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Classification of cancer cell lines using a promoter-targeted liquid hybridization capture-based bisulfite sequencing approach

ABSTRACT: DNA methylation plays a significant role in assuring cell identity, thus potentiating its application in molecular classification of cancers in respect of tissue origins or clinically and aetiologically distinct subtypes. In this study, we adapted our liquid hybridization capture-based bisulfite sequencing approach on the targeted sequencing of promoter methylomes. We detected ten cell lines originated from different tissue origins and demonstrated a similar potentiality of promoter methylomes as classifiers for cancer cell lines from different tissue origins in comparison with gene expression profiles. Furthermore, promoter methylome can sensitively differentiate two different cell lines from the same tissue origin in respect of the CpG island methylator phenotype (CIMP), as in the case of AGS and BGC-823 gastric cancer cell lines. These results potentiate the targeted sequencing of promoter methylomes as a means for comprehensive screening and classifying cancer cells with respect to tissue-origins and CIMP subtypes in the future studies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE44866 | GEO | 2014/02/19

SECONDARY ACCESSION(S): PRJNA192520

REPOSITORIES: GEO

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Classification of cancer cell lines using a promoter-targeted liquid hybridization capture-based bisulfite sequencing approach

Project description:DNA methylation plays a significant role in assuring cell identity, thus potentiating its application in molecular classification of cancers in respect of tissue origins or clinically and aetiologically distinct subtypes. In this study, we adapted our liquid hybridization capture-based bisulfite sequencing approach on the targeted sequencing of promoter methylomes. We detected ten cell lines originated from different tissue origins and demonstrated a similar potentiality of promoter methylomes as classifiers for cancer cell lines from different tissue origins in comparison with gene expression profiles. Furthermore, promoter methylome can sensitively differentiate two different cell lines from the same tissue origin in respect of the CpG island methylator phenotype (CIMP), as in the case of AGS and BGC-823 gastric cancer cell lines. These results potentiate the targeted sequencing of promoter methylomes as a means for comprehensive screening and classifying cancer cells with respect to tissue-origins and CIMP subtypes in the future studies. We proved the potentiality of promoter-targeted LHC-BS that requires reduced experimental cost and less amount of initial DNA samples in comparison with a previous design [23] using YH cell line. In addition, we generated single-base promoter methylomes for ten cell lines, including eight cancer cell lines generated from four types of tissues and one pair of model cell lines for ovarian cancer (T29 and T29H). We proved the potentiality of promoter-targeted LHC-BS that requires reduced experimental cost and less amount of initial DNA samples in comparison with a previous design using YH cell line. In addition, we generated single-base promoter methylomes for ten cell lines, including eight cancer cell lines generated from four types of tissues and one pair of model cell lines for ovarian cancer (T29 and T29H).

2014-02-19 | E-GEOD-44866 | biostudies-arrayexpress

Breast Cancer Methylomes Establish an Epigenomic Foundation for Metastasis

Project description:Cancer-specific changes in DNA methylation can alter genetic stability, genomic structure, and gene expression. Promoter CpG island methylation can result in transcriptional silencing and plays an important role in the oncogenic process. We used genome-wide analysis to characterize the methylomes of breast cancers with diverse metastatic behavior. Here, we describe the identification of novel groups of breast tumors characterized by the presence or absence of coordinate hypermethylation at a large number of genes, demonstrating the existence of a breast-CpG island methylator phenotype (B-CIMP). B-CIMP imparts a distinct epigenomic profile and is a strong determinant of metastatic potential. Gene Expression Samples (GSM647057-GSM647077): Twenty-one breast cancer primary samples were analyzed. There are 10 CIMP positive and 11 CIMP negative samples. Methylation Profiling Samples (GSM651372-GSM651410): Thirty-nine breast cancer primary samples were analyzed. There are 17 CIMP positive and 22 CIMP negative samples.

2011-03-31 | E-GEOD-26349 | biostudies-arrayexpress

Breast Cancer Methylomes Establish an Epigenomic Foundation for Metastasis

2011-03-31 | GSE26349 | GEO

DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways [tumor, paired normal]

Project description:Promoter hypermethylation divides colon cancers into subtypes with and without a CpG island methylator phenotype (CIMP). Here, we performed genome-wide DNA methylation profiling of colonic normal and tumor tissues to dissect development of CpG hypermethylation in colon carcinogenesis. This identified age-environment related versus genetically driven CpG hypermethylation, the latter being associated with CIMP cancers. We found a strong association between BRAFV600E mutation and downregulation of the DNA demethylases TET1 and TET2. Expression of BRAFV600E in CIMP cancer cells suppressed TET1 transcription, which was sufficient to establish hypermethylation at CIMP genes promoters, including that of TET2. This phenotype was reverted by the BRAFV600E inhibitor vemurafenib. Thus, BRAFV600E, via impairment of cytosine de-methylation, is a genetic driver of CIMP in colon tumorigenesis. Genome-wide DNA methylation profiling of adjacent non-tumor colon tissue and colon adenocarcinoma samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 8 colon cancer tissues and their associated healthy mucosa (CAM).

2019-12-18 | GSE98531 | GEO

DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways [Colo320 cell line]

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DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways [BrafV637E knock-in ]

2019-12-18 | GSE108606 | GEO

DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways [Caco2 cell line]

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CCAT1 is a cMYC super-enhancer templated RNA that predicts BET sensitivity in cancer

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2016-01-26 | GSE73319 | GEO

Genome wide gene expression array analysis in T-ALL

Project description:In short: The objective with the gene expression array (Illumina HT-12 v.4) analysis of 17 T-ALL samples was to correlate gene expression levels with DNA promoter methylation status. Manuscript Abstract: Background: Treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL) has improved, but there is a considerable fraction of patients experiencing a poor outcome. There is a need for better prognostic markers and aberrant DNA methylation is a candidate in other malignancies, but its potential prognostic significance in T-ALL is hitherto undecided. Design and Methods: Genome wide promoter DNA methylation analysis was performed in pediatric T-ALL samples (n=43) using arrays covering >27000 CpG sites. Clinical outcome was evaluated in relation to methylation status and compared with a contemporary T-ALL group not tested for methylation (n= 32). Results: Based on CpG island methylator phenotype (CIMP), T-ALL samples were subgrouped as CIMP+ (high methylation) and CIMP- (low methylation). CIMP- T-ALL patients had significantly worse overall and event free survival (p=0.02 and p=0.001, respectively) compared to CIMP+ cases. CIMP status was an independent factor for survival in multivariate analysis including age, gender and white blood cell count. Analysis of differently methylated genes in the CIMP subgroups showed an overrepresentation of transcription factors, ligands and polycomb target genes. Conclusions: We identified global promoter methylation profiling as being of relevance for subgrouping and prognostication of pediatric T-ALL.

2013-07-01 | GSE41621 | GEO

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