Plasma cfDNA and Peripheral Blood gDNA Provide Complementary Information for Molecular Monitoring in Myeloproliferative Neoplasms
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE325660 | GEO | 2026/03/23
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression profiles were established for 50 MPNs samples. RNA extracted from 2 healthy people was used as control. All MPNs were screened for JAK2V617F mutation as part of routine diagnostic practice.
2011-12-31 | E-MTAB-510 | biostudies-arrayexpress
Project description:Interferons (IFNs) are cytokines with potent anti-neoplastic properties and significant clinical activity in the treatment of myeloproliferative neoplasms (MPNs). The use of pegylated IFN for the treatment of MPNs has been of particular interest, with several clinical trials establishing clinical responses. Here we demonstrate that chromatin assembly factor 1 subunit B (CHAF1B) is overexpressed in MPN patients. Targeted silencing of CHAF1B enhances transcription of IFN-stimulated genes and promotes IFN-dependent anti-neoplastic effects against MPN patient-derived cells. Our findings suggest that targeting CHAF1B in combination with IFN therapy may offer an avenue for the development of effective combination therapies for the treatment of MPNs.
2023-05-15 | PXD037376 | Pride
Project description:Myeloproliferative neoplasms (MPNs) arise via the acquisition of a driver mutation in a single hematopoietic stem cell (HSC), often decades prior to the development of a clinical phenotype. The most common MPN driver mutation, JAK2V617F, activates aberrant JAK/STAT signaling via cytokine receptors critical for myelopoiesis. Over time, this MPN HSC clone outcompetes its normal counterparts, leading to excessive myeloid cell production and contributes to lymphopenia in patients with MPNs and leades to elevated neutrophil-to-lymphocyte ratio (NLR), which is predictive of disease-related complications including thrombosis and mortality. We conducted this study to learn how hematopoiesis from the JAK2V617F clone affects lymphopoiesis in patients with MPNs. Although myeloid proliferation via aberrant JAK2 signaling is the most apparent mechanistic link between JAK2V617F and MPN phenotypes, our findings demonstrate that impaired lymphoid differentiation is an additional feature of JAK2V617F hematopoiesis, leading to the rarity of JAK2V617F lymphocytes despite the dominance of JAK2V617F HSCs in patients with MPNs. The combination of prolific myelopoiesis and defective lymphopoiesis from the JAK2V617F clone is a potential connection between MPN pathology and the surrogate markers, including NLR and lymphopenia, which hold prognostic significance. Based on our data, we speculate that, defective JAK2V617F lymphopoiesis and the consequent increased burden of lymphopoiesis from residual normal HSC clones drives the appearance of abnormal lymphocyte subsets, lymphoproliferative disease or T cell exhaustion in MPNs. Further study of MPN lymphopoiesis provides an opportunity to define the immune deficits underlying the myriad complications that affect patients with MPNs.
2024-09-01 | GSE269568 | GEO
Project description:Since most DNA methylation studies in Classic Philadelphia-negative myeloproliferative neoplasms (MPNs) M-bM-^@M-^S polycythaemia vera (PV), essential thrombocythaemia (ET), and primary myelofibrosis (PMF) - have been performed on a gene-by-gene basis, a more comprehensive methylation profiling is needed to know the real implication of this alteration. In order to investigate the DNA methylation profile in chronic and transformed phase MPNs, we performed genome-wide DNA methylation arrays in 71 chronic (24 PV, 23 ET and 24 PMF) and 13 transformed MPNs. The three types of chronic MPNs showed the same aberrant DNA methylation pattern when compared to controls. Differentially methylated genes (DMG) were enriched in a gene network centered on the NF-M-NM-:B pathway, indicating that they may be involved in the pathogenesis of these diseases. In the case of transformed MPNs we detected an increased number of DMGs with respect to chronic MPNs. Interestingly, these genes were enriched in a list of DMGs in primary AMLs and in a gene network centered around the IFN pathway. Further studies are clearly needed to elucidate the role of DMGs in MPNs, but our results suggest that this alteration plays an important role in the pathogenesis and transformation of MPNs and that modulation of these pathways would allow us to improve the quality of life of these patients. The methylation profile of 24 PBMCs samples from patients diagnosed with Policytemia Vera, 23 from Essential Thrombocythemia and 24 from primary myelofibrosis was assessed. We also included 13 secondary acute myeloid leukaemia (AML): 5 transformed PMF,4 transformed TE and 4 transformed PV. As reference,4 healthy donor PBMCs samples from whole peripheral blood and 4 PBMCs samples from bone marrow were used.
2013-11-29 | E-GEOD-42042 | biostudies-arrayexpress
Project description:Since most DNA methylation studies in Classic Philadelphia-negative myeloproliferative neoplasms (MPNs) – polycythaemia vera (PV), essential thrombocythaemia (ET), and primary myelofibrosis (PMF) - have been performed on a gene-by-gene basis, a more comprehensive methylation profiling is needed to know the real implication of this alteration. In order to investigate the DNA methylation profile in chronic and transformed phase MPNs, we performed genome-wide DNA methylation arrays in 71 chronic (24 PV, 23 ET and 24 PMF) and 13 transformed MPNs. The three types of chronic MPNs showed the same aberrant DNA methylation pattern when compared to controls. Differentially methylated genes (DMG) were enriched in a gene network centered on the NF-κB pathway, indicating that they may be involved in the pathogenesis of these diseases. In the case of transformed MPNs we detected an increased number of DMGs with respect to chronic MPNs. Interestingly, these genes were enriched in a list of DMGs in primary AMLs and in a gene network centered around the IFN pathway. Further studies are clearly needed to elucidate the role of DMGs in MPNs, but our results suggest that this alteration plays an important role in the pathogenesis and transformation of MPNs and that modulation of these pathways would allow us to improve the quality of life of these patients.
2013-11-29 | GSE42042 | GEO
Project description:Comparison of matched cfDNA and CTC gDNA in HR+HER2- metastatic breast cancer patients
| PRJEB33921 | ENA
Project description:Myeloproliferative neoplasms (MPNs) are hematological diseases predominantly driven by the JAK2V617F mutation. Progression from chronic-phase MPN to secondary acute myeloid leukemia (sAML) is a severe complication as it dramatically worsens disease prognosis. While sAML transformation is classically linked to MPN clones acquiring additional mutations, the absence of JAK2V617F in sAML cases originating from JAK2-mutant MPNs suggests alternative mechanisms. Utilizing patient samples and in vivo modeling, we establish that sAML clones can emerge independently of JAK2-mutant cells. These leukemic clones undergo positive selection in the pro-inflammatory MPN environment leading to their predominance in the hematopoietic system. Genetic and pharmacological inhibition of IL-12 and TNFa mitigates this competitive advantage. Our data establish a new paradigm and show that disease progression in MPN can arise from parallel acute myeloid leukemia (pAML) clones.
2026-02-24 | GSE308233 | GEO
Project description:Type I interferons (IFNs) are key initiators and effectors of the immune response against malignant cells and can also directly inhibit tumor growth. IFN is highly effective in the treatment of myeloproliferative neoplasms (MPNs), but the mechanisms of action are unclear and it remains unknown why some patients respond to IFN therapy and others do not. We have identified and characterized a novel pathway involving PKC upstream of the kinase ULK1. Engagement of the Type I IFN receptor triggers PKC-dependent phosphorylation of ULK1 on serines 341 and 495, required for subsequent engagement of p38 MAPK that regulates transcription of IFN-stimulated genes and subsequent growth inhibitory responses. We show that this pathway is essential for IFN-suppressive effects on primary malignant erythroid precursors from patients with MPNs in vitro, while increased levels of ULK1 and p38 MAPK correlate with clinical response to IFN therapy in MPN patients. IFN treatment also induces cleavage/activation of the ULK1-interacting ROCK1/2 proteins in vivo, triggering a negative feedback loop that suppresses IFN responses. Both ROCK homologs are overexpressed in MPN patients and their genetic or pharmacological inhibition enhances IFN-anti-neoplastic responses in malignant erythroid progenitors from MPN patients. Together, our results identify activation of the PKC-ULK1-p38 MAPK cascade as a key and essential component for the IFN-response, regulated by a feedback loop involving ROCK1/2. These findings suggest the clinical potential of pharmacological inhibition of ROCK1/2 in combination with IFN-therapy for the treatment of MPN patients.
2022-01-10 | PXD021748 | Pride
Project description:We performed all stimulatory experiments using THP1 cell line as a representative of primary human monocytes to show fundamental role of the cfDNA in healthy organisms. The experiments were conducted in duplicates using plasma containing cfDNA (NP) and the reference one with cfDNA removed by DNase (TP) to recognize unequivocally the effect of plasma cfDNA on transcriptome and proteome of monocytes. We used native human plasma samples obtained from healthy volunteers with no animal serum addition to cultivation medium in order to avoid the presence of uncharacterized animal cfDNA in the experiments.
2021-05-18 | PXD017285 | Pride
Project description:Myeloproliferative neoplasms (MPN) are a heterogeneous group of clonal disorders characterized by aberrant hematopoietic proliferation and an intrinsic risk of progression to blast phase. The WHO classification 2022 identifies chronic myeloid leukemia and the BCR::ABL1 negative MPNs polycythemia vera, primary myelofibrosis and essential thrombocythemia as individual entities. However, overlaps, borderline findings or transitions between MPN subtypes occur and incomplete clinical data often complicates diagnosis. By conducting a thorough genetic analysis, we've developed a model that relies on 12 genetic markers to accurately stratify MPN patients. The model can be simplified into a decision tree for routine use. Comparing samples at chronic and blast phase revealed, that one third of patients lost their MPN driver-gene mutation, while mutations in splicing and chromatin modifying genes were stable, indicating a shared founder clone of chronic and blast phase with different driver mutations and therefore different progressing capacities. This was further supported by gain of typical de novo AML gene mutations, accompanied by gain of complex karyotypes and RAS pathway gene mutations. Our data suggest to perform a broader genetic screening at diagnosis and also at clinical progression, as driver mutations may change and the MPN driver mutations present at diagnosis may disappear.
2024-09-20 | GSE277354 | GEO