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DNA methylation in primary myelofibrosis is partly associated with driver mutations and distinct from other myeloid malignancies II

ABSTRACT: DNA methylation in primary myelofibrosis is partly associated with driver mutations and distinct from other myeloid malignancies II

PROVIDER: PRJNA1164678 | ENA |

REPOSITORIES: ENA

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DNA methylation in primary myelofibrosis is partly associated with driver mutations and distinct from other myeloid malignancies

Project description:DNA methylation in primary myelofibrosis is partly associated with driver mutations and distinct from other myeloid malignancies

| PRJNA1164705 | ENA

DNA methylation in primary myelofibrosis is partly associated with driver mutations and distinct from other myeloid malignancies I

Project description:DNA methylation in primary myelofibrosis is partly associated with driver mutations and distinct from other myeloid malignancies I

| PRJNA1164666 | ENA

DNA methylation in primary myelofibrosis is partly associated with driver mutations and distinct from other myeloid malignancies II

Project description:Primary myelofibrosis (PMF) is a clonal blood disorder linked to mutually exclusive mutations in JAK2, CALR, or MPL genes. To understand the epigenetic effects of these mutations, we analyzed DNA methylation (DNAm) profiles of PMF patients. Notably, no differences were found between JAK2 and CALR mutated cases, whereas MPL mutations showed distinct DNAm patterns. Further investigation in induced pluripotent stem cell (iPSC) models with JAK2 mutations revealed only a moderate link to PMF-related epigenetic changes, suggesting these alterations are not directly caused by the mutations. Additionally, PMF-associated epigenetic changes showed minimal correlation with allele burden and were largely evoked by changes in the cellular composition. When comparing PMF DNAm profiles with those from other myeloid malignancies, such as acute myeloid leukemia, juvenile myelomonocytic leukemia, and myelodysplastic syndrome, many overlapping changes were found, making it difficult to distinguish PMF based on individual CpGs. However, a PMF score created by combining five CpGs successfully differentiated PMF from other diseases in training and validation datasets. These findings demonstrate that PMF driver mutations do not directly evoke epigenetic changes. While PMF shares epigenetic changes with other myeloid malignancies, epigenetic signatures can effectively differentiate PMF from related diseases.

2025-05-07 | GSE277866 | GEO

DNA methylation in primary myelofibrosis is partly associated with driver mutations and distinct from other myeloid malignancies I

2025-05-07 | GSE277841 | GEO

DNA methylation in primary myelofibrosis is partly associated with driver mutations and distinct from other myeloid malignancies

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-05-07 | GSE277889 | GEO

Non-driver mutations in myeloproliferative neoplasm-associated myelofibrosis.

Project description:We studied non-driver mutations in 62 subjects with myeloproliferative neoplasm (MPN)-associated myelofibrosis upon diagnosis, including 45 subjects with primary myelofibrosis (PMF) and 17 with post-polycythemia vera or post-essential thrombocythemia myelofibrosis (post-PV/ET MF). Fifty-eight subjects had ≥1 non-driver mutation upon diagnosis. Mutations in mRNA splicing genes, especially in U2AF1, were significantly more frequent in PMF than in post-PV/ET MF (33 vs. 6%; P = 0.015). There were also striking differences in clonal architecture. These data indicate different genomic spectrums between PMF and post-PV/ET MF.

| S-EPMC5414291 | biostudies-literature

Chromosome 11 analysis in myeloid malignancies - microarrays

Project description:blood samples from patients with myeloid malignancies were analyzed using Affymetrix Genome-Wide Human SNP 6.0 arrays.

2013-11-01 | E-MTAB-1845 | biostudies-arrayexpress

Cohesin mutations in myeloid malignancies.

Project description:Cohesin is a multisubunit protein complex that forms a ring-like structure around DNA. It is essential for sister chromatid cohesion, chromatin organization, transcriptional regulation, and DNA damage repair and plays a major role in dynamically shaping the genome architecture and maintaining DNA integrity. The core complex subunits STAG2, RAD21, SMC1, and SMC3, as well as its modulators PDS5A/B, WAPL, and NIPBL, have been found to be recurrently mutated in hematologic and solid malignancies. These mutations are found across the full spectrum of myeloid neoplasia, including pediatric Down syndrome-associated acute megakaryoblastic leukemia, myelodysplastic syndromes, chronic myelomonocytic leukemia, and de novo and secondary acute myeloid leukemias. The mechanisms by which cohesin mutations act as drivers of clonal expansion and disease progression are still poorly understood. Recent studies have described the impact of cohesin alterations on self-renewal and differentiation of hematopoietic stem and progenitor cells, which are associated with changes in chromatin and epigenetic state directing lineage commitment, as well as genomic integrity. Herein, we review the role of the cohesin complex in healthy and malignant hematopoiesis. We discuss clinical implications of cohesin mutations in myeloid malignancies and discuss opportunities for therapeutic targeting.

| S-EPMC8394903 | biostudies-literature

Chromosome 11 analysis in myeloid malignancies - WES

Project description:Blood samples from patients with myeloid malignancies were analyzed using whole exome sequencing (WES). Data set from genotyping by microarray of the same samples has been deposited in ArrayExpress under accession number E-MTAB-1845 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1845/).

2013-11-01 | E-MTAB-1850 | biostudies-arrayexpress

Somatic SETBP1 mutations in myeloid malignancies.

Project description:Here we report whole-exome sequencing of individuals with various myeloid malignancies and identify recurrent somatic mutations in SETBP1, consistent with a recent report on atypical chronic myeloid leukemia (aCML). Closely positioned somatic SETBP1 mutations encoding changes in Asp868, Ser869, Gly870, Ile871 and Asp880, which match germline mutations in Schinzel-Giedion syndrome (SGS), were detected in 17% of secondary acute myeloid leukemias (sAML) and 15% of chronic myelomonocytic leukemia (CMML) cases. These results from deep sequencing demonstrate a higher mutational detection rate than reported with conventional sequencing methodology. Mutant cases were associated with advanced age and monosomy 7/deletion 7q (-7/del(7q)) constituting poor prognostic factors. Analysis of serially collected samples indicated that SETBP1 mutations were acquired during leukemic evolution. Transduction with mutant Setbp1 led to the immortalization of mouse myeloid progenitors that showed enhanced proliferative capacity compared to cells transduced with wild-type Setbp1. Somatic mutations of SETBP1 seem to cause gain of function, are associated with myeloid leukemic transformation and convey poor prognosis in myelodysplastic syndromes (MDS) and CMML.

| S-EPMC3729750 | biostudies-literature

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