Microarray analysis of differentially expressed genes regulating lipid metabolism during melanoma progression.

IF 1.5 4区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Indian journal of biochemistry & biophysics Pub Date : 2015-04-01

Venil N Sumantran, Pratik Mishra, N Sudhakar

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引用次数: 0

Abstract

A new hallmark of cancer involves acquisition of a lipogenic phenotype which promotes tumorigenesis. Little is known about lipid metabolism in melanomas. Therefore, we used BRB (Biometrics Research Branch) class comparison tool with multivariate analysis to identify differentially expressed genes in human cutaneous melanomas, compared with benign nevi and normal skin derived from the microarray dataset (GDS1375). The methods were validated by identifying known melanoma biomarkers (CITED1, FGFR2, PTPRF, LICAM, SPP1 and PHACTR1) in our results. Eighteen genes regulating metabolism of fatty acids, lipid second messengers and gangliosides were 2-9 fold upregulated in melanomas of GDS-1375. Out of the 18 genes, 13 were confirmed by KEGG pathway analysis and 10 were also significantly upregulated in human melanoma cell lines of NCI-60 Cell Miner database. Results showed that melanomas upregulated PPARGC1A transcription factor and its target genes regulating synthesis of fatty acids (SCD) and complex lipids (FABP3 and ACSL3). Melanoma also upregulated genes which prevented lipotoxicity (CPT2 and ACOT7) and regulated lipid second messengers, such as phosphatidic acid (AGPAT-4, PLD3) and inositol triphosphate (ITPKB, ITPR3). Genes for synthesis of pro-tumorigenic GM3 and GD3 gangliosides (UGCG, HEXA, ST3GAL5 and ST8SIA1) were also upregulated in melanoma. Overall, the microarray analysis of GDS-1375 dataset indicated that melanomas can become lipogenic by upregulating genes, leading to increase in fatty acid metabolism, metabolism of specific lipid second messengers, and ganglioside synthesis.

本刊更多论文

微阵列分析黑色素瘤进展过程中调节脂质代谢的差异表达基因。

癌症的一个新特征是获得了一种促进肿瘤发生的脂肪生成表型。人们对黑色素瘤中的脂质代谢知之甚少。因此，我们使用BRB (biomeics Research Branch)类比较工具和多变量分析来识别人类皮肤黑色素瘤中差异表达的基因，并与来自微阵列数据集(GDS1375)的良性痣和正常皮肤进行比较。我们的结果通过鉴定已知的黑色素瘤生物标志物(CITED1、FGFR2、PTPRF、LICAM、SPP1和PHACTR1)验证了这些方法。调节脂肪酸、脂质第二信使和神经节苷代谢的18个基因在GDS-1375黑素瘤中上调2-9倍。在这18个基因中，13个被KEGG通路分析证实，10个在NCI-60 cell Miner数据库的人黑色素瘤细胞系中也显著上调。结果显示，黑色素瘤上调PPARGC1A转录因子及其调控脂肪酸(SCD)和复合脂质(FABP3和ACSL3)合成的靶基因。黑色素瘤还上调了防止脂肪毒性的基因(CPT2和ACOT7)，并调节脂质第二信使，如磷脂酸(AGPAT-4, PLD3)和肌醇三磷酸(ITPKB, ITPR3)。促瘤性GM3和GD3神经节苷脂(UGCG、HEXA、ST3GAL5和ST8SIA1)合成基因在黑色素瘤中也上调。总体而言，GDS-1375数据集的微阵列分析表明，黑素瘤可通过上调基因导致脂肪酸代谢、特定脂质第二信使代谢和神经节苷脂合成增加而致脂质生成。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Indian journal of biochemistry & biophysics 生物-生化与分子生物学

CiteScore

2.90

自引率

50.00%

发文量

审稿时长

3 months

期刊介绍： Started in 1964, this journal publishes original research articles in the following areas: structure-function relationships of biomolecules; biomolecular recognition, protein-protein and protein-DNA interactions; gene-cloning, genetic engineering, genome analysis, gene targeting, gene expression, vectors, gene therapy; drug targeting, drug design; molecular basis of genetic diseases; conformational studies, computer simulation, novel DNA structures and their biological implications, protein folding; enzymes structure, catalytic mechanisms, regulation; membrane biochemistry, transport, ion channels, signal transduction, cell-cell communication, glycobiology; receptors, antigen-antibody binding, neurochemistry, ageing, apoptosis, cell cycle control; hormones, growth factors; oncogenes, host-virus interactions, viral assembly and structure; intermediary metabolism, molecular basis of disease processes, vitamins, coenzymes, carrier proteins, toxicology; plant and microbial biochemistry; surface forces, micelles and microemulsions, colloids, electrical phenomena, etc. in biological systems. Solicited peer reviewed articles on contemporary Themes and Methods in Biochemistry and Biophysics form an important feature of IJBB. Review articles on a current topic in the above fields are also considered. They must dwell more on research work done during the last couple of years in the field and authors should integrate their own work with that of others with acumen and authenticity, mere compilation of references by a third party is discouraged. While IJBB strongly promotes innovative novel research works for publication as full length papers, it also considers research data emanating from limited objectives, and extension of ongoing experimental works as ‘Notes’. IJBB follows “Double Blind Review process” where author names, affiliations and other correspondence details are removed to ensure fare evaluation. At the same time, reviewer names are not disclosed to authors.