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Altered primary chromatin structures and their implications in cancer development. Cell Oncol (Dordr) 2016; 39:195-210. [PMID: 27007278 DOI: 10.1007/s13402-016-0276-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cancer development is a complex process involving both genetic and epigenetic changes. Genetic changes in oncogenes and tumor-suppressor genes are generally considered as primary causes, since these genes may directly regulate cellular growth. In addition, it has been found that changes in epigenetic factors, through mutation or altered gene expression, may contribute to cancer development. In the nucleus of eukaryotic cells DNA and histone proteins form a structure called chromatin which consists of nucleosomes that, like beads on a string, are aligned along the DNA strand. Modifications in chromatin structure are essential for cell type-specific activation or repression of gene transcription, as well as other processes such as DNA repair, DNA replication and chromosome segregation. Alterations in epigenetic factors involved in chromatin dynamics may accelerate cell cycle progression and, ultimately, result in malignant transformation. Abnormal expression of remodeler and modifier enzymes, as well as histone variants, may confer to cancer cells the ability to reprogram their genomes and to yield, maintain or exacerbate malignant hallmarks. At the end, genetic and epigenetic alterations that are encountered in cancer cells may culminate in chromatin changes that may, by altering the quantity and quality of gene expression, promote cancer development. METHODS During the last decade a vast number of studies has uncovered epigenetic abnormalities that are associated with the (anomalous) packaging and remodeling of chromatin in cancer genomes. In this review I will focus on recently published work dealing with alterations in the primary structure of chromatin resulting from imprecise arrangements of nucleosomes along DNA, and its functional implications for cancer development. CONCLUSIONS The primary chromatin structure is regulated by a variety of epigenetic mechanisms that may be deregulated through gene mutations and/or gene expression alterations. In recent years, it has become evident that changes in chromatin structure may coincide with the occurrence of cancer hallmarks. The functional interrelationships between such epigenetic alterations and cancer development are just becoming manifest and, therefore, the oncology community should continue to explore the molecular mechanisms governing the primary chromatin structure, both in normal and in cancer cells, in order to improve future approaches for cancer detection, prevention and therapy, as also for circumventing drug resistance.
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Tögel L, Nightingale R, Chueh AC, Jayachandran A, Tran H, Phesse T, Wu R, Sieber OM, Arango D, Dhillon AS, Dawson MA, Diez-Dacal B, Gahman TC, Filippakopoulos P, Shiau AK, Mariadason JM. Dual Targeting of Bromodomain and Extraterminal Domain Proteins, and WNT or MAPK Signaling, Inhibits c-MYC Expression and Proliferation of Colorectal Cancer Cells. Mol Cancer Ther 2016; 15:1217-26. [PMID: 26983878 DOI: 10.1158/1535-7163.mct-15-0724] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 03/06/2016] [Indexed: 12/28/2022]
Abstract
Inhibitors of the bromodomain and extraterminal domain (BET) protein family attenuate the proliferation of several tumor cell lines. These effects are mediated, at least in part, through repression of c-MYC. In colorectal cancer, overexpression of c-MYC due to hyperactive WNT/β-catenin/TCF signaling is a key driver of tumor progression; however, effective strategies to target this oncogene remain elusive. Here, we investigated the effect of BET inhibitors (BETi) on colorectal cancer cell proliferation and c-MYC expression. Treatment of 20 colorectal cancer cell lines with the BETi JQ1 identified a subset of highly sensitive lines. JQ1 sensitivity was higher in cell lines with microsatellite instability but was not associated with the CpG island methylator phenotype, c-MYC expression or amplification status, BET protein expression, or mutation status of TP53, KRAS/BRAF, or PIK3CA/PTEN Conversely, JQ1 sensitivity correlated significantly with the magnitude of c-MYC mRNA and protein repression. JQ1-mediated c-MYC repression was not due to generalized attenuation of β-catenin/TCF-mediated transcription, as JQ1 had minimal effects on other β-catenin/TCF target genes or β-catenin/TCF reporter activity. BETi preferentially target super-enhancer-regulated genes, and a super-enhancer in c-MYC was recently identified in HCT116 cells to which BRD4 and effector transcription factors of the WNT/β-catenin/TCF and MEK/ERK pathways are recruited. Combined targeting of c-MYC with JQ1 and inhibitors of these pathways additively repressed c-MYC and proliferation of HCT116 cells. These findings demonstrate that BETi downregulate c-MYC expression and inhibit colorectal cancer cell proliferation and identify strategies for enhancing the effects of BETi on c-MYC repression by combinatorial targeting the c-MYC super-enhancer. Mol Cancer Ther; 15(6); 1217-26. ©2016 AACR.
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Affiliation(s)
- Lars Tögel
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia. Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia
| | - Rebecca Nightingale
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia. Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia
| | - Anderly C Chueh
- Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia
| | | | - Hoanh Tran
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia. Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia
| | - Toby Phesse
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - Rui Wu
- Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia
| | - Oliver M Sieber
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Diego Arango
- CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Mark A Dawson
- Peter MacCallum Cancer Institute, Melbourne, Victoria, Australia
| | - Beatriz Diez-Dacal
- Ludwig Institute for Cancer Research and UK and Structural Genomics Consortium, Oxford, United Kingdom
| | - Timothy C Gahman
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, California
| | - Panagis Filippakopoulos
- Ludwig Institute for Cancer Research and UK and Structural Genomics Consortium, Oxford, United Kingdom
| | - Andrew K Shiau
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, California
| | - John M Mariadason
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia. Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia.
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Influenza Virus and Chromatin: Role of the CHD1 Chromatin Remodeler in the Virus Life Cycle. J Virol 2016; 90:3694-707. [PMID: 26792750 DOI: 10.1128/jvi.00053-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Influenza A virus requires ongoing cellular transcription to carry out the cap-snatching process. Chromatin remodelers modify chromatin structure to produce an active or inactive conformation, which enables or prevents the recruitment of transcriptional complexes to specific genes; viral transcription thus depends on chromatin dynamics. Influenza virus polymerase associates with chromatin components of the infected cell, such as RNA polymerase II (RNAP II) or the CHD6 chromatin remodeler. Here we show that another CHD family member, CHD1 protein, also interacts with the influenza virus polymerase complex. CHD1 recognizes the H3K4me3 (histone 3 with a trimethyl group in lysine 4) histone modification, a hallmark of active chromatin. Downregulation of CHD1 causes a reduction in viral polymerase activity, viral RNA transcription, and the production of infectious particles. Despite the dependence of influenza virus on cellular transcription, RNAP II is degraded when viral transcription is complete, and recombinant viruses unable to degrade RNAP II show decreased pathogenicity in the murine model. We describe the CHD1-RNAP II association, as well as the parallel degradation of both proteins during infection with viruses showing full or reduced induction of degradation. The H3K4me3 histone mark also decreased during influenza virus infection, whereas a histone mark of inactive chromatin, H3K27me3, remained unchanged. Our results indicate that CHD1 is a positive regulator of influenza virus multiplication and suggest a role for chromatin remodeling in the control of the influenza virus life cycle. IMPORTANCE Although influenza virus is not integrated into the genome of the infected cell, it needs continuous cellular transcription to synthesize viral mRNA. This mechanism implies functional association with host genome expression and thus depends on chromatin dynamics. Influenza virus polymerase associates with transcription-related factors, such as RNA polymerase II, and with chromatin remodelers, such as CHD6. We identified the association of viral polymerase with another chromatin remodeler, the CHD1 protein, which positively modulated viral polymerase activity, viral RNA transcription, and virus multiplication. Once viral transcription is complete, RNAP II is degraded in infected cells, probably as a virus-induced mechanism to reduce the antiviral response. CHD1 associated with RNAP II and paralleled its degradation during infection with viruses that induce full or reduced degradation. These findings suggest that RNAP II degradation and CHD1 degradation cooperate to reduce the antiviral response.
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254
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Wong A, Kuick CH, Wong WL, Tham JM, Mansor S, Loh E, Jain S, Vikas NN, Tan SH, Chan SH, Li ST, Chew SH, Hong W, Ngeow J. Mutation spectrum of POLE and POLD1 mutations in South East Asian women presenting with grade 3 endometrioid endometrial carcinomas. Gynecol Oncol 2015; 141:113-20. [PMID: 26748215 DOI: 10.1016/j.ygyno.2015.12.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/11/2015] [Accepted: 12/30/2015] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Somatic POLE mutations have been found in a subset of endometrioid ECs particularly in FIGO grade 3 tumors while POLD1 mutations are reportedly rare in ECs. While it has been suggested that POLE mutation confers good prognosis, the data remains conflicting. Our study aims to determine the mutation spectrum of somatic and germline POLE and POLD1 gene mutations in South East Asian (SEA) women with FIGO grade 3 endometrioid ECs. METHODS Forty-seven patients diagnosed with FIGO grade 3 endometrioid EC, diagnosed between 2009 and 2013 were included. Next generation sequencing (NGS) using formalin fixed embedded (FFPE) tissue was utilized to sequence tumor and matched normal tissue. Tumors were also assessed for other clinicopathologic and microsatellite status phenotype. Survival curves for pathogenic somatic POLE mutated and wild-type tumors were estimated by Kaplan-Meier method. RESULTS Pathogenic POLE (somatic or germline) and POLD1 (germline) mutations were detected in 29.7% (14/47) and 4.3% (2/47) patients, respectively. Three pathogenic germline mutations; one POLE and two POLD1 mutations were novel. Pathogenic germline and somatic POLE and POLD1 mutations were associated with 100% recurrence free survival. In contrast, among the wild-type POLE and POLD1 patients, 25% (8/32) had recurrence with 15.6% (5/32) subsequently dying of the disease. Somatic POLE-mutated tumors were more commonly associated with microsatellite stable (MSS) ECs (83% vs 49%; p=0.04) and peritumoral lymphocytic infiltration (75% vs 42%; p=0.05). All tumors with tumoral infiltrating lymphocytes exhibited peritumoral lymphocytic infiltrate but not vice versa. CONCLUSION Mutations in POLE and POLD1 in SEA women with grade 3 endometrioid ECs are associated with improved recurrence free survival. Notably, germline mutations in either POLE/POLD1 were seen in 8.5% of patients who will require appropriate genetic counseling regarding risk of developing colorectal carcinoma and on the need for additional surveillance for colonic changes. MSS and peritumoral lymphocytic infiltration may be useful histological features for distinguishing POLE mutated grade 3 endometrioid ECs.
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Affiliation(s)
- Adele Wong
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Chik Hong Kuick
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Wai Loong Wong
- Department of Gynaecological Oncology, KK Women's and Children's Hospital, Singapore, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Jill M Tham
- Protein Trafficking and Cancer Cell Biology, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Sorsiah Mansor
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Eva Loh
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Sudhanshi Jain
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Nadkarni N Vikas
- Centre for Quantitative Medicine, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Sze Huey Tan
- Division of Clinical Trials and Epidemiological Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore
| | - Sock Hoai Chan
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore
| | - Shao Tzu Li
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore
| | - Sung Hock Chew
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Wanjin Hong
- Protein Trafficking and Cancer Cell Biology, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore; Oncology Academic Clinical Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore.
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González-Sarrías A, Núñez-Sánchez MÁ, Tomé-Carneiro J, Tomás-Barberán FA, García-Conesa MT, Espín JC. Comprehensive characterization of the effects of ellagic acid and urolithins on colorectal cancer and key-associated molecular hallmarks: MicroRNA cell specific induction of CDKN1A (p21) as a common mechanism involved. Mol Nutr Food Res 2015; 60:701-16. [PMID: 26634414 DOI: 10.1002/mnfr.201500780] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/25/2015] [Accepted: 11/29/2015] [Indexed: 12/14/2022]
Abstract
SCOPE Ellagitannins, ellagic acid, and the colonic metabolites urolithins (Uros) exhibit anticancer effects against colon cells, but a comprehensive molecular analysis has not been done. Herein, we used a panel of cell lines to first time evaluate the antiproliferative properties and accompanying molecular responses of two ellagitannin metabolites mixtures mimicking the situation in vivo and of each individual metabolite. METHODS AND RESULTS We examined cell growth, cell cycle, apoptosis, and the expression of related genes and microRNAs (miRs) in a panel of nonmalignant and malignant colon cell lines. Regardless of the composition, the mixed metabolites similarly inhibited proliferation, induced cycle arrest, and apoptosis. All the metabolites contributed to these effects, but Uro-A, isourolithin A, Uro-C, and Uro-D were more potent than Uro-B and ellagic acid. Despite molecular differences between the cell lines, we discerned relevant changes in key cancer markers and corroborated the induction of CDKN1A (cyclin-dependent kinase inhibitor 1A gene (p21, Cip1); encoding p21) as a common step underlying the anticancer properties of Uros. Interestingly, cell-unique downregulation of miR-224 or upregulation of miR-215 was found associated with CDKN1A induction. CONCLUSION Physiologically relevant mixtures of Uros exert anticancer effects against colon cancer cells via a common CDKN1A upregulatory mechanism. Other associated molecular responses are however heterogeneous and mostly cell-specific.
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Affiliation(s)
- Antonio González-Sarrías
- Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, Murcia, Spain
| | - María Ángeles Núñez-Sánchez
- Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, Murcia, Spain
| | - Joao Tomé-Carneiro
- Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, Murcia, Spain
| | - Francisco A Tomás-Barberán
- Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, Murcia, Spain
| | - María Teresa García-Conesa
- Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, Murcia, Spain
| | - Juan Carlos Espín
- Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, Murcia, Spain
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256
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Niu N, Wang L. In vitro human cell line models to predict clinical response to anticancer drugs. Pharmacogenomics 2015; 16:273-85. [PMID: 25712190 DOI: 10.2217/pgs.14.170] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In vitro human cell line models have been widely used for cancer pharmacogenomic studies to predict clinical response, to help generate pharmacogenomic hypothesis for further testing, and to help identify novel mechanisms associated with variation in drug response. Among cell line model systems, immortalized cell lines such as Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) have been used most often to test the effect of germline genetic variation on drug efficacy and toxicity. Another model, especially in cancer research, uses cancer cell lines such as the NCI-60 panel. These models have been used mainly to determine the effect of somatic alterations on response to anticancer therapy. Even though these cell line model systems are very useful for initial screening, results from integrated analyses of multiple omics data and drug response phenotypes using cell line model systems still need to be confirmed by functional validation and mechanistic studies, as well as validation studies using clinical samples. Future models might include the use of patient-specific inducible pluripotent stem cells and the incorporation of 3D culture which could further optimize in vitro cell line models to improve their predictive validity.
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Affiliation(s)
- Nifang Niu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
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Ling A, Lundberg IV, Eklöf V, Wikberg ML, Öberg Å, Edin S, Palmqvist R. The infiltration, and prognostic importance, of Th1 lymphocytes vary in molecular subgroups of colorectal cancer. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2015; 2:21-31. [PMID: 27499912 PMCID: PMC4858126 DOI: 10.1002/cjp2.31] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/05/2015] [Indexed: 12/11/2022]
Abstract
Giving strong prognostic information, T‐cell infiltration is on the verge of becoming an additional component in the routine clinical setting for classification of colorectal cancer (CRC). With a view to further improving the tools for prognostic evaluation, we have studied how Th1 lymphocyte infiltration correlates with prognosis not only by quantity, but also by subsite, within CRCs with different molecular characteristics (microsatellite instability, CpG island methylator phenotype status, and BRAF and KRAS mutational status). We evaluated the Th1 marker T‐bet by immunohistochemistry in 418 archival tumour tissue samples from patients who underwent surgical resection for CRC. We found that a high number of infiltrating Th1 lymphocytes is strongly associated with an improved prognosis in patients with CRC, irrespective of intratumoural subsite, and that both extent of infiltration and patient outcome differ according to molecular subgroup. In brief, microsatellite instability, CpG island methylator phenotype‐high and BRAF mutated tumours showed increased infiltration of Th1 lymphocytes, and the most pronounced prognostic effect of Th1 infiltration was found in these tumours. Interestingly, BRAF mutated tumours were found to be more highly infiltrated by Th1 lymphocytes than BRAF wild‐type tumours whereas the opposite was seen for KRAS mutated tumours. These differences could be explained at least partly by our finding that BRAF mutated, in contrast to KRAS mutated, CRC cell lines and tumour specimens expressed higher levels of the Th1‐attracting chemokine CXCL10, and reduced levels of CCL22 and TGFB1, stimulating Th2/Treg recruitment and polarisation. In conclusion, the strong prognostic importance of Th1 lymphocyte infiltration in CRC was found at all subsites evaluated, and it remained significant in multivariable analyses, indicating that T‐bet may be a valuable marker in the clinical setting. Our results also indicate that T‐bet is of value when analysed in molecular subgroups of CRC, allowing identification of patients with especially poor prognosis who are in need of extended treatment.
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Affiliation(s)
- Agnes Ling
- Department of Medical Biosciences Pathology, Umeå University Umeå Sweden
| | - Ida V Lundberg
- Department of Medical Biosciences Pathology, Umeå University Umeå Sweden
| | - Vincy Eklöf
- Department of Medical Biosciences Pathology, Umeå University Umeå Sweden
| | - Maria L Wikberg
- Department of Medical Biosciences Pathology, Umeå University Umeå Sweden
| | - Åke Öberg
- Department of Surgical and Perioperative Sciences Surgery, Umeå University Umeå Sweden
| | - Sofia Edin
- Department of Medical Biosciences Pathology, Umeå University Umeå Sweden
| | - Richard Palmqvist
- Department of Medical Biosciences Pathology, Umeå University Umeå Sweden
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258
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Hu JL, Hua YJ, Chen Y, Yu B, Gao S. Structural analysis of tumor-related single amino acid mutations in human MxA protein. CHINESE JOURNAL OF CANCER 2015; 34:583-93. [PMID: 26411585 PMCID: PMC4593380 DOI: 10.1186/s40880-015-0055-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 09/13/2015] [Indexed: 12/21/2022]
Abstract
Background Human myxovirus resistant protein A (MxA), encoded by the myxovirus resistance 1 (Mx1) gene, is an interferon (IFN)-triggered dynamin-like multi-domain GTPase involved in innate immune responses against viral infections. Recent studies suggest that MxA is associated with several human cancers and may be a tumor suppressor and a promising biomarker for IFN therapy. Mx1 gene mutations in the coding region for MxA have been discovered in many types of cancer, suggesting potential biological associations between mutations in MxA protein and corresponding cancers. In this study, we performed a systematic analysis based on the crystal structures of MxA and elucidated how these mutations specifically affect the structure and therefore the function of MxA protein. Methods Cancer-associated Mx1 mutations were collected and screened from the COSMIC database. Twenty-two unique mutations that cause single amino acid alterations in the MxA protein were chosen for the analysis. Amino acid sequence alignment was performed using Clustal W to check the conservation level of mutation sites in Mx proteins and dynamins. Structural analysis of the mutants was carried out with Coot. Structural models of selected mutants were generated by the SWISS-MODEL server for comparison with the corresponding non-mutated structures. All structural figures were generated using PyMOL. Results We analyzed the conservation level of the single-point mutation sites and mapped them on different domains of MxA. Through individual structural analysis, we found that some mutations severely affect the stability and function of MxA either by disrupting the intra-/inter-molecular interactions supported by the original residues or by incurring unfavorable configuration alterations, whereas other mutations lead to gentle or no interference to the protein stability and function because of positions or polarity features. The potential clinical value of the mutations that lead to drastic influence on MxA protein is also assessed. Conclusions Among all of the reported tumor-associated single-point mutations, seven of them notably affect the structure and function of MxA and therefore deserve more attention with respect to potential clinical applications. Our research provides an example for systematic analysis and consequence evaluation of single-point mutations on a given cancer-related protein.
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Affiliation(s)
- Jia-Li Hu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P.R. China.
| | - Yi-Jun Hua
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P.R. China.
| | - Yang Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P.R. China.
| | - Bing Yu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P.R. China.
| | - Song Gao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P.R. China.
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259
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Rogawski DS, Ndoj J, Cho HJ, Maillard I, Grembecka J, Cierpicki T. Two Loops Undergoing Concerted Dynamics Regulate the Activity of the ASH1L Histone Methyltransferase. Biochemistry 2015; 54:5401-13. [PMID: 26292256 PMCID: PMC4664444 DOI: 10.1021/acs.biochem.5b00697] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
ASH1L (absent, small, or homeotic-like 1) is a histone methyltransferase (HMTase) involved in gene activation that is overexpressed in multiple forms of cancer. Previous studies of ASH1L's catalytic SET domain identified an autoinhibitory loop that blocks access of histone substrate to the enzyme active site. Here, we used both nuclear magnetic resonance and X-ray crystallography to identify conformational dynamics in the ASH1L autoinhibitory loop. Using site-directed mutagenesis, we found that point mutations in the autoinhibitory loop that perturb the structure of the SET domain result in decreased enzyme activity, indicating that the autoinhibitory loop is not a simple gate to the active site but is rather a key feature critical to ASH1L function. We also identified a second loop in the SET-I subdomain of ASH1L that experiences conformational dynamics, and we trapped two different conformations of this loop using crystallographic studies. Mutation of the SET-I loop led to a large decrease in ASH1L enzymatic activity in addition to a significant conformational change in the SET-I loop, demonstrating the importance of the structure and dynamics of the SET-I loop to ASH1L function. Furthermore, we found that three C-terminal chromatin-interacting domains greatly enhance ASH1L enzymatic activity and that ASH1L requires native nucleosome substrate for robust activity. Our study illuminates the role of concerted conformational dynamics in ASH1L function and identifies structural features important for ASH1L enzymatic activity.
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Affiliation(s)
- David S. Rogawski
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109
| | - Juliano Ndoj
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109
| | - Hyo Je Cho
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109
| | - Ivan Maillard
- Center for Stem Cell Biology, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109,Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109,Corresponding author: Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510C, Ann Arbor, MI, USA 48109. Tel.: (734) 615-9324;
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260
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Goodspeed A, Heiser LM, Gray JW, Costello JC. Tumor-Derived Cell Lines as Molecular Models of Cancer Pharmacogenomics. Mol Cancer Res 2015; 14:3-13. [PMID: 26248648 DOI: 10.1158/1541-7786.mcr-15-0189] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/29/2015] [Indexed: 02/07/2023]
Abstract
Compared with normal cells, tumor cells have undergone an array of genetic and epigenetic alterations. Often, these changes underlie cancer development, progression, and drug resistance, so the utility of model systems rests on their ability to recapitulate the genomic aberrations observed in primary tumors. Tumor-derived cell lines have long been used to study the underlying biologic processes in cancer, as well as screening platforms for discovering and evaluating the efficacy of anticancer therapeutics. Multiple -omic measurements across more than a thousand cancer cell lines have been produced following advances in high-throughput technologies and multigroup collaborative projects. These data complement the large, international cancer genomic sequencing efforts to characterize patient tumors, such as The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC). Given the scope and scale of data that have been generated, researchers are now in a position to evaluate the similarities and differences that exist in genomic features between cell lines and patient samples. As pharmacogenomics models, cell lines offer the advantages of being easily grown, relatively inexpensive, and amenable to high-throughput testing of therapeutic agents. Data generated from cell lines can then be used to link cellular drug response to genomic features, where the ultimate goal is to build predictive signatures of patient outcome. This review highlights the recent work that has compared -omic profiles of cell lines with primary tumors, and discusses the advantages and disadvantages of cancer cell lines as pharmacogenomic models of anticancer therapies.
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Affiliation(s)
- Andrew Goodspeed
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Laura M Heiser
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Joe W Gray
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - James C Costello
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
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Sinicrope FA, Mahoney MR, Yoon HH, Smyrk TC, Thibodeau SN, Goldberg RM, Nelson GD, Sargent DJ, Alberts SR. Analysis of Molecular Markers by Anatomic Tumor Site in Stage III Colon Carcinomas from Adjuvant Chemotherapy Trial NCCTG N0147 (Alliance). Clin Cancer Res 2015; 21:5294-304. [PMID: 26187617 DOI: 10.1158/1078-0432.ccr-15-0527] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/30/2015] [Indexed: 12/16/2022]
Abstract
PURPOSE To determine the frequency and prognostic association of molecular markers by anatomic tumor site in patients with stage III colon carcinomas. EXPERIMENTAL DESIGN In a randomized trial of adjuvant FOLFOX ± cetuximab, BRAF(V600E) and KRAS (exon 2) mutations and DNA mismatch repair (MMR) proteins were analyzed in tumors (N = 3,018) in relationship to tumor location, including subsite. Cox models were used to assess clinical outcome, including overall survival (OS). RESULTS KRAS codon 12 mutations were most frequent at the splenic flexure and cecum; codon 13 mutations were evenly distributed. BRAF mutation frequency sharply increased from transverse colon to cecum in parallel with deficient (d) MMR. Nonmutated BRAF and KRAS tumors progressively decreased from sigmoid to transverse (all P < 0.0001). Significantly, poorer OS was found for mutant KRAS in distal [HR, 1.98; 95% confidence interval (CI), 1.49-2.63; P < 0.0001] versus proximal (1.25; 95% CI, 0.97-1.60; P = 0.079) cancers. BRAF status and outcome were not significantly associated with tumor site. Proximal versus distal dMMR tumors had significantly better outcome. An interaction test was significant for tumor site by KRAS (P(adjusted) = 0.043) and MMR (P(adjusted) = 0.010) for OS. Significant prognostic differences for biomarkers by tumor site were maintained in the FOLFOX arm. Tumor site was independently prognostic with a stepwise improvement from cecum to sigmoid (OS: P(adjusted) = 0.001). CONCLUSIONS Mutation in BRAF or KRAS codon 12 was enriched in proximal cancers whereas nonmutated BRAF/KRAS was increased in distal tumors. Significant differences in outcome for KRAS mutations and dMMR were found by tumor site, indicating that their interpretation should occur in the context of tumor location.
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Affiliation(s)
- Frank A Sinicrope
- Department of Medicine, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota. Department of Oncology, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota.
| | - Michelle R Mahoney
- Alliance Statistics and Data Center, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
| | - Harry H Yoon
- Department of Oncology, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
| | - Thomas C Smyrk
- Laboratory Medicine and Pathology, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
| | - Stephen N Thibodeau
- Laboratory Medicine and Pathology, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
| | | | - Garth D Nelson
- Alliance Statistics and Data Center, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
| | - Daniel J Sargent
- Alliance Statistics and Data Center, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
| | - Steven R Alberts
- Department of Oncology, Mayo Clinic and Mayo Cancer Center, Rochester, Minnesota
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262
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Li W, Mills AA. Architects of the genome: CHD dysfunction in cancer, developmental disorders and neurological syndromes. Epigenomics 2015; 6:381-95. [PMID: 25333848 DOI: 10.2217/epi.14.31] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Chromatin is vital to normal cells, and its deregulation contributes to a spectrum of human ailments. An emerging concept is that aberrant chromatin regulation culminates in gene expression programs that set the stage for the seemingly diverse pathologies of cancer, developmental disorders and neurological syndromes. However, the mechanisms responsible for such common etiology have been elusive. Recent evidence has implicated lesions affecting chromatin-remodeling proteins in cancer, developmental disorders and neurological syndromes, suggesting a common source for these different pathologies. Here, we focus on the chromodomain helicase DNA binding chromatin-remodeling family and the recent evidence for its deregulation in diverse pathological conditions, providing a new perspective on the underlying mechanisms and their implications for these prevalent human diseases.
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Affiliation(s)
- Wangzhi Li
- Cold Spring Harbor Laboratory Cold Spring Harbor, NY 11724, USA
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263
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Bazzocco S, Dopeso H, Carton-Garcia F, Macaya I, Andretta E, Chionh F, Rodrigues P, Garrido M, Alazzouzi H, Nieto R, Sanchez A, Schwartz S, Bilic J, Mariadason JM, Arango D. Highly Expressed Genes in Rapidly Proliferating Tumor Cells as New Targets for Colorectal Cancer Treatment. Clin Cancer Res 2015; 21:3695-704. [PMID: 25944804 DOI: 10.1158/1078-0432.ccr-14-2457] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 04/27/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE The clinical management of colorectal cancer patients has significantly improved because of the identification of novel therapeutic targets such as EGFR and VEGF. Because rapid tumor proliferation is associated with poor patient prognosis, here we characterized the transcriptional signature of rapidly proliferating colorectal cancer cells in an attempt to identify novel candidate therapeutic targets. EXPERIMENTAL DESIGN The doubling time of 52 colorectal cancer cell lines was determined and genome-wide expression profiling of a subset of these lines was assessed by microarray analysis. We then investigated the potential of genes highly expressed in cancer cells with faster growth as new therapeutic targets. RESULTS Faster proliferation rates were associated with microsatellite instability and poorly differentiated histology. The expression of 1,290 genes was significantly correlated with the growth rates of colorectal cancer cells. These included genes involved in cell cycle, RNA processing/splicing, and protein transport. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and protoporphyrinogen oxidase (PPOX) were shown to have higher expression in faster growing cell lines and primary tumors. Pharmacologic or siRNA-based inhibition of GAPDH or PPOX reduced the growth of colon cancer cells in vitro. Moreover, using a mouse xenograft model, we show that treatment with the specific PPOX inhibitor acifluorfen significantly reduced the growth of three of the seven (42.8%) colon cancer lines investigated. CONCLUSIONS We have characterized at the transcriptomic level the differences between colorectal cancer cells that vary in their growth rates, and identified novel candidate chemotherapeutic targets for the treatment of colorectal cancer.
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Affiliation(s)
- Sarah Bazzocco
- Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Spain
| | - Higinio Dopeso
- Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Spain
| | - Fernando Carton-Garcia
- Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Spain
| | - Irati Macaya
- Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Spain
| | - Elena Andretta
- Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Spain
| | - Fiona Chionh
- Ludwig Institute for Cancer Research Melbourne-Austin Branch and Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
| | - Paulo Rodrigues
- Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Spain
| | - Miriam Garrido
- Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Hafid Alazzouzi
- Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Spain
| | - Rocio Nieto
- Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Spain
| | - Alex Sanchez
- Unitat d'Estadística i Bioinformàtica, Vall d'Hebron University Hospital Research Institute (VHIR), Barcelona, Spain. Departament d'Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Simo Schwartz
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Spain. Group of Drug Delivery and Targeting, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josipa Bilic
- Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Spain
| | - John M Mariadason
- Ludwig Institute for Cancer Research Melbourne-Austin Branch and Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
| | - Diego Arango
- Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Spain.
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264
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The molecular landscape of colorectal cancer cell lines unveils clinically actionable kinase targets. Nat Commun 2015; 6:7002. [PMID: 25926053 DOI: 10.1038/ncomms8002] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 03/23/2015] [Indexed: 02/07/2023] Open
Abstract
The development of molecularly targeted anticancer agents relies on large panels of tumour-specific preclinical models closely recapitulating the molecular heterogeneity observed in patients. Here we describe the mutational and gene expression analyses of 151 colorectal cancer (CRC) cell lines. We find that the whole spectrum of CRC molecular and transcriptional subtypes, previously defined in patients, is represented in this cell line compendium. Transcriptional outlier analysis identifies RAS/BRAF wild-type cells, resistant to EGFR blockade, functionally and pharmacologically addicted to kinase genes including ALK, FGFR2, NTRK1/2 and RET. The same genes are present as expression outliers in CRC patient samples. Genomic rearrangements (translocations) involving the ALK and NTRK1 genes are associated with the overexpression of the corresponding proteins in CRC specimens. The approach described here can be used to pinpoint CRCs with exquisite dependencies to individual kinases for which clinically approved drugs are already available.
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265
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DeWitt M, Johnson RL, Snyder P, Fleet JC. The effect of 1,25 dihydroxyvitamin D3 treatment on the mRNA levels of β catenin target genes in mice with colonic inactivation of both APC alleles. J Steroid Biochem Mol Biol 2015; 148:103-10. [PMID: 25597951 PMCID: PMC4361272 DOI: 10.1016/j.jsbmb.2015.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 01/05/2015] [Accepted: 01/13/2015] [Indexed: 12/31/2022]
Abstract
In colon cancer, adenomatous polyposis coli (APC) inactivating gene mutations increase nuclear β-catenin levels and stimulate proliferation. In vitro, 1,25 dihydroxyvitamin D (1,25(OH)2D), suppresses β-catenin-mediated gene transcription by inducing vitamin D receptor (VDR)-β-catenin interactions. We examined whether acute treatment with 1,25(OH)2D could suppress β-catenin-mediated gene transcription in the hyperplastic colonic lesions of mice with colon-specific deletion of both APC gene alleles (CAC; APC(Δ580/Δ580)). At four weeks of age, CAC; APC(Δ580/Δ580) and control mice were injected with vehicle or 1,25(OH)2D (1μg/kg body weight) once a day for three days and then killed six hours after the last injection. mRNA levels of β-catenin target genes were elevated in the colon of CAC; APC(Δ580/Δ580) mice. 1,25(OH)2D increased 25 hydroxyvitamin D-24 hydroxylase mRNA levels in the colon of CAC; APC(Δ580/Δ580) and control mice indicating the treatments activated the VDR. However, 1,25(OH)2D had no effect on either β-catenin target gene mRNA levels or the proliferation index in CAC; APC(Δ580/Δ580) or control mice. VDR mRNA and protein levels were lower (-65% and -90%) in the colon of CAC; APC(Δ580/Δ580) mice compared to control mice, suggesting loss of colon responsiveness to vitamin D. Consistent with this, vitamin D-induced expression of transient receptor potential cation channel, subfamily V, member 6 mRNA was reduced in the colon of CAC; APC(Δ580/Δ580) mice. Our data show that short term exposure to 1,25(OH)2D does not suppress colonic β-catenin signaling in vivo. This article is part of a special issue entitled '17th Vitamin D Workshop'.
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Affiliation(s)
- Marsha DeWitt
- Purdue University Interdisciplinary Life Science Ph.D. program, Purdue University, West Lafayette, IN 47907, USA; Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA.
| | - Robert L Johnson
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA; Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA.
| | - Paul Snyder
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA; Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - James C Fleet
- Purdue University Interdisciplinary Life Science Ph.D. program, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA; Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA.
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266
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Calon A, Lonardo E, Berenguer-Llergo A, Espinet E, Hernando-Momblona X, Iglesias M, Sevillano M, Palomo-Ponce S, Tauriello DVF, Byrom D, Cortina C, Morral C, Barceló C, Tosi S, Riera A, Attolini CSO, Rossell D, Sancho E, Batlle E. Stromal gene expression defines poor-prognosis subtypes in colorectal cancer. Nat Genet 2015; 47:320-9. [PMID: 25706628 DOI: 10.1038/ng.3225] [Citation(s) in RCA: 777] [Impact Index Per Article: 86.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 01/28/2015] [Indexed: 12/13/2022]
Abstract
Recent molecular classifications of colorectal cancer (CRC) based on global gene expression profiles have defined subtypes displaying resistance to therapy and poor prognosis. Upon evaluation of these classification systems, we discovered that their predictive power arises from genes expressed by stromal cells rather than epithelial tumor cells. Bioinformatic and immunohistochemical analyses identify stromal markers that associate robustly with disease relapse across the various classifications. Functional studies indicate that cancer-associated fibroblasts (CAFs) increase the frequency of tumor-initiating cells, an effect that is dramatically enhanced by transforming growth factor (TGF)-β signaling. Likewise, we find that all poor-prognosis CRC subtypes share a gene program induced by TGF-β in tumor stromal cells. Using patient-derived tumor organoids and xenografts, we show that the use of TGF-β signaling inhibitors to block the cross-talk between cancer cells and the microenvironment halts disease progression.
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Affiliation(s)
- Alexandre Calon
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona, Spain
| | - Enza Lonardo
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona, Spain
| | | | - Elisa Espinet
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona, Spain
| | | | - Mar Iglesias
- 1] Department of Pathology, Hospital del Mar, Barcelona, Spain. [2] Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain. [3] Universitat Autónoma de Barcelona, Barcelona, Spain
| | - Marta Sevillano
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona, Spain
| | | | | | - Daniel Byrom
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona, Spain
| | - Carme Cortina
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona, Spain
| | - Clara Morral
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona, Spain
| | - Carles Barceló
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona, Spain
| | - Sebastien Tosi
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona, Spain
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona, Spain
| | | | - David Rossell
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona, Spain
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona, Spain
| | - Eduard Batlle
- 1] Institute for Research in Biomedicine (IRB) Barcelona, Barcelona, Spain. [2] Institució Catalana de Recerca i Estudis Avançats (iCREA), Barcelona, Spain
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267
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Kaur S, Lotsari JE, Al-Sohaily S, Warusavitarne J, Kohonen-Corish MR, Peltomäki P. Identification of subgroup-specific miRNA patterns by epigenetic profiling of sporadic and Lynch syndrome-associated colorectal and endometrial carcinoma. Clin Epigenetics 2015; 7:20. [PMID: 25767621 PMCID: PMC4357086 DOI: 10.1186/s13148-015-0059-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 02/13/2015] [Indexed: 12/20/2022] Open
Abstract
Background Altered expression of microRNAs (miRNAs) commonly accompanies colorectal (CRC) and endometrial carcinoma (EC) development, but the underlying mechanisms and clinicopathological correlations remain to be clarified. We focused on epigenetic mechanisms and aimed to explore if DNA methylation patterns in tumors depend on DNA mismatch repair (MMR) status, sporadic vs. Lynch-associated disease, and geographic origin (Finland vs. Australia). Treatment of cancer cell lines with demethylating agents revealed 109 significantly upregulated miRNAs. Seven met our stringent criteria for possible methylation-sensitive miRNAs and were used to screen patient specimens (205 CRCs and 36 ECs) by methylation-specific multiplex ligation-dependent probe amplification. Results Three miRNAs (129-2, 345, and 132) with low methylation levels in normal tissue and frequent hypermethylation in tumors were of particular interest. Hypermethylation of miR-345 and miR-132 associated with MMR deficiency in CRC regardless of geographic origin, and hypermethylation of miR-132 distinguished sporadic MMR-deficient CRC from Lynch-CRC. Finally, hypermethylation of miRNAs stratified 49 endometrial hyperplasias into low-methylator (simple hyperplasia) and high-methylator groups (complex hyperplasia with or without atypia) and suggested that miR-129-2 methylation in particular could serve as a marker of progression in early endometrial tumorigenesis. Conclusions Our study identifies miR-345 and miR-132 as novel differentially methylated miRNAs in CRC, thereby facilitating sub-classification of CRC and links miR-129-2 methylation to early endometrial tumorigenesis. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0059-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sippy Kaur
- Department of Medical Genetics, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, P.O. Box 63, Helsinki, FIN-00014 Finland
| | - Johanna E Lotsari
- Department of Medical Genetics, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, P.O. Box 63, Helsinki, FIN-00014 Finland
| | - Sam Al-Sohaily
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia
| | - Janindra Warusavitarne
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia
| | - Maija Rj Kohonen-Corish
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia.,St Vincent's Clinical School, UNSW Medicine, Darlinghurst, NSW 2052 Australia.,School of Medicine, University of Western Sydney, Campelltown, Sydney, NSW 2560 Australia
| | - Päivi Peltomäki
- Department of Medical Genetics, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, P.O. Box 63, Helsinki, FIN-00014 Finland
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268
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Micucci JA, Sperry ED, Martin DM. Chromodomain helicase DNA-binding proteins in stem cells and human developmental diseases. Stem Cells Dev 2015; 24:917-26. [PMID: 25567374 DOI: 10.1089/scd.2014.0544] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Dynamic regulation of gene expression is vital for proper cellular development and maintenance of differentiated states. Over the past 20 years, chromatin remodeling and epigenetic modifications of histones have emerged as key controllers of rapid reversible changes in gene expression. Mutations in genes encoding enzymes that modify chromatin have also been identified in a variety of human neurodevelopmental disorders, ranging from isolated intellectual disability and autism spectrum disorder to multiple congenital anomaly conditions that affect major organ systems and cause severe morbidity and mortality. In this study, we review recent evidence that chromodomain helicase DNA-binding (CHD) proteins regulate stem cell proliferation, fate, and differentiation in a wide variety of tissues and organs. We also highlight known roles of CHD proteins in human developmental diseases and present current unanswered questions about the pleiotropic effects of CHD protein complexes, their genetic targets, nucleosome sliding functions, and enzymatic effects in cells and tissues.
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Affiliation(s)
- Joseph A Micucci
- 1 Division of Hematology, Children's Hospital of Philadelphia , Philadelphia, Pennsylvania
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269
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Nunes M, Vrignaud P, Vacher S, Richon S, Lièvre A, Cacheux W, Weiswald LB, Massonnet G, Chateau-Joubert S, Nicolas A, Dib C, Zhang W, Watters J, Bergstrom D, Roman-Roman S, Bièche I, Dangles-Marie V. Evaluating patient-derived colorectal cancer xenografts as preclinical models by comparison with patient clinical data. Cancer Res 2015; 75:1560-6. [PMID: 25712343 DOI: 10.1158/0008-5472.can-14-1590] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 02/06/2015] [Indexed: 11/16/2022]
Abstract
Development of targeted therapeutics required translationally relevant preclinical models with well-characterized cancer genome alterations. Here, by studying 52 colorectal patient-derived tumor xenografts (PDX), we examined key molecular alterations of the IGF2-PI3K and ERBB-RAS pathways and response to cetuximab. PDX molecular data were compared with that published for patient colorectal tumors in The Cancer Genome Atlas. We demonstrated a significant pattern of mutual exclusivity of genomic abnormalities in the IGF2-PI3K and ERBB-RAS pathways. The genomic anomaly frequencies observed in microsatellite stable PDX reproduce those detected in nonhypermutated patient tumors. We found frequent IGF2 upregulation (16%), which was mutually exclusive with IRS2, PIK3CA, PTEN, and INPP4B alterations, supporting IGF2 as a potential drug target. In addition to maintaining the genomic and histologic diversity, correct preclinical models need to reproduce drug response observed in patients. Responses of PDXs to cetuximab recapitulate also clinical data in patients, with partial or complete response in 15% (8 of 52) of PDXs and response strictly restricted to KRAS wild-type models. The response rate reaches 53% (8 of 15) when KRAS, BRAF, and NRAS mutations are concomitantly excluded, proving a functional cross-validation of predictive biomarkers obtained retrospectively in patients. Collectively, these results show that, because of their clinical relevance, colorectal PDXs are appropriate tools to identify both new targets, like IGF2, and predictive biomarkers of response/resistance to targeted therapies.
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Affiliation(s)
- Manoel Nunes
- Translational and Experimental Medicine, Sanofi Oncology, Sanofi, Vitry-sur-Seine, France. Translational and Experimental Medicine, Sanofi Oncology, Sanofi, Cambridge, Massachusetts
| | - Patricia Vrignaud
- Translational and Experimental Medicine, Sanofi Oncology, Sanofi, Vitry-sur-Seine, France. Translational and Experimental Medicine, Sanofi Oncology, Sanofi, Cambridge, Massachusetts
| | - Sophie Vacher
- Service de Génétique, Hôpital Institut Curie, Paris, France
| | - Sophie Richon
- IFR71, Faculté de Sciences Biologiques et Pharmaceutiques, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Astrid Lièvre
- Département d'Oncologie médicale, Hôpital Institut Curie, Paris, France. Université de Versailles Saint-Quentin en Yvelines, Faculté des Sciences Biologiques, Versailles, France
| | - Wulfran Cacheux
- Département d'Oncologie médicale, Hôpital Institut Curie, Paris, France
| | - Louis-Bastien Weiswald
- IFR71, Faculté de Sciences Biologiques et Pharmaceutiques, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Gerald Massonnet
- Recherche Translationnelle, Centre de Recherche, Institut Curie, Paris, France
| | - Sophie Chateau-Joubert
- France Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, Unité d'Anatomie Pathologique, Maisons-Alfort, France
| | - André Nicolas
- Département de Pathologie, Hôpital Institut Curie, Paris, France
| | - Colette Dib
- Translational and Experimental Medicine, Sanofi Oncology, Sanofi, Vitry-sur-Seine, France. Translational and Experimental Medicine, Sanofi Oncology, Sanofi, Cambridge, Massachusetts
| | - Weidong Zhang
- Translational and Experimental Medicine, Sanofi Oncology, Sanofi, Vitry-sur-Seine, France. Translational and Experimental Medicine, Sanofi Oncology, Sanofi, Cambridge, Massachusetts
| | - James Watters
- Translational and Experimental Medicine, Sanofi Oncology, Sanofi, Vitry-sur-Seine, France. Translational and Experimental Medicine, Sanofi Oncology, Sanofi, Cambridge, Massachusetts
| | - Donald Bergstrom
- Translational and Experimental Medicine, Sanofi Oncology, Sanofi, Vitry-sur-Seine, France. Translational and Experimental Medicine, Sanofi Oncology, Sanofi, Cambridge, Massachusetts
| | - Sergio Roman-Roman
- Recherche Translationnelle, Centre de Recherche, Institut Curie, Paris, France
| | - Ivan Bièche
- Service de Génétique, Hôpital Institut Curie, Paris, France. IFR71, Faculté de Sciences Biologiques et Pharmaceutiques, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Virginie Dangles-Marie
- IFR71, Faculté de Sciences Biologiques et Pharmaceutiques, Université Paris Descartes, Sorbonne Paris Cité, Paris, France. Recherche Translationnelle, Centre de Recherche, Institut Curie, Paris, France.
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270
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The cancer COMPASS: navigating the functions of MLL complexes in cancer. Cancer Genet 2015; 208:178-91. [PMID: 25794446 DOI: 10.1016/j.cancergen.2015.01.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 12/13/2022]
Abstract
The mixed-lineage leukemia family of histone methyltransferases (MLL1-4, or KMT2A-D) were previously linked to cancer through the founding member, MLL1/KMT2A, which is often involved in translocation-associated gene fusion events in childhood leukemias. However, in recent years, a multitude of tumor exome sequencing studies have revealed that orthologues MLL3/KMT2C and MLL2/KMT2D are mutated in a significant percentage of a large variety of malignancies, particularly solid tumors. These unexpected findings necessitate a deeper inspection into the activities and functional differences between the MLL/KMT2 family members. This review provides an overview of this protein family and its relation to cancers, focusing on the recent links between MLL3/KMT2C and MLL2/4/KMT2D and their potential roles as tumor suppressors in an assortment of cell types.
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Colamaio M, Puca F, Ragozzino E, Gemei M, Decaussin-Petrucci M, Aiello C, Bastos AU, Federico A, Chiappetta G, Del Vecchio L, Torregrossa L, Battista S, Fusco A. miR-142-3p down-regulation contributes to thyroid follicular tumorigenesis by targeting ASH1L and MLL1. J Clin Endocrinol Metab 2015; 100:E59-69. [PMID: 25238203 DOI: 10.1210/jc.2014-2280] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
CONTEXT A previous micro-RNA expression profile of thyroid follicular adenomas identified miR-142 precursor among the miRNAs downregulated in the neoplastic tissues compared to normal thyroid gland. OBJECTIVE The aim of this work has been to assess the expression of miR-142-3p in a large panel of follicular thyroid adenomas and carcinomas and evaluate its effect on thyroid cell proliferation and target expression. DESIGN The expression of miR-142-3p was analyzed by qRT-PCR in thyroid follicular adenomas and carcinomas, compared to normal thyroids. MiR-142-3p expression was restored in WRO cells and the effects on cell proliferation and target expression were evaluated. RESULTS Here we show that miR-142-3p is downregulated in FTAs, FTCs, and FVPTCs. MiR-142-3p was demonstrated to reduce the proliferation rate of WRO and FTC133 cells, supporting its tumor suppressor role in thyroid cancerogenesis. Moreover, this microRNA was able to downregulate the expression of ASH1L and MLL1, by direct and indirect mechanisms, respectively. Consistently, an inverse correlation between miR-142-3p expression and ASH1L and MLL1 proteins was found in thyroid follicular adenomas and carcinomas. ASH1L and MLL1, which belong to the Trithorax group (TrxG) proteins and are major regulators of Homeobox gene expression, maintain active target gene transcription by histone 3 lysine 4 methylation. Interestingly, we found that FTCs and FTC cell lines express tumor specific, shorter forms of the two proteins. The capability of miR-142-3p to modulate the levels of these tumor-associated forms and to reactivate thyroid-specific Hox gene expression, likely contributes to its tumor suppressive function. CONCLUSIONS These data demonstrate that miR-142-3p downregulation has a role in thyroid tumorigenesis, by regulating ASH1L and MLL1.
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Affiliation(s)
- Marianna Colamaio
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche (M.C., F.P., E.R., A.U.B., A.F., S.B., A.F.), Università degli Studi di Napoli "Federico II," 80131 Naples, Italy; Department of Pathology (M. D-P.), Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Université Lyon 1, 69495 Pierre Bénite, France; CEINGE (M.G., L.D.V.), Biotecnologie Avanzate, 80145 Naples, Italy; Istituto dei Tumori di Napoli "G. Pascale" (C.A., G.C.) Via Mariano Semmola, 52, 80131 Naples, Italy; Dipartimento di Patologia Chirurgica, Medica, Molecolare e dell'Area Critica (L.T.), University of Pisa, I-56126 Pisa, Italy; and Instituto Nacional de Câncer (A.F.), 20230-130 Rio de Janeiro, RJ, Brazil
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272
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Oh HR, An CH, Yoo NJ, Lee SH. Somatic mutations of amino acid metabolism-related genes in gastric and colorectal cancers and their regional heterogeneity--a short report. Cell Oncol (Dordr) 2014; 37:455-61. [PMID: 25450519 DOI: 10.1007/s13402-014-0209-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Metabolic reprogramming is an emerging topic in cancer research. However, genetic alterations in genes encoding enzymes involved in amino acid metabolism are largely unknown. The aim of this study was to explore whether genes known to be involved in amino acid metabolism are mutated in gastric cancer (GC) and/or colorectal cancer (CRC). METHODS Through a public database search, we found that a number of genes known to be involved in amino acid metabolism, i.e., AGXT, ALDH2, APIP, MTR, DNMT1, ASH1L, ASPA, CAD, DDC, GCDH, DLD, LAP3, MCEE and MUT, harbor mononucleotide repeats that may serve as mutation targets in cancers exhibiting microsatellite instability (MSI). We assessed these genes for the presence of the mutations in 79 GCs and 124 CRCs using single-strand conformation polymorphism (SSCP) and direct sequencing analyses. RESULTS Using SSCP in conjunction with DNA sequencing we detected frameshift mutations in AGXT (17 cases), ALDH2 (3 cases), APIP (4 cases), MTR (5 cases), DNMT1 (1 case), ASH1L (1 case), ASPA (2 cases), CAD (2 cases), DDC (1 case), GCDH (3 cases), DLD (1 case), LAP3 (1 case), MCEE (5 cases) and MUT (1 case). These mutations were exclusively detected in MSI-high (MSI-H), and not in MSI-low or MSI-stable (MSI-L/MSS) cases. In addition, we analyzed 16 CRCs for the presence of intra-tumor heterogeneity (ITH) and found that two CRCs harbored regional ITH for GCDH frameshift mutations. CONCLUSIONS Our data indicate that genes known to be involved in amino acid metabolism recurrently acquire somatic mutations in MSH-H GCs and MSH-H CRCs and that, in addition, mutation ITH does occur in at least some of these tumors. Together, these data suggest that metabolic reprogramming may play a role in the etiology of MSI-H GCs and CRCs. Our data also suggest that ultra-regional mutation analysis is required for a more comprehensive evaluation of the mutation status in these tumors.
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Affiliation(s)
- Hye Rim Oh
- Departments of Pathology, College of Medicine, The Catholic University of Korea, 505 Banpo-dong, Socho-gu, Seoul, 137-701, South Korea
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273
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Yang Y, Yang JJ, Tao H, Jin WS. New perspectives on β-catenin control of cell fate and proliferation in colon cancer. Food Chem Toxicol 2014; 74:14-9. [DOI: 10.1016/j.fct.2014.08.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/12/2014] [Accepted: 08/21/2014] [Indexed: 02/08/2023]
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274
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Glaucarubinone inhibits colorectal cancer growth by suppression of hypoxia-inducible factor 1α and β-catenin via a p-21 activated kinase 1-dependent pathway. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:157-65. [PMID: 25409929 DOI: 10.1016/j.bbamcr.2014.10.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/17/2014] [Accepted: 10/15/2014] [Indexed: 01/22/2023]
Abstract
p-21-Activated kinase 1 (PAK1) enhances colorectal cancer (CRC) progression by stimulating Wnt/β-catenin, ERK and AKT pathways. PAK1 also promotes CRC survival via up-regulation of hypoxia-inducible factor 1α (HIF-1α), a key player in cancer survival. Glaucarubinone, a quassinoid natural product, inhibits pancreatic cancer growth by down-regulation of PAK1. The aim of this study was to investigate the effect of glaucarubinone on CRC growth and metastasis, and the mechanism involved. Cell proliferation was measured in vitro by [(3)H]-thymidine incorporation and in vivo by volume of tumor xenografts. Protein concentrations were measured by Western blotting of cell extracts. We report here that glaucarubinone inhibited CRC growth both in vitro and in vivo. The potency of glaucarubinone as an inhibitor of cell proliferation was negatively correlated to PAK1 expression in CRC cells. Glaucarubinone suppressed the expression of HIF-1α and β-catenin. Knockdown of PAK1 by shRNA enhanced inhibition by glaucarubinone while constitutively active PAK1 blocked the inhibitory effect. Our findings indicate that glaucarubinone inhibited CRC growth by down-regulation of HIF-1α and β-catenin via a PAK1-dependent pathway.
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275
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Donnard E, Asprino PF, Correa BR, Bettoni F, Koyama FC, Navarro FC, Perez RO, Mariadason J, Sieber OM, Strausberg RL, Simpson AJ, Jardim DL, Reis LFL, Parmigiani RB, Galante PA, Camargo AA. Mutational analysis of genes coding for cell surface proteins in colorectal cancer cell lines reveal novel altered pathways, druggable mutations and mutated epitopes for targeted therapy. Oncotarget 2014; 5:9199-213. [PMID: 25193853 PMCID: PMC4253428 DOI: 10.18632/oncotarget.2374] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/20/2014] [Indexed: 12/14/2022] Open
Abstract
We carried out a mutational analysis of 3,594 genes coding for cell surface proteins (Surfaceome) in 23 colorectal cancer cell lines, searching for new altered pathways, druggable mutations and mutated epitopes for targeted therapy in colorectal cancer. A total of 3,944 somatic non-synonymous substitutions and 595 InDels, occurring in 2,061 (57%) Surfaceome genes were catalogued. We identified 48 genes not previously described as mutated in colorectal tumors in the TCGA database, including genes that are mutated and expressed in >10% of the cell lines (SEMA4C, FGFRL1, PKD1, FAM38A, WDR81, TMEM136, SLC36A1, SLC26A6, IGFLR1). Analysis of these genes uncovered important roles for FGF and SEMA4 signaling in colorectal cancer with possible therapeutic implications. We also found that cell lines express on average 11 druggable mutations, including frequent mutations (>20%) in the receptor tyrosine kinases AXL and EPHA2, which have not been previously considered as potential targets for colorectal cancer. Finally, we identified 82 cell surface mutated epitopes, however expression of only 30% of these epitopes was detected in our cell lines. Notwithstanding, 92% of these epitopes were expressed in cell lines with the mutator phenotype, opening new venues for the use of "general" immune checkpoint drugs in this subset of patients.
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Affiliation(s)
- Elisa Donnard
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
- Programa de Pós Graduação do Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Paula F. Asprino
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Bruna R. Correa
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Fabiana Bettoni
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Fernanda C. Koyama
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
- Laboratory of Molecular Biology and Genomics, Ludwig Institute for Cancer Research, São Paulo, Brazil
| | - Fabio C.P. Navarro
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
- Programa de Pós Graduação do Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Rodrigo O. Perez
- Laboratory of Molecular Biology and Genomics, Ludwig Institute for Cancer Research, São Paulo, Brazil
- Instituto Angelita & Joaquim Gama, São Paulo, Brazil
| | - John Mariadason
- Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Melbourne, Australia
| | - Oliver M. Sieber
- Colorectal Cancer Genetics Laboratory, Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville, Australia
| | | | | | - Denis L.F. Jardim
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | | | | | - Pedro A.F. Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Anamaria A. Camargo
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
- Laboratory of Molecular Biology and Genomics, Ludwig Institute for Cancer Research, São Paulo, Brazil
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276
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Rönsch K, Jägle S, Rose K, Seidl M, Baumgartner F, Freihen V, Yousaf A, Metzger E, Lassmann S, Schüle R, Zeiser R, Michoel T, Hecht A. SNAIL1 combines competitive displacement of ASCL2 and epigenetic mechanisms to rapidly silence the EPHB3 tumor suppressor in colorectal cancer. Mol Oncol 2014; 9:335-54. [PMID: 25277775 DOI: 10.1016/j.molonc.2014.08.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 08/27/2014] [Accepted: 08/29/2014] [Indexed: 01/06/2023] Open
Abstract
EPHB3 is a critical cellular guidance factor in the intestinal epithelium and an important tumor suppressor in colorectal cancer (CRC) whose expression is frequently lost at the adenoma-carcinoma transition when tumor cells become invasive. The molecular mechanisms underlying EPHB3 silencing are incompletely understood. Here we show that EPHB3 expression is anti-correlated with inducers of epithelial-mesenchymal transition (EMT) in primary tumors and CRC cells. In vitro, SNAIL1 and SNAIL2, but not ZEB1, repress EPHB3 reporter constructs and compete with the stem cell factor ASCL2 for binding to an E-box motif. At the endogenous EPHB3 locus, SNAIL1 triggers the displacement of ASCL2, p300 and the Wnt pathway effector TCF7L2 and engages corepressor complexes containing HDACs and the histone demethylase LSD1 to collapse active chromatin structure, resulting in rapid downregulation of EPHB3. Beyond its impact on EPHB3, SNAIL1 deregulates markers of intestinal identity and stemness and in vitro forces CRC cells to undergo EMT with altered morphology, increased motility and invasiveness. In xenotransplants, SNAIL1 expression abrogated tumor cell palisading and led to focal loss of tumor encapsulation and the appearance of areas with tumor cells displaying a migratory phenotype. These changes were accompanied by loss of EPHB3 and CDH1 expression. Intriguingly, SNAIL1-induced phenotypic changes of CRC cells are significantly impaired by sustained EPHB3 expression both in vitro and in vivo. Altogether, our results identify EPHB3 as a novel target of SNAIL1 and suggest that disabling EPHB3 signaling is an important aspect to eliminate a roadblock at the onset of EMT processes.
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Affiliation(s)
- Kerstin Rönsch
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Sabine Jägle
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Katja Rose
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
| | - Maximilian Seidl
- Department of Pathology, University Medical Center, Breisacher Str. 115a, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency, University Medical Center, Breisacher Str. 117, 79106 Freiburg, Germany
| | - Francis Baumgartner
- Department of Hematology and Oncology, University Medical Center, Hugstetter Str. 55, 79106 Freiburg, Germany
| | - Vivien Freihen
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
| | - Afsheen Yousaf
- Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs-University Freiburg, Albertstraße 19, 79104 Freiburg, Germany
| | - Eric Metzger
- Department of Urology/Women's Hospital and Center for Clinical Research, University Medical Center, Breisacher Str. 66, 79106 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany; German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Silke Lassmann
- Department of Pathology, University Medical Center, Breisacher Str. 115a, 79106 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany; German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Roland Schüle
- Department of Urology/Women's Hospital and Center for Clinical Research, University Medical Center, Breisacher Str. 66, 79106 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany; German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Robert Zeiser
- Department of Hematology and Oncology, University Medical Center, Hugstetter Str. 55, 79106 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - Tom Michoel
- Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs-University Freiburg, Albertstraße 19, 79104 Freiburg, Germany; The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK
| | - Andreas Hecht
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany.
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