Classification of lung adenocarcinoma based on stemness scores in bulk and single cell transcriptomes

Qian Liu; Jiali Lei; Xiaobo Zhang; Xiaosheng Wang

doi:10.1016/j.csbj.2022.04.004

Classification of lung adenocarcinoma based on stemness scores in bulk and single cell transcriptomes

Comput Struct Biotechnol J. 2022 Apr 6:20:1691-1701. doi: 10.1016/j.csbj.2022.04.004. eCollection 2022.

Authors

Qian Liu^{1

2

3}, Jiali Lei^{1

2

3}, Xiaobo Zhang⁴, Xiaosheng Wang^{1

2

3}

Affiliations

¹ Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
² Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
³ Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China.
⁴ Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China.

Abstract

Tumor stemness is associated with tumor progression and therapy resistance. The recent advances in sequencing, genomics, and computational technologies have facilitated investigation into the tumor stemness cell-like characteristics. We identified subtypes of lung adenocarcinoma (LUAD) in bulk tumors or single cells based on the enrichment scores of 12 stemness signatures by clustering analysis of their transcriptomic profiles. Three stemness subtypes of LUAD were identified: St-H, St-M, and St-L, having high, medium, and low stemness signatures, respectively, consistently in six different datasets. Among the three subtypes, St-H was the most enriched in epithelial-mesenchymal transition, invasion, and metastasis signaling, genomically instable, irresponsive to immunotherapies and targeted therapies, and hence had the worst prognosis. We observed that intratumor heterogeneity was significantly higher in high-stemness than in low-stemness bulk tumors, but significantly lower in high-stemness than in low-stemness single cancer cells. Moreover, tumor immunity was stronger in high-stemness than in low-stemness cancer cells, but weaker in high-stemness than in low-stemness bulk tumors. These differences between bulk tumors and single cancer cells could be attributed to the non-tumor cells in bulk tumors that confounded the results of correlation analysis. Furthermore, pseudotime analysis showed that many St-H cells were at the beginning of the cell evolution trajectory, compared to most St-L cells in the terminal or later phase, suggesting that many low-stemness cells are originated from high-stemness cells. The stemness-based classification of LUAD may provide novel insights into the tumor biology as well as precise clinical management of this disease.

Keywords: Clustering analysis; DFS, disease free survival; EMT, epithelial-mesenchymal transition; FDR, false discovery rate; GO, gene ontology; HLA, human leukocyte antigen; HRD, homologous recombination deficiency; Immunotherapy and targeted therapy; K–W, Kruskal–Wallis; Lung adenocarcinoma; OS, overall survival; RF, Random Forest; SCNAs, somatic copy number alterations; Subtyping; TCGA, The Cancer Genome Atlas; TMB, tumor mutation burden; Transcriptome; Tumor stemness; ssGSEA, single-sample gene-set enrichment analysis.