An absolute human stemness index associated with oncogenic dedifferentiation

• DOI: 10.1093/bib/bbz174
• Publication Date: 2019-12-19T12:11:38Z
• Authors: Hailong Zheng; Kai Song; Yelin Fu; Tianyi You; Jing Yang; Wenbing Guo; Kai Wang; Liangliang Jin; Yunyan Gu; Lishuang Qi; Wenyuan Zhao
• Keywords: 0301 basic medicine; 0303 health sciences; Gene Expression Profiling; Computational Biology; Datasets as Topic; Oncogenes; Cell Dedifferentiation; 3. Good health; Gene Expression Regulation, Neoplastic; 03 medical and health sciences; Biomarkers, Tumor; Neoplastic Stem Cells; Humans; 10. No inequality

Abstract The progression of cancer is accompanied by the acquisition of stemness features. Many stemness evaluation methods based on transcriptional profiles have been presented to reveal the relationship between stemness and cancer. However, instead of absolute stemness index values—the values with certain range—these methods gave the values without range, which makes them unable to intuitively evaluate the stemness. Besides, these indices were based on the absolute expression values of genes, which were found to be seriously influenced by batch effects and the composition of samples in the dataset. Recently, we have showed that the signatures based on the relative expression orderings (REOs) of gene pairs within a sample were highly robust against these factors, which makes that the REO-based signatures have been stably applied in the evaluations of the continuous scores with certain range. Here, we provided an absolute REO-based stemness index to evaluate the stemness. We found that this stemness index had higher correlation with the culture time of the differentiated stem cells than the previous stemness index. When applied to the cancer and normal tissue samples, the stemness index showed its significant difference between cancers and normal tissues and its ability to reveal the intratumor heterogeneity at stemness level. Importantly, higher stemness index was associated with poorer prognosis and greater oncogenic dedifferentiation reflected by histological grade. All results showed the capability of the REO-based stemness index to assist the assignment of tumor grade and its potential therapeutic and diagnostic implications.