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Series GSE136724 Query DataSets for GSE136724
Status Public on Mar 13, 2020
Title DNA methylation of chronic lymphocytic leukemia with differential response to chemotherapy
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Acquired resistance of chronic lymphocytic leukemia (CLL) to chemotherapy is an important clinical problem and is often caused by cytogenetic aberrations or gene mutations affecting the ATM-p53 DNA damage response pathway or other pathways. However, there are also a lot of resistant cases without detectable mutations and we decided to check whether there are specific epigenetic changes at the level of DNA methylation that might underlie resistance development in CLL. We used Illumina Infinium HumanMethylation450 BeadChips to obtain DNA methylation profiles of 71 CLL patients with different responses to chemotherapy. Fifty-one patients were subjects of the CLL2O clinical trial and 36 of them were categorized as relapsed/refractory after treatment with fludarabine- or bendamustine-containing regimens, whereas the other 15 patients as well as 20 additional patients not on the trial were untreated at the time of sampling. Although we could not correlate chemoresistance with epigenetic changes, we believe that the dataset is valuable and can be used by researchers to test other hypotheses, especially as the patients are well characterized regarding different prognostic and molecular markers (IGHV mutation status, chromosome aberrations, TP53 mutation status, etc.).
Overall design 72 samples of CLL patients were analyzed by Illumina Infinium HumanMethylation450 BeadChips. Two consecutive samples (40 months apart) from one patient were used to confirm reproducibility of the assay, as well as stability of DNA methylation profiles over time. Fifty-one of the patients were subjects of the multi-centre CLL2O clinical trial ( NCT01392079) and we have subdivided them here in 4 subgroups depending on their del(17p)/TP53mut and treatment/response statuses as follows: groups A (N = 15), B (N = 10) and C (N = 11) consisted of patients with del(17p) and/or TP53 mutation and group E (N = 15) consisted of patients without del(17p) or TP53 mutation. Patients in group A were not treated previously but required treatment, patients in group B had relapsed after treatment with fludarabine- or bendamustine-containing regimens and patients in groups C and E were refractory to fludarabine or bendamustine. Samples from patients in all these groups were taken prior to the start of the CLL2O clinical trial. Additional 20 cases (group D) were patients of the University Hospital in Ulm who did not have del(17p) or TP53 mutation and who were not previously treated.
Contributor(s) Yosifov DY, Bloehdorn J, Döhner H, Lichter P, Stilgenbauer S, Mertens D
Citation(s) 32358561
Submission date Sep 02, 2019
Last update date Jun 12, 2020
Contact name Deyan Yordanov Yosifov
Phone +4973150045870
Organization name University Hospital Ulm
Department Internal Medicine III
Street address Albert-Einstein-Allee 23
City Ulm
ZIP/Postal code 89081
Country Germany
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (72)
GSM4056697 CLL_A_del17p_untreated_1
GSM4056698 CLL_B_del17p_relapsed_1
GSM4056699 CLL_B_del17p_relapsed_2
BioProject PRJNA563338

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE136724_RAW.tar 776.2 Mb (http)(custom) TAR (of IDAT)
Processed data included within Sample table
Raw data provided as supplementary file

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