51
|
Hauptman N, Jevšinek Skok D, Spasovska E, Boštjančič E, Glavač D. Genes CEP55, FOXD3, FOXF2, GNAO1, GRIA4, and KCNA5 as potential diagnostic biomarkers in colorectal cancer. BMC Med Genomics 2019; 12:54. [PMID: 30987631 PMCID: PMC6466812 DOI: 10.1186/s12920-019-0501-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
Background Colorectal cancer (CRC) is one of the leading causes of death by cancer worldwide and in need of novel potential diagnostic biomarkers for early discovery. Methods We conducted a two-step study. We first employed bioinformatics on data from The Cancer Genome Atlas to obtain potential biomarkers and then experimentally validated some of them on our clinical samples. Our aim was to find a methylation alteration common to all clusters, with the potential of becoming a diagnostic biomarker in CRC. Results Unsupervised clustering of methylation data resulted in four clusters, none of which had a known common genetic or epigenetic event, such as mutations or methylation. The intersect among clusters and regulatory regions resulted in 590 aberrantly methylated probes, belonging to 198 differentially expressed genes. After performing pathway and functional analysis on differentially expressed genes, we selected six genes: CEP55, FOXD3, FOXF2, GNAO1, GRIA4 and KCNA5, for further experimental validation on our own clinical samples. In silico analysis demonstrated that CEP55 was hypomethylated in 98.7% and up-regulated in 95.0% of samples. Genes FOXD3, FOXF2, GNAO1, GRIA4 and KCNA5 were hypermethylated in 97.9, 81.1, 80.3, 98.4 and 94.0%, and down-regulated in 98.3, 98.9, 98.1, 98.1 and 98.6% of samples, respectively. Our experimental data show CEP55 was hypomethylated in 97.3% of samples and down-regulated in all samples, while FOXD3, FOXF2, GNAO1, GRIA4 and KCNA5 were hypermethylated in 100.0, 90.2, 100.0, 99.1 and 100.0%, and down-regulated in 68.0, 76.0, 96.0, 95.2 and 84.0% of samples, respectively. Results of in silico and our experimental analyses showed that more than 97% of samples had at least four methylation markers altered. Conclusions Using bioinformatics followed by experimental validation, we identified a set of six genes that were differentially expressed in CRC compared to normal mucosa and whose expression seems to be methylation dependent. Moreover, all of these six genes were common in all methylation clusters and mutation statuses of CRC and as such are believed to be an early event in human CRC carcinogenesis and to represent potential CRC biomarkers. Electronic supplementary material The online version of this article (10.1186/s12920-019-0501-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Nina Hauptman
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000, Ljubljana, Slovenia.
| | - Daša Jevšinek Skok
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000, Ljubljana, Slovenia.,Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000, Ljubljana, Slovenia
| | - Elena Spasovska
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000, Ljubljana, Slovenia
| | - Emanuela Boštjančič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000, Ljubljana, Slovenia
| | - Damjan Glavač
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000, Ljubljana, Slovenia
| |
Collapse
|
52
|
Chen S, Pu W, Guo S, Jin L, He D, Wang J. Genome-Wide DNA Methylation Profiles Reveal Common Epigenetic Patterns of Interferon-Related Genes in Multiple Autoimmune Diseases. Front Genet 2019; 10:223. [PMID: 31024609 PMCID: PMC6459983 DOI: 10.3389/fgene.2019.00223] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 02/28/2019] [Indexed: 11/13/2022] Open
Abstract
Graves' disease (GD), rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) and systemic sclerosis (SSc) are complex autoimmune diseases sharing common clinical, genetic and pathogenetic features. However, the commonalities of the DNA methylation profiles for these diseases are still unknown. We conducted an integrative analysis of the multiple-autoimmune disease methylation dataset including GD, RA, SLE, and SSc samples, to identify the common methylation patterns of autoimmune diseases. We identified 15,289 differentially methylated sites between multiple-autoimmune disease patients and controls in CD4+ T cells. We found that the most significant differentially methylated sites had a remarkable enrichment in type I interferon (IFN) pathway genes. Similarly, we identified 9,295 differentially methylated sites between GD/SSc patients and controls in CD8+ T cells. The overall IFN-related gene panel annotated by gene ontology (GO) showed an excellent diagnostic capacity in CD4+ T cells (Sensitivity = 0.82, specificity = 0.82 and AUC = 0.90), while IFI44L, another IFN-related gene not annotated by GO, showed high prediction ability in both CD4+ (AUC = 0.86) and CD8+ (AUC = 0.75) T cells. In conclusion, our study demonstrated that hypomethylation of IFN-related genes is a common feature of GD/RA/SLE/SSc patients in CD4+ T cells, and the DNA methylation profile of IFN-related genes could be promising biomarkers for the diagnosis of GD, RA, SLE, and SSc.
Collapse
Affiliation(s)
- Sidi Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Weilin Pu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Shicheng Guo
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Dongyi He
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine, Shanghai, China
- Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Traditional Chinese Medicine Research Institute, Shanghai, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China
| |
Collapse
|
53
|
Gu S, Lin S, Ye D, Qian S, Jiang D, Zhang X, Li Q, Yang J, Ying X, Li Z, Tang M, Wang J, Jin M, Chen K. Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer. Clin Epigenetics 2019; 11:41. [PMID: 30846004 PMCID: PMC6407227 DOI: 10.1186/s13148-019-0628-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/04/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Epigenetic alternation is a common contributing factor to neoplastic transformation. Although previous studies have reported a cluster of aberrant promoter methylation changes associated with silencing of tumor suppressor genes, little is known concerning their sequential DNA methylation changes during the carcinogenetic process. The aim of the present study was to address a genome-wide search for identifying potentially important methylated changes and investigate the onset and pattern of methylation changes during the progression of colorectal neoplasia. METHODS A three-phase design was employed in this study. In the screening phase, DNA methylation profile of 12 pairs of colorectal cancer (CRC) and adjacent normal tissues was analyzed by using the Illumina MethylationEPIC BeadChip. Significant CpG sites were selected based on a cross-validation analysis from The Cancer Genome Atlas (TCGA) database. Methylation levels of candidate CpGs were assessed using pyrosequencing in the training dataset (tumor lesions and adjacent normal tissues from 46 CRCs) and the validation dataset (tumor lesions and paired normal tissues from 13 hyperplastic polyps, 129 adenomas, and 256 CRCs). A linear mixed-effects model was used to examine the incremental changes of DNA methylation during the progression of colorectal neoplasia. RESULTS The comparisons between normal and tumor samples in the screening phase revealed an extensive CRC-specific methylomic pattern with 174,006 (21%) methylated CpG sites, of which 22,232 (13%) were hyermethylated and 151,774 (87%) were hypomethylated. Hypermethylation mostly occurred in CpG islands with an overlap of gene promoters, while hypomethylation tended to be mapped far away from functional regions. Further cross validation analysis from TCGA dataset confirmed 265 hypermethylated promoters coupling with downregulated gene expression. Among which, hypermethylated changes in MEEPD2 promoter was successfully replicated in both training and validation phase. Significant hypermethylation appeared since precursor lesions with an extensive modification in CRCs. The linear mixed-effects modeling analysis found that a cumulative pattern of MPPED2 methylation changes from normal mucosa to hyperplastic polyp to adenoma, and to carcinoma (P < 0.001). CONCLUSIONS Our findings indicate that epigenetic alterations of MPPED2 promoter region appear sequentially during the colorectal neoplastic progression. It might be able to serve as a promising biomarker for early diagnosis and stage surveillance of colorectal tumorigenesis.
Collapse
Affiliation(s)
- Simeng Gu
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Shujuan Lin
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Ding Ye
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China.,Department of Epidemiology and Biostatistics, Zhejiang Chinese Medical University School of Public Health, 548 Binwen Road, Hangzhou, 310053, China
| | - Sangni Qian
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Danjie Jiang
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Xiaocong Zhang
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Qilong Li
- Jiashan Institute of Cancer Prevention and Treatment, 345 Jiefangdong Road, Jiashan, 314100, China
| | - Jinhua Yang
- Jiashan Institute of Cancer Prevention and Treatment, 345 Jiefangdong Road, Jiashan, 314100, China
| | - Xiaojiang Ying
- Department of Anorectal Surgery, Shaoxing People's Hospital, 568 Zhongxingbei Road, Shaoxing, 312000, China
| | - Zhenjun Li
- Department of Anorectal Surgery, Shaoxing People's Hospital, 568 Zhongxingbei Road, Shaoxing, 312000, China
| | - Mengling Tang
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jianbing Wang
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Mingjuan Jin
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China.
| | - Kun Chen
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China. .,Cancer Institute, the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China.
| |
Collapse
|
54
|
Ding W, Chen G, Shi T. Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis. Epigenetics 2019; 14:67-80. [PMID: 30696380 DOI: 10.1080/15592294.2019.1568178] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA methylation status is closely associated with diverse diseases, and is generally more stable than gene expression, thus abnormal DNA methylation could be important biomarkers for tumor diagnosis, treatment and prognosis. However, the signatures regarding DNA methylation changes for pan-cancer diagnosis and prognosis are less explored. Here we systematically analyzed the genome-wide DNA methylation patterns in diverse TCGA cancers with machine learning. We identified seven CpG sites that could effectively discriminate tumor samples from adjacent normal tissue samples for 12 main cancers of TCGA (1216 samples, AUC > 0.99). Those seven potential diagnostic biomarkers were further validated in the other 9 different TCGA cancers and 4 independent datasets (AUC > 0.92). Three out of the seven CpG sites were correlated with cell division, DNA replication and cell cycle. We also identified 12 CpG sites that can effectively distinguish 26 different cancers (7605 samples), and the result was repeatable in independent datasets as well as two disparate tumors with metastases (micro-average AUC > 0.89). Furthermore, a series of potential signatures that could significantly predict the prognosis of tumor patients for 7 different cancer were identified via survival analysis (p-value < 1e-4). Collectively, DNA methylation patterns vary greatly between tumor and adjacent normal tissues, as well as among different types of cancers. Our identified signatures may aid the decision of clinical diagnosis and prognosis for pan-cancer and the potential cancer-specific biomarkers could be used to predict the primary site of metastatic breast and prostate cancers.
Collapse
Affiliation(s)
- Wubin Ding
- a Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai , China
| | - Geng Chen
- a Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai , China
| | - Tieliu Shi
- a Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai , China.,b National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy , Guangxi Medical University , Nanning , China
| |
Collapse
|
55
|
Liu R, Su X, Long Y, Zhou D, Zhang X, Ye Z, Ma J, Tang T, Wang F, He C. A systematic review and quantitative assessment of methylation biomarkers in fecal DNA and colorectal cancer and its precursor, colorectal adenoma. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 779:45-57. [PMID: 31097151 DOI: 10.1016/j.mrrev.2019.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/15/2018] [Accepted: 01/16/2019] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) arises from accumulated genetic and epigenetic alterations, which provide the possibility to identify tumor-specific biomarkers by analyzing fecal DNA. Methylation status in human genes from tumor tissue is highlighted as promising biomarker in the early detection of CRC. A number of studies have documented altered methylation levels in DNA extracted from stool samples, but generated heterogeneous results. We performed a systematic review and quantitative assessment of existing studies to compare levels of DNA methylation in most frequently studied genes and their diagnostic value in CRC and its precursor, colorectal adenoma, with their counterparts in healthy subjects. Robust searches of the literature were performed in our study with explicit strategies and definite inclusion/exclusion criteria. Pooled data revealed that methylation levels of SFRP2, SFRP1, TFPI2, BMP3, NDRG4, SPG20, and BMP3 plus NDRG4 genes exceeded a sensitivity of 70% and a specificity of 80% for CRC detection. The DOR of the seven candidate biomarkers ranged from 19.80 to 334.33, indicating a good diagnostic power in discriminating cancer from normal tissues. The AUC range was from 0.88 to 0.95, indicating a good or very good discriminatory performance. When test results for BMP3 and NDRG4 were combined, the DOR of CRC detection was 98.36, which was higher than that for BMP3 and NDRG4 separately. As for adenoma detection, the DOR of methylated NDRG4 is higher than that for CRC (CRC vs. adenoma: 54.86 vs. 57.22). Both the sensitivity and specificity of NDRG4 for adenoma detection exceeded 70%. These findings demonstrate the eligibility and feasibility of DNA methylation as a minimally invasive biomarker in feces in the diagnosis of CRC and adenoma. The use of DNA from human stools has the potential to be readily applicable to detect aberrant DNA methylation levels among many subjects for CRC early screening.
Collapse
Affiliation(s)
- Rongbin Liu
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China; Department of Ultrasound, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xuan Su
- Department of Head and Neck, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, China
| | - Yakang Long
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Dalei Zhou
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xiao Zhang
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zulu Ye
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jiangjun Ma
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Tao Tang
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Fang Wang
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| | - Caiyun He
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| |
Collapse
|
56
|
Abstract
DNA methylation is a process by which methyl groups are added to cytosine or adenine. DNA methylation can change the activity of the DNA molecule without changing the sequence. Methylation of 5-methylcytosine (5mC) is widespread in both eukaryotes and prokaryotes, and it is a very important epigenetic modification event, which can regulate gene activity and influence a number of key processes such as genomic imprinting, cell differentiation, transcriptional regulation, and chromatin remodeling. Profiling DNA methylation across the genome is critical to understanding the influence of methylation in normal biology and diseases including cancer. Recent discoveries of 5-methylcytosine (5mC) oxidation derivatives including 5-hydroxymethylcytosine (5hmC), 5-formylcytsine (5fC), and 5-carboxycytosine (5caC) in mammalian genome further expand our understanding of the methylation regulation. Genome-wide analyses such as microarrays and next-generation sequencing technologies have been used to assess large fractions of the methylome. A number of different quantitative approaches have also been established to map the DNA epigenomes with single-base resolution, as represented by the bisulfite-based methods, such as classical bisulfite sequencing, pyrosequencing etc. These methods have been used to generate base-resolution maps of 5mC and its oxidation derivatives in genomic samples. The focus of this chapter is to provide the methodologies that have been developed to detect the cytosine derivatives in the genomic DNA.
Collapse
Affiliation(s)
- Lingfang Feng
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, P. R. China
| | - Jianlin Lou
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, P. R. China.
| |
Collapse
|
57
|
LogLoss-BERAF: An ensemble-based machine learning model for constructing highly accurate diagnostic sets of methylation sites accounting for heterogeneity in prostate cancer. PLoS One 2018; 13:e0204371. [PMID: 30388122 PMCID: PMC6214495 DOI: 10.1371/journal.pone.0204371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/06/2018] [Indexed: 12/23/2022] Open
Abstract
Although modern methods of whole genome DNA methylation analysis have a wide range of applications, they are not suitable for clinical diagnostics due to their high cost and complexity and due to the large amount of sample DNA required for the analysis. Therefore, it is crucial to be able to identify a relatively small number of methylation sites that provide high precision and sensitivity for the diagnosis of pathological states. We propose an algorithm for constructing limited subsamples from high-dimensional data to form diagnostic panels. We have developed a tool that utilizes different methods of selection to find an optimal, minimum necessary combination of factors using cross-entropy loss metrics (LogLoss) to identify a subset of methylation sites. We show that the algorithm can work effectively with different genome methylation patterns using ensemble-based machine learning methods. Algorithm efficiency, precision and robustness were evaluated using five genome-wide DNA methylation datasets (totaling 626 samples), and each dataset was classified into tumor and non-tumor samples. The algorithm produced an AUC of 0.97 (95% CI: 0.94-0.99, 9 sites) for prostate adenocarcinoma and an AUC of 1.0 (from 2 to 6 sites) for urothelial bladder carcinoma, two types of kidney carcinoma and colorectal carcinoma. For prostate adenocarcinoma we showed that identified differential variability methylation patterns distinguish cluster of samples with higher recurrence rate (hazard ratio for recurrence = 0.48, 95% CI: 0.05-0.92; log-rank test, p-value < 0.03). We also identified several clusters of correlated interchangeable methylation sites that can be used for the elaboration of biological interpretation of the resulting models and for further selection of the sites most suitable for designing diagnostic panels. LogLoss-BERAF is implemented as a standalone python code and open-source code is freely available from https://github.com/bioinformatics-IBCH/logloss-beraf along with the models described in this article.
Collapse
|
58
|
Barault L, Amatu A, Siravegna G, Ponzetti A, Moran S, Cassingena A, Mussolin B, Falcomatà C, Binder A, Cristiano C, Oddo D, Cancelliere C, Bustreo S, Bencardino K, Maden S, Vanzati A, Zavattari P, Truini M, Grady WM, Racca P, Michels KB, Siena S, Esteller M, Bardelli A, Sartore-Bianchi A, Di Nicolantonio F, Sartore-Bianchi A, Di Nicolantonio F. Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer. Gut 2018; 67:1995-2005. [PMID: 28982739 PMCID: PMC5897187 DOI: 10.1136/gutjnl-2016-313372] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Mutations in cell-free circulating DNA (cfDNA) have been studied for tracking disease relapse in colorectal cancer (CRC). This approach requires personalised assay design due to the lack of universally mutated genes. In contrast, early methylation alterations are restricted to defined genomic loci allowing comprehensive assay design for population studies. Our objective was to identify cancer-specific methylated biomarkers which could be measured longitudinally in cfDNA (liquid biopsy) to monitor therapeutic outcome in patients with metastatic CRC (mCRC). DESIGN Genome-wide methylation microarrays of CRC cell lines (n=149) identified five cancer-specific methylated loci (EYA4, GRIA4, ITGA4, MAP3K14-AS1, MSC). Digital PCR assays were employed to measure methylation of these genes in tumour tissue DNA (n=82) and cfDNA from patients with mCRC (n=182). Plasma longitudinal assessment was performed in a patient subset treated with chemotherapy or targeted therapy. RESULTS Methylation in at least one marker was detected in all tumour tissue samples and in 156 mCRC patient cfDNA samples (85.7%). Plasma marker prevalence was 71.4% for EYA4, 68.5% for GRIA4, 69.7% for ITGA4, 69.1% for MAP3K14-AS1% and 65.1% for MSC. Dynamics of methylation markers was not affected by treatment type and correlated with objective tumour response and progression-free survival. CONCLUSION This five-gene methylation panel can be used to circumvent the absence of patient-specific mutations for monitoring tumour burden dynamics in liquid biopsy under different therapeutic regimens. This method might be proposed for assessing pharmacodynamics in clinical trials or when conventional imaging has limitations.
Collapse
Affiliation(s)
- Ludovic Barault
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Corresponding authors: Ludovic Barault, PhD or Dr Federica Di Nicolantonio, PhD, Department of Oncology, University of Torino, Candiolo Cancer Institute – FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, Torino, Italy, Phone: +39-011-9933523, Fax: +39-011-9933225, (; )
| | - Alessio Amatu
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Giulia Siravegna
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy,FIRC Institute of Molecular Oncology (IFOM), Milano, Italy
| | - Agostino Ponzetti
- Colorectal Cancer Unit, Medical Oncology Division 1, AOU Città della Salute e della Scienza, San Giovanni Battista Hospital, Turin, Italy
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L’Hospitalet, Barcelona, Catalonia, Spain
| | - Andrea Cassingena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Benedetta Mussolin
- Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy
| | - Chiara Falcomatà
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy
| | - Alexandra Binder
- Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA
| | - Carmen Cristiano
- Colorectal Cancer Unit, Medical Oncology Division 1, AOU Città della Salute e della Scienza, San Giovanni Battista Hospital, Turin, Italy
| | - Daniele Oddo
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy
| | - Carlotta Cancelliere
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy
| | - Sara Bustreo
- Colorectal Cancer Unit, Medical Oncology Division 1, AOU Città della Salute e della Scienza, San Giovanni Battista Hospital, Turin, Italy
| | - Katia Bencardino
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Sean Maden
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Alice Vanzati
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Patrizia Zavattari
- Unit of Biology and Genetics, Dept. Biomedical Sciences, University of Cagliari, Italy
| | - Mauro Truini
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA,Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Patrizia Racca
- Colorectal Cancer Unit, Medical Oncology Division 1, AOU Città della Salute e della Scienza, San Giovanni Battista Hospital, Turin, Italy
| | - Karin B. Michels
- Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy,Università degli Studi di Milano, Milan, Italy
| | - Manel Esteller
- Colorectal Cancer Unit, Medical Oncology Division 1, AOU Città della Salute e della Scienza, San Giovanni Battista Hospital, Turin, Italy,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain,Institucio Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
| | - Alberto Bardelli
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy
| | | | - Federica Di Nicolantonio
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Corresponding authors: Ludovic Barault, PhD or Dr Federica Di Nicolantonio, PhD, Department of Oncology, University of Torino, Candiolo Cancer Institute – FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, Torino, Italy, Phone: +39-011-9933523, Fax: +39-011-9933225, (; )
| | | | - Federica Di Nicolantonio
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| |
Collapse
|
59
|
Carey JL, Cox OH, Seifuddin F, Marque L, Tamashiro KLK, Zandi PP, Wand GS, Lee RS. A Rat Methyl-Seq Platform to Identify Epigenetic Changes Associated with Stress Exposure. J Vis Exp 2018. [PMID: 30417882 PMCID: PMC6235597 DOI: 10.3791/58617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
As genomes of a wider variety of animals become available, there is an increasing need for tools that can capture dynamic epigenetic changes in these animal models. The rat is one particular model animal where an epigenetic tool can complement many pharmacological and behavioral studies to provide insightful mechanistic information. To this end, we adapted the SureSelect Target Capture System (referred to as Methyl-Seq) for the rat, which can assess DNA methylation levels across the rat genome. The rat design targeted promoters, CpG islands, island shores, and GC-rich regions from all RefSeq genes. To implement the platform on a rat experiment, male Sprague Dawley rats were exposed to chronic variable stress for 3 weeks, after which blood samples were collected for genomic DNA extraction. Methyl-Seq libraries were constructed from the rat DNA samples by shearing, adapter ligation, target enrichment, bisulfite conversion, and multiplexing. Libraries were sequenced on a next-generation sequencing platform and the sequenced reads were analyzed to identify DMRs between DNA of stressed and unstressed rats. Top candidate DMRs were independently validated by bisulfite pyrosequencing to confirm the robustness of the platform. Results demonstrate that the rat Methyl-Seq platform is a useful epigenetic tool that can capture methylation changes induced by exposure to stress.
Collapse
Affiliation(s)
- Jenny L Carey
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine
| | - Olivia H Cox
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine
| | - Fayaz Seifuddin
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine
| | - Leonard Marque
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine
| | - Kellie L K Tamashiro
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine
| | - Peter P Zandi
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine; Department of Mental Health, Johns Hopkins School of Public Health
| | - Gary S Wand
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine; Department of Medicine, Johns Hopkins School of Medicine
| | - Richard S Lee
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine;
| |
Collapse
|
60
|
Xue W, Wu X, Wang F, Han P, Cui B. Genome-wide methylation analysis identifies novel prognostic methylation markers in colon adenocarcinoma. Biomed Pharmacother 2018; 108:288-296. [PMID: 30223100 DOI: 10.1016/j.biopha.2018.09.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/26/2018] [Accepted: 09/08/2018] [Indexed: 12/14/2022] Open
Abstract
Previous studies have indicated that abnormal methylation is a critical and early event in the pathogenesis of most types of human cancer, which contributes to tumorigenesis. However, there has been little focus on the potential of DNA methylation patterns as predictive markers for the prognosis of colon adenocarcinoma (COAD). In the present study, a genome-wide comparative analysis of DNA methylation profiles was performed between 315 COAD samples and 38 matched tumor-adjacent normal tissue samples. A total of 675 differentially methylated regions (DMRs) associated with 630 genes were identified, including 654 hypermethylated regions (UMRs) and 21 hypomethylated regions, which were capable of distinguishing COAD samples from non-malignant tissue samples. Although most of the DMRs appeared to be located within the gene body or promoter regions, UMRs were mostly located within CpG islands. Functional analysis suggested that genes associated with DMRs were enriched in many of the core cancer-signaling pathways known to be important in COAD biology. A survival analysis was also performed, which identified 7 DMRs as potential candidate markers with the ability to classify patients into high and low-risk groups with significantly different overall survival. The present study provides a better understanding of the molecular mechanisms underlying COAD, and demonstrates the utility of aberrant DNA methylation in the prognosis of COAD.
Collapse
Affiliation(s)
- Weinan Xue
- Department of Colorectal Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China
| | - Xiangxin Wu
- Department of Colorectal Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China
| | - Fan Wang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, 150081, China
| | - Peng Han
- Department of Colorectal Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China
| | - Binbin Cui
- Department of Colorectal Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China.
| |
Collapse
|
61
|
Abdallah MOE, Algizouli UK, Suliman MA, Abdulrahman RA, Koko M, Fessahaye G, Shakir JH, Fahal AH, Elhassan AM, Ibrahim ME, Mohamed HS. EBV Associated Breast Cancer Whole Methylome Analysis Reveals Viral and Developmental Enriched Pathways. Front Oncol 2018; 8:316. [PMID: 30151354 PMCID: PMC6099083 DOI: 10.3389/fonc.2018.00316] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/24/2018] [Indexed: 01/18/2023] Open
Abstract
Background: Breast cancer (BC) ranks among the most common cancers in Sudan and worldwide with hefty toll on female health and human resources. Recent studies have uncovered a common BC signature characterized by low frequency of oncogenic mutations and high frequency of epigenetic silencing of major BC tumor suppressor genes. Therefore, we conducted a pilot genome-wide methylome study to characterize aberrant DNA methylation in breast cancer. Results: Differential methylation analysis between primary tumor samples and normal samples from healthy adjacent tissues yielded 20,188 differentially methylated positions (DMPs), which is further divided into 13,633 hypermethylated sites corresponding to 5339 genes and 6,555 hypomethylated sites corresponding to 2811 genes. Moreover, bioinformatics analysis revealed epigenetic dysregulation of major developmental pathways including hippo signaling pathway. We also uncovered many clues to a possible role for EBV infection in BC. Conclusion: Our results clearly show the utility of epigenetic assays in interrogating breast cancer tumorigenesis, and pinpointing specific developmental and viral pathways dysregulation that might serve as potential biomarkers or targets for therapeutic interventions.
Collapse
Affiliation(s)
- Mohammad O E Abdallah
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Ubai K Algizouli
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Maram A Suliman
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Rawya A Abdulrahman
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Mahmoud Koko
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Ghimja Fessahaye
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Jamal H Shakir
- Department of Surgery, Khartoum Teaching Hospital, Khartoum, Sudan
| | - Ahmed H Fahal
- Department of Surgery, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Ahmed M Elhassan
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Muntaser E Ibrahim
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Hiba S Mohamed
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan.,Department of Biology, Taibah University, Medina, Saudi Arabia
| |
Collapse
|
62
|
Molnár B, Galamb O, Péterfia B, Wichmann B, Csabai I, Bodor A, Kalmár A, Szigeti KA, Barták BK, Nagy ZB, Valcz G, Patai ÁV, Igaz P, Tulassay Z. Gene promoter and exon DNA methylation changes in colon cancer development - mRNA expression and tumor mutation alterations. BMC Cancer 2018; 18:695. [PMID: 29945573 PMCID: PMC6020382 DOI: 10.1186/s12885-018-4609-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/18/2018] [Indexed: 12/28/2022] Open
Abstract
Background DNA mutations occur randomly and sporadically in growth-related genes, mostly on cytosines. Demethylation of cytosines may lead to genetic instability through spontaneous deamination. Aims were whole genome methylation and targeted mutation analysis of colorectal cancer (CRC)-related genes and mRNA expression analysis of TP53 pathway genes. Methods Long interspersed nuclear element-1 (LINE-1) BS-PCR followed by pyrosequencing was performed for the estimation of global DNA metlyation levels along the colorectal normal-adenoma-carcinoma sequence. Methyl capture sequencing was done on 6 normal adjacent (NAT), 15 adenomatous (AD) and 9 CRC tissues. Overall quantitative methylation analysis, selection of top hyper/hypomethylated genes, methylation analysis on mutation regions and TP53 pathway gene promoters were performed. Mutations of 12 CRC-related genes (APC, BRAF, CTNNB1, EGFR, FBXW7, KRAS, NRAS, MSH6, PIK3CA, SMAD2, SMAD4, TP53) were evaluated. mRNA expression of TP53 pathway genes was also analyzed. Results According to the LINE-1 methylation results, overall hypomethylation was observed along the normal-adenoma-carcinoma sequence. Within top50 differential methylated regions (DMRs), in AD-N comparison TP73, NGFR, PDGFRA genes were hypermethylated, FMN1, SLC16A7 genes were hypomethylated. In CRC-N comparison DKK2, SDC2, SOX1 genes showed hypermethylation, while ERBB4, CREB5, CNTN1 genes were hypomethylated. In certain mutation hot spot regions significant DNA methylation alterations were detected. The TP53 gene body was addressed by hypermethylation in adenomas. APC, TP53 and KRAS mutations were found in 30, 15, 21% of adenomas, and in 29, 53, 29% of CRCs, respectively. mRNA expression changes were observed in several TP53 pathway genes showing promoter methylation alterations. Conclusions DNA methylation with consecutive phenotypic effect can be observed in a high number of promoter and gene body regions through CRC development. Electronic supplementary material The online version of this article (10.1186/s12885-018-4609-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Béla Molnár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary. .,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary.
| | - Orsolya Galamb
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Bálint Péterfia
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - András Bodor
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary.,Institute of Mathematics and Informatics, Faculty of Sciences, University of Pécs, Ifjúság útja 6, Pécs, H-7624, Hungary
| | - Alexandra Kalmár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Krisztina Andrea Szigeti
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Barbara Kinga Barták
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Zsófia Brigitta Nagy
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Gábor Valcz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Árpád V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Péter Igaz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Zsolt Tulassay
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| |
Collapse
|
63
|
Klett H, Balavarca Y, Toth R, Gigic B, Habermann N, Scherer D, Schrotz-King P, Ulrich A, Schirmacher P, Herpel E, Brenner H, Ulrich CM, Michels KB, Busch H, Boerries M. Robust prediction of gene regulation in colorectal cancer tissues from DNA methylation profiles. Epigenetics 2018; 13:386-397. [PMID: 29697014 PMCID: PMC6140810 DOI: 10.1080/15592294.2018.1460034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/19/2018] [Accepted: 03/27/2018] [Indexed: 02/01/2023] Open
Abstract
DNA methylation is recognized as one of several epigenetic regulators of gene expression and as potential driver of carcinogenesis through gene-silencing of tumor suppressors and activation of oncogenes. However, abnormal methylation, even of promoter regions, does not necessarily alter gene expression levels, especially if the gene is already silenced, leaving the exact mechanisms of methylation unanswered. Using a large cohort of matching DNA methylation and gene expression samples of colorectal cancer (CRC; n = 77) and normal adjacent mucosa tissues (n = 108), we investigated the regulatory role of methylation on gene expression. We show that on a subset of genes enriched in common cancer pathways, methylation is significantly associated with gene regulation through gene-specific mechanisms. We built two classification models to infer gene regulation in CRC from methylation differences of tumor and normal tissues, taking into account both gene-silencing and gene-activation effects through hyper- and hypo-methylation of CpGs. The classification models result in high prediction performances in both training and independent CRC testing cohorts (0.92
Collapse
Affiliation(s)
- Hagen Klett
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine and Medical Center, University of Freiburg, Germany
| | - Yesilda Balavarca
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Reka Toth
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Biljana Gigic
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of General, Visceral and Transplantation Surgery, University Clinic Heidelberg, Heidelberg, Germany
| | - Nina Habermann
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominique Scherer
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Petra Schrotz-King
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexis Ulrich
- Department of General, Visceral and Transplantation Surgery, University Clinic Heidelberg, Heidelberg, Germany
| | - Peter Schirmacher
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Pathology, University Clinic Heidelberg, Heidelberg, Germany
| | - Esther Herpel
- Institute of Pathology, University Clinic Heidelberg, Heidelberg, Germany
- Tissue Bank of the National Center for Tumor Diseases (NCT) Heidelberg, Germany
| | - Hermann Brenner
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cornelia M. Ulrich
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Karin B. Michels
- Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Germany
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Hauke Busch
- Lübeck Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine and Medical Center, University of Freiburg, Germany
| |
Collapse
|
64
|
Fadda A, Gentilini D, Moi L, Barault L, Leoni VP, Sulas P, Zorcolo L, Restivo A, Cabras F, Fortunato F, Zavattari C, Varesco L, Gismondi V, De Miglio MR, Scanu AM, Colombi F, Lombardi P, Sarotto I, Loi E, Leone F, Giordano S, Di Nicolantonio F, Columbano A, Zavattari P. Colorectal cancer early methylation alterations affect the crosstalk between cell and surrounding environment, tracing a biomarker signature specific for this tumor. Int J Cancer 2018. [PMID: 29542109 DOI: 10.1002/ijc.31380] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Colorectal cancer (CRC) develops through the accumulation of both genetic and epigenetic alterations. However, while the former are already used as prognostic and predictive biomarkers, the latter are less well characterized. Here, performing global methylation analysis on both CRCs and adenomas by Illumina Infinium HumanMethylation450 Bead Chips, we identified a panel of 74 altered CpG islands, demonstrating that the earliest methylation alterations affect genes coding for proteins involved in the crosstalk between cell and surrounding environment. The panel discriminates CRCs and adenomas from peritumoral and normal mucosa with very high specificity (100%) and sensitivity (99.9%). Interestingly, over 70% of the hypermethylated islands resulted in downregulation of gene expression. To establish the possible usefulness of these non-invasive markers for detection of colon cancer, we selected three biomarkers and identified the presence of altered methylation in stool DNA and plasma cell-free circulating DNA from CRC patients.
Collapse
Affiliation(s)
- Antonio Fadda
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Loredana Moi
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Ludovic Barault
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Vera Piera Leoni
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Pia Sulas
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Luigi Zorcolo
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | - Angelo Restivo
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | - Francesco Cabras
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | - Federica Fortunato
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | | | - Liliana Varesco
- Unit of Hereditary Cancer, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Viviana Gismondi
- Unit of Hereditary Cancer, IRCCS AOU San Martino-IST, Genoa, Italy
| | | | - Antonio Mario Scanu
- Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | | | | | - Ivana Sarotto
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Eleonora Loi
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Francesco Leone
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Silvia Giordano
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Federica Di Nicolantonio
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Amedeo Columbano
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Patrizia Zavattari
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| |
Collapse
|
65
|
Wei J, Li G, Zhang J, Zhou Y, Dang S, Chen H, Wu Q, Liu M. Integrated analysis of genome-wide DNA methylation and gene expression profiles identifies potential novel biomarkers of rectal cancer. Oncotarget 2018; 7:62547-62558. [PMID: 27566576 PMCID: PMC5308745 DOI: 10.18632/oncotarget.11534] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 08/08/2016] [Indexed: 12/18/2022] Open
Abstract
DNA methylation was regarded as the promising biomarker for rectal cancer diagnosis. However, the optimal methylation biomarkers with ideal diagnostic performance for rectal cancer are still limited. To identify new molecular markers for rectal cancer, we mapped DNA methylation and transcriptomic profiles in the six rectal cancer and paired normal samples. Further analysis revealed the hypermethylated probes in cancer prone to be located in gene promoter. Meanwhile, transcriptome analysis presented 773 low-expressed and 1,161 over-expressed genes in rectal cancer. Correction analysis identified a panel of 36 genes with an inverse correlation between methylation and gene expression levels, including 10 known colorectal cancer related genes. From the other 26 novel marker genes, GFRA1 and GSTM2 were selected for further analysis on the basis of their biological functions. Further experiment analysis confirmed their methylation and expression status in a larger number (44) of rectal cancer samples, and ROC curves showed higher AUC than SEPT9, which has been used as a biomarker in rectal cancer. Our data suggests that aberrant DNA methylation of contiguous CpG sites in methylation array may be potential diagnostic markers of rectal cancer.
Collapse
Affiliation(s)
- Jiufeng Wei
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Guodong Li
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Jinning Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Yuhui Zhou
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Shuwei Dang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Hongsheng Chen
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150001, P.R. China
| | - Ming Liu
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| |
Collapse
|
66
|
Visakh R, Abdul Nazeer K. DEEPAligner: Deep encoding of pathways to align epigenetic signatures. Comput Biol Chem 2018; 72:87-95. [DOI: 10.1016/j.compbiolchem.2018.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 01/09/2018] [Accepted: 01/09/2018] [Indexed: 12/15/2022]
|
67
|
Porcellini E, Laprovitera N, Riefolo M, Ravaioli M, Garajova I, Ferracin M. Epigenetic and epitranscriptomic changes in colorectal cancer: Diagnostic, prognostic, and treatment implications. Cancer Lett 2018; 419:84-95. [PMID: 29360561 DOI: 10.1016/j.canlet.2018.01.049] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/07/2018] [Accepted: 01/12/2018] [Indexed: 12/12/2022]
Abstract
A cancer cell is the final product of a complex mixture of genetic, epigenetic and epitranscriptomic alterations, whose final interplay contribute to cancer onset and progression. This is specifically true for colorectal cancer, a tumor with a strong epigenetic component, which acts earlier than any other genetic alteration in promoting cancer cell malignant transformation. The pattern of progressive, and usually subtype-specific, DNA and histone modifications that occur in colorectal cancer has been extensively studied in the last decade, providing plenty of data to explore. For this tumor, it became recently evident that also RNA modifications play a relevant role in the activation of oncogenes or repression of tumor suppressor genes. In this review we provide a brief overview of all epigenetic and epitranscriptomic changes that have been found associated to colorectal cancer till now. We explore the impact of these alterations in cancer prognosis and response to treatment and discuss their potential use as cancer biomarkers.
Collapse
Affiliation(s)
- Elisa Porcellini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Noemi Laprovitera
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Mattia Riefolo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | | | - Ingrid Garajova
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.
| |
Collapse
|
68
|
Soozangar N, Sadeghi MR, Jeddi F, Somi MH, Shirmohamadi M, Samadi N. Comparison of genome‐wide analysis techniques to DNA methylation analysis in human cancer. J Cell Physiol 2017; 233:3968-3981. [DOI: 10.1002/jcp.26176] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/24/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Narges Soozangar
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
- Molecular Medicine Research CenterTabriz University of Medical SciencesTabrizIran
| | - Mohammad R. Sadeghi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Farhad Jeddi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Mohammad H. Somi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Masoud Shirmohamadi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | - Nasser Samadi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
- Department of Biochemistry, Faculty of MedicineTabriz University of Medical SciencesTabrizIran
| |
Collapse
|
69
|
Zhang T, Cui G, Yao YL, Wang QC, Gu HG, Li XN, Zhang H, Feng WM, Shi QL, Cui W. Value of CNRIP1 promoter methylation in colorectal cancer screening and prognosis assessment and its influence on the activity of cancer cells. Arch Med Sci 2017; 13:1281-1294. [PMID: 29181058 PMCID: PMC5701694 DOI: 10.5114/aoms.2017.65829] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/21/2016] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION The aim of the study was to investigate the effect of CNRIP1 promoter methylation on the proliferative, invasive and migration potential of colorectal cancer cells, including its potential use for the early detection and prognostic assessment of colorectal cancer. MATERIAL AND METHODS Quantitative methylation-specific PCR (qMSP) was used to detect the methylation status of the CNRIP1 promoter region in peripheral blood samples drawn from patients with colorectal adenocarcinoma, benign colorectal adenoma, and matched healthy controls. Putative CpG methylation sites were then pyrosequenced. We subsequently suppressed CNRIP1 methylation within colon cancer cells via treatment with 5-azacytidine and overexpressed colon cancer cells by transfection with a CNRIP1-overexpression pcDNA3.0 plasmid. Thereafter, the CNRIP1 methylation status and mRNA and protein expressions levels were determined. Finally, the proliferative, invasive and migration abilities of cell lines were determined with the CCK-8 and Transwell cell assays. RESULTS There were differences in the methylation status at loci 2216, 2226, 2231, 2245, and 2254 within the promoter region of CNRIP1 between patients with colorectal adenocarcinoma, colorectal adenoma, and healthy volunteers. The methylation status of CpG sequence 2245 significantly correlated with tumor diameter, invasion depth, TNM stage, grade, and lymph node metastasis (p < 0.05). The proliferative, invasive and migration abilities of colon cancer cells treated with 5-azaC or transfected with a CNRIP1-overexpression plasmid were significantly impaired relative to negative controls (p < 0.05). CONCLUSIONS The methylation status at locus 2245 within the CNRIP1 promoter region has potential value for the early detection and prognostic evaluation of colorectal cancers. Demethylation of the CNRIP1 promoter or overexpression of CNRIP1 can reduce the proliferative and migration abilities of colon cancer cells.
Collapse
Affiliation(s)
- Ting Zhang
- Department of Pathology, School of Medicine, Huzhou University, Huzhou, China
| | - Ge Cui
- Department of Pathology, First Affiliated Hospital of Huzhou University, Huzhou, China
| | - Yun-Liang Yao
- Department of Microbiology and Immunology, School of Medicine, Huzhou University, Huzhou, China
| | - Qi-Chun Wang
- Department of Pathology, School of Medicine, Huzhou University, Huzhou, China
| | - Hong-Guang Gu
- Department of Pathology, School of Medicine, Huzhou University, Huzhou, China
| | - Xi-Ning Li
- Department of Pathology, School of Medicine, Huzhou University, Huzhou, China
| | - Hui Zhang
- Department of Microbiology and Immunology, School of Medicine, Huzhou University, Huzhou, China
| | - Wen-Ming Feng
- Department of Surgery, First Affiliated Hospital of Huzhou University, Huzhou, China
| | - Qi-Lin Shi
- Department of Pathology, First Affiliated Hospital of Huzhou University, Huzhou, China
| | - Weiwei Cui
- Department of Pharmacy, Zichuan District Hospital, Zibo, Shangdong, China
| |
Collapse
|
70
|
Tilley SK, Kim WY, Fry RC. Analysis of bladder cancer tumor CpG methylation and gene expression within The Cancer Genome Atlas identifies GRIA1 as a prognostic biomarker for basal-like bladder cancer. Am J Cancer Res 2017; 7:1850-1862. [PMID: 28979808 PMCID: PMC5622220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 03/06/2017] [Indexed: 06/07/2023] Open
Abstract
Increased methylation levels at cytosines proximal to guanines (CpG) in the promoter regions of tumor suppressor genes have been reported to play an important role in the development and progression of bladder cancer. In this study, we conducted a genome-wide analysis using data from The Cancer Genome Atlas to better characterize CpG methylation and mRNA expression patterns in urothelial carcinomas and to identify new epigenetic biomarkers of survival. Across 408 tumors, we identified 223 genes that displayed significant relationships between CpG methylation and mRNA expression levels. Hypermethylation within 200 base pairs upstream of the transcription start site and hypomethylation within the 3' untranslated region and body region were associated with gene silencing. These 223 genes were functionally enriched for their role in glutamate receptor signaling and among them was a novel, tumor-stage-independent epigenetic biomarker of overall mortality, GRIA1. GRIA1 hypermethylation and elevated mRNA expression levels were associated with significantly worse survival outcomes in patients with basal-like urothelial carcinomas. Furthermore, 70 genes associated with glutamate receptor signaling were differentially expressed between basal (n = 203 tumors) and luminal (n = 205 tumors) subtypes of bladder cancer, including genes involved in glutamate receptor-mediated activation of the calmodulin, PI3K/Akt, and EGFR signaling pathways. The majority of genes displayed increased expression levels in basal-like subtypes. This research highlights glutamate receptors as targets for investigation in the development and pharmacological treatment of urothelial cancer.
Collapse
Affiliation(s)
- Sloane K Tilley
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North CarolinaChapel Hill, NC, 27599, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel HillChapel Hill, North Carolina 27514, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North CarolinaChapel Hill, NC, 27599, USA
- Curriculum in Toxicology, The University of North CarolinaChapel Hill, NC, 27599, USA
| |
Collapse
|
71
|
Advani G, Lim YC, Catimel B, Lio DSS, Ng NLY, Chüeh AC, Tran M, Anasir MI, Verkade H, Zhu HJ, Turk BE, Smithgall TE, Ang CS, Griffin M, Cheng HC. Csk-homologous kinase (Chk) is an efficient inhibitor of Src-family kinases but a poor catalyst of phosphorylation of their C-terminal regulatory tyrosine. Cell Commun Signal 2017; 15:29. [PMID: 28784162 PMCID: PMC5547543 DOI: 10.1186/s12964-017-0186-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/28/2017] [Indexed: 11/10/2022] Open
Abstract
Background C-terminal Src kinase (Csk) and Csk-homologous kinase (Chk) are the major endogenous inhibitors of Src-family kinases (SFKs). They employ two mechanisms to inhibit SFKs. First, they phosphorylate the C-terminal tail tyrosine which stabilizes SFKs in a closed inactive conformation by engaging the SH2 domain in cis. Second, they employ a non-catalytic inhibitory mechanism involving direct binding of Csk and Chk to the active forms of SFKs that is independent of phosphorylation of their C-terminal tail. Csk and Chk are co-expressed in many cell types. Contributions of the two mechanisms towards the inhibitory activity of Csk and Chk are not fully clear. Furthermore, the determinants in Csk and Chk governing their inhibition of SFKs by the non-catalytic inhibitory mechanism are yet to be defined. Methods We determined the contributions of the two mechanisms towards the inhibitory activity of Csk and Chk both in vitro and in transduced colorectal cancer cells. Specifically, we assayed the catalytic activities of Csk and Chk in phosphorylating a specific peptide substrate and a recombinant SFK member Src. We employed surface plasmon resonance spectroscopy to measure the kinetic parameters of binding of Csk, Chk and their mutants to a constitutively active mutant of the SFK member Hck. Finally, we determined the effects of expression of recombinant Chk on anchorage-independent growth and SFK catalytic activity in Chk-deficient colorectal cancer cells. Results Our results revealed Csk as a robust enzyme catalysing phosphorylation of the C-terminal tail tyrosine of SFKs but a weak non-catalytic inhibitor of SFKs. In contrast, Chk is a poor catalyst of SFK tail phosphorylation but binds SFKs with high affinity, enabling it to efficiently inhibit SFKs with the non-catalytic inhibitory mechanism both in vitro and in transduced colorectal cancer cells. Further analyses mapped some of the determinants governing this non-catalytic inhibitory mechanism of Chk to its kinase domain. Conclusions SFKs are activated by different upstream signals to adopt multiple active conformations in cells. SFKs adopting these conformations can effectively be constrained by the two complementary inhibitory mechanisms of Csk and Chk. Furthermore, the lack of this non-catalytic inhibitory mechanism accounts for SFK overactivation in the Chk-deficient colorectal cancer cells. Electronic supplementary material The online version of this article (doi:10.1186/s12964-017-0186-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gahana Advani
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia.,Cell Signalling Research Laboratories, School of Biomedical Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ya Chee Lim
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,PAP Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Bruno Catimel
- Walter and Eliza Hall Institute for Medical Research and Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daisy Sio Seng Lio
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia.,Cell Signalling Research Laboratories, School of Biomedical Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Nadia L Y Ng
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia.,Cell Signalling Research Laboratories, School of Biomedical Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Anderly C Chüeh
- Walter and Eliza Hall Institute for Medical Research and Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mai Tran
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mohd Ishtiaq Anasir
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Heather Verkade
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hong-Jian Zhu
- Department of Surgery, University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, 3052, Australia
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ching-Seng Ang
- Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michael Griffin
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Heung-Chin Cheng
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia. .,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia. .,Cell Signalling Research Laboratories, School of Biomedical Sciences, University of Melbourne, Parkville, VIC, 3010, Australia.
| |
Collapse
|
72
|
Jeon K, Min B, Park JS, Kang YK. Simultaneous Methylation-Level Assessment of Hundreds of CpG Sites by Targeted Bisulfite PCR Sequencing (TBPseq). Front Genet 2017; 8:97. [PMID: 28751909 PMCID: PMC5507944 DOI: 10.3389/fgene.2017.00097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/28/2017] [Indexed: 12/23/2022] Open
Abstract
Methylated-DNA sequencing technologies are producing vast amounts of methylome data from cancer samples, from which cancer-associated differentially methylated CpG sites (cDMCs) are continuously identified and filed. The inclusion of as many cDMCs as possible helps improve the accuracy of cancer diagnosis and sometimes identify cancer subtypes. However, the lack of an established method for the analysis of 100s of cDMCs practically impedes their robust use in clinical medicine. Here, we tested the availability of targeted bisulfite-PCR-sequencing (TBPseq) technology for the assessment of methylation levels of a myriad of CpGs scattered over the genome. In randomly selected 46 cancer cell lines, multiplexed PCR yielded a variety of amplicons harboring 246 CpGs residing at promoters of 97 cancer-associated genes, all of which were sequenced in the same flow cell. Clustering analysis of the TBPseq-assessed methylation levels of target CpGs showed that the lung and liver cancer cell lines correlated relatively strongly with each other while they weakly correlated with colon cancer cells. CpGs at the LIFR gene promoter, which are known to be hypermethylated in colon cancers, indeed were heavily methylated in the tested colon cancer cells. Moreover, the LIFR promoter hypermethylation was found in colon cancer cells only, but not in biliary tract, liver, lung, and stomach cancers cell lines. A meta-analysis with public cancer methylome data verified the colon cancer specificity of LIFR promoter methylation. These results demonstrate that our TBPseq-based methylation assessment could be considered an effective, accurate, and competitive method to simultaneously examine a large number of target cDMCs and patient samples.
Collapse
Affiliation(s)
- Kyuheum Jeon
- Development and Differentiation Research CenterKorea Research Institute of Bioscience & Biotechnology, Daejeon, South Korea.,Department of Functional Genomics, Korea University of Science and TechnologyDaejeon, South Korea
| | - Byungkuk Min
- Development and Differentiation Research CenterKorea Research Institute of Bioscience & Biotechnology, Daejeon, South Korea
| | - Jung S Park
- Development and Differentiation Research CenterKorea Research Institute of Bioscience & Biotechnology, Daejeon, South Korea
| | - Yong-Kook Kang
- Development and Differentiation Research CenterKorea Research Institute of Bioscience & Biotechnology, Daejeon, South Korea.,Department of Functional Genomics, Korea University of Science and TechnologyDaejeon, South Korea
| |
Collapse
|
73
|
Chen J, Behnam E, Huang J, Moffatt MF, Schaid DJ, Liang L, Lin X. Fast and robust adjustment of cell mixtures in epigenome-wide association studies with SmartSVA. BMC Genomics 2017; 18:413. [PMID: 28549425 PMCID: PMC5446715 DOI: 10.1186/s12864-017-3808-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/18/2017] [Indexed: 12/20/2022] Open
Abstract
Background One problem that plagues epigenome-wide association studies is the potential confounding due to cell mixtures when purified target cells are not available. Reference-free adjustment of cell mixtures has become increasingly popular due to its flexibility and simplicity. However, existing methods are still not optimal: increased false positive rates and reduced statistical power have been observed in many scenarios. Methods We develop SmartSVA, an optimized surrogate variable analysis (SVA) method, for fast and robust reference-free adjustment of cell mixtures. SmartSVA corrects the limitation of traditional SVA under highly confounded scenarios by imposing an explicit convergence criterion and improves the computational efficiency for large datasets. Results Compared to traditional SVA, SmartSVA achieves an order-of-magnitude speedup and better false positive control. It protects the signals when capturing the cell mixtures, resulting in significant power increase while controlling for false positives. Through extensive simulations and real data applications, we demonstrate a better performance of SmartSVA than the existing methods. Conclusions SmartSVA is a fast and robust method for reference-free adjustment of cell mixtures for epigenome-wide association studies. As a general method, SmartSVA can be applied to other genomic studies to capture unknown sources of variability. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3808-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jun Chen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA.
| | - Ehsan Behnam
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Jinyan Huang
- State Key Laboratory of Medical Genomics, Rui-jin Hospital & Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, 200025, China
| | - Miriam F Moffatt
- Faculty of Medicine, National Heart & Lung Institute, Imperial College London, Dovehouse St, London, SW3 6LY, UK
| | - Daniel J Schaid
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. School of Public Health, Boston, 677 Huntington Ave, Boston, MA, 02115, USA. .,Department of Biostatistics, Harvard T.H. School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.
| |
Collapse
|
74
|
Maiuri AR, Peng M, Podicheti R, Sriramkumar S, Kamplain CM, Rusch DB, DeStefano Shields CE, Sears CL, O'Hagan HM. Mismatch Repair Proteins Initiate Epigenetic Alterations during Inflammation-Driven Tumorigenesis. Cancer Res 2017; 77:3467-3478. [PMID: 28522752 DOI: 10.1158/0008-5472.can-17-0056] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/30/2017] [Accepted: 05/04/2017] [Indexed: 01/05/2023]
Abstract
Aberrant silencing of genes by DNA methylation contributes to cancer, yet how this process is initiated remains unclear. Using a murine model of inflammation-induced tumorigenesis, we tested the hypothesis that inflammation promotes recruitment of epigenetic proteins to chromatin, initiating methylation and gene silencing in tumors. Compared with normal epithelium and noninflammation-induced tumors, inflammation-induced tumors gained DNA methylation at CpG islands, some of which are associated with putative tumor suppressor genes. Hypermethylated genes exhibited enrichment of repressive chromatin marks and reduced expression prior to tumorigenesis, at a time point coinciding with peak levels of inflammation-associated DNA damage. Loss of MutS homolog 2 (MSH2), a mismatch repair (MMR) protein, abrogated early inflammation-induced epigenetic alterations and DNA hypermethylation alterations observed in inflammation-induced tumors. These results indicate that early epigenetic alterations initiated by inflammation and MMR proteins lead to gene silencing during tumorigenesis, revealing a novel mechanism of epigenetic alterations in inflammation-driven cancer. Understanding such mechanisms will inform development of pharmacotherapies to reduce carcinogenesis. Cancer Res; 77(13); 3467-78. ©2017 AACR.
Collapse
Affiliation(s)
- Ashley R Maiuri
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - Michael Peng
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | | | - Shruthi Sriramkumar
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - Caitlin M Kamplain
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | | | | | - Cynthia L Sears
- Departments of Medicine and Oncology, Johns Hopkins University, Baltimore, Maryland.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, Maryland.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Heather M O'Hagan
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana. .,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana
| |
Collapse
|
75
|
Trescher S, Münchmeyer J, Leser U. Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization. BMC SYSTEMS BIOLOGY 2017; 11:41. [PMID: 28347313 PMCID: PMC5369021 DOI: 10.1186/s12918-017-0419-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 03/08/2017] [Indexed: 12/28/2022]
Abstract
Background Gene regulation is one of the most important cellular processes, indispensable for the adaptability of organisms and closely interlinked with several classes of pathogenesis and their progression. Elucidation of regulatory mechanisms can be approached by a multitude of experimental methods, yet integration of the resulting heterogeneous, large, and noisy data sets into comprehensive and tissue or disease-specific cellular models requires rigorous computational methods. Recently, several algorithms have been proposed which model genome-wide gene regulation as sets of (linear) equations over the activity and relationships of transcription factors, genes and other factors. Subsequent optimization finds those parameters that minimize the divergence of predicted and measured expression intensities. In various settings, these methods produced promising results in terms of estimating transcription factor activity and identifying key biomarkers for specific phenotypes. However, despite their common root in mathematical optimization, they vastly differ in the types of experimental data being integrated, the background knowledge necessary for their application, the granularity of their regulatory model, the concrete paradigm used for solving the optimization problem and the data sets used for evaluation. Results Here, we review five recent methods of this class in detail and compare them with respect to several key properties. Furthermore, we quantitatively compare the results of four of the presented methods based on publicly available data sets. Conclusions The results show that all methods seem to find biologically relevant information. However, we also observe that the mutual result overlaps are very low, which contradicts biological intuition. Our aim is to raise further awareness of the power of these methods, yet also to identify common shortcomings and necessary extensions enabling focused research on the critical points. Electronic supplementary material The online version of this article (doi:10.1186/s12918-017-0419-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Saskia Trescher
- Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany.
| | - Jannes Münchmeyer
- Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| |
Collapse
|
76
|
Genome-wide methylation profiles in primary intracranial germ cell tumors indicate a primordial germ cell origin for germinomas. Acta Neuropathol 2017; 133:445-462. [PMID: 28078450 DOI: 10.1007/s00401-017-1673-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 12/29/2016] [Accepted: 01/07/2017] [Indexed: 01/01/2023]
Abstract
Intracranial germ cell tumors (iGCTs) are the second most common brain tumors among children under 14 in Japan. The World Health Organization classification recognizes several subtypes of iGCTs, which are conventionally subclassified into pure germinoma or non-germinomatous GCTs. Recent exhaustive genomic studies showed that mutations of the genes involved in the MAPK and/or PI3K pathways are common in iGCTs; however, the mechanisms of how different subtypes develop, often as a mixed-GCT, are unknown. To elucidate the pathogenesis of iGCTs, we investigated 61 GCTs of various subtypes by genome-wide DNA methylation profiling. We showed that pure germinomas are characterized by global low DNA methylation, a unique epigenetic feature making them distinct from all other iGCTs subtypes. The patterns of methylation strongly resemble that of primordial germ cells (PGC) at the migration phase, possibly indicating the cell of origin for these tumors. Unlike PGC, however, hypomethylation extends to long interspersed nuclear element retrotransposons. Histologically and epigenetically distinct microdissected components of mixed-GCTs shared identical somatic mutations in the MAPK or PI3K pathways, indicating that they developed from a common ancestral cell.
Collapse
|
77
|
Conserved effect of aging on DNA methylation and association with EZH2 polycomb protein in mice and humans. Mech Ageing Dev 2017; 162:27-37. [PMID: 28249716 DOI: 10.1016/j.mad.2017.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/11/2017] [Accepted: 02/16/2017] [Indexed: 11/22/2022]
Abstract
In humans, DNA methylation at specific CpG sites can be used to estimate the 'epigenetic clock', a biomarker of aging and health. The mechanisms that regulate the aging epigenome and level of conservation are not entirely clear. We performed affinity-based enrichment with methyl-CpG binding domain protein followed by high-throughput sequencing (MBD-seq) to assay DNA methylation in mouse samples. Consistent with previous reports, aging is associated with increase in methylation at CpG islands that likely overlap regulatory regions of genes that have been implicated in cancers (e.g., C1ql3, Srd5a2 and Ptk7). The differentially methylated regions in mice have high sequence conservation in humans and the pattern of methylation is also largely conserved between the two species. Based on human ENCODE data, these sites are targeted by polycomb proteins, including EZH2. Chromatin immunoprecipitation confirmed that these regions interact with EZH2 in mice as well, and there may be reduction in EZH2 occupancy with age at C1ql3. This adds to the growing evidence that EZH2 is part of the protein machinery that shapes the aging epigenome. The conservation in both sequence and methylation patterns of the age-dependent CpGs indicate that the epigenetic clock is a fundamental feature of aging in mammals.
Collapse
|
78
|
Durso DF, Bacalini MG, do Valle ÍF, Pirazzini C, Bonafé M, Castellani G, Faria AMC, Franceschi C, Garagnani P, Nardini C. Aberrant methylation patterns in colorectal cancer: a meta-analysis. Oncotarget 2017; 8:12820-12830. [PMID: 28086223 PMCID: PMC5355058 DOI: 10.18632/oncotarget.14590] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 12/27/2016] [Indexed: 12/30/2022] Open
Abstract
Colorectal cancer is among the leading causes of cancer death worldwide. Despite numerous molecular characterizations of the phenomenon, the exact dynamics of its onset and progression remain elusive. Colorectal cancer onset has been characterized by changes in DNA methylation profiles, that, owing to the stability of their patterns, are promising candidates to shed light on the molecular events laying at the base of this phenomenon.To exploit this stability and reinforce it, we conducted a meta-analysis on publicly available DNA methylation datasets generated on: normal colorectal, adenoma (ADE) and adenocarcinoma (CRC) samples using the Illumina 450k array, in the systems medicine frame, searching for tumor gene episignatures, to produce a carefully selected list of potential drivers, markers and targets of the disease. The analysis proceeds from a differential meta-analysis of the methylation profiles using an analytical pipeline recently developed by our group [1], through network reconstruction, topological and functional analyses, to finally highlight relevant epigenomic features. Our results show that genes already highlighted for their genetic or transcriptional alteration in colorectal cancer are also differentially methylated, reinforcing -regardless of the level of cellular control- their role in the complex of alterations involved in tumorigenesis.These findings were finally validated in an independent cohort from The Cancer Genome Atlas (TCGA).
Collapse
Affiliation(s)
- Danielle Fernandes Durso
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- National Counsel of Technological and Scientific Development (CNPq), ministry of science technology and innovation (MCTI), Brasilia, Brazil
| | | | - Ítalo Faria do Valle
- CAPES Foundation, Ministry of Education of Brazil–Brasília (DF), Brazil
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | | | - Massimiliano Bonafé
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Ana Maria Caetano Faria
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- IRCCS Institute of Neurological Sciences, Bologna, Italy
- Interdepartmental Center “L. Galvani”, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Interdepartmental Center “L. Galvani”, University of Bologna, Bologna, Italy
- Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna, Italy
| | | |
Collapse
|
79
|
Abstract
In this chapter we summarize the pros and cons of the notion that Runx3 is a major tumor suppressor gene (TSG). Inactivation of TSGs in normal cells provides a viability/growth advantage that contributes cell-autonomously to cancer. More than a decade ago it was suggested that RUNX3 is involved in gastric cancer development, a postulate extended later to other epithelial cancers portraying RUNX3 as a major TSG. However, evidence that Runx3 is not expressed in normal gastric and other epithelia has challenged the RUNX3-TSG paradigm. In contrast, RUNX3 is overexpressed in a significant fraction of tumor cells in various human epithelial cancers and its overexpression in pancreatic cancer cells promotes their migration, anchorage-independent growth and metastatic potential. Moreover, recent high-throughput quantitative genome-wide studies on thousands of human samples of various tumors and new investigations of the role of Runx3 in mouse cancer models have unequivocally demonstrated that RUNX3 is not a bona fide cell-autonomous TSG. Importantly, accumulating data demonstrated that RUNX3 functions in control of immunity and inflammation, thereby indirectly influencing epithelial tumor development.
Collapse
|
80
|
Galamb O, Kalmár A, Barták BK, Patai &AV, Leiszter K, Péterfia B, Wichmann B, Valcz G, Veres G, Tulassay Z, Molnár B. Aging related methylation influences the gene expression of key control genes in colorectal cancer and adenoma. World J Gastroenterol 2016; 22:10325-10340. [PMID: 28058013 PMCID: PMC5175245 DOI: 10.3748/wjg.v22.i47.10325] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/20/2016] [Accepted: 11/16/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To analyze colorectal carcinogenesis and age-related DNA methylation alterations of gene sequences associated with epigenetic clock CpG sites.
METHODS In silico DNA methylation analysis of 353 epigenetic clock CpG sites published by Steve Horvath was performed using methylation array data for a set of 123 colonic tissue samples [64 colorectal cancer (CRC), 42 adenoma, 17 normal; GEO accession number: GSE48684]. Among the differentially methylated age-related genes, secreted frizzled related protein 1 (SFRP1) promoter methylation was further investigated in colonic tissue from 8 healthy adults, 19 normal children, 20 adenoma and 8 CRC patients using bisulfite-specific PCR followed by methylation-specific high resolution melting (MS-HRM) analysis. mRNA expression of age-related “epigenetic clock” genes was studied using Affymetrix HGU133 Plus2.0 whole transcriptome data of 153 colonic biopsy samples (49 healthy adult, 49 adenoma, 49 CRC, 6 healthy children) (GEO accession numbers: GSE37364, GSE10714, GSE4183, GSE37267). Whole promoter methylation analysis of genes showing inverse DNA methylation-gene expression data was performed on 30 colonic samples using methyl capture sequencing.
RESULTS Fifty-seven age-related CpG sites including hypermethylated PPP1R16B, SFRP1, SYNE1 and hypomethylated MGP, PIPOX were differentially methylated between CRC and normal tissues (P < 0.05, Δβ≥ 10%). In the adenoma vs normal comparison, 70 CpG sites differed significantly, including hypermethylated DKK3, SDC2, SFRP1, SYNE1 and hypomethylated CEMIP, SPATA18 (P < 0.05, Δβ≥ 10%). In MS-HRM analysis, the SFRP1 promoter region was significantly hypermethylated in CRC (55.0% ± 8.4 %) and adenoma tissue samples (49.9% ± 18.1%) compared to normal adult (5.2% ± 2.7%) and young (2.2% ± 0.7%) colonic tissue (P < 0.0001). DNA methylation of SFRP1 promoter was slightly, but significantly increased in healthy adults compared to normal young samples (P < 0.02). This correlated with significantly increased SFRP1 mRNA levels in children compared to normal adult samples (P < 0.05). In CRC tissue the mRNA expression of 117 age-related genes were changed, while in adenoma samples 102 genes showed differential expression compared with normal colonic tissue (P < 0.05, logFC > 0.5). The change of expression for several genes including SYNE1, CLEC3B, LTBP3 and SFRP1, followed the same pattern in aging and carcinogenesis, though not for all genes (e.g., MGP).
CONCLUSION Several age-related DNA methylation alterations can be observed during CRC development and progression affecting the mRNA expression of certain CRC- and adenoma-related key control genes.
Collapse
|
81
|
Dirks RAM, Stunnenberg HG, Marks H. Genome-wide epigenomic profiling for biomarker discovery. Clin Epigenetics 2016; 8:122. [PMID: 27895806 PMCID: PMC5117701 DOI: 10.1186/s13148-016-0284-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/02/2016] [Indexed: 12/24/2022] Open
Abstract
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery. Recent years saw great progress in miniaturization of genome-wide epigenomic profiling, enabling large-scale epigenetic biomarker screens for disease diagnosis, prognosis, and stratification on patient-derived samples. All main genome-wide profiling technologies have now been scaled down and/or are compatible with single-cell readout, including: (i) Bisulfite sequencing to determine DNA methylation at base-pair resolution, (ii) ChIP-Seq to identify protein binding sites on the genome, (iii) DNaseI-Seq/ATAC-Seq to profile open chromatin, and (iv) 4C-Seq and HiC-Seq to determine the spatial organization of chromosomes. In this review we provide an overview of current genome-wide epigenomic profiling technologies and main technological advances that allowed miniaturization of these assays down to single-cell level. For each of these technologies we evaluate their application for future biomarker discovery. We will focus on (i) compatibility of these technologies with methods used for clinical sample preservation, including methods used by biobanks that store large numbers of patient samples, and (ii) automation of these technologies for robust sample preparation and increased throughput.
Collapse
Affiliation(s)
- René A M Dirks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| |
Collapse
|
82
|
Sharma P, Bhunia S, Poojary SS, Tekcham DS, Barbhuiya MA, Gupta S, Shrivastav BR, Tiwari PK. Global methylation profiling to identify epigenetic signature of gallbladder cancer and gallstone disease. Tumour Biol 2016; 37:14687-14699. [DOI: 10.1007/s13277-016-5355-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 09/07/2016] [Indexed: 12/21/2022] Open
|
83
|
Tudor staphylococcal nuclease: biochemistry and functions. Cell Death Differ 2016; 23:1739-1748. [PMID: 27612014 DOI: 10.1038/cdd.2016.93] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 08/01/2016] [Indexed: 12/17/2022] Open
Abstract
Tudor staphylococcal nuclease (TSN, also known as Tudor-SN, SND1 or p100) is an evolutionarily conserved protein with invariant domain composition, represented by tandem repeat of staphylococcal nuclease domains and a tudor domain. Conservation along significant evolutionary distance, from protozoa to plants and animals, suggests important physiological functions for TSN. It is known that TSN is critically involved in virtually all pathways of gene expression, ranging from transcription to RNA silencing. Owing to its high protein-protein binding affinity coexistent with enzymatic activity, TSN can exert its biochemical function by acting as both a scaffolding molecule of large multiprotein complexes and/or as a nuclease. TSN is indispensible for normal development and stress resistance, whereas its increased expression is closely associated with various types of cancer. Thus, TSN is an attractive target for anti-cancer therapy and a potent tumor marker. Considering ever increasing interest to further understand a multitude of TSN-mediated processes and a mechanistic role of TSN in these processes, here we took an attempt to summarize and update the available information about this intriguing multifunctional protein.
Collapse
|
84
|
Vymetalkova V, Vodicka P, Pardini B, Rosa F, Levy M, Schneiderova M, Liska V, Vodickova L, Nilsson TK, Farkas SA. Epigenome-wide analysis of DNA methylation reveals a rectal cancer-specific epigenomic signature. Epigenomics 2016; 8:1193-207. [DOI: 10.2217/epi-2016-0044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: The aim of the present study is to address a genome-wide search for novel methylation biomarkers in the rectal cancer (RC), as only scarce information on methylation profile is available. Materials & methods: We analyzed methylation status in 25 pairs of RC and adjacent healthy mucosa using the Illumina Human Methylation 450 BeadChip. Results: We found significantly aberrant methylation in 33 genes. After validation of our results by pyrosequencing, we found a good agreement with our findings. The BPIL3 and HBBP1 genes resulted hypomethylated in RC, whereas TIFPI2, ADHFE1, FLI1 and TLX1 were hypermethylated. An external validation by TCGA datasets confirmed the results. Conclusion: Our study, with external validation, has demonstrated the feasibility of using specific methylated DNA signatures for developing biomarkers in RC.
Collapse
Affiliation(s)
- Veronika Vymetalkova
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology & Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
| | - Pavel Vodicka
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology & Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Czech Republic
| | | | - Fabio Rosa
- Human Genetics Foundation, (HuGeF), Torino, Italy
| | - Miroslav Levy
- Department of Surgery, 1st Faculty of Medicine, Charles University & Thomayer Hospital, Prague, Czech Republic
| | | | - Vaclav Liska
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Czech Republic
- Department of Surgery, Teaching Hospital & Medical School in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology & Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Czech Republic
| | | | - Sanja A Farkas
- Department of Laboratory Medicine, Örebro University; Örebro, Sweden
| |
Collapse
|
85
|
Huang RL, Su PH, Liao YP, Wu TI, Hsu YT, Lin WY, Wang HC, Weng YC, Ou YC, Huang THM, Lai HC. Integrated Epigenomics Analysis Reveals a DNA Methylation Panel for Endometrial Cancer Detection Using Cervical Scrapings. Clin Cancer Res 2016; 23:263-272. [DOI: 10.1158/1078-0432.ccr-16-0863] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/27/2016] [Accepted: 07/19/2016] [Indexed: 11/16/2022]
|
86
|
Discovery and Validation of Hypermethylated Markers for Colorectal Cancer. DISEASE MARKERS 2016; 2016:2192853. [PMID: 27493446 PMCID: PMC4963574 DOI: 10.1155/2016/2192853] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/06/2016] [Accepted: 06/15/2016] [Indexed: 12/31/2022]
Abstract
Colorectal carcinoma (CRC) is one of the most prevalent malignant tumors worldwide. Screening and early diagnosis are critical for the clinical management of this disease. DNA methylation changes have been regarded as promising biomarkers for CRC diagnosis. Here, we map DNA methylation profiling on CRC in six CRCs and paired normal samples using a 450 K bead array. Further analysis confirms the methylation status of candidates in two data sets from the Gene Expression Omnibus. Receiver operating characteristic (ROC) curves are calculated to determine the diagnostic performances. We identify 1549 differentially methylated regions (DMRs) showing differences in methylation between CRC and normal tissue. Two genes (ADD2 and AKR1B1), related to the DMRs, are selected for further validation. ROC curves show that the areas under the curves of ADD2 and AKR1B1 are higher than that of SEPT9, which has been clinically used as a screening biomarker of CRC. Our data suggests that aberrant DNA methylation of ADD2 and AKR1B1 could be potential screening markers of CRC.
Collapse
|
87
|
Lam K, Pan K, Linnekamp JF, Medema JP, Kandimalla R. DNA methylation based biomarkers in colorectal cancer: A systematic review. Biochim Biophys Acta Rev Cancer 2016; 1866:106-20. [PMID: 27385266 DOI: 10.1016/j.bbcan.2016.07.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/30/2016] [Accepted: 07/01/2016] [Indexed: 12/11/2022]
Abstract
Since genetic and epigenetic alterations influence the development of colorectal cancer (CRC), huge potential lies in the use of DNA methylation as biomarkers to improve the current diagnosis, screening, prognosis and treatment prediction. Here we performed a systematic review on DNA methylation-based biomarkers published in CRC, and discussed the current state of findings and future challenges. Based on the findings, we then provide a perspective on future studies. Genome-wide studies on DNA methylation revealed novel biomarkers as well as distinct subgroups that exist in CRC. For diagnostic purposes, the most independently validated genes to study further are VIM, SEPT9, ITGA4, OSM4, GATA4 and NDRG4. These hypermethylated biomarkers can even be combined with LINE1 hypomethylation and the performance of markers should be examined in comparison to FIT further to find sensitive combinations. In terms of prognostic markers, myopodin, KISS1, TMEFF2, HLTF, hMLH1, APAF1, BCL2 and p53 are independently validated. Most prognostic markers published lack both a multivariate analysis in comparison to clinical risk factors and the appropriate patient group who will benefit by adjuvant chemotherapy. Methylation of IGFBP3, mir148a and PTEN are found to be predictive markers for 5-FU and EGFR therapy respectively. For therapy prediction, more studies should focus on finding markers for chemotherapeutic drugs as majority of the patients would benefit. Translation of these biomarkers into clinical utility would require large-scale prospective cohorts and randomized clinical trials in future. Based on these findings and consideration we propose an avenue to introduce methylation markers into clinical practice in near future. For future studies, multi-omics profiling on matched tissue and non-invasive cohorts along with matched cohorts of adenoma to carcinoma is indispensable to concurrently stratify CRC and find novel, robust biomarkers. Moreover, future studies should examine the timing and heterogeneity of methylation as well as the difference in methylation levels between epithelial and stromal tissues.
Collapse
Affiliation(s)
- Kevin Lam
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Kathy Pan
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Janneke Fiona Linnekamp
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Raju Kandimalla
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
88
|
Galamb O, Kalmár A, Péterfia B, Csabai I, Bodor A, Ribli D, Krenács T, Patai ÁV, Wichmann B, Barták BK, Tóth K, Valcz G, Spisák S, Tulassay Z, Molnár B. Aberrant DNA methylation of WNT pathway genes in the development and progression of CIMP-negative colorectal cancer. Epigenetics 2016; 11:588-602. [PMID: 27245242 DOI: 10.1080/15592294.2016.1190894] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The WNT signaling pathway has an essential role in colorectal carcinogenesis and progression, which involves a cascade of genetic and epigenetic changes. We aimed to analyze DNA methylation affecting the WNT pathway genes in colorectal carcinogenesis in promoter and gene body regions using whole methylome analysis in 9 colorectal cancer, 15 adenoma, and 6 normal tumor adjacent tissue (NAT) samples by methyl capture sequencing. Functional methylation was confirmed on 5-aza-2'-deoxycytidine-treated colorectal cancer cell line datasets. In parallel with the DNA methylation analysis, mutations of WNT pathway genes (APC, β-catenin/CTNNB1) were analyzed by 454 sequencing on GS Junior platform. Most differentially methylated CpG sites were localized in gene body regions (95% of WNT pathway genes). In the promoter regions, 33 of the 160 analyzed WNT pathway genes were differentially methylated in colorectal cancer vs. normal, including hypermethylated AXIN2, CHP1, PRICKLE1, SFRP1, SFRP2, SOX17, and hypomethylated CACYBP, CTNNB1, MYC; 44 genes in adenoma vs. NAT; and 41 genes in colorectal cancer vs. adenoma comparisons. Hypermethylation of AXIN2, DKK1, VANGL1, and WNT5A gene promoters was higher, while those of SOX17, PRICKLE1, DAAM2, and MYC was lower in colon carcinoma compared to adenoma. Inverse correlation between expression and methylation was confirmed in 23 genes, including APC, CHP1, PRICKLE1, PSEN1, and SFRP1. Differential methylation affected both canonical and noncanonical WNT pathway genes in colorectal normal-adenoma-carcinoma sequence. Aberrant DNA methylation appears already in adenomas as an early event of colorectal carcinogenesis.
Collapse
Affiliation(s)
- Orsolya Galamb
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
| | - Alexandra Kalmár
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Bálint Péterfia
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - István Csabai
- c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary
| | - András Bodor
- c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary
| | - Dezső Ribli
- c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary
| | - Tibor Krenács
- d 1st Department of Pathology and Experimental Cancer Research , Semmelweis University , Budapest , Hungary.,e Tumor Progression Research Group , Hungarian Academy of Sciences - Semmelweis University , Budapest , Hungary
| | - Árpád V Patai
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Barnabás Wichmann
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
| | - Barbara Kinga Barták
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Kinga Tóth
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Gábor Valcz
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
| | - Sándor Spisák
- f Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , MA , USA
| | - Zsolt Tulassay
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary.,b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Béla Molnár
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
| |
Collapse
|
89
|
Dickinson PJ, York D, Higgins RJ, LeCouteur RA, Joshi N, Bannasch D. Chromosomal Aberrations in Canine Gliomas Define Candidate Genes and Common Pathways in Dogs and Humans. J Neuropathol Exp Neurol 2016; 75:700-10. [PMID: 27251041 DOI: 10.1093/jnen/nlw042] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 12/16/2022] Open
Abstract
Spontaneous gliomas in dogs occur at a frequency similar to that in humans and may provide a translational model for therapeutic development and comparative biological investigations. Copy number alterations in 38 canine gliomas, including diffuse astrocytomas, glioblastomas, oligodendrogliomas, and mixed oligoastrocytomas, were defined using an Illumina 170K single nucleotide polymorphism array. Highly recurrent alterations were seen in up to 85% of some tumor types, most notably involving chromosomes 13, 22, and 38, and gliomas clustered into 2 major groups consisting of high-grade IV astrocytomas, or oligodendrogliomas and other tumors. Tumor types were characterized by specific broad and focal chromosomal events including focal loss of the INK4A/B locus in glioblastoma and loss of the RB1 gene and amplification of the PDGFRA gene in oligodendrogliomas. Genes associated with the 3 critical pathways in human high-grade gliomas (TP53, RB1, and RTK/RAS/PI3K) were frequently associated with canine aberrations. Analysis of oligodendrogliomas revealed regions of chromosomal losses syntenic to human 1p involving tumor suppressor genes, such as CDKN2C, as well as genes associated with apoptosis, autophagy, and response to chemotherapy and radiation. Analysis of high frequency chromosomal aberrations with respect to human orthologues may provide insight into both novel and common pathways in gliomagenesis and response to therapy.
Collapse
Affiliation(s)
- Peter J Dickinson
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California.
| | - Dan York
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| | - Robert J Higgins
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| | - Richard A LeCouteur
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| | - Nikhil Joshi
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| | - Danika Bannasch
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| |
Collapse
|
90
|
Ma F, Song H, Guo B, Zhang Y, Zheng Y, Lin C, Wu Y, Guan G, Sha R, Zhou Q, Wang D, Zhou X, Li J, Qiu X. MiR-361-5p inhibits colorectal and gastric cancer growth and metastasis by targeting staphylococcal nuclease domain containing-1. Oncotarget 2016; 6:17404-16. [PMID: 25965817 PMCID: PMC4627317 DOI: 10.18632/oncotarget.3744] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/06/2015] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRs) function as key regulators of gene expression and their deregulation is associated with the carcinogenesis of various cancers. In the present study, we investigated the biological role and mechanism of miR-361-5p in colorectal carcinoma (CRC) and gastric cancer (GC). We showed that microRNA-361-5p (miR-361-5p) was down-regulated in CRC and GC in comparison to the controls. Meanwhile, the expression levels of miR-361-5p negatively correlated with lung metastasis and prognosis in clinical CRC patients. Overexpression of miR-361-5p markedly suppressed proliferation, migration and invasion of cancer cells. Additionally, this phenotype could be partially rescued by the ectopic expression of staphylococcal nuclease domain containing-1 (SND1). SND1 was identified as a target of miR-361-5p using bioinformatics analysis and in vitro luciferase reporter assays. In turn, SND1 bound to pre-miR-361-5p and suppressed the expression of miR-361-5p, thus exerting a feedback loop. Most interestingly, in vivo studies showed that restoration of miR-361-5p significantly inhibited tumor growth and especially the lung metastasis in nude mice. Therefore, it could be concluded that miR-361-5p functions as a tumor-suppressive miRNA through directly binding to SND1, highlighting its potential as a novel agent for the treatment of patients with CRC and GC.
Collapse
Affiliation(s)
- Fei Ma
- Department of Endoscopy, The Affiliated Cancer Hospital, Harbin Medical University, Harbin, China
| | - Hongjiang Song
- Department of Endoscopy, The Affiliated Cancer Hospital, Harbin Medical University, Harbin, China.,Department of Gastrointestinal Surgery, The Affiliated Cancer Hospital, Harbin Medical University, Harbin, China
| | - Baoliang Guo
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuxin Zhang
- Department of Gastrointestinal Surgery, The Affiliated Cancer Hospital, Harbin Medical University, Harbin, China
| | - Yasheng Zheng
- Department of General Surgery, Central Hospital of Jiuzhen, China
| | - Chengchun Lin
- Department of Gastroenterology, The First Hospital of Longyan, Fujian Medical University, Longyan, China
| | - Ying Wu
- Department of Pathology, Hongqi Hospital, Mudanjiang Medical University, Mudanjiang, China
| | - Guijie Guan
- Department of Pathology, Hongqi Hospital, Mudanjiang Medical University, Mudanjiang, China
| | - Ruihua Sha
- Department of Digestive Disease, Hongqi Hospital, Mudanjiang Medical University, Mudanjiang, China
| | - Qingxin Zhou
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dejun Wang
- Department of Ultrasound of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinglu Zhou
- Department of Medical Imaging, The Affiliated Cancer Hospital of Harbin Medical University, Harbin, China
| | - Juan Li
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaohui Qiu
- The Second Hospital of Longyan, Fujian Medical University, Longyan, China
| |
Collapse
|
91
|
Silva-Martínez GA, Rodríguez-Ríos D, Alvarado-Caudillo Y, Vaquero A, Esteller M, Carmona FJ, Moran S, Nielsen FC, Wickström-Lindholm M, Wrobel K, Wrobel K, Barbosa-Sabanero G, Zaina S, Lund G. Arachidonic and oleic acid exert distinct effects on the DNA methylome. Epigenetics 2016; 11:321-34. [PMID: 27088456 DOI: 10.1080/15592294.2016.1161873] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Abnormal fatty acid metabolism and availability are landmarks of metabolic diseases, which in turn are associated with aberrant DNA methylation profiles. To understand the role of fatty acids in disease epigenetics, we sought DNA methylation profiles specifically induced by arachidonic (AA) or oleic acid (OA) in cultured cells and compared those with published profiles of normal and diseased tissues. THP-1 monocytes were stimulated with AA or OA and analyzed using Infinium HumanMethylation450 BeadChip (Illumina) and Human Exon 1.0 ST array (Affymetrix). Data were corroborated in mouse embryonic fibroblasts. Comparisons with publicly available data were conducted by standard bioinformatics. AA and OA elicited a complex response marked by a general DNA hypermethylation and hypomethylation in the 1-200 μM range, respectively, with a maximal differential response at the 100 μM dose. The divergent response to AA and OA was prominent within the gene body of target genes, where it correlated positively with transcription. AA-induced DNA methylation profiles were similar to the corresponding profiles described for palmitic acid, atherosclerosis, diabetes, obesity, and autism, but relatively dissimilar from OA-induced profiles. Furthermore, human atherosclerosis grade-associated DNA methylation profiles were significantly enriched in AA-induced profiles. Biochemical evidence pointed to β-oxidation, PPAR-α, and sirtuin 1 as important mediators of AA-induced DNA methylation changes. In conclusion, AA and OA exert distinct effects on the DNA methylome. The observation that AA may contribute to shape the epigenome of important metabolic diseases, supports and expands current diet-based therapeutic and preventive efforts.
Collapse
Affiliation(s)
| | - Dalia Rodríguez-Ríos
- a Department of Genetic Engineering , CINVESTAV Irapuato Unit , Irapuato , Mexico
| | - Yolanda Alvarado-Caudillo
- b Department of Medical Sciences , Division of Health Sciences, León Campus, University of Guanajuato , Mexico
| | - Alejandro Vaquero
- c Laboratory of Chromatin Biology, Cancer Epigenetics and Biology Program (PEBC) , IDIBELL, L'Hospitalet de Llobregat , Barcelona , Catalonia , Spain
| | - Manel Esteller
- d Laboratory of Cancer Epigenetics, Cancer Epigenetics and Biology Program (PEBC) , IDIBELL, L'Hospitalet de Llobregat , Barcelona , Catalonia , Spain
| | - F Javier Carmona
- d Laboratory of Cancer Epigenetics, Cancer Epigenetics and Biology Program (PEBC) , IDIBELL, L'Hospitalet de Llobregat , Barcelona , Catalonia , Spain
| | - Sebastian Moran
- d Laboratory of Cancer Epigenetics, Cancer Epigenetics and Biology Program (PEBC) , IDIBELL, L'Hospitalet de Llobregat , Barcelona , Catalonia , Spain
| | - Finn C Nielsen
- e Center for Genomic Medicine, Rigshospitalet , University of Copenhagen , Copenhagen , Denmark
| | - Marie Wickström-Lindholm
- f Experimental Cardiovascular Research , Malmö University Hospital, Lund University , Malmö , Sweden
| | - Katarzyna Wrobel
- g Department of Chemistry, Division of Natural and Exact Sciences, Guanajuato Campus , University of Guanajuato , Mexico
| | - Kazimierz Wrobel
- g Department of Chemistry, Division of Natural and Exact Sciences, Guanajuato Campus , University of Guanajuato , Mexico
| | - Gloria Barbosa-Sabanero
- b Department of Medical Sciences , Division of Health Sciences, León Campus, University of Guanajuato , Mexico
| | - Silvio Zaina
- b Department of Medical Sciences , Division of Health Sciences, León Campus, University of Guanajuato , Mexico
| | - Gertrud Lund
- a Department of Genetic Engineering , CINVESTAV Irapuato Unit , Irapuato , Mexico
| |
Collapse
|
92
|
Kitchen MO, Bryan RT, Emes RD, Glossop JR, Luscombe C, Cheng KK, Zeegers MP, James ND, Devall AJ, Mein CA, Gommersall L, Fryer AA, Farrell WE. Quantitative genome-wide methylation analysis of high-grade non-muscle invasive bladder cancer. Epigenetics 2016; 11:237-46. [PMID: 26929985 DOI: 10.1080/15592294.2016.1154246] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
High-grade non-muscle invasive bladder cancer (HG-NMIBC) is a clinically unpredictable disease with greater risks of recurrence and progression relative to their low-intermediate-grade counterparts. The molecular events, including those affecting the epigenome, that characterize this disease entity in the context of tumor development, recurrence, and progression, are incompletely understood. We therefore interrogated genome-wide DNA methylation using HumanMethylation450 BeadChip arrays in 21 primary HG-NMIBC tumors relative to normal bladder controls. Using strict inclusion-exclusion criteria we identified 1,057 hypermethylated CpGs within gene promoter-associated CpG islands, representing 256 genes. We validated the array data by bisulphite pyrosequencing and examined 25 array-identified candidate genes in an independent cohort of 30 HG-NMIBC and 18 low-intermediate-grade NMIBC. These analyses revealed significantly higher methylation frequencies in high-grade tumors relative to low-intermediate-grade tumors for the ATP5G2, IRX1 and VAX2 genes (P<0.05), and similarly significant increases in mean levels of methylation in high-grade tumors for the ATP5G2, VAX2, INSRR, PRDM14, VSX1, TFAP2b, PRRX1, and HIST1H4F genes (P<0.05). Although inappropriate promoter methylation was not invariantly associated with reduced transcript expression, a significant association was apparent for the ARHGEF4, PON3, STAT5a, and VAX2 gene transcripts (P<0.05). Herein, we present the first genome-wide DNA methylation analysis in a unique HG-NMIBC cohort, showing extensive and discrete methylation changes relative to normal bladder and low-intermediate-grade tumors. The genes we identified hold significant potential as targets for novel therapeutic intervention either alone, or in combination, with more conventional therapeutic options in the treatment of this clinically unpredictable disease.
Collapse
Affiliation(s)
- Mark O Kitchen
- a Institute for Science and Technology in Medicine, Keele University , UK.,b Urology Department , University Hospitals of North Midlands NHS Trust , UK
| | - Richard T Bryan
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK
| | - Richard D Emes
- d Advanced Data Analysis Center, University of Nottingham , UK
| | - John R Glossop
- a Institute for Science and Technology in Medicine, Keele University , UK
| | | | - K K Cheng
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK
| | - Maurice P Zeegers
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK.,e Department of Complex Genetics , Maastricht University Medical Center , The Netherlands.,f NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center , The Netherlands.,g CAPHRI School for Public Health and Primary Care, Maastricht University Medical Center , The Netherlands
| | | | - Adam J Devall
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK
| | - Charles A Mein
- i The Genome Center, Barts and the London School of Medicine and Dentistry , London , UK
| | - Lyndon Gommersall
- b Urology Department , University Hospitals of North Midlands NHS Trust , UK
| | - Anthony A Fryer
- a Institute for Science and Technology in Medicine, Keele University , UK
| | - William E Farrell
- a Institute for Science and Technology in Medicine, Keele University , UK
| |
Collapse
|
93
|
Kishino T, Niwa T, Yamashita S, Takahashi T, Nakazato H, Nakajima T, Igaki H, Tachimori Y, Suzuki Y, Ushijima T. Integrated analysis of DNA methylation and mutations in esophageal squamous cell carcinoma. Mol Carcinog 2016; 55:2077-2088. [PMID: 26756304 DOI: 10.1002/mc.22452] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 12/01/2015] [Accepted: 12/15/2015] [Indexed: 12/12/2022]
Abstract
The recent development of next-generation sequencing technology for extensive mutation analysis, and beadarray technology for genome-wide DNA methylation analysis has made it possible to obtain integrated pictures of genetic and epigenetic alterations, using the same cancer samples. In this study, we aimed to characterize such a picture in esophageal squamous cell carcinomas (ESCCs). Base substitutions of 55 cancer-related genes and copy number alterations (CNAs) of 28 cancer-related genes were analyzed by targeted sequencing. Forty-four of 57 ESCCs (77%) had 64 non-synonymous somatic mutations, and 24 ESCCs (42%) had 35 CNAs. A genome-wide DNA methylation analysis using an Infinium HumanMethylation450 BeadChip array showed that the CpG island methylator phenotype was unlikely to be present in ESCCs, a different situation from gastric and colon cancers. Regarding individual pathways affected in ESCCs, the WNT pathway was activated potentially by aberrant methylation of its negative regulators, such as SFRP1, SFRP2, SFRP4, SFRP5, SOX17, and WIF1 (33%). The p53 pathway was inactivated by TP53 mutations (70%), and potentially by aberrant methylation of its downstream genes. The cell cycle was deregulated by mutations of CDKN2A (9%), deletions of CDKN2A and RB1 (32%), and by aberrant methylation of CDKN2A and CHFR (9%). In conclusion, ESCCs had unique methylation profiles different from gastric and colon cancers. The genes involved in the WNT pathway were affected mainly by epigenetic alterations, and those involved in the p53 pathway and cell cycle regulation were affected mainly by genetic alterations. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Takayoshi Kishino
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan.,Department of Gastroenterological Surgery, Kagawa University, Kagawa, Japan
| | - Tohru Niwa
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takamasa Takahashi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Hidetsugu Nakazato
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Takeshi Nakajima
- Division of Endoscopy, National Cancer Center Hospital, Tokyo, Japan
| | - Hiroyasu Igaki
- Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yuji Tachimori
- Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yasuyuki Suzuki
- Department of Gastroenterological Surgery, Kagawa University, Kagawa, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| |
Collapse
|
94
|
Roznovăţ IA, Ruskin HJ. Theoretical cross-comparative analysis on dynamics of small intestine and colon crypts during cancer initiation. IET Syst Biol 2015; 9:259-67. [PMID: 26577160 DOI: 10.1049/iet-syb.2015.0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Epigenetics is emerging as a fundamentally important area of biological and medical research that has implications for our understanding of human diseases including cancer, autoimmune and neuropsychiatric disorders. In the context of recent efforts on personalised medicine, a novel research direction is concerned with identification of intra-individual epigenetic variation linked to disease predisposition and development, i.e. epigenome-wide association studies. A computational model has been developed to describe the dynamics and structure of human intestinal crypts and to perform a comparative analysis on aberrant DNA methylation level induced in these during cancer initiation. The crypt framework, AgentCrypt, is an agent-based model of crypt dynamics, which handles intra- and inter-dependencies. In addition, the AgentCrypt model is used to investigate the effect of a set of potential inhibitors with respect to methylation modification in intestinal tissue during initiation of disease. Methylation level decrease over a relatively short period of 90 days is marked for the colon compared to the small intestine, although similar alterations are induced in both tissues. In addition, inhibitor effect is notable for abnormal crypt groups, with largest average methylation differences observed ≈0.75% lower in the colon and ≈0.79% lower in the small intestine with inhibitor present.
Collapse
Affiliation(s)
- Irina A Roznovăţ
- Current address: European Institute for Systems Biology and Medicine (EISBM), CNRS-ENS-UCBL, Campus Charles Mérieux, Université de Lyon, 50 Avenue Tony Garnier, 69366 Lyon cedex 07, France.
| | - Heather J Ruskin
- Centre for Scientific Computing & Complex Systems Modelling (SCI-SYM), School of Computing, Dublin City University, Dublin, Ireland
| |
Collapse
|
95
|
Jeon MS, Song SH, Yun J, Kang JY, Kim HP, Han SW, Kim TY. Aberrant Epigenetic Modifications of LPHN2 Function as a Potential Cisplatin-Specific Biomarker for Human Gastrointestinal Cancer. Cancer Res Treat 2015; 48:676-86. [PMID: 26511811 PMCID: PMC4843720 DOI: 10.4143/crt.2015.153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/01/2015] [Indexed: 12/22/2022] Open
Abstract
Purpose Epigenetic alterations of specific genes have recently been identified as diagnostic biomarkers for human cancers. However, there are currently no standardized epigenetic biomarkers for drug sensitivity in human gastrointestinal cancer. Therefore, the aim of this study is to identify a novel epigenetic biomarker in gastrointestinal cancer. Materials and Methods Using bisulfite sequencing and pyrosequencing analysis, DNA methylation patterns of gastric, colon primary tissues and their cancer cells were analyzed, and histone modifications were analyzed using chromatin immunoprecipitation assay. In addition, cancer cells were exposed to cisplatin and treated with a DNA methyltransferase inhibitor. Results We report that in human gastric and colon cancers, latrophilin 2 (LPHN2) is silenced by epigenetic modifications, including CpG island methylation and aberrant histone modifications. We also confirmed that LPHN2 was silenced by DNA hypermethylation in primary gastric and colon tumor tissues compared to their normal counterparts. Interestingly, we found that cancer cells with methylated LPHN2 showed higher sensitivity to cisplatin. Also, 5-aza- 2′-deoxycytidine combined with cisplatin decreased the cytotoxicity of cisplatin in cancer cells with methylated LPHN2. In addition, LPHN2 knockdown in cancer cells with high LPHN2 expression sensitized these cells to the anti-proliferative effects of cisplatin. Conclusion In human gastrointestinal cancer, we found that LPHN2 is regulated by epigenetic modifications, and that cancer cells with lower LPHN2 expression show higher sensitivity to cisplatin. Therefore, the methylation status of LPHN2 is a potential novel epigenetic biomarker for cisplatin treatment in human gastric and colon cancers.
Collapse
Affiliation(s)
- Mi-Seong Jeon
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Sang-Hyun Song
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Jiyeon Yun
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Jee-Youn Kang
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Hwang-Phill Kim
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Sae-Won Han
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Tae-You Kim
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| |
Collapse
|
96
|
Abu-Remaileh M, Bender S, Raddatz G, Ansari I, Cohen D, Gutekunst J, Musch T, Linhart H, Breiling A, Pikarsky E, Bergman Y, Lyko F. Chronic inflammation induces a novel epigenetic program that is conserved in intestinal adenomas and in colorectal cancer. Cancer Res 2015; 75:2120-30. [PMID: 25808873 DOI: 10.1158/0008-5472.can-14-3295] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/12/2015] [Indexed: 12/13/2022]
Abstract
Chronic inflammation represents a major risk factor for tumor formation, but the underlying mechanisms have remained largely unknown. Epigenetic mechanisms can record the effects of environmental challenges on the genome level and could therefore play an important role in the pathogenesis of inflammation-associated tumors. Using single-base methylation maps and transcriptome analyses of a colitis-induced mouse colon cancer model, we identified a novel epigenetic program that is characterized by hypermethylation of DNA methylation valleys that are characterized by low CpG density and active chromatin marks. This program is conserved and functional in mouse intestinal adenomas and results in silencing of active intestinal genes that are involved in gastrointestinal homeostasis and injury response. Further analyses reveal that the program represents a prominent feature of human colorectal cancer and can be used to correctly classify colorectal cancer samples with high accuracy. Together, our results show that inflammatory signals establish a novel epigenetic program that silences a specific set of genes that contribute to inflammation-induced cellular transformation.
Collapse
Affiliation(s)
- Monther Abu-Remaileh
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Sebastian Bender
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Ihab Ansari
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Daphne Cohen
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Tanja Musch
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Heinz Linhart
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany. Salem Medical Center, University of Heidelberg, Heidelberg, Germany. Department of Hematology/Oncology, University of Heidelberg Medical Center, Heidelberg, Germany
| | - Achim Breiling
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Eli Pikarsky
- The Lautenberg Center for Immunology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany.
| |
Collapse
|
97
|
Marzese DM, Hoon DS. Emerging technologies for studying DNA methylation for the molecular diagnosis of cancer. Expert Rev Mol Diagn 2015; 15:647-64. [PMID: 25797072 DOI: 10.1586/14737159.2015.1027194] [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] [Indexed: 12/11/2022]
Abstract
DNA methylation is an epigenetic mechanism that plays a key role in regulating gene expression and other functions. Although this modification is seen in different sequence contexts, the most frequently detected DNA methylation in mammals involves cytosine-guanine dinucleotides. Pathological alterations in DNA methylation patterns are described in a variety of human diseases, including cancer. Unlike genetic changes, DNA methylation is heavily influenced by subtle modifications in the cellular microenvironment. In all cancers, aberrant DNA methylation is involved in the alteration of a large number of oncological pathways with relevant theranostic utility. Several technologies for DNA methylation mapping have been developed recently and successfully applied in cancer studies. The scope of these technologies varies from assessing a single cytosine-guanine locus to genome-wide distribution of DNA methylation. Here, we review the strengths and weaknesses of these approaches in the context of clinical utility for the molecular diagnosis of human cancers.
Collapse
Affiliation(s)
- Diego M Marzese
- Department of Molecular Oncology, Saint John's Health Center, John Wayne Cancer Institute, 2200 Santa Monica Blvd, Santa Monica, CA 90404, USA
| | | |
Collapse
|
98
|
Abstract
One of the hallmarks of cancer is the ability to generate and withstand unusual levels of oxidative stress. In part, this property of tumor cells is conferred by elevation of the cellular redox buffer glutathione. Though enzymes of the glutathione synthesis and salvage pathways have been characterized for several decades, we still lack a comprehensive understanding of their independent and coordinate regulatory mechanisms. Recent studies have further revealed that overall central metabolic pathways are frequently altered in various tumor types, resulting in significant increases in biosynthetic capacity and feeding into glutathione synthesis. In this review, we will discuss the enzymes and pathways affecting glutathione flux in cancer and summarize current models for regulating cellular glutathione through both de novo synthesis and efficient salvage. In addition, we examine the integration of glutathione metabolism with other altered fates of intermediary metabolites and highlight remaining questions about molecular details of the accepted regulatory modes.
Collapse
Affiliation(s)
- Yilin Liu
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, Nebraska, USA
| | - Annastasia S Hyde
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, Nebraska, USA
| | - Melanie A Simpson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, Nebraska, USA
| | - Joseph J Barycki
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, Nebraska, USA.
| |
Collapse
|
99
|
Lotem J, Levanon D, Negreanu V, Bauer O, Hantisteanu S, Dicken J, Groner Y. Runx3 at the interface of immunity, inflammation and cancer. Biochim Biophys Acta Rev Cancer 2015; 1855:131-43. [PMID: 25641675 DOI: 10.1016/j.bbcan.2015.01.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 02/06/2023]
Abstract
Inactivation of tumor suppressor genes (TSG) in normal cells provides a viability/growth advantage that contributes cell-autonomously to cancer. More than a decade ago claims arose that the RUNX3 member of the RUNX transcription factor family is a major TSG inactivated in gastric cancer, a postulate extended later to other cancers. However, evidence that Runx3 is not expressed in normal gastric and other epithelia has challenged the RUNX3-TSG paradigm. Here we critically re-appraise this paradigm in light of recent high-throughput, quantitative genome-wide studies on thousands of human samples of various tumors and new investigations of the role of Runx3 in mouse cancer models. Collectively, these studies unequivocally demonstrate that RUNX3 is not a bona fide cell-autonomous TSG. Accordingly, RUNX3 is not recognized as a TSG and is not included among the 2000 cancer genes listed in the "Cancer Gene Census" or "Network for Cancer Genes" repositories. In contrast, RUNX3 does play important functions in immunity and inflammation and may thereby indirectly influence epithelial tumor development.
Collapse
Affiliation(s)
- Joseph Lotem
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Ditsa Levanon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Varda Negreanu
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Omri Bauer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shay Hantisteanu
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joseph Dicken
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoram Groner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
100
|
Ng JMK, Yu J. Promoter hypermethylation of tumour suppressor genes as potential biomarkers in colorectal cancer. Int J Mol Sci 2015; 16:2472-96. [PMID: 25622259 PMCID: PMC4346847 DOI: 10.3390/ijms16022472] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/02/2014] [Accepted: 01/14/2015] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a common malignancy and the fourth leading cause of cancer deaths worldwide. It results from the accumulation of multiple genetic and epigenetic changes leading to the transformation of colon epithelial cells into invasive adenocarcinomas. In CRC, epigenetic changes, in particular promoter CpG island methylation, occur more frequently than genetic mutations. Hypermethylation contributes to carcinogenesis by inducing transcriptional silencing or downregulation of tumour suppressor genes and currently, over 600 candidate hypermethylated genes have been identified. Over the past decade, a deeper understanding of epigenetics coupled with technological advances have hinted at the potential of translating benchtop research into biomarkers for clinical use. DNA methylation represents one of the largest bodies of literature in epigenetics, and hence has the highest potential for minimally invasive biomarker development. Most progress has been made in the development of diagnostic markers and there are currently two, one stool-based and one blood-based, biomarkers that are commercially available for diagnostics. Prognostic and predictive methylation markers are still at their infantile stages.
Collapse
Affiliation(s)
- Jennifer Mun-Kar Ng
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China.
| |
Collapse
|