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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Effect of influenza vaccination on PBMC and B cell gene expression profiles in healthy humans

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Stephen Welle

PROVIDER: E-GEOD-45764 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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High-resolution temporal response patterns to influenza vaccine reveal a distinct human plasma cell gene signature.

Henn Alicia D AD Wu Shuang S Qiu Xing X Ruda Melissa M Stover Michael M Yang Hongmei H Liu Zhiping Z Welle Stephen L SL Holden-Wiltse Jeanne J Wu Hulin H Zand Martin S MS

Scientific reports 20130101

To identify sources of inter-subject variation in vaccine responses, we performed high-frequency sampling of human peripheral blood cells post-vaccination, followed by a novel systems biology analysis. Functional principal component analysis was used to examine time varying B cell vaccine responses. In subjects vaccinated within the previous three years, 90% of transcriptome variation was explained by a single subject-specific mathematical pattern. Within individual vaccine response patterns, a ...[more]

PMID: 23900141

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Changes in gene expression profiles of circulating B cells after influenza vaccination in healthy human subjects

Project description:Daily sampling of peripheral blood from human subjects vaccinated for influenza was done immediately before vaccination and for 10 days after vaccination. In B cells, 90% of transcriptomic variation in subjects who received influenza vaccine within the previous three years was explained by a single temporal pattern unique to the individual. A common set of 742 genes was strongly correlated with the migration of differentiating plasma cell subtypes. Five subjects, 11 time points per subject (pre-vaccination and daily for 10 days post-vaccination)

2013-08-07 | E-GEOD-45734 | biostudies-arrayexpress

Changes in PBMC gene expression profiles after influenza vaccination in healthy human subjects

Project description:Daily sampling of peripheral blood from human subjects vaccinated for influenza was done immediately before vaccination and for 10 days after vaccination. Temporal patterns of gene expression, determined by RNA-seq, in unfractionated PBMC suggested migration of myeloid/dendritic cell lineage cells one day after vaccination. Five subjects, 11 time points per subject (pre-vaccination and daily for 10 days post-vaccination)

2013-08-07 | E-GEOD-45735 | biostudies-arrayexpress

Krüppel-like factor 4 regulates T cell function

Project description:Krüppel-like factor 4 (Klf4), a transcription factor mediating context-dependent activation or repression, plays a key role in maintaining pluripotency of stem cells and in regulating cell differentiation. However, the precise function of Klf4 in T cell development and differentiation is largely unknown. Here we showed that Klf4 was highly expressed in thymocyte subsets and mature T cells, and was rapidly down-regulated in mature T cells after activation. In T cell-specific Klf4 conditional knockout mice, we observed a modest reduction of thymocytes (27%). This was due partly to the loss of Klf4 repression of Cdkn1b expression in thymocytes resulting in decreased proliferation of DN thymocytes. Together, these findings identify Klf4 as a critical regulator in T cell development. Klf4fl/fl mice (Katz et al., 2002) were crossed with CD4-Cre mice (Lee et al., 2001) to generate Klf4fl/fl-CD4-Cre+ (Klf4 conditional knockout in T cells) and Klf4fl/fl-CD4-Cre- (control) mice. Mice used for experiments were between 8 and 10 weeks old. Total RNA was extracted from freshly isolated DP+SP4 thymocytes from 3 KO mice and 3 control mice. RNA samples were labeled and hybridized to Illumina Sentrix MouseRef-8 v2 bead arrays.

2011-06-24 | E-GEOD-24880 | biostudies-arrayexpress

Hedgehog pathway analysis in both CD138+ and B-cells obtained from newly diagnosed Multiple Myeloma patients

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-05-31 | E-GEOD-69000 | biostudies-arrayexpress

Expression data from BM-CD138+, BM B cells and PBL B cells obtained from newly diagnosed Multiple Myeloma patients

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2016-05-31 | E-GEOD-68891 | biostudies-arrayexpress

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2012-11-05 | E-GEOD-38627 | biostudies-arrayexpress

Age-associated Changes in Basal NF-ÎºB Function in Human CD4+ T Lymphocytes via Dysregulation of PI3 Kinase (dataset 1)

Project description:Immune impairment and high circulating level of pro-inflammatory cytokines are landmarks of human aging. However, the molecular basis of immune dysregulation and the source of inflammatory markers remain unclear. Here we demonstrate that in the absence of overt cell stimulation, gene expression mediated by the transcription factor NF-ÎºB is higher in purified and rested human CD4+ T lymphocytes from older compared to younger individuals. This increase of NF-ÎºB -associated transcription includes transcripts for pro-inflammatory cytokines such as IL-1 and chemokines such as CCL2 and CXCL10. We demonstrate that NF-ÎºB up-regulation is cell-intrinsic and mediated in part by phosphatidylinositol 3-kinase (PI3K) activity induced in response to metabolic activity, which can be moderated by rapamycin treatment. Our observations provide direct evidence that dysregulated basal NF-ÎºB activity may contribute to the mild pro-inflammatory state of aging. Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized blood using Ficoll-Paque Plus density gradient centrifugation. CD4+ T cells were obtained by positive selection using anti-human CD4 microbeads. After a 4h incubation at 37ÂºC (5% CO2 incubator), cells were harvested and collected by centrifugation. Total cellular RNA was prepared using Qiagen RNeasy protocols. Labeling and amplification were done with the standard Illumina protocol, and the biotin-labeled cRNA was hybridized to Illumina's HumanRef-8 v2.0 Expression BeadChip. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3. Samples were divided into 2 age groups, young and old, with the cut off at 65 years and above as old.

2015-01-08 | E-GEOD-62331 | biostudies-arrayexpress

Age-associated Changes in Basal NF-ÎºB Function in Human CD4+ T Lymphocytes via Dysregulation of PI3 Kinase (dataset 2)

Project description:Immune impairment and high circulating level of pro-inflammatory cytokines are landmarks of human aging. However, the molecular basis of immune dysregulation and the source of inflammatory markers remain unclear. Here we demonstrate that in the absence of overt cell stimulation, gene expression mediated by the transcription factor NF-ÎºB is higher in purified and rested human CD4+ T lymphocytes from older compared to younger individuals. This increase of NF-ÎºB -associated transcription includes transcripts for pro-inflammatory cytokines such as IL-1 and chemokines such as CCL2 and CXCL10. We demonstrate that NF-ÎºB up-regulation is cell-intrinsic and mediated in part by phosphatidylinositol 3-kinase (PI3K) activity induced in response to metabolic activity, which can be moderated by rapamycin treatment. Our observations provide direct evidence that dysregulated basal NF-ÎºB activity may contribute to the mild pro-inflammatory state of aging. Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized blood using Ficoll-Paque Plus density gradient centrifugation. CD4+ T cells were obtained by positive selection using anti-human CD4 microbeads. After a 4h incubation at 37ÂºC (5% CO2 incubator), cells were harvested and collected by centrifugation. Total cellular RNA was prepared using Qiagen RNeasy protocols. Labeling and amplification were done with the standard Illumina protocol, and the biotin-labeled cRNA was hybridized to Illumina's HumanHT-12 v4 Expression BeadChip. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3. Samples were divided into 2 age groups, young and old, with the cut off at 65 years and above as old.

2015-01-08 | E-GEOD-62332 | biostudies-arrayexpress

Age-associated Changes in Basal NF-ÎºB Function in Human CD4+ T Lymphocytes via Dysregulation of PI3 Kinase (dataset 5)

Project description:Immune impairment and high circulating level of pro-inflammatory cytokines are landmarks of human aging. However, the molecular basis of immune dysregulation and the source of inflammatory markers remain unclear. Here we demonstrate that in the absence of overt cell stimulation, gene expression mediated by the transcription factor NF-ÎºB is higher in purified and rested human CD4+ T lymphocytes from older compared to younger individuals. This increase of NF-ÎºB -associated transcription includes transcripts for pro-inflammatory cytokines such as IL-1 and chemokines such as CCL2 and CXCL10. We demonstrate that NF-ÎºB up-regulation is cell-intrinsic and mediated in part by phosphatidylinositol 3-kinase (PI3K) activity induced in response to metabolic activity, which can be moderated by rapamycin treatment. Our observations provide direct evidence that dysregulated basal NF-ÎºB activity may contribute to the mild pro-inflammatory state of aging. Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized blood using Ficoll-Paque Plus density gradient centrifugation. CD4+ T cells were obtained by positive selection using anti-human CD4 microbeads. To test the effects of drug treatment, 5x10^6 CD4+ T cells were treated with varying concentrations of rapamycin and also LY 294002 in 3 ml of RPMI 1640 medium. Control cells were also created without any added drugs. Cells were incubated for 4h in 5% CO2 at both 37Â°C and 4Â°C. After incubation, cells were harvested and collected by centrifugation. Total cellular RNA was prepared using Qiagen RNeasy protocols. Labeling and amplification were done with the standard Illumina protocol and the biotin-labeled cRNA was hybridized to Illumina's HumanHT-12 V4.0 Expression BeadChip. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.

2015-01-08 | E-GEOD-62375 | biostudies-arrayexpress

Age-associated Changes in Basal NF-ÎºB Function in Human CD4+ T Lymphocytes via Dysregulation of PI3 Kinase (dataset 4)

Project description:Immune impairment and high circulating level of pro-inflammatory cytokines are landmarks of human aging. However, the molecular basis of immune dysregulation and the source of inflammatory markers remain unclear. Here we demonstrate that in the absence of overt cell stimulation, gene expression mediated by the transcription factor NF-ÎºB is higher in purified and rested human CD4+ T lymphocytes from older compared to younger individuals. This increase of NF-ÎºB -associated transcription includes transcripts for pro-inflammatory cytokines such as IL-1 and chemokines such as CCL2 and CXCL10. We demonstrate that NF-ÎºB up-regulation is cell-intrinsic and mediated in part by phosphatidylinositol 3-kinase (PI3K) activity induced in response to metabolic activity, which can be moderated by rapamycin treatment. Our observations provide direct evidence that dysregulated basal NF-ÎºB activity may contribute to the mild pro-inflammatory state of aging. Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized blood using Ficoll-Paque Plus density gradient centrifugation. CD4+ T cells were obtained by positive selection using anti-human CD4 microbeads. To test the effects of serum, 5x10^6 CD4+ T cells in 3 ml of RPMI 1640 with serum or AIM V (Life Technologies, Carlsbad, CA, USA) serum-free medium were held at 4Â°C or incubated for 4h at 37ÂºC (5% CO2 incubator). After incubation, cells were harvested and collected by centrifugation. Total cellular RNA was prepared using Qiagen RNeasy protocols. Labeling and amplification were done with the standard Illumina protocol and the biotin-labeled cRNA was hybridized to Illumina's HumanHT-12 V4.0 Expression BeadChip. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.

2015-01-08 | E-GEOD-62374 | biostudies-arrayexpress

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