Transcriptome sequencing of neonatal thymic epithelial cells

St-Pierre, Charles; Brochu, Sylvie; Vanegas, Juan Ruiz; Dumont-Lagacé, Maude; Lemieux, Sébastien; Perreault, Claude

doi:10.1038/srep01860

Cited by 66 publications

(72 citation statements)

References 60 publications

(91 reference statements)

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“…Additionally, fatty acid binding protein 4 (FABP4) was significantly up-regulated (fourfold) in GMCSF ϩ IL4-treated monocytes while slightly down-regulated (Ϫ1.7-fold) in GMCSFtreated monocytes. We used the IPA regulation z-score algorithm to identify biological functions associated with lipid metabolism pathways as previously described (28). Fig.…”

Section: Analysis Of Protein Expression In Differentiated Monocytes-mentioning

confidence: 99%

Quantitative Proteomics Reveals a Role for Epigenetic Reprogramming During Human Monocyte Differentiation

Nicholas

Tang²,

Zhang

et al. 2015

Molecular & Cellular Proteomics

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The differentiation of monocytes into macrophages and dendritic cells involves mechanisms for activation of the innate immune system in response to inflammatory stimuli, such as pathogen infection and environmental cues. Epigenetic reprogramming is thought to play an important role during monocyte differentiation. Complementary to cell surface markers, the characterization of monocytic cell lineages by mass spectrometry based protein/histone expression profiling opens a new avenue for studying immune cell differentiation. Here, we report the application of mass spectrometry and bioinformatics to identify changes in human monocytes during their differentiation into macrophages and dendritic cells. Our data show that linker histone H1 proteins are significantly down-regulated during monocyte differentiation. Although highly enriched H3K9-methyl/S10-phos/K14-acetyl tri-modification forms of histone H3 were identified in monocytes and macrophages, they were dramatically reduced in dendritic cells. In contrast, histone H4 K16 acetylation was found to be markedly higher in dendritic cells than in monocytes and macrophages. We also found that global hyperacetylation generated by the nonspecific histone deacetylase HDAC inhibitor Apicidin induces monocyte differentiation. Together, our data suggest that specific regulation of inter-and intra-histone modifications including H3 K9 methylation, H3 S10 phosphorylation, H3 K14 acetylation, and H4 K16 acetylation must occur in concert with chromatin remodeling by linker histones for cell cycle progression and differentiation of human myeloid cells into macrophages and dendritic cells. Molecular & Cellular

show abstract

Section: Analysis Of Protein Expression In Differentiated Monocytes-mentioning

confidence: 99%

Quantitative Proteomics Reveals a Role for Epigenetic Reprogramming During Human Monocyte Differentiation

Nicholas

Tang²,

Zhang

et al. 2015

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

show abstract

“…Transcriptome libraries were generated from 4 mg total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer's protocols. Paired-end (2 3 100 bp) sequencing was performed using an Illumina HiSeq2000 sequencer running TruSeq SBS v3 chemistry (Illumina) as previously described (18). Cluster density was targeted at ∼600,000-800,000 clusters/mm 2 .…”

Section: Rna Sequencingmentioning

confidence: 99%

Immunoproteasomes Shape the Transcriptome and Regulate the Function of Dendritic Cells

Verteuil

Rouette

Hardy

et al. 2014

The Journal of Immunology

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By regulating protein degradation, constitutive proteasomes (CPs) control practically all cellular functions. In addition to CPs, vertebrates express immunoproteasomes (IPs). The major nonredundant role ascribed to IPs is their enhanced ability to generate antigenic peptides. We report that CPs and IPs differentially regulate the expression of >8000 transcripts in maturing mouse dendritic cells (DCs) via regulation of signaling pathways such as IFN regulatory factors, STATs, and NF-κB. IPs regulate the transcription of many mRNAs and maturation of a few of them. Moreover, even when engineered to present optimal amounts of antigenic peptide, IP-deficient DCs are inefficient for in vivo T cell priming. Our study shows that the role of IPs in DCs is not limited to Ag processing and reveals a major nonredundant role for IPs in transcription regulation. The dramatic effect of IPs on the transcriptional landscape could explain the various immune and nonimmune phenotypes observed in vertebrates with IP deficiency or mutations.

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“…Second, we reasoned that the function of MCs might be influenced by the nature of their neighboring parenchymal cells: thymic and skin MCs have to support epithelial cells, whereas thymic and bone MCs have to support hematolymphoid cells. The transcriptome is a critical component of systems-level understanding of cell biology, and it can be reliably tackled in its entirety using relatively modest cell numbers (14). In the last decade, studies by the Immunological Genome Project (http://www.immgen.…”

mentioning

confidence: 99%

Thymic Mesenchymal Cells Have a Distinct Transcriptomic Profile

Patenaude

Perreault

2016

The Journal of Immunology

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In order to understand the role of mesenchymal cells (MCs) in the adult thymus, we performed whole transcriptome analyses of primary thymic, bone, and skin MCs. These three MC populations shared expression of 2850 core MC genes involved in generic processes including interactions with tissue-resident macrophages. Moreover, we discovered that 2036 genes were differentially expressed, by at least 5-fold, in the three MC populations. Genes preferentially expressed in thymic MCs are instrumental in clearance of apoptotic thymocytes by macrophages, maintenance of a noninflammatory milieu, and attraction-expansion of thymocyte progenitors. Thymic and bone MCs share other sets of differentially expressed genes implicated in resolution of inflammation and expansion of hematolymphoid progenitors. Consistent with the fact that thymic and skin MCs have to support epithelial cells, they express at higher levels genes mediating epithelial cell adhesion to basement membrane and mesenchymal–epithelial cross-talk. Differentially expressed genes preferentially expressed by bone MCs are connected to formation and remodeling of bone, whereas those preferentially expressed in skin MCs are involved in skin and hair follicle homeostasis. We conclude that MCs from different organs display substantial heterogeneity and that the transcriptome of thymic MCs is exquisitely suited for interactions with epithelial and hematolymphoid cells in an environment with a high apoptosis rate.

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Transcriptome sequencing of neonatal thymic epithelial cells

Cited by 66 publications

References 60 publications

Quantitative Proteomics Reveals a Role for Epigenetic Reprogramming During Human Monocyte Differentiation

Quantitative Proteomics Reveals a Role for Epigenetic Reprogramming During Human Monocyte Differentiation

Immunoproteasomes Shape the Transcriptome and Regulate the Function of Dendritic Cells

Thymic Mesenchymal Cells Have a Distinct Transcriptomic Profile

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