Riedl Markus, Ruggeri Caterina, Marx Nicolas, Borth Nicole
Department of Biotechnology, BOKU University, Vienna, Austria.
Comput Struct Biotechnol J. 2025 Apr 2;27:1407-1415. doi: 10.1016/j.csbj.2025.03.050. eCollection 2025.
The transcriptome of Chinese hamster ovary (CHO) cells plays a crucial role in determining cellular characteristics that are essential for biopharmaceutical applications. RNA-sequencing has been extensively used to profile gene expression patterns, aiming to gain a better understanding of intracellular behavior and mechanisms. Individual datasets, however, do not provide a comprehensive overview and characterization of the CHO cell's transcriptome, such that the fundamental structure of the transcriptome remains unknown. Using 15 RNA-sequencing datasets, encompassing almost 300 samples of various experimental setups, conditions and cell lines, we explore and classify the protein-coding transcriptome of CHO cells. Differences in cell line lineages are found to be the primary source of variation in transcribed genes. By employing a novel approach, we identified the core transcriptome that is ubiquitously expressed in all cell lines and culture conditions, as well as genes that remain entirely non-expressed. Additionally, we identified a set of genes that may be active or inactive depending on different conditions, which are linked to biological processes including translation as well as immune and stress response. Lastly, by integrating chromatin states derived from histone modifications, we provided additional context on the epigenetic level that supports our protein-coding gene classification. Our study offers a comprehensive insight into the CHO cell transcriptome and lays the foundation for future research into cellular adaptation to changing conditions and the development of phenotypes.
中国仓鼠卵巢（CHO）细胞的转录组在决定生物制药应用所需的细胞特性方面起着关键作用。RNA测序已被广泛用于分析基因表达模式，旨在更好地了解细胞内行为和机制。然而，单个数据集并不能全面概述和表征CHO细胞的转录组，因此转录组的基本结构仍然未知。我们使用15个RNA测序数据集，涵盖了近300个不同实验设置、条件和细胞系的样本，对CHO细胞的蛋白质编码转录组进行了探索和分类。发现细胞系谱系差异是转录基因变异的主要来源。通过采用一种新颖的方法，我们确定了在所有细胞系和培养条件下普遍表达的核心转录组，以及完全不表达的基因。此外，我们还确定了一组可能根据不同条件处于活跃或不活跃状态的基因，这些基因与包括翻译以及免疫和应激反应在内的生物过程相关。最后，通过整合源自组蛋白修饰的染色质状态，我们在表观遗传水平上提供了额外的背景信息，以支持我们对蛋白质编码基因的分类。我们的研究为CHO细胞转录组提供了全面的见解，并为未来研究细胞对变化条件的适应以及表型的发展奠定了基础。
