Oncotarget

Research Papers:

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

Joan Anton Puig-Butille _, Pol Gimenez-Xavier, Alessia Visconti, Jérémie Nsengimana, Francisco Garcia-García, Gemma Tell-Marti, Maria José Escamez, Julia Newton-Bishop, Veronique Bataille, Marcela del Río, Joaquín Dopazo, Mario Falchi and Susana Puig

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Oncotarget. 2017; 8:11589-11599. https://doi.org/10.18632/oncotarget.14140

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Abstract

Joan Anton Puig-Butille1, Pol Gimenez-Xavier2, Alessia Visconti3, Jérémie Nsengimana4, Francisco Garcia-García5, Gemma Tell-Marti2, Maria José Escamez6, Julia Newton-Bishop4, Veronique Bataille3, Marcela del Río6, Joaquín Dopazo5,7,8, Mario Falchi3, Susana Puig2

1Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clinic & IDIBAPS, CIBER de Enfermedades Raras (CIBERER), Barcelona, Spain

2Dermatology Department, Melanoma Unit, Hospital Clinic & IDIBAPS, CIBER de Enfermedades Raras (CIBERER), Barcelona, Spain

3Department of Twin Research and Genetic Epidemiology, King's College London, London, UK

4Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK

5Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain

6Departamento de Bioingeniería, Universidad Carlos III de Madrid, CIEMAT, IIS-Fundación Jiménez Díaz, CIBER de Enfermedades Raras (CIBERER), Madrid, Spain

7Functional Genomics Node, (INB) at CIPF, Valencia, Spain

8CIBER de Enfermedades Raras (CIBERER), Valencia, Spain

Correspondence to:

Joan Anton Puig-Butille, email: [email protected]; [email protected]

Keywords: MC1R, red hair phenotype, melanocyte, melanoma, autophagy

Received: July 28, 2016     Accepted: November 21, 2016     Published: December 24, 2016

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.


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