Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1214541 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32089400_1.fastq.gz | Fastqsanger.gz | |||
| SRR32089400_2.fastq.gz | Fastqsanger.gz | |||
| SRR32089401_1.fastq.gz | Fastqsanger.gz | |||
| SRR32089401_2.fastq.gz | Fastqsanger.gz | |||
| SRR32089402_1.fastq.gz | Fastqsanger.gz |
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Project description:Hepatic niche leads to aggressive NK-cell leukemia proliferation
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Project description:NK-cell lymphoma shares strikingly similar molecular features with a distinct subset of gamma-delta T-cell lymphoma. Gene expression profiling of NK-cell lymphoma patient samples was performed to investigate whether molecular signatures can be used to identify entities of peripheral T-cell lymphoma (PTCL) with NK-cell-like features. Gene expression profiling was performed on NK-cell maligancies to examine extranodal NK/T-cell lymphoma (ENKTL) and aggressive NK-cell leukemia (ANKL) and well-characterized cell lines of NK- and T-cell lineages to define molecular classifiers that can distinguish ENKTL from other lymphomas.
2010-03-18 | E-GEOD-19067 | biostudies-arrayexpress
Project description:Gene expression profile of Aggressive NK cell Leukemia (ANKL) cells in liver and spleen microenvironments
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Project description:Immunogenicity of acute myeloid leukemia (AML) keeps changing during tumor evolution, showing a trend that the aggressive AMLs generate through serial transplantations are susceptible to NK cell-mediated tumor suppression. To access molecular differences between the newly developed AML cells and aggressive AML cells generated through serial transplantations, we performed RNA-seq using newly generated mouse AML cells trasduced with MLL-AF9, and the aggressive MLL-AF9 cells obtained after 5 times serial transplantations in the non-irradiated recipient mice.
2023-12-27 | GSE245358 | GEO
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
Project description:Homeobox genes encode transcription factors regulating basic processes in cell differentiation during embryogenesis and in the adult. Recently, we have reported the NKL-code which describes physiological expression patterns of nine NKL homeobox genes in early hematopoiesis and in lymphopoiesis including main stages of T-, B- and NK-cell development. Aberrant activity of NKL homeobox genes is involved in the generation of hematological malignancies including T-cell leukemia. Here, we searched for deregulated NKL homeobox genes in main entities of T-cell lymphomas comprising peripheral T-cell lymphoma (PTCL), angioimmunoblastic T-cell lymphoma (AITL), anaplastic large cell lymphoma (ALCL), adult T-cell leukemia/lymphoma (ATLL), hepatospleenic T-cell lymphoma (HSTL), and NK/T-cell lymphoma (NKTL). Our data revealed in all types altogether 19 aberrantly overexpressed genes, demonstrating that deregulated NKL homeobox genes play a significant role in T-cell lymphomas as well. For detailed analyses we focused on NKL homeobox gene MSX1 which is normally expressed in NK-cells and aberrantly activated in T-cell leukemia. This gene was overexpressed in subsets of HSTL patients and HSTL-derived sister cell lines DERL-2 and DERL-7 which served as models to identify mechanisms of deregulation. We performed genomic and expression profiling and whole genome sequencing and revealed mutated and deregulated gene candidates including the fusion gene CD53-PDGFRB exclusively expressed in DERL-2. Subsequent knockdown experiments allowed the construction of an aberrant network involved in MSX1 deregulation containing chromatin factors AUTS2 and H3B/H3.1, PDGF- and BMP-signalling pathways, and homeobox genes NKX2-2 and PITX1. The gene encoding AUTS2 is located at 7q11 and may represent a basic target of the HSTL hallmark aberration i(7q). Our data indicate both oncogenic and tumor suppressor functions of MSX1 in HSTL, reflecting its activity in early lineage differentiation of T- and NK-cells and the presence of NK-cell like characteristics in malignant HSTL cells. In this context, NKL homeobox gene MSX1 may represent a selective target in HSTL tumor evolution. Together, the data highlight an oncogenic role of deregulated NKL homeobox genes in T-cell lymphoma and identified MSX1 as a novel player in HSTL, involved in aberrant NK- and T-cell differentiation.
2019-11-01 | E-MTAB-7734 | biostudies-arrayexpress
Project description:Somatic STAT5B gain-of-function mutations have been frequently found in patients with T- and NK-cell neoplasms. STAT5BN642H represents the most frequently occuring STAT5B mutation. To investigate the molecular mechanism of STAT5BN642H-driven NK-cell leukemia, we performed RNA-Seq of liver derived FACS-sorted diseased N642HNK/NK and aged non-diseased control (Cre neg, GFPNK/NK), STAT5BNK/NK, N642HNK/NK NK cells.
2024-05-01 | E-MTAB-13797 | biostudies-arrayexpress
Project description:Natural killer (NK) cell function is markedly impaired in acute leukemia patients, weakening their antitumor immune response; however, the specific mechanisms underlying these functional deficits remain incompletely understood. Here, we reveal the critical role of glutathione (GSH) metabolism in maintaining NK cell homeostasis and function. Compared with healthy individuals, NK cells from acute leukemia patients exhibit markedly reduced GSH levels. GSH depletion impairs NK cell cytotoxic activity, cytokine production, and proliferative capacity. Notably, supplementation with glutathione reduced ethyl ester (GSHEE) enhances the antileukemic activity of NK cells. Mechanistically, GSH supports optimal NK cell function by improving mitochondrial function and promoting oxidative phosphorylation (OXPHOS). In summary, this study identifies disrupted GSH metabolism as a driver of NK cell dysfunction in acute leukemia and suggests that GSH supplementation may enhance NK cell-mediated antileukemic effects, offering a potential new strategy for NK cell-based immunotherapy.
2024-11-17 | GSE281768 | GEO
Project description:Large granular lymphocyte leukemia (LGLL) is a rare lymphoproliferative malignancy caused by clonal expansion of granular lymphocytes. Two subgroups, (cytotoxic) T-cell LGLL and natural killer (NK) cell LGLL, are defined based on their cellular origin and expression of characteristic surface molecules. In this study, we performed a comparative proteome profiling of isolated extracellular vesicles (EV) from the T-LGLL cell line MOTN-1 and the NK-LGLL line NKL.
2024-10-17 | PXD053228 | Pride
Project description:Large lymphocytic leukemia (LGL) is a chronic clonal lymphoproliferative disorder, characterized by expansion of cytotoxic CD8+ T-cells or NK-cells. We compared gene expression of 3 LGL leukemia patients with STAT3 mutation (Patients 1, 2, and 3), 3 LGL leukemia patients with STAT5b mutation (Patients 4, 5, and 6), and 2 LGL leukemia patients without STAT3/STAT5b mutation (Patients 7 and 8) with CD8 and NK-cell samples from healthy controls to assess different gene expression patterns between samples.
2013-04-15 | E-MTAB-1611 | biostudies-arrayexpress