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Homo sapiens

ABSTRACT: Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia

PROVIDER: PRJNA146893 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR352003.fastq.gz	Fastqsanger.gz
	SRR352004.fastq.gz	Fastqsanger.gz
	SRR352005.fastq.gz	Fastqsanger.gz
	SRR352006.fastq.gz	Fastqsanger.gz
	SRR352007.fastq.gz	Fastqsanger.gz

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Nanda2013 - B cell chronic lymphocytic leukemia A model with immune response

Project description:B cell chronic lymphocytic leukemia - A model with immune response Seema Nanda 1, , Lisette dePillis 2, and Ami Radunskaya 3, 1. Tata Institute of Fundamental Research, Centre for Applicable Mathematics, Bangalore 560065, India 2. Department of Mathematics, Harvey Mudd College, Claremont, CA 91711 3. Department of Mathematics, Pomona College, Claremont, CA, 91711, United States Abstract B cell chronic lymphocytic leukemia (B-CLL) is known to have substantial clinical heterogeneity. There is no cure, but treatments allow for disease management. However, the wide range of clinical courses experienced by B-CLL patients makes prognosis and hence treatment a significant challenge. In an attempt to study disease progression across different patients via a unified yet flexible approach, we present a mathematical model of B-CLL with immune response, that can capture both rapid and slow disease progression. This model includes four different cell populations in the peripheral blood of humans: B-CLL cells, NK cells, cytotoxic T cells and helper T cells. We analyze existing data in the medical literature, determine ranges of values for parameters of the model, and compare our model outcomes to clinical patient data. The goal of this work is to provide a tool that may shed light on factors affecting the course of disease progression in patients. This modeling tool can serve as a foundation upon which future treatments can be based. Keywords: NK cell, chronic lymphocytic leukemia, mathematical model, T cell., B-CLL.

2020-01-09 | MODEL2001090002 | BioModels

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Project description:Activation induced deaminase (AID) has two distinct and well defined roles, both relying on its deoxycytidine (dC) deaminating function: one as a DNA mutator and another in DNA demethylation. In chronic lymphocytic leukemia (CLL), AID was previously shown to be an independent negative prognostic factor. While there is substantial impact on DNA mutations, effects of AID on gene expression by promoter demethylation of disease related target genes in leukemia has not been addressed. To shed light on this question, we aimed at determining genome wide methylation changes as well as gene expression changes in response to AID expression in CLL. Although we found minor differences in individual methylation variable positions following AID expression, we could not find recurrent methylation changes of specific target sites or changes in global methylation.

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A dataset of sequential DNA methylation profiles (2 timepoints) of 10 patients with chronic lymphocytic leukemia

Project description:Clonal and subclonal evolution is involved in the progression of chronic lymphocytic leukemia (CLL). Evolution can work to select not only genetic mutations, but also epigenetic states. Here we performed a long-term longitudinal DNA methylation profiling study of CLL patients to look for associations of epigenetic evolution to different disease courses. In line with the genetic data, large-scale methylation evolution was not present in any of the evaluated long-term untreated (n = 3) and relapsed (n = 2) patients displaying clonal changes of linear type while 3 of the 5 examined refractory patients featured profound changes in DNA methylation.

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Project description:The contribution of DNA methylation on the evolution of chronic lymphocytic leukemia has not been adequately studied yet. The purpose of this study was to investigate the role of DNA methylation in patients under chemoimmunotherapy. The overtime analysis of DNA methylation was performed on 40 patients in two time points: pre-treatment and after relapse, and 2 samples of memory B cells (MBC), using 450k arrays.

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Project description:Genome-wide Analysis of Chronic Lymphocytic Leukemia

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