Dataset Information

Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis.

ABSTRACT: The MC1R gene plays a crucial role in pigmentation synthesis. Loss-of-function MC1R variants, which impair protein function, are associated with red hair color (RHC) phenotype and increased skin cancer risk. Cultured cutaneous cells bearing loss-of-function MC1R variants show a distinct gene expression profile compared to wild-type MC1R cultured cutaneous cells. We analysed the gene signature associated with RHC co-cultured melanocytes and keratinocytes by Protein-Protein interaction (PPI) network analysis to identify genes related with non-functional MC1R variants. From two detected networks, we selected 23 nodes as hub genes based on topological parameters. Differential expression of hub genes was then evaluated in healthy skin biopsies from RHC and black hair color (BHC) individuals. We also compared gene expression in melanoma tumors from individuals with RHC versus BHC. Gene expression in normal skin from RHC cutaneous cells showed dysregulation in 8 out of 23 hub genes (CLN3, ATG10, WIPI2, SNX2, GABARAPL2, YWHA, PCNA and GBAS). Hub genes did not differ between melanoma tumors in RHC versus BHC individuals. The study suggests that healthy skin cells from RHC individuals present a constitutive genomic deregulation associated with the red hair phenotype and identify novel genes involved in melanocyte biology.

SUBMITTER: Puig-Butille JA

PROVIDER: S-EPMC5355288 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

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Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis.

Puig-Butille Joan Anton JA Gimenez-Xavier Pol P Visconti Alessia A Nsengimana Jérémie J Garcia-García Francisco F Tell-Marti Gemma G Escamez Maria José MJ Newton-Bishop Julia J Bataille Veronique V Del Río Marcela M Dopazo Joaquín J Falchi Mario M Puig Susana S

Oncotarget 20170201 7

The MC1R gene plays a crucial role in pigmentation synthesis. Loss-of-function MC1R variants, which impair protein function, are associated with red hair color (RHC) phenotype and increased skin cancer risk. Cultured cutaneous cells bearing loss-of-function MC1R variants show a distinct gene expression profile compared to wild-type MC1R cultured cutaneous cells. We analysed the gene signature associated with RHC co-cultured melanocytes and keratinocytes by Protein-Protein interaction (PPI) netwo ...[more]

PMID: 28030792

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Project description:The investigation of carcass traits to produce meat with high efficiency has been in focus on Japanese Black cattle since 1972. To implement a successful breeding program in carcass production, a comprehensive understanding of genetic characteristics and relationships between the traits is of paramount importance. In this study, genomic heritability and genomic correlation between carcass traits, including carcass weight (CW), rib eye area (REA), rib thickness (RT), subcutaneous fat thickness (SFT), yield rate (YI), and beef marbling score (BMS) were estimated using the genomic data of 9,850 Japanese Black cattle (4,142 heifers and 5,708 steers). In addition, we investigated the effect of genetic relatedness degree on the estimation of genetic parameters of carcass traits in sub-populations created based on different GRM-cutoff values. Genome-based restricted maximum likelihood (GREML) analysis was applied to estimate genetic parameters. Using all animal data, the heritability values for carcass traits were estimated as moderate to relatively high magnitude, ranging from 0.338 to 0.509 with standard errors, ranging from 0.014 to 0.015. The genetic correlations were obtained low and negative between SFT and REA [-0.198 (0.034)] and between SFT and BMS [-0.096 (0.033)] traits, and high and negative between SFT and YI [-0.634 (0.022)]. REA trait was genetically highly correlated with YI and BMS [0.811 (0.012) and 0.625 (0.022), respectively]. In sub-populations created based on the genetic-relatedness ceiling, the heritability estimates ranged from 0.212 (0.131) to 0.647 (0.066). At the genetic-relatedness ceiling of 0.15, the correlation values between most traits with low genomic correlation were overestimated while the correlations between the traits with relatively moderate to high correlations, ranging from 0.380 to 0.811, were underestimated. The values were steady at the ceilings of 0.30-0.95 (sample size of 5,443-9,850) for most of the highly correlated traits. The results demonstrated that there is considerable genetic variation and also favorable genomic correlations between carcass traits. Therefore, the genetic improvement for the traits can be simultaneously attained through genomic selection. In addition, we observed that depending on the degree of relationship between individuals and sample size, the genomic heritability and correlation estimates for carcass traits may be different.

Project description:Several studies demonstrated that in insects cuticle melanism is interrelated with pathogen resistance, as melanin-based coloration and innate immunity possess similar physiological pathways. For some insects, higher pathogen resistance was observed in darker individuals than in individuals with lighter cuticular coloration. Here, we investigated the difference in immune response between two color morphs (black and red) and between the life stages (pupa and adult) of the red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae). Here in this study, cuticle thickness, microbial test (antimicrobial activity, phenoloxidase activity, and hemocyte density), and immune-related gene expression were evaluated at different stages of RPW. Study results revealed that cuticle thickness of black phenotype was thicker than red phenotype at old-pupa stage, while no significant difference found at adult stage. These results may relate to the development processes of epidermis in different stages of RPW. The results of antimicrobial activity, phenoloxidase (PO) activity, and hemocyte density analyses showed that adults with a red phenotype had stronger pathogen resistance than those with a black phenotype. In addition to antimicrobial activity and PO activity, we tested relative gene expression in the fat body of old pupae. The results of hemolymph antimicrobial analysis showed that old pupae with a red phenotype were significantly different from those with a black phenotype at 12 hr after Staphylococcus aureus injection, suggesting that red phenotype pupae were more sensitive to S. aureus. Examination of gene expression in the fat body also revealed that the red phenotype had a higher immune response than the black phenotype. Our results were inconsistent with the previous conclusion that dark insects had increased immune function, suggesting that the relationship between cuticle pigmentation and immune function in insects was not a direct link. Additional possible factors that are associated with the immune response, such as life-history, developmental, physiological factors also need to be considered.

Dataset Information

Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis.

Publications

Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis.

Similar Datasets

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