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Dakal TC, Dhabhai B, Pant A, Moar K, Chaudhary K, Yadav V, Ranga V, Sharma NK, Kumar A, Maurya PK, Maciaczyk J, Schmidt‐Wolf IGH, Sharma A. Oncogenes and tumor suppressor genes: functions and roles in cancers. MedComm (Beijing) 2024; 5:e582. [PMID: 38827026 PMCID: PMC11141506 DOI: 10.1002/mco2.582] [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: 09/18/2023] [Revised: 04/21/2024] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Cancer, being the most formidable ailment, has had a profound impact on the human health. The disease is primarily associated with genetic mutations that impact oncogenes and tumor suppressor genes (TSGs). Recently, growing evidence have shown that X-linked TSGs have specific role in cancer progression and metastasis as well. Interestingly, our genome harbors around substantial portion of genes that function as tumor suppressors, and the X chromosome alone harbors a considerable number of TSGs. The scenario becomes even more compelling as X-linked TSGs are adaptive to key epigenetic processes such as X chromosome inactivation. Therefore, delineating the new paradigm related to X-linked TSGs, for instance, their crosstalk with autosome and involvement in cancer initiation, progression, and metastasis becomes utmost importance. Considering this, herein, we present a comprehensive discussion of X-linked TSG dysregulation in various cancers as a consequence of genetic variations and epigenetic alterations. In addition, the dynamic role of X-linked TSGs in sex chromosome-autosome crosstalk in cancer genome remodeling is being explored thoroughly. Besides, the functional roles of ncRNAs, role of X-linked TSG in immunomodulation and in gender-based cancer disparities has also been highlighted. Overall, the focal idea of the present article is to recapitulate the findings on X-linked TSG regulation in the cancer landscape and to redefine their role toward improving cancer treatment strategies.
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Affiliation(s)
- Tikam Chand Dakal
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Bhanupriya Dhabhai
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Anuja Pant
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kareena Moar
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kanika Chaudhary
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vikas Yadav
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vipin Ranga
- Dearptment of Agricultural BiotechnologyDBT‐NECAB, Assam Agricultural UniversityJorhatAssamIndia
| | | | - Abhishek Kumar
- Manipal Academy of Higher EducationManipalKarnatakaIndia
- Institute of Bioinformatics, International Technology ParkBangaloreIndia
| | - Pawan Kumar Maurya
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Jarek Maciaczyk
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
| | - Ingo G. H. Schmidt‐Wolf
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
| | - Amit Sharma
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
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Du P, Chen Y, Li Q, Gai Z, Bai H, Zhang L, Liu Y, Cao Y, Zhai Y, Jin W. CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer. Database (Oxford) 2024; 2024:baae029. [PMID: 38613826 PMCID: PMC11015892 DOI: 10.1093/database/baae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/04/2024] [Accepted: 03/23/2024] [Indexed: 04/15/2024]
Abstract
The discovery of key epigenetic modifications in cancer is of great significance for the study of disease biomarkers. Through the mining of epigenetic modification data relevant to cancer, some researches on epigenetic modifications are accumulating. In order to make it easier to integrate the effects of key epigenetic modifications on the related cancers, we established CancerMHL (http://www.positionprediction.cn/), which provide key DNA methylation, histone modifications and lncRNAs as well as the effect of these key epigenetic modifications on gene expression in several cancers. To facilitate data retrieval, CancerMHL offers flexible query options and filters, allowing users to access specific key epigenetic modifications according to their own needs. In addition, based on the epigenetic modification data, three online prediction tools had been offered in CancerMHL for users. CancerMHL will be a useful resource platform for further exploring novel and potential biomarkers and therapeutic targets in cancer. Database URL: http://www.positionprediction.cn/.
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Affiliation(s)
- Pengyu Du
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Yingli Chen
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Qianzhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Zhimin Gai
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Hui Bai
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Luqiang Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Yuxian Liu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Yanni Cao
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Yuanyuan Zhai
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Wen Jin
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
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Yu X, Guo Z, Fang Z, Yang K, Liu C, Dong Z, Liu C. Identification and validation of disulfidptosis-associated molecular clusters in non-alcoholic fatty liver disease. Front Genet 2023; 14:1251999. [PMID: 37745847 PMCID: PMC10514914 DOI: 10.3389/fgene.2023.1251999] [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: 07/03/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023] Open
Abstract
Objective: Non-alcoholic fatty liver disease (NAFLD) is the most prevalent liver disease in the world, and its pathogenesis is not fully understood. Disulfidptosis is the most recently reported form of cell death and may be associated with NAFLD progression. Our study aimed to explore the molecular clusters associated with disulfidptosis in NAFLD and to construct a predictive model. Methods: First, we analyzed the expression profile of the disulfidptosis regulators and immune characteristics in NAFLD. Using 104 NAFLD samples, we investigated molecular clusters based on differentially expressed disulfidptosis-related genes, along with the related immune cell infiltration. Cluster-specific differentially expressed genes were then identified by using the WGCNA method. We also evaluated the performance of four machine learning models before choosing the optimal machine model for diagnosis. Nomogram, calibration curves, decision curve analysis, and external datasets were used to confirm the prediction effectiveness. Finally, the expression levels of the biomarkers were assessed in a mouse model of a high-fat diet. Results: Two differentially expressed DRGs were identified between healthy and NAFLD patients. We revealed the expression profile of DRGs in NAFLD and the correlation with 22 immune cells. In NAFLD, two clusters of molecules connected to disulfidptosis were defined. Significant immunological heterogeneity was shown by immune infiltration analysis among the various clusters. A significant amount of immunological infiltration was seen in Cluster 1. Functional analysis revealed that Cluster 1 differentially expressed genes were strongly linked to energy metabolism and immune control. The highest discriminatory performance was demonstrated by the SVM model, which had a higher area under the curve, relatively small residual and root mean square errors. Nomograms, calibration curves, and decision curve analyses were used to show how accurate the prediction of NAFLD was. Further analysis revealed that the expression of three model-related genes was significantly associated with the level of multiple immune cells. In animal experiments, the expression trends of DDO, FRK and TMEM19 were consistent with the results of bioinformatics analysis. Conclusion: This study systematically elucidated the complex relationship between disulfidptosis and NAFLD and developed a promising predictive model to assess the risk of disease in patients with disulfidptosis subtypes and NAFLD.
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Affiliation(s)
| | | | | | | | | | | | - Chang Liu
- Department of General Surgery, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
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Goubran M, Wang W, Indik S, Faschinger A, Wasilenko ST, Bintner J, Carpenter EJ, Zhang G, Nuin P, Macintyre G, Wong GKS, Mason AL. Isolation of a Human Betaretrovirus from Patients with Primary Biliary Cholangitis. Viruses 2022; 14:v14050886. [PMID: 35632628 PMCID: PMC9146342 DOI: 10.3390/v14050886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
A human betaretrovirus (HBRV) has been linked with the autoimmune liver disease, primary biliary cholangitis (PBC), and various cancers, including breast cancer and lymphoma. HBRV is closely related to the mouse mammary tumor virus, and represents the only exogenous betaretrovirus characterized in humans to date. Evidence of infection in patients with PBC has been demonstrated through the identification of proviral integration sites in lymphoid tissue, the major reservoir of infection, as well as biliary epithelium, which is the site of the disease process. Accordingly, we tested the hypothesis that patients with PBC harbor a transmissible betaretrovirus by co-cultivation of PBC patients’ lymph node homogenates with the HS578T breast cancer line. Because of the low level of HBRV replication, betaretrovirus producing cells were subcloned to optimize viral isolation and production. Evidence of infection was provided by electron microscopy, RT-PCR, in situ hybridization, cloning of the HBRV proviral genome and demonstration of more than 3400 integration sites. Further evidence of viral transmissibility was demonstrated by infection of biliary epithelial cells. While HBRV did not show a preference for integration proximal to specific genomic features, analyses of common insertion sites revealed evidence of integration proximal to cancer associated genes. These studies demonstrate the isolation of HBRV with features similar to mouse mammary tumor virus and confirm that patients with PBC display evidence of a transmissible viral infection.
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Affiliation(s)
- Mariam Goubran
- Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, AB T6G 2E1, Canada; (M.G.); (W.W.); (S.T.W.); (J.B.); (G.Z.); (G.M.); (G.K.-S.W.)
| | - Weiwei Wang
- Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, AB T6G 2E1, Canada; (M.G.); (W.W.); (S.T.W.); (J.B.); (G.Z.); (G.M.); (G.K.-S.W.)
| | - Stanislav Indik
- Department of Virology, University of Veterinary Medicine, A-1210 Vienna, Austria; (S.I.); (A.F.)
| | - Alexander Faschinger
- Department of Virology, University of Veterinary Medicine, A-1210 Vienna, Austria; (S.I.); (A.F.)
| | - Shawn T. Wasilenko
- Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, AB T6G 2E1, Canada; (M.G.); (W.W.); (S.T.W.); (J.B.); (G.Z.); (G.M.); (G.K.-S.W.)
| | - Jasper Bintner
- Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, AB T6G 2E1, Canada; (M.G.); (W.W.); (S.T.W.); (J.B.); (G.Z.); (G.M.); (G.K.-S.W.)
| | - Eric J. Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada;
| | - Guangzhi Zhang
- Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, AB T6G 2E1, Canada; (M.G.); (W.W.); (S.T.W.); (J.B.); (G.Z.); (G.M.); (G.K.-S.W.)
| | - Paulo Nuin
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2E1, Canada;
| | - Georgina Macintyre
- Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, AB T6G 2E1, Canada; (M.G.); (W.W.); (S.T.W.); (J.B.); (G.Z.); (G.M.); (G.K.-S.W.)
| | - Gane K.-S. Wong
- Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, AB T6G 2E1, Canada; (M.G.); (W.W.); (S.T.W.); (J.B.); (G.Z.); (G.M.); (G.K.-S.W.)
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada;
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Andrew L. Mason
- Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, AB T6G 2E1, Canada; (M.G.); (W.W.); (S.T.W.); (J.B.); (G.Z.); (G.M.); (G.K.-S.W.)
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Correspondence: ; Tel.: +1-(780)-492-8176
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Ghantous Y, Omar M, Broner EC, Agrawal N, Pearson AT, Rosenberg AJ, Mishra V, Singh A, Abu El-naaj I, Savage PA, Sidransky D, Marchionni L, Izumchenko E. A robust and interpretable gene signature for predicting the lymph node status of primary T1/T2 oral cavity squamous cell carcinoma. Int J Cancer 2022; 150:450-460. [PMID: 34569064 PMCID: PMC8760163 DOI: 10.1002/ijc.33828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/31/2021] [Accepted: 09/21/2021] [Indexed: 02/03/2023]
Abstract
Oral cavity squamous cell carcinoma (OSCC) affects more than 30 000 individuals in the United States annually, with smoking and alcohol consumption being the main risk factors. Management of early-stage tumors usually includes surgical resection followed by postoperative radiotherapy in certain cases. The cervical lymph nodes (LNs) are the most common site for local metastasis, and elective neck dissection is usually performed if the primary tumor thickness is greater than 3.5 mm. However, postoperative histological examination often reveals that many patients with early-stage disease are negative for neck nodal metastasis, posing a pressing need for improved risk stratification to either avoid overtreatment or prevent the disease progression. To this end, we aimed to identify a primary tumor gene signature that can accurately predict cervical LN metastasis in patients with early-stage OSCC. Using gene expression profiles from 189 samples, we trained K-top scoring pairs models and identified six gene pairs that can distinguish primary tumors with nodal metastasis from those without metastasis. The signature was further validated on an independent cohort of 35 patients using real-time polymerase chain reaction (PCR) in which it achieved an area under the receiver operating characteristic (ROC) curve and accuracy of 90% and 91%, respectively. These results indicate that such signature holds promise as a quick and cost effective method for detecting patients at high risk of developing cervical LN metastasis, and may be potentially used to guide the neck treatment regimen in early-stage OSCC.
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Affiliation(s)
- Yasmin Ghantous
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.4 Department of Medicine, University of Chicago, Chicago, IL, USA.,Department of Oral and Maxillofacial Surgery, Baruch Padeh Medical Center, Faculty of Medicine, Bar Ilan University, Israel
| | - Mohamed Omar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Esther Channah Broner
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.4 Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Nishant Agrawal
- Section of Otolaryngology-Head and Neck Surgery, University of Chicago, Chicago, IL, USA
| | - Alexander T. Pearson
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Ari J. Rosenberg
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Vasudha Mishra
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Alka Singh
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Imad Abu El-naaj
- Department of Oral and Maxillofacial Surgery, Baruch Padeh Medical Center, Faculty of Medicine, Bar Ilan University, Israel
| | - Peter A. Savage
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - David Sidransky
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.4 Department of Medicine, University of Chicago, Chicago, IL, USA.,Corresponding Authors: Evgeny Izumchenko, Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA. , Luigi Marchionni, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA. , and David Sidransky, Departments of Otolaryngology and Oncology, Johns Hopkins University, Baltimore, MD, USA
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.,Corresponding Authors: Evgeny Izumchenko, Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA. , Luigi Marchionni, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA. , and David Sidransky, Departments of Otolaryngology and Oncology, Johns Hopkins University, Baltimore, MD, USA
| | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA.,Corresponding Authors: Evgeny Izumchenko, Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA. , Luigi Marchionni, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA. , and David Sidransky, Departments of Otolaryngology and Oncology, Johns Hopkins University, Baltimore, MD, USA
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Lin Y, Qi X, Chen J, Shen B. Multivariate competing endogenous RNA network characterization for cancer MicroRNA biomarker discovery: a novel bioinformatics model with application to prostate cancer metastasis. PRECISION CLINICAL MEDICINE 2022; 5:pbac001. [PMID: 35821682 PMCID: PMC9267254 DOI: 10.1093/pcmedi/pbac001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/01/2022] [Accepted: 01/05/2022] [Indexed: 02/05/2023] Open
Abstract
Background MicroRNAs (miRNAs) are post-transcriptional regulators with potential as biomarkers for cancer management. Data-driven competing endogenous RNA (ceRNA) network modeling is an effective way to decipher the complex interplay between miRNAs and spongers. However, there are currently no general rules for ceRNA network-based biomarker prioritization. Methods and results In this study, a novel bioinformatics model was developed by integrating gene expression with multivariate miRNA-target data for ceRNA network-based biomarker discovery. Compared with traditional methods, the structural vulnerability in the human long non-coding RNA (lncRNA)–miRNA–messenger RNAs (mRNA) network was comprehensively analyzed, and the single-line regulatory or competing mode among miRNAs, lncRNAs, and mRNAs was characterized and quantified as statistical evidence for miRNA biomarker identification. The application of this model to prostate cancer (PCa) metastasis identified a total of 12 miRNAs as putative biomarkers from the metastatic PCa-specific lncRNA–miRNA–mRNA network and nine of them have been previously reported as biomarkers for PCa metastasis. The receiver operating characteristic curve and cell line qRT-PCR experiments demonstrated the power of miR-26b-5p, miR-130a-3p, and miR-363-3p as novel candidates for predicting PCa metastasis. Moreover, PCa-associated pathways such as prostate cancer signaling, ERK/MAPK signaling, and TGF-β signaling were significantly enriched by targets of identified miRNAs, indicating the underlying mechanisms of miRNAs in PCa carcinogenesis. Conclusions A novel ceRNA-based bioinformatics model was proposed and applied to screen candidate miRNA biomarkers for PCa metastasis. Functional validations using human samples and clinical data will be performed for future translational studies on the identified miRNAs.
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Affiliation(s)
- Yuxin Lin
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610212, China
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215000, China
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Xin Qi
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Jing Chen
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610212, China
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Gondal MN, Chaudhary SU. Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. Front Oncol 2021; 11:712505. [PMID: 34900668 PMCID: PMC8652070 DOI: 10.3389/fonc.2021.712505] [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: 05/20/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022] Open
Abstract
Rapid advancements in high-throughput omics technologies and experimental protocols have led to the generation of vast amounts of scale-specific biomolecular data on cancer that now populates several online databases and resources. Cancer systems biology models built using this data have the potential to provide specific insights into complex multifactorial aberrations underpinning tumor initiation, development, and metastasis. Furthermore, the annotation of these single- and multi-scale models with patient data can additionally assist in designing personalized therapeutic interventions as well as aid in clinical decision-making. Here, we have systematically reviewed the emergence and evolution of (i) repositories with scale-specific and multi-scale biomolecular cancer data, (ii) systems biology models developed using this data, (iii) associated simulation software for the development of personalized cancer therapeutics, and (iv) translational attempts to pipeline multi-scale panomics data for data-driven in silico clinical oncology. The review concludes that the absence of a generic, zero-code, panomics-based multi-scale modeling pipeline and associated software framework, impedes the development and seamless deployment of personalized in silico multi-scale models in clinical settings.
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Affiliation(s)
- Mahnoor Naseer Gondal
- Biomedical Informatics Research Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
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8
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Song R, Struhl K. S100A8/S100A9 cytokine acts as a transcriptional coactivator during breast cellular transformation. SCIENCE ADVANCES 2021; 7:7/1/eabe5357. [PMID: 33523865 PMCID: PMC7775746 DOI: 10.1126/sciadv.abe5357] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Cytokines are extracellular proteins that convey messages between cells by interacting with cognate receptors at the cell surface and triggering signaling pathways that alter gene expression and other phenotypes in an autocrine or paracrine manner. Here, we show that the calcium-dependent cytokines S100A8 and S100A9 are recruited to numerous promoters and enhancers in a model of breast cellular transformation. This recruitment is associated with multiple DNA sequence motifs recognized by DNA binding transcription factors that are linked to transcriptional activation and are important for transformation. The cytokines interact with these transcription factors in nuclear extracts, and they activate transcription when artificially recruited to a target promoter. Nuclear-specific expression of S100A8/A9 promotes oncogenic transcription and leads to enhanced breast transformation phenotype. These results suggest that, in addition to its classical cytokine function, S100A8/A9 can act as a transcriptional coactivator.
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Affiliation(s)
- Ruisheng Song
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston, MA 02115, USA
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston, MA 02115, USA.
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9
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Creeden JF, Alganem K, Imami AS, Henkel ND, Brunicardi FC, Liu SH, Shukla R, Tomar T, Naji F, McCullumsmith RE. Emerging Kinase Therapeutic Targets in Pancreatic Ductal Adenocarcinoma and Pancreatic Cancer Desmoplasia. Int J Mol Sci 2020; 21:ijms21228823. [PMID: 33233470 PMCID: PMC7700673 DOI: 10.3390/ijms21228823] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 02/08/2023] Open
Abstract
Kinase drug discovery represents an active area of therapeutic research, with previous pharmaceutical success improving patient outcomes across a wide variety of human diseases. In pancreatic ductal adenocarcinoma (PDAC), innovative pharmaceutical strategies such as kinase targeting have been unable to appreciably increase patient survival. This may be due, in part, to unchecked desmoplastic reactions to pancreatic tumors. Desmoplastic stroma enhances tumor development and progression while simultaneously restricting drug delivery to the tumor cells it protects. Emerging evidence indicates that many of the pathologic fibrotic processes directly or indirectly supporting desmoplasia may be driven by targetable protein tyrosine kinases such as Fyn-related kinase (FRK); B lymphoid kinase (BLK); hemopoietic cell kinase (HCK); ABL proto-oncogene 2 kinase (ABL2); discoidin domain receptor 1 kinase (DDR1); Lck/Yes-related novel kinase (LYN); ephrin receptor A8 kinase (EPHA8); FYN proto-oncogene kinase (FYN); lymphocyte cell-specific kinase (LCK); tec protein kinase (TEC). Herein, we review literature related to these kinases and posit signaling networks, mechanisms, and biochemical relationships by which this group may contribute to PDAC tumor growth and desmoplasia.
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Affiliation(s)
- Justin F. Creeden
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (N.D.H.); (R.S.); (R.E.M.)
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 6038, USA
- Correspondence: ; Tel.: +1-419-383-6474
| | - Khaled Alganem
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (N.D.H.); (R.S.); (R.E.M.)
| | - Ali S. Imami
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (N.D.H.); (R.S.); (R.E.M.)
| | - Nicholas D. Henkel
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (N.D.H.); (R.S.); (R.E.M.)
| | - F. Charles Brunicardi
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 6038, USA
| | - Shi-He Liu
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 6038, USA
| | - Rammohan Shukla
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (N.D.H.); (R.S.); (R.E.M.)
| | - Tushar Tomar
- PamGene International BV, 5200 BJ’s-Hertogenbosch, The Netherlands; (T.T.); (F.N.)
| | - Faris Naji
- PamGene International BV, 5200 BJ’s-Hertogenbosch, The Netherlands; (T.T.); (F.N.)
| | - Robert E. McCullumsmith
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (N.D.H.); (R.S.); (R.E.M.)
- Neurosciences Institute, ProMedica, Toledo, OH 6038, USA
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10
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Wang F, Zhao Q, Liu W, Kong D. CENPE, PRC1, TTK, and PLK4 May Play Crucial Roles in the Osteosarcoma Progression. Technol Cancer Res Treat 2020; 19:1533033820973278. [PMID: 33176597 PMCID: PMC7675850 DOI: 10.1177/1533033820973278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Osteosarcoma (OS) is a cancerous tumor in a bone. We aimed to identify the
critical genes involved in OS progression, and then try to elucidate the
molecular mechanisms of this disease. The microarray data of GSE32395 was used
for the present study. We analyzed differentially expressed genes (DEGs) in OS
cells compared with control group by Student’s t-test. The significant enriched
gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathways
were analyzed for upregulated genes and downregulated genes, respectively. In
addition, a protein-protein interaction (PPI) network was constructed. GO and
KEGG enrichment analyses were conducted for genes in the PPI network. In total,
183 DEGs, including 100 upregulated DEGs and 83 downregulated DEGs were
screened. The upregulated DEGs were significantly enriched in 2 KEGG pathways,
such as “Glycosaminoglycan biosynthesis-chondroitin sulfate” and the
downregulated DEGs were significantly enriched in 12 pathways, including “cell
adhesion molecules,” “pentose phosphate pathway” and “allograft rejection.” GO
enrichment analysis indicated that the upregulated DEGs were significantly
involved in biological process, such as “multicellular organismal metabolic
process” and “limb morphogenesis,” while the downregulated DEGs were
significantly enriched in biological process, such as “Positive regulation of
pathway-restricted SMAD protein phosphorylation.” The PPI network included 84
interactions and 51 nodes. The “glycosaminoglycan biosynthesis-chondroitin
sulfate pathway,” “microtubule motor activityfunction,” and “regulation of
mitosis process” were significantly enriched by genes in PPI network. In
particular, CENPE, PRC1, TTK, and PLK4 had higher degrees in the PPI network.
The interactions between TTK and PLK4 as well as CENPE and PRC1 may involve in
the OS development. These 4 genes might be possible biomarkers for the treatment
and diagnosis of OS.
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Affiliation(s)
- Fei Wang
- Department of Orthopedic, 74569China-Japan Union Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Qiheng Zhao
- Department of Orthopedic, 74569China-Japan Union Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Wenping Liu
- Department of Internal Neurology, 154454The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Daliang Kong
- Department of Orthopedic, 74569China-Japan Union Hospital of Jilin University, Changchun, Jilin, People's Republic of China
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11
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Src Family Kinases as Therapeutic Targets in Advanced Solid Tumors: What We Have Learned so Far. Cancers (Basel) 2020; 12:cancers12061448. [PMID: 32498343 PMCID: PMC7352436 DOI: 10.3390/cancers12061448] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/17/2022] Open
Abstract
Src is the prototypal member of Src Family tyrosine Kinases (SFKs), a large non-receptor kinase class that controls multiple signaling pathways in animal cells. SFKs activation is necessary for the mitogenic signal from many growth factors, but also for the acquisition of migratory and invasive phenotype. Indeed, oncogenic activation of SFKs has been demonstrated to play an important role in solid cancers; promoting tumor growth and formation of distant metastases. Several drugs targeting SFKs have been developed and tested in preclinical models and many of them have successfully reached clinical use in hematologic cancers. Although in solid tumors SFKs inhibitors have consistently confirmed their ability in blocking cancer cell progression in several experimental models; their utilization in clinical trials has unveiled unexpected complications against an effective utilization in patients. In this review, we summarize basic molecular mechanisms involving SFKs in cancer spreading and metastasization; and discuss preclinical and clinical data highlighting the main challenges for their future application as therapeutic targets in solid cancer progression
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12
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Anwar S, Mourosi JT, Khan MF, Hosen MJ. Prediction of Epitope-Based Peptide Vaccine Against the Chikungunya Virus by Immuno-informatics Approach. Curr Pharm Biotechnol 2020; 21:325-340. [PMID: 31721709 DOI: 10.2174/1389201020666191112161743] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/16/2019] [Accepted: 11/04/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Chikungunya is an arthropod-borne viral disease characterized by abrupt onset of fever frequently accompanied by joint pain, which has been identified in over 60 countries in Africa, the Americas, Asia, and Europe. METHODS Regardless of the availability of molecular knowledge of this virus, no definite vaccine or other remedial agents have been developed yet. In the present study, a combination of B-cell and T-cell epitope predictions, followed by molecular docking simulation approach has been carried out to design a potential epitope-based peptide vaccine, which can trigger a critical immune response against the viral infections. RESULTS A total of 52 sequences of E1 glycoprotein from the previously reported isolates of Chikungunya outbreaks were retrieved and examined through in silico methods to identify a potential B-cell and T-cell epitope. From the two separate epitope prediction servers, five potential B-cell epitopes were selected, among them "NTQLSEAHVEKS" was found highly conserved across strains and manifests high antigenicity with surface accessibility, flexibility, and hydrophilicity. Similarly, two highly conserved, non-allergenic, non-cytotoxic putative T-cell epitopes having maximum population coverage were screened to bind with the HLA-C 12*03 molecule. Molecular docking simulation revealed potential T-cell based epitope "KTEFASAYR" as a vaccine candidate for this virus. CONCLUSION A combination of these B-cell and T-cell epitope-based vaccine can open up a new skyline with broader therapeutic application against Chikungunya virus with further experimental and clinical investigation.
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Affiliation(s)
- Saeed Anwar
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.,Maternal and Child Health Program, Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, 8440 112 St. NW, Edmonton, AB T6G 2R7, Canada
| | - Jarin T Mourosi
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.,Microbial and Cellular Biology Program, Department of Biology, The Catholic University of America, 620 Michigan Ave. NE, Washington, DC, 20064, United States
| | - Md Fahim Khan
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Mohammad J Hosen
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
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13
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Wang R, Fu L, Li J, Zhao D, Zhao Y, Yin L. Microarray Analysis for Differentially Expressed Genes Between Stromal and Epithelial Cells in Development and Metastasis of Invasive Breast Cancer. J Comput Biol 2020; 27:1631-1643. [PMID: 32429691 DOI: 10.1089/cmb.2019.0154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Both epithelium and stroma are involved in breast cancer invasion and metastasis. This study aimed at identifying the roles of the stroma in breast cancer tumorigenesis and metastasis. Gene expression profiling GSE10797 was downloaded from the Gene Expression Omnibus database, and it included 28-paired stroma and epithelium breast tissue samples from invasive breast cancer patients and 10 paired normal breast tissue samples. Differentially expressed genes (DEGs) between breast cancer and normal breast tissue samples were identified by using the limma package followed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses to seek the potential functions of DEGs. Moreover, a protein-protein interaction network was constructed based on the String database, and modules were selected through the BioNet tool. Further, functional annotations of DEGs were carried out by using tumor suppressor gene and tumor associated gene databases. Ultimately, KEGG pathway enrichment analysis for DEGs in modules was performed. A total of 38 and 156 DEGs were identified from normal invasive stromal cells and epithelial cells, respectively. DEGs in stromal and epithelial cells were significantly enriched in extracellular matrix (ECM)- and cell proliferation-related functions. COL1A2, a hub node in the stromal module, was mainly enriched in ECM-receptor interaction and focal adhesion pathways. JUN, a hub node in the epithelium module, was significantly enriched in cancer and ErbB signaling pathways. COL1A2, COL1A1, COL3A1, JUN, and FN1 might be vital for tumorigenesis and metastasis of invasive breast cancer. These genes might be potential therapeutic targets for breast cancer treatment.
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Affiliation(s)
- Rong Wang
- National Research Institute for Health and Family Planning, Beijing, China
| | - Lei Fu
- Core Laboratory of Translational Medicine, Chinese PLA General Hospital, Beijing, China.,Department of Medical Engineering, 401 Hospital of Chinese PLA, Qingdao, China
| | - Jinbin Li
- Core Laboratory of Translational Medicine, Chinese PLA General Hospital, Beijing, China
| | - Di Zhao
- Dermatological Department, The 309 Hospital Of Chinese PLA, Beijing, China
| | - Yulan Zhao
- Department of Respiratory, The 88th Hospital of PLA, Tai'an, China
| | - Ling Yin
- Core Laboratory of Translational Medicine, Chinese PLA General Hospital, Beijing, China
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14
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Zhu C, Hu H, Li J, Wang J, Wang K, Sun J. Identification of key differentially expressed genes and gene mutations in breast ductal carcinoma in situ using RNA-seq analysis. World J Surg Oncol 2020; 18:52. [PMID: 32156290 PMCID: PMC7063758 DOI: 10.1186/s12957-020-01820-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 02/18/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The aim of this study was to identify the key differentially expressed genes (DEGs) and high-risk gene mutations in breast ductal carcinoma in situ (DCIS). METHODS Raw data (GSE36863) were downloaded from the database of Gene Expression Omnibus (GEO), including three DCIS samples (DCIS cell lines MCF10.DCIS, Sum102, and Sum225) and one normal control sample (normal mammary epithelial cell line MCF10A). The DEGs were analyzed using NOIseq and annotated via DAVID. Motif scanning in the promoter region of DEGs was performed via SeqPos. Additionally, single nucleotide variations (SNVs) were identified via GenomeAnalysisTK and SNV risk was assessed via VarioWatch. Mutant genes with a high frequency and risk were validated by RT-PCR analyses. RESULTS Finally, 5391, 7073, and 7944 DEGs were identified in DCIS, Sum102, and Sum22 cell lines, respectively, when compared with MCF10A. VENN analysis of the three cell lines revealed 603 upregulated and 1043 downregulated DEGs, including 16 upregulated and 36 downregulated transcription factor (TF) genes. In addition, six TFs each (e.g., E2F1 and CREB1) were found to regulate the core up- and downregulated DEGs, respectively. Furthermore, SNV detection results revealed 1104 (MCF10.DCIS), 2833 (Sum102), and 1132 (Sum22) mutation sites. Four mutant genes (RWDD4, SDHC, SEPT7, and SFN) with high frequency and risk were identified. The results of RT-PCR analysis as well as bioinformatics analysis consistently demonstrated that the expression of RWDD4, SDHC, SEPT7, and SFN was downregulated in the tumor tissues as compared with that in adjacent non-tumor tissues. CONCLUSIONS The differentially expressed TFs, TFs regulating DEGs (e.g., E2F1 and CREB1), and high-frequency mutant genes (RWDD4, SDHC, SEPT7, and SFN) might play key roles in the pathogenesis of DCIS.
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Affiliation(s)
- Congyuan Zhu
- Department of General Surgery, the Affiliated Hospital of Jiangnan University (original area of Wuxi Third People's Hospital), No. 585 North Xingyuan Road, Liangxi District, Wuxi, 214002, Jiangsu, China.
| | - Hao Hu
- Department of General Surgery, the Affiliated Hospital of Jiangnan University (original area of Wuxi Third People's Hospital), No. 585 North Xingyuan Road, Liangxi District, Wuxi, 214002, Jiangsu, China
| | - Jianping Li
- Department of General Surgery, the Affiliated Hospital of Jiangnan University (original area of Wuxi Third People's Hospital), No. 585 North Xingyuan Road, Liangxi District, Wuxi, 214002, Jiangsu, China.
| | - Jingli Wang
- Department of General Surgery, the Affiliated Hospital of Jiangnan University (original area of Wuxi Third People's Hospital), No. 585 North Xingyuan Road, Liangxi District, Wuxi, 214002, Jiangsu, China
| | - Ke Wang
- Department of General Surgery, the Affiliated Hospital of Jiangnan University (original area of Wuxi Third People's Hospital), No. 585 North Xingyuan Road, Liangxi District, Wuxi, 214002, Jiangsu, China
| | - Jingqiu Sun
- Department of General Surgery, the Affiliated Hospital of Jiangnan University (original area of Wuxi Third People's Hospital), No. 585 North Xingyuan Road, Liangxi District, Wuxi, 214002, Jiangsu, China
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15
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Zhang F, Wang F, Chen C, Wang T, Hu J, Su R, Li X, Gu B, Tang S, Chen H, Li Y. Prediction of progression of chronic atrophic gastritis with Helicobacter pylori and poor prognosis of gastric cancer by CYP3A4. J Gastroenterol Hepatol 2020; 35:425-432. [PMID: 31441961 DOI: 10.1111/jgh.14844] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIM It has been well documented that Helicobacter pylori (H. pylori) infection is a risk factor for aggravating gastric mucosal atrophy. However, the exact molecular mechanism mediating this process is not fully elucidated. The purpose of this study was to identify biomarkers, which may predict the risk for progression of chronic atrophic gastritis (CAG) with H. pylori. METHODS GSE27411 was downloaded from the Gene Expression Omnibus. The differentially expressed genes (DEGs) between H. pylori-infected samples without CAG and H. pylori-infected CAG samples were analyzed. Gene Ontology and pathway enrichment analyses were performed, followed by protein-protein interaction network construction. We used immunohistochemistry analysis to identify DEGs in 20 chronic gastritis, 20 CAG, and 22 gastric cancer (GC) specimens. RESULTS A total of 303 upregulated and 26 downregulated DEGs were identified. The pathways enriched by upregulated DEGs were mainly related to fat digestion and absorption, peroxisome proliferator-activated receptor signaling pathway, and chemical carcinogenesis. Cytochrome P450, family 3, subfamily A, polypeptide 4 (CYP3A4) had the highest degrees in protein-protein interaction network. Moreover, the positive rates of CYP3A4 protein expression in chronic gastritis, CAG, and GC were 10% (2/20), 55% (11/20), and 77.3% (17/22), respectively (P < 0.001). The Kaplan-Meier analysis revealed that elevated expression of CYP3A4 was significantly associated with worse overall survival and first progression, respectively (P < 0.0001). CONCLUSION According to the findings of this study, the expression of CYP3A4 might be related to the potential carcinogenic transformation of CAG to GC. Therefore, CYP3A4 may be biomarkers to predict progression of CAG and poor prognosis of gastric cancer.
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Affiliation(s)
- Fan Zhang
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Furong Wang
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Cong Chen
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Tianyu Wang
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Jike Hu
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Ruiliang Su
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Xuemei Li
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Baohong Gu
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Shaojun Tang
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, District of Columbia, USA.,Department of Oncology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Hao Chen
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Yumin Li
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
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16
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Matyunina EA, Emelyanov AV, Kurbatova TV, Makashov AA, Mizgirev IV, Kozlov AP. Evolutionarily novel genes are expressed in transgenic fish tumors and their orthologs are involved in development of progressive traits in humans. Infect Agent Cancer 2019; 14:46. [PMID: 31827597 PMCID: PMC6896781 DOI: 10.1186/s13027-019-0262-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/20/2019] [Indexed: 01/01/2023] Open
Abstract
Abstract Earlier we suggested a new hypothesis of the possible evolutionary role of hereditary tumors (Kozlov, Evolution by tumor Neofunctionalization, 2014), and described a new class of genes – tumor specifically expressed, evolutionarily novel (TSEEN) genes - that are predicted by this hypothesis (Kozlov, Infect Agents Cancer 11:34, 2016). In this paper we studied evolutionarily novel genes expressed in fish tumors after regression, as a model of evolving organs. As evolutionarily novel genes may not yet have organismal functions, we studied the acquisition of new gene functions by comparing fish evolutionarily novel genes with their human orthologs. We found that many genes involved in development of progressive traits in humans (lung, mammary gland, placenta, ventricular septum, etc.) originated in fish and are expressed in fish tumors and tumors after regression. These findings support a possible evolutionary role of hereditary tumors, and in particular the hypothesis of evolution by tumor neofunctionalization. Research highlights Earlier we described a new class of genes that are tumor-specifically expressed and evolutionarily novel (TSEEN). As the functions of TSEEN genes are often uncertain, we decided to study TSEEN genes of fishes so that we could trace the appearance of their new functions in higher vertebrates. We found that many human genes which are involved in development of progressive traits (placenta development, mammary gland and lung development etc.,) originated in fishes and are expressed in fish tumors.
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Affiliation(s)
- E A Matyunina
- 1Research Institute of Ultra-Pure Biologicals, Ministry of Public Health of the Russian Federation, St.-Petersburg, Russia.,2Peter the Great Saint-Petersburg Polytechnic University (SPbPU), St.-Petersburg, Russia
| | - A V Emelyanov
- 3The Biomedical Center (BMC), St.-Petersburg, Russia.,4Institute for Research on Cancer and Aging (IRCAN), Nice, France
| | - T V Kurbatova
- 1Research Institute of Ultra-Pure Biologicals, Ministry of Public Health of the Russian Federation, St.-Petersburg, Russia.,2Peter the Great Saint-Petersburg Polytechnic University (SPbPU), St.-Petersburg, Russia.,3The Biomedical Center (BMC), St.-Petersburg, Russia
| | - A A Makashov
- 1Research Institute of Ultra-Pure Biologicals, Ministry of Public Health of the Russian Federation, St.-Petersburg, Russia.,2Peter the Great Saint-Petersburg Polytechnic University (SPbPU), St.-Petersburg, Russia.,3The Biomedical Center (BMC), St.-Petersburg, Russia
| | - I V Mizgirev
- 5Petrov Research Institute of Oncology, St.-Petersburg, Russia
| | - A P Kozlov
- 1Research Institute of Ultra-Pure Biologicals, Ministry of Public Health of the Russian Federation, St.-Petersburg, Russia.,2Peter the Great Saint-Petersburg Polytechnic University (SPbPU), St.-Petersburg, Russia.,3The Biomedical Center (BMC), St.-Petersburg, Russia.,6Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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17
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Makashov AA, Malov SV, Kozlov AP. Oncogenes, tumor suppressor and differentiation genes represent the oldest human gene classes and evolve concurrently. Sci Rep 2019; 9:16410. [PMID: 31712655 PMCID: PMC6848199 DOI: 10.1038/s41598-019-52835-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 10/24/2019] [Indexed: 01/20/2023] Open
Abstract
Earlier we showed that human genome contains many evolutionarily young or novel genes with tumor-specific or tumor-predominant expression. We suggest calling such genes Tumor Specifically Expressed, Evolutionarily New (TSEEN) genes. In this paper we performed a study of the evolutionary ages of different classes of human genes, using homology searches in genomes of different taxa in human lineage. We discovered that different classes of human genes have different evolutionary ages and confirmed the existence of TSEEN gene classes. On the other hand, we found that oncogenes, tumor-suppressor genes and differentiation genes are among the oldest gene classes in humans and their evolution occurs concurrently. These findings confirm non-trivial predictions made by our hypothesis of the possible evolutionary role of hereditary tumors. The results may be important for better understanding of tumor biology. TSEEN genes may become the best tumor markers.
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Affiliation(s)
- A A Makashov
- Biomedical Center, Viborgskaya str. 8, Saint-Petersburg, 194044, Russia.,Peter the Great St. Petersburg Polytechnic University, Politekhnicheskaya ul., 29, St. Petersburg, 195251, Russia.,Research Institute of Ultra Pure Biologicals, 7 Pudozhskaya str., St. Petersburg, 197110, Russia
| | - S V Malov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St.-Petersburg State University, 41A, Sredniy av., St. Petersburg, 199004, Russia.,Department of Algorithmic Mathematics, St.-Petersburg Electrotechnical University, 5, Prof. Popova str, St. Petersburg, 197376, Russia
| | - A P Kozlov
- Biomedical Center, Viborgskaya str. 8, Saint-Petersburg, 194044, Russia. .,Peter the Great St. Petersburg Polytechnic University, Politekhnicheskaya ul., 29, St. Petersburg, 195251, Russia. .,Research Institute of Ultra Pure Biologicals, 7 Pudozhskaya str., St. Petersburg, 197110, Russia. .,Vavilov Institute of General Genetics, 3 Gubkina str., Moscow, 119333, Russia.
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18
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The stromal loss of miR-4516 promotes the FOSL1-dependent proliferation and malignancy of triple negative breast cancer. Cancer Lett 2019; 469:256-265. [PMID: 31672492 DOI: 10.1016/j.canlet.2019.10.039] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/24/2019] [Accepted: 10/09/2019] [Indexed: 12/24/2022]
Abstract
Stroma-derived exosomal microRNA (exomiR) contributes to tumor progression, however, which remains poorly understood. In our study, we analyzed exomiRs from the cancer-associated fibroblast (CAF) and normal fibroblast (NF) isolated from an invasive ductal carcinoma (IDC) patient and found that the level of microRNA (miR)-4516 was approximately 5-fold lower in CAF-derived exosomes than NF-derived ones. In gene annotation analysis, miR-4516 target genes were mainly associated with the regulation of proliferation. miR-4516 overexpression or mimic treatment suppressed the proliferation of breast cancer cells, especially triple negative breast cancer (TNBC) cells. Among miR-4516 targets, FOSL1 was overexpressed in TNBC cells compared to non-TNBC cells and promoted tumor proliferation. The expression of miR-4516 and FOSL1 was reversely correlated in breast cancer patient tissues. Particularly, TNBC patients with high FOSL1 expression showed a significant poorer survival than those with low FOSL1 expression. Our results show that the loss of miR-4516 from CAF-derived exosomes is associated with FOSL1-dependent TNBC progression and suggest that miR-4516 can be used as an anti-cancer drug for TNBC.
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19
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Alizadeh S, Isanejad A, Sadighi S, Khalighfard S, Alizadeh AM. Effect of a high-intensity interval training on serum microRNA levels in women with breast cancer undergoing hormone therapy. A single-blind randomized trial. Ann Phys Rehabil Med 2019; 62:329-335. [PMID: 31400480 DOI: 10.1016/j.rehab.2019.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 07/07/2019] [Accepted: 07/07/2019] [Indexed: 01/28/2023]
Abstract
BACKGROUND The role of microRNAs (miRs) in hormone therapy (HT) is of keen interest in developing biomarkers and treatments for individuals with breast cancer. Although miRs are often moderate regulators under homeostatic conditions, their function is changed more in response to physical activity. OBJECTIVE This single-blind randomized trial aimed to explore the effect of high-intensity interval training (HIIT) on serum levels of miRs in individuals with early-stage breast cancer undergoing HT. METHODS Hormone receptor-positive women with breast cancer and healthy women were randomly assigned to a healthy control group (n=15), healthy group with HIIT (n=15), breast cancer group with HT (HT, n=26), and breast cancer group with HT and HIIT (HT+HIIT, n=26). The exercise groups underwent interval uphill walking training on a treadmill 3 times a week for 12weeks. At the end of the study, we analyzed changes in levels of cancer-related miRs (oncomiRs) and tumour suppressor miRs (TSmiRs) in response to the HT and HIIT. RESULTS In women with breast cancer versus healthy controls, the expression of some oncomiRs was significantly increased - miR-21 (P<0.001), miR-155 (P=0.001), miR-221 (P=0.008), miR-27a (P<0.001), and miR-10b (P=0.007) - and that of some TSmiRs was significantly decreased - miR-206 (P=0.048), miR-145 (P=0.011), miR-143 (P=0.008), miR-9 (P=0.020), and let-7a (P=0.005). Moreover, HT considerably downregulated oncomiRs and upregulated TSmiRs. HIIT for 12weeks with HT significantly decreased the expression of the oncomiRs and significantly increased that of the TSmiRs as compared with HT alone. CONCLUSIONS HITT could amplify the decrease and/or increase in expression of miRs associated with HT in women with breast cancer. A prospective trial could determine whether the use of circulating miRs for monitoring treatment can be useful in therapy decisions. TRIAL REGISTRATION Iranian Registry of Clinical Trials (No.: IRCT201202289171N1).
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Affiliation(s)
- Shaban Alizadeh
- Department of Hematology, Allied Medical School, Tehran University of Medical Sciences, Tehran, Iran
| | - Amin Isanejad
- Immunoregulation Research Center, Shahed University, Tehran, Iran; Physical Education Department, Shahed University, Tehran, Iran
| | - Sanambar Sadighi
- Medical Oncology and Hematology Department, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Solmaz Khalighfard
- Cancer Research Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ali Mohammad Alizadeh
- Cancer Research Center, Tehran University of Medical Sciences, Tehran, Iran; Breast Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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Liu HC, Peng YS, Lee HC. miRDRN-miRNA disease regulatory network: a tool for exploring disease and tissue-specific microRNA regulatory networks. PeerJ 2019; 7:e7309. [PMID: 31404401 PMCID: PMC6688598 DOI: 10.7717/peerj.7309] [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: 04/30/2019] [Accepted: 06/17/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND MicroRNA (miRNA) regulates cellular processes by acting on specific target genes, and cellular processes proceed through multiple interactions often organized into pathways among genes and gene products. Hundreds of miRNAs and their target genes have been identified, as are many miRNA-disease associations. These, together with huge amounts of data on gene annotation, biological pathways, and protein-protein interactions are available in public databases. Here, using such data we built a database and web service platform, miRNA disease regulatory network (miRDRN), for users to construct disease and tissue-specific miRNA-protein regulatory networks, with which they may explore disease related molecular and pathway associations, or find new ones, and possibly discover new modes of drug action. METHODS Data on disease-miRNA association, miRNA-target association and validation, gene-tissue association, gene-tumor association, biological pathways, human protein interaction, gene ID, gene ontology, gene annotation, and product were collected from publicly available databases and integrated. A large set of miRNA target-specific regulatory sub-pathways (RSPs) having the form (T, G 1, G 2) was built from the integrated data and stored, where T is a miRNA-associated target gene, G 1 (G 2) is a gene/protein interacting with T (G 1). Each sequence (T, G 1, G 2) was assigned a p-value weighted by the participation of the three genes in molecular interactions and reaction pathways. RESULTS A web service platform, miRDRN (http://mirdrn.ncu.edu.tw/mirdrn/), was built. The database part of miRDRN currently stores 6,973,875 p-valued RSPs associated with 116 diseases in 78 tissue types built from 207 diseases-associated miRNA regulating 389 genes. miRDRN also provides facilities for the user to construct disease and tissue-specific miRNA regulatory networks from RSPs it stores, and to download and/or visualize parts or all of the product. User may use miRDRN to explore a single disease, or a disease-pair to gain insights on comorbidity. As demonstrations, miRDRN was applied: to explore the single disease colorectal cancer (CRC), in which 26 novel potential CRC target genes were identified; to study the comorbidity of the disease-pair Alzheimer's disease-Type 2 diabetes, in which 18 novel potential comorbid genes were identified; and, to explore possible causes that may shed light on recent failures of late-phase trials of anti-AD, BACE1 inhibitor drugs, in which genes downstream to BACE1 whose suppression may affect signal transduction were identified.
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Affiliation(s)
- Hsueh-Chuan Liu
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan City, Taiwan
| | - Yi-Shian Peng
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan City, Taiwan
| | - Hoong-Chien Lee
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan City, Taiwan
- Department of Physics, Chung Yuan Christian University, Zhongli District, Taoyuan City, Taiwan
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Wen M, Qu X, Zhu Y, Tian L, Shen Z, Yang X, Shi X. Exploration of Novel Biomarkers in Vasculitis by Integrated Bioinfomatic Approaches. J Comput Biol 2019; 26:1448-1457. [PMID: 31356108 DOI: 10.1089/cmb.2019.0176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Angiitis, also known as vasculitis, is a chronic inflammatory disease characterized by the infiltration of inflammatory cells in surroundings of blood vessels, accompanied by vascular damage including fibrin deposition, collagen fiber degeneration, myocyte, and endotheliocyte necrosis. This work aimed to perform an integrated bioinformatic analysis of three data sets concerning vasculitis to explore and examine the potential diagnostic and therapeutic makers contributing to illuminating the pathomechanisms of vasculitis. We collected three sets of gene expression data designed by dual-channel method from Gene Expression Omnibus, which were based on the same platform (Agilent-014850 Whole Human Genome Microarray 4x44K G4112F). The meta-analysis was used to analyze the gene expression profiles and screen the differentially expressed genes followed by functional features identification. Subsequently, a protein-protein interaction and transcriptional regulation network were conducted for further investigation of expression mechanisms of vasculitis. Totally, 73 consistently upregulated genes, 49 consistently downregulated genes, and 26 genes with different expression directions were identified. Functional enrichment and transcription regulation analysis suggested upregulated genes (PPBP, PLAU, and HIST1H2BH) and downregulated genes such as IL23A gene were predominately associated with immune responses and cytokine receptors function. In addition, specific cancer-related genes such as MRVI1 was also extracted and considered as promising biomarkers of the development and progression of vasculitis. This study established an integrated meta-analysis approach and identified novel biomarkers involved in vasculitis, which further facilitate to explore and unravel the etiopathogenesis of vasculitis.
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Affiliation(s)
- Mingxiang Wen
- Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang, China
| | - Xiang Qu
- Department of Emergency and Guizhou Provincial People's Hospital, Guiyang, China
| | - Yanyan Zhu
- Department of Radiology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Lingfang Tian
- Department of Endocrine, The First People's Hospital of Guiyang, Guiyang, China
| | - Zhongqin Shen
- Department of Endocrine, The First People's Hospital of Guiyang, Guiyang, China
| | - Xiulin Yang
- Department of Emergency and Guizhou Provincial People's Hospital, Guiyang, China
| | - Xianqing Shi
- Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang, China
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Zhang L, Yang Y, Chai L, Bu H, Yang Y, Huang H, Ran J, Zhu Y, Li L, Chen F, Li W. FRK plays an oncogenic role in non-small cell lung cancer by enhancing the stemness phenotype via induction of metabolic reprogramming. Int J Cancer 2019; 146:208-222. [PMID: 31251822 DOI: 10.1002/ijc.32530] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/02/2019] [Accepted: 05/16/2019] [Indexed: 02/05/2023]
Abstract
The role of Fyn-related kinase (FRK) in malignant tumors remains controversial. Our study investigated the function of FRK in lung cancer. Immunohistochemistry staining and generating a knockout of FRK by CRISPR/Cas9 in H1299 (FRK-KO-H1299) cells were strategies used to explore the role of FRK. Immunohistochemistry staining indicated that FRK expression was elevated in 223 lung cancer tissues compared to 26 distant normal lung tissues. FRK contributed to poor survival status in lung cancer patients and acted as a predictor for poor prognosis of lung cancer. Knockout of FRK by CRISPR/Cas9 markedly inhibited proliferation, invasion, colony formation and epithelial-mesenchymal transition (EMT) process in the lung cancer cell line H1299. Further exploration indicated that FRK-KO damaged the stemness phenotype of H1299 by inhibiting CD44 and CD133 expression. Seahorse detection and a U-13 C flux assay revealed that FRK-KO induced metabolism reprogramming by inhibiting the Warburg effect and changing the energy type in H1299 cells. Epidermal growth factor stimulation recovered the expression of FRK and biological functions, metabolic reprogramming and stemness phenotype of H1299 cells. FRK plays an oncogenic role in lung cancer cells via a novel regulation mechanism of enhancing the stemness of H1299 cells by inducing metabolism reprogramming, which finally promotes EMT and metastasis. Our study also indicates that FRK could be used as a potential therapeutic target for drug development.
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Affiliation(s)
- Li Zhang
- Lab of Pathology, Key Lab of Transplantation Engineering and Immunology, Ministry of Health, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yongfeng Yang
- Lab of Pathology, Key Lab of Transplantation Engineering and Immunology, Ministry of Health, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Li Chai
- Research Core Facility, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Hong Bu
- Lab of Pathology, Key Lab of Transplantation Engineering and Immunology, Ministry of Health, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Ying Yang
- Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Hong Huang
- Lab of Pathology, Key Lab of Transplantation Engineering and Immunology, Ministry of Health, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Jingjing Ran
- Lab of Pathology, Key Lab of Transplantation Engineering and Immunology, Ministry of Health, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yihan Zhu
- Lab of Pathology, Key Lab of Transplantation Engineering and Immunology, Ministry of Health, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Li Li
- Lab of Pathology, Key Lab of Transplantation Engineering and Immunology, Ministry of Health, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Fei Chen
- Lab of Pathology, Key Lab of Transplantation Engineering and Immunology, Ministry of Health, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Weimin Li
- Department of Respiratory Medicine, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
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Protective potential of miR-146a-5p and its underlying molecular mechanism in diverse cancers: a comprehensive meta-analysis and bioinformatics analysis. Cancer Cell Int 2019; 19:167. [PMID: 31285693 PMCID: PMC6592002 DOI: 10.1186/s12935-019-0886-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 06/17/2019] [Indexed: 12/16/2022] Open
Abstract
Background/aims Studies have shown that miR-146a-5p was differentially expressed in diverse cancers, but the associations between miR-146a-5p expression and prognosis across multiple types of cancer as well its potential targets and downstream pathways have not been comprehensively analyzed. In this study, we performed the first meta-analysis of the prognostic value of miR-146a-5p expression in diverse malignancies and explored prospective targets of miR-146a-5p and related signaling pathways. Methods A thorough search for articles related to miR-146a-5p was performed, and RNA-seq data from The Cancer Genome Atlas (TCGA) and microarray data from gene expression omnibus profiles were used to collect information about the prognostic value of miR-146a-5p. A comprehensive meta-analysis was conducted. Twelve platforms in miRWalk 2.0 were applied to predict targets of miR-146a-5p. TCGA RNA-seq data were used to validate the inverse relationships between miR-146a-5p and its likely targets. Subsequently, gene ontology and pathway analyses were conducted using Funrich version 3.1.3. Potential protein–protein interaction (PPI) networks were constructed. Potential target genes of miR-146a-5p in lung cancer were validated by RT-qPCR. Results We included 10 articles in the meta-analysis. In a pooled analysis, the high miR-146a-5p expression group showed a better overall survival in solid cancers, particularly in reproductive system cancers and digestive system cancers. A total of 120 predicted target genes were included in a bioinformatics analysis. Five pathways involving phospholipase C (PLC) and aquaporins (AQPs) were the most significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways. Moreover, the PPI network displayed the related signaling pathways and interactions among proteins. AQP1 and FYN were validated by RT-qPCR to be potential targets of miR-146a-5p in lung cancer. Conclusion There is a close link between high miR-146a-5p expression and better overall survival in 21 types of solid cancer, especially in reproductive system and digestive system cancers. Furthermore, miR-146a-5p could inhibit diverse malignancies by modulating pathways linked to PLC or AQPs. In summary, miR-146a-5p is a potential prognostic biomarker and therapeutic target for various cancers.
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Kan S, Chai S, Chen W, Yu B. DNA methylation profiling identifies potentially significant epigenetically-regulated genes in glioblastoma multiforme. Oncol Lett 2019; 18:1679-1688. [PMID: 31423235 PMCID: PMC6614665 DOI: 10.3892/ol.2019.10512] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 04/05/2019] [Indexed: 12/25/2022] Open
Abstract
Glioblastoma multiforme (GBM) is one of the most lethal and damaging types of human cancer. The current study was conducted to identify differentially methylated genes (DMGs) between GBM and normal controls, and to improve our understanding of GBM at the epigenetic level. The DNA methylation profile of GBM was downloaded from the Gene Expression Omnibus (GEO) database using the accession number GSE50923. The MethyAnalysis package was applied to identify DMGs between GBM and controls, which were then analyzed by functional enrichment analysis. Protein-protein interaction (PPI) networks were constructed using the hypermethylated and hypomethylated genes. Finally, transcription factors (TFs) that can regulate the hypermethylated and hypomethylated genes were predicted, followed by construction of transcriptional regulatory networks. Furthermore, another relevant dataset, GSE22867, was downloaded from the GEO database for data validation. A total of 476 hypermethylated and 850 hypomethylated genes were identified, which were mainly associated with the functions of ‘G-protein-coupled receptors ligand binding’, ‘cytokine activity’, ‘cytokine-cytokine receptor interaction’, and ‘D-glutamine and D-glutamate metabolism’. The hypermethylated gene neuropeptide Y (NPY) and the hypomethylated gene tumor necrosis factor (TNF) demonstrated high degrees in the PPI network. Forkhead box protein A1 (FOXA1), potassium voltage-gated channel subfamily C member 3 (KCNC3) and caspase-8 (CASP8) exhibited high degrees in the transcriptional regulatory networks. In addition, the methylation profiles of NPY, TNF, FOXA1, KCNC3 and CASP8 were confirmed by another dataset. In summary, the present study systematically analyzed the DNA methylation profile of GBM using bioinformatics approaches and identified several abnormally methylated genes, providing insight into the molecular mechanism underlying GBM.
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Affiliation(s)
- Shifeng Kan
- Department of Rehabilitation, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai 200080, P.R. China
| | - Song Chai
- Department of Rehabilitation, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai 200080, P.R. China
| | - Wenhua Chen
- Department of Rehabilitation, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai 200080, P.R. China
| | - Bo Yu
- Department of Rehabilitation, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai 200080, P.R. China
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Yang Y, Yang W, Jin L. The Role of Long Non-coding RNA Prostate Cancer-Associated Transcript 1 in Prostate Cancer. J Comput Biol 2019; 26:975-984. [PMID: 31090454 DOI: 10.1089/cmb.2018.0240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This study aimed to investigate the role of prostate cancer associated transcript 1 (PCAT1) underlying the molecular mechanisms of prostate cancer. Using GSE29886 data set downloaded from Gene Expression Omnibus database, we screened the differentially expressed genes (DEGs) in PCAT1-siRNA interfering (PCAT1-siRNA) LNCaP cells compared with control-siRNA cells. Transcription factor (TF) and tumor-associated genes database were used to obtain oncogenes and tumor suppressor genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used to investigate the function and pathways of DEGs. Subnetwork was further analyzed using BioNet. A total of 93 DEGs were identified. KEGG analysis showed downregulated TF genes (ID1 and ID3) were enriched in transforming growth factor-β pathway, whereas upregulated genes were involved in pathways associated with immune system, environmental sensing, and metabolism. GO analysis showed that downregulated genes were primarily enriched in cell cycle-related biological functions and upregulated DEGs were related to immune response, exogenous genetic material response, and viral response. Centromere protein F (CENPF) was identified as the central node of the regulatory subnetwork. In the PCAT1 knockdown LNCaP cells, the CENPF, ID1, and ID3 were obviously decreased based on the RT-PCR (quantitative real-time reverse transcription PCR) analysis. PCAT1 may be involved in cell cycle and proliferation of prostate cancers by mediating the expression of CENPF, ID1, and ID3.
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Affiliation(s)
- Yushuang Yang
- Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Wei Yang
- Department of Psychology, Changchun Sixth Hospital, Changchun, China
| | - Ling Jin
- Department of Clinical Laboratory, China-Japan Union Hospital of Jilin University, Changchun, China
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26
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Jing ZF, Bi JB, Li ZL, Liu XK, Li J, Zhu YY, Zhang XT, Zhang Z, Li ZH, Kong CZ. miR-19 promotes the proliferation of clear cell renal cell carcinoma by targeting the FRK-PTEN axis. Onco Targets Ther 2019; 12:2713-2727. [PMID: 31043790 PMCID: PMC6463782 DOI: 10.2147/ott.s199238] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background The non-receptor tyrosine kinase Fyn-related kinase (FRK) has been reported to affect cell proliferation in several cancer types. However, its effect on the proliferation of clear cell renal cell carcinoma (ccRCC) remains largely unknown. Purpose The objective of this study was to investigate the expression pattern and function of FRK in ccRCC. We further determined how FRK interacted with other molecules to regulate ccRCC proliferation. Patients and methods The expression of FRK in ccRCC samples and paired normal renal tissues from 30 patients were analyzed by immunoblotting, immunohistochemistry and quantitative PCR. Then the role of FRK in ccRCC proliferation was analyzed by Cell Counting Kit-8, colony formation assay and EdU incorporation assay. In addition, the miRNA targeting FRK was predicted through a bioinformatic approach and validated by quantitative PCR, immunoblotting and luciferase reporter assay. Finally, the underlying mechanism of FRK regulation of ccRCC proliferation was also determined. Results Low expression of FRK was detected in ccRCC samples and predicted poor survival for ccRCC patients. FRK inhibited the proliferation of ccRCC cells via phosphorylating downstream PTEN. miR-19 was identified as a novel suppressor of FRK in renal cancer cells and it promoted the proliferation of ccRCC by inhibiting the FRK-PTEN axis. Conclusion Our results unravel a new regulatory mechanism involved in ccRCC proliferation and may be useful in the identification of therapeutic targets for ccRCC.
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Affiliation(s)
- Zhi-Fei Jing
- Department of Urology, First Hospital of China Medical University, Shenyang, Liaoning 110001, People's Republic of China, ; .,Institute of Urology, China Medical University, Shenyang 110001, People's Republic of China, ;
| | - Jian-Bin Bi
- Department of Urology, First Hospital of China Medical University, Shenyang, Liaoning 110001, People's Republic of China, ; .,Institute of Urology, China Medical University, Shenyang 110001, People's Republic of China, ;
| | - Ze-Liang Li
- Department of Urology, First Hospital of China Medical University, Shenyang, Liaoning 110001, People's Republic of China, ; .,Institute of Urology, China Medical University, Shenyang 110001, People's Republic of China, ;
| | - Xian-Kui Liu
- Department of Urology, First Hospital of China Medical University, Shenyang, Liaoning 110001, People's Republic of China, ; .,Institute of Urology, China Medical University, Shenyang 110001, People's Republic of China, ;
| | - Jun Li
- Department of Urology, First Hospital of China Medical University, Shenyang, Liaoning 110001, People's Republic of China, ; .,Institute of Urology, China Medical University, Shenyang 110001, People's Republic of China, ;
| | - Yu-Yan Zhu
- Department of Urology, First Hospital of China Medical University, Shenyang, Liaoning 110001, People's Republic of China, ; .,Institute of Urology, China Medical University, Shenyang 110001, People's Republic of China, ;
| | - Xiao-Tong Zhang
- Department of Urology, First Hospital of China Medical University, Shenyang, Liaoning 110001, People's Republic of China, ; .,Institute of Urology, China Medical University, Shenyang 110001, People's Republic of China, ;
| | - Zhe Zhang
- Department of Urology, First Hospital of China Medical University, Shenyang, Liaoning 110001, People's Republic of China, ; .,Institute of Urology, China Medical University, Shenyang 110001, People's Republic of China, ;
| | - Zhen-Hua Li
- Department of Urology, First Hospital of China Medical University, Shenyang, Liaoning 110001, People's Republic of China, ; .,Institute of Urology, China Medical University, Shenyang 110001, People's Republic of China, ;
| | - Chui-Ze Kong
- Department of Urology, First Hospital of China Medical University, Shenyang, Liaoning 110001, People's Republic of China, ; .,Institute of Urology, China Medical University, Shenyang 110001, People's Republic of China, ;
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Zhou L, Liu S, Li X, Yin M, Li S, Long H. Diagnostic and prognostic value of CEP55 in clear cell renal cell carcinoma as determined by bioinformatics analysis. Mol Med Rep 2019; 19:3485-3496. [PMID: 30896867 PMCID: PMC6471254 DOI: 10.3892/mmr.2019.10042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/01/2019] [Indexed: 12/16/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignant adult kidney tumor. Tumor recurrence and metastasis is the primary cause of cancer-associated mortality in patients with ccRCC. Therefore, identification of efficient diagnostic and prognostic molecular markers may improve survival times. The GSE46699, GSE36895, GSE53000 and GSE53757 gene datasets were downloaded from the Gene Expression Omnibus database and contained 196 ccRCC samples and 164 adjacent normal kidney samples. Bioinformatics analysis was used to integrate the four microarray datasets to identify and analyze differentially expressed genes. Functional analysis revealed that there were 12 genes associated with cancer, based on the tumor-associated gene database. Erb-B2 receptor tyrosine kinase 4, centrosomal protein 55 (CEP55) and vascular endothelial growth factor A are oncogenes, all of which were associated with tumor stage, whereas only CEP55 was significantly associated with survival time as determined by Gene Expression Profiling Interactive Analysis. The mRNA expression levels of CEP55 in ccRCC samples were significantly higher than those observed in adjacent normal kidney tissues based on The Cancer Genome Atlas data and reverse transcription-polymerase chain reaction results. The receiver operating characteristic curve analysis revealed that CEP55 may be considered a diagnostic biomarker for ccRCC with an area under the curve of >0.85 in the training and validation sets. High CEP55 expression was strongly associated with sex, histological grade, stage, T classification, N classification and M classification. Univariate and multivariate Cox proportional hazards analyses demonstrated that CEP55 expression was an independent risk factor for poor prognosis. In addition, gene set enrichment analysis indicated that high CEP55 expression was associated with immunization, cell adhesion, inflammation, the Janus kinase/signal transducer and activator of transcription signaling pathway and cell proliferation. In conclusion, CEP55 was increased in ccRCC samples, and may be considered a potential diagnostic and prognostic biomarker for ccRCC.
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Affiliation(s)
- Libin Zhou
- Department of Urology, Ningbo Medical Centre Lihuili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Shibo Liu
- Department of Urology, Cancer Hospital of China Medical University, Shenyang, Liaoning 110042, P.R. China
| | - Xing Li
- Department of Urology, Ningbo Medical Centre Lihuili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Min Yin
- Department of Urology, Ningbo Medical Centre Lihuili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Sheng Li
- Department of Urology, Ningbo Medical Centre Lihuili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Huimin Long
- Department of Urology, Ningbo Medical Centre Lihuili Hospital, Ningbo, Zhejiang 315040, P.R. China
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Mun DG, Bhin J, Kim S, Kim H, Jung JH, Jung Y, Jang YE, Park JM, Kim H, Jung Y, Lee H, Bae J, Back S, Kim SJ, Kim J, Park H, Li H, Hwang KB, Park YS, Yook JH, Kim BS, Kwon SY, Ryu SW, Park DY, Jeon TY, Kim DH, Lee JH, Han SU, Song KS, Park D, Park JW, Rodriguez H, Kim J, Lee H, Kim KP, Yang EG, Kim HK, Paek E, Lee S, Lee SW, Hwang D. Proteogenomic Characterization of Human Early-Onset Gastric Cancer. Cancer Cell 2019; 35:111-124.e10. [PMID: 30645970 DOI: 10.1016/j.ccell.2018.12.003] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 08/22/2018] [Accepted: 12/10/2018] [Indexed: 02/08/2023]
Abstract
We report proteogenomic analysis of diffuse gastric cancers (GCs) in young populations. Phosphoproteome data elucidated signaling pathways associated with somatic mutations based on mutation-phosphorylation correlations. Moreover, correlations between mRNA and protein abundances provided potential oncogenes and tumor suppressors associated with patient survival. Furthermore, integrated clustering of mRNA, protein, phosphorylation, and N-glycosylation data identified four subtypes of diffuse GCs. Distinguishing these subtypes was possible by proteomic data. Four subtypes were associated with proliferation, immune response, metabolism, and invasion, respectively; and associations of the subtypes with immune- and invasion-related pathways were identified mainly by phosphorylation and N-glycosylation data. Therefore, our proteogenomic analysis provides additional information beyond genomic analyses, which can improve understanding of cancer biology and patient stratification in diffuse GCs.
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Affiliation(s)
- Dong-Gi Mun
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Jinhyuk Bhin
- Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea; Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Sangok Kim
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Hyunwoo Kim
- Department of Computer Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea; Research Data Hub Center, Korea Institute of Science and Technology Information, Daejeon 34141, Republic of Korea
| | - Jae Hun Jung
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yong-in 446-701, Republic of Korea
| | - Yeonjoo Jung
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Ye Eun Jang
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Jong Moon Park
- Gachon Institute of Pharmaceutical Sciences, Gachon College of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
| | - Hokeun Kim
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Yeonhwa Jung
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Hangyeore Lee
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Jingi Bae
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Seunghoon Back
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Su-Jin Kim
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Jieun Kim
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Heejin Park
- Department of Computer Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea
| | - Honglan Li
- School of Computer Science and Engineering, Soongsil University, Seoul 156-743, Republic of Korea
| | - Kyu-Baek Hwang
- School of Computer Science and Engineering, Soongsil University, Seoul 156-743, Republic of Korea
| | - Young Soo Park
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-873, Republic of Korea
| | - Jeong Hwan Yook
- Department of Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-873, Republic of Korea
| | - Byung Sik Kim
- Department of Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-873, Republic of Korea
| | - Sun Young Kwon
- Department of Surgery, Keimyung University School of Medicine, Daegu 700-712, Republic of Korea
| | - Seung Wan Ryu
- Department of Surgery, Keimyung University School of Medicine, Daegu 700-712, Republic of Korea
| | - Do Youn Park
- Department of Pathology, Pusan National University School of Medicine, Busan 602-739, Republic of Korea
| | - Tae Yong Jeon
- Department of Surgery, Pusan National University School of Medicine, Busan 602-739, Republic of Korea
| | - Dae Hwan Kim
- Department of Surgery, Pusan National University School of Medicine, Busan 602-739, Republic of Korea
| | - Jae-Hyuck Lee
- Department of Pathology, Chonnam National University Medical School, Gwangju 501-746, Republic of Korea
| | - Sang-Uk Han
- Department of Surgery, Ajou University School of Medicine, Suwon 443-380 Republic of Korea
| | - Kyu Sang Song
- Department of Pathology, School of Medicine, Chungnam National University, Daejeon 301-747 Republic of Korea
| | - Dongmin Park
- National Cancer Center, Goyang 410-769, Republic of Korea
| | - Jun Won Park
- National Cancer Center, Goyang 410-769, Republic of Korea
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jaesang Kim
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Hookeun Lee
- Gachon Institute of Pharmaceutical Sciences, Gachon College of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yong-in 446-701, Republic of Korea
| | - Eun Gyeong Yang
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea.
| | - Hark Kyun Kim
- National Cancer Center, Goyang 410-769, Republic of Korea.
| | - Eunok Paek
- Department of Computer Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea.
| | - Sanghyuk Lee
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea.
| | - Sang-Won Lee
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea.
| | - Daehee Hwang
- Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea.
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Plasma miR-21, miR-155, miR-10b, and Let-7a as the potential biomarkers for the monitoring of breast cancer patients. Sci Rep 2018; 8:17981. [PMID: 30568292 PMCID: PMC6299272 DOI: 10.1038/s41598-018-36321-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/19/2018] [Indexed: 12/19/2022] Open
Abstract
There is a pressing need for further studies to categorize and validate circulating microRNAs (miRs) in breast cancer patients that can be one of the novel strategies for cancer screening and monitoring. The present study is aimed to investigate the expression of the circulating candidate microRNAs after the operation, chemotherapy, and radiotherapy in the non-metastatic breast cancer patients. Tumor tissue and plasma samples were collected from the 30 patients with recently diagnosed Luminal A breast cancer. Control plasma samples were collected from the 10 healthy subjects. A panel of four miRs including miR-21, miR-55, miR-10b, and Let-7a were selected and their expression levels were measured before and after the operation, chemotherapy, and radiotherapy by using Real-Time PCR technique. The plasma expression of the miR-21, miR-155, and miR-10b was significantly increased and the Let-7a plasma expression decreased in the breast cancer patients compromised to the control ones. There was a similar expression pattern of the miRs between the tissue and plasma samples. The plasma levels of the miR-21, miR-155, and miR-10b were significantly down-regulated and the Let-7a plasma level was up-regulated after the operation, chemotherapy, and radiotherapy compromised to the pre-treatment. There was a significant difference in the miR-155 plasma level after the operation, chemotherapy, and radiotherapy compromised with each other. Moreover, there was no significant difference between the plasma levels of the miRs after the radiotherapy compromised to the control cases. The operation, chemotherapy, and radiotherapy led to a more reduction in the oncomiRs and an increase in the tumor suppressor-miRs. It seems that monitoring miRs during treatment might be considered as a respectable diagnostic tool for monitoring of breast cancer patients.
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Li Y, Bai W, Zhang L. The Overexpression of CD80 and ISG15 Are Associated with the Progression and Metastasis of Breast Cancer by a Meta-Analysis Integrating Three Microarray Datasets. Pathol Oncol Res 2018; 26:443-452. [PMID: 30411299 DOI: 10.1007/s12253-018-0478-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022]
Abstract
Breast cancer is a common cancer and could result in a substantial mortality. The study aimed to screen gene signatures associated with the development and metastasis of breast cancer and explore their regulation mechanisms. Three datasets of GSE10797, GSE8977 and GSE3744 were downloaded from GEO (Gene Expression Omnibus) database, containing 55 breast cancer samples and 27 normal samples. After data preprocessing using limma software and RMA (robust multi-array average) algorithm, DEGs (differentially expressed genes) between breast tumor and normal tissues in three individual experiments were identified using MADAM package. Function and pathway enrichment analyses were performed for the DEGs. Transcription factors and TAGs (tumor associated genes) among the DEGs were recognized and the PPI (protein-protein-interaction) network for the DEGs was constructed using Cytoscape software. The mRNA expression was analyzed via real-time quantitative PCR and protein expression was measured by western blotting. Totally, 100 DEGs were identified, including 33 up-regulated genes and 67 down-regulated genes. Among them, up-regulated DEGs such as CD80 was enriched in toll-like receptor (TLR) interaction pathway and the TAG, ISG15 was related to RIG-I-like receptor signaling pathway, while CXCL10 was involved in both of the two pathways. Whereas, the down-regulated DEG, CXCL12 was significantly associated with axon guidance pathway. Additionally, these DEGs were also pivotal nodes in the PPI network with high degrees. Besides, CXCL10 and CD80 were both interacted with IFNG. The mRNA expression of ISG15 was obviously enhanced in human breast cancer cells MCF-7, while no significant difference of CXCL10 mRNA level was found between MCF10A and MCF-7 cells. Moreover, the proteins expression levels of CD80 and ISG15 were significantly increased in MCF-7, MDA-MB-468 and MDA-MB-231 breast cancer cells than in normal MCF10A cells. CD80 might be responsible for the breast cancer's progression and metastasis via regulating innate immune system. In addition, ISG15 is identified as a crucial gene signature associated with breast cancer development and metastasis via RIG-I-like receptor signaling pathway.
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Affiliation(s)
- Yuanhang Li
- Medical Department, Cancer Hospital of China Medical University, No. 44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning Province, China.
| | - Weijun Bai
- Medical Department, Cancer Hospital of China Medical University, No. 44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning Province, China
| | - Linlin Zhang
- Medical Department, Cancer Hospital of China Medical University, No. 44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning Province, China
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Shi Z, Yu J, Shao H, Cheng K, Zhai J, Jiang Q, Li H. Exploring the molecular pathogenesis associated with T-cell prolymphocytic leukemia based on a comprehensive bioinformatics analysis. Oncol Lett 2018; 16:301-307. [PMID: 29928415 PMCID: PMC6006439 DOI: 10.3892/ol.2018.8615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 02/27/2017] [Indexed: 12/25/2022] Open
Abstract
As a rare hematological malignancy, T-cell prolymphocytic leukemia (T-PLL) has a high mortality rate. However, the comprehensive mechanisms of the underlying pathogenesis of T-PLL are unknown. The purpose of the present study was to investigate the pathogenesis of T-PLL based on a comprehensive bioinformatics analysis. The differentially expressed genes (DEGs) between T-PLL blood cell samples and normal peripheral blood cell samples were investigated using the GSE5788 Affymetrix microarray data from the Gene Expression Omnibus database. To investigate the functional changes associated with tumor progression, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were used on the identified DEGs, followed by protein-protein interaction (PPI) and sub-PPI analysis. Transcription factors and tumor-associated genes (TAGs) were investigated further. The results identified 84 upregulated genes and 354 downregulated genes in T-PLL samples when compared with healthy samples. These DEGs featured in various functions including cell death and various pathways including apoptosis. The functional analysis of DEGs revealed 17 dysregulated transcription factors and 37 dysregulated TAGs. Furthermore, the PPI network analysis based on node degree (a network topology attribute) identified 61 genes, including the core downregulated gene of the sub-PPI network, signal transducer and activator of transcription 3 (STAT3; degree, 13) and the core upregulated gene, insulin receptor substrate-1 (IRS1; degree, 5), that may have important associations with the progression of T-PLL. Alterations to cell functions, including cell death, and pathways, including apoptosis, may contribute to the process of T-PLL. Candidate genes identified in the present study, including STAT3 and IRS1, should be targets for additional studies.
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Affiliation(s)
- Zhangzhen Shi
- Department of Hematology and Oncology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Jing Yu
- Department of Nephrology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Hui Shao
- Department of Hematology and Oncology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Kailiang Cheng
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Jingjie Zhai
- Department of Implantology, Jilin University Stomatology Hospital, Changchun, Jilin 130021, P.R. China
| | - Qi Jiang
- Department of Nephrology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Hongjun Li
- Medical Examination Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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Ewing RM, Song J, Gokulrangan G, Bai S, Bowler EH, Bolton R, Skipp P, Wang Y, Wang Z. Multiproteomic and Transcriptomic Analysis of Oncogenic β-Catenin Molecular Networks. J Proteome Res 2018; 17:2216-2225. [PMID: 29747501 DOI: 10.1021/acs.jproteome.8b00180] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The dysregulation of Wnt signaling is a frequent occurrence in many different cancers. Oncogenic mutations of CTNNB1/β-catenin, the key nuclear effector of canonical Wnt signaling, lead to the accumulation and stabilization of β-catenin protein with diverse effects in cancer cells. Although the transcriptional response to Wnt/β-catenin signaling activation has been widely studied, an integrated understanding of the effects of oncogenic β-catenin on molecular networks is lacking. We used affinity-purification mass spectrometry (AP-MS), label-free liquid chromatography-tandem mass spectrometry, and RNA-Seq to compare protein-protein interactions, protein expression, and gene expression in colorectal cancer cells expressing mutant (oncogenic) or wild-type β-catenin. We generate an integrated molecular network and use it to identify novel protein modules that are associated with mutant or wild-type β-catenin. We identify a DNA methyltransferase I associated subnetwork that is enriched in cells with mutant β-catenin and a subnetwork enriched in wild-type cells associated with the CDKN2A tumor suppressor, linking these processes to the transformation of colorectal cancer cells through oncogenic β-catenin signaling. In summary, multiomics analysis of a defined colorectal cancer cell model provides a significantly more comprehensive identification of functional molecular networks associated with oncogenic β-catenin signaling.
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Affiliation(s)
- Rob M Ewing
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Jing Song
- School of Medicine , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Giridharan Gokulrangan
- School of Medicine , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Sheldon Bai
- School of Medicine , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Emily H Bowler
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Rachel Bolton
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Paul Skipp
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Yihua Wang
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Zhenghe Wang
- School of Medicine , Case Western Reserve University , Cleveland , Ohio 44106 , United States
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Shen H, Wang W, Ni B, Zou Q, Lu H, Wang Z. Exploring the molecular mechanisms of osteosarcoma by the integrated analysis of mRNAs and miRNA microarrays. Int J Mol Med 2018; 42:21-30. [PMID: 29620143 PMCID: PMC5979835 DOI: 10.3892/ijmm.2018.3594] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 08/11/2017] [Indexed: 01/05/2023] Open
Abstract
Osteosarcoma (OS) is the most frequently occurring primary bone malignancy with a rapid progression and poor survival. In the present study, in order to examine the molecular mechanisms of OS, we analyzed the microarray of GSE28425. GSE28425 was downloaded from Gene Expression Omnibus, which also included the miRNA expression profile, GSE28423, and the mRNA expression profile, GSE28424. Each of the expression profiles included 19 OS cell lines and 4 normal bones. The differentially expressed genes (DEGs) and differentially expressed miRNAs (DE-miRNAs) were screened using the limma package in Bioconductor. The DEGs associated with tumors were screened and annotated. Subsequently, the potential functions of the DEGs were analyzed by Gene Ontology (GO) and pathway enrichment analyses. Furthermore, the protein-protein interaction (PPI) network was constructed using the STRING database and Cytoscape software. Furthermore, modules of the PPI network were screened using the ClusterOne plugin in Cytoscape. Additionally, the transcription factor (TF)-DEG regulatory network, DE-miRNA-DEG regulatory network and miRNA-function collaborative network were separately constructed to obtain key DEGs and DE-miRNAs. In total, 1,609 DEGs and 149 DE-miRNAs were screened. Upregulated FOS-like antigen 1 (FOSL1) also had the function of an oncogene. MAD2 mitotic arrest deficient-like 1 (MAD2L1; degree, 65) and aurora kinase A (AURKA; degree, 64) had higher degrees in the PPI network of the DEGs. In the TF-DEG regulatory network, the TF, signal transducer and activator of transcription 3 (STAT3) targeted the most DEGs. Moreover, in the DE-miRNA-DEG regulatory network, downregulated miR-1 targeted many DEGs and estrogen receptor 1 (ESR1) was targeted by several highly expressed miRNAs. Moreover, in the miRNA-function collaborative networks of upregulated miRNAs, miR-128 targeted myeloid dendritic associated functions. On the whole, our data indicate that MAD2L1, AURKA, STAT3, ESR1, FOSL1, miR-1 and miR-128 may play a role in the development and/or progressio of OS.
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Affiliation(s)
- Hao Shen
- Department of Orthopaedics, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, P.R. China
| | - Wei Wang
- Department of Orthopaedics, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, P.R. China
| | - Bingbing Ni
- Department of Orthopaedics, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, P.R. China
| | - Qiang Zou
- Department of Orthopaedics, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Chongming Branch, Shanghai 202150, P.R. China
| | - Hua Lu
- Department of Orthopaedics, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, P.R. China
| | - Zhanchao Wang
- Department of Orthopaedics, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Chongming Branch, Shanghai 202150, P.R. China
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35
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Guan L, Tan J, Li H, Jin X. Biomarker identification in clear cell renal cell carcinoma based on miRNA-seq and digital gene expression-seq data. Gene 2018; 647:205-212. [DOI: 10.1016/j.gene.2017.12.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/12/2017] [Accepted: 12/15/2017] [Indexed: 12/21/2022]
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Zhang Z, Wu H, Zhou H, Gu Y, Bai Y, Yu S, An R, Qi J. Identification of potential key genes and high-frequency mutant genes in prostate cancer by using RNA-Seq data. Oncol Lett 2018; 15:4550-4556. [PMID: 29616087 DOI: 10.3892/ol.2018.7846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/22/2017] [Indexed: 01/26/2023] Open
Abstract
The aim of the present study was to identify potential key genes and single nucleotide variations (SNVs) in prostate cancer. RNA sequencing (RNA-seq) data, GSE22260, were downloaded from the Gene Expression Omnibus database, including 4 prostate cancer samples and 4 normal tissues samples. RNA-Seq reads were processed using Tophat and differentially-expressed genes (DEGs) were identified using the Cufflinks package. Gene Ontology enrichment analysis of DEGs was performed. Subsequently, Seqpos was used to identify the potential upstream regulatory elements of DEGs. SNV was analyzed using Genome Analysis Toolkit. In addition, the frequency and risk-level of mutant genes were calculated using VarioWatch. A total of 150 upregulated and 211 downregulated DEGs were selected and 25 upregulated and 17 downregulated potential upstream regulatory elements were identified, respectively. The SNV annotations of somatic mutations revealed that 65% were base transition and 35% were base transversion. At frequencies ≥2, a total of 17 mutation sites were identified. The mutation site with the highest frequency was located in the folate hydrolase 1B (FOLH1B) gene. Furthermore, 20 high-risk mutant genes with high frequency were identified using VarioWatch, including ribosomal protein S4 Y-linked 2 (RPS4Y2), polycystin 1 transient receptor potential channel interacting (PKD1) and FOLH1B. In addition, kallikrein 1 (KLK1) and PKD1 are known tumor suppressor genes. The potential regulatory elements and high-frequency mutant genes (RPS4Y2, KLK1, PKD1 and FOLH1B) may have key functions in prostate cancer. The results of the present study may provide novel information for the understanding of prostate cancer development.
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Affiliation(s)
- Ze Zhang
- Department of Urology Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - He Wu
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Hong Zhou
- Department of Respiration, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yunhe Gu
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yufeng Bai
- Department of Urology Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Shiliang Yu
- Department of Urology Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Ruihua An
- Department of Urology Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Jiping Qi
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
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Bo L, Wei B, Wang Z, Kong D, Gao Z, Miao Z. Bioinformatics analysis of the CDK2 functions in neuroblastoma. Mol Med Rep 2018; 17:3951-3959. [PMID: 29328425 DOI: 10.3892/mmr.2017.8368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 11/14/2017] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to elucidate the potential mechanism of cyclin-dependent kinase 2 (CDK2) in neuroblastoma progression and to identify the candidate genes associated with neuroblastoma with CDK2 silencing. The microarray data of GSE16480 were obtained from the gene expression omnibus database. This dataset contained 15 samples: Neuroblastoma cell line IMR32 transfected with CDK2 shRNA at 0, 8, 24, 48 and 72 h (n=3 per group; total=15). Significant clusters associated with differentially expressed genes (DEGs) were identified using fuzzy C‑Means algorithm in the Mfuzz package. Gene ontology and pathway enrichment analysis of DEGs in each cluster were performed, and a protein‑protein interaction (PPI) network was constructed. Additionally, functional annotation of DEGs in clusters was performed for the detection of transcription factors and tumor‑associated genes. A total of 4 clusters with significant change tendency and 1,683 DEGs were identified. The hub nodes of the PPI network constructed by DEGs in Cluster 1, Cluster 2, Cluster 3 and Cluster 4 were MDM2 oncogene, E3 ubiquitin protein ligase (MDM2), cyclin‑dependent kinase 1 (CDK1), proteasome (prosome, macropain) 26S subunit, non‑ATPase, 14 (PSMD14) and translocator protein (18 kDa) (TSPO) respectively. These genes were significantly enriched in the p53 signaling pathway, cell cycle, proteasome and systemic lupus erythematosus pathways. MDM2, CDK1, PSMD14 and TSPO may be key target genes of CDK2. CDK2 may have key functions in neuroblastoma progression by regulating the expression of these genes.
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Affiliation(s)
- Lijuan Bo
- Department of Infections, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Bo Wei
- Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zhanfeng Wang
- Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Daliang Kong
- Department of Orthopaedics, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zheng Gao
- Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zhuang Miao
- Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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38
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Chen P, Song W, Liu L. Genome-Wide Transcriptome Analysis of Estrogen Receptor-Positive and Human Epithelial Growth Factor Receptor 2-Positive Breast Cancers by Ribonucleic Acid Sequencing. Gynecol Obstet Invest 2017; 83:338-348. [PMID: 29241203 DOI: 10.1159/000484244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/13/2017] [Indexed: 11/19/2022]
Abstract
AIM The aim is to identify complex pathogenesis of breast cancer subtypes and disclose the whole landscape of altered transcriptional activities in these cancers. METHODS We downloaded raw expression data from public database, and performed transcriptome analysis of 8 estrogen receptor-positive (ER+) breast cancer tissue samples, 8 human epithelial growth factor receptor 2-positive (HER2+) breast cancer tissue samples, and 3 normal breast tissues by identification, functional annotation, and prediction of upstream regulators and cell-surface biomarkers of differentially expressed genes (DEGs). RESULTS We identified over 5,000 DEGs in each of ER+ and HER2+ breast cancers compared to normal tissues. Functional enrichment analysis of shared DEGs indicated significant changes in the regulation of immune -systems in the 2 subtypes. We further identified 1,871 DEGs between the 2 subtypes and disclosed great tumor heterogeneity. We identified 533 shared upregulated genes and predicted 17 upstream transcription factors, as well as identified differentially expressed cell-surface biomarkers for distinguishing our ER+ and HER2+ breast cancers. Further analysis also highlighted the limitation of the usage of HER2 alone in breast cancer classification. CONCLUSION Our findings in ER+ and HER2+ breast cancers provided novel insights into heterogeneous transcriptional activities underlying complex mechanisms of oncogenesis in breast cancers.
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Affiliation(s)
- Pengtao Chen
- Thyroid and Breast Surgery, Zhoukou Central Hospital of Henan Province, Zhoukou, China
| | - Wei Song
- School of Life Science, Shanghai University, Shanghai, China
| | - Liangli Liu
- Intensive Care Unit, Zhoukou Hospital of Traditional Chinese Medicine of Henan Province, Zhoukou, China
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Ogunbolude Y, Dai C, Bagu ET, Goel RK, Miah S, MacAusland-Berg J, Ng CY, Chibbar R, Napper S, Raptis L, Vizeacoumar F, Vizeacoumar F, Bonham K, Lukong KE. FRK inhibits breast cancer cell migration and invasion by suppressing epithelial-mesenchymal transition. Oncotarget 2017; 8:113034-113065. [PMID: 29348886 PMCID: PMC5762571 DOI: 10.18632/oncotarget.22958] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/16/2017] [Indexed: 12/31/2022] Open
Abstract
The human fyn-related kinase (FRK) is a non-receptor tyrosine kinase known to have tumor suppressor activity in breast cancer cells. However, its mechanism of action has not been fully characterized. We generated FRK-stable MDA-MB-231 breast cancer cell lines and analyzed the effect on cell proliferation, migration, and invasiveness. We also used kinome analysis to identify potential FRK-regulated signaling pathways. We employed both immunoblotting and RT-PCR to identify/validate FRK-regulated targets (proteins and genes) in these cells. Finally, we interrogated the TCGA and GENT gene expression databases to determine the correlation between the expression of FRK and epithelial/mesenchymal markers. We observed that FRK overexpression suppressed cell proliferation, migration, and invasiveness, inhibited various JAK/STAT, MAPK and Akt signaling pathways, and suppressed the expression of some STAT3 target genes. Also, FRK overexpression increased the expression of epithelial markers including E-cadherin mRNA and down-regulated the transcript levels of vimentin, fibronectin, and slug. Finally, we observed an inverse correlation between FRK expression and mesenchymal markers in a large cohort of breast cancer cells. Our data, therefore, suggests that FRK represses cell proliferation, migration and invasiveness by suppressing epithelial to mesenchymal transition.
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Affiliation(s)
- Yetunde Ogunbolude
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Chenlu Dai
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Edward T Bagu
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Canada.,Cancer Research Unit, Health Research Division, Saskatchewan Cancer Agency, and Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Raghuveera Kumar Goel
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Sayem Miah
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Canada.,Departments of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Joshua MacAusland-Berg
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Chi Ying Ng
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Rajni Chibbar
- Department of Pathology Royal University Hospital Saskatchewan, Saskatoon, Canada
| | - Scott Napper
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Canada.,Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
| | - Leda Raptis
- Departments of Microbiology and Immunology and Pathology, Queen's University, Kingston, Canada
| | - Frederick Vizeacoumar
- Cancer Research Unit, Health Research Division, Saskatchewan Cancer Agency, and Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Franco Vizeacoumar
- Cancer Research Unit, Health Research Division, Saskatchewan Cancer Agency, and Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Keith Bonham
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Canada.,Cancer Research Unit, Health Research Division, Saskatchewan Cancer Agency, and Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Kiven Erique Lukong
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Canada
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40
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Disease gene classification with metagraph representations. Methods 2017; 131:83-92. [DOI: 10.1016/j.ymeth.2017.06.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 06/23/2017] [Accepted: 06/30/2017] [Indexed: 12/28/2022] Open
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Han Y, Jin X, Zhou H, Liu B. Identification of key genes associated with bladder cancer using gene expression profiles. Oncol Lett 2017; 15:297-303. [PMID: 29375713 PMCID: PMC5766060 DOI: 10.3892/ol.2017.7310] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 08/23/2017] [Indexed: 12/19/2022] Open
Abstract
The aim of the present study was to further investigate the molecular mechanisms of bladder cancer. The microarray data GSE52519 were downloaded from Gene Expression Omnibus, comprising 9 bladder cancer and 3 normal bladder tissue samples. Differentially expressed genes (DEGs) were identified using Limma package analysis. Subsequently, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and Reactome pathway enrichment analyses were performed for down- and upregulated DEGs. Transcription factors and genes associated with cancer from DEGs were identified. Protein-protein interaction (PPI) networks were constructed using STRING, and pathway enrichment analysis was also conducted for genes in the core sub-network that was identified using BioNet. In total, 420 downregulated and 335 upregulated DEGs were identified. Functional and pathway enrichment analyses identified that a number of DEGs, including AURKA, CCNA2, CCNE1, CDC20 and CCNB2, were enriched in the cell cycle. Furthermore, a total of 12 upregulated proto-oncogenes were identified, including AURKA and CCNA2. In the PPI sub-network, a number of DEGs (e.g., CCNB2, CDC20, CCNA2 and MCM6) with higher degrees were enriched in the KEGG pathway of the cell cycle. In conclusion, the DEGs associated with the cell cycle (e.g., CDC20, CCNA2, CCNB2 and AURKA) may serve pivotal roles in the pathogenesis of bladder cancer.
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Affiliation(s)
- Yuping Han
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Xuefei Jin
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Hui Zhou
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Bin Liu
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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WITHDRAWN: Bioinformatic analysis of the roles of CDK2 in neuroblastoma. Clin Neurol Neurosurg 2017. [DOI: 10.1016/j.clineuro.2017.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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43
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Huang GQ, Ke ZP, Hu HB, Gu B. Co-expression network analysis of long noncoding RNAs (IncRNAs) and cancer genes revealsSFTA1P and CASC2abnormalities in lung squamous cell carcinoma. Cancer Biol Ther 2017; 18:115-122. [PMID: 28118064 DOI: 10.1080/15384047.2017.1281494] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Lung squamous cell carcinoma(LSCC) is the most common and aggressive lung tumor with poor clinical outcome. Previously studies showed that deregulation of long noncoding RNAs (lncRNAs) were involved in LSCC. We intended to figure out the role of lncRNAs in the regulation process of cancer-related genes and pathways they are involved. Data of 552 samples, including 501 cancer samples and 51 normal ones, were extracted from The Cancer Genome Atlas (TCGA). Differentially expressed lncRNAs (DEIs) were screened out (FDR<0.05, |logFC|>1) and then followed by GO ontology and KEGG annotation analysis. Oncogenes from COSMIC data set and Tumor suppressor genes (TSGs) from TSGene data set were collected and analyzed by gene Set Enrichment Analysis (GSEA) . The differentially expressed oncogenes and tumor supressor gene (TSGs) were obtained and co-expression analysis was conducted to generate co-expression lncRNA-gene pairs, which can be helpful in figuring out the role of lncRNA in the regulation of oncogenes and tumor suppressor genes. A total of 31 lncRNAs with low expression levels and 37 lncRNAs with high expression levels were screened out and most of them were enriched in pathways such as meiosis, male gamete generation, defensins. Of note, SFTA1P and CASC2 were found to be related with most of the oncogenes and TSGs by co-expression analysis. We suggested SFTA1P and CASC2 played important role in the regulation of both oncogene and TSGs during the carcinogenesis of LSCC and have the potential to be applied in future diagnosis, prognostic process and target therapy of LSCC.
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Affiliation(s)
- Guang-Qing Huang
- a Department of Intensive Care Unit , Renmin Hospital, Hubei University of Medicine , Shiyan , Hubei , P.R. China
| | - Zun-Ping Ke
- b Department of Cardiology , The Fifth People's Hospital of Shanghai, Fudan University , Shanghai , China
| | - Hai-Bo Hu
- c Department of Thoracic Surgery , The Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'an , Huai'an , China
| | - Biao Gu
- d Department of Thoracic Surgery , Huai'an First People's Hospital, Nanjing Medical University , Huai'an, Jiangsu , China
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Proteomic profiling of human HepG2 cells treated with hesperidin using antibody array. Mol Med Rep 2017; 16:5386-5392. [PMID: 28849065 PMCID: PMC5647072 DOI: 10.3892/mmr.2017.7232] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/11/2017] [Indexed: 11/05/2022] Open
Abstract
Protein array technology not only identifies a large number of proteins but also determines their expression levels. In the present study, antibody array analysis is used to decipher the proteins involved in hesperidin-induced cell death in HepG2 cells. Altered proteins in hesperidin treated cells were compared with that of untreated control cells by using a RayBio® Label‑based (L series) human antibody array kit. The identified proteins were further confirmed using western blot analysis. STRING software based analysis was used to determine the protein‑protein interactions. Many proteins related to signal transduction, cellular mechanisms, cell growth and proliferation regulatory proteins were identified. Among the proteins identified Hsp90, Smac/DIABLO, Prdx6 and FRK were significantly reduced in hesperidin treated cells. To the best of the authors' knowledge, the present study is the first to use antibody array for identifying proteins marker in hesperidin‑induced cell death in HepG2 cells. The present study provides a novel insight into the anticancer mechanism of hesperidin.
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Zheng T, Wang A, Hu D, Wang Y. Molecular mechanisms of breast cancer metastasis by gene expression profile analysis. Mol Med Rep 2017; 16:4671-4677. [PMID: 28791367 PMCID: PMC5647040 DOI: 10.3892/mmr.2017.7157] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 05/18/2017] [Indexed: 01/08/2023] Open
Abstract
Metastasis is the main cause of breast cancer‑related mortalities. The present study aimed to uncover the relevant molecular mechanisms of breast cancer metastasis and to explore potential biomarkers that may be used for prognosis. Expression profile microarray data GSE8977, which contained 22 stroma samples (15 were from normal breast and 7 were from invasive ductal carcinoma tumor samples), were obtained from the Gene Expression Omnibus database. Following data preprocessing, differentially expressed genes (DEGs) were selected based on analyses conducted using the linear models for microarray analysis package from R and Bioconductor software. The resulting data were used in subsequent function and pathway enrichment analyses, as well as protein‑protein interaction (PPI) network and subnetwork analyses. Transcription factors (TFs) and tumor‑associated genes were also identified among the DEGs. A total of 234 DEGs were identified, which were enriched in immune response, cell differentiation and cell adhesion‑related functions and pathways. Downregulated DEGs included TFs, such as the proto‑oncogene SPI1, pre‑B‑cell leukemia homeobox 3 (PBX3) and lymphoid enhancer‑binding factor 1 (LEF1), as well as tumor suppressors (TSs), such as capping actin protein, gelsolin like (CAPG) and tumor protein p53‑inducible nuclear protein 1 (TP53INP1). Upregulated DEGs also included TFs and tumor suppressors, consisting of transcription factor 7‑like 2 (TCF7L2) and pleiomorphic adenoma gene‑like 1 (PLAGL1). DEGs that were identified at the hub nodes in the PPI network and the subnetwork were epidermal growth factor receptor (EGFR) and spleen‑associated tyrosine kinase (SYK), respectively. Several genes crucial in the metastasis of breast cancer were identified, which may serve as potential biomarkers, many of which were associated with cell adhesion, proliferation or immune response, and may influence breast cancer metastasis by regulating these function or pathways.
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Affiliation(s)
- Tianying Zheng
- Department of Chemotherapy, Cancer Center, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Aijun Wang
- Department of Chemotherapy, Cancer Center, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Dongyan Hu
- Department of Chemotherapy, Cancer Center, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Yonggang Wang
- Department of Chemotherapy, Cancer Center, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
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Zhang Y, Han X, Wu H, Zhou Y. Bioinformatics analysis of transcription profiling of solid pseudopapillary neoplasm of the pancreas. Mol Med Rep 2017. [PMID: 28627654 PMCID: PMC5562055 DOI: 10.3892/mmr.2017.6800] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Solid pseudopapillary neoplasm (SPN) of the pancreas is a low-grade malignant neoplasm that accounts for ~5% of cystic pancreatic tumors and ~0.9–2.7% of exocrine pancreatic tumors. The transcription profiling data (GSE43795) of 14 SPN and 6 control samples were downloaded from the Gene Expression Omnibus (GEO) database. Using the Limma package, Student's t-tests were performed to identify differentially expressed genes (DEGs) between SPN and control samples [with the following criterion: False discovery rate (FDR)<0.01 and log2 fold-change (FC)≥3]. Pathway and functional enrichment analyses were performed to investigate the biological processes that the DEGs were involved in. Protein-protein interaction (PPI) network and sub-network analyses were conducted to comprehensively understand the interactions between DEGs. The screened DEGs were further annotated according to information relating to transcription factors and tumor associated genes (TAGs). A total of 710 upregulated and 710 downregulated DEGs were observed, including 74 transcriptional factors and 124 TAGs. Membrane metallo-endopeptidase (MME), matrix metalloproteinase (MMP)-2 and MMP-9 were also identified as key TAGs. Following PPI network analysis, hub nodes of epidermal growth factor receptor (EGFR), proto-oncogene tyrosine protein kinase Fyn (FYN), c-JUN (JUN), glucagon (GCG), c-Myc (MYC) and CD44 were identified, the majority of which participate in the epidermal growth factor receptor (ErbB) and gonadotropin-releasing hormone (GnRH) signaling pathways. A sub-network involving 70 gene nodes was also identified, with EGFR as the central gene. MME, MMP-2 and MMP-9 contribute to proliferative diabetic retinopathy and also involved in SPN. The genes EGFR, FYN, JUN, GCG, MYC and CD44 may therefore be key genes in SPN, and the ErbB and GnRH signaling pathways may be an important contributor to SPN progression.
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Affiliation(s)
- Yongping Zhang
- Department of Digestion, Xin Chang People's Hospital, Pancreatic Disease Research Center of Shanghai, Xinchang, Zhejiang 312500, P.R. China
| | - Xu Han
- Department of Gastroenterology, Shanghai Changhai Hospital, Second Military Medical University of China, Pancreatic Disease Research Center of Shanghai, Shanghai 214000, P.R. China
| | - Hao Wu
- Department of Gastroenterology, Shanghai Changhai Hospital, Second Military Medical University of China, Pancreatic Disease Research Center of Shanghai, Shanghai 214000, P.R. China
| | - Yifeng Zhou
- Digestive Department, Hangzhou First People's Hospital, Pancreatic Disease Research Center of Shanghai, Hangzhou, Zhejiang 310006, P.R. China
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Xu J, Li D, Cai Z, Zhang Y, Huang Y, Su B, Ma R. An integrative analysis of DNA methylation in osteosarcoma. J Bone Oncol 2017; 9:34-40. [PMID: 29234590 PMCID: PMC5715438 DOI: 10.1016/j.jbo.2017.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/09/2017] [Accepted: 05/12/2017] [Indexed: 01/17/2023] Open
Abstract
Background The study aimed to analyze aberrantly methylated genes, relevant pathways and transcription factors (TFs) in osteosarcoma (OS) development. Methods Based on the DNA methylation microarray data GSE36002 that were downloaded from GEO database, the differentially methylated genes in promoter regions were identified between OS and normal samples. Pathway and function enrichment analyses of differentially methylated genes was performed. Subsequently, protein-protein interaction (PPI) network was constructed, followed by identification of cancer-associated differentially methylated genes and significant differentially methylated TFs. Results A total of 1379 hyper-methylation regions and 169 hypo-methylation regions in promoter regions were identified in OS samples compared to normal samples. The differentially hyper-methylated genes were significantly enriched in Neuroactive ligand-receptor interaction pathway, and Peroxisome proliferator activated receptor (PPAR) signaling pathway. The differentially hypo-methylated genes were significantly enriched in Toll-like receptor signaling pathway. In PPI network, signal transducers and activators of transcription (STAT3) had high degree (degree=21). MAX interactor 1, dimerization protein (MXI1), STAT3 and T-cell acute lymphocytic leukemia 1 (TAL1) were significant TFs enriched with target genes in OS samples. They were found to be cancer-associated and hyper-methylated in OS samples. Conclusion Neuroactive ligand-receptor interaction, PPAR signaling, Toll-like receptor signaling pathways are implicated in OS. MXI1, STAT3, and TAL1 may be important TFs involved in OS development.
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Affiliation(s)
- Jie Xu
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Deng Li
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Zhiqing Cai
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yingbin Zhang
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yulin Huang
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Baohua Su
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Ruofan Ma
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
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Chen J, Zhang N, Wen J, Zhang Z. Silencing TAK1 alters gene expression signatures in bladder cancer cells. Oncol Lett 2017; 13:2975-2981. [PMID: 28521404 PMCID: PMC5431247 DOI: 10.3892/ol.2017.5819] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/22/2016] [Indexed: 02/06/2023] Open
Abstract
The aim of the present study was to identify the differentially expressed genes (DEGs) that are induced by the silencing of transforming growth factor-β-activated kinase 1 (TAK1) in bladder cancer cells and to analyze the potential biological effects. Dataset GSE52452 from mutant fibroblast growth factor receptor 3 (FGFR3) bladder cancer cells transfected with control siRNA or TAK1-specific siRNA was downloaded from Gene Expression Omnibus. The DEGs between the two groups were identified using Limma package following data pre-processing by Affy in Bioconductor. Enrichment analysis of DEGs was performed using the Database for Annotation, Visualization and Integrated Discovery, followed by functional annotation using TRANSFAC, TSGene and TAG databases. Integrated networks were constructed by Cytoscape and sub-networks were extracted employing BioNet, followed by enrichment analysis of DEGs in the sub-network. A total of 43 downregulated and 21 upregulated genes were obtained. The downregulated genes were enriched in five pathways, including NOD-like receptor signaling pathway and functions related to cellular response. The upregulated genes were associated with cellular developmental processes. Transcription factor EGR1 and 9 tumor-associated genes were screened from the DEGs. Among the DEGs, 10 hub nodes may represent important roles in the complex metabolic network, including EGFR, CYP3A5, MAP3K7, GSTA1, PTHLH, ALDH1A1, KCND2, EGR1, ARRB1 and ITPR1. Additionally, EGFR was correlated with ERBB2, GRB2 and PIK3R1, and these were enriched in ErbB signaling pathway and various cancer-associated pathways. Silencing TAK1 may decrease cellular response to chemical stimulus via downregulating CYP3A5, MAP3K7, GSTA1, ALDH1A1, ARRB1 and ITPR1; increase cancer cell development via upregulating EGFR, EGR1 and PTHLH; and regulate cancer metastasis through EGFR, ERBB2, GRB2 and PIK3R1.
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Affiliation(s)
- Jimin Chen
- Department of Urology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Nan Zhang
- Department of Urology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Jiaming Wen
- Department of Urology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Zhewei Zhang
- Department of Urology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
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Wu X, Ruan L, Yang Y, Mei Q. Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma. Biol Res 2017; 50:6. [PMID: 28231844 PMCID: PMC5322592 DOI: 10.1186/s40659-017-0108-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 02/04/2017] [Indexed: 12/18/2022] Open
Abstract
Background This study aimed to investigate the gene expression changes associated with carcinoma-associated fibroblasts (CAFs) involving in non-small cell lung carcinoma (NSCLC). Methods We downloaded the GEO series GSE22862, which contained matched gene expression values for 15 CAF and normal fibroblasts samples, and series GSE27289 containing SNP genotyping for four matched NSCLC samples. The differentially expressed genes in CAF samples were identified using the limma package in R. Then we performed gene ontology (GO) and pathway enrichment analysis and protein–protein interaction (PPI) network construction using the identified DEGs. Moreover, aberrant cell fraction, ploidy, allele-specific copy number, and loss of heterozygosity (LOH) within CAF cells were analyzed using the allele-specific copy number analysis. Results We obtained 545 differentially expressed genes between CAF and normal fibroblasts samples. The up-regulated genes are mainly involved in GO terms such as positive regulation of cell migration and extracellular region, while the down-regulated genes participate in the lung development and extracellular region. Multiple genes including bone morphogenetic protein 4 (BMP4) and transforming growth factor, beta 3 (TGFB3) are involved in the TGF-β signaling pathway. Genes including BMP4, TGFBI and matrix Gla protein (MGP) were hub genes. Moreover, no LOH event for BMP4 and MGP was found, that for sphingosine kinase 1 (SPHK1) was 70%, and for TGFBI was 40%. Conclusion Our data suggested that BMP4, MGP, TGFBI, and SPHK1 may be important in CAFs-associated NSCLC, and the abnormal expression and high LOH frequency of them may be used as the diagnosis targets of CAFs in NSCLC.
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Affiliation(s)
- Xiaofen Wu
- Department of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lei Ruan
- Department of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yi Yang
- Department of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qi Mei
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, China.
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Identification of molecular characteristics induced by radiotherapy in rectal cancer based on microarray data. Oncol Lett 2017; 13:2777-2783. [PMID: 28454466 DOI: 10.3892/ol.2017.5750] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 12/06/2016] [Indexed: 12/15/2022] Open
Abstract
The present study aimed to reveal the molecular characteristics induced by radiotherapy in rectal cancer at the transcriptome level. Microarray data (ID, GSE26027) downloaded from the Gene Expression Omnibus database were re-analyzed to identify differentially expressed genes (DEGs) between rectal cancer tissues during and prior to radiotherapy. The DEGs were then inputted into the database for annotation, visualization and integrated discovery, an online tool to perform enrichment analyses, and into the search tool for the retrieval of interacting genes/proteins database to identify protein-protein interactions (PPIs). Subsequently, a PPI network was constructed, which was screened for densely connected modules. Furthermore, protein domain enrichment analysis was performed. In total, 690 DEGs, including 179 upregulated and 511 downregulated DEGs, were found in rectal cancer tissues during and prior to radiotherapy. The upregulated DEGs were significantly enriched in 'positive regulation of transport' and 'regulation of cardiac muscle contraction', while the downregulated DEGs were most markedly enriched in 'cell migration', 'cell-cell signaling', 'extracellular matrix organization' and 'blood vessel development', including prostaglandin-endoperoxide synthase 2, transforming growth factor β-induced, 68 kDa endothelin receptor type A, brain-derived neurotrophic factor, TIMP metallopeptidase inhibitor 1, and serpin family E member 1, which were the top 6 hub nodes in the PPI network. Furthermore, 2 protein domains were significantly enriched by PPI modules, including: The collagen triple helix repeat (CTHR) family members collagen type (COL) 5A2, COL9A3, COL6A3, COL21A1, COL5A3, COL11A1, COL7A1 and CTHR-containing-1; and the olfactory receptor family (OR) members OR7E24, OR7A17, OR6A2, OR1F1, OR10H3 and OR7A10. A total of 7 upregulated DEGs were characterized as tumor suppressor genes, and 8 downregulated DEGs were characterized as oncogenes. The biological processes or protein domains enriched by upregulated or downregulated DEGs may improve the understanding of molecular characteristics in response to radiotherapy.
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