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Brown ZJ, Patwardhan S, Bean J, Pawlik TM. Molecular diagnostics and biomarkers in cholangiocarcinoma. Surg Oncol 2022; 44:101851. [PMID: 36126350 DOI: 10.1016/j.suronc.2022.101851] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/26/2022] [Accepted: 09/09/2022] [Indexed: 10/14/2022]
Abstract
Regardless of anatomic origin, cholangiocarcinoma is generally an aggressive malignancy with a relatively high case fatality. Surgical resection with curative intent remains the best opportunity to achieve meaningful long-term survival. Most patients present, however, with advanced disease and less than 20% of patients are candidates for surgical resection. Unfortunately, even patients who undergo resection have a 5-year survival that ranges from 20 to 40%. Biomarkers are indicators of normal, pathologic, or biologic responses to an intervention and can range from a characteristic (i.e., blood pressure reading which can detect hypertension) to specific genetic mutations or proteins (i.e., carcinoembryonic antigen level). Novel biomarkers and improved molecular diagnostics represent an attractive opportunity to improve detection as well as to identify novel therapeutic targets for patients with cholangiocarcinoma. We herein review the latest advances in molecular diagnostics and biomarkers related to the early detection and treatment of patients with cholangiocarcinoma.
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Affiliation(s)
- Zachary J Brown
- Department of Surgery, The State Wexner Medical Center, Columbus, OH, USA.
| | - Satyajit Patwardhan
- Dept of HPB Surgery and Liver Transplantation, Global Hospital, Mumbai, India
| | - Joal Bean
- Department of Surgery, The State Wexner Medical Center, Columbus, OH, USA
| | - Timothy M Pawlik
- Department of Surgery, The State Wexner Medical Center, Columbus, OH, USA.
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2
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Pantaleón García J, Kulkarni VV, Reese TC, Wali S, Wase SJ, Zhang J, Singh R, Caetano MS, Kadara H, Moghaddam S, Johnson FM, Wang J, Wang Y, Evans S. OBIF: an omics-based interaction framework to reveal molecular drivers of synergy. NAR Genom Bioinform 2022; 4:lqac028. [PMID: 35387383 PMCID: PMC8982434 DOI: 10.1093/nargab/lqac028] [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: 07/09/2021] [Revised: 02/28/2022] [Accepted: 03/10/2022] [Indexed: 01/08/2023] Open
Abstract
Bioactive molecule library screening may empirically identify effective combination therapies, but molecular mechanisms underlying favorable drug–drug interactions often remain unclear, precluding further rational design. In the absence of an accepted systems theory to interrogate synergistic responses, we introduce Omics-Based Interaction Framework (OBIF) to reveal molecular drivers of synergy through integration of statistical and biological interactions in synergistic biological responses. OBIF performs full factorial analysis of feature expression data from single versus dual exposures to identify molecular clusters that reveal synergy-mediating pathways, functions and regulators. As a practical demonstration, OBIF analyzed transcriptomic and proteomic data of a dyad of immunostimulatory molecules that induces synergistic protection against influenza A and revealed unanticipated NF-κB/AP-1 cooperation that is required for antiviral protection. To demonstrate generalizability, OBIF analyzed data from a diverse array of Omics platforms and experimental conditions, successfully identifying the molecular clusters driving their synergistic responses. Hence, unlike existing synergy quantification and prediction methods, OBIF is a phenotype-driven systems model that supports multiplatform interrogation of synergy mechanisms.
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Affiliation(s)
- Jezreel Pantaleón García
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Vikram V Kulkarni
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Tanner C Reese
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- Rice University, Houston, TX 77005, USA
| | - Shradha Wali
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Saima J Wase
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ratnakar Singh
- Department of Thoracic, Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Mauricio S Caetano
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Seyed Javad Moghaddam
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Faye M Johnson
- Department of Thoracic, Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yongxing Wang
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Scott E Evans
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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Ray T, Ryusaki T, Ray PS. Therapeutically Targeting Cancers That Overexpress FOXC1: A Transcriptional Driver of Cell Plasticity, Partial EMT, and Cancer Metastasis. Front Oncol 2021; 11:721959. [PMID: 34540690 PMCID: PMC8446626 DOI: 10.3389/fonc.2021.721959] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 12/28/2022] Open
Abstract
Metastasis accounts for more than 90% of cancer related mortality, thus the most pressing need in the field of oncology today is the ability to accurately predict future onset of metastatic disease, ideally at the time of initial diagnosis. As opposed to current practice, what would be desirable is that prognostic, biomarker-based detection of metastatic propensity and heightened risk of cancer recurrence be performed long before overt metastasis has set in. Without such timely information it will be impossible to formulate a rational therapeutic treatment plan to favorably alter the trajectory of disease progression. In order to help inform rational selection of targeted therapeutics, any recurrence/metastasis risk prediction strategy must occur with the paired identification of novel prognostic biomarkers and their underlying molecular regulatory mechanisms that help drive cancer recurrence/metastasis (i.e. recurrence biomarkers). Traditional clinical factors alone (such as TNM staging criteria) are no longer adequately prognostic for this purpose in the current molecular era. FOXC1 is a pivotal transcription factor that has been functionally implicated to drive cancer metastasis and has been demonstrated to be an independent predictor of heightened metastatic risk, at the time of initial diagnosis. In this review, we present our viewpoints on the master regulatory role that FOXC1 plays in mediating cancer stem cell traits that include cellular plasticity, partial EMT, treatment resistance, cancer invasion and cancer migration during cancer progression and metastasis. We also highlight potential therapeutic strategies to target cancers that are, or have evolved to become, “transcriptionally addicted” to FOXC1. The potential role of FOXC1 expression status in predicting the efficacy of these identified therapeutic approaches merits evaluation in clinical trials.
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Affiliation(s)
- Tania Ray
- R&D Division, Onconostic Technologies (OT), Inc., Champaign, IL, United States
| | | | - Partha S Ray
- R&D Division, Onconostic Technologies (OT), Inc., Champaign, IL, United States
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Mishra NK, Niu M, Southekal S, Bajpai P, Elkholy A, Manne U, Guda C. Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression Profiles. Front Genet 2020; 11:522125. [PMID: 33193605 PMCID: PMC7606733 DOI: 10.3389/fgene.2020.522125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 08/21/2020] [Indexed: 12/30/2022] Open
Abstract
Background Cholangiocarcinoma (CCA) is a rare disease, but it is amongst the most lethal cancers with a median survival under 1 year. Variations in DNA methylation and gene expression have been extensively studied in other cancers for their role in pathogenesis and disease prognosis, but these studies are very limited in CCA. This study focusses on the identification of DNA methylation and gene expression prognostic biomarkers using multi-omics data of CCA tumors from The Cancer Genome Atlas (TCGA). Method We have conducted a genome-wide analysis of differential DNA methylation and gene/miRNA expression using data from 36 CCA tumor and 9 normal samples from TCGA. The impact of DNA methylation in promoters and long-range distal enhancers on the regulation and expression of CCA-associated genes was examined using linear regression. Next, we conducted network analyses on genes which are regulated by DNA methylation as well as by miRNA. Finally, we performed Kaplan–Meier and Cox proportional hazards regression analyses in order to identify the role of selected methylation sites and specific genes and miRNAs in patient survival. We also performed real-time quantitative PCR (qPCR) to confirm the change in gene expression in CCA patients’ tumor and adjacent normal samples. Results Altered DNA methylation was observed on 12,259 CpGs across all chromosomes, of which 78% were hypermethylated. We observed a strong negative relationship between promoter hypermethylation and corresponding gene expression in 92% of the CpGs. Differential expression analyses revealed altered expression patterns in 3,305 genes and 101 miRNAs. Finally, we identified 17 differentially methylated promoter CpGs, 72 differentially expressed genes, and two miRNAs that are likely associated with patient survival. Pathway analysis suggested that cell division, bile secretion, amino acid metabolism, PPAR signaling, hippo signaling were highly affected by gene expression and DNA methylation alterations. The qPCR analysis further confirmed that MDK, HNF1B, PACS1, and GLUD1 are differentially expressed in CCA. Conclusion Based on the survival analysis, we conclude that DEPDC1, FUT4, MDK, PACS1, PIWIL4 genes, miR-22, miR-551b microRNAs, and cg27362525 and cg26597242 CpGs can strongly support their use as prognostic markers of CCA.
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Affiliation(s)
- Nitish Kumar Mishra
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Meng Niu
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Siddesh Southekal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Prachi Bajpai
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Amr Elkholy
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Upender Manne
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
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Abstract
Gene expression profiling by microarray has been used to uncover molecular variations in many areas. The traditional analysis method to gene expression profiling just focuses on the individual genes, and the interactions among genes are ignored, while genes play their roles not by isolations but by interactions with each other. Consequently, gene-to-gene coexpression analysis emerged as a powerful approach to solve the above problems. Then complementary to the conventional differential expression analysis, the differential coexpression analysis can identify gene markers from the systematic level. There are three aspects for differential coexpression network analysis including the network global topological comparison, differential coexpression module identification, and differential coexpression genes and gene pairs identification. To date, the coexpression network and differential coexpression analysis are widely used in a variety of areas in response to environmental stresses, genetic differences, or disease changes. In this chapter, we reviewed the existing methods for differential coexpression network analysis and discussed the applications to cancer research.
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Affiliation(s)
- Bao-Hong Liu
- State Key Laboratory of Veterinary Etiological Biology; Key Laboratory of Veterinary Parasitology of Gansu Province; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, People's Republic of China. .,Jiangsu Co-Innovation Center for Prevention and Control of Animal Infectious Diseases and Zoonoses, Yangzhou, People's Republic of China.
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6
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Qian F, Guo J, Jiang Z, Shen B. Translational Bioinformatics for Cholangiocarcinoma: Opportunities and Challenges. Int J Biol Sci 2018; 14:920-929. [PMID: 29989102 PMCID: PMC6036745 DOI: 10.7150/ijbs.24622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/02/2018] [Indexed: 02/07/2023] Open
Abstract
Translational bioinformatics is becoming a driven force and a new scientific paradigm for cancer research in the era of big data. To promote the cross-disciplinary communication and research, we take cholangiocarcinoma as an example to review the present status and the future perspectives of the bioinformatics models applied in cancer study. We first summarize the present application of computational methods to the study of cholangiocarcinoma ranged from pattern recognition of biological data, knowledge based data annotation to systems biological level modeling and clinical translation. Then the future opportunities and challenges about database or knowledge base building, novel model developing and molecular mechanism exploring as well as the intelligent decision supporting system construction for the precision diagnosis, prognosis and treatment of cholangiocarcinoma are discussed.
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Affiliation(s)
- Fuliang Qian
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Junping Guo
- The Affiliated Yixing Hospital of Jiangsu University, Yixing, 214200, China
| | - Zhi Jiang
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou 215006, China.,Guizhou University School of Medicine, Guiyang, 550025, China.,Institute for Systems Genetics, West China Hospital, Sichuan University, Chengdu, 610041, China
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7
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Yang Z, Jiang S, Cheng Y, Li T, Hu W, Ma Z, Chen F, Yang Y. FOXC1 in cancer development and therapy: deciphering its emerging and divergent roles. Ther Adv Med Oncol 2017; 9:797-816. [PMID: 29449899 PMCID: PMC5808840 DOI: 10.1177/1758834017742576] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/24/2017] [Indexed: 12/12/2022] Open
Abstract
Forkhead box C1 (FOXC1) is an essential member of the forkhead box transcription factors and has been highlighted as an important transcriptional regulator of crucial proteins associated with a wide variety of carcinomas. FOXC1 regulates tumor-associated genes and is regulated by multiple pathways that control its mRNA expression and protein activity. Aberrant FOXC1 expression is involved in diverse tumorigenic processes, such as abnormal cell proliferation, cancer stem cell maintenance, cancer migration, and angiogenesis. Herein, we review the correlation between the expression of FOXC1 and tumor behaviors. We also summarize the mechanisms of the regulation of FOXC1 expression and activity in physiological and pathological conditions. In particular, we focus on the pathological processes of cancer targeted by FOXC1 and discuss whether FOXC1 is good or detrimental during tumor progression. Moreover, FOXC1 is highlighted as a clinical biomarker for diagnosis or prognosis in various human cancers. The information reviewed here should assist in experimental designs and emphasize the potential of FOXC1 as a therapeutic target for cancer.
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Affiliation(s)
- Zhi Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences, Northwest University, Xi'an, China Department of Biomedical Engineering, The Fourth Military Medical University, Xi'an, China
| | - Shuai Jiang
- Department of Aerospace Medicine, The Fourth Military Medical University, Xi'an, China
| | - Yicheng Cheng
- Department of Stomatology, Bayi Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Tian Li
- Department of Biomedical Engineering, The Fourth Military Medical University, Xi'an, China
| | - Wei Hu
- Department of Biomedical Engineering, The Fourth Military Medical University, Xi'an, China
| | - Zhiqiang Ma
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Fulin Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, Xi'an, China
| | - Yang Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, 229 Taibai North Road, Xi'an 710069, China
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8
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Han B, Bhowmick N, Qu Y, Chung S, Giuliano AE, Cui X. FOXC1: an emerging marker and therapeutic target for cancer. Oncogene 2017; 36:3957-3963. [PMID: 28288141 PMCID: PMC5652000 DOI: 10.1038/onc.2017.48] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/03/2017] [Accepted: 02/04/2017] [Indexed: 02/07/2023]
Abstract
The Forkhead box C1 (FOXC1) transcription factor is involved in normal embryonic development and regulates the development and function of many organs. Most recently, a large body of literature has shown that FOXC1 plays a critical role in tumor development and metastasis. Clinical studies have demonstrated that elevated FOXC1 expression is associated with poor prognosis in many cancer subtypes, such as basal-like breast cancer (BLBC). FOXC1 is highly and specifically expressed in BLBC as opposed to other breast cancer subtypes. Its functions in breast cancer have been extensively explored. This review will summarize current knowledge on the function and regulation of FOXC1 in tumor development and progression with a focus on BLBC as well as the implications of these new findings in cancer diagnosis and treatment.
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Affiliation(s)
- B Han
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - N Bhowmick
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Y Qu
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - S Chung
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - A E Giuliano
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - X Cui
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Rahnemai-Azar AA, Weisbrod A, Dillhoff M, Schmidt C, Pawlik TM. Intrahepatic cholangiocarcinoma: Molecular markers for diagnosis and prognosis. Surg Oncol 2017; 26:125-137. [PMID: 28577718 DOI: 10.1016/j.suronc.2016.12.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/24/2016] [Accepted: 12/29/2016] [Indexed: 02/08/2023]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is the second most common primary liver tumor with increasing incidence worldwide. The outcome of patients with iCCA is dismal owing to tumor's aggressiveness, late diagnosis and lack of effective treatment options. Detection of the tumor at early stages may make surgical resection, as only potential curative treatment, more feasible. Unfortunately, despite recent developments in imaging modalities and laboratory tests, the diagnosis of iCCA remains challenging and patients often present in advanced stages when surgery cannot be offered. Moreover, accurate assessment of disease burden is critical to optimize management strategy, including the use of adjuvant therapies and clinical trials. Identifying iCCA specific diagnostic and prognostic biomarkers has been a focus of interest among many investigators with a progressive increase in data on iCCA related to advances in "omics" technologies. We herein summarize iCCA biomarkers and define the molecular mechanisms underlying iCCA carcinogenesis, as well as highlight potential diagnostic and prognostic application of molecular biomarkers.
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Affiliation(s)
- Amir A Rahnemai-Azar
- Department of Surgery, University of Washington Medical Center, Seattle, WA, USA
| | - Allison Weisbrod
- Department of Surgery, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Mary Dillhoff
- Department of Surgery, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Carl Schmidt
- Department of Surgery, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Timothy M Pawlik
- Department of Surgery, The Ohio State University, Wexner Medical Center, Columbus, OH, USA.
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Wirth TC, Vogel A. Surveillance in cholangiocellular carcinoma. Best Pract Res Clin Gastroenterol 2016; 30:987-999. [PMID: 27938792 DOI: 10.1016/j.bpg.2016.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/28/2016] [Accepted: 11/04/2016] [Indexed: 01/31/2023]
Abstract
Cholangiocellular carcinoma is the most frequent malignant neoplasm originating from the epithelium of intra- or extrahepatic bile ducts. In the past decades, the incidence of cholangiocarcinoma has been shown to increase while overall mortality has remained high with an approximate 5-year overall survival below 20%. Surgery remains the only curative option while systemic treatment is limited to palliative chemotherapy. Therefore, surveillance strategies for patients at risk of developing cholangiocarcinoma are urgently needed, particularly in patients with primary sclerosing cholangitis and patients infected with liver flukes. Here we summarize the currently available data on surveillance of risk populations and methods for the detection of cholangiocarcinoma.
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Affiliation(s)
- Thomas C Wirth
- Department of Gastroenterology, Hepatology and Endocrinology, Medical School Hannover, 30625 Hannover, Germany
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Medical School Hannover, 30625 Hannover, Germany.
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Chen J, Yang HT, Li Z, Xu N, Yu B, Xu JP, Zhao PG, Wang Y, Zhang XJ, Lin DJ. Construction of protein interaction network involved in lung adenocarcinomas using a novel algorithm. Oncol Lett 2016; 12:1792-1800. [PMID: 27588126 PMCID: PMC4998145 DOI: 10.3892/ol.2016.4822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 12/01/2015] [Indexed: 12/14/2022] Open
Abstract
Studies that only assess differentially-expressed (DE) genes do not contain the information required to investigate the mechanisms of diseases. A complete knowledge of all the direct and indirect interactions between proteins may act as a significant benchmark in the process of forming a comprehensive description of cellular mechanisms and functions. The results of protein interaction network studies are often inconsistent and are based on various methods. In the present study, a combined network was constructed using selected gene pairs, following the conversion and combination of the scores of gene pairs that were obtained across multiple approaches by a novel algorithm. Samples from patients with and without lung adenocarcinoma were compared, and the RankProd package was used to identify DE genes. The empirical Bayesian (EB) meta-analysis approach, the search tool for the retrieval of interacting genes/proteins database (STRING), the weighted gene coexpression network analysis (WGCNA) package and the differentially-coexpressed genes and links package (DCGL) were used for network construction. A combined network was also constructed with a novel rank-based algorithm using a combined score. The topological features of the 5 networks were analyzed and compared. A total of 941 DE genes were screened. The topological analysis indicated that the gene interaction network constructed using the WGCNA method was more likely to produce a small-world property, which has a small average shortest path length and a large clustering coefficient, whereas the combined network was confirmed to be a scale-free network. Gene pairs that were identified using the novel combined method were mostly enriched in the cell cycle and p53 signaling pathway. The present study provided a novel perspective to the network-based analysis. Each method has advantages and disadvantages. Compared with single methods, the combined algorithm used in the present study may provide a novel method to analyze gene interactions, with increased credibility.
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Affiliation(s)
- Juan Chen
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250014, P.R. China; Department of Respiratory Medicine, People's Hospital of Liaocheng, Liaocheng, Shandong 252000, P.R. China
| | - Hai-Tao Yang
- Department of Respiratory Medicine, People's Hospital of Liaocheng, Liaocheng, Shandong 252000, P.R. China
| | - Zhu Li
- Department of Hepatobiliary Surgery, People's Hospital of Liaocheng, Liaocheng, Shandong 252000, P.R. China
| | - Ning Xu
- Department of Respiratory Medicine, Weihai Municipal Hospital, Weihai, Shandong 264200, P.R. China
| | - Bo Yu
- Department of Respiratory Medicine, People's Hospital of Liaocheng, Liaocheng, Shandong 252000, P.R. China
| | - Jun-Ping Xu
- Department of Respiratory Medicine, People's Hospital of Liaocheng, Liaocheng, Shandong 252000, P.R. China
| | - Pei-Ge Zhao
- Department of Respiratory Medicine, People's Hospital of Liaocheng, Liaocheng, Shandong 252000, P.R. China
| | - Yan Wang
- Department of Respiratory Medicine, People's Hospital of Liaocheng, Liaocheng, Shandong 252000, P.R. China
| | - Xiu-Juan Zhang
- Department of Respiratory Medicine, People's Hospital of Liaocheng, Liaocheng, Shandong 252000, P.R. China
| | - Dian-Jie Lin
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250014, P.R. China
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Yue H, Yang BO, Yang F, Hu XL, Kong FB. Co-expression network-based analysis of hippocampal expression data associated with Alzheimer's disease using a novel algorithm. Exp Ther Med 2016; 11:1707-1715. [PMID: 27168792 PMCID: PMC4840697 DOI: 10.3892/etm.2016.3131] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 01/07/2016] [Indexed: 12/15/2022] Open
Abstract
Recent progress in bioinformatics has facilitated the clarification of biological processes associated with complex diseases. Numerous methods of co-expression analysis have been proposed for use in the study of pairwise relationships among genes. In the present study, a combined network based on gene pairs was constructed following the conversion and combination of gene pair score values using a novel algorithm across multiple approaches. Three hippocampal expression profiles of patients with Alzheimer's disease (AD) and normal controls were extracted from the ArrayExpress database, and a total of 144 differentially expressed (DE) genes across multiple studies were identified by a rank product (RP) method. Five groups of co-expression gene pairs and five networks were identified and constructed using four existing methods [weighted gene co-expression network analysis (WGCNA), empirical Bayesian (EB), differentially co-expressed genes and links (DCGL), search tool for the retrieval of interacting genes/proteins database (STRING)] and a novel rank-based algorithm with combined score, respectively. Topological analysis indicated that the co-expression network constructed by the WGCNA method had the tendency to exhibit small-world characteristics, and the combined co-expression network was confirmed to be a scale-free network. Functional analysis of the co-expression gene pairs was conducted by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The co-expression gene pairs were mostly enriched in five pathways, namely proteasome, oxidative phosphorylation, Parkinson's disease, Huntington's disease and AD. This study provides a new perspective to co-expression analysis. Since different methods of analysis often present varying abilities, the novel combination algorithm may provide a more credible and robust outcome, and could be used to complement to traditional co-expression analysis.
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Affiliation(s)
- Hong Yue
- Department of Neurology (No. 2), Rizhao People's Hospital, Rizhao, Shandong 276826, P.R. China
| | - B O Yang
- Department of Neurology (No. 2), Rizhao People's Hospital, Rizhao, Shandong 276826, P.R. China
| | - Fang Yang
- Department of Neurology (No. 2), Rizhao People's Hospital, Rizhao, Shandong 276826, P.R. China
| | - Xiao-Li Hu
- Department of Neurology (No. 2), Rizhao People's Hospital, Rizhao, Shandong 276826, P.R. China
| | - Fan-Bin Kong
- Department of Neurology (No. 2), Rizhao People's Hospital, Rizhao, Shandong 276826, P.R. China
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An Omics Perspective on Molecular Biomarkers for Diagnosis, Prognosis, and Therapeutics of Cholangiocarcinoma. Int J Genomics 2015; 2015:179528. [PMID: 26421274 PMCID: PMC4572471 DOI: 10.1155/2015/179528] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/09/2015] [Indexed: 12/12/2022] Open
Abstract
Cholangiocarcinoma (CCA) is an aggressive biliary tract malignancy arising from the epithelial bile duct. The lack of early diagnostic biomarkers as well as therapeutic measures results in severe outcomes and poor prognosis. Thus, effective early diagnostic, prognostic, and therapeutic biomarkers are required to improve the prognosis and prolong survival rates in CCA patients. Recent advancement in omics technologies combined with the integrative experimental and clinical validations has provided an insight into the underlying mechanism of CCA initiation and progression as well as clues towards novel biomarkers. This work highlights the discovery and validation of molecular markers in CCA identified through omics approaches. The possible roles of these molecules in various cellular pathways, which render CCA carcinogenesis and progression, will also be discussed. This paper can serve as a reference point for further investigations to yield deeper understanding in the complex feature of this disease, potentially leading to better approaches for diagnosis, prognosis, and therapeutics.
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