysis was used to identify canonical pathways and curated networks having statistically significant enrichment of differentially expressed genes. Osteopontin (OPN) expression was validated by immunohistochemistry. Hierarchical clustering defined signatures, which differentiated between cancer and healthy tissue, muscle-invasive or non-muscle invasive cancer and healthy tissue, grade 1 and grade 3. Pathways associated with cell cycle and proliferation were markedly upregulated in muscle-invasive and grade 3 cancers. Genes associated with the classical complement pathway were downregulated in non-muscle invasive cancer. Osteopontin was markedly overexpressed in invasive cancer compared to healthy tissue. The present study contributes to a growing body of work on gene expression signatures in bladder cancer. The data support an important role for osteopontin in bladder cancer, and identify several pathways worthy of further investigation.
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Affiliation(s)
- Syed A Hussain
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L69 3GA, UK
| | - Daniel H Palmer
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L69 3GA, UK
| | - Wing-Kin Syn
- Regeneration and Repair Group, The Institute of Hepatology, Foundation of Liver Research, London SE5 9NT, UK
| | - Joseph J Sacco
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L69 3GA, UK
| | - Richard M D Greensmith
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L69 3GA, UK
| | - Taha Elmetwali
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L69 3GA, UK
| | - Vijay Aachi
- The Royal Liverpool and Broadgreen University Hospital Trust, Liverpool L7 8XP, UK
| | - Bryony H Lloyd
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L69 3GA, UK
| | - Puthen V Jithesh
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L69 3GA, UK
| | - John Arrand
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Darren Barton
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Jawaher Ansari
- Beatson West Scotland Cancer Centre, Glasgow G12 0YN, UK
| | - D Ross Sibson
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L69 3GA, UK
| | - Nicholas D James
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
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Koide N, Kasamatsu A, Endo-Sakamoto Y, Ishida S, Shimizu T, Kimura Y, Miyamoto I, Yoshimura S, Shiiba M, Tanzawa H, Uzawa K. Evidence for Critical Role of Lymphocyte Cytosolic Protein 1 in Oral Cancer. Sci Rep 2017; 7:43379. [PMID: 28230172 PMCID: PMC5322526 DOI: 10.1038/srep43379] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/23/2017] [Indexed: 12/26/2022] Open
Abstract
Lymphocyte cytosolic protein 1 (LCP1), a member of actin-binding protein of the plastin family, has been identified in several malignant tumors of non-hematopoietic sites, such as the colon, prostate, and breast. However, little is known about the roles of LCP1 in oral squamous cell carcinomas (OSCCs). This present study sought to clarify the clinical relevance of LCP1 in OSCCs and investigate possible clinical applications for treating OSCCs by regulating LCP1 expression. We found up-regulation of LCP1in OSCCs compared with normal counterparts using real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), immunoblotting, and immunohistochemistry (P < 0.05). We used shRNA models for LCP1 (shLCP1) and enoxacin (ENX), a fluoroquinolone antibiotic drug, as a regulator of LCP1 expression. In addition to the LCP1 knockdown experiments in which shLCP1 cells showed several depressed functions, including cellular proliferation, invasiveness, and migratory activities, ENX-treated cells also had attenuated functions. Consistent with our hypothesis from our in vitro data, LCP1-positive OSCC samples were correlated closely with the primary tumoral size and regional lymph node metastasis. These results suggested that LCP1 is a useful biomarker for determining progression of OSCCs and that ENX might be a new therapeutic agent for treating OSCCs by controlling LCP1 expression.
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Affiliation(s)
- Nao Koide
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kasamatsu
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Chiba, Japan
| | - Yosuke Endo-Sakamoto
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Chiba, Japan
| | - Sho Ishida
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba, Japan
| | | | - Yasushi Kimura
- Department of Oral and maxillofacial Surgery Research Institute, National Defense Medical College, Saitama, Japan
| | - Isao Miyamoto
- Department of Dentistry and Oral-Maxillofacial Surgery, Japanese Red Cross Fukaya Hospital, Saitama, Japan
| | - Shusaku Yoshimura
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masashi Shiiba
- Department of Clinical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hideki Tanzawa
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Chiba, Japan
| | - Katsuhiro Uzawa
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Chiba, Japan
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Liu X, Zhang Y, Wang P, Wang H, Su H, Zhou X, Zhang L. HBX Protein-Induced Downregulation of microRNA-18a is Responsible for Upregulation of Connective Tissue Growth Factor in HBV Infection-Associated Hepatocarcinoma. Med Sci Monit 2016; 22:2492-500. [PMID: 27421245 PMCID: PMC4959457 DOI: 10.12659/msm.895943] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background This study was designed to improve our understanding of the role of miR-18a and its target (connective tissue growth factor (CTGF), which are mediators in HBX-induced hepatocellular carcinoma (HCC). Material/Methods We first investigated the expression of several candidate microRNAs (miRNAs) reported to have been aberrantly expressed between HepG2 and HepG2.2.15, which is characterized by stable HBV infection, while the CTGF is identified as a target of miR-18a. Furthermore, the expression of CTGF evaluated in HepG2 was transfected with HBX, while the HepG2.2.15 was transfected with miR-18a and CTGF siRNA. We examined the cell cycle at the same time. Results We found that the expression of miR-18a was abnormally reduced in the HBV-positive HCC tissue samples compared with HBV-negative HCC samples. Through the use of a luciferase reporter system, we also identified CTGF 3′UTR (1046–1052 bp) as the exact binding site for miR-18a. We also observed a clear increase in CTGF mRNA and protein expression levels in HBV-positive HCC human tissue samples in comparison with the HBV-negative controls, indicating a possible negatively associated relationship between miR-18a and CTGF. Furthermore, we investigated the effect of HBX overexpression on miR-18a and CTGF, as well as the viability and cell cycle status of HepG2 cells. In addition, we found that HBX introduction downregulated miR-18a, upregulated CTGF, elevated the viability, and promoted cell cycle progression. We transfected HepG2.2.15 with miR-18a mimics and CTGF siRNA, finding that upregulated miR-18a and downregulated CTGF suppress the viability and cause cell cycle arrest. Conclusions Our study shows the role of the CTGF gene as a target of miR-18a, and identifies the function of HBV/HBX/miR-18a/CTGF as a key signaling pathway mediating HBV infection-induced HCC.
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Affiliation(s)
- Xiaomin Liu
- Department of Gastroenterology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan, China (mainland)
| | - Yingjian Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan, China (mainland)
| | - Ping Wang
- Department of Public Health, School of Medicine, Henan University of Science and Technology, Luoyang, Henan, China (mainland)
| | - Hongyun Wang
- Department of Gastroenterology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan, China (mainland)
| | - Huanhuan Su
- Department of Gastroenterology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan, China (mainland)
| | - Xin Zhou
- Department of Gastroenterology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan, China (mainland)
| | - Lamei Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan, China (mainland)
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40
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Chai Y, Wang G, Fan L, Zhao M. A proteomic analysis of mushroom polysaccharide-treated HepG2 cells. Sci Rep 2016; 6:23565. [PMID: 27020667 PMCID: PMC4810362 DOI: 10.1038/srep23565] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/19/2016] [Indexed: 12/30/2022] Open
Abstract
The anti-tumor properties of fungal polysaccharides have gained significant recognition in Asia and tropical America. In this study, the differential expression of proteins in normal HepG2 cells and those treated with polysaccharides that had been isolated from Phellinus linteus (PL), Ganoderma lucidum (GL) and Auricularia auricula (AA) was investigated. Using two-dimensional electrophoresis (2DE), a total of 104 protein spots were determined to be overexpressed in these cells compared with noncancerous regions. A total of 59 differentially expressed proteins were identified through MALDI-TOF-MS. In addition, 400 biological processes (BP), 133 cell components (CC) and 146 molecular functions (MF) were enriched by Gene Ontology (GO) analysis, and 78 KEGG pathways were enriched by pathway enrichment. Protein-Protein Interaction (PPI) analysis demonstrated the interaction networks affected by polysaccharides in HepG2 cells. Then, DJ-1 and 14-3-3 were identified as the key proteins in the networks, and the expression of the mRNA and proteins were evaluated using Real-time quantitative PCR (qRT-PCR) and Western blotting (WB), respectively. The results were in agreement with the 2DE. These results provided information on significant proteins of hepatocellular carcinoma (HCC) and form an important basis for the future development of valuable medicinal mushroom resources.
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Affiliation(s)
- Yangyang Chai
- College of Life Sciences, Northeast Forestry University, Harbin, PR China
| | - Guibin Wang
- College of Life Sciences, Northeast Forestry University, Harbin, PR China
| | - Lili Fan
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences,Harbin, PR China
| | - Min Zhao
- College of Life Sciences, Northeast Forestry University, Harbin, PR China
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Dhawan D, Paoloni M, Shukradas S, Choudhury DR, Craig BA, Ramos-Vara JA, Hahn N, Bonney PL, Khanna C, Knapp DW. Comparative Gene Expression Analyses Identify Luminal and Basal Subtypes of Canine Invasive Urothelial Carcinoma That Mimic Patterns in Human Invasive Bladder Cancer. PLoS One 2015; 10:e0136688. [PMID: 26352142 PMCID: PMC4564191 DOI: 10.1371/journal.pone.0136688] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/06/2015] [Indexed: 01/01/2023] Open
Abstract
More than 160,000 people are expected to die from invasive urothelial carcinoma (iUC) this year worldwide. Research in relevant animal models is essential to improving iUC management. Naturally-occurring canine iUC closely resembles human iUC in histopathology, metastatic behavior, and treatment response, and could provide a relevant model for human iUC. The molecular characterization of canine iUC, however, has been limited. Work was conducted to compare gene expression array results between tissue samples from iUC and normal bladder in dogs, with comparison to similar expression array data from human iUC and normal bladder in the literature. Considerable similarities between enrichment patterns of genes in canine and human iUC were observed. These included patterns mirroring basal and luminal subtypes initially observed in human breast cancer and more recently noted in human iUC. Canine iUC samples also exhibited enrichment for genes involved in P53 pathways, as has been reported in human iUC. This is particularly relevant as drugs targeting these genes/pathways in other cancers could be repurposed to treat iUC, with dogs providing a model to optimize therapy. As part of the validation of the results and proof of principal for evaluating individualized targeted therapy, the overexpression of EGFR in canine bladder iUC was confirmed. The similarities in gene expression patterns between dogs and humans add considerably to the value of naturally-occurring canine iUC as a relevant and much needed animal model for human iUC. Furthermore, the finding of expression patterns that cross different pathologically-defined cancers could allow studies of dogs with iUC to help optimize cancer management across multiple cancer types. The work is also expected to lead to a better understanding of the biological importance of the gene expression patterns, and the potential application of the cross-species comparisons approach to other cancer types as well.
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Affiliation(s)
- Deepika Dhawan
- Department of Veterinary Clinical Sciences, Purdue University College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States of America
- Purdue Oncological Sciences Center, Purdue University, West Lafayette, Indiana, United States of America
| | - Melissa Paoloni
- CCR Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Shweta Shukradas
- Department of Bioinformatics, Strand Genomics Inc, San Francisco, California, United States of America
| | - Dipanwita Roy Choudhury
- Department of Bioinformatics, Strand Genomics Inc, San Francisco, California, United States of America
| | - Bruce A. Craig
- Department of Statistics, Purdue University, West Lafayette, Indiana, United States of America
| | - José A. Ramos-Vara
- Purdue Oncological Sciences Center, Purdue University, West Lafayette, Indiana, United States of America
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States of America
| | - Noah Hahn
- Department of Oncology and Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Patty L. Bonney
- Department of Veterinary Clinical Sciences, Purdue University College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States of America
| | - Chand Khanna
- CCR Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Deborah W. Knapp
- Department of Veterinary Clinical Sciences, Purdue University College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States of America
- Purdue Oncological Sciences Center, Purdue University, West Lafayette, Indiana, United States of America
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, United States of America
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42
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Liu F, Ji F, Ji Y, Jiang Y, Sun X, Lu Y, Zhang L, Han Y, Liu X. Dissecting the mechanism of colorectal tumorigenesis based on RNA-sequencing data. Exp Mol Pathol 2015; 98:246-53. [PMID: 25576648 DOI: 10.1016/j.yexmp.2015.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/26/2014] [Accepted: 01/05/2015] [Indexed: 02/07/2023]
Abstract
OBJECTIVE This study aimed to identify the differentially expressed genes (DEGs), mutated genes and fusion genes in colorectal cancer. MATERIALS AND METHODS RNA-sequencing data (ID: SRP009386) from cancerous, paracancerous non-tumor and distant normal tissue from one Chinese patient with stage III colorectal cancer were downloaded from Sequence Read Archive. Quality control was checked using FastQC, followed by sequence alignment against the hg19 reference genome using TopHat v1.3.3. The expression levels were quantified using Cufflinks, followed by DEGs screening using NOISeq. Enrichment analysis was performed using DAVID. Transcription factors were screened using TRANSFA. Mutated loci were identified using SAMTools and VCFTools. Gene fusion events were detected by TopHat-fusion. RESULTS In total 2440, 1887 and 834 DEGs were respectively detected in cancerous vs. normal tissue, cancerous vs. paracancerous tissue and paracancerous vs. normal tissue. The up-regulated genes from cancerous and paracancerous tissue compared with normal tissue were enriched in "extracellular matrix receptor interaction" and "focal adhesion pathway" as well as some biological processes except for "negative regulation of programmed cell death" uniquely presenting in cancer. Dysregulated transcription factors including SOX4, BCL6, CEBPB and MSX2 were enriched in the unique biological process. Trp53 was identified with one mutated locus 7577142 (C → T) on chromosome 17. BCL6 also experienced missense mutation. Additionally, COL1A1-PPP2R2C and EXPH5-COL1A2 were observed fusion genes in cancer tissue. CONCLUSIONS The unique biological process in cancer tissue may be the cause for colorectal carcinogenesis. The screened transcription factors, mutated genes and fusion genes may contribute to the progression of colorectal cancer.
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Affiliation(s)
- Fuguo Liu
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Fengzhi Ji
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Yuling Ji
- Statistics Division, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Yueping Jiang
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Xueguo Sun
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Yanyan Lu
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Lingyun Zhang
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Yue Han
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Xishuang Liu
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
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43
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Wu J, Zhao X, Lin Z, Shao Z. A system level analysis of gastric cancer across tumor stages with RNA-seq data. MOLECULAR BIOSYSTEMS 2015; 11:1925-32. [DOI: 10.1039/c5mb00105f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gastric cancer is the third leading cause of cancer-related death in the world.
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Affiliation(s)
- Jun Wu
- Department of Automation
- Shanghai Jiao Tong University
- and Key Laboratory of System Control and Information Processing of Ministry of Education
- Shanghai
- China
| | - Xiaodong Zhao
- School of Biomedical Engineering
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Zongli Lin
- Charles L. Brown Department of Electrical and Computer Engineering
- University of Virginia
- Charlottesville
- USA
| | - Zhifeng Shao
- School of Biomedical Engineering
- Shanghai Jiao Tong University
- Shanghai
- China
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44
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Xie R, Huang H, Li W, Chen B, Jiang J, He Y, Lv J, ma B, Zhou Y, Feng C, Chen L, He W. Identifying progression related disease risk modules based on the human subcellular signaling networks. MOLECULAR BIOSYSTEMS 2014; 10:3298-309. [PMID: 25315201 DOI: 10.1039/c4mb00482e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many studies have shown that the structure and dynamics of the human signaling network are disturbed in complex diseases such as coronary artery disease, and gene expression profiles can distinguish variations in diseases since they can accurately reflect the status of cells. Integration of subcellular localization and the human signaling network holds promise for providing insight into human diseases. In this study, we performed a novel algorithm to identify progression-related-disease-risk modules (PRDRMs) among patients of different disease states within eleven subcellular sub-networks from a human signaling network. The functional annotation and literature retrieval showed that the PRDRMs were strongly associated with disease pathogenesis. The results indicated that the PRDRM expression values as classification features had a good classification performance to distinguish patients of different disease states. Our approach compared with the method PageRank had a better classification performance. The identification of the PRDRMs in response to the dynamic gene expression change could facilitate our understanding of the pathological basis of complex diseases. Our strategy could provide new insights into the potential use of prognostic biomarkers and the effective guidance of clinical therapy from the human subcellular signaling network perspective.
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Affiliation(s)
- Ruiqiang Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150081, China.
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Joshi BH, Leland P, Lababidi S, Varrichio F, Puri RK. Interleukin-4 receptor alpha overexpression in human bladder cancer correlates with the pathological grade and stage of the disease. Cancer Med 2014; 3:1615-28. [PMID: 25208941 PMCID: PMC4298388 DOI: 10.1002/cam4.330] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 08/06/2014] [Accepted: 08/06/2014] [Indexed: 12/01/2022] Open
Abstract
Previously, we have demonstrated that interleukin-4 receptor α (IL-4Rα) is overexpressed on a variety of human cancers and can serve as target for IL-4 immunotoxin comprised of IL-4 and a mutated Pseudomonas exotoxin. However, its expression and association with grade and clinical stage of bladder cancer has not been studied. IL-4Rα expression was examined in human bladder cancer cell lines, mouse xenografts, and biopsy specimens at mRNA and protein levels by real-time RT-PCR and IHC/ISH techniques. We also examined the effect of IL-4 on proliferation and invasion of bladder carcinoma cell lines. For tissue microarray (TMA) results, we analyzed the precision data using exact binomial proportion with exact two-sided P-values. We used Cochran–Armitage Statistics with exact two-sided P-values to examine the trend analysis of IL-4Rα over grade or stage of the bladder cancer specimens. The influence of age and gender covariates was also analyzed using multiple logistic regression models. IL-4Rα is overexpressed in five bladder cancer cell lines, while normal bladder and human umbilical vein cell lines (HUVEC) expressed at low levels. Two other chains of IL-4 receptor complex, IL-2RγC and IL-13Rα1, were absent or weakly expressed. IL-4 modestly inhibited the cell proliferation, but enhanced cell invasion of bladder cancer cell lines in a concentration-dependent manner. Bladder cancer xenografts in immunodeficient mice also maintained IL-4Rα overexpression in vivo. Analysis of tumor biopsy specimens in TMAs revealed significantly higher IL-4Rα immunostaining (≥2+) in Grade 2 (85%) and Grade 3 (97%) compared to Grade 1 tumors (0%) (P ≤ 0.0001). Similarly, 9% stage I tumors were positive for IL-4Rα (≥2+) compared to 84% stage II (P ≤ 0.0001) and 100% stages III–IV tumors (P ≤ 0.0001). IL-13Rα1 was also expressed in tumor tissues but at low levels and it did not show any correlation with the grade and stage of disease. However, the IL-2RγC was not expressed. Ten normal bladder specimens demonstrated ≤1+ staining for IL-4Rα and IL-13Rα1 and no staining for IL-2RγC. These results demonstrate that IL-4Rα is overexpressed in human bladder cancer, which correlates with advanced grade and stage of the disease. Thus, IL-4Rα may be a bladder tumor-associated protein and a prognostic biomarker.
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Affiliation(s)
- Bharat H Joshi
- Tumor Vaccines and Biotechnology Branch, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapy, Center for Biologics Evaluation and Research, NIH Building 29B, Room 2E1229 Lincoln Drive, Bethesda, 20892, Maryland
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