Song Kyu Jin, Kim Minsuh, Heo Yong Jin, Cho Kyung-Cho, Oh Jae-Won, Kim Dae Ho, Hwa Chanwoong, Do Yeji, Choi Seunghyuk, Hwang Hee Sang, Kim Kwoneel, Kim Kyunggon, Na Seungjin, Paek Eunok, An Joon-Yong, Jang Se Jin, Kim Min-Sik, Kim Kwang Pyo
Department of Applied Chemistry, Institute of Natural Science, Kyung Hee University, Yongin 17104, Republic of Korea.
Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul 02454, Republic of Korea.
J Proteome Res. 2025 Sep 5;24(9):4563-4574. doi: 10.1021/acs.jproteome.5c00289. Epub 2025 Aug 10.
As research into cancer biology progresses, multiomics analyses have become essential for unraveling its molecular complexities. However, sample availability remains a challenge due to factors such as collection procedures and long-term storage effects. Archived samples present an opportunity to expand multiomics studies, but concerns persist regarding storage duration's impact on data reliability. This study examines the genomic, transcriptomic, and proteomic profiles of samples stored for over a decade. Transcriptomic analysis revealed a decline in read counts for protein-coding genes but preserved core gene expression patterns. Proteomic measurements remained stable, with minimal changes in post-translational modifications. While phosphorylation and acetylation rates were largely unaffected, a slight increase in modification frequencies was observed. Housekeeping genes and proteins exhibited consistent expression across samples, yet proteomic differences between the tumor and normal tissues were distinct. Despite technical variations in transcriptomic data, essential transcription factors and kinases retained functionality. These findings underscore the viability of archived samples for multiomics research, enabling broader investigations into cancer biology and providing insights into molecular mechanisms. By leveraging archived specimens, researchers can overcome sample limitations and advance precision oncology efforts, ultimately deepening our understanding of cancer at the systems level.
随着癌症生物学研究的进展，多组学分析对于揭示其分子复杂性变得至关重要。然而，由于采集程序和长期储存影响等因素，样本的可获得性仍然是一个挑战。存档样本为扩大多组学研究提供了机会，但对于储存时间对数据可靠性的影响仍存在担忧。本研究检查了储存十多年的样本的基因组、转录组和蛋白质组图谱。转录组分析显示蛋白质编码基因的读数计数下降，但核心基因表达模式得以保留。蛋白质组测量保持稳定，翻译后修饰的变化最小。虽然磷酸化和乙酰化率基本未受影响，但观察到修饰频率略有增加。管家基因和蛋白质在样本中表现出一致的表达，但肿瘤组织和正常组织之间的蛋白质组差异明显。尽管转录组数据存在技术差异，但关键转录因子和激酶仍保留功能。这些发现强调了存档样本用于多组学研究的可行性，有助于对癌症生物学进行更广泛的研究，并为分子机制提供见解。通过利用存档标本，研究人员可以克服样本限制，推进精准肿瘤学工作，最终在系统层面加深我们对癌症的理解。
