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Han J, Thurnherr T, Chung AYF, Goh BKP, Chow PKH, Chan CY, Cheow PC, Lee SY, Lim TKH, Chong SS, Ooi LLPJ, Lee CG. Clinicopathological-Associated Regulatory Network of Deregulated circRNAs in Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13112772. [PMID: 34199580 PMCID: PMC8199648 DOI: 10.3390/cancers13112772] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/01/2023] Open
Abstract
Simple Summary Here, we present a novel strategy to identify key signatures of clinically-relevant co-expressed circRNA-mRNA networks in pertinent cancer-pathways that modulate the prognosis of HCC patients, by integrating clinicopathological features, circRNA and mRNA expression profiles. Five master circRNAs were identified and experimentally demonstrated to upregulate proliferate and promote transformation. Through further integration with miRNA-expression profiles, clinically-relevant competing-endogenous-RNA (ceRNA) networks of circRNA-miRNA-mRNAs were constructed. The most up-regulated nodal-circRNA, circGPC3 was experimentally demonstrated to up-regulate cell-cycle, migration and invasion. circGPC3 was found to act as a sponge of miR-378a-3p to regulate ASPM expression and modulate cell transformation. These 5 nodal circRNAs has potential to be good prognostic biomarkers with good prognostic performance. circGPC3 has great potential to be a promising non-invasive prognostic biomarker for early HCC. We have thus demonstrated the robustness of bioinformatically-predicted master circRNAs in clinically-relevant, circRNA-mRNA networks, underscoring the important roles that these identified deregulated key/master circRNAs play in HCC. Abstract Hepatocellular carcinoma (HCC) is one of the most common and lethal cancers worldwide. Here, we present a novel strategy to identify key circRNA signatures of clinically relevant co-expressed circRNA-mRNA networks in pertinent cancer-pathways that modulate prognosis of HCC patients, by integrating clinic-pathological features, circRNA and mRNA expression profiles. Through further integration with miRNA expression profiles, clinically relevant competing-endogenous-RNA (ceRNA) networks of circRNA-miRNA-mRNAs were constructed. At least five clinically relevant nodal-circRNAs, co-expressed with numerous genes, were identified from the circRNA-mRNA networks. These nodal circRNAs upregulated proliferation (except circRaly) and transformation in cells. The most upregulated nodal-circRNA, circGPC3, associated with higher-grade tumors and co-expressed with 33 genes, competes with 11 mRNAs for two shared miRNAs. circGPC3 was experimentally demonstrated to upregulate cell-cycle and migration/invasion in both transformed and non-transformed liver cell-lines. circGPC3 was further shown to act as a sponge of miR-378a-3p to regulate APSM (Abnormal spindle-like microcephaly associated) expression and modulate cell transformation. This study identifies 5 key nodal master circRNAs in a clinically relevant circRNA-centric network that are significantly associated with poorer prognosis of HCC patients and promotes tumorigenesis in cell-lines. The identification and characterization of these key circRNAs in clinically relevant circRNA-mRNA and ceRNA networks may facilitate the design of novel strategies targeting these important regulators for better HCC prognosis.
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Affiliation(s)
- Jian Han
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
| | - Thomas Thurnherr
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore;
| | - Alexander Y. F. Chung
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Brian K. P. Goh
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Pierce K. H. Chow
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
- Department of Surgical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Chung Yip Chan
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Peng Chung Cheow
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Ser Yee Lee
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Tony K. H. Lim
- Department of Pathology, Singapore General Hospital, Singapore 169608, Singapore;
| | - Samuel S. Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
| | - London L. P. J. Ooi
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
- Department of Surgical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Caroline G. Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore;
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Level 6, Lab 5, 11 Hospital Drive, Singapore 169610, Singapore
- Correspondence: ; Tel.: +65-65163251
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2
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Singer F, Irmisch A, Toussaint NC, Grob L, Singer J, Thurnherr T, Beerenwinkel N, Levesque MP, Dummer R, Quagliata L, Rothschild SI, Wicki A, Beisel C, Stekhoven DJ. SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics. BMC Med Inform Decis Mak 2018; 18:89. [PMID: 30373609 PMCID: PMC6206832 DOI: 10.1186/s12911-018-0680-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 10/18/2018] [Indexed: 12/18/2022] Open
Abstract
Background Molecular precision oncology is an emerging practice to improve cancer therapy by decreasing the risk of choosing treatments that lack efficacy or cause adverse events. However, the challenges of integrating molecular profiling into routine clinical care are manifold. From a computational perspective these include the importance of a short analysis turnaround time, the interpretation of complex drug-gene and gene-gene interactions, and the necessity of standardized high-quality workflows. In addition, difficulties faced when integrating molecular diagnostics into clinical practice are ethical concerns, legal requirements, and limited availability of treatment options beyond standard of care as well as the overall lack of awareness of their existence. Methods To the best of our knowledge, we are the first group in Switzerland that established a workflow for personalized diagnostics based on comprehensive high-throughput sequencing of tumors at the clinic. Our workflow, named SwissMTB (Swiss Molecular Tumor Board), links genetic tumor alterations and gene expression to therapeutic options and clinical trial opportunities. The resulting treatment recommendations are summarized in a clinical report and discussed in a molecular tumor board at the clinic to support therapy decisions. Results Here we present results from an observational pilot study including 22 late-stage cancer patients. In this study we were able to identify actionable variants and corresponding therapies for 19 patients. Half of the patients were analyzed retrospectively. In two patients we identified resistance-associated variants explaining lack of therapy response. For five out of eleven patients analyzed before treatment the SwissMTB diagnostic influenced treatment decision. Conclusions SwissMTB enables the analysis and clinical interpretation of large numbers of potentially actionable molecular targets. Thus, our workflow paves the way towards a more frequent use of comprehensive molecular diagnostics in Swiss hospitals. Electronic supplementary material The online version of this article (10.1186/s12911-018-0680-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Franziska Singer
- NEXUS Personalized Health Technologies, ETH Zurich, Otto-Stern-Weg 7, 8093, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Anja Irmisch
- Department of Dermatology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Nora C Toussaint
- NEXUS Personalized Health Technologies, ETH Zurich, Otto-Stern-Weg 7, 8093, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Linda Grob
- NEXUS Personalized Health Technologies, ETH Zurich, Otto-Stern-Weg 7, 8093, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Jochen Singer
- SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Thomas Thurnherr
- SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Niko Beerenwinkel
- SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Luca Quagliata
- Department of Pathology, University Hospital Basel, Schönbeinstrasse 40, 4056, Basel, Switzerland
| | - Sacha I Rothschild
- Division of Oncology, Department of Biomedicine, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Andreas Wicki
- Division of Oncology, Department of Biomedicine, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Daniel J Stekhoven
- NEXUS Personalized Health Technologies, ETH Zurich, Otto-Stern-Weg 7, 8093, Zurich, Switzerland. .,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland.
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3
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Singer J, Ruscheweyh HJ, Hofmann AL, Thurnherr T, Singer F, Toussaint NC, Ng CKY, Piscuoglio S, Beisel C, Christofori G, Dummer R, Hall MN, Krek W, Levesque MP, Manz MG, Moch H, Papassotiropoulos A, Stekhoven DJ, Wild P, Wüst T, Rinn B, Beerenwinkel N. NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis. Bioinformatics 2018; 34:107-108. [PMID: 28968639 PMCID: PMC5870795 DOI: 10.1093/bioinformatics/btx540] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/26/2017] [Indexed: 01/07/2023] Open
Abstract
Motivation Next-generation sequencing is now an established method in genomics, and massive amounts of sequencing data are being generated on a regular basis. Analysis of the sequencing data is typically performed by lab-specific in-house solutions, but the agreement of results from different facilities is often small. General standards for quality control, reproducibility and documentation are missing. Results We developed NGS-pipe, a flexible, transparent and easy-to-use framework for the design of pipelines to analyze whole-exome, whole-genome and transcriptome sequencing data. NGS-pipe facilitates the harmonization of genomic data analysis by supporting quality control, documentation, reproducibility, parallelization and easy adaptation to other NGS experiments. Availability and implementation https://github.com/cbg-ethz/NGS-pipe
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Affiliation(s)
- Jochen Singer
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland.,Scientific IT Services, ETH Zurich, Basel, Switzerland
| | - Ariane L Hofmann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Thomas Thurnherr
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Franziska Singer
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland.,NEXUS Personalized Health Technologies, Zurich, Switzerland
| | - Nora C Toussaint
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland.,NEXUS Personalized Health Technologies, Zurich, Switzerland
| | - Charlotte K Y Ng
- Department of Biomedicine, University of Basel, Basel, Switzerland.,Institute of Pathology.,Division of Gastroenterology and Hepatology, University Hospital Basel, Basel, Switzerland
| | | | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Reinhard Dummer
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | | | - Wilhelm Krek
- Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Markus G Manz
- Division of Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Andreas Papassotiropoulos
- Division of Molecular Neuroscience, Department of Psychology.,Transfaculty Research Platform Molecular and Cognitive Neurosciences.,Psychiatric University Clinics University of Basel, Basel, Switzerland.,Department Biozentrum, Life Sciences Training Facility, University of Basel, Basel, Switzerland
| | - Daniel J Stekhoven
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland.,NEXUS Personalized Health Technologies, Zurich, Switzerland
| | - Peter Wild
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Thomas Wüst
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland.,Scientific IT Services, ETH Zurich, Basel, Switzerland
| | - Bernd Rinn
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland.,Scientific IT Services, ETH Zurich, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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4
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Abstract
Annotation and interpretation of DNA aberrations identified through next-generation sequencing is becoming an increasingly important task. Even more so in the context of data analysis pipelines for medical applications, where genomic aberrations are associated with phenotypic and clinical features. Here we describe a workflow to identify potential gene targets in aberrated genes or pathways and their corresponding drugs. To this end, we provide the R/Bioconductor package rDGIdb, an R wrapper to query the drug-gene interaction database (DGIdb). DGIdb accumulates drug-gene interaction data from 15 different resources and allows filtering on different levels. The rDGIdb package makes these resources and tools available to R users. Moreover, rDGIdb queries can be automated through incorporation of the rDGIdb package into NGS sequencing pipelines.
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Affiliation(s)
- Thomas Thurnherr
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Franziska Singer
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich, Switzerland
| | - Daniel J. Stekhoven
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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5
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Abstract
Annotation and interpretation of DNA aberrations identified through next-generation sequencing is becoming an increasingly important task. Even more so in the context of data analysis pipelines for medical applications, where genomic aberrations are associated with phenotypic and clinical features. Here we describe a workflow to identify potential gene targets in aberrated genes or pathways and their corresponding drugs. To this end, we provide the R/Bioconductor package rDGIdb, an R wrapper to query the drug-gene interaction database (DGIdb). DGIdb accumulates drug-gene interaction data from 15 different source databases and allows filtering on different levels. The rDGIdb package makes these resources and tools available to R users. Moreover, DGIdb queries can be automated through incorporation of the rDGIdb package into NGS sequencing pipelines.
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Affiliation(s)
- Thomas Thurnherr
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Franziska Singer
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland; NEXUS Personalized Health Technologies, ETH Zurich, Zurich, Switzerland
| | - Daniel J Stekhoven
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland; NEXUS Personalized Health Technologies, ETH Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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6
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Chan C, Thurnherr T, Wang J, Gallart-Palau X, Sze SK, Rozen S, Lee CG. Global re-wiring of p53 transcription regulation by the hepatitis B virus X protein. Mol Oncol 2016; 10:1183-95. [PMID: 27302019 DOI: 10.1016/j.molonc.2016.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The tumour suppressor p53 is a central player in transcription regulation and cell fate determination. By interacting with p53 and altering its sequence-specific binding to the response elements, the hepatitis B virus X protein (HBx) was reported to re-direct p53 regulation of some genes. RESULTS Coupling massively parallel deep sequencing with p53 chromatin immunoprecipitation, we demonstrate that HBx modulates global p53 site selection and that this was strongly influenced by altered interaction with transcription co-factors/co-regulators as well as post-translational modifications. Specifically, HBx attenuated p53-TBP-RB1 transcription complex recruitment and interaction and this was associated with hyper-phosphorylation of p53 at serine 315 by HBx. Concurrently, HBx enhanced p53 DNA occupancy to other response elements either alone by displacing specific transcription factors such as CEBPB and NFkB1, or in complex with distinct interacting co-factors Sp1, JUN and E2F1. Importantly, re-wiring of p53 transcription regulation by HBx was linked to the deregulation of genes involved in cell proliferation and death, suggesting a role of HBx in errant cell fate determination mediated by altered p53 site selection of target genes. CONCLUSIONS Our study thus presents first evidence of global modes of p53 transcription alteration by HBx and provides new insights to understand and potentially curtail the viral oncoprotein.
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Affiliation(s)
- Cheryl Chan
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore 169610, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore
| | - Thomas Thurnherr
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore; Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Jingbo Wang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Xavier Gallart-Palau
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Steve Rozen
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Caroline G Lee
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore 169610, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore; Duke-NUS Graduate Medical School, Singapore 169857, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
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7
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Thurnherr T, Mah WC, Lei Z, Jin Y, Rozen SG, Lee CG. Differentially Expressed miRNAs in Hepatocellular Carcinoma Target Genes in the Genetic Information Processing and Metabolism Pathways. Sci Rep 2016; 6:20065. [PMID: 26817861 PMCID: PMC4730185 DOI: 10.1038/srep20065] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/01/2015] [Indexed: 12/11/2022] Open
Abstract
To date, studies of the roles of microRNAs (miRNAs) in hepatocellular carcinoma (HCC) have either focused on specific individual miRNAs and a small number of suspected targets or simply reported a list of differentially expressed miRNAs based on expression profiling. Here, we seek a more in-depth understanding of the roles of miRNAs and their targets in HCC by integrating the miRNA and messenger RNA (mRNA) expression profiles of tumorous and adjacent non-tumorous liver tissues of 100 HCC patients. We assessed the levels of 829 mature miRNAs, of which 32 were significantly differentially expressed. Statistical analysis indicates that six of these miRNAs regulate a significant proportion of their in silico predicted target mRNAs. Three of these miRNAs (miR-26a, miR-122, and miR-130a) were down-regulated in HCC, and their up-regulated gene targets are primarily associated with aberrant cell proliferation that involves DNA replication, transcription and nucleotide metabolism. The other three miRNAs (miR-21, miR-93, and miR-221) were up-regulated in HCC, and their down-regulated gene targets are primarily involved in metabolism and immune system processes. We further found evidence for a coordinated miRNA-induced regulation of important cellular processes, a finding to be considered when designing therapeutic applications based on miRNAs.
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Affiliation(s)
- Thomas Thurnherr
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Way-Champ Mah
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Zhengdeng Lei
- Program in Neuroscience and Behavioural Disorders, Duke-NUS Graduate Medical School, Singapore
| | - Yu Jin
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Steven G. Rozen
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
| | - Caroline G. Lee
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore 169610, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
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Mah WC, Thurnherr T, Chow PKH, Chung AYF, Ooi LLPJ, Toh HC, Teh BT, Saunthararajah Y, Lee CGL. Correction: Methylation Profiles Reveal Distinct Subgroup of Hepatocellular Carcinoma Patients with Poor Prognosis. PLoS One 2016; 11:e0146690. [PMID: 26751067 PMCID: PMC4713443 DOI: 10.1371/journal.pone.0146690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Mah WC, Thurnherr T, Chow PKH, Chung AYF, Ooi LLPJ, Toh HC, Teh BT, Saunthararajah Y, Lee CGL. Methylation profiles reveal distinct subgroup of hepatocellular carcinoma patients with poor prognosis. PLoS One 2014; 9:e104158. [PMID: 25093504 PMCID: PMC4122406 DOI: 10.1371/journal.pone.0104158] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/05/2014] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular Carcinoma (HCC) is one of the leading causes of cancer-associated mortality worldwide. However, the role of epigenetic changes such as aberrant DNA methylation in hepatocarcinogenesis remains largely unclear. In this study, we examined the methylation profiles of 59 HCC patients. Using consensus hierarchical clustering with feature selection, we identified three tumor subgroups based on their methylation profiles and correlated these subgroups with clinicopathological parameters. Interestingly, one tumor subgroup is different from the other 2 subgroups and the methylation profile of this subgroup is the most distinctly different from the non-tumorous liver tissues. Significantly, this subgroup of patients was found to be associated with poor overall as well as disease-free survival. To further understand the pathways modulated by the deregulation of methylation in HCC patients, we integrated data from both the methylation as well as the gene expression profiles of these 59 HCC patients. In these patients, while 4416 CpG sites were differentially methylated between the tumors compared to the adjacent non-tumorous tissues, only 536 of these CpG sites were associated with differences in the expression of their associated genes. Pathway analysis revealed that forty-four percent of the most significant upstream regulators of these 536 genes were involved in inflammation-related NFκB pathway. These data suggest that inflammation via the NFκB pathway play an important role in modulating gene expression of HCC patients through methylation. Overall, our analysis provides an understanding on aberrant methylation profile in HCC patients.
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Affiliation(s)
- Way-Champ Mah
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - Thomas Thurnherr
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Pierce K. H. Chow
- Duke-NUS Graduate Medical School, Singapore, Singapore
- Department of Surgery, Singapore General Hospital, Singapore, Singapore
| | | | - London L. P. J. Ooi
- Department of Surgery, Singapore General Hospital, Singapore, Singapore
- Department of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Han Chong Toh
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Bin Tean Teh
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yogen Saunthararajah
- Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Caroline G. L. Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
- * E-mail:
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Abstract
Traditionally, the population of human embryonic stem cell (hESC) culture is estimated through haemacytometer counts, which include harvesting the cells and manually analyzing a fraction of an entire population. Obviously, through this highly invasive method, it is not possible to preserve any spatial information on the cell population. The goal of this study is to identify a fast and consistent method for in situ automated hESC population estimation to quantitatively estimate the cell growth. Therefore, cell cultures were fixed, stained, and their nuclei imaged through high-resolution microscopy, and the images were processed with different image analysis techniques. The proposed method first identifies signal and background by computing an image specific threshold for image segmentation. By applying a morphological operator (watershed), we split most physically overlapping nuclei, leading to a pixel area distribution of isolated signal areas on the image. On the basis of this distribution, we derive a nucleus area model, describing the distribution of the area of cell debris, single nuclei, and small groups of connected nuclei. Through the model, we can give a quantitative estimation of the population. The focus of this study is on low-density human embryonic stem cell populations; hence cultures were measured at days 2-3 after seeding. Compared with manual cell counts, the automatic method achieved higher accuracy with <6% error.
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Affiliation(s)
- Thomas Thurnherr
- Stem Cell Group, Bioprocessing Technology Institute, Biomedical Sciences Institutes, A*STAR, Singapore
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Leboeuf-Yde C, Axén I, Ahlefeldt G, Lidefelt P, Rosenbaum A, Thurnherr T. The types and frequencies of improved nonmusculoskeletal symptoms reported after chiropractic spinal manipulative therapy. J Manipulative Physiol Ther 1999; 22:559-64. [PMID: 10626697 DOI: 10.1016/s0161-4754(99)70014-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
OBJECTIVE To investigate the frequency and types of improved nonmusculoskeletal symptoms reported after chiropractic spinal manipulative therapy. DESIGN Retrospective information obtained by chiropractors through standardized interview of patients on return visit within 2 weeks of previous treatment. SETTING The private practice of 87 Swedish chiropractors (response rate 81%). SUBJECTS Twenty consecutive (presumably naive) patients per chiropractor (1504 valid questionnaires returned, 86% of optimal number of replies). INTERVENTION Spinal manipulation with or without additional therapy provided by chiropractors. MAIN OUTCOME MEASURES Self-reported improved nonmusculoskeletal symptoms (reactions). RESULTS At least I reaction was reported after the previous treatment in 21% to 25% of cases. Of these responses, 26% were related to the airway passages (usually reported as "easier to breathe"), 25% were related to the digestive system (mostly reported as "improved function"), 14% were classified under eyes/vision (usually reported as "improved vision"), and 14% under heart/ circulation (about half of these reported as "improved circulation"). The number of spinal areas treated was positively associated with the number of reactions. CONCLUSION A minority of chiropractic patients report having positive nonmusculoskeletal reactions after spinal manipulative therapy but such reports cluster predominantly around specific symptoms. It would be interesting to find out if these can be verified objectively and, if so, to investigate if they are caused by the treatment or if they are signs of natural variations in human physiology.
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Affiliation(s)
- C Leboeuf-Yde
- Medical Research Unit, Amtsrådhuset, Torvet, Denmark.
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