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Gene expression in uninvolved and involved lesional epidermis from human skin biopsies from patients with atopic dermatitis (laser capture microdissection)

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE111055 | GEO | 2019/06/30

REPOSITORIES: GEO

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Gene expression in uninvolved and involved epidermis from patients with atopic dermatitis (laser capture microdissection): set 2

Project description:We performed microarray analysis on laser-microdissected epidermis from patients with atopic dermatitis to identify genes dysregulated in uninvolved and involved lesional epidermis

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Gene expression in uninvolved and involved epidermis from patients with atopic dermatitis (laser capture microdissection): set 1

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Gene expression in uninvolved and involved lesional epidermis from human skin biopsies from patients with atopic dermatitis (laser capture microdissection)

Project description:Gene expression in uninvolved and involved lesional epidermis from human skin biopsies from patients with atopic dermatitis (laser capture microdissection)

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Gene expression in uninvolved and involved epidermis from patients with atopic dermatitis (laser capture microdissection): set 1

Project description:Gene expression in uninvolved and involved epidermis from patients with atopic dermatitis (laser capture microdissection): set 1

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Gene expression in uninvolved and involved epidermis from patients with atopic dermatitis (laser capture microdissection): set 2

Project description:Gene expression in uninvolved and involved epidermis from patients with atopic dermatitis (laser capture microdissection): set 2

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Gene expression in healthy and lesional psoriatic epidermis from human skin biopsies (laser capture microdissection): set 2

Project description:We performed microarray analysis on laser-microdissected epidermis from healthy volunteers and psoriatic patients to identify genes dysregulated in lesional psoriatic epidermis

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Identification of novel immune and barrier genes in atopic dermatitis by means of laser capture microdissection.

Project description:BackgroundThe molecular signature of atopic dermatitis (AD) lesions is associated with TH2 and TH22 activation and epidermal alterations. However, the epidermal and dermal AD transcriptomes and their respective contributions to abnormalities in respective immune and barrier phenotypes are unknown.ObjectiveWe sought to establish the genomic profile of the epidermal and dermal compartments of lesional and nonlesional AD skin compared with normal skin.MethodsLaser capture microdissection was performed to separate the epidermis and dermis of lesional and nonlesional skin from patients with AD and normal skin from healthy volunteers, followed by gene expression (microarrays and real-time PCR) and immunostaining studies.ResultsOur study identified novel immune and barrier genes, including the IL-34 cytokine and claudins 4 and 8, and showed increased detection of key AD genes usually undetectable on arrays (ie, IL22, thymic stromal lymphopoietin [TSLP], CCL22, and CCL26). Overall, the combined epidermal and dermal transcriptomes enlarged the AD transcriptome, adding 674 upregulated and 405 downregulated differentially expressed genes between lesional and nonlesional skin to the AD transcriptome. We were also able to localize individual transcripts as primarily epidermal (defensin, beta 4A [DEFB4A]) or dermal (IL22, cytotoxic T-lymphocyte antigen 4 [CTLA4], and CCR7) and link their expressions to possible cellular sources.ConclusionsThis is the first report that establishes robust epidermal and dermal genomic signatures of lesional and nonlesional AD skin and normal skin compared with whole tissues. These data establish the utility of laser capture microdissection to separate different compartments and cellular subsets in patients with AD, allowing localization of key barrier or immune molecules and enabling detection of gene products usually not detected on arrays.

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Laser capture microdissection for transcriptomic profiles in human skin biopsies.

Project description:BackgroundThe acquisition of reliable tissue-specific RNA sequencing data from human skin biopsy represents a major advance in research. However, the complexity of the process of isolation of specific layers from fresh-frozen human specimen by laser capture microdissection, the abundant presence of skin nucleases and RNA instability remain relevant methodological challenges. We developed and optimized a protocol to extract RNA from layers of human skin biopsies and to provide satisfactory quality and amount of mRNA sequencing data.ResultsThe protocol includes steps of collection, embedding, freezing, histological coloration and relative optimization to preserve RNA extracted from specific components of fresh-frozen human skin biopsy of 14 subjects. Optimization of the protocol includes a preservation step in RNALater® Solution, the control of specimen temperature, the use of RNase Inhibitors and the time reduction of the staining procedure. The quality of extracted RNA was measured using the percentage of fragments longer than 200 nucleotides (DV200), a more suitable measurement for successful library preparation than the RNA Integrity Number (RIN). RNA was then enriched using the TruSeq® RNA Access Library Prep Kit (Illumina®) and sequenced on HiSeq® 2500 platform (Illumina®). Quality control on RNA sequencing data was adequate to get reliable data for downstream analysis.ConclusionsThe described implemented and optimized protocol can be used for generating transcriptomics data on skin tissues, and it is potentially applicable to other tissues. It can be extended to multicenter studies, due to the introduction of an initial step of preservation of the specimen that allowed the shipment of biological samples.

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Creation of differentiation-specific genomic maps of human epidermis through laser capture microdissection.

Project description: Not available

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