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Genomic characterization of clones derived from a murine acute myeloid leukemia cell line for the description of genes involved in immunogenicity (dataset 2)

ABSTRACT: The goal of this study was to determine the effects of gene deletions and duplications on acute myeloid leukemia cells immunogenicity. The Clones were derived from the C1498 AML cell line. Lymphocytes were isolated from the C57BL/6 mouse strain. Genome profiling of mouse single cell clones originating from an acute myeloid leukemia cell line compared to control T lymphocytes from the same murine strain.

ORGANISM(S): Mus musculus

SUBMITTER: frédéric leprêtre

PROVIDER: E-GEOD-55354 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genomic characterization of clones derived from a murine acute myeloid leukemia cell line for the description of genes involved in immunogenicity (dataset 1)

Project description:The goal of this study was to determine the effects of gene deletions and duplications on acute myeloid leukemia cells immunogenicity. The Clones were derived from the C1498 AML cell line. Lymphocytes were isolated from the C57BL/6 mouse strain. Genome profiling of mouse single cell clones originating from an acute myeloid leukemia cell line compared to control T lymphocytes from the same murine strain.

2015-02-25 | E-GEOD-55353 | biostudies-arrayexpress

Genomic characterization of clones derived from a murine acute myeloid leukemia cell line for the description of genes involved in immunogenicity (dataset 2)

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Genomic characterization of clones derived from a murine acute myeloid leukemia cell line for the description of genes involved in immunogenicity (dataset 1)

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NUP98RARG gene fusion

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Project description:Except for the well-known association with Down syndrome, there is little information on the genetic factors predisposing to acute myeloid leukemia. Germinal gene copy-number variations may represent risk factors for the disease. To identify copy number variants present in both normal and leukemic cells, we compared the Comparative Genomic Hybridization profiles of the blasts and healthy cells (CD3+ cells or peripheral lymphocytes during remission) of 13 patients (SET-A) and the blasts of a further 12 normal-karyotype acute myeloid leukemia patients (SET-B) for which only blasts DNA were available.

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Project description:The ETCTN 10026 study tested decitabine and ipilimumab for transplant-naive advanced myelodysplastic syndrome/acute myeloid leukemia and relapsed acute myeloid leukemia after allogeneic hematopoietic stem cell transplantation. Using single cell RNA sequencing, determinants of response (higher T/NK to myeloid cell ratio in responders) and resistance (insufficient clearance of AML clones) were identified and pharmacodynamics of decitabine (cytoreduction) and ipilimumab (increase in regulatory T cells) characterized.

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Affymetrix SNP array data for NUP98 rearranged acute leukemias

Project description:We assessed lineage involvement by NUP98 translocations in myelodysplastic syndromes (MDS), acute myeloid leukemia (AML), and T-cell acute lymphoblastic leukemia (T-ALL). Single cell analysis by FICTION (Fluorescence Immunophenotype and Interphase Cytogenetics as a Tool for Investigation of Neoplasms) showed that NUP98-translocations with various partners, i.e. NSD1, DDX10, RAP1GDS1, and LNP1, always affected a CD34+/CD133+ hematopoietic precursor. Interestingly, in MDS/AML myelomonocytes, erythroid cells, B- and T- lymphocytes belonged to the abnormal clone, while in T-ALL only CD7+/CD3+ cells were involved. The partner did not appear to play a major role in determining the leukemia phenotype as shown in AML and T-ALL with the same NUP98-RAP1GDS1 fusion. Additional hits, namely mutations of FLT3 and CEBPA in MDS/AML and mutation of NOTCH1 plus MYB duplication in T-ALL, were identified in leukemias with, respectively, myeloid or T-lymphoid phenotype. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples. Copy number and Copy neutral LOH analysis of with Affymetrix Cytogenetic 2.7 and Cytoscan HD SNP arrays was performed on 6 NUP98 rearranged leukemias.

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CENAT-AML-experiment1

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