Transcriptome analysis of human Natural Killer (NK) cells overexpressing the transcription factor RUNX2-I isoform.
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PROVIDER: PRJNA723308 | ENA |
REPOSITORIES: ENA
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Project description:Research has already gained much insight into the roles of various members of the RUNX family of transcription factors in the development of human T- and B-cells, however the importance in human NK cell development remains unclear. In this study we discovered that NK cells predominantly express the shorter of the two principal isoforms of RUNX2, also referred to as RUNX2-I. Therefore, we overexpressed the RUNX2-I isoform in human umbilical cord blood-derived hematopoietic progenitor cells (HPC) and cultured them in vitro in an NK cell differentiation model. On day 14 of culture (CD56+CD94+) NK cells from RUNX2-I overexpression and control cultures were sorted, after which mRNA was isolated and transcriptome analysis was performed by RNA sequencing. Evaluation of the transcriptome in these NK cells could reveal the molecular mechanisms of the RUNX2-I isoform.
2022-06-03 | GSE172436 | GEO
Project description:RUNX2-specific human Natural Killer (NK) cells
| PRJNA723303 | ENA
Project description:Research has already gained much insight into the roles of various members of the RUNX family of transcription factors in the development of human T- and B-cells, however the importance in human NK cell development remains unclear. Therefore, we transduced a shRNA that specifically binds to all known RUNX2 isoforms in human umbilical cord blood-derived hematopoietic progenitor cells (HPC) and cultured them in vitro in an NK cell differentiation model. On day 21 of culture (CD56+CD94+) NK cells from shRNA and control cultures were sorted, after which mRNA was isolated and transcriptome analysis was performed by RNA sequencing. Evaluation of the transcriptome in these NK cells could reveal the molecular mechanisms of RUNX2.
2022-06-03 | GSE172435 | GEO
Project description:Transcriptome analysis of human Natural Killer (NK) cells expressing a RUNX2-specific shRNA.
| PRJNA723309 | ENA
Project description:Natural killer (NK) cells represent one of three lymphoid lineages and play a vital role in controlling viral infections and cancer. In contrast to B and T lymphopoiesis where cellular and regulatory pathways have been extensively characterized, the cellular stages of early human NK-cell commitment remain poorly understood Here we described a novel NK-lineage restricted progenitor (NKP) in fetal development, umbilical cord blood and adult bone marrow. We used microarrays to detail the global programme of gene expression genes of this new progenitor. Global gene expression analysis was performed on the NKP, multipotent progenitors LMPP, common lymphoid progenitor candidate and mature NK cells purified from Cord blood CD34+ cells (3-4 replicates, 2 experiments)
2015-09-01 | E-GEOD-60448 | biostudies-arrayexpress
Project description:In order to gain a better understanding of gene expression during early malaria infection, we conducted microarray analysis of early blood responses in mice infected with erythrocytic stage Plasmodium chabaudi. Immediately following infection, we observed coordinated and sequential waves of immune responses, with interferon-associated gene transcripts dominating by 16 hours post-infection, followed by strong increases in natural killer (NK) cell-associated and MHC class I-related transcripts by 32 hours post-infection. We hypothesized that the observed elevation in NK cell-associated transcripts could be the result of a dramatic increase in the proportion of NK cells in the blood during infection, which we confirmed by flow cytometry. Subsequent microarray analysis of NK cells isolated from the peripheral blood of infected mice revealed a cell proliferation expression signature consistent with the observation that NK cells replicate in response to infection. Early proliferation of NK cells was directly observed in studies with adoptively transferred cells in infected mice. These data indicate that the early response to P. chabaudi infection of the blood is marked by a primary wave of interferon with a subsequent response by NK cells. Keywords: murine NK cell response to Plasmodium chabaudi infection We analyzed a series of 10 MEEBO arrays on which were hybed RNA amplified from NK cells of C57BL/6 mice either mock-infected or infected with P. chabaudi AS.
2010-05-19 | E-GEOD-12727 | biostudies-arrayexpress
Project description:Natural killer (NK) cells belong to the innate immune system where they can control virus infections and developing tumors by cytotoxicity and production of inflammatory cytokines. Most studies of mouse NK cells, however, have focused on conventional NK (cNK) cells found in the spleen. Recently, we described two populations of NK cells within the liver, tissue-resident NK (trNK) cells and those resembling splenic cNK cells. However, the lineage relationship of trNK to cNK cells was unclear because trNK cells display a phenotype associated with immature, developing cNK cells. Moreover, liver trNK cells could be related to thymic NK cells or alternatively, a lineage distinct from both cNK and thymic NK cells. Herein we used detailed transcriptomic, flow cytometric, and functional analysis of mice deficient in several transcription factors to determine that liver trNK cells form a distinct lineage from cNK and thymic NK cells, especially because they do not require NFIL3 (E4BP4), the previously described NK cellspecification factor. Analysis of other tissues indicate the presence of trNK cells in skin and uterus with different transcription factor requirements. Thus, there are at least four distinct lineages of NK cells: cNK, thymic, liver (and skin) trNK, and uterine trNK cells. Liver NK 1.1+CD49+, liver NK 1.1+CD49-, spleen NK 1.1+ CD49- populations of NK cells were sorted with FACS pooling cells from individual mice to end up with ~100k cells for each samples. mRNA was derived from lysates using Invitrogen oligo-dT beads
2014-04-26 | E-GEOD-52043 | biostudies-arrayexpress
Project description:Natural killer (NK) cells belong to the innate immune system where they can control virus infections and developing tumors by cytotoxicity and production of inflammatory cytokines. Most studies of mouse NK cells, however, have focused on conventional NK (cNK) cells found in the spleen. Recently, we described two populations of NK cells within the liver, tissue-resident NK (trNK) cells and those resembling splenic cNK cells. However, the lineage relationship of trNK to cNK cells was unclear because trNK cells display a phenotype associated with immature, developing cNK cells. Moreover, liver trNK cells could be related to thymic NK cells or alternatively, a lineage distinct from both cNK and thymic NK cells. Herein we used detailed transcriptomic, flow cytometric, and functional analysis of mice deficient in several transcription factors to determine that liver trNK cells form a distinct lineage from cNK and thymic NK cells, especially because they do not require NFIL3 (E4BP4), the previously described NK cellspecification factor. Analysis of other tissues indicate the presence of trNK cells in skin and uterus with different transcription factor requirements. Thus, there are at least four distinct lineages of NK cells: cNK, thymic, liver (and skin) trNK, and uterine trNK cells. Liver DX5-CD49+, liver DX5+CD49-, spleen DX5+ CD49- populations of NK cells were sorted with FACS pooling cells from individual mice to end up with ~100k cells for each samples. mRNA was derived from lysates using Invitrogen oligo-dT beads
2014-04-26 | E-GEOD-52045 | biostudies-arrayexpress
Project description:Research has already gained much insight into the roles of various members of the RUNX family of transcription factors in the development of human T- and B-cells, however the importance in human NK cell development remains unclear. We performed a ChIP-Seq analysis with a RUNX2-specific antibody on sorted human peripheral blood NK cells (CD3- CD19- CD56+) to shed more light onto the genes that are under control of RUNX2 in this cell type.
2022-06-03 | GSE172434 | GEO
Project description:Natural killer (NK) cells represent one of three lymphoid lineages and play a vital role in controlling viral infections and cancer. In contrast to B and T lymphopoiesis where cellular and regulatory pathways have been extensively characterized, the cellular stages of early human NK-cell commitment remain poorly understood Here we described a novel NK-lineage restricted progenitor (NKP) in fetal development, umbilical cord blood and adult bone marrow. We used microarrays to detail the global programme of gene expression genes of this new progenitor.
2015-09-01 | GSE60448 | GEO