College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, P.R. China.
Department of Dermatology, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul 135-710, Korea.
Protein Pept Lett. 2021;28(12):1408-1424. doi: 10.2174/0929866528666211105112927.
We investigated melanogenesis- and anti-apoptosis-related melanoma factors in melanoma cells (TXM1, TXM18, A375P, and A375SM).
To find melanoma associated hub factor, high-throughput screening-based techniques integrating with bioinformatics were investigated.
Array CGH analysis was conducted with a commercial system. Total genomic DNAs prepared individually from each cell line with control DNA were properly labeled with Cy3-dCTP and Cy5-dCTP and hybridizations and subsequently performed data treatment by the log2 green (G; test) to red (R; reference) fluorescence ratios (G/R). Gain or loss of copy number was judged by spots with log2-transformed ratios. PPI mapping analysis of detected candidate genes based on the array CGH results was conducted using the human interactome in the STRING database. Energy minimization and a short Molecular Dynamics (MD) simulation using the implicit solvation model in CHARMM were performed to analyze the interacting residues between YWHAZ and YWHAB.
Three genes (BMP-4, BFGF, LEF-1) known to be involved in melanogenesis were found to lose chromosomal copy numbers, and Chr. 6q23.3 was lost in all tested cell lines. Ten hub genes (CTNNB1, PEX13, PEX14, PEX5, IFNG, EXOSC3, EXOSC1, EXOSC8, UBC, and PEX10) were predicted to be functional interaction factors in the network of the 6q23.3 locus. The apoptosis-associated genes E2F1, p50, BCL2L1, and BIRC7 gained, and FGF2 lost chromosomal copy numbers in the tested melanoma cell lines. YWHAB, which gained chromosomal copy numbers, was predicted to be the most important hub protein in melanoma cells. Molecular dynamics simulations for binding YWHAB and YWHAZ were conducted, and the complex was predicted to be energetically and structurally stable through its 3 hydrogen-bond patterns. The number of interacting residues is 27.
Our study compares genome-wide screening interactomics predictions for melanoma factors and offers new information for understanding melanogenesis- and anti-apoptosis-associated mechanisms in melanoma. Especially, YWHAB was newly detected as a core factor in melanoma cells.
我们研究了黑色素瘤细胞（TXM1、TXM18、A375P 和 A375SM）中的黑色素生成和抗凋亡相关的黑色素瘤因子。
寻找与黑色素瘤相关的核心因子，我们研究了基于高通量筛选的技术与生物信息学的整合。
使用商业系统进行阵列 CGH 分析。分别用 Cy3-dCTP 和 Cy5-dCTP 对每个细胞系的总基因组 DNA 进行适当标记，并通过绿色（G；测试）到红色（R；参考）荧光比值（G/R）的对数 2 转换进行杂交和后续数据处理。通过斑点的对数 2 转换比值来判断拷贝数的增加或减少。基于阵列 CGH 结果，使用 STRING 数据库中的人类相互作用组进行检测候选基因的 PPI 映射分析。使用 CHARMM 中的隐式溶剂模型进行能量最小化和短分子动力学（MD）模拟，以分析 YWHAZ 和 YWHAB 之间的相互作用残基。
发现三个已知参与黑色素生成的基因（BMP-4、BFGF、LEF-1）失去染色体拷贝数，并且所有测试的细胞系都失去了 Chr.6q23.3。十个核心基因（CTNNB1、PEX13、PEX14、PEX5、IFNG、EXOSC3、EXOSC1、EXOSC8、UBC 和 PEX10）被预测为网络中的功能相互作用因子在 6q23.3 基因座。在测试的黑色素瘤细胞系中，凋亡相关基因 E2F1、p50、BCL2L1 和 BIRC7 获得了，而 FGF2 失去了染色体拷贝数。获得染色体拷贝数的 YWHAB 被预测为黑色素瘤细胞中最重要的核心蛋白。进行了结合 YWHAB 和 YWHAZ 的分子动力学模拟，并且通过其 3 个氢键模式预测该复合物在能量和结构上是稳定的。相互作用残基的数量为 27。
我们的研究比较了黑色素瘤因子的全基因组筛选互作组学预测，并为理解黑色素瘤中的黑色素生成和抗凋亡相关机制提供了新信息。特别是，YWHAB 被新检测为黑色素瘤细胞中的核心因子。
