201
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Porkka N, Valo S, Nieminen TT, Olkinuora A, Mäki-Nevala S, Eldfors S, Peltomäki P. Sequencing of Lynch syndrome tumors reveals the importance of epigenetic alterations. Oncotarget 2017; 8:108020-108030. [PMID: 29296220 PMCID: PMC5746122 DOI: 10.18632/oncotarget.22445] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/27/2017] [Indexed: 02/07/2023] Open
Abstract
Genomic instability and epigenetic aberrations are important classifiers of human tumors, yet, their interrelations are poorly understood. We used Lynch syndrome (LS) to address such relationships. Forty-five tumors (11 colorectal adenomas, 18 colorectal carcinomas, and 16 ovarian carcinomas) were profiled for CpG Island Methylator Phenotype (CIMP) and somatic mutations. All tumors showed high-degree microsatellite instability. Panel sequencing of 578 cancer-relevant genes revealed the average number of 1433, 1124, and 657 non-synonymous somatic mutations per colorectal adenoma, colorectal carcinoma, and ovarian carcinoma, respectively. Genes harboring mutations with allele frequency 25 % or higher in at least 31 % of tumors were regarded to be possible drivers. Among 72 and 10 such genes identified in colorectal and ovarian tumors, respectively, the most frequently mutated genes BRD4 and MLL2 (62 % of colorectal tumors) and ARID1A (50 % of ovarian carcinomas) are involved in epigenetic regulation. The total number of somatic mutations or mutant genes per tumor were significantly associated with CIMP. Our results suggest that even in an inherited disease, tumor type-specific epigenetic changes are significant and may result from regulatory changes (CIMP) or structural events (mutations of epigenetic regulatory genes). The findings are clinically relevant since many of the affected pathways can be therapeutically targeted.
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Affiliation(s)
- Noora Porkka
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Satu Valo
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Taina T Nieminen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Alisa Olkinuora
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Satu Mäki-Nevala
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Samuli Eldfors
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
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202
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Frejno M, Zenezini Chiozzi R, Wilhelm M, Koch H, Zheng R, Klaeger S, Ruprecht B, Meng C, Kramer K, Jarzab A, Heinzlmeir S, Johnstone E, Domingo E, Kerr D, Jesinghaus M, Slotta-Huspenina J, Weichert W, Knapp S, Feller SM, Kuster B. Pharmacoproteomic characterisation of human colon and rectal cancer. Mol Syst Biol 2017; 13:951. [PMID: 29101300 PMCID: PMC5731344 DOI: 10.15252/msb.20177701] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Most molecular cancer therapies act on protein targets but data on the proteome status of patients and cellular models for proteome‐guided pre‐clinical drug sensitivity studies are only beginning to emerge. Here, we profiled the proteomes of 65 colorectal cancer (CRC) cell lines to a depth of > 10,000 proteins using mass spectrometry. Integration with proteomes of 90 CRC patients and matched transcriptomics data defined integrated CRC subtypes, highlighting cell lines representative of each tumour subtype. Modelling the responses of 52 CRC cell lines to 577 drugs as a function of proteome profiles enabled predicting drug sensitivity for cell lines and patients. Among many novel associations, MERTK was identified as a predictive marker for resistance towards MEK1/2 inhibitors and immunohistochemistry of 1,074 CRC tumours confirmed MERTK as a prognostic survival marker. We provide the proteomic and pharmacological data as a resource to the community to, for example, facilitate the design of innovative prospective clinical trials.
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Affiliation(s)
- Martin Frejno
- Department of Oncology, University of Oxford, Oxford, UK.,Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Riccardo Zenezini Chiozzi
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,Department of Chemistry, Sapienza - Università di Roma, Rome, Italy
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Heiner Koch
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Runsheng Zheng
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Susan Klaeger
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Ruprecht
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,Center for Integrated Protein Science (CIPSM), Munich, Germany
| | - Chen Meng
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Karl Kramer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Anna Jarzab
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Stephanie Heinzlmeir
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Enric Domingo
- Department of Oncology, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, Oxford, UK
| | - David Kerr
- Nuffield Division of Clinical Laboratory Sciences (NDCLS), University of Oxford, Oxford, UK
| | - Moritz Jesinghaus
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | | | - Wilko Weichert
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Stephan M Feller
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK .,Institute of Molecular Medicine, Martin-Luther-University, Halle, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany .,German Cancer Consortium (DKTK), Munich, Germany.,Center for Integrated Protein Science (CIPSM), Munich, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Freising, Germany
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203
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Development and validation of a targeted next generation DNA sequencing panel outperforming whole exome sequencing for the identification of clinically relevant genetic variants. Oncotarget 2017; 8:102033-102045. [PMID: 29254223 PMCID: PMC5731933 DOI: 10.18632/oncotarget.22116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 09/08/2017] [Indexed: 02/07/2023] Open
Abstract
Next generation sequencing (NGS) technologies have revolutionized our approach to genomic research. The use of whole genome sequencing (WGS), whole exome sequencing (WES), transcriptome profiling, and targeted DNA sequencing has exponentially improved our understanding of the human genome and the genetic complexities underlying malignancy. Yet, WGS and WES clinical applications remain limited due to high costs and the large volume of data generated. When utilized to address biological questions in basic science studies, targeted sequencing panels have proven extremely valuable due to reduced costs and higher sequencing depth. However, the routine application of targeted sequencing to the clinical setting is limited to a few cancer subtypes. Some highly aggressive tumor types, like type 2 endometrial cancer (EC), could greatly benefit from routine genomic analysis using targeted sequencing. To explore the potential utility of a mid size panel (~150 genes) in the clinical setting, we developed and validated a custom panel against WGS, WES, and another commercially available targeted panel. Our results indicate that a mid size custom designed panel is as efficient as WGS and WES in mapping variants of biological and clinical relevance, rendering higher coverage, at a lower cost, with fewer variants of uncertain significance. Because of the much higher sequencing depth that could be achieved, our results demonstrate that targeted sequencing outperformed WGS and WES in the mapping of pathogenic variants in a breast cancer case, as well as a case of mixed serous and high-grade endometrioid EC, the most aggressive EC subtype.
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204
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Tissue transglutaminase induces Epithelial-Mesenchymal-Transition and the acquisition of stem cell like characteristics in colorectal cancer cells. Oncotarget 2017; 8:20025-20041. [PMID: 28223538 PMCID: PMC5386741 DOI: 10.18632/oncotarget.15370] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/07/2017] [Indexed: 12/26/2022] Open
Abstract
Human colon cancer cell lines (CRCs) RKO, SW480 and SW620 were investigated for TG2 involvement in tumour advancement and aggression. TG2 expression correlated with tumour advancement and expression of markers of epithelial-mesenchymal transition (EMT). The metastatic cell line SW620 showed high TG2 expression compared to the primary tumour cell lines SW480 and RKO and could form tumour spheroids under non- adherent conditions. TG2 manipulation in the CRCs by shRNA or TG2 transduction confirmed the relationship between TG2 and EMT. TGFβ1 expression in CRC cells, and its level in the cell medium and extracellular matrix was increased in primary tumour CRCs overexpressing TG2 and could regulate TG2 expression and EMT by both canonical (RKO) and non-canonical (RKO and SW480) signalling. TGFβ1 regulation was not observed in the metastatic SW620 cell line, but TG2 knockdown or inhibition in SW620 reversed EMT. In SW620, TG2 expression and EMT was associated with increased presence of nuclear β-catenin which could be mediated by association of TG2 with the Wnt signalling co-receptor LRP5. TG2 inhibition/knockdown increased interaction between β-catenin and ubiquitin shown by co-immunoprecipitation, suggesting that TG2 could be important in β-catenin regulation. β-Catenin and TG2 was also upregulated in SW620 spheroid cells enriched with cancer stem cell marker CD44 and TG2 inhibition/knockdown reduced the spheroid forming potential of SW620 cells. Our data suggests that TG2 could hold both prognostic and therapeutic significance in colon cancer.
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205
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Loo SK, Ab Hamid SS, Musa M, Wong KK. DNMT1 is associated with cell cycle and DNA replication gene sets in diffuse large B-cell lymphoma. Pathol Res Pract 2017; 214:134-143. [PMID: 29137822 DOI: 10.1016/j.prp.2017.10.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 09/27/2017] [Accepted: 10/03/2017] [Indexed: 10/18/2022]
Abstract
Dysregulation of DNA (cytosine-5)-methyltransferase 1 (DNMT1) is associated with the pathogenesis of various types of cancer. It has been previously shown that DNMT1 is frequently expressed in diffuse large B-cell lymphoma (DLBCL), however its functions remain to be elucidated in the disease. In this study, we gene expression profiled (GEP) shRNA targeting DNMT1(shDNMT1)-treated germinal center B-cell-like DLBCL (GCB-DLBCL)-derived cell line (i.e. HT) compared with non-silencing shRNA (control shRNA)-treated HT cells. Independent gene set enrichment analysis (GSEA) performed using GEPs of shRNA-treated HT cells and primary GCB-DLBCL cases derived from two publicly-available datasets (i.e. GSE10846 and GSE31312) produced three separate lists of enriched gene sets for each gene sets collection from Molecular Signatures Database (MSigDB). Subsequent Venn analysis identified 268, 145 and six consensus gene sets from analyzing gene sets in C2 collection (curated gene sets), C5 sub-collection [gene sets from gene ontology (GO) biological process ontology] and Hallmark collection, respectively to be enriched in positive correlation with DNMT1 expression profiles in shRNA-treated HT cells, GSE10846 and GSE31312 datasets [false discovery rate (FDR) <0.05]. Cell cycle progression and DNA replication were among the significantly enriched biological processes (FDR <0.05). Expression of genes involved in the activation of cell cycle and DNA replication (e.g. CDK1, CCNA2, E2F2, PCNA, RFC5 and POLD3) were highly correlated (r>0.8) with DNMT1 expression and significantly downregulated (log fold-change <-1.35; p<0.05) following DNMT1 silencing in HT cells. These results suggest the involvement of DNMT1 in the activation of cell cycle and DNA replication in DLBCL cells.
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Affiliation(s)
- Suet Kee Loo
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Suzina Sheikh Ab Hamid
- Tissue Bank Unit, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Mustaffa Musa
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Kah Keng Wong
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
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206
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Stintzing S, Tejpar S, Gibbs P, Thiebach L, Lenz HJ. Understanding the role of primary tumour localisation in colorectal cancer treatment and outcomes. Eur J Cancer 2017; 84:69-80. [PMID: 28787661 PMCID: PMC7505124 DOI: 10.1016/j.ejca.2017.07.016] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023]
Abstract
Metastatic colorectal carcinoma (mCRC) is a heterogeneous disease with differing outcomes and clinical responses and poor prognosis. CRCs can be characterised by their primary tumour location within the colon. The left-sided colon, derived from the hindgut, includes the distal third of the transverse colon, splenic flexure, descending colon, sigmoid colon and rectum. The right-sided colon, derived from the midgut, includes the proximal two-thirds of the transverse colon, ascending colon and caecum. Sometimes, the rectum is described separately, despite originating from the hindgut, and in many clinical series, the left-sided colon includes only tumours within and distal to the splenic flexure. Differences in the microbiome, clinical characteristics and chromosomal and molecular characteristics have been reported between the right and left side of the colon, regardless of how this is defined. There is now strong evidence from clinical studies in patients with mCRC for the prognostic effect of primary tumour location. The impact of primary colonic tumour location on response to treatment is now under investigation in a large number of clinical studies in patients with mCRC. In this review, we summarise the microbiome, clinical, chromosomal and molecular differences associated with the primary location of CRC. We present an overview of the proven prognostic impact of primary tumour location for patients with mCRC and discuss emerging data for the predictive impact of primary tumour location on clinical outcome.
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Affiliation(s)
| | - Sabine Tejpar
- Molecular Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium.
| | - Peter Gibbs
- Systems Biology and Personalised Medicine, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.
| | | | - Heinz-Josef Lenz
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
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207
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Wang J, Mouradov D, Wang X, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJ, Burgess AW, Liebler DC, Zhang B, Sieber OM. Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity. Gastroenterology 2017; 153. [PMID: 28625833 PMCID: PMC5623120 DOI: 10.1053/j.gastro.2017.06.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIMS Proteomics holds promise for individualizing cancer treatment. We analyzed to what extent the proteomic landscape of human colorectal cancer (CRC) is maintained in established CRC cell lines and the utility of proteomics for predicting therapeutic responses. METHODS Proteomic and transcriptomic analyses were performed on 44 CRC cell lines, compared against primary CRCs (n=95) and normal tissues (n=60), and integrated with genomic and drug sensitivity data. RESULTS Cell lines mirrored the proteomic aberrations of primary tumors, in particular for intrinsic programs. Tumor relationships of protein expression with DNA copy number aberrations and signatures of post-transcriptional regulation were recapitulated in cell lines. The 5 proteomic subtypes previously identified in tumors were represented among cell lines. Nonetheless, systematic differences between cell line and tumor proteomes were apparent, attributable to stroma, extrinsic signaling, and growth conditions. Contribution of tumor stroma obscured signatures of DNA mismatch repair identified in cell lines with a hypermutation phenotype. Global proteomic data showed improved utility for predicting both known drug-target relationships and overall drug sensitivity as compared with genomic or transcriptomic measurements. Inhibition of targetable proteins associated with drug responses further identified corresponding synergistic or antagonistic drug combinations. Our data provide evidence for CRC proteomic subtype-specific drug responses. CONCLUSIONS Proteomes of established CRC cell line are representative of primary tumors. Proteomic data tend to exhibit improved prediction of drug sensitivity as compared with genomic and transcriptomic profiles. Our integrative proteogenomic analysis highlights the potential of proteome profiling to inform personalized cancer medicine.
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Affiliation(s)
- Jing Wang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,CORRESPONDING AUTHORS: Oliver Sieber, Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, 1G Royal Parade, Parkville, VIC 3052, Australia. . Bing Zhang, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Dmitri Mouradov
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia,Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia,CORRESPONDING AUTHORS: Oliver Sieber, Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, 1G Royal Parade, Parkville, VIC 3052, Australia. . Bing Zhang, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Xiaojing Wang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,CORRESPONDING AUTHORS: Oliver Sieber, Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, 1G Royal Parade, Parkville, VIC 3052, Australia. . Bing Zhang, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Robert N. Jorissen
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia,Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | | | - Lisa J. Zimmerman
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Suhas Vasaikar
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher G. Love
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia,Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Shan Li
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia
| | - Kym Lowes
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia
| | - Karl-Johan Leuchowius
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia
| | - Helene Jousset
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia
| | - Janet Weinstock
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Christopher Yau
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom,Department of Statistics, University of Oxford, Oxford, OX1 3LB, United Kingdom
| | - John Mariadason
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia,La Trobe University School of Cancer Medicine, Melbourne, VIC 3086, Australia
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuguang Ban
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xi Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA,Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Robert J. C. Coffey
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA,Veterans Affairs Medical Center, Nashville, TN 37212, USA
| | | | - Antony W. Burgess
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia,Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Daniel C. Liebler
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.
| | - Oliver M. Sieber
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia,Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3052, Australia,School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia,CORRESPONDING AUTHORS: Oliver Sieber, Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, 1G Royal Parade, Parkville, VIC 3052, Australia. . Bing Zhang, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
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208
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Chen Z, Jiang H, Xu W, Li X, Dempsey DR, Zhang X, Devreotes P, Wolberger C, Amzel LM, Gabelli SB, Cole PA. A Tunable Brake for HECT Ubiquitin Ligases. Mol Cell 2017; 66:345-357.e6. [PMID: 28475870 DOI: 10.1016/j.molcel.2017.03.020] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/15/2017] [Accepted: 03/31/2017] [Indexed: 12/24/2022]
Abstract
The HECT E3 ligases ubiquitinate numerous transcription factors and signaling molecules, and their activity must be tightly controlled to prevent cancer, immune disorders, and other diseases. In this study, we have found unexpectedly that peptide linkers tethering WW domains in several HECT family members are key regulatory elements of their catalytic activities. Biochemical, structural, and cellular analyses have revealed that the linkers can lock the HECT domain in an inactive conformation and block the proposed allosteric ubiquitin binding site. Such linker-mediated autoinhibition of the HECT domain can be relieved by linker post-translational modifications, but complete removal of the brake can induce hyperactive autoubiquitination and E3 self destruction. These results clarify the mechanisms of several HECT protein cancer associated mutations and provide a new framework for understanding how HECT ubiquitin ligases must be finely tuned to ensure normal cellular behavior.
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Affiliation(s)
- Zan Chen
- Department of Pharmacology and Molecular Sciences, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Hanjie Jiang
- Department of Pharmacology and Molecular Sciences, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Wei Xu
- Department of Pharmacology and Molecular Sciences, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Xiaoguang Li
- Department of Cell Biology, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Daniel R Dempsey
- Department of Pharmacology and Molecular Sciences, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Xiangbin Zhang
- Department of Biophysics and Biophysical Chemistry, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Peter Devreotes
- Department of Cell Biology, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, John Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - L Mario Amzel
- Department of Biophysics and Biophysical Chemistry, John Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, John Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, John Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, John Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, John Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, John Hopkins School of Medicine, Baltimore, MD 21205, USA.
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209
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RCC2 is a novel p53 target in suppressing metastasis. Oncogene 2017; 37:8-17. [PMID: 28869598 PMCID: PMC5759027 DOI: 10.1038/onc.2017.306] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 07/14/2017] [Accepted: 07/20/2017] [Indexed: 12/17/2022]
Abstract
RCC2 (also known as TD60) is a highly conserved protein involved in prognosis in colorectal cancer. However, its relationship with tumor development is less understood. Here we demonstrate a signaling pathway defining regulation of RCC2 and its functions in tumor progression. We report that p53 is a transcriptional regulator of RCC2 that acts through its binding to a palindromic motif in the RCC2 promoter. RCC2 physically interacts and deactivates a small GTPase Rac1 that is known to be involved in metastasis. We solved a high-resolution crystal structure of RCC2 and revealed one RCC1-like domain with a unique β-hairpin that is requisite for RCC2 interaction with Rac1. p53 or RCC2 deficiency leads to activation of Rac1 and deterioration of extracellular matrix sensing (haptotaxis) of surface-bound gradients. Ectopic expression of RCC2 restores directional migration in p53-null cells. Our results demonstrate that p53 and RCC2 signaling is important for regulation of cell migration and suppression of metastasis. We propose that the p53/RCC2/Rac1 axis is a potential target for cancer therapy.
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210
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Mertz TM, Baranovskiy AG, Wang J, Tahirov TH, Shcherbakova PV. Nucleotide selectivity defect and mutator phenotype conferred by a colon cancer-associated DNA polymerase δ mutation in human cells. Oncogene 2017; 36:4427-4433. [PMID: 28368425 PMCID: PMC5542868 DOI: 10.1038/onc.2017.22] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/17/2016] [Accepted: 12/30/2016] [Indexed: 12/14/2022]
Abstract
Mutations in the POLD1 and POLE genes encoding DNA polymerases δ (Polδ) and ɛ (Polɛ) cause hereditary colorectal cancer (CRC) and have been found in many sporadic colorectal and endometrial tumors. Much attention has been focused on POLE exonuclease domain mutations, which occur frequently in hypermutated DNA mismatch repair (MMR)-proficient tumors and appear to be responsible for the bulk of genomic instability in these tumors. In contrast, somatic POLD1 mutations are seen less frequently and typically occur in MMR-deficient tumors. Their functional significance is often unclear. Here we demonstrate that expression of the cancer-associated POLD1-R689W allele is strongly mutagenic in human cells. The mutation rate increased synergistically when the POLD1-R689W expression was combined with a MMR defect, indicating that the mutator effect of POLD1-R689W results from a high rate of replication errors. Purified human Polδ-R689W has normal exonuclease activity, but the nucleotide selectivity of the enzyme is severely impaired, providing a mechanistic explanation for the increased mutation rate in the POLD1-R689W-expressing cells. The vast majority of mutations induced by the POLD1-R689W are GC→︀TA transversions and GC→︀AT transitions, with transversions showing a strong strand bias and a remarkable preference for polypurine/polypyrimidine sequences. The mutational specificity of the Polδ variant matches that of the hypermutated CRC cell line, HCT15, in which this variant was first identified. The results provide compelling evidence for the pathogenic role of the POLD1-R689W mutation in the development of the human tumor and emphasize the need to experimentally determine the significance of Polδ variants present in sporadic tumors.
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Affiliation(s)
- T M Mertz
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - A G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - J Wang
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - T H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - P V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
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211
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Berg KCG, Eide PW, Eilertsen IA, Johannessen B, Bruun J, Danielsen SA, Bjørnslett M, Meza-Zepeda LA, Eknæs M, Lind GE, Myklebost O, Skotheim RI, Sveen A, Lothe RA. Multi-omics of 34 colorectal cancer cell lines - a resource for biomedical studies. Mol Cancer 2017; 16:116. [PMID: 28683746 PMCID: PMC5498998 DOI: 10.1186/s12943-017-0691-y] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/28/2017] [Indexed: 12/19/2022] Open
Abstract
Background Colorectal cancer (CRC) cell lines are widely used pre-clinical model systems. Comprehensive insights into their molecular characteristics may improve model selection for biomedical studies. Methods We have performed DNA, RNA and protein profiling of 34 cell lines, including (i) targeted deep sequencing (n = 612 genes) to detect single nucleotide variants and insertions/deletions; (ii) high resolution DNA copy number profiling; (iii) gene expression profiling at exon resolution; (iv) small RNA expression profiling by deep sequencing; and (v) protein expression analysis (n = 297 proteins) by reverse phase protein microarrays. Results The cell lines were stratified according to the key molecular subtypes of CRC and data were integrated at two or more levels by computational analyses. We confirm that the frequencies and patterns of DNA aberrations are associated with genomic instability phenotypes and that the cell lines recapitulate the genomic profiles of primary carcinomas. Intrinsic expression subgroups are distinct from genomic subtypes, but consistent at the gene-, microRNA- and protein-level and dominated by two distinct clusters; colon-like cell lines characterized by expression of gastro-intestinal differentiation markers and undifferentiated cell lines showing upregulation of epithelial-mesenchymal transition and TGFβ signatures. This sample split was concordant with the gene expression-based consensus molecular subtypes of primary tumors. Approximately ¼ of the genes had consistent regulation at the DNA copy number and gene expression level, while expression of gene-protein pairs in general was strongly correlated. Consistent high-level DNA copy number amplification and outlier gene- and protein- expression was found for several oncogenes in individual cell lines, including MYC and ERBB2. Conclusions This study expands the view of CRC cell lines as accurate molecular models of primary carcinomas, and we present integrated multi-level molecular data of 34 widely used cell lines in easily accessible formats, providing a resource for preclinical studies in CRC. Electronic supplementary material The online version of this article (doi:10.1186/s12943-017-0691-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kaja C G Berg
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Peter W Eide
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Bjarne Johannessen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Stine A Danielsen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Merete Bjørnslett
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Leonardo A Meza-Zepeda
- Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway.,Department of Core Facilities and Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Mette Eknæs
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ola Myklebost
- Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway.,Department of Core Facilities and Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway. .,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway. .,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway.
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212
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Chang F, Liu L, Fang E, Zhang G, Chen T, Cao K, Li Y, Li MM. Molecular Diagnosis of Mosaic Overgrowth Syndromes Using a Custom-Designed Next-Generation Sequencing Panel. J Mol Diagn 2017; 19:613-624. [DOI: 10.1016/j.jmoldx.2017.04.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 03/27/2017] [Accepted: 04/18/2017] [Indexed: 12/19/2022] Open
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213
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Tutuka CSA, Andrews MC, Mariadason JM, Ioannidis P, Hudson C, Cebon J, Behren A. PLX8394, a new generation BRAF inhibitor, selectively inhibits BRAF in colonic adenocarcinoma cells and prevents paradoxical MAPK pathway activation. Mol Cancer 2017; 16:112. [PMID: 28659148 PMCID: PMC5490236 DOI: 10.1186/s12943-017-0684-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/21/2017] [Indexed: 01/07/2023] Open
Abstract
BRAF inhibitors (BRAFi) are standard of care for the treatment of BRAF V600 mutation-driven metastatic melanoma, but can lead to paradoxical activation of the mitogen-activated protein kinase (MAPK) signalling pathway. This can result in the promotion of precancerous lesions and secondary neoplasms, mainly (but not exclusively) associated with pre-existing mutations in RAS genes. We previously reported a patient with synchronous BRAF-mutated metastatic melanoma and BRAFwt/KRASG12D-metastatic colorectal cancer (CRC), whose CRC relapsed and progressed when treated with the BRAF inhibitor dabrafenib (GSK2118436). We used tissue from the resected CRC metastasis to derive a cell line, LM-COL-1, which directly and reliably mimicked the clinical scenario including paradoxical activation of the MAPK signalling pathway resulting in increased cell proliferation upon dabrafenib treatment. Novel BRAF inhibitors (PLX8394 and PLX7904), dubbed as “paradox breakers”, were developed to inhibit V600 mutated oncogenic BRAF without causing paradoxical MAPK pathway activation. In this study we used our LM-COL-1 model alongside multiple other CRC cell lines with varying mutational backgrounds to demonstrate and confirm that the paradox breaker PLX8394 retains on-target inhibition of mutated BRAF V600 without paradoxically promoting MAPK signalling.
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Affiliation(s)
- Candani S A Tutuka
- Olivia Newton-John Cancer Research Institute, 145 Studley Road, Heidelberg, VIC, 3084, Australia
| | - Miles C Andrews
- Olivia Newton-John Cancer Research Institute, 145 Studley Road, Heidelberg, VIC, 3084, Australia.,Austin Medical Oncology Unit, Austin Health, Heidelberg, VIC, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, VIC, Australia
| | - John M Mariadason
- Olivia Newton-John Cancer Research Institute, 145 Studley Road, Heidelberg, VIC, 3084, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, VIC, Australia
| | - Paul Ioannidis
- Olivia Newton-John Cancer Research Institute, 145 Studley Road, Heidelberg, VIC, 3084, Australia
| | - Christopher Hudson
- Olivia Newton-John Cancer Research Institute, 145 Studley Road, Heidelberg, VIC, 3084, Australia
| | - Jonathan Cebon
- Olivia Newton-John Cancer Research Institute, 145 Studley Road, Heidelberg, VIC, 3084, Australia.,Austin Medical Oncology Unit, Austin Health, Heidelberg, VIC, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, VIC, Australia.,Department of Medicine, University of Melbourne, Parkville, VIC, Australia
| | - Andreas Behren
- Olivia Newton-John Cancer Research Institute, 145 Studley Road, Heidelberg, VIC, 3084, Australia. .,School of Cancer Medicine, La Trobe University, Bundoora, VIC, Australia.
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214
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Marcos-Alcalde Í, Mendieta-Moreno JI, Puisac B, Gil-Rodríguez MC, Hernández-Marcos M, Soler-Polo D, Ramos FJ, Ortega J, Pié J, Mendieta J, Gómez-Puertas P. Two-step ATP-driven opening of cohesin head. Sci Rep 2017; 7:3266. [PMID: 28607419 PMCID: PMC5468275 DOI: 10.1038/s41598-017-03118-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/24/2017] [Indexed: 02/07/2023] Open
Abstract
The cohesin ring is a protein complex composed of four core subunits: Smc1A, Smc3, Rad21 and Stag1/2. It is involved in chromosome segregation, DNA repair, chromatin organization and transcription regulation. Opening of the ring occurs at the "head" structure, formed of the ATPase domains of Smc1A and Smc3 and Rad21. We investigate the mechanisms of the cohesin ring opening using techniques of free molecular dynamics (MD), steered MD and quantum mechanics/molecular mechanics MD (QM/MM MD). The study allows the thorough analysis of the opening events at the atomic scale: i) ATP hydrolysis at the Smc1A site, evaluating the role of the carboxy-terminal domain of Rad21 in the process; ii) the activation of the Smc3 site potentially mediated by the movement of specific amino acids; and iii) opening of the head domains after the two ATP hydrolysis events. Our study suggests that the cohesin ring opening is triggered by a sequential activation of the ATP sites in which ATP hydrolysis at the Smc1A site induces ATPase activity at the Smc3 site. Our analysis also provides an explanation for the effect of pathogenic variants related to cohesinopathies and cancer.
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Affiliation(s)
| | - Jesús I Mendieta-Moreno
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049, Madrid, Spain
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Beatriz Puisac
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - María Concepción Gil-Rodríguez
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - María Hernández-Marcos
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - Diego Soler-Polo
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Feliciano J Ramos
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - José Ortega
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan Pié
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - Jesús Mendieta
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049, Madrid, Spain
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Departamento de Biotecnología, Universidad Francisco de Vitoria, Pozuelo de Alarcón, 28223, Madrid, Spain
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215
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Replicative DNA polymerase defects in human cancers: Consequences, mechanisms, and implications for therapy. DNA Repair (Amst) 2017; 56:16-25. [PMID: 28687338 DOI: 10.1016/j.dnarep.2017.06.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The fidelity of DNA replication relies on three error avoidance mechanisms acting in series: nucleotide selectivity of replicative DNA polymerases, exonucleolytic proofreading, and post-replicative DNA mismatch repair (MMR). MMR defects are well known to be associated with increased cancer incidence. Due to advances in DNA sequencing technologies, the past several years have witnessed a long-predicted discovery of replicative DNA polymerase defects in sporadic and hereditary human cancers. The polymerase mutations preferentially affect conserved amino acid residues in the exonuclease domain and occur in tumors with an extremely high mutation load. Thus, a concept has formed that defective proofreading of replication errors triggers the development of these tumors. Recent studies of the most common DNA polymerase variants, however, suggested that their pathogenicity may be determined by functional alterations other than loss of proofreading. In this review, we summarize our current understanding of the consequences of DNA polymerase mutations in cancers and the mechanisms of their mutator effects. We also discuss likely explanations for a high recurrence of some but not other polymerase variants and new ideas for therapeutic interventions emerging from the mechanistic studies.
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216
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Halaburková A, Jendželovský R, Kovaľ J, Herceg Z, Fedoročko P, Ghantous A. Histone deacetylase inhibitors potentiate photodynamic therapy in colon cancer cells marked by chromatin-mediated epigenetic regulation of CDKN1A. Clin Epigenetics 2017; 9:62. [PMID: 28603560 PMCID: PMC5465463 DOI: 10.1186/s13148-017-0359-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/24/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Hypericin-mediated photodynamic therapy (HY-PDT) has recently captured increased attention as an alternative minimally invasive anticancer treatment, although cancer cells may acquire resistance. Therefore, combination treatments may be necessary to enhance HY-PDT efficacy. Histone deacetylase inhibitors (HDACis) are often used in combination treatments due to their non-genotoxic properties and epigenetic potential to sensitize cells to external stimuli. Therefore, this study attempts for the first time to investigate the therapeutic effects of HDACis in combination with visible light-mediated PDT against cancer. Specifically, the colorectal cancer cell model was used due to its known resistance to HY-PDT. RESULTS Two chemical groups of HDACis were tested in combination with HY-PDT: the hydroxamic acids Saha and Trichostatin A, and the short-chain fatty acids valproic acid and sodium phenylbutyrate (NaPB), as inhibitors of all-class versus nuclear HDACs, respectively. The selected HDACis manifest a favorable clinical toxicity profile and showed similar potencies and mechanisms in intragroup comparisons but different biological effects in intergroup analyses. HDACi combination with HY-PDT significantly attenuated cancer cell resistance to treatment and caused the two HDACi groups to become similarly potent. However, the short-chain fatty acids, in combination with HY-PDT, showed increased selectivity towards inhibition of HDACs versus other key epigenetic enzymes, and NaPB induced the strongest expression of the otherwise silenced tumor suppressor CDKN1A, a hallmark gene for HDACi-mediated chromatin modulation. Epigenetic regulation of CDKN1A by NaPB was associated with histone acetylation at enhancer and promoter elements rather than histone or DNA methylation at those or other regulatory regions of this gene. Moreover, NaPB, compared to the other HDACis, caused milder effects on global histone acetylation, suggesting a more specific effect on CDKN1A chromatin architecture relative to global chromatin structure. The mechanism of NaPB + HY-PDT was P53-dependent and likely driven by the HY-PDT rather than the NaPB constituent. CONCLUSIONS Our results show that HDACis potentiate the antitumor efficacy of HY-PDT in colorectal cancer cells, overcoming their resistance to this drug and epigenetically reactivating the expression of CDKN1A. Besides their therapeutic potential, hypericin and these HDACis are non-genotoxic constituents of dietary agents, hence, represent interesting targets for investigating mechanisms of dietary-based cancer prevention.
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Affiliation(s)
- Andrea Halaburková
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Košice, Slovakia
| | - Rastislav Jendželovský
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Košice, Slovakia
| | - Ján Kovaľ
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Košice, Slovakia
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France
| | - Peter Fedoročko
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Košice, Slovakia
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France
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217
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Nijhuis A, Thompson H, Adam J, Parker A, Gammon L, Lewis A, Bundy JG, Soga T, Jalaly A, Propper D, Jeffery R, Suraweera N, McDonald S, Thaha MA, Feakins R, Lowe R, Bishop CL, Silver A. Remodelling of microRNAs in colorectal cancer by hypoxia alters metabolism profiles and 5-fluorouracil resistance. Hum Mol Genet 2017; 26:1552-1564. [PMID: 28207045 PMCID: PMC5393147 DOI: 10.1093/hmg/ddx059] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/13/2017] [Indexed: 12/25/2022] Open
Abstract
Solid tumours have oxygen gradients and areas of near and almost total anoxia. Hypoxia reduces sensitivity to 5-fluorouracil (5-FU)-chemotherapy for colorectal cancer (CRC). MicroRNAs (miRNAs) are hypoxia sensors and were altered consistently in six CRC cell lines (colon cancer: DLD-1, HCT116 and HT29; rectal cancer: HT55, SW837 and VACO4S) maintained in hypoxia (1 and 0.2% oxygen) compared with normoxia (20.9%). CRC cell lines also showed altered amino acid metabolism in hypoxia and hypoxia-responsive miRNAs were predicted to target genes in four metabolism pathways: beta-alanine; valine, leucine, iso-leucine; aminoacyl-tRNA; and alanine, aspartate, glutamate. MiR-210 was increased in hypoxic areas of CRC tissues and hypoxia-responsive miR-21 and miR-30d, but not miR-210, were significantly increased in 5-FU resistant CRCs. Treatment with miR-21 and miR-30d antagonists sensitized hypoxic CRC cells to 5-FU. Our data highlight the complexity and tumour heterogeneity caused by hypoxia. MiR-210 as a hypoxic biomarker, and the targeting of miR-21 and miR-30d and/or the amino acid metabolism pathways may offer translational opportunities.
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Affiliation(s)
- Anke Nijhuis
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Hannah Thompson
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Julie Adam
- Radcliffe Department of Medicine, OCDEM, University of Oxford, Oxford OX3 7LJ, UK
| | - Alexandra Parker
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Luke Gammon
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Amy Lewis
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Jacob G Bundy
- Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, UK
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Aisha Jalaly
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - David Propper
- Department of Medical Oncology, St Bartholomew's Hospital, Gloucester House, Little Britain, London EC1A 7BE, UK
| | - Rosemary Jeffery
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Nirosha Suraweera
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Sarah McDonald
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Mohamed A Thaha
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK.,Academic Surgical Unit, The Royal London Hospital, Whitechapel, London E1 1BB, UK
| | - Roger Feakins
- Department of Histopathology, Royal London Hospital, Whitechapel, London, UK
| | - Robert Lowe
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Cleo L Bishop
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Andrew Silver
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
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218
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Mills AA. The Chromodomain Helicase DNA-Binding Chromatin Remodelers: Family Traits that Protect from and Promote Cancer. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026450. [PMID: 28096241 DOI: 10.1101/cshperspect.a026450] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A plethora of mutations in chromatin regulators in diverse human cancers is emerging, attesting to the pivotal role of chromatin dynamics in tumorigenesis. A recurrent theme is inactivation of the chromodomain helicase DNA-binding (CHD) family of proteins-ATP-dependent chromatin remodelers that govern the cellular machinery's access to DNA, thereby controlling fundamental processes, including transcription, proliferation, and DNA damage repair. This review highlights what is currently known about how genetic and epigenetic perturbation of CHD proteins and the pathways that they regulate set the stage for cancer, providing new insight for designing more effective anti-cancer therapies.
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Affiliation(s)
- Alea A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724
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219
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Wang Z, Dai J, Hu N, Miao X, Abnet CC, Yang M, Freedman ND, Chen J, Burdette L, Zhu X, Chung CC, Ren C, Dawsey SM, Wang M, Ding T, Du J, Gao YT, Zhong R, Giffen C, Pan W, Koh WP, Dai N, Liao LM, Yan C, Qiao YL, Jiang Y, Shu XO, Chen J, Wang C, Ma H, Su H, Zhang Z, Wang L, Wu C, Xiang YB, Hu Z, Yuan JM, Xie L, Zheng W, Lin D, Chanock SJ, Shi Y, Goldstein AM, Jin G, Taylor PR, Shen H. Identification of new susceptibility loci for gastric non-cardia adenocarcinoma: pooled results from two Chinese genome-wide association studies. Gut 2017; 66:581-587. [PMID: 26701879 PMCID: PMC4963301 DOI: 10.1136/gutjnl-2015-310612] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/01/2015] [Accepted: 11/17/2015] [Indexed: 01/29/2023]
Abstract
OBJECTIVE Although several genome-wide association studies (GWAS) of non-cardia gastric cancer have been published, more novel association signals could be exploited by combining individual studies together, which will further elucidate the genetic susceptibility of non-cardia gastric cancer. DESIGN We conducted a meta-analysis of two published Chinese GWAS studies (2031 non-cardia gastric cancer cases and 4970 cancer-free controls) and followed by genotyping of additional 3564 cases and 4637 controls in two stages. RESULTS The overall meta-analysis revealed two new association signals. The first was a novel locus at 5q14.3 and marked by rs7712641 (per-allele OR=0.84, 95% CI 0.80 to 0.88; p=1.21×10-11). This single-nucleotide polymorphism (SNP) marker maps to the intron of the long non-coding RNA, lnc-POLR3G-4 (XLOC_004464), which we observed has lower expression in non-cardia gastric tumour compared with matched normal tissue (Pwilcoxon signed-rank=7.20×10-4). We also identified a new signal at the 1q22 locus, rs80142782 (per-allele OR=0.62; 95% CI 0.56 to 0.69; p=1.71×10-19), which was independent of the previously reported SNP at the same locus, rs4072037 (per-allele OR=0.74; 95% CI 0.69 to 0.79; p=6.28×10-17). Analysis of the new SNP conditioned on the known SNP showed that the new SNP remained genome-wide significant (Pconditional=3.47×10-8). Interestingly, rs80142782 has a minor allele frequency of 0.05 in East Asians but is monomorphic in both European and African populations. CONCLUSION These findings add new evidence for inherited genetic susceptibility to non-cardia gastric cancer and provide further clues to its aetiology in the Han Chinese population.
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Affiliation(s)
- Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA,Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Gaithersburg, Maryland, USA,Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Christian C Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ming Yang
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jinfei Chen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA,Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Gaithersburg, Maryland, USA
| | - Xun Zhu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA,Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Gaithersburg, Maryland, USA
| | - Chuanli Ren
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China,Clinical Medical Testing Laboratory, Northern Jiangsu People's Hospital and Clinical Medical College of Yangzhou University, Yangzhou, People's Republic of China
| | - Sanford M Dawsey
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Meilin Wang
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Ti Ding
- Shanxi Cancer Hospital, Taiyuan, Shanxi, P.R. China
| | - Jiangbo Du
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yu-Tang Gao
- Shanghai Cancer Institute, Shanghai, People's Republic of China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Carol Giffen
- Information Management Services Inc., Silver Spring, Maryland, USA
| | - Wenting Pan
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Woon-Puay Koh
- Duke-NUS Graduate Medical School Singapore, and Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Ningbing Dai
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Linda M Liao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Caiwang Yan
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - You-Lin Qiao
- Department of Epidemiology, Cancer Institute and Hospital Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Yue Jiang
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Xiao-Ou Shu
- Department of Medicine and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Jiaping Chen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Chaoyu Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Hua Su
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zhendong Zhang
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Lemin Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Chen Wu
- Department of Etiology & Carcinogenesis, Cancer Institute and Hospital Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Yong-Bing Xiang
- Shanghai Cancer Institute, Shanghai, People's Republic of China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute; Pittsburgh, Pennsylvania, USA,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lu Xie
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Wei Zheng
- Department of Medicine and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Dongxin Lin
- Department of Etiology & Carcinogenesis, Cancer Institute and Hospital Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yongyong Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
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Merino GA, Murua YA, Fresno C, Sendoya JM, Golubicki M, Iseas S, Coraglio M, Podhajcer OL, Llera AS, Fernández EA. TarSeqQC: Quality control on targeted sequencing experiments in R. Hum Mutat 2017; 38:494-502. [DOI: 10.1002/humu.23204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 02/06/2017] [Accepted: 02/19/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Gabriela A. Merino
- Ua Area Cs. Agr. Ing. Bio. Y S, Conicet; Universidad Católica de Córdoba; Córdoba Argentina
- Facultad de Ciencias Exactas; Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
| | - Yanina A. Murua
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Cristóbal Fresno
- Ua Area Cs. Agr. Ing. Bio. Y S, Conicet; Universidad Católica de Córdoba; Córdoba Argentina
| | - Juan M. Sendoya
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Mariano Golubicki
- Intergrupo Argentino para el Tratamiento de los Tumores Gastrointestinales; Buenos Aires Argentina
| | - Soledad Iseas
- Hospital de Gastroenterología “Dr. Carlos Bonorino Udaondo”; Buenos Aires Argentina
| | - Mariana Coraglio
- Hospital de Gastroenterología “Dr. Carlos Bonorino Udaondo”; Buenos Aires Argentina
| | - Osvaldo L. Podhajcer
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Andrea S. Llera
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Elmer A. Fernández
- Ua Area Cs. Agr. Ing. Bio. Y S, Conicet; Universidad Católica de Córdoba; Córdoba Argentina
- Facultad de Ciencias Exactas; Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
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221
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Savio AJ, Bapat B. Modulation of transcription factor binding and epigenetic regulation of the MLH1 CpG island and shore by polymorphism rs1800734 in colorectal cancer. Epigenetics 2017; 12:441-448. [PMID: 28304185 DOI: 10.1080/15592294.2017.1305527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The MLH1 promoter polymorphism rs1800734 is associated with MLH1 CpG island hypermethylation and expression loss in colorectal cancer (CRC). Conversely, variant rs1800734 is associated with MLH1 shore, but not island, hypomethylation in peripheral blood mononuclear cell DNA. To explore these distinct patterns, MLH1 CpG island and shore methylation was assessed in CRC cell lines stratified by rs1800734 genotype. Cell lines containing the variant A allele demonstrated MLH1 shore hypomethylation compared to wild type (GG). There was significant enrichment of transcription factor AP4 at the MLH1 promoter in GG and GA cell lines, but not the AA cell line, by chromatin immunoprecipitation studies. Preferential binding to the G allele was confirmed by sequencing in the GA cell line. The enhancer-associated histone modification H3K4me1 was enriched at the MLH1 shore; however, H3K27ac was not, indicating the shore is an inactive enhancer. These results demonstrate the role of variant rs1800734 in altering transcription factor binding as well as epigenetics at regions beyond the MLH1 CpG island in which it is located.
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Affiliation(s)
- Andrea J Savio
- a Lunenfeld-Tanenbaum Research Institute, Sinai Health System , Toronto , Ontario , Canada.,b Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada
| | - Bharati Bapat
- a Lunenfeld-Tanenbaum Research Institute, Sinai Health System , Toronto , Ontario , Canada.,b Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada.,c Department of Pathology , University Health Network , Toronto , Ontario , Canada
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222
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Mook RA, Ren XR, Wang J, Piao H, Barak LS, Kim Lyerly H, Chen W. Benzimidazole inhibitors from the Niclosamide chemotype inhibit Wnt/β-catenin signaling with selectivity over effects on ATP homeostasis. Bioorg Med Chem 2017; 25:1804-1816. [PMID: 28233680 PMCID: PMC5490664 DOI: 10.1016/j.bmc.2017.01.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/19/2017] [Accepted: 01/25/2017] [Indexed: 10/20/2022]
Abstract
The Wnt signaling pathway plays a key role in organ and tissue homeostasis, and when dysregulated, can become a major underlying mechanism of disease, particularly cancer. We reported previously that the anthelmintic drug Niclosamide inhibits Wnt/β-catenin signaling and suppresses colon cancer cell growth in vitro and in vivo. To define Niclosamide's mechanism of Wnt/β-catenin inhibition, and to improve its selectivity and pharmacokinetic properties as an anticancer treatment, we designed a novel class of benzimidazole inhibitors of Wnt/β-catenin signaling based on SAR studies of the Niclosamide salicylanilide chemotype. Niclosamide has multiple biological activities. To address selectivity in our design, we interrogated a protonophore SAR model and used the principle of conformational restriction to identify novel Wnt/β-catenin inhibitors with less effect on ATP cellular homeostasis. These studies led to the identification of 4-chloro-2-(5-(trifluoromethyl)-1H-benzo[d]imidazol-2-yl) phenol (4) and related derivatives with greater selectivity for Wnt/β-catenin signaling inhibition vs. differential effects on cellular ATP homeostasis. This is the first report that the Wnt signaling inhibitory activity of Niclosamide can be translated into a new chemical class and to show that its effects on ATP homeostasis can be separated from its inhibitory effects on Wnt signaling. These compounds could be useful tools to elucidate the mechanism of Niclosamide's inhibition of Wnt signaling, and aid the discovery of inhibitors with improved pharmacologic properties to treat cancer and diseases in which Niclosamide has important biological activity.
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Affiliation(s)
- Robert A Mook
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States.
| | - Xiu-Rong Ren
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States
| | - Jiangbo Wang
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States
| | - Hailan Piao
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States
| | - Larry S Barak
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, United States
| | - H Kim Lyerly
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, United States
| | - Wei Chen
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States.
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223
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O'Brien MT, Oakhill JS, Ling NXY, Langendorf CG, Hoque A, Dite TA, Means AR, Kemp BE, Scott JW. Impact of Genetic Variation on Human CaMKK2 Regulation by Ca 2+-Calmodulin and Multisite Phosphorylation. Sci Rep 2017; 7:43264. [PMID: 28230171 PMCID: PMC5322397 DOI: 10.1038/srep43264] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/23/2017] [Indexed: 12/18/2022] Open
Abstract
The Ca2+-calmodulin dependent protein kinase kinase-2 (CaMKK2) is a key regulator of neuronal function and whole-body energy metabolism. Elevated CaMKK2 activity is strongly associated with prostate and hepatic cancers, whereas reduced CaMKK2 activity has been linked to schizophrenia and bipolar disease in humans. Here we report the functional effects of nine rare-variant point mutations that were detected in large-scale human genetic studies and cancer tissues, all of which occur close to two regulatory phosphorylation sites and the catalytic site on human CaMKK2. Four mutations (G87R, R139W, R142W and E268K) cause a marked decrease in Ca2+-independent autonomous activity, however S137L and P138S mutants displayed increased autonomous and Ca2+-CaM stimulated activities. Furthermore, the G87R mutant is defective in Thr85-autophosphorylation dependent autonomous activity, whereas the A329T mutation rendered CaMKK2 virtually insensitive to Ca2+-CaM stimulation. The G87R and R139W mutants behave as dominant-negative inhibitors of CaMKK2 signaling in cells as they block phosphorylation of the downstream substrate AMP-activated protein kinase (AMPK) in response to ionomycin. Our study provides insight into functionally disruptive, rare-variant mutations in human CaMKK2, which have the potential to influence risk and burden of disease associated with aberrant CaMKK2 activity in human populations carrying these variants.
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Affiliation(s)
- Matthew T O'Brien
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia
| | - Jonathan S Oakhill
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia.,Mary MacKillop Institute for Health Research, Australian Catholic University, 215 Spring Street, Melbourne, 3000, Australia
| | - Naomi X Y Ling
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia
| | - Christopher G Langendorf
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia
| | - Ashfaqul Hoque
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia
| | - Toby A Dite
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia
| | - Anthony R Means
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Bruce E Kemp
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia.,Mary MacKillop Institute for Health Research, Australian Catholic University, 215 Spring Street, Melbourne, 3000, Australia
| | - John W Scott
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia.,Mary MacKillop Institute for Health Research, Australian Catholic University, 215 Spring Street, Melbourne, 3000, Australia
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224
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Andretta E, Cartón-García F, Martínez-Barriocanal Á, de Marcondes PG, Jimenez-Flores LM, Macaya I, Bazzocco S, Bilic J, Rodrigues P, Nieto R, Landolfi S, Ramon y Cajal S, Schwartz S, Brown A, Dopeso H, Arango D. Investigation of the role of tyrosine kinase receptor EPHA3 in colorectal cancer. Sci Rep 2017; 7:41576. [PMID: 28169277 PMCID: PMC5294649 DOI: 10.1038/srep41576] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 12/22/2016] [Indexed: 12/23/2022] Open
Abstract
EPH signaling deregulation has been shown to be important for colorectal carcinogenesis and genome-wide sequencing efforts have identified EPHA3 as one of the most frequently mutated genes in these tumors. However, the role of EPHA3 in colorectal cancer has not been thoroughly investigated. We show here that ectopic expression of wild type EPHA3 in colon cancer cells did not affect their growth, motility/invasion or metastatic potential in vivo. Moreover, overexpression of mutant EPHA3 or deletion of the endogenous mutant EPHA3 in colon cancer cells did not affect their growth or motility. EPHA3 inactivation in mice did not initiate the tumorigenic process in their intestine, and had no effects on tumor size/multiplicity after tumor initiation either genetically or pharmacologically. In addition, immunohistochemical analysis of EPHA3 tumor levels did not reveal associations with survival or clinicopathological features of colorectal cancer patients. In conclusion, we show that EPHA3 does not play a major role in colorectal tumorigenesis. These results significantly contribute to our understanding of the role of EPH signaling during colorectal carcinogenesis, and highlighting the need for detailed functional studies to confirm the relevance of putative cancer driver genes identified in sequencing efforts of the cancer genome.
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Affiliation(s)
- Elena Andretta
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d’Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | - Fernando Cartón-García
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d’Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | - Águeda Martínez-Barriocanal
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d’Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | - Priscila Guimarães de Marcondes
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d’Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | - Lizbeth M. Jimenez-Flores
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d’Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | - Irati Macaya
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d’Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | - Sarah Bazzocco
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d’Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | - Josipa Bilic
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d’Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | - Paulo Rodrigues
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d’Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | - Rocio Nieto
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d’Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | | | | | - Simo Schwartz
- Group of Drug Delivery and Targeting, CIBBIM-Nanomedicine, Vall d’Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Arthur Brown
- Robarts Research Institute, London, Ontario, Canada
| | - Higinio Dopeso
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d’Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | - Diego Arango
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d’Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron, 119-129, 08035 Barcelona, Spain
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225
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Li X, Li M, Ruan H, Qiu W, Xu X, Zhang L, Yu J. Co-targeting translation and proteasome rapidly kills colon cancer cells with mutant RAS/RAF via ER stress. Oncotarget 2017; 8:9280-9292. [PMID: 28030835 PMCID: PMC5354731 DOI: 10.18632/oncotarget.14063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/13/2016] [Indexed: 12/20/2022] Open
Abstract
Colorectal cancers with mutant RAS/RAF are therapy refractory. Deregulated mRNA translation has become an emerging target in cancer treatment. We recently reported that mTOR inhibitors induce apoptosis via ER stress and the extrinsic pathway upon acute inhibition of the eIF4F complex in colon cancer cells and xenografts, while mutant BRAF600E leads to therapeutic resistance via ERK-mediated Mcl-1 stabilization. In this study, we demonstrated that several other translation inhibitors also activate ER stress and the extrinsic apoptotic pathway. Co-targeting translation and proteasome using the combination of Episilvestrol and Bortezomib promoted strong ER stress and rapid killing of colon cancer cells with mutant RAS/RAF in culture and mice. This combination led to marked induction of ER stress and ATF4/CHOP, followed by DR5- and BAX-dependent apoptosis, but unexpectedly with maintained or even increased levels of prosurvival factors such as p-AKT, p-4E-BP1, Mcl-1, and eiF4E targets c-Myc and Bcl-xL. Our study supports that targeting deregulated proteostasis is a promising approach for treating advanced colon cancer via induction of destructive ER stress that overcomes multiple resistance mechanisms associated with translation inhibition.
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Affiliation(s)
- Xiangyun Li
- First department, State Key Laboratory of Trauma, Burn and Combined Injury, Research Institute of Surgery and Daping Hospital, Third Military Medical University, Daping, Yu Zhong District, Chongqing 400042, P.R. China
- Department of Pathology, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Mei Li
- Department of Animal Genetics, Breeding and Reproduction, Nanjing Agricultural University, Weigang, Nanjing 210095, P.R. China
- Department of Pathology, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Hang Ruan
- Department of Pathology, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Wei Qiu
- First department, State Key Laboratory of Trauma, Burn and Combined Injury, Research Institute of Surgery and Daping Hospital, Third Military Medical University, Daping, Yu Zhong District, Chongqing 400042, P.R. China
| | - Xiang Xu
- First department, State Key Laboratory of Trauma, Burn and Combined Injury, Research Institute of Surgery and Daping Hospital, Third Military Medical University, Daping, Yu Zhong District, Chongqing 400042, P.R. China
| | - Lin Zhang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Jian Yu
- Department of Pathology, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
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226
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Chen J, Herlong FH, Stroehlein JR, Mishra L. Mutations of Chromatin Structure Regulating Genes in Human Malignancies. Curr Protein Pept Sci 2017; 17:411-37. [PMID: 26796307 PMCID: PMC5403969 DOI: 10.2174/1389203717666160122120008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 12/25/2015] [Accepted: 12/30/2015] [Indexed: 02/08/2023]
Abstract
Chromatin structure regulating processes mediated by the adenosine triphosphate (ATP) –dependent chromatin remodeling complex and the covalent histone-modifying complexes are critical to gene transcriptional control and normal cellular processes, including cell stemness, differentiation, and proliferation. Gene mutations, structural abnormalities, and epigenetic modifications that lead to aberrant expression of chromatin structure regulating members have been observed in most of human malignancies. Advances in next-generation sequencing (NGS) technologies in recent years have allowed in-depth study of somatic mutations in human cancer samples. The Cancer Genome Atlas (TCGA) is the largest effort to date to characterize cancer genome using NGS technology. In this review, we summarize somatic mutations of chromatin-structure regulating genes from TCGA publications and other cancer genome studies, providing an overview of genomic alterations of chromatin regulating genes in human malignancies.
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Affiliation(s)
- Jian Chen
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.
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227
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Facile synthesis of novel substituted aryl-thiazole (SAT) analogs via one-pot multi-component reaction as potent cytotoxic agents against cancer cell lines. Bioorg Chem 2017; 70:133-143. [DOI: 10.1016/j.bioorg.2016.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/07/2016] [Accepted: 12/17/2016] [Indexed: 11/21/2022]
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228
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Mamlouk S, Childs LH, Aust D, Heim D, Melching F, Oliveira C, Wolf T, Durek P, Schumacher D, Bläker H, von Winterfeld M, Gastl B, Möhr K, Menne A, Zeugner S, Redmer T, Lenze D, Tierling S, Möbs M, Weichert W, Folprecht G, Blanc E, Beule D, Schäfer R, Morkel M, Klauschen F, Leser U, Sers C. DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer. Nat Commun 2017; 8:14093. [PMID: 28120820 PMCID: PMC5288500 DOI: 10.1038/ncomms14093] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 11/28/2016] [Indexed: 02/06/2023] Open
Abstract
Genetic heterogeneity between and within tumours is a major factor determining cancer progression and therapy response. Here we examined DNA sequence and DNA copy-number heterogeneity in colorectal cancer (CRC) by targeted high-depth sequencing of 100 most frequently altered genes. In 97 samples, with primary tumours and matched metastases from 27 patients, we observe inter-tumour concordance for coding mutations; in contrast, gene copy numbers are highly discordant between primary tumours and metastases as validated by fluorescent in situ hybridization. To further investigate intra-tumour heterogeneity, we dissected a single tumour into 68 spatially defined samples and sequenced them separately. We identify evenly distributed coding mutations in APC and TP53 in all tumour areas, yet highly variable gene copy numbers in numerous genes. 3D morpho-molecular reconstruction reveals two clusters with divergent copy number aberrations along the proximal-distal axis indicating that DNA copy number variations are a major source of tumour heterogeneity in CRC.
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Affiliation(s)
- Soulafa Mamlouk
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Liam Harold Childs
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Daniela Aust
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
- NCT Biobank Dresden, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Daniel Heim
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Friederike Melching
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Cristiano Oliveira
- Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Thomas Wolf
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Pawel Durek
- Experimental Rheumatology, German Rheumatism Research Centre, Berlin 10117, Germany
| | - Dirk Schumacher
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Hendrik Bläker
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | | | - Bastian Gastl
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- BSIO Berlin School of Integrative Oncology, University Medicine Charité, Berlin 13353, Germany
| | - Kerstin Möhr
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Andrea Menne
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Silke Zeugner
- Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Torben Redmer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Dido Lenze
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Sascha Tierling
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken 66123, Germany
| | - Markus Möbs
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute of Pathology, Technical University Munich, Munich 81675, Germany
| | - Gunnar Folprecht
- University Hospital Carl Gustav Carus, University Cancer Center/Medical Dpt. I, Dresden 01307, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
- Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
- Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Reinhold Schäfer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Markus Morkel
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Frederick Klauschen
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Christine Sers
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
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229
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Acquired RAS or EGFR mutations and duration of response to EGFR blockade in colorectal cancer. Nat Commun 2016; 7:13665. [PMID: 27929064 PMCID: PMC5155160 DOI: 10.1038/ncomms13665] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 10/23/2016] [Indexed: 12/15/2022] Open
Abstract
Blockade of the epidermal growth factor receptor (EGFR) with the monoclonal antibodies cetuximab or panitumumab is effective in a subset of colorectal cancers (CRCs), but the emergence of resistance limits the efficacy of these therapeutic agents. At relapse, the majority of patients develop RAS mutations, while a subset acquires EGFR extracellular domain (ECD) mutations. Here we find that patients who experience greater and longer responses to EGFR blockade preferentially develop EGFR ECD mutations, while RAS mutations emerge more frequently in patients with smaller tumour shrinkage and shorter progression-free survival. In circulating cell-free tumour DNA of patients treated with anti-EGFR antibodies, RAS mutations emerge earlier than EGFR ECD variants. Subclonal RAS but not EGFR ECD mutations are present in CRC samples obtained before exposure to EGFR blockade. These data indicate that clonal evolution of drug-resistant cells is associated with the clinical outcome of CRC patients treated with anti-EGFR antibodies.
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230
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Gebert J, Schnölzer M, Warnken U, Kopitz J. Combining Click Chemistry-Based Proteomics With Dox-Inducible Gene Expression. Methods Enzymol 2016; 585:295-327. [PMID: 28109436 DOI: 10.1016/bs.mie.2016.09.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Inactivating mutations in single genes can trigger, prevent, promote, or alleviate diseases. Identifying such disease-related genes is a main pillar of medical research. Since proteins play a crucial role in mediating these effects, their impact on the diseased cells' proteome including posttranslational modifications has to be elucidated for a detailed understanding of the role of these genes in the disease process. In complex disorders, like cancer, several genes contribute to the disease process, thereby hampering the assignment of a proteomic change to the corresponding causative gene. To enable comprehensive screening for the impact of inactivation of a gene, e.g., loss of a tumor suppressor in cancer, on the cellular proteome, we present a strategy based on combination of three technologies that is recombinase-mediated cassette exchange, click chemistry, and mass spectrometry. The methodology is exemplified by the analysis of the proteomic changes induced by the loss of a tumor suppressor gene in colorectal cancer cells. To demonstrate the applicability to screen for posttranslational modification changes, we also describe the analysis of protein glycosylation changes caused by the tumor suppressor inactivation. In principle, this strategy can be applied to analyze the effects of any gene of interest on protein expression as well as posttranslational modification by glycosylation. Moreover adaptation of the strategy to an appropriate cell culture model has the potential for application on a broad range of diseases where the disease-promoting mutations have been identified.
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Affiliation(s)
- J Gebert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - U Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - J Kopitz
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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231
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Pereira JFS, Awatade NT, Loureiro CA, Matos P, Amaral MD, Jordan P. The third dimension: new developments in cell culture models for colorectal research. Cell Mol Life Sci 2016; 73:3971-89. [PMID: 27147463 PMCID: PMC11108567 DOI: 10.1007/s00018-016-2258-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/20/2016] [Accepted: 04/28/2016] [Indexed: 12/23/2022]
Abstract
Cellular models are important tools in various research areas related to colorectal biology and associated diseases. Herein, we review the most widely used cell lines and the different techniques to grow them, either as cell monolayer, polarized two-dimensional epithelia on membrane filters, or as three-dimensional spheres in scaffold-free or matrix-supported culture conditions. Moreover, recent developments, such as gut-on-chip devices or the ex vivo growth of biopsy-derived organoids, are also discussed. We provide an overview on the potential applications but also on the limitations for each of these techniques, while evaluating their contribution to provide more reliable cellular models for research, diagnostic testing, or pharmacological validation related to colon physiology and pathophysiology.
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Affiliation(s)
- Joana F S Pereira
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016, Lisbon, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Nikhil T Awatade
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Cláudia A Loureiro
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016, Lisbon, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Paulo Matos
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016, Lisbon, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Margarida D Amaral
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Peter Jordan
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal.
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232
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Aberrant DNA methylation of acute myeloid leukemia and colorectal cancer in a Chinese pedigree with a MLL3 germline mutation. Tumour Biol 2016; 37:12609-12618. [PMID: 27405564 DOI: 10.1007/s13277-016-5130-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/29/2016] [Indexed: 12/14/2022] Open
Abstract
Unlike genetic aberrations, epigenetic alterations do not modify the deoxyribonucleic acid (DNA) coding sequence and can be reversed pharmacologically. Identifying a particular epigenetic alteration such as abnormal DNA methylation may provide better understanding of cancers and improve current therapy. In a Chinese pedigree with colorectal carcinoma and acute myeloid leukemia, we examined the genome-wide DNA methylation level of cases and explored the role of methylation in pathogenesis and progression. DNA methylation status in the four cases, which all harbor a MLL3 germline mutation, differed from that of the normal control, and hypermethylation was more prevalent. Also, more CpG sites were hypermethylated in the acute-phase AML patient than in the AML patient in remission. Fifty-nine hyper- or hypomethylated genes were identified as common to all four cases. Genome-wide DNA methylation analysis demonstrated that differentially methylated sites among acute myeloid leukemia and colorectal carcinoma cases and the control were in both promoters (CpG island) and gene body regions (shelf/shore areas). Hypermethylation was more prevalent in cancer cases. The study supports the suggestion that the level of DNA methylation changes in AML progression.
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233
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Analysis of Mammalian Cell Proliferation and Macromolecule Synthesis Using Deuterated Water and Gas Chromatography-Mass Spectrometry. Metabolites 2016; 6:metabo6040034. [PMID: 27754354 PMCID: PMC5192440 DOI: 10.3390/metabo6040034] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 10/10/2016] [Accepted: 10/10/2016] [Indexed: 11/16/2022] Open
Abstract
Deuterated water (²H₂O), a stable isotopic tracer, provides a convenient and reliable way to label multiple cellular biomass components (macromolecules), thus permitting the calculation of their synthesis rates. Here, we have combined ²H₂O labelling, GC-MS analysis and a novel cell fractionation method to extract multiple biomass components (DNA, protein and lipids) from the one biological sample, thus permitting the simultaneous measurement of DNA (cell proliferation), protein and lipid synthesis rates. We have used this approach to characterize the turnover rates and metabolism of a panel of mammalian cells in vitro (muscle C2C12 and colon cancer cell lines). Our data show that in actively-proliferating cells, biomass synthesis rates are strongly linked to the rate of cell division. Furthermore, in both proliferating and non-proliferating cells, it is the lipid pool that undergoes the most rapid turnover when compared to DNA and protein. Finally, our data in human colon cancer cell lines reveal a marked heterogeneity in the reliance on the de novo lipogenic pathway, with the cells being dependent on both 'self-made' and exogenously-derived fatty acid.
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234
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Yang Z, Wong A, Kuh D, Paul DS, Rakyan VK, Leslie RD, Zheng SC, Widschwendter M, Beck S, Teschendorff AE. Correlation of an epigenetic mitotic clock with cancer risk. Genome Biol 2016; 17:205. [PMID: 27716309 PMCID: PMC5046977 DOI: 10.1186/s13059-016-1064-3] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Variation in cancer risk among somatic tissues has been attributed to variations in the underlying rate of stem cell division. For a given tissue type, variable cancer risk between individuals is thought to be influenced by extrinsic factors which modulate this rate of stem cell division. To date, no molecular mitotic clock has been developed to approximate the number of stem cell divisions in a tissue of an individual and which is correlated with cancer risk. Results Here, we integrate mathematical modeling with prior biological knowledge to construct a DNA methylation-based age-correlative model which approximates a mitotic clock in both normal and cancer tissue. By focusing on promoter CpG sites that localize to Polycomb group target genes that are unmethylated in 11 different fetal tissue types, we show that increases in DNA methylation at these sites defines a tick rate which correlates with the estimated rate of stem cell division in normal tissues. Using matched DNA methylation and RNA-seq data, we further show that it correlates with an expression-based mitotic index in cancer tissue. We demonstrate that this mitotic-like clock is universally accelerated in cancer, including pre-cancerous lesions, and that it is also accelerated in normal epithelial cells exposed to a major carcinogen. Conclusions Unlike other epigenetic and mutational clocks or the telomere clock, the epigenetic clock proposed here provides a concrete example of a mitotic-like clock which is universally accelerated in cancer and precancerous lesions. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1064-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhen Yang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing at University College London, London, UK
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing at University College London, London, UK
| | - Dirk S Paul
- Medical Genomics, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - R David Leslie
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Shijie C Zheng
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
| | - Martin Widschwendter
- Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China. .,Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK. .,Statistical Cancer Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
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235
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Garin-Muga A, Odriozola L, Martínez-Val A, Del Toro N, Martínez R, Molina M, Cantero L, Rivera R, Garrido N, Dominguez F, Sanchez Del Pino MM, Vizcaíno JA, Corrales FJ, Segura V. Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence. J Proteome Res 2016; 15:4101-4115. [PMID: 27581094 PMCID: PMC5099979 DOI: 10.1021/acs.jproteome.6b00437] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
The current catalogue of the human
proteome is not yet complete,
as experimental proteomics evidence is still elusive for a group of
proteins known as the missing proteins. The Human Proteome Project
(HPP) has been successfully using technology and bioinformatic resources
to improve the characterization of such challenging proteins. In this
manuscript, we propose a pipeline starting with the mining of the
PRIDE database to select a group of data sets potentially enriched
in missing proteins that are subsequently analyzed for protein identification
with a method based on the statistical analysis of proteotypic peptides.
Spermatozoa and the HEK293 cell line were found to be a promising
source of missing proteins and clearly merit further attention in
future studies. After the analysis of the selected samples, we found
342 PSMs, suggesting the presence of 97 missing proteins in human
spermatozoa or the HEK293 cell line, while only 36 missing proteins
were potentially detected in the retina, frontal cortex, aorta thoracica,
or placenta. The functional analysis of the missing proteins detected
confirmed their tissue specificity, and the validation of a selected
set of peptides using targeted proteomics (SRM/MRM assays) further
supports the utility of the proposed pipeline. As illustrative examples,
DNAH3 and TEPP in spermatozoa, and UNCX and ATAD3C in HEK293 cells
were some of the more robust and remarkable identifications in this
study. We provide evidence indicating the relevance to carefully analyze
the ever-increasing MS/MS data available from PRIDE and other repositories
as sources for missing proteins detection in specific biological matrices
as revealed for HEK293 cells.
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Affiliation(s)
- Alba Garin-Muga
- Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain
| | - Leticia Odriozola
- Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research , 31008, Pamplona, Spain
| | - Ana Martínez-Val
- Proteomics Unit, Spanish National Cancer Research Centre , 28029, Madrid, Spain
| | - Noemí Del Toro
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust GenomeCampus, Hinxton, Cambridge, CB10 1SD, U.K
| | - Rocío Martínez
- Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain
| | - Manuela Molina
- Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain
| | - Laura Cantero
- Proteomics Unit (SCSIE), University of Valencia , 46010, Valencia, Spain
| | - Rocío Rivera
- Andrology Laboratory and Sperm Bank, Instituto Universitario IVI , 46015, Valencia, Spain
| | - Nicolás Garrido
- Andrology Laboratory and Sperm Bank, Instituto Universitario IVI , 46015, Valencia, Spain
| | | | | | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust GenomeCampus, Hinxton, Cambridge, CB10 1SD, U.K
| | - Fernando J Corrales
- Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research , 31008, Pamplona, Spain.,Division of Hepatology and Gene Therapy, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain
| | - Victor Segura
- Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research , 31008, Pamplona, Spain
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236
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Stromal uptake and transmission of acid is a pathway for venting cancer cell-generated acid. Proc Natl Acad Sci U S A 2016; 113:E5344-53. [PMID: 27543333 DOI: 10.1073/pnas.1610954113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Proliferation and invasion of cancer cells require favorable pH, yet potentially toxic quantities of acid are produced metabolically. Membrane-bound transporters extrude acid from cancer cells, but little is known about the mechanisms that handle acid once it is released into the poorly perfused extracellular space. Here, we studied acid handling by myofibroblasts (colon cancer-derived Hs675.T, intestinal InMyoFib, embryonic colon-derived CCD-112-CoN), skin fibroblasts (NHDF-Ad), and colorectal cancer (CRC) cells (HCT116, HT29) grown in monoculture or coculture. Expression of the acid-loading transporter anion exchanger 2 (AE2) (SLC4A2 product) was detected in myofibroblasts and fibroblasts, but not in CRC cells. Compared with CRC cells, Hs675.T and InMyoFib myofibroblasts had very high capacity to absorb extracellular acid. Acid uptake into CCD-112-CoN and NHDF-Ad cells was slower and comparable to levels in CRC cells, but increased alongside SLC4A2 expression under stimulation with transforming growth factor β1 (TGFβ1), a cytokine involved in cancer-stroma interplay. Myofibroblasts and fibroblasts are connected by gap junctions formed by proteins such as connexin-43, which allows the absorbed acid load to be transmitted across the stromal syncytium. To match the stimulatory effect on acid uptake, cell-to-cell coupling in NHDF-Ad and CCD-112-CoN cells was strengthened with TGFβ1. In contrast, acid transmission was absent between CRC cells, even after treatment with TGFβ1. Thus, stromal cells have the necessary molecular apparatus for assembling an acid-venting route that can improve the flow of metabolic acid through tumors. Importantly, the activities of stromal AE2 and connexin-43 do not place an energetic burden on cancer cells, allowing resources to be diverted for other activities.
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237
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Pinto AT, Pinto ML, Velho S, Pinto MT, Cardoso AP, Figueira R, Monteiro A, Marques M, Seruca R, Barbosa MA, Mareel M, Oliveira MJ, Rocha S. Intricate Macrophage-Colorectal Cancer Cell Communication in Response to Radiation. PLoS One 2016; 11:e0160891. [PMID: 27513864 PMCID: PMC4981353 DOI: 10.1371/journal.pone.0160891] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/26/2016] [Indexed: 11/19/2022] Open
Abstract
Both cancer and tumour-associated host cells are exposed to ionizing radiation when a tumour is subjected to radiotherapy. Macrophages frequently constitute the most abundant tumour-associated immune population, playing a role in tumour progression and response to therapy. The present work aimed to evaluate the importance of macrophage-cancer cell communication in the cellular response to radiation. To address this question, we established monocultures and indirect co-cultures of human monocyte-derived macrophages with RKO or SW1463 colorectal cancer cells, which exhibit higher and lower radiation sensitivity, respectively. Mono- and co-cultures were then irradiated with 5 cumulative doses, in a similar fractionated scheme to that used during cancer patients' treatment (2 Gy/fraction/day). Our results demonstrated that macrophages sensitize RKO to radiation-induced apoptosis, while protecting SW1463 cells. Additionally, the co-culture with macrophages increased the mRNA expression of metabolism- and survival-related genes more in SW1463 than in RKO. The presence of macrophages also upregulated glucose transporter 1 expression in irradiated SW1463, but not in RKO cells. In addition, the influence of cancer cells on the expression of pro- and anti-inflammatory macrophage markers, upon radiation exposure, was also evaluated. In the presence of RKO or SW1463, irradiated macrophages exhibit higher levels of pro-inflammatory TNF, IL6, CCL2 and CCR7, and of anti-inflammatory CCL18. However, RKO cells induce an increase of macrophage pro-inflammatory IL1B, while SW1463 cells promote higher pro-inflammatory CXCL8 and CD80, and also anti-inflammatory VCAN and IL10 levels. Thus, our data demonstrated that macrophages and cancer cells mutually influence their response to radiation. Notably, conditioned medium from irradiated co-cultures increased non-irradiated RKO cell migration and invasion and did not impact on angiogenesis in a chicken embryo chorioallantoic membrane assay. Overall, the establishment of primary human macrophage-cancer cell co-cultures revealed an intricate cell communication in response to ionizing radiation, which should be considered when developing therapies adjuvant to radiotherapy.
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Affiliation(s)
- Ana T. Pinto
- i3s-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB-Institute of Biomedical Engineering, University of Porto, Porto, Portugal
- FEUP-Faculty of Engineering, University of Porto, Porto, Portugal
| | - Marta L. Pinto
- i3s-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB-Institute of Biomedical Engineering, University of Porto, Porto, Portugal
- ICBAS-Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Sérgia Velho
- i3s-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Marta T. Pinto
- i3s-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Ana P. Cardoso
- i3s-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB-Institute of Biomedical Engineering, University of Porto, Porto, Portugal
| | - Rita Figueira
- Radiotherapy Service, Centro Hospitalar S. João, EPE, Porto, Portugal
| | - Armanda Monteiro
- Radiotherapy Service, Centro Hospitalar S. João, EPE, Porto, Portugal
| | - Margarida Marques
- Radiotherapy Service, Centro Hospitalar S. João, EPE, Porto, Portugal
| | - Raquel Seruca
- i3s-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Department of Pathology and Oncology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Mário A. Barbosa
- i3s-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB-Institute of Biomedical Engineering, University of Porto, Porto, Portugal
- ICBAS-Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Marc Mareel
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Maria J. Oliveira
- i3s-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB-Institute of Biomedical Engineering, University of Porto, Porto, Portugal
- Department of Pathology and Oncology, Faculty of Medicine, University of Porto, Porto, Portugal
- * E-mail:
| | - Sónia Rocha
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
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THE CULTIVATION OF RAT COLON TUMOR WITH PLACENTAL MULTIPOTENT STEM CELLS. BIOTECHNOLOGIA ACTA 2016. [DOI: 10.15407/biotech9.04.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Lundberg IV, Edin S, Eklöf V, Öberg Å, Palmqvist R, Wikberg ML. SOX2 expression is associated with a cancer stem cell state and down-regulation of CDX2 in colorectal cancer. BMC Cancer 2016; 16:471. [PMID: 27411517 PMCID: PMC4944515 DOI: 10.1186/s12885-016-2509-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 06/16/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND To improve current treatment strategies for patients with aggressive colorectal cancer (CRC), the molecular understanding of subgroups of CRC with poor prognosis is of vast importance. SOX2 positive tumors have been associated with a poor patient outcome, but the functional role of SOX2 in CRC patient prognosis is still unclear. METHODS An in vitro cell culture model expressing SOX2 was used to investigate the functional role of SOX2 in CRC. In vitro findings were verified using RNA from fresh frozen tumor tissue or immunohistochemistry on formalin fixed paraffin embedded (FFPE) tumor tissue from a cohort of 445 CRC patients. RESULTS Using our in vitro model, we found that SOX2 expressing cells displayed several characteristics of cancer stem cells; such as a decreased proliferative rate, a spheroid growth pattern, and increased expression of stem cell markers CD24 and CD44. Cells expressing SOX2 also showed down-regulated expression of the intestinal epithelial marker CDX2. We next evaluated CDX2 expression in our patient cohort. CDX2 down-regulation was more often found in right sided tumors of high grade and high stage. Furthermore, a decreased expression of CDX2 was closely linked to MSI, CIMP-high as well as BRAF mutated tumors. A decreased expression of CDX2 was also, in a stepwise manner, strongly correlated to a poor patient prognosis. When looking at SOX2 expression in relation to CDX2, we found that SOX2 expressing tumors more often displayed a down-regulated expression of CDX2. In addition, SOX2 expressing tumors with a down-regulated CDX2 expression had a worse patient prognosis compared to those with retained CDX2 expression. CONCLUSIONS Our results indicate that SOX2 expression induces a cellular stem cell state in human CRC with a decreased expression of CDX2. Furthermore, a down-regulated expression of CDX2 results in a poor patient prognosis in CRC and at least part of the prognostic importance of SOX2 is mediated through CDX2 down-regulation.
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Affiliation(s)
- Ida V Lundberg
- Department of Medical Biosciences, Pathology, Umeå University, Building 6M, SE-90185, Umeå, Sweden
| | - Sofia Edin
- Department of Medical Biosciences, Pathology, Umeå University, Building 6M, SE-90185, Umeå, Sweden.
| | - Vincy Eklöf
- Department of Medical Biosciences, Pathology, Umeå University, Building 6M, SE-90185, Umeå, Sweden
| | - Åke Öberg
- Department of Surgical and Perioperative Sciences, Surgery, Umeå University, Umeå, Sweden
| | - Richard Palmqvist
- Department of Medical Biosciences, Pathology, Umeå University, Building 6M, SE-90185, Umeå, Sweden
| | - Maria L Wikberg
- Department of Medical Biosciences, Pathology, Umeå University, Building 6M, SE-90185, Umeå, Sweden
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Millen R, Malaterre J, Cross RS, Carpinteri S, Desai J, Tran B, Darcy P, Gibbs P, Sieber O, Zeps N, Waring P, Fox S, Pereira L, Ramsay RG. Immunomodulation by MYB is associated with tumor relapse in patients with early stage colorectal cancer. Oncoimmunology 2016; 5:e1149667. [PMID: 27622014 PMCID: PMC5006930 DOI: 10.1080/2162402x.2016.1149667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 01/26/2023] Open
Abstract
The presence of tumor immune infiltrating cells (TILs), particularly CD8+ T-cells, is a robust predictor of outcome in patients with colorectal cancer (CRC). We revisited TIL abundance specifically in patients with microsatellite stable (MSS) CRC without evidence of lymph node or metastatic spread. Examination of the density of CD8+ T-cells in primary tumors in the context of other pro-oncogenic markers was performed to investigate potential regulators of TILs. Two independent cohorts of patients with MSS T2-4N0M0 CRC, enriched for cases with atypical relapse, were investigated. We quantified CD8+ and CD45RO+ -TILs, inflammatory markers, NFkBp65, pStat3, Cyclo-oxygenase-2 (COX2) and GRP78 as well as transcription factors (TF), β-catenin and MYB. High CD8+ TILs correlated with a better relapse-free survival in both cohorts (p = 0.002) with MYB and its target gene, GRP78 being higher in the relapse group (p = 0.001); no difference in pSTAT3 and p65 was observed. A mouse CRC (CT26) model was employed to evaluate the effect of MYB on GRP78 expression as well as T-cell infiltration. MYB over-expressing in CT26 cells increased GRP78 expression and the analysis of tumor-draining lymph nodes adjacent to tumors showed reduced T-cell activation. Furthermore, MYB over-expression reduced the efficacy of anti-PD-1 to modulate CT26 tumor growth. This high MYB and GRP78 show a reciprocal relationship with CD8+ TILs which may be useful refining the prediction of patient outcome. These data reveal a new immunomodulatory function for MYB suggesting a basis for further development of anti-GRP78 and/or anti-MYB therapies.
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Affiliation(s)
- Rosemary Millen
- Peter MacCallum Cancer Center and The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne ,Victoria, Australia; St Vincent's Hospital, Fitzroy, Victoria, Australia
| | - Jordane Malaterre
- Peter MacCallum Cancer Center and The Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne ,Victoria, Australia
| | - Ryan S Cross
- Peter MacCallum Cancer Center and The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne ,Victoria, Australia; The Department of Pathology, University of Melbourne, Melbourne Victoria, Australia
| | - Sandra Carpinteri
- Peter MacCallum Cancer Center and The Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne ,Victoria, Australia
| | - Jayesh Desai
- Peter MacCallum Cancer Center and The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne ,Victoria, Australia; Royal Melbourne Hospital and Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Ben Tran
- Royal Melbourne Hospital and Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute , Parkville, Victoria, Australia
| | - Phillip Darcy
- Peter MacCallum Cancer Center and The Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne ,Victoria, Australia
| | - Peter Gibbs
- Royal Melbourne Hospital and Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute , Parkville, Victoria, Australia
| | - Oliver Sieber
- Royal Melbourne Hospital and Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute , Parkville, Victoria, Australia
| | - Nikolajs Zeps
- St John of God Subiaco Hospital, Subiaco, Western Australia, Australia; The School of Surgery, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Paul Waring
- The Department of Pathology, University of Melbourne , Melbourne Victoria, Australia
| | - Stephen Fox
- Peter MacCallum Cancer Center and The Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne ,Victoria, Australia
| | - Lloyd Pereira
- Peter MacCallum Cancer Center and The Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne ,Victoria, Australia
| | - Robert G Ramsay
- Peter MacCallum Cancer Center and The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne ,Victoria, Australia; The Department of Pathology, University of Melbourne, Melbourne Victoria, Australia
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242
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OncoScape: Exploring the cancer aberration landscape by genomic data fusion. Sci Rep 2016; 6:28103. [PMID: 27321817 PMCID: PMC4913322 DOI: 10.1038/srep28103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/25/2016] [Indexed: 01/22/2023] Open
Abstract
Although large-scale efforts for molecular profiling of cancer samples provide multiple data types for many samples, most approaches for finding candidate cancer genes rely on somatic mutations and DNA copy number only. We present a new method, OncoScape, which exploits five complementary data types across 11 cancer types to identify new candidate cancer genes. We find many rarely mutated genes that are strongly affected by other aberrations. We retrieve the majority of known cancer genes but also new candidates such as STK31 and MSRA with very high confidence. Several genes show a dual oncogene- and tumor suppressor-like behavior depending on the tumor type. Most notably, the well-known tumor suppressor RB1 shows strong oncogene-like signal in colon cancer. We applied OncoScape to cell lines representing ten cancer types, providing the most comprehensive comparison of aberrations in cell lines and tumor samples to date. This revealed that glioblastoma, breast and colon cancer show strong similarity between cell lines and tumors, while head and neck squamous cell carcinoma and bladder cancer, exhibit very little similarity between cell lines and tumors. To facilitate exploration of the cancer aberration landscape, we created a web portal enabling interactive analysis of OncoScape results (http://ccb.nki.nl/software/oncoscape).
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243
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Qiu Z, Zou K, Zhuang L, Qin J, Li H, Li C, Zhang Z, Chen X, Cen J, Meng Z, Zhang H, Li Y, Hui L. Hepatocellular carcinoma cell lines retain the genomic and transcriptomic landscapes of primary human cancers. Sci Rep 2016; 6:27411. [PMID: 27273737 PMCID: PMC4895220 DOI: 10.1038/srep27411] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 05/18/2016] [Indexed: 01/03/2023] Open
Abstract
Hepatocellular carcinoma (HCC) cell lines are useful in vitro models for the study of primary HCCs. Because cell lines acquire additional mutations in culture, it is important to understand to what extent HCC cell lines retain the genetic landscapes of primary HCCs. Most HCC cell lines were established during the last century, precluding comparison between cell lines and primary cancers. In this study, 9 Chinese HCC cell lines with matched patient-derived cells at low passages (PDCs) were established in the defined culture condition. Whole genome analyses of 4 HCC cell lines showed that genomic mutation landscapes, including mutations, copy number alterations (CNAs) and HBV integrations, were highly stable during cell line establishment. Importantly, genetic alterations in cancer drivers and druggable genes were reserved in cell lines. HCC cell lines also retained gene expression patterns of primary HCCs during in vitro culture. Finally, sequential analysis of HCC cell lines and PDCs at different passages revealed their comparable and stable genomic and transcriptomic levels if maintained within proper passages. These results show that HCC cell lines largely retain the genomic and transcriptomic landscapes of primary HCCs, thus laying the rationale for testing HCC cell lines as preclinical models in precision medicine.
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Affiliation(s)
- Zhixin Qiu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Keke Zou
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Liping Zhuang
- Department of Minimally Invasive Therapy, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China, 200032 Shanghai, China
| | - Jianjie Qin
- Liver Transplantation Center, Key Laboratory of Living Donor Liver Transplantation of Ministry of Public Health, The First Affiliated Hospital of Nanjing Medical University, 210029 Nanjing, China
| | - Hong Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Chao Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Zhengtao Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China.,University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xiaotao Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Jin Cen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Zhiqiang Meng
- Department of Minimally Invasive Therapy, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China, 200032 Shanghai, China
| | - Haibin Zhang
- Fifth Department of Hepatic Surgery, Eastern Hepatobilliary Surgery Hospital, Second Military Medical University, 200438 Shanghai, China
| | - Yixue Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Lijian Hui
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
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Nickerson ML, Witte N, Im KM, Turan S, Owens C, Misner K, Tsang SX, Cai Z, Wu S, Dean M, Costello JC, Theodorescu D. Molecular analysis of urothelial cancer cell lines for modeling tumor biology and drug response. Oncogene 2016; 36:35-46. [PMID: 27270441 PMCID: PMC5140783 DOI: 10.1038/onc.2016.172] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/04/2016] [Accepted: 03/07/2016] [Indexed: 12/14/2022]
Abstract
The utility of tumor-derived cell lines is dependent on their ability to recapitulate underlying genomic aberrations and primary tumor biology. Here, we sequenced the exomes of 25 bladder cancer (BCa) cell lines and compared mutations, copy number alterations (CNAs), gene expression and drug response to BCa patient profiles in The Cancer Genome Atlas (TCGA). We observed a mutation pattern associated with altered CpGs and APOBEC-family cytosine deaminases similar to mutation signatures derived from somatic alterations in muscle-invasive (MI) primary tumors, highlighting a major mechanism(s) contributing to cancer-associated alterations in the BCa cell line exomes. Non-silent sequence alterations were confirmed in 76 cancer-associated genes, including mutations that likely activate oncogenes TERT and PIK3CA, and alter chromatin-associated proteins (MLL3, ARID1A, CHD6 and KDM6A) and established BCa genes (TP53, RB1, CDKN2A and TSC1). We identified alterations in signaling pathways and proteins with related functions, including the PI3K/mTOR pathway, altered in 60% of lines; BRCA DNA repair, 44% and SYNE1–SYNE2, 60%. Homozygous deletions of chromosome 9p21 are known to target the cell cycle regulators CDKN2A and CDKN2B. This loci was commonly lost in BCa cell lines and we show the deletions extended to the polyamine enzyme methylthioadenosine (MTA) phosphorylase (MTAP) in 36% of lines, transcription factor DMRTA1 (27%) and antiviral interferon epsilon (IFNE, 19%). Overall, the BCa cell line genomic aberrations were concordant with those found in BCa patient tumors. We used gene expression and copy number data to infer pathway activities for cell lines, then used the inferred pathway activities to build a predictive model of cisplatin response. When applied to platinum-treated patients gathered from TCGA, the model predicted treatment-specific response. Together, these data and analysis represent a valuable community resource to model basic tumor biology and to study the pharmacogenomics of BCa.
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Affiliation(s)
- M L Nickerson
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - N Witte
- Computational Bioscience Program, University of Colorado, Aurora, CO, USA
| | - K M Im
- Data Science for Genomics, LLC, Ellicott City, MD, USA
| | - S Turan
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - C Owens
- Department of Surgery (Urology), University of Colorado, Aurora, CO, USA
| | - K Misner
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | | | - Z Cai
- Shenzhen Second People's Hospital, Shenzhen, China
| | - S Wu
- Shenzhen Second People's Hospital, Shenzhen, China
| | - M Dean
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - J C Costello
- Computational Bioscience Program, University of Colorado, Aurora, CO, USA.,Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,University of Colorado Comprehensive Cancer Center, Aurora, CO, USA
| | - D Theodorescu
- Department of Surgery (Urology), University of Colorado, Aurora, CO, USA.,Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,University of Colorado Comprehensive Cancer Center, Aurora, CO, USA
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Aurora kinase-induced phosphorylation excludes transcription factor RUNX from the chromatin to facilitate proper mitotic progression. Proc Natl Acad Sci U S A 2016; 113:6490-5. [PMID: 27217562 DOI: 10.1073/pnas.1523157113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The Runt-related transcription factors (RUNX) are master regulators of development and major players in tumorigenesis. Interestingly, unlike most transcription factors, RUNX proteins are detected on the mitotic chromatin and apparatus, suggesting that they are functionally active in mitosis. Here, we identify key sites of RUNX phosphorylation in mitosis. We show that the phosphorylation of threonine 173 (T173) residue within the Runt domain of RUNX3 disrupts RUNX DNA binding activity during mitotic entry to facilitate the recruitment of RUNX proteins to mitotic structures. Moreover, knockdown of RUNX3 delays mitotic entry. RUNX3 phosphorylation is therefore a regulatory mechanism for mitotic entry. Cancer-associated mutations of RUNX3 T173 and its equivalent in RUNX1 further corroborate the role of RUNX phosphorylation in regulating proper mitotic progression and genomic integrity.
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246
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Fujii M, Shimokawa M, Date S, Takano A, Matano M, Nanki K, Ohta Y, Toshimitsu K, Nakazato Y, Kawasaki K, Uraoka T, Watanabe T, Kanai T, Sato T. A Colorectal Tumor Organoid Library Demonstrates Progressive Loss of Niche Factor Requirements during Tumorigenesis. Cell Stem Cell 2016; 18:827-838. [PMID: 27212702 DOI: 10.1016/j.stem.2016.04.003] [Citation(s) in RCA: 538] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 03/02/2016] [Accepted: 04/14/2016] [Indexed: 12/30/2022]
Abstract
Colorectal tumor is a heterogeneous disease, with varying clinical presentation and prognosis in patients. To establish a platform encompassing this diversity, we generated 55 colorectal tumor organoid lines from a range of histological subtypes and clinical stages, including rare subtypes. Each line was defined by gene expression signatures and optimized for organoid culture according to niche factor requirements. In vitro and in xenografts, the organoids reproduced the histopathological grade and differentiation capacity of their parental tumors. Notably, we found that niche-independent growth is predominantly associated with the adenoma-carcinoma transition reflecting accumulation of multiple mutations. For matched pairs of primary and metastatic organoids, which had similar genetic profiles and niche factor requirements, the metastasis-derived organoids exhibited higher metastatic capacity. These observations underscore the importance of genotype-phenotype analyses at a single-patient level and the value of our resource to provide insights into colorectal tumorigenesis and patient-centered therapeutic development.
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Affiliation(s)
- Masayuki Fujii
- Department of Gastroenterology, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Surgical Oncology, The University of Tokyo, Tokyo 113-8654, Japan
| | - Mariko Shimokawa
- Department of Gastroenterology, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Shoichi Date
- Department of Gastroenterology, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan; Fujii Memorial Research Institute, Otsuka Pharmaceutical Company, Limited, Shiga 520-0106, Japan
| | - Ai Takano
- Department of Gastroenterology, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Mami Matano
- Department of Gastroenterology, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kosaku Nanki
- Department of Gastroenterology, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yuki Ohta
- Department of Gastroenterology, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kohta Toshimitsu
- Department of Gastroenterology, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yoshihiro Nakazato
- Department of Gastroenterology, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kenta Kawasaki
- Department of Gastroenterology, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Toshio Uraoka
- Division for Research and Development of Minor Invasive Treatment, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Toshiaki Watanabe
- Department of Surgical Oncology, The University of Tokyo, Tokyo 113-8654, Japan
| | - Takanori Kanai
- Department of Gastroenterology, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Toshiro Sato
- Department of Gastroenterology, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan.
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Choudhury NJ, Campanile A, Antic T, Yap KL, Fitzpatrick CA, Wade JL, Karrison T, Stadler WM, Nakamura Y, O'Donnell PH. Afatinib Activity in Platinum-Refractory Metastatic Urothelial Carcinoma in Patients With ERBB Alterations. J Clin Oncol 2016; 34:2165-71. [PMID: 27044931 DOI: 10.1200/jco.2015.66.3047] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
PURPOSE Somatic mutations and copy number variation in the ERBB family are frequent in urothelial carcinoma (UC) and may represent viable therapeutic targets. We studied whether afatinib (an oral, irreversible inhibitor of the ErbB family) has activity in UC and if specific ERBB molecular alterations are associated with clinical response. PATIENTS AND METHODS In this phase II trial, patients with metastatic platinum-refractory UC received afatinib 40 mg/day continuously until progression or intolerance. The primary end point was 3-month progression-free survival (PFS3). Prespecified tumor analysis for alterations in EGFR, HER2, ERBB3, and ERBB4 was conducted. RESULTS The first-stage enrollment goal of 23 patients was met. Patient demographic data included: 78% male, median age 67 years (range, 36 to 82 years), hemoglobin < 10 g/dL in 17%, liver metastases in 30%, median time from prior chemotherapy of 3.6 months, and Eastern Cooperative Oncology Group performance status ≤ 1 in 100%. No unexpected toxicities were observed; two patients required dose reduction for grade 3 fatigue and rash. Overall, five of 23 patients (21.7%) met PFS3 (two partial response, three stable disease). Notably, among the 21 tumors analyzed, five of six patients (83.3%) with HER2 and/or ERBB3 alterations achieved PFS3 (PFS = 10.3, 7.0, 6.9, 6.3, and 5.0 months, respectively) versus none of 15 patients without alterations (P < .001). Three of four patients with HER2 amplification and three of three patients with ERBB3 somatic mutations (G284R, V104M, and R103G) met PFS3. One patient with both HER2 amplification and ERBB3 mutation never progressed on therapy, but treatment was discontinued after 10.3 months as a result of depressed ejection fraction. The median time to progression/discontinuation was 6.6 months in patients with HER2/ERBB3 alterations versus 1.4 months in patients without alterations (P < .001). CONCLUSION Afatinib demonstrated significant activity in patients with platinum-refractory UC with HER2 or ERBB3 alterations. The potential contribution of ERBB3 to afatinib sensitivity is novel. Afatinib deserves further investigation in molecularly selected UC.
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Affiliation(s)
- Noura J Choudhury
- Noura J. Choudhury, Alexa Campanile, Tatjana Antic, Kai Lee Yap, Carrie A. Fitzpatrick, Theodore Karrison, Walter M. Stadler, Yusuke Nakamura, and Peter H. O'Donnell, University of Chicago, Chicago; and James L. Wade III, Decatur Memorial Hospital, Decatur, IL
| | - Alexa Campanile
- Noura J. Choudhury, Alexa Campanile, Tatjana Antic, Kai Lee Yap, Carrie A. Fitzpatrick, Theodore Karrison, Walter M. Stadler, Yusuke Nakamura, and Peter H. O'Donnell, University of Chicago, Chicago; and James L. Wade III, Decatur Memorial Hospital, Decatur, IL
| | - Tatjana Antic
- Noura J. Choudhury, Alexa Campanile, Tatjana Antic, Kai Lee Yap, Carrie A. Fitzpatrick, Theodore Karrison, Walter M. Stadler, Yusuke Nakamura, and Peter H. O'Donnell, University of Chicago, Chicago; and James L. Wade III, Decatur Memorial Hospital, Decatur, IL
| | - Kai Lee Yap
- Noura J. Choudhury, Alexa Campanile, Tatjana Antic, Kai Lee Yap, Carrie A. Fitzpatrick, Theodore Karrison, Walter M. Stadler, Yusuke Nakamura, and Peter H. O'Donnell, University of Chicago, Chicago; and James L. Wade III, Decatur Memorial Hospital, Decatur, IL
| | - Carrie A Fitzpatrick
- Noura J. Choudhury, Alexa Campanile, Tatjana Antic, Kai Lee Yap, Carrie A. Fitzpatrick, Theodore Karrison, Walter M. Stadler, Yusuke Nakamura, and Peter H. O'Donnell, University of Chicago, Chicago; and James L. Wade III, Decatur Memorial Hospital, Decatur, IL
| | - James L Wade
- Noura J. Choudhury, Alexa Campanile, Tatjana Antic, Kai Lee Yap, Carrie A. Fitzpatrick, Theodore Karrison, Walter M. Stadler, Yusuke Nakamura, and Peter H. O'Donnell, University of Chicago, Chicago; and James L. Wade III, Decatur Memorial Hospital, Decatur, IL
| | - Theodore Karrison
- Noura J. Choudhury, Alexa Campanile, Tatjana Antic, Kai Lee Yap, Carrie A. Fitzpatrick, Theodore Karrison, Walter M. Stadler, Yusuke Nakamura, and Peter H. O'Donnell, University of Chicago, Chicago; and James L. Wade III, Decatur Memorial Hospital, Decatur, IL
| | - Walter M Stadler
- Noura J. Choudhury, Alexa Campanile, Tatjana Antic, Kai Lee Yap, Carrie A. Fitzpatrick, Theodore Karrison, Walter M. Stadler, Yusuke Nakamura, and Peter H. O'Donnell, University of Chicago, Chicago; and James L. Wade III, Decatur Memorial Hospital, Decatur, IL
| | - Yusuke Nakamura
- Noura J. Choudhury, Alexa Campanile, Tatjana Antic, Kai Lee Yap, Carrie A. Fitzpatrick, Theodore Karrison, Walter M. Stadler, Yusuke Nakamura, and Peter H. O'Donnell, University of Chicago, Chicago; and James L. Wade III, Decatur Memorial Hospital, Decatur, IL
| | - Peter H O'Donnell
- Noura J. Choudhury, Alexa Campanile, Tatjana Antic, Kai Lee Yap, Carrie A. Fitzpatrick, Theodore Karrison, Walter M. Stadler, Yusuke Nakamura, and Peter H. O'Donnell, University of Chicago, Chicago; and James L. Wade III, Decatur Memorial Hospital, Decatur, IL.
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Sutherland JJ, Jolly RA, Goldstein KM, Stevens JL. Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes. PLoS Comput Biol 2016; 12:e1004847. [PMID: 27028627 PMCID: PMC4814051 DOI: 10.1371/journal.pcbi.1004847] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/03/2016] [Indexed: 12/13/2022] Open
Abstract
The effect of drugs, disease and other perturbations on mRNA levels are studied using gene expression microarrays or RNA-seq, with the goal of understanding molecular effects arising from the perturbation. Previous comparisons of reproducibility across laboratories have been limited in scale and focused on a single model. The use of model systems, such as cultured primary cells or cancer cell lines, assumes that mechanistic insights derived from the models would have been observed via in vivo studies. We examined the concordance of compound-induced transcriptional changes using data from several sources: rat liver and rat primary hepatocytes (RPH) from Drug Matrix (DM) and open TG-GATEs (TG), human primary hepatocytes (HPH) from TG, and mouse liver / HepG2 results from the Gene Expression Omnibus (GEO) repository. Gene expression changes for treatments were normalized to controls and analyzed with three methods: 1) gene level for 9071 high expression genes in rat liver, 2) gene set analysis (GSA) using canonical pathways and gene ontology sets, 3) weighted gene co-expression network analysis (WGCNA). Co-expression networks performed better than genes or GSA when comparing treatment effects within rat liver and rat vs. mouse liver. Genes and modules performed similarly at Connectivity Map-style analyses, where success at identifying similar treatments among a collection of reference profiles is the goal. Comparisons between rat liver and RPH, and those between RPH, HPH and HepG2 cells reveal lower concordance for all methods. We observe that the baseline state of untreated cultured cells relative to untreated rat liver shows striking similarity with toxicant-exposed cells in vivo, indicating that gross systems level perturbation in the underlying networks in culture may contribute to the low concordance. Gene expression studies in model systems are widely used for understanding the mechanism of drugs and other perturbations in biological systems. Other researchers have examined the reproducibility of microarray studies between laboratories, or comparing microarrays and/or RNA sequencing. However, no large scale studies have compared results from protocols which differ in minor details, or results generated in vivo vs. in vitro culture systems thought to serve as useful models. The rat liver is by far the most extensively studied model evaluating effects of drugs and other perturbations, and existing data allowed us to assess the level of concordance between rat liver and rat primary hepatocytes cultured in collagen-coated plates (i.e. “flat” culture) for hundreds of drugs. We found that the mouse liver serves as a better model of the rat liver than do rat primary hepatocytes, even after allowing for differences due to pharmacokinetics. The low concordance observed between rat liver and rat hepatocytes suggests that validating the utility of ‘omics data generated on emerging cell culture approaches (e.g. “organ-on-a-chip”, 3D-printed tissues) using rat cells and comparison to the rat liver may be necessary in order to gain confidence these approaches substantially improve on traditional culture models of human cells.
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Affiliation(s)
- Jeffrey J. Sutherland
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
- * E-mail: (JJS); (JLS)
| | - Robert A. Jolly
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Keith M. Goldstein
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - James L. Stevens
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
- * E-mail: (JJS); (JLS)
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ORLANDO ANTONELLA, LINSALATA MICHELE, RUSSO FRANCESCO. Antiproliferative effects on colon adenocarcinoma cells induced by co-administration of vitamin K1 and Lactobacillus rhamnosus GG. Int J Oncol 2016; 48:2629-38. [DOI: 10.3892/ijo.2016.3463] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/18/2016] [Indexed: 11/06/2022] Open
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250
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Kang JJ, Liu IY, Wang MB, Srivatsan ES. A review of gigaxonin mutations in giant axonal neuropathy (GAN) and cancer. Hum Genet 2016; 135:675-84. [PMID: 27023907 DOI: 10.1007/s00439-016-1659-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 03/17/2016] [Indexed: 01/28/2023]
Abstract
Gigaxonin, the product of GAN gene localized to chromosome 16, is associated with the early onset neuronal degeneration disease giant axonal neuropathy (GAN). Gigaxonin is an E3 ubiquitin ligase adaptor protein involved in intermediate filament processing in neural cells, and vimentin filaments in fibroblasts. Mutations of the gene cause pre-neural filaments to accumulate and form giant axons resulting in the inhibition of neural cell signaling. Analysis of the catalog of somatic mutations in cancer, driver DB and IDGC data portal databases containing 21,000 tumor genomic sequences has identified GAN patient mutations in cancer cell lines and primary tumors. The database search has also shown the presence of identical missense and nonsense gigaxonin mutations in GAN and colon cancer. These mutations frequently occur in the domains associated with protein homodimerization and substrate interaction such as Broad-Complex, Tramtrack and Bric a brac (BTB), BTB associated C-terminal KELCH (BACK), and KELCH repeats. Analysis of the International HapMap Project database containing 1200 normal genomic sequences has identified a single nucleotide polymorphism (SNP), rs2608555, in exon 8 of the gigaxonin sequence. While this SNP is present in >40 % of Caucasian population, it is present in less than 10 % of Japanese and Chinese populations. Although the role of gigaxonin polymorphism is not yet known, CFTR and MDR1 gene studies have shown that silent mutations play a role in the instability and aberrant splicing and folding of mRNAs. We believe that molecular and functional investigation of gigaxonin mutations including the exon 8 polymorphism could lead to an improved understanding of the relationship between GAN and cancer.
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Affiliation(s)
- James J Kang
- Department of Surgery, VA Greater Los Angeles Healthcare System/David Geffen School of Medicine at UCLA, 11301 Wilshire Blvd., Los Angeles, CA, 90073, USA
| | - Isabelle Y Liu
- Department of Head and Neck Surgery, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA
| | - Marilene B Wang
- Department of Surgery, VA Greater Los Angeles Healthcare System/David Geffen School of Medicine at UCLA, 11301 Wilshire Blvd., Los Angeles, CA, 90073, USA
- Department of Head and Neck Surgery, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA
| | - Eri S Srivatsan
- Department of Surgery, VA Greater Los Angeles Healthcare System/David Geffen School of Medicine at UCLA, 11301 Wilshire Blvd., Los Angeles, CA, 90073, USA.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA.
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