Molecular Analysis and Characteristics of Ethnic Skin
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE54638 | GEO | 2014/07/31
SECONDARY ACCESSION(S): PRJNA237240
REPOSITORIES: GEO
Similar Datasets
Project description:In this study, we used microarray analysis to investigate molecular differences underlying the determination of pigmentation in various skin types, and we used immunohistochemistry to validate the expression patterns of several interesting targets that were identified. Whole skin gene expression profile were investigated in three ethnic groups:1) Caucasian 2)Asian 3)African. In each group, 4 mm whole skin punch biopsies were taken from forearm of 10 subjects, and gene expression level were tested by agilent whole human genome microarray. Samples with mRNA degraded: African_skin_03, Asian_skin_02, Asian_skin_06, and Caucasian_skin_7.
2014-07-31 | E-GEOD-54638 | biostudies-arrayexpress
Project description:We analysed three interesting, rare cases of CAIS (Complete Androgen Insensitivity Syndrome) and report three hitherto undisclosed causes of the disease. Comparative RNA-Seq analysis of CAIS and control samples (3 testicular oligobiopsies from men with normal spermatogenesis) revealed 4,293 significantly deregulated genes.
2019-02-18 | GSE125222 | GEO
Project description:Skin pigmentation is paused following sun exposure, however the mechanism behind this pausing is unknown. Here we found that the UVB-induced DNA repair system, led by the ATM protein kinase, represses MITF transcriptional activity of pigmentation genes while placing MITF in DNA repair mode, thus directly inhibiting pigment production. Phosphoproteomics analysis revealed ATM to be the most significantly enriched pathway among all UVB-induced DNA repair systems. ATM inhibition in mouse or human skin, either genetically or chemically, induces pigmentation. Upon UVB, MITF transcriptional activation is blocked due to ATM dependent phosphorylation of MITF on S414, which modifies MITF activity and interactome towards DNA repair including binding to TRIM28 and RBBP4. Accordingly, MITF genome-occupancy is enriched in sites of high DNA damage that are likely repaired. This suggests that ATM harnesses the pigmentation key activator, for the necessary rapid, efficient DNA repair, thus optimizing the chances of the cell to survive.
2023-07-19 | PXD041121 | Pride
Project description:Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. We identified 1,157 candidate variants influencing skin pigmentation in indigenous Africans by genome-wide association studies and scans of natural selection based on differentiation in allele frequencies between lightly pigmented southern African Khoesan populations and other darkly pigmented African populations. We applied massively parallel reporter and chromosome conformation capture assays to identify novel regulatory variants and their target genes related to skin pigmentation in melanocytic cells. We identified 165 SNPs showing strong differential regulatory activities between alleles. Combining CRISPR-mediated genome editing, transcriptome profiling and melanin assays, we identified causal regulatory variants impacting pigmentation near MFSD12/HMG20B, MITF, OCA2, and DDB1/CYB561A3/TMEM138. We identified CYB561A3 as a novel gene regulating pigmentation by impacting genes involved in oxidative phosphorylation and melanogenesis. Our results broaden our understanding of the genetic basis of human skin color diversity and human adaptation. To identify candidate enhancers and regulatory regions in skin pigmentation, we performed CUT&RUN and ATAC assays in two melanocytic cell lines (MNT-1 and WM88). We used the darkly pigmented MNT-1 cell line because it is widely used for studying skin pigmentation and it has a transcription pattern similar to normal melanocytes. We used the WM88 cell line because the cells are lightly pigmented and may have a different trans-environment (e.g., different levels of transcription factors and open chromatin regions) compared with MNT-1 cells. To identify regulatory regions in MNT-1 cells, we conducted CUT&RUN assays using antibodies against H3K4me3, H3K27ac, MITF and SOX10. We further performed ATAC-seq in both MNT-1 and WM88 cells to identify open chromatin regions.
2023-08-31 | GSE240716 | GEO
Project description:Each senescent FB model exhibited different characteristics. Besides the upregulated expression of natural senescence features, FB-UVB and FB-ATV expressed high levels of senescence-related genes including SASP, and FB-P30 had the greatest similarity with FB-E. However, D-galactose-stimulated FB did not clearly present aging characteristics. It provides references for choosing senescent FB model in studying aging and related skin disease.
2024-04-10 | GSE262932 | GEO
Project description:A better understanding of human melanocyte and melanocyte stem cell (McSC) biology is essential for treating melanocyte-related diseases. This study employed an inherited pigmentation disorder carrying the SASH1S519N variant in a Hispanic family to investigate the SASH1 function in melanocyte lineage and the underlying mechanism for this disorder. We used a multidisciplinary approach, including clinical exams, human cell assays, yeast two-hybrid screening, and biochemical techniques. Results linked early hair graying to the SASH1S519N variant, a previously unrecognized clinical phenotype in hyperpigmentation disorders. We identified SASH1 as a novel regulator in McSC maintenance and discovered that TNKS2 is crucial for SASH1’s role in vitro. Additionally, the S519N variant is located in one of multiple tankyrase binding motifs and alters the binding kinetics and affinity of the interaction. In summary, this disorder showcases accelerated aging in human McSC, linking both gain and loss of pigmentation to McSC dysfunction in the same individuals. The findings offer new insights into the roles of SASH1 and TNKS2 in McSC maintenance and the molecular mechanisms of pigmentation disorders. We propose that a comprehensive clinical evaluation of patients with skin disorders should include an assessment and history of hair pigmentation loss.
2024-06-17 | GSE266293 | GEO
Project description:We investigated the gene expression changes associated with skin pigmentation variation between Virginia opossum populations inhabiting tropical and temperate environments. We found that gene expression variation in genes with melanocytic and immune functions is associated with the degree of skin pigmentation variation. Further, we found evidence suggesting that the Wnt/ß-catenin signaling pathway might be regulating the depigmentation observed in temperate populations. We present several alternative hypotheses that may explain Gloger’s rule pattern of skin pigmentation variation in the Virginia opossum.
2018-03-31 | GSE112562 | GEO
Project description:This work was to study the transcriptome profiles in the skin of chickens with black versus white skin using high-throughput RNA deep-sequencing technology, to investigate the different expression profiles of the genes involved in skin pigmentation, then look for the main differences between black and white skin colors in Lueyang chickens.
2015-05-20 | GSE68460 | GEO
Project description:Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. We identified 1,157 candidate variants influencing skin pigmentation in indigenous Africans by genome-wide association studies and scans of natural selection based on differentiation in allele frequencies between lightly pigmented southern African Khoesan populations and other darkly pigmented African populations. We applied massively parallel reporter and chromosome conformation capture assays to identify novel regulatory variants and their target genes related to skin pigmentation in melanocytic cells. We identified 165 SNPs showing strong differential regulatory activities between alleles. Combining CRISPR-mediated genome editing, transcriptome profiling and melanin assays, we identified causal regulatory variants impacting pigmentation near MFSD12/HMG20B, MITF, OCA2, and DDB1/CYB561A3/TMEM138. We identified CYB561A3 as a novel gene regulating pigmentation by impacting genes involved in oxidative phosphorylation and melanogenesis. Our results broaden our understanding of the genetic basis of human skin color diversity and human adaptation. To decipher the target genes of the MFVs, we performed Hi-C and H3K27ac HiChIP assays in MNT1 cells. Hi-C is a high-throughput method for detecting chromatin interactions at whole genome scale and is often used to identify topologically associating domains (TADs) in the nucleus. H3K27ac HiChIP can identify chromatin interactions enriched for H3K27ac, a histone modification associated with active promoters and enhancers. We performed bridge linker mediated Hi-C and H3K27ac HiChIP using double (Hae3_Alu1) as well as single (Hae3) enzyme digestion in MNT-1 cells.
2023-11-30 | GSE248849 | GEO
Project description:From a clinical and molecular perspective, colon cancer (CC) is a heterogeneous disease but to date no classification based on high-density transcriptome data has been established. The aim of this study was to build up a robust molecular classification of mRNA expression profiles (Affymetrix U133Plus2) of a large series of 443 CC and to validate it on an independent serie of 123 CC and 906 public dataset. We identified and validated six molecular subtypes in this large cohort as a combination of multiple molecular processes that complement current disease stratification based on clinicopathological variables and molecular markers. The biological relevance of these subtypes was consolidated by significant differences in survival. These insights open new perspectives for improving prognostic models and targeted therapies.
2013-05-22 | GSE40966 | GEO