Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Role of JunD in macrophage activation under LPS stimulation

ABSTRACT: To investigate the effects of the differences seen in the JUND binding patterns between LEW, WKY and WKY.LCrgn2 bone marrow derived macrophages (BMDMs), we have 1) analysed gene expression changes over a time course (4 time points: 0,2,4 and 8 hrs) of stimulation with lipopolysaccharide (LPS) using whole transcript expression microarrays, 2) knocked down JunD in WKY BMDMs and analysed gene expression by microarrays.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Prashant Srivastava

PROVIDER: E-MEXP-3469 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis.

Srivastava Prashant K PK Hull Richard P RP Behmoaras Jacques J Petretto Enrico E Aitman Timothy J TJ

BMC systems biology 20130922

<h4>Background</h4>Function and efficiency of a transcription factor (TF) are often modulated by interactions with other proteins or TFs to achieve finely tuned regulation of target genes. However, complex TF interactions are often not taken into account to identify functionally active TF-targets and characterize their regulatory network. Here, we have developed a computational framework for integrated analysis of genome-wide ChIP-seq and gene expression data to identify the functional interacti ...[more]

PMID: 24053712

Publication: 1/2

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Project description:In mammals, resident dermal macrophages (MÎ¦s) are subverted by Leishmania (L.) amazonensis amastigotes as host cells permissive for parasite multiplication. These Leishmania are living within a communal parasitophorous vacuole (PV) and are expected to trigger unique MÎ¦ transcriptional signatures. We performed a transcription profiling of mouse MÎ¦s harboring amastigotes to get insights into their reprogramming as host cells for parasite multiplication. BALB/c mouse bone marrow-derived MÎ¦s were either loaded or not with four amastigotes on average. Twenty four hours later, when amastigotes multiply, total RNA from MÎ¦ cultures was prepared, amplified and hybridized onto Affymetrix Mouse430_2 GeneChipsÂ®. The outcome recorded a total of 1,248 probe-sets showing significant differential expression. Comparable fold-change values for a handful of genes were obtained between Affymetrix technology and the more sensitive RTqPCR method. Ingenuity Pathway Analysis softwareÂ® pinpointed the up-regulation of the sterol biosynthesis pathway (P-value = 1.31e-02) involving several genes (1.95 to 4.30 fold-change values), and the modulation of various genes involved in polyamine synthesis and in pro/counter-inflammatory signaling. Our findings suggest that amastigotes exploit the MÎ¦ lipid and polyamine pathways to multiply efficiently, and induce a counter-inflammatory environment to expand their dermis niche. Experiment Overall Design: Mice, MÎ¦s and amastigotes: Experiment Overall Design: Swiss nu/nu and BALB/c mice were used (following National Scientific Ethics Committee guidelines) for L. amazonensis (LV79 strain, MPRO/BR/1972/M1841) amastigote propagation and to prepare bone marrow-derived MÎ¦s, respectively. Amastigotes were added at a multiplicity of 4 amastigotes per MÎ¦. Parasite-harboring MÎ¦s (>98%; samples I1, I2 and I3) and parasite-free ones (samples UI1, UI2 and UI3) were cultured at 34Â°C (LV79 permissive temperature) for 24h. Experiment Overall Design: Real-time quantitative PCR: Experiment Overall Design: Total RNA from various biological samples including those used for hybridization experiments were reverse transcribed into cDNA using random hexamers (Roche Diagnostics) and Moloney Murine Leukemia Virus Reverse Transcriptase (Invitrogen Life Technologies). RTqPCR was performed using LightCycler-480 system (Roche) with primers designed with LightCycler Probe Design 1.0 software.Target genes primer sequences, amplicon melting temperatures and amplification efficiencies are available upon request. Gene expression analysis using qBase program allowed determining the normalized relative quantities between parasite-free and parasite-harboring MÎ¦s.

Dataset Information

Role of JunD in macrophage activation under LPS stimulation

Publications

JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis.

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