1
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Agarwal S, Gupta S, Raj R. Identification of potential targetable genes in papillary, follicular, and anaplastic thyroid carcinoma using bioinformatics analysis. Endocrine 2024:10.1007/s12020-024-03836-x. [PMID: 38676768 DOI: 10.1007/s12020-024-03836-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 04/14/2024] [Indexed: 04/29/2024]
Abstract
PURPOSE To perform an extensive exploratory analysis to build a deeper insight into clinically relevant molecular biomarkers in Papillary, Follicular, and Anaplastic thyroid carcinomas (PTC, FTC, ATC). METHODS Thirteen Thyroid Cancer (THCA) datasets incorporating PTC, FTC, and ATC were derived from the Gene Expression Omnibus. Genes differentially expressed (DEGs) between THCA and normal were identified and subjected to GO and KEGG analyses. Multiple topological properties were harnessed and protein-protein interaction (PPI) networks were constructed to identify the hub genes followed by survival analysis and validation. RESULTS There were 70, 87, and 377 DEGs, and 23, 27, and 53 hub genes for PTC, FTC, and ATC samples, respectively. Survival analysis detected 39 overall and 49 relapse-free survival-relevant hub genes. Six hub genes, BCL2, FN1, ITPR1, LYVE1, NTRK2, TBC1D4, were found common to more than one THCA type. The most significant hub genes found in the study were: BCL2, CD44, DCN, FN1, IRS1, ITPR1, MFAP4, MKI67, NTRK2, PCLO, TGFA. The most enriched and significant GO terms were Melanocyte differentiation for PTC, Extracellular region for FTC, and Extracellular exosome for ATC. Prostate cancer for PTC was the most significantly enriched KEGG pathway. The results were validated using TCGA data. CONCLUSIONS The findings unravel potential biomarkers and therapeutic targets of thyroid carcinomas.
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Affiliation(s)
- Shipra Agarwal
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Shikha Gupta
- Department of Computer Science, S.S. College of Business Studies, University of Delhi, New Delhi, India.
| | - Rishav Raj
- Department of Computer Science, S.S. College of Business Studies, University of Delhi, New Delhi, India
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2
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Chandra Jena B, Flaherty DP, O'Brien VP, Watts VJ. Biochemical pharmacology of adenylyl cyclases in cancer. Biochem Pharmacol 2024:116160. [PMID: 38522554 DOI: 10.1016/j.bcp.2024.116160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/11/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
Globally, despite extensive research and pharmacological advancement, cancer remains one of the most common causes of mortality. Understanding the signaling pathways involved in cancer progression is essential for the discovery of new drug targets. The adenylyl cyclase (AC) superfamily comprises glycoproteins that regulate intracellular signaling and convert ATP into cyclic AMP, an important second messenger. The present review highlights the involvement of ACs in cancer progression and suppression, broken down for each specific mammalian AC isoform. The precise mechanisms by which ACs contribute to cancer cell proliferation and invasion are not well understood and are variable among cancer types; however, AC overactivation, along with that of downstream regulators, presents a potential target for novel anticancer therapies. The expression patterns of ACs in numerous cancers are discussed. In addition, we highlight inhibitors of AC-related signaling that are currently under investigation, with a focus on possible anti-cancer strategies. Recent discoveries with small molecules regarding more direct modulation AC activity are also discussed in detail. A more comprehensive understanding of different components in AC-related signaling could potentially lead to the development of novel therapeutic strategies for personalized oncology and might enhance the efficacy of chemoimmunotherapy in the treatment of various cancers.
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Affiliation(s)
- Bikash Chandra Jena
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Daniel P Flaherty
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Valerie P O'Brien
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Val J Watts
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, USA.
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3
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Lu H, Ping J, Zhou G, Zhao Z, Gao W, Jiang Y, Quan C, Lu Y, Zhou G. CommPath: An R package for inference and analysis of pathway-mediated cell-cell communication chain from single-cell transcriptomics. Comput Struct Biotechnol J 2022; 20:5978-5983. [PMID: 36382188 PMCID: PMC9647193 DOI: 10.1016/j.csbj.2022.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/14/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
Single-cell transcriptomics offers opportunities to investigate ligand-receptor (LR) interactions between heterogeneous cell populations within tissues. However, most existing tools for the inference of intercellular communication do not allow prioritization of functional LR associations that provoke certain biological responses in the receiver cells. In addition, current tools do not enable the identification of the impact on the downstream cell types of the receiver cells. We present CommPath, an open-source R package and webserver, to analyze and visualize the LR interactions and pathway-mediated intercellular communication chain with single-cell transcriptomic data. CommPath curates a comprehensive signaling pathway database to interpret the consequences of LR associations and therefore infers functional LR interactions. Furthermore, CommPath determines cell-cell communication chain by considering both the upstream and downstream cells of user-defined cell populations. Applying CommPath to human hepatocellular carcinoma dataset shows its ability to decipher complex LR interaction patterns and the associated intercellular communication chain, as well as their changes in disease versus homeostasis.
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4
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Suter P, Dazert E, Kuipers J, Ng CKY, Boldanova T, Hall MN, Heim MH, Beerenwinkel N. Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model. PLoS Comput Biol 2022; 18:e1009767. [PMID: 36067230 PMCID: PMC9481159 DOI: 10.1371/journal.pcbi.1009767] [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: 12/21/2021] [Revised: 09/16/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
Comprehensive molecular characterization of cancer subtypes is essential for predicting clinical outcomes and searching for personalized treatments. We present bnClustOmics, a statistical model and computational tool for multi-omics unsupervised clustering, which serves a dual purpose: Clustering patient samples based on a Bayesian network mixture model and learning the networks of omics variables representing these clusters. The discovered networks encode interactions among all omics variables and provide a molecular characterization of each patient subgroup. We conducted simulation studies that demonstrated the advantages of our approach compared to other clustering methods in the case where the generative model is a mixture of Bayesian networks. We applied bnClustOmics to a hepatocellular carcinoma (HCC) dataset comprising genome (mutation and copy number), transcriptome, proteome, and phosphoproteome data. We identified three main HCC subtypes together with molecular characteristics, some of which are associated with survival even when adjusting for the clinical stage. Cluster-specific networks shed light on the links between genotypes and molecular phenotypes of samples within their respective clusters and suggest targets for personalized treatments.
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Affiliation(s)
- Polina Suter
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eva Dazert
- Biozentrum, University of Basel, Basel, Switzerland
| | - Jack Kuipers
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Charlotte K. Y. Ng
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Tuyana Boldanova
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Markus H. Heim
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, Clarunis, University Center for Gastrointestinal and Liver Diseases, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail:
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5
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Guo R, Liu T, Shasaltaneh MD, Wang X, Imani S, Wen Q. Targeting Adenylate Cyclase Family: New Concept of Targeted Cancer Therapy. Front Oncol 2022; 12:829212. [PMID: 35832555 PMCID: PMC9271773 DOI: 10.3389/fonc.2022.829212] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 05/26/2022] [Indexed: 12/18/2022] Open
Abstract
The adenylate cyclase (ADCY) superfamily is a group of glycoproteins regulating intracellular signaling. ADCYs act as key regulators in the cyclic adenosine monophosphate (cAMP) signaling pathway and are related to cell sensitivity to chemotherapy and ionizing radiation. Many members of the superfamily are detectable in most chemoresistance cases despite the complexity and unknownness of the specific mechanism underlying the role of ADCYs in the proliferation and invasion of cancer cells. The overactivation of ADCY, as well as its upstream and downstream regulators, is implicated as a major potential target of novel anticancer therapies and markers of exceptional responders to chemotherapy. The present review focuses on the oncogenic functions of the ADCY family and emphasizes the possibility of the mediating roles of deleterious nonsynonymous single nucleotide polymorphisms (nsSNPs) in ADCY as a prognostic therapeutic target in modulating resistance to chemotherapy and immunotherapy. It assesses the mediating roles of ADCY and its counterparts as stress regulators in reprogramming cancer cell metabolism and the tumor microenvironment. Additionally, the well-evaluated inhibitors of ADCY-related signaling, which are under clinical investigation, are highlighted. A better understanding of ADCY-induced signaling and deleterious nsSNPs (p.E1003K and p.R1116C) in ADCY6 provides new opportunities for developing novel therapeutic strategies in personalized oncology and new approaches to enhance chemoimmunotherapy efficacy in treating various cancers.
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Affiliation(s)
- Rui Guo
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Tian Liu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | | | - Xuan Wang
- China Regional Research Center, International Centre for Genetic Engineering and Biotechnology Taizhou, Jiangsu, China
| | - Saber Imani
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- China Regional Research Center, International Centre for Genetic Engineering and Biotechnology Taizhou, Jiangsu, China
- *Correspondence: Saber Imani, ; QingLian Wen,
| | - QingLian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- *Correspondence: Saber Imani, ; QingLian Wen,
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6
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Ying H, Lin A, Liang J, Zhang J, Luo P. Association Between FSIP2 Mutation and an Improved Efficacy of Immune Checkpoint Inhibitors in Patients With Skin Cutaneous Melanoma. Front Mol Biosci 2021; 8:629330. [PMID: 34113648 PMCID: PMC8186463 DOI: 10.3389/fmolb.2021.629330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 04/06/2021] [Indexed: 12/24/2022] Open
Abstract
Background Immune checkpoint inhibitors (ICIs) have shown remarkable success in treating skin cutaneous melanoma (SKCM); however, the response to treatment varies greatly between patients. Considering that the efficacy of ICI treatment is influenced by many factors, we selected the Fibrosheath interacting protein 2 (FSIP2) gene and systematically analyzed its potential to predict the efficacy of ICI treatment. Methods Patient data were collected from an ICI treatment cohort (n = 120) and a The Cancer Genome Atlas (TCGA)-SKCM cohort (n = 467). The data were divided into an FSIP2-mutant (MT) group and FSIP2-wild-type (WT) group according to FSIP2 mutation status. In this study, we analyzed the patients' overall survival rate, tumor mutational burden (TMB), neoantigen load (NAL), copy number variation (CNV), cell infiltration data and immune-related genes. We used gene set enrichment analysis (GSEA) to delineate biological pathways and processes associated with the efficacy of immunotherapy. Results The efficacy of ICI treatment of SKCM patients with FSIP2 mutation was significantly better than that of patients without FSIP2 mutation. The patients in the FSIP2-MT group had higher tumor immunogenicity and lower regulatory T cell (Treg) infiltration. Results of GSEA showed that pathways related to tumor progression (MAPK and FGFR), immunomodulation, and IL-2 synthesis inhibition were significantly downregulated in the FSIP2-MT group. Conclusion Our research suggests that the FSIP2 gene has the potential to predict the efficacy of ICI treatment. The high tumor immunogenicity and low Treg levels observed may be closely related to the fact that patients with FSIP2-MT can benefit from ICI treatment.
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Affiliation(s)
- Haoxuan Ying
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Southern Medical University, Guangzhou, China
| | - Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Junyi Liang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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7
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Chen Y, Yang W, Chen Q, Liu Q, Liu J, Zhang Y, Li B, Li D, Nan J, Li X, Wu H, Xiang X, Peng Y, Wang J, Su S, Wang Z. Prediction of hepatocellular carcinoma risk in patients with chronic liver disease from dynamic modular networks. J Transl Med 2021; 19:122. [PMID: 33757544 PMCID: PMC7989040 DOI: 10.1186/s12967-021-02791-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/16/2021] [Indexed: 12/17/2022] Open
Abstract
Background Discovering potential predictive risks in the super precarcinomatous phase of hepatocellular carcinoma (HCC) without any clinical manifestations is impossible under normal paradigm but critical to control this complex disease. Methods In this study, we utilized a proposed sequential allosteric modules (AMs)-based approach and quantitatively calculated the topological structural variations of these AMs. Results We found the total of 13 oncogenic allosteric modules (OAMs) among chronic hepatitis B (CHB), cirrhosis and HCC network used SimiNEF. We obtained the 11 highly correlated gene pairs involving 15 genes (r > 0.8, P < 0.001) from the 12 OAMs (the out-of-bag (OOB) classification error rate < 0.5) partial consistent with those in independent clinical microarray data, then a three-gene set (cyp1a2-cyp2c19-il6) was optimized to distinguish HCC from non-tumor liver tissues using random forests with an average area under the curve (AUC) of 0.973. Furthermore, we found significant inhibitory effect on the tumor growth of Bel-7402, Hep 3B and Huh7 cell lines in zebrafish treated with the compounds affected those three genes. Conclusions These findings indicated that the sequential AMs-based approach could detect HCC risk in the patients with chronic liver disease and might be applied to any time-dependent risk of cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02791-9.
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Affiliation(s)
- Yinying Chen
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5 Beixian Ge, Xicheng District, Beijing, 100053, China.,Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimen, Beijing, 100700, China.,Postdoctoral Research Station, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Yang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimen, Beijing, 100700, China
| | - Qilong Chen
- Research Center for Traditional Chinese Medicine Complexity System, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong, Shanghai, 201203, China
| | - Qiong Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimen, Beijing, 100700, China
| | - Jun Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimen, Beijing, 100700, China
| | - Yingying Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimen, Beijing, 100700, China
| | - Bing Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimen, Beijing, 100700, China
| | - Dongfeng Li
- School of Mathematical Sciences, Peking University, Beijing, China
| | - Jingyi Nan
- Shandong Danhong Pharmaceutical Co. Ltd., Heze, China
| | - Xiaodong Li
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
| | - Huikun Wu
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
| | - Xinghua Xiang
- School of Mathematics and Computational Science, Hunan University of Science and Technology, Xiangtan, China
| | - Yehui Peng
- School of Mathematics and Computational Science, Hunan University of Science and Technology, Xiangtan, China
| | - Jie Wang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5 Beixian Ge, Xicheng District, Beijing, 100053, China.
| | - Shibing Su
- Research Center for Traditional Chinese Medicine Complexity System, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong, Shanghai, 201203, China.
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimen, Beijing, 100700, China.
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8
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Bhat M, Pasini E, Pastrello C, Rahmati S, Angeli M, Kotlyar M, Ghanekar A, Jurisica I. Integrative analysis of layers of data in hepatocellular carcinoma reveals pathway dependencies. World J Hepatol 2021; 13:94-108. [PMID: 33584989 PMCID: PMC7856865 DOI: 10.4254/wjh.v13.i1.94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/19/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The broader use of high-throughput technologies has led to improved molecular characterization of hepatocellular carcinoma (HCC).
AIM To comprehensively analyze and characterize all publicly available genomic, gene expression, methylation, miRNA and proteomic data in HCC, covering 85 studies and 3355 patient sample profiles, to identify the key dysregulated genes and pathways they affect.
METHODS We collected and curated all well-annotated and publicly available high-throughput datasets from PubMed and Gene Expression Omnibus derived from human HCC tissue. Comprehensive pathway enrichment analysis was performed using pathDIP for each data type (genomic, gene expression, methylation, miRNA and proteomic), and the overlap of pathways was assessed to elucidate pathway dependencies in HCC.
RESULTS We identified a total of 8733 abstracts retrieved by the search on PubMed on HCC for the different layers of data on human HCC samples, published until December 2016. The common key dysregulated pathways in HCC tissue across different layers of data included epidermal growth factor (EGFR) and β1-integrin pathways. Genes along these pathways were significantly and consistently dysregulated across the different types of high-throughput data and had prognostic value with respect to overall survival. Using CTD database, estradiol would best modulate and revert these genes appropriately.
CONCLUSION By analyzing and integrating all available high-throughput genomic, transcriptomic, miRNA, methylation and proteomic data from human HCC tissue, we identified EGFR, β1-integrin and axon guidance as pathway dependencies in HCC. These are master regulators of key pathways in HCC, such as the mTOR, Ras/Raf/MAPK and p53 pathways. The genes implicated in these pathways had prognostic value in HCC, with Netrin and Slit3 being novel proteins of prognostic importance to HCC. Based on this integrative analysis, EGFR, and β1-integrin are master regulators that could serve as potential therapeutic targets in HCC.
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Affiliation(s)
- Mamatha Bhat
- Multi Organ transplant Program, University Health Network, Toronto M5G2N2, Canada
| | - Elisa Pasini
- Multi Organ transplant Program, University Health Network, Toronto M5G2N2, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health NetworkandKrembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Sara Rahmati
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health NetworkandKrembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Marc Angeli
- Multi Organ transplant Program, University Health Network, Toronto M5G2N2, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health NetworkandKrembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Anand Ghanekar
- Surgery, University Health Network, Toronto M5G 2C4, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health NetworkandKrembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto M5T 0S8, Canada
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Marzec J, Ross-Adams H, Pirrò S, Wang J, Zhu Y, Mao X, Gadaleta E, Ahmad AS, North BV, Kammerer-Jacquet SF, Stankiewicz E, Kudahetti SC, Beltran L, Ren G, Berney DM, Lu YJ, Chelala C. The Transcriptomic Landscape of Prostate Cancer Development and Progression: An Integrative Analysis. Cancers (Basel) 2021; 13:345. [PMID: 33477882 PMCID: PMC7838904 DOI: 10.3390/cancers13020345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing of primary tumors is now standard for transcriptomic studies, but microarray-based data still constitute the majority of available information on other clinically valuable samples, including archive material. Using prostate cancer (PC) as a model, we developed a robust analytical framework to integrate data across different technical platforms and disease subtypes to connect distinct disease stages and reveal potentially relevant genes not identifiable from single studies alone. We reconstructed the molecular profile of PC to yield the first comprehensive insight into its development, by tracking changes in mRNA levels from normal prostate to high-grade prostatic intraepithelial neoplasia, and metastatic disease. A total of nine previously unreported stage-specific candidate genes with prognostic significance were also found. Here, we integrate gene expression data from disparate sample types, disease stages and technical platforms into one coherent whole, to give a global view of the expression changes associated with the development and progression of PC from normal tissue through to metastatic disease. Summary and individual data are available online at the Prostate Integrative Expression Database (PIXdb), a user-friendly interface designed for clinicians and laboratory researchers to facilitate translational research.
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Affiliation(s)
- Jacek Marzec
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Helen Ross-Adams
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Stefano Pirrò
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Jun Wang
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Yanan Zhu
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Xueying Mao
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Emanuela Gadaleta
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Amar S. Ahmad
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK; (A.S.A.); (B.V.N.)
| | - Bernard V. North
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK; (A.S.A.); (B.V.N.)
| | - Solène-Florence Kammerer-Jacquet
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Elzbieta Stankiewicz
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Sakunthala C. Kudahetti
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Luis Beltran
- Department of Pathology, Barts Health NHS, London E1 F1R, UK;
| | - Guoping Ren
- Department of Pathology, The First Affiliated Hospital, Zhejiang University Medical College, Hangzhou 310058, China;
| | - Daniel M. Berney
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
- Department of Pathology, Barts Health NHS, London E1 F1R, UK;
| | - Yong-Jie Lu
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Claude Chelala
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
- Centre for Computational Biology, Life Sciences Initiative, Queen Mary University London, London EC1M 6BQ, UK
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10
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Ni Z, Lu J, Huang W, Khan H, Wu X, Huang D, Shi G, Niu Y, Huang H. Transcriptomic identification of HBx-associated hub genes in hepatocellular carcinoma. PeerJ 2021; 9:e12697. [PMID: 35036167 PMCID: PMC8710059 DOI: 10.7717/peerj.12697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/06/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common malignancies around the world. Among the risk factors involved in liver carcinogenesis, hepatitis B virus (HBV) X protein (HBx) is considered to be a key regulator in hepatocarcinogenesis. Whether HBx promotes or protects against HCC remains controversial, therefore exploring new HBx-associated genes is still important. METHODS HBx was overexpressed in HepG2, HepG2.2.15 and SMMC-7721 cell lines, primary mouse hepatocytes and livers of C57BL/6N mice. High-throughput RNA sequencing profiling of HepG2 cells with HBx overexpression and related differentially-expressed genes (DEGs), pathway enrichment analysis, protein-protein interaction networks (PPIs), overlapping analysis were conducted. In addition, Gene Expression Omnibus (GEO) and proteomic datasets of HBV-positive HCC datasets were used to verify the expression and prognosis of selected DEGs. Finally, we also evaluated the known oncogenic role of HBx by oncogenic array analysis. RESULTS A total of 523 DEGs were obtained from HBx-overexpressing HepG2 cells. Twelve DEGs were identified and validated in cells transiently transfected with HBx and three datasets of HBV-positive HCC transcription profiles. In addition, using the Kaplan-Meier plotter database, the expression levels of the twelve different genes were further analyzed to predict patient outcomes. CONCLUSION Among the 12 identified HBx-associated hub genes, HBV-positive HCC patients expressing ARG1 and TAT showed a good overall survival (OS) and relapse-free survival (RFS). Thus, ARG1 and TAT expression could be potential prognostic markers.
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Affiliation(s)
- Zhengzhong Ni
- Department of Pharmacology, Shantou University Medical College, Shantou, Guangdong, China
| | - Jun Lu
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Weiyi Huang
- Department of Pharmacology, Shantou University Medical College, Shantou, Guangdong, China
| | - Hanif Khan
- Department of Pharmacology, Shantou University Medical College, Shantou, Guangdong, China
| | - Xuejun Wu
- Department of Pharmacology, Shantou University Medical College, Shantou, Guangdong, China
| | - Danmei Huang
- Department of Pharmacology, Shantou University Medical College, Shantou, Guangdong, China
| | - Ganggang Shi
- Department of Pharmacology, Shantou University Medical College, Shantou, Guangdong, China
| | - Yongdong Niu
- Department of Pharmacology, Shantou University Medical College, Shantou, Guangdong, China
| | - Haihua Huang
- Department of Pathology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
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11
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Ali ES, Rychkov GY, Barritt GJ. Targeting Ca 2+ Signaling in the Initiation, Promotion and Progression of Hepatocellular Carcinoma. Cancers (Basel) 2020; 12:cancers12102755. [PMID: 32987945 PMCID: PMC7600741 DOI: 10.3390/cancers12102755] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Liver cancer (hepatocellular carcinoma) is a significant health burden worldwide. It is often not detected until at an advanced stage when there are few treatment options available. Changes in calcium concentrations within liver cancer cells are essential for regulating their growth, death, and migration (metastasis). Our aim was to review published papers which have identified proteins involved in calcium signaling as potential drug targets for the treatment of liver cancer. About twenty calcium signaling proteins were identified, including those involved in regulating calcium concentrations in the cytoplasm, endoplasmic reticulum and mitochondria. A few of these have turned out to be sites of action of natural products previously known to inhibit liver cancer. More systematic studies are now needed to determine which calcium signaling proteins might be used clinically for treatment of liver cancer, especially advanced stage cancers and those resistant to inhibition by current drugs. Abstract Hepatocellular carcinoma (HCC) is a considerable health burden worldwide and a major contributor to cancer-related deaths. HCC is often not noticed until at an advanced stage where treatment options are limited and current systemic drugs can usually only prolong survival for a short time. Understanding the biology and pathology of HCC is a challenge, due to the cellular and anatomic complexities of the liver. While not yet fully understood, liver cancer stem cells play a central role in the initiation and progression of HCC and in resistance to drugs. There are approximately twenty Ca2+-signaling proteins identified as potential targets for therapeutic treatment at different stages of HCC. These potential targets include inhibition of the self-renewal properties of liver cancer stem cells; HCC initiation and promotion by hepatitis B and C and non-alcoholic fatty liver disease (principally involving reduction of reactive oxygen species); and cell proliferation, tumor growth, migration and metastasis. A few of these Ca2+-signaling pathways have been identified as targets for natural products previously known to reduce HCC. Promising Ca2+-signaling targets include voltage-operated Ca2+ channel proteins (liver cancer stem cells), inositol trisphosphate receptors, store-operated Ca2+ entry, TRP channels, sarco/endoplasmic reticulum (Ca2++Mg2+) ATP-ase and Ca2+/calmodulin-dependent protein kinases. However, none of these Ca2+-signaling targets has been seriously studied any further than laboratory research experiments. The future application of more systematic studies, including genomics, gene expression (RNA-seq), and improved knowledge of the fundamental biology and pathology of HCC will likely reveal new Ca2+-signaling protein targets and consolidate priorities for those already identified.
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Affiliation(s)
- Eunus S. Ali
- Department of Medical Biochemistry, College of Medicine and Public Health, Flinders University, Adelaide 5001, South Australia, Australia;
| | - Grigori Y. Rychkov
- School of Medicine, The University of Adelaide, Adelaide 5005, South Australia, Australia;
- South Australian Health and Medical Research Institute, Adelaide 5005, South Australia, Australia
| | - Greg J. Barritt
- Department of Medical Biochemistry, College of Medicine and Public Health, Flinders University, Adelaide 5001, South Australia, Australia;
- Correspondence: ; Tel.: +61-438-204-426
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12
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Florou V, Rosenberg AE, Wieder E, Komanduri KV, Kolonias D, Uduman M, Castle JC, Buell JS, Trent JC, Wilky BA. Angiosarcoma patients treated with immune checkpoint inhibitors: a case series of seven patients from a single institution. J Immunother Cancer 2019; 7:213. [PMID: 31395100 PMCID: PMC6686562 DOI: 10.1186/s40425-019-0689-7] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/23/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Angiosarcoma is an uncommon endothelial malignancy and a highly aggressive soft tissue sarcoma. Due to its infiltrative nature, successful management of localized angiosarcoma is often challenging. Systemic chemotherapy is used in the metastatic setting and occasionally in patients with high-risk localized disease in neoadjuvant or adjuvant settings. However, responses tend to be short-lived and most patients succumb to metastatic disease. Novel therapies are needed for patients with angiosarcomas. METHODS We performed a retrospective analysis of patients with locally advanced or metastatic angiosarcoma, who were treated with checkpoint inhibitors at our institution. We collected their clinical information and outcome measurements. In one patient with achieved complete response, we analyzed circulating and infiltrating T cells within peripheral blood and tumor tissue. RESULTS We have treated seven angiosarcoma (AS) patients with checkpoint inhibitors either in the context of clinical trials or off label [Pembrolizumab + Axitinib (NCT02636725; n = 1), AGEN1884, a CTLA-4 inhibitor (NCT02694822; n = 2), Pembrolizumab (n = 4)]. Five patients had cutaneous angiosarcoma, one primary breast angiosarcoma and one radiation-associated breast angiosarcoma. At 12 weeks, 5/7 patients (71%) had partial response of their lesions either on imaging and/or clinical exam and two (29%) had progressive disease. 6/7 patients are alive to date and, thus far, 3/7 patients (43%) have progressed (median 3.4 months)- one achieved partial response after pembrolizumab was switched to ongoing Nivolumab/Ipilimumab, one died of progressive disease at 31 weeks (primary breast angiosarcoma) and one was placed on pazopanib. One patient had a complete response (CR) following extended treatment with monotherapy AGEN1884. No patient experienced any ≥ grade 2 toxicities. CONCLUSIONS This case series underscores the value of targeted immunotherapy in treating angiosarcoma. It also identifies genetic heterogeneity of cutaneous angiosarcomas and discusses specific genetic findings that may explain reported benefits from immunotherapy.
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Affiliation(s)
- Vaia Florou
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
| | - Andrew E. Rosenberg
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
| | - Eric Wieder
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
| | - Krishna V. Komanduri
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
| | - Despina Kolonias
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
| | | | | | | | - Jonathan C. Trent
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
| | - Breelyn A. Wilky
- Department of Medicine, Division of Oncology, Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, 1475 NW 12th Avenue, Miami, FL 33136 USA
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Sarathi A, Palaniappan A. Novel significant stage-specific differentially expressed genes in hepatocellular carcinoma. BMC Cancer 2019; 19:663. [PMID: 31277598 PMCID: PMC6612102 DOI: 10.1186/s12885-019-5838-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 06/16/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Liver cancer is among top deadly cancers worldwide with a very poor prognosis, and the liver is a vulnerable site for metastases of other cancers. Early diagnosis is crucial for treatment of the predominant liver cancers, namely hepatocellular carcinoma (HCC). Here we developed a novel computational framework for the stage-specific analysis of HCC. METHODS Using publicly available clinical and RNA-Seq data of cancer samples and controls and the AJCC staging system, we performed a linear modelling analysis of gene expression across all stages and found significant genome-wide changes in the log fold-change of gene expression in cancer samples relative to control. To identify genes that were stage-specific controlling for confounding differential expression in other stages, we developed a set of six pairwise contrasts between the stages and enforced a p-value threshold (< 0.05) for each such contrast. Genes were specific for a stage if they passed all the significance filters for that stage. The monotonicity of gene expression with cancer progression was analyzed with a linear model using the cancer stage as a numeric variable. RESULTS Our analysis yielded two stage-I specific genes (CA9, WNT7B), two stage-II specific genes (APOBEC3B, FAM186A), ten stage-III specific genes including DLG5, PARI, NCAPG2, GNMT and XRCC2, and 35 stage-IV specific genes including GABRD, PGAM2, PECAM1 and CXCR2P1. Overexpression of DLG5 was found to be tumor-promoting contrary to the cancer literature on this gene. Further, GABRD was found to be signifincantly monotonically upregulated across stages. Our work has revealed 1977 genes with significant monotonic patterns of expression across cancer stages. NDUFA4L2, CRHBP and PIGU were top genes with monotonic changes of expression across cancer stages that could represent promising targets for therapy. Comparison with gene signatures from the BCLC staging system identified two genes, HSP90AB1 and ARHGAP42. Gene set enrichment analysis indicated overrepresented pathways specific to each stage, notably viral infection pathways in HCC initiation. CONCLUSIONS Our study identified novel significant stage-specific differentially expressed genes which could enhance our understanding of the molecular determinants of hepatocellular carcinoma progression. Our findings could serve as biomarkers that potentially underpin diagnosis as well as pinpoint therapeutic targets.
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Affiliation(s)
- Arjun Sarathi
- Department of Bioengineering, School of Chemical and BioTechnology, SASTRA deemed University, Thanjavur, Tamil Nadu 613401 India
| | - Ashok Palaniappan
- Department of Bioinformatics, School of Chemical and BioTechnology, SASTRA deemed University, Thanjavur, Tamil Nadu 613401 India
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14
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Kovač U, Skubic C, Bohinc L, Rozman D, Režen T. Oxysterols and Gastrointestinal Cancers Around the Clock. Front Endocrinol (Lausanne) 2019; 10:483. [PMID: 31379749 PMCID: PMC6653998 DOI: 10.3389/fendo.2019.00483] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/03/2019] [Indexed: 12/24/2022] Open
Abstract
This review focuses on the role of oxidized sterols in three major gastrointestinal cancers (hepatocellular carcinoma, pancreatic, and colon cancer) and how the circadian clock affects the carcinogenesis by regulating the lipid metabolism and beyond. While each field of research (cancer, oxysterols, and circadian clock) is well-studied within their specialty, little is known about the intertwining mechanisms and how these influence the disease etiology in each cancer type. Oxysterols are involved in pathology of these cancers, but final conclusions about their protective or damaging effects are elusive, since the effect depends on the type of oxysterol, concentration, and the cell type. Oxysterol concentrations, the expression of key regulators liver X receptors (LXR), farnesoid X receptor (FXR), and oxysterol-binding proteins (OSBP) family are modulated in tumors and plasma of cancer patients, exposing these proteins and selected oxysterols as new potential biomarkers and drug targets. Evidence about how cholesterol/oxysterol pathways are intertwined with circadian clock is building. Identified key contact points are different forms of retinoic acid receptor related orphan receptors (ROR) and LXRs. RORs and LXRs are both regulated by sterols/oxysterols and the circadian clock and in return also regulate the same pathways, representing a complex interplay between sterol metabolism and the clock. With this in mind, in addition to classical therapies to modulate cholesterol in gastrointestinal cancers, such as the statin therapy, the time is ripe also for therapies where time and duration of the drug application is taken as an important factor for successful therapies. The final goal is the personalized approach with chronotherapy for disease management and treatment in order to increase the positive drug effects.
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15
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Personalized prediction of genes with tumor-causing somatic mutations based on multi-modal deep Boltzmann machine. Neurocomputing 2019. [DOI: 10.1016/j.neucom.2018.02.096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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Huang W, Skanderup AJ, Lee CG. Advances in genomic hepatocellular carcinoma research. Gigascience 2018; 7:5232228. [PMID: 30521023 PMCID: PMC6335342 DOI: 10.1093/gigascience/giy135] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/01/2018] [Indexed: 12/14/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the cancer with the second highest mortality in the world due to its late presentation and limited treatment options. As such, there is an urgent need to identify novel biomarkers for early diagnosis and to develop novel therapies. The availability of next-generation sequencing (NGS) data from tumors of liver cancer patients has provided us with invaluable resources to better understand HCC through the integration of data from different sources to facilitate the identification of promising biomarkers or therapeutic targets. Findings Here, we review key insights gleaned from more than 20 NGS studies of HCC tumor samples, comprising approximately 582 whole genomes and 1,211 whole exomes mainly from the East Asian population. Through consolidation of reported somatic mutations from multiple studies, we identified genes with different types of somatic mutations, including single nucleotide variations, insertion/deletions, structural variations, and copy number alterations as well as genes with multiple frequent viral integration. Pathway analysis showed that this curated list of somatic mutations is critically involved in cancer-related pathways, viral carcinogenesis, and signaling pathways. Lastly, we addressed the future directions of HCC research as more NGS datasets become available. Conclusions Our review is a comprehensive resource for the current NGS research in HCC, consolidating published articles, potential gene candidates, and their related biological pathways.
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Affiliation(s)
- Weitai Huang
- Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.,Graduate School of Integrative Sciences and Engineering, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 117456, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Anders Jacobsen Skanderup
- Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Caroline G Lee
- Graduate School of Integrative Sciences and Engineering, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 117456, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore.,Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Center Singapore, Singapore 169610, Singapore.,Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
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17
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Sullivan KM, Kenerson HL, Pillarisetty VG, Riehle KJ, Yeung RS. Precision oncology in liver cancer. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:285. [PMID: 30105235 DOI: 10.21037/atm.2018.06.14] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
With the widespread adoption of molecular profiling in clinical oncology practice, many physicians are faced with making therapeutic decisions based upon isolated genomic alterations. For example, epidermal growth factor receptor tyrosine kinase inhibitors (TKIs) are effective in EGFR-mutant non-small cell lung cancers (NSCLC) while anti-EGFR monoclonal antibodies are ineffective in Ras-mutant colorectal cancers. The matching of mutations with drugs aimed at their respective gene products represents the current state of "precision" oncology. Despite the great expectations of this approach, only a fraction of cancers responds to 'targeted' interventions, and many early responders will ultimately develop resistance to these agents. The underwhelming success of mutation-driven therapies across all cancer types is not due to an inability to detect genetic changes in tumors; rather a deficit in functional insight into the genomic alterations that give rise to each cancer. The Achilles heel of precision oncology thus remains the lack of a robust functional understanding of an individual cancer genome that then allows prediction of the best therapy and resultant outcome for that patient. Current practice focuses on one 'actionable' mutation at a time, while solid cancers typically possess many mutations that involve different cellular sub-populations within a tumor. No method or platform currently exists to guide the interpretation of these complex data, nor to accurately predict response to treatment. This problem is particularly germane to primary liver cancers (PLC), for which only a handful of targeted therapies have been introduced. Here, we will review strategies aimed at overcoming some of these challenges in precision oncology, using liver cancer as an example.
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Affiliation(s)
- Kevin M Sullivan
- Northwest Liver Research Program, Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Heidi L Kenerson
- Northwest Liver Research Program, Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Venu G Pillarisetty
- Northwest Liver Research Program, Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Kimberly J Riehle
- Northwest Liver Research Program, Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Raymond S Yeung
- Northwest Liver Research Program, Department of Surgery, University of Washington, Seattle, Washington, USA
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18
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Mao R, Liu J, Liu G, Jin S, Xue Q, Ma L, Fu Y, Zhao N, Xing J, Li L, Qiu Y, Lin B. Whole genome sequencing of matched tumor, adjacent non-tumor tissues and corresponding normal blood samples of hepatocellular carcinoma patients revealed dynamic changes of the mutations profiles during hepatocarcinogenesis. Oncotarget 2018; 8:26185-26199. [PMID: 28412734 DOI: 10.18632/oncotarget.15428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/01/2017] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) has become the third most deadly disease worldwide and HBV is the major factor in Asia and Africa. We conducted 9 WGS (whole genome sequencing) analyses for matched samples of tumor, adjacent non-tumor tissues and normal blood samples of HCC patients from three HBV positive patients. We then validated the mutations identified in a larger cohort of 177 HCC patients. We found that the number of the unique somatic mutations (average of 59,136) in tumor samples is significantly less than that in adjacent non-tumor tissues (average 83, 633). We discovered that the TP53 R249S mutation occurred in 7.7% of the HCC patients, and it was significantly associated with poor diagnosis. In addition, we found that the L104P mutation in the VCX gene (Variable charge, X-linked) was absent in white blood cell samples, but present at 11.1% frequency in the adjacent tissues and increased to 14.6% in HCC tissues, suggesting that this mutation might be a tumor driver gene driving HCC carcinogenesis. Finally, we identified a TK1-RNU7 fusion, which would result in a deletion of 103 amino acids from its C-terminal. The frequencies of this fusion event decreased from the adjacent tissues (29.2%) to the tumors (16.7%), suggesting that a truncated thymidine Kinase1 (TK1) caused by the fusion event might be deleterious and be selected against during tumor progression. The three-way comparisons allow the identification of potential driver mutations of carcinogenesis. Furthermore, our dataset provides the research community a valuable dataset for identifying dynamic changes of mutation profiles and driver mutations for HCC.
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Affiliation(s)
- Ruifang Mao
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P.R. China
| | - Jie Liu
- Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P.R. China
| | - Guanfeng Liu
- Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P.R. China
| | - Shanshan Jin
- Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P.R. China
| | - Qingzhong Xue
- Departmant of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
| | - Liang Ma
- Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P.R. China
| | - Yan Fu
- College of Animal Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Na Zhao
- Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P.R. China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, China
| | - Lanjuan Li
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yunqing Qiu
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Biaoyang Lin
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P.R. China.,Departmant of Urology, University of Washington, Seattle, WA, USA
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19
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Ao L, Song X, Li X, Tong M, Guo Y, Li J, Li H, Cai H, Li M, Guan Q, Yan H, Guo Z. An individualized prognostic signature and multi‑omics distinction for early stage hepatocellular carcinoma patients with surgical resection. Oncotarget 2018; 7:24097-110. [PMID: 27006471 PMCID: PMC5029687 DOI: 10.18632/oncotarget.8212] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 03/02/2016] [Indexed: 12/31/2022] Open
Abstract
Previously reported prognostic signatures for predicting the prognoses of postsurgical hepatocellular carcinoma (HCC) patients are commonly based on predefined risk scores, which are hardly applicable to samples measured by different laboratories. To solve this problem, using gene expression profiles of 170 stage I/II HCC samples, we identified a prognostic signature consisting of 20 gene pairs whose within-sample relative expression orderings (REOs) could robustly predict the disease-free survival and overall survival of HCC patients. This REOs-based prognostic signature was validated in two independent datasets. Functional enrichment analysis showed that the patients with high-risk of recurrence were characterized by the activations of pathways related to cell proliferation and tumor microenvironment, whereas the low-risk patients were characterized by the activations of various metabolism pathways. We further investigated the distinct epigenomic and genomic characteristics of the two prognostic groups using The Cancer Genome Atlas samples with multi-omics data. Epigenetic analysis showed that the transcriptional differences between the two prognostic groups were significantly concordant with DNA methylation alternations. The signaling network analysis identified several key genes (e.g. TP53, MYC) with epigenomic or genomic alternations driving poor prognoses of HCC patients. These results help us understand the multi-omics mechanisms determining the outcomes of HCC patients.
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Affiliation(s)
- Lu Ao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350001, China
| | - Xuekun Song
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Xiangyu Li
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350001, China
| | - Mengsha Tong
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350001, China
| | - You Guo
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350001, China
| | - Jing Li
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350001, China
| | - Hongdong Li
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350001, China
| | - Hao Cai
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350001, China
| | - Mengyao Li
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350001, China
| | - Qingzhou Guan
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350001, China
| | - Haidan Yan
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350001, China
| | - Zheng Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350001, China
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20
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Zhuang X, Rambhatla SB, Lai AG, McKeating JA. Interplay between circadian clock and viral infection. J Mol Med (Berl) 2017; 95:1283-1289. [PMID: 28963570 PMCID: PMC5684296 DOI: 10.1007/s00109-017-1592-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 08/12/2017] [Accepted: 09/11/2017] [Indexed: 12/20/2022]
Abstract
The circadian clock underpins most physiological conditions and provides a temporal dimension to our understanding of body and tissue homeostasis. Disruptions of circadian rhythms have been associated with many diseases, including metabolic disorders and cancer. Recent literature highlights a role for the circadian clock to regulate innate and adaptive immune functions that may prime the host response to infectious organisms. Viruses are obligate parasites that rely on host cell synthesis machinery for their own replication, survival and dissemination. Here, we review key findings on how circadian rhythms impact viral infection and how viruses modulate molecular clocks to facilitate their own replication. This emerging area of viral-clock biology research provides a fertile ground for discovering novel anti-viral targets and optimizing immune-based therapies.
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Affiliation(s)
- Xiaodong Zhuang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | | | - Alvina G Lai
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jane A McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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21
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Khemlina G, Ikeda S, Kurzrock R. The biology of Hepatocellular carcinoma: implications for genomic and immune therapies. Mol Cancer 2017; 16:149. [PMID: 28854942 PMCID: PMC5577674 DOI: 10.1186/s12943-017-0712-x] [Citation(s) in RCA: 261] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/15/2017] [Indexed: 02/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC), the most common type of primary liver cancer, is a leading cause of cancer-related death worldwide. It is highly refractory to most systemic therapies. Recently, significant progress has been made in uncovering genomic alterations in HCC, including potentially targetable aberrations. The most common molecular anomalies in this malignancy are mutations in the TERT promoter, TP53, CTNNB1, AXIN1, ARID1A, CDKN2A and CCND1 genes. PTEN loss at the protein level is also frequent. Genomic portfolios stratify by risk factors as follows: (i) CTNNB1 with alcoholic cirrhosis; and (ii) TP53 with hepatitis B virus-induced cirrhosis. Activating mutations in CTNNB1 and inactivating mutations in AXIN1 both activate WNT signaling. Alterations in this pathway, as well as in TP53 and the cell cycle machinery, and in the PI3K/Akt/mTor axis (the latter activated in the presence of PTEN loss), as well as aberrant angiogenesis and epigenetic anomalies, appear to be major events in HCC. Many of these abnormalities may be pharmacologically tractable. Immunotherapy with checkpoint inhibitors is also emerging as an important treatment option. Indeed, 82% of patients express PD-L1 (immunohistochemistry) and response rates to anti-PD-1 treatment are about 19%, and include about 5% complete remissions as well as durable benefit in some patients. Biomarker-matched trials are still limited in this disease, and many of the genomic alterations in HCC remain challenging to target. Future studies may require combination regimens that include both immunotherapies and molecularly matched targeted treatments.
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Affiliation(s)
- Galina Khemlina
- Department of Geriatrics, University of California, UC San Diego, 9500 Gilman Drive, #9111, La Jolla, CA, 92093-9111, USA. .,Kaiser Permanente Southern California, San Diego, USA.
| | - Sadakatsu Ikeda
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, San Diego, USA.,Tokyo Medical and Dental University, Tokyo, Japan
| | - Razelle Kurzrock
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, San Diego, USA
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22
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Zhang W, Hong R, Xue L, Ou Y, Liu X, Zhao Z, Xiao W, Dong D, Dong L, Fu M, Ma L, Lu N, Chen H, Song Y, Zhan Q. Piccolo mediates EGFR signaling and acts as a prognostic biomarker in esophageal squamous cell carcinoma. Oncogene 2017; 36:3890-3902. [PMID: 28263981 DOI: 10.1038/onc.2017.15] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 02/07/2023]
Abstract
The presynaptic cytomatrix protein Piccolo, encoded by PCLO, is frequently mutated and amplified in esophageal squamous cell carcinoma (ESCC), but its exact roles in ESCC remain unclear. Here we report that Piccolo expression correlates significantly with clinical stage, patient survival and tumor embolus. Functional studies demonstrate that PCLO knockdown remarkably attenuates ESCC malignancy in vitro and in vivo, and ectopic EGFR expression partially compensates for Piccolo loss. PCLO knockdown promotes ubiquitination and degradation of EGFR, which is associated with the negative regulatory effect of Piccolo on E3 ligase Siah1. An anti-Piccolo monoclonal antibody inhibited tumor proliferation in a mouse model of ESCC. These results demonstrate that Piccolo contributes to tumor aggressiveness in ESCC, likely by stabilizing EGFR and promoting EGFR-dependent signaling. Our results further suggest that Piccolo may represent a novel prognostic biomarker and therapeutic target for patients with ESCC.
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Affiliation(s)
- W Zhang
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Sichuan, China.,Guangdong Koheala Precision Medicine Institute, Guangzhou, China
| | - R Hong
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - L Xue
- Department of Pathology, Cancer Institute and Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Y Ou
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Neurosurgery, Tiantan Hospital, Capital Medical University, Beijing, China
| | - X Liu
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Z Zhao
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - W Xiao
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - D Dong
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - L Dong
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - M Fu
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - L Ma
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - N Lu
- Department of Pathology, Cancer Institute and Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - H Chen
- Guangdong Koheala Precision Medicine Institute, Guangzhou, China
| | - Y Song
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Q Zhan
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Sichuan, China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital &Institute, Beijing, China
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23
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Niu ZS, Niu XJ, Wang WH. Genetic alterations in hepatocellular carcinoma: An update. World J Gastroenterol 2016; 22:9069-9095. [PMID: 27895396 PMCID: PMC5107590 DOI: 10.3748/wjg.v22.i41.9069] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/20/2016] [Accepted: 10/19/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Although recent advances in therapeutic approaches for treating HCC have improved the prognoses of patients with HCC, this cancer is still associated with a poor survival rate mainly due to late diagnosis. Therefore, a diagnosis must be made sufficiently early to perform curative and effective treatments. There is a need for a deeper understanding of the molecular mechanisms underlying the initiation and progression of HCC because these mechanisms are critical for making early diagnoses and developing novel therapeutic strategies. Over the past decade, much progress has been made in elucidating the molecular mechanisms underlying hepatocarcinogenesis. In particular, recent advances in next-generation sequencing technologies have revealed numerous genetic alterations, including recurrently mutated genes and dysregulated signaling pathways in HCC. A better understanding of the genetic alterations in HCC could contribute to identifying potential driver mutations and discovering novel therapeutic targets in the future. In this article, we summarize the current advances in research on the genetic alterations, including genomic instability, single-nucleotide polymorphisms, somatic mutations and deregulated signaling pathways, implicated in the initiation and progression of HCC. We also attempt to elucidate some of the genetic mechanisms that contribute to making early diagnoses of and developing molecularly targeted therapies for HCC.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Genomic Instability
- Humans
- Liver Neoplasms/drug therapy
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Molecular Diagnostic Techniques
- Molecular Targeted Therapy
- Mutation
- Patient Selection
- Phenotype
- Polymorphism, Single Nucleotide
- Precision Medicine
- Predictive Value of Tests
- Signal Transduction
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24
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Liu J, Hua P, Hui L, Zhang LL, Hu Z, Zhu YW. Identification of hub genes and pathways associated with hepatocellular carcinoma based on network strategy. Exp Ther Med 2016; 12:2109-2119. [PMID: 27703495 PMCID: PMC5039750 DOI: 10.3892/etm.2016.3599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/05/2016] [Indexed: 12/11/2022] Open
Abstract
The objective of this study was to identify hub genes and pathways associated with hepatocellular carcinoma (HCC) by centrality analysis of a co-expression network. A co-expression network based on differentially expressed (DE) genes of HCC was constructed using the Differentially Co-expressed Genes and Links (DCGL) package. Centrality analyses, for centrality of degree, clustering coefficient, closeness, stress and betweenness for the co-expression network were performed to identify hub genes, and the hub genes were combined together to overcome inconsistent results. Enrichment analyses were conducted using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. Finally, validation of hub genes was conducted utilizing reverse transcription-polymerase chain reaction (RT-PCR) analysis. In total, 260 DE genes between normal controls and HCC patients were obtained and a co-expression network with 154 nodes and 326 edges was constructed. From this, 13 hub genes were identified according to degree, clustering coefficient, closeness, stress and betweenness centrality analysis. It was found that reelin (RELN), potassium voltage-gated channel subfamily J member 10 (KCNJ10) and neural cell adhesion molecule 1 (NCAM1) were common hub genes across the five centralities, and the results of RT-PCR analysis for RELN, KCNJ10 and NCAM1 were consistent with the centrality analyses. Pathway enrichment analysis of DE genes showed that cell cycle, metabolism of xenobiotics by cytochrome P450 and p53 signaling pathway were the most significant pathways. This study may contribute to understanding the molecular pathogenesis of HCC and provide potential biomarkers for its early detection and effective therapies.
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Affiliation(s)
- Jun Liu
- Department of Radiology, Wuxi Second Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
| | - Ping Hua
- Department of Internal Medicine, Wuxi Second Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
| | - Li Hui
- Department of Internal Medicine, Wuxi Second Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
| | - Li-Li Zhang
- Department of Internal Medicine, Wuxi Second Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
| | - Zhen Hu
- Department of Internal Medicine, Wuxi Second Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
| | - Ying-Wei Zhu
- Department of Internal Medicine, Wuxi Second Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
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25
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Peveling-Oberhag J, Wolters F, Döring C, Walter D, Sellmann L, Scholtysik R, Lucioni M, Schubach M, Paulli M, Biskup S, Zeuzem S, Küppers R, Hansmann ML. Whole exome sequencing of microdissected splenic marginal zone lymphoma: a study to discover novel tumor-specific mutations. BMC Cancer 2015; 15:773. [PMID: 26498442 PMCID: PMC4619476 DOI: 10.1186/s12885-015-1766-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 10/10/2015] [Indexed: 12/14/2022] Open
Abstract
Background Splenic marginal zone lymphoma (SMZL) is an indolent B-cell non-Hodgkin lymphoma and represents the most common primary malignancy of the spleen. Its precise molecular pathogenesis is still unknown and specific molecular markers for diagnosis or possible targets for causal therapies are lacking. Methods We performed whole exome sequencing (WES) and copy number analysis from laser-microdissected tumor cells of two primary SMZL discovery cases. Selected somatic single nucleotide variants (SNVs) were analyzed using pyrosequencing and Sanger sequencing in an independent validation cohort. Results Overall, 25 nonsynonymous somatic SNVs were identified, including known mutations in the NOTCH2 and MYD88 genes. Twenty-three of the mutations have not been associated with SMZL before. Many of these seem to be subclonal. Screening of 24 additional SMZL for mutations at the same positions found mutated in the WES approach revealed no recurrence of mutations for ZNF608 and PDE10A, whereas the MYD88 L265P missense mutation was identified in 15 % of cases. An analysis of the NOTCH2 PEST domain and the whole coding region of the transcription factor SMYD1 in eight cases identified no additional case with a NOTCH2 mutation, but two additional cases with SMYD1 alterations. Conclusions In this first WES approach from microdissected SMZL tissue we confirmed known mutations and discovered new somatic variants. Recurrence of MYD88 mutations in SMZL was validated, but NOTCH2 PEST domain mutations were relatively rare (10 % of cases). Recurrent mutations in the transcription factor SMYD1 have not been described in SMZL before and warrant further investigation. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1766-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jan Peveling-Oberhag
- Medizinische Klinik 1, Klinikum der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany.
| | - Franziska Wolters
- Medizinische Klinik 1, Klinikum der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany.
| | - Claudia Döring
- Senckenbergisches Institut für Pathologie, Klinikum der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany.
| | - Dirk Walter
- Medizinische Klinik 1, Klinikum der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany.
| | - Ludger Sellmann
- Institute of Cell Biology (Cancer Research), Medical School, University of Duisburg-Essen, Essen, Germany.
| | - René Scholtysik
- Institute of Cell Biology (Cancer Research), Medical School, University of Duisburg-Essen, Essen, Germany.
| | - Marco Lucioni
- Department of Human Pathology, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy.
| | - Max Schubach
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, Germany.
| | - Marco Paulli
- Department of Human Pathology, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy.
| | - Saskia Biskup
- CeGaT GmbH, Paul-Ehrlich-Straße 23, Tübingen, Germany.
| | - Stefan Zeuzem
- Medizinische Klinik 1, Klinikum der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany.
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical School, University of Duisburg-Essen, Essen, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Martin-Leo Hansmann
- Senckenbergisches Institut für Pathologie, Klinikum der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.
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26
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Ferrín G, Aguilar-Melero P, Rodríguez-Perálvarez M, Montero-Álvarez JL, de la Mata M. Biomarkers for hepatocellular carcinoma: diagnostic and therapeutic utility. Hepat Med 2015; 7:1-10. [PMID: 25926760 PMCID: PMC4403743 DOI: 10.2147/hmer.s50161] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Because of the high prevalence and associated-mortality of hepatocellular carcinoma (HCC), early diagnosis of the disease is vital for patient survival. In this regard, tumor size is one of the two main prognostic factors for surgical resection, which constitutes the only curative treatment for HCC along with liver transplantation. However, techniques for HCC surveillance and diagnosis that are currently used in clinical practice have certain limitations that may be inherent to the tumor development. Thus, it is important to continue efforts in the search for biomarkers that increase diagnostic accuracy for HCC. In this review, we focus on different biological sources of candidate biomarkers for HCC diagnosis. Although those biomarkers identified from biological samples obtained by noninvasive methods have greater diagnostic value, we have also considered those obtained from liver tissue because of their potential therapeutic value. To date, sorafenib is the only US Food and Drug Administration-approved antineoplastic for HCC. However, this therapeutic agent shows very low tumor response rates and frequently causes acquired resistance in HCC patients. We discuss the use of HCC biomarkers as therapeutic targets themselves, or as targets to increase sensitivity to sorafenib treatment.
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Affiliation(s)
- Gustavo Ferrín
- Liver Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Córdoba, Spain ; Centro de Investigación Biomédica en Red (CIBER), Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid, Spain
| | - Patricia Aguilar-Melero
- Liver Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Manuel Rodríguez-Perálvarez
- Liver Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Córdoba, Spain ; Centro de Investigación Biomédica en Red (CIBER), Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid, Spain
| | - José Luis Montero-Álvarez
- Liver Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Córdoba, Spain ; Centro de Investigación Biomédica en Red (CIBER), Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid, Spain
| | - Manuel de la Mata
- Liver Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Córdoba, Spain ; Centro de Investigación Biomédica en Red (CIBER), Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid, Spain
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27
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Li W, Yu J, Lian B, Sun H, Li J, Zhang M, Li L, Li Y, Liu Q, Xie L. Identifying prognostic features by bottom-up approach and correlating to drug repositioning. PLoS One 2015; 10:e0118672. [PMID: 25738841 PMCID: PMC4349868 DOI: 10.1371/journal.pone.0118672] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/22/2015] [Indexed: 12/31/2022] Open
Abstract
Background Traditionally top-down method was used to identify prognostic features in cancer research. That is to say, differentially expressed genes usually in cancer versus normal were identified to see if they possess survival prediction power. The problem is that prognostic features identified from one set of patient samples can rarely be transferred to other datasets. We apply bottom-up approach in this study: survival correlated or clinical stage correlated genes were selected first and prioritized by their network topology additionally, then a small set of features can be used as a prognostic signature. Methods Gene expression profiles of a cohort of 221 hepatocellular carcinoma (HCC) patients were used as a training set, ‘bottom-up’ approach was applied to discover gene-expression signatures associated with survival in both tumor and adjacent non-tumor tissues, and compared with ‘top-down’ approach. The results were validated in a second cohort of 82 patients which was used as a testing set. Results Two sets of gene signatures separately identified in tumor and adjacent non-tumor tissues by bottom-up approach were developed in the training cohort. These two signatures were associated with overall survival times of HCC patients and the robustness of each was validated in the testing set, and each predictive performance was better than gene expression signatures reported previously. Moreover, genes in these two prognosis signature gave some indications for drug-repositioning on HCC. Some approved drugs targeting these markers have the alternative indications on hepatocellular carcinoma. Conclusion Using the bottom-up approach, we have developed two prognostic gene signatures with a limited number of genes that associated with overall survival times of patients with HCC. Furthermore, prognostic markers in these two signatures have the potential to be therapeutic targets.
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Affiliation(s)
- Wei Li
- Key Laboratory of Biomedical Photonics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Jian Yu
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
| | - Baofeng Lian
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai, 200240, P. R. China
| | - Han Sun
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, 200031, P. R. China
| | - Jing Li
- Key Laboratory of Biomedical Photonics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Menghuan Zhang
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai, 200240, P. R. China
| | - Ling Li
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
| | - Yixue Li
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai, 200240, P. R. China
- Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, 200031, P. R. China
| | - Qian Liu
- Key Laboratory of Biomedical Photonics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- * E-mail: (LX); (QL)
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- * E-mail: (LX); (QL)
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