Gene expression signature of the three major epidermal differentiation compartments: interfollicular epidermis (IFE), hair follicle (HF) and sebaceous gland (SG).
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE62604 | GEO | 2017/05/16
SECONDARY ACCESSION(S): PRJNA264531
REPOSITORIES: GEO
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Project description:There are multiple stem cells in adult mammalian epidermis, but the mechanisms controlling lineage specification are poorly understood. To identify gene expression signatures of the three major epidermal differentiation compartments we micro-dissected individual SG, IFE and HF from adult epidermis. The RNA was isolated from age and sex matched wild-type mice and performed transcriptome analysis with Affymetrix Exon microarrays We micro-dissected individual interfollicular epidermis (IFE), hair follicle (HF) and sebaceous gland (SG) from adult tail epidermis. The RNA was isolated from age and sex matched wild-type mice. Three biological replicates for each epidermal differentiation compartment were analyzed.
2017-05-16 | E-GEOD-62604 | biostudies-arrayexpress
Project description:The skin epidermis is a highly compartmentalised tissue consisting of a cornifying epithelium called the interfollicular epidermis (IFE) and associated hair follicles (HFs). Several stem cell populations have been described that mark specific sub compartments in the skin but none of them is IFE-specific. Here we identify Troy as a marker of IFE and HF infundibulum basal layer cells in embryonic and adult human and mouse epidermis. Genetic lineage-tracing experiments demonstrate that Troy-expressing basal cells contribute to long-term renewal of all layers of the cornifying epithelium. Single-cell transcriptomics and organoid assays of Troy-expressing cells as well as their progeny confirmed stem cell identity as well as the ability to generate differentiating daughter cells. In conclusion, we define Troy as a marker of epidermal basal cells that govern interfollicular epidermal renewal and cornification.
2021-08-05 | GSE165379 | GEO
Project description:The epidermis consists of different compartments such as the hair follicle (HF), sebaceous gland (SG) and interfollicular epidermis (IFE), each containing distinct stem cell (SC) populations. However, with the exception of the SCs residing within the HF bulge, other epidermal SC populations remain poorly characterized at the molecular level. Here we used an epigenomic strategy that combines H3K27me3 ChIP-seq and RNA-seq profiling to identify major regulators of HFSC located outside the bulge. When applied to the bulk of HFSC isolated from mouse skin our approach identified both previously known and potentially novel non-bulge HFSC regulators. Among the latter, we found that PRDM16 was preferentially expressed within the Junctional Zone (JZ). To investigate PRDM16 function within the JZ SCs, we generated an epidermal-specific Prdm16 Knock-out mouse model (K14-Cre-Prdm16fl/fl). Notably, although these K14-Cre-Prdm16fl/fl mice did not show any major skin or hair abnormalities, the homeostasis of the SG was clearly compromised. Namely, PRDM16 deficient mice displayed enlarged SGs and excessive sebum production, thus resembling some of the features associated with certain human conditions (i.e. acne, sebaceous hyperplasia). Overall, our study provides a list of putative novel regulators of HFSC outside the bulge and identifies PRDM16 as a major regulator of SG homeostasis.
2021-03-26 | GSE169647 | GEO
Project description:The epidermis consists of different compartments such as the hair follicle (HF), sebaceous gland (SG) and interfollicular epidermis (IFE), each containing distinct stem cell (SC) populations. However, with the exception of the SCs residing within the HF bulge, other epidermal SC populations remain poorly characterized at the molecular level. Here we used an epigenomic strategy that combines H3K27me3 ChIP-seq and RNA-seq profiling to identify major regulators of HFSC located outside the bulge. When applied to the bulk of HFSC isolated from mouse skin our approach identified both previously known and potentially novel non-bulge HFSC regulators. Among the latter, we found that PRDM16 was preferentially expressed within the Junctional Zone (JZ). To investigate PRDM16 function within the JZ SCs, we generated an epidermal-specific Prdm16 Knock-out mouse model (K14-Cre-Prdm16fl/fl). Notably, although these K14-Cre-Prdm16fl/fl mice did not show any major skin or hair abnormalities, the homeostasis of the SG was clearly compromised. Namely, PRDM16 deficient mice displayed enlarged SGs and excessive sebum production, thus resembling some of the features associated with certain human conditions (i.e. acne, sebaceous hyperplasia). Overall, our study provides a list of putative novel regulators of HFSC outside the bulge and identifies PRDM16 as a major regulator of SG homeostasis.
2021-03-26 | GSE169648 | GEO
Project description:The skin interfollicular epidermis (IFE) is the first barrier against the external environment and its maintenance is critical for survival. Two seemingly opposite theories have been proposed to explain IFE homeostasis. One posits that IFE is maintained by a long-lived slow-cycling stem cell (SC) population that give rise to short-lived transit-amplifying (TA) cell progeny, while the other suggests that homeostasis is achieved by a single committed progenitor (CP) that balances stochastic fate. Here, we probed the cellular heterogeneity within the IFE using two different inducible CREER targeting IFE progenitors. Quantitative analysis of clonal fate data and proliferation dynamics demonstrate the existence of two distinct proliferative cell compartments composed of slow-cycling SC and CP, both of which undergo population asymmetric self-renewal. However, following wounding, only SCs contribute substantially to the repair and long-term regeneration of the tissue, while CP cells make a minimal and transient contribution. Transcriptional profile of InvCREER/RosaYFP and K14CREER/RosaYFP targeted FACS-isolated alpha6 integrin-high CD34-neg basal cells from mouse tail epidermis. Skin epidermis was removed from tail bone and incubated overnight in HBSS (Gibco) 0.25% trypsin (Gibco) at 4M-BM-0C. Epidermis was separated from the dermis and incubated on a rocking plate (100 rpm) at room temperature for 5 min. Basal cells were mechanically separated from the epidermis by flushing 10 times under the epidermis. Tissues were then cut in pieces of 1 mm2 with scalpel, and trypsin was neutralized by adding DMEM medium (Gibco) supplemented with 2% Chelex Fetal Calf Serum (FCS). Samples were filtrated on 70 and 40M-BM-5m filter (Falcon). Immunostaining was performed using biotin-conjugated anti-CD34 (clone RAM34; BD Biosciences) PE-conjugated anti-M-NM-16-integrin (clone GoH3; BD biosciences). Primary antibodies were washed with 2% FCS/PBS and cells were incubated for 30 min in APC conjugated streptavidin (BD Biosciences) secondary antibodies, on ice, with shaking every 10 min. Living K14- and involucrin-expressing epidermal cells were gated by forward scatter, side scatter, negative staining for Hoechst dye and by following the YFP signal. Basal cells from the interfollicular epidermis were targeted using CD34 negative alpha 6 high gating. Fluorescence-activated cell sorting analysis was performed using FACSAria I at high pressure (70 psi) and FACSDiva software (BD Biosciences). Sorted cells were harvested directly in the lysis buffer provided by the RNeasy microkit (QIAGEN) supplemented with 1M-BM-5l of beta-mercaptoethanol for every 100M-BM-5l of lysis buffer. RNA extraction was performed on freshly sorted cells according to the manufacturerM-bM-^@M-^Ys protocol.
2012-09-07 | E-GEOD-36688 | biostudies-arrayexpress
Project description:The skin interfollicular epidermis (IFE) is the first barrier against the external environment and its maintenance is critical for survival. Two seemingly opposite theories have been proposed to explain IFE homeostasis. One posits that IFE is maintained by a long-lived slow-cycling stem cell (SC) population that give rise to short-lived transit-amplifying (TA) cell progeny, while the other suggests that homeostasis is achieved by a single committed progenitor (CP) that balances stochastic fate. Here, we probed the cellular heterogeneity within the IFE using two different inducible CREER targeting IFE progenitors. Quantitative analysis of clonal fate data and proliferation dynamics demonstrate the existence of two distinct proliferative cell compartments composed of slow-cycling SC and CP, both of which undergo population asymmetric self-renewal. However, following wounding, only SCs contribute substantially to the repair and long-term regeneration of the tissue, while CP cells make a minimal and transient contribution.
2012-09-07 | GSE36688 | GEO
Project description:The epidermis and associated appendages ensure a number of critical functions necessary for survival and social interactions. Perturbations of epidermal stem cell homeostasis lead to a variety of skin diseases affecting humans and dogs. Therefore, the establishment of an in vitro system to investigate canine epidermal stem cells, representing a model for human diseases, is essential. Here we report the establishment and characterization of organoids derived from microdissected canine hair follicles (HFs) and interfollicular epidermal (IFE). Gene and protein expression analysis revealed high mRNA and protein levels of keratin 5 and 14, IFE differentiation markers and intercellular molecules (e.g., keratin 10 and desmoglein), indicating a strong basal cell signature as well as differentiation towards mature epidermis. Key markers of HF stem cells were lacking. This suggests that, independently of the tissue of origin, both organoid lines develop into the same cell type (basal IFE-like keratinocytes). Signaling pathways members important for regulation of HF growth and cycling (such as Wnt, Hh, BMP and Notch) were present in both HF and IFE organoids at low levels. Withdrawal of growth factors (Noggin, R-spondin and FGFs) resulted in upregulation of markers such as KRT16, IVL, KRT17 and SOX9, showing the potential of the organoids to develop towards more differentiated tissue. However, for induction of HF signatures or hair growth, addition of different growth factors or dermal papilla co-culture might be required. Taken together, our in vitro culture system can provide the basis to address hair growth and explore epidermal function/regeneration, allowing us to further investigate pathomechanisms of cutaneous disorders in dogs and potentially human patients.
2018-07-02 | GSE104622 | GEO
Project description:Relative polysomal loading changes for wild type (N2) versus ife-1(bn127) C. elegans strains Strain ife-1(bn127) is null for the gene encoding one of five eIF4E isoforms in the worm, IFE-1. Only this isoform associates with P granules.
2016-01-07 | GSE74459 | GEO
Project description:Relative polysomal loading changes for wild type (N2) versus ife-1(bn127) C. elegans strains Strain ife-1(bn127) is null for the gene encoding one of five eIF4E isoforms in the worm, IFE-1. Only this isoform associates with P granules. Resolution of translating and non-translating mRNAs from WT and mutant worms on 10-45% sucrose gradients. Comparision was by ratios of polysomal content. Please note that each sample data table contains raw signal directly imported from the Affymetrix files and the ratio of signals, P/(NP+P), and fold-changes were further calculated. The TSAA_overview.xls contains more datails about the TSAA procedure and 'complete_data.xlsx' contains complete TSAA data output.
2016-01-07 | E-GEOD-74459 | biostudies-arrayexpress
Project description:To investigate the properties of Sg spent culture supernatant (SCS) on the proliferation of periodontal pathogens and the expression of proinflammatory cytokines by human macrophages, epithelial cells, and gingival fibroblasts.
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