@article {384, title = {Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis.}, journal = {Oncotarget}, volume = {8}, year = {2017}, month = {2017 Feb 14}, pages = {11589-11599}, 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.

}, keywords = {Adult, Coculture Techniques, Computational Biology, gene expression, Genetic Predisposition to Disease, Genomics, Hair Color, Humans, Keratinocytes, Melanocytes, Middle Aged, Phenotype, Receptor, Melanocortin, Type 1}, issn = {1949-2553}, doi = {10.18632/oncotarget.14140}, url = {http://www.impactjournals.com/oncotarget/index.php?journal=oncotarget\&page=article\&op=view\&path\%5B\%5D=14140\&path\%5B\%5D=45094}, author = {Puig-Butille, Joan Anton and Gimenez-Xavier, Pol and Visconti, Alessia and Nsengimana, J{\'e}r{\'e}mie and Garcia-Garcia, Francisco and Tell-Marti, Gemma and Escamez, Maria Jos{\'e} and Newton-Bishop, Julia and Bataille, Veronique and Del Rio, Marcela and Dopazo, Joaquin and Falchi, Mario and Puig, Susana} } @article {457, title = {Global Transcriptome Analysis of Primary Cerebrocortical Cells: Identification of Genes Regulated by Triiodothyronine in Specific Cell Types.}, journal = {Cereb Cortex}, volume = {27}, year = {2017}, month = {2017 01 01}, pages = {706-717}, abstract = {

Thyroid hormones, thyroxine, and triiodothyronine (T3) are crucial for cerebral cortex development acting through regulation of gene expression. To define the transcriptional program under T3 regulation, we have performed RNA-Seq of T3-treated and untreated primary mouse cerebrocortical cells. The expression of 1145 genes or 7.7\% of expressed genes was changed upon T3 addition, of which 371 responded to T3 in the presence of cycloheximide indicating direct transcriptional regulation. The results were compared with available transcriptomic datasets of defined cellular types. In this way, we could identify targets of T3 within genes enriched in astrocytes and neurons, in specific layers including the subplate, and in specific neurons such as prepronociceptin, cholecystokinin, or cortistatin neurons. The subplate and the prepronociceptin neurons appear as potentially major targets of T3 action. T3 upregulates mostly genes related to cell membrane events, such as G-protein signaling, neurotransmission, and ion transport and downregulates genes involved in nuclear events associated with the M phase of cell cycle, such as chromosome organization and segregation. Remarkably, the transcriptomic changes induced by T3 sustain the transition from fetal to adult patterns of gene expression. The results allow defining in molecular terms the elusive role of thyroid hormones on neocortical development.

}, keywords = {Animals, Astrocytes, Cells, Cultured, Cerebral Cortex, Fluorescent Antibody Technique, Gene Expression Profiling, Mice, 129 Strain, Mice, Inbred BALB C, Mice, Inbred C57BL, Neurons, Piperazines, Transcriptome, Triiodothyronine}, issn = {1460-2199}, doi = {10.1093/cercor/bhv273}, author = {Gil-Iba{\~n}ez, Pilar and Garcia-Garcia, Francisco and Dopazo, Joaquin and Bernal, Juan and Morte, Beatriz} } @article {957, title = {Grape antioxidant dietary fiber (GADF) inhibits intestinal polyposis in ApcMin/+ mice: relation to cell cycle and immune response.}, journal = {Carcinogenesis}, year = {2013}, month = {2013 Apr 24}, abstract = {Epidemiological and experimental studies suggest that fiber and phenolic compounds might have a protective effect on the development of colon cancer in humans. Accordingly, we assessed the chemopreventive efficacy and associated mechanisms of action of a lyophilized red grape pomace containing proanthocyanidin-rich dietary fiber (Grape Antioxidant Dietary Fiber, GADF) on spontaneous intestinal tumorigenesis in the Apc(Min/+) mouse model. Mice were fed a standard diet (control group) or a 1\% (w/w) GADF-supplemented diet (GADF group) for 6 weeks. GADF supplementation greatly reduced intestinal tumorigenesis, significantly decreasing the total number of polyps by 76\%. Moreover, size distribution analysis showed a considerable reduction in all polyp size categories [diameter <1 mm (65\%), 1-2 mm (67\%) and >2 mm (87\%)]. In terms of polyp formation in the proximal, middle and distal portions of the small intestine a decrease of 76\%, 81\% and 73\% was observed respectively. Putative molecular mechanisms underlying the inhibition of intestinal tumorigenesis were investigated by comparison of microarray expression profiles of GADF-treated and non-treated mice. We observed that the effects of GADF are mainly associated with the induction of a G1 cell cycle arrest and the downregulation of genes related to the immune response and inflammation. Our findings show for the first time the efficacy and associated mechanisms of action of GADF against intestinal tumorigenesis in Apc(Min/+) mice, suggesting its potential for the prevention of colorectal cancer.}, issn = {1460-2180}, doi = {10.1093/carcin/bgt140}, url = {http://carcin.oxfordjournals.org/content/early/2013/04/23/carcin.bgt140.abstract}, author = {S{\'a}nchez-Tena, Susana and Lizarraga, Daneida and Miranda, Anibal and Vinardell, Maria Pilar and Garcia-Garcia, Francisco and Joaqu{\'\i}n Dopazo and Torres, Josep Llu{\'\i}s and Saura-Calixto, Fulgencio and Capell{\`a}, Gabriel and Cascante, Marta} } @article {497, title = {Grape antioxidant dietary fiber inhibits intestinal polyposis in ApcMin/+ mice: relation to cell cycle and immune response.}, journal = {Carcinogenesis}, volume = {34}, year = {2013}, month = {2013 Aug}, pages = {1881-8}, abstract = {

Epidemiological and experimental studies suggest that fiber and phenolic compounds might have a protective effect on the development of colon cancer in humans. Accordingly, we assessed the chemopreventive efficacy and associated mechanisms of action of a lyophilized red grape pomace containing proanthocyanidin (PA)-rich dietary fiber [grape antioxidant dietary fiber (GADF)] on spontaneous intestinal tumorigenesis in the Apc(Min/+) mouse model. Mice were fed a standard diet (control group) or a 1\% (w/w) GADF-supplemented diet (GADF group) for 6 weeks. GADF supplementation greatly reduced intestinal tumorigenesis, significantly decreasing the total number of polyps by 76\%. Moreover, size distribution analysis showed a considerable reduction in all polyp size categories [diameter <1mm (65\%), 1-2mm (67\%) and >2mm (87\%)]. In terms of polyp formation in the proximal, middle and distal portions of the small intestine, a decrease of 76, 81 and 73\% was observed, respectively. Putative molecular mechanisms underlying the inhibition of intestinal tumorigenesis were investigated by comparison of microarray expression profiles of GADF-treated and non-treated mice. We observed that the effects of GADF are mainly associated with the induction of a G1 cell cycle arrest and the downregulation of genes related to the immune response and inflammation. Our findings show for the first time the efficacy and associated mechanisms of action of GADF against intestinal tumorigenesis in Apc(Min/+) mice, suggesting its potential for the prevention of colorectal cancer.

}, keywords = {Animals, Antioxidants, Body Weight, Carcinogenesis, Cell Cycle, Cell Cycle Checkpoints, Colorectal Neoplasms, Dietary Fiber, Dietary Supplements, Down-Regulation, G1 Phase, Inflammation, Intestinal Polyposis, Intestinal Polyps, Intestine, Small, Male, Mice, Transcriptome, Vitis}, issn = {1460-2180}, doi = {10.1093/carcin/bgt140}, author = {S{\'a}nchez-Tena, Susana and Lizarraga, Daneida and Miranda, Anibal and Vinardell, Maria P and Garcia-Garcia, Francisco and Dopazo, Joaquin and Torres, Josep L and Saura-Calixto, Fulgencio and Capell{\`a}, Gabriel and Cascante, Marta} } @article {593, title = {GEPAS, a web-based tool for microarray data analysis and interpretation.}, journal = {Nucleic Acids Res}, volume = {36}, year = {2008}, month = {2008 Jul 01}, pages = {W308-14}, abstract = {

Gene Expression Profile Analysis Suite (GEPAS) is one of the most complete and extensively used web-based packages for microarray data analysis. During its more than 5 years of activity it has continuously been updated to keep pace with the state-of-the-art in the changing microarray data analysis arena. GEPAS offers diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and functional profiling of the experiment. New options for time-course (or dose-response) experiments, microarray-based class prediction, new clustering methods and new tests for differential expression have been included. The new pipeliner module allows automating the execution of sequential analysis steps by means of a simple but powerful graphic interface. An extensive re-engineering of GEPAS has been carried out which includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. GEPAS is nowadays the most quoted web tool in its field and it is extensively used by researchers of many countries and its records indicate an average usage rate of 500 experiments per day. GEPAS, is available at http://www.gepas.org.

}, keywords = {Computer Graphics, Dose-Response Relationship, Drug, Gene Expression Profiling, Internet, Kinetics, Oligonucleotide Array Sequence Analysis, Software}, issn = {1362-4962}, doi = {10.1093/nar/gkn303}, author = {T{\'a}rraga, Joaqu{\'\i}n and Medina, Ignacio and Carbonell, Jos{\'e} and Huerta-Cepas, Jaime and Minguez, Pablo and Alloza, Eva and Al-Shahrour, F{\'a}tima and Vegas-Azc{\'a}rate, Susana and Goetz, Stefan and Escobar, Pablo and Garcia-Garcia, Francisco and Conesa, Ana and Montaner, David and Dopazo, Joaquin} }