Department of Oral and Maxillofacial Surgery, Okayama University Hospital, Okayama, Japan.
Department of Dental Pharmacology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
Methods Mol Biol. 2023;2693:293-306. doi: 10.1007/978-1-0716-3342-7_22.
Molecular chaperones, such as heat shock proteins (HSPs), have attracted attention as molecules involved in malignant events in cancers and are potential therapeutic targets and biomarkers for tumor therapy. Furthermore, mutations in chaperones can significantly impact cancer risk and prognosis. Bioinformatics is a particularly useful method for developing biomarkers as a practical consideration for the immediate clinical application of data. Many large-scale databases and portals on cancer genome are nowadays publicly available, including the International Cancer Genome Consortium (ICGC); The Cancer Genome Atlas (TCGA), renamed as Genomic Data Commons (GDC); Catalogue of Somatic Mutations in Cancer (COSMIC); and Cancer Cell Line Encyclopedia (CCLE). Referring to these databases, advanced web portals are publicized, including cBioPortal, Human Protein Atlas (HPA), Kaplan-Meier (KM) plotter, Gene Expression Profiling Interactive Analysis 2 (GEPIA2), Genomics of Drug Sensitivity in Cancer (GDSC), and Dependency Map (DepMap). Here, we assemble these databases and portals to clarify what is available and useful for current cancer research and provide protocols to utilize the HPA, KM plotter, and GEPIA2 for studies on chaperone genes in cancer patients. Utilizing these portals will reveal the correlation between tumor subtype-specific high expression of chaperone genes and patient prognosis. Our protocols are useful to increase systematic awareness of chaperones and find new biomarkers for diagnosis and prognosis and new targets for anticancer drugs.
分子伴侣，如热休克蛋白（HSPs），作为参与癌症恶性事件的分子引起了关注，是肿瘤治疗的潜在治疗靶点和生物标志物。此外，伴侣的突变可以显著影响癌症的风险和预后。生物信息学是开发生物标志物的一种特别有用的方法，因为它考虑到了数据的直接临床应用的实际情况。如今，许多癌症基因组的大型数据库和门户都是公开可用的，包括国际癌症基因组联盟（ICGC）；癌症基因组图谱（TCGA），更名为基因组数据共享中心（GDC）；癌症体细胞突变目录（COSMIC）；和癌症细胞系百科全书（CCLE）。参考这些数据库，宣传了先进的网络门户，包括 cBioPortal、人类蛋白质图谱（HPA）、Kaplan-Meier（KM）绘图器、基因表达谱交互式分析 2（GEPIA2）、癌症药物敏感性基因组学（GDSC）和依赖图谱（DepMap）。在这里，我们整合了这些数据库和门户，以阐明哪些对当前癌症研究是可用和有用的，并提供了利用 HPA、KM 绘图器和 GEPIA2 研究癌症患者伴侣基因的方案。利用这些门户将揭示肿瘤亚型特异性高表达伴侣基因与患者预后之间的相关性。我们的方案有助于提高对伴侣的系统认识，为诊断和预后找到新的生物标志物，并为抗癌药物找到新的靶点。
