Molecular profiling of human non-small cell lung cancer by single-cell RNA-seq

Abstract

Background Lung cancer, one of the most common malignant tumors, exhibits high inter- and intra-tumor heterogeneity which contributes significantly to treatment resistance and failure. Single-cell RNA sequencing (scRNA-seq) has been widely used to dissect the cellular composition and characterize the molecular properties of cancer cells and their tumor microenvironment in lung cancer. However, the transcriptomic heterogeneity among various cancer cells in non-small cell lung cancer (NSCLC) warrants further illustration. Methods To comprehensively analyze the molecular heterogeneity of NSCLC, we performed high-precision single-cell RNA-seq analyses on 7364 individual cells from tumor tissues and matched normal tissues from 19 primary lung cancer patients and 1 pulmonary chondroid hamartoma patient. Results In 6 of 16 patients sequenced, we identified a significant proportion of cancer cells simultaneously expressing classical marker genes for two or even three histologic subtypes of NSCLC—adenocarcinoma (ADC), squamous cell carcinoma (SCC), and neuroendocrine tumor (NET) in the same individual cell, which we defined as mixed-lineage tumor cells; this was verified by both co-immunostaining and RNA in situ hybridization. These data suggest that mixed-lineage tumor cells are highly plastic with mixed features of different types of NSCLC. Both copy number variation (CNV) patterns and mitochondrial mutations clearly showed that the mixed-lineage and single-lineage tumor cells from the same patient had common tumor ancestors rather than different origins. Moreover, we revealed that patients with high mixed-lineage features of different cancer subtypes had worse survival than patients with low mixed-lineage features, indicating that mixed-lineage tumor features were associated with poorer prognosis. In addition, gene signatures specific to mixed-lineage tumor cells were identified, including AKR1B1. Gene knockdown and small molecule inhibition of AKR1B1 can significantly decrease cell proliferation and promote cell apoptosis, suggesting that AKR1B1 plays an important role in tumorigenesis and can serve as a candidate target for tumor therapy of NSCLC patients with mixed-lineage tumor features. Conclusions In summary, our work provides novel insights into the tumor heterogeneity of NSCLC in terms of the identification of prevalent mixed-lineage subpopulations of cancer cells with combined signatures of SCC, ADC, and NET and offers clues for potential treatment strategies in these patients.

RNA sequencing identifies lung cancer lineage and facilitates drug repositioning

“…Li et al showed co-expression of lineage, however, bronchioid became overwhelmingly dominant and did not determine the lineage classification of patients. 56 In contrast, the transcriptional clusters allow for personalized therapies in identifiable lung cancer lineage. 7,8,9 Additionally, we compare correlation analysis of global, lineage-specific, our 42-classifier and immune pathways genes, separately ( Fig.…”

“…We speculate that the squamoid cluster may have the worst prognosis due to the hybrid state. 56 From the therapeutic aspect, the squamoid cluster may benefit from the MEK inhibitors after large-scale drug sensitivity analysis. Recently described dysregulation of CDKs in the neuroendocrine cluster, we further show that patients with high proliferation but low squamous and extracellular matrix remodeling may benefit from pan-CDK inhibitors.…”

“…Emerging evidence suggests that scRNA analysis was good at resolving heterogeneity, but had difficulty in simultaneously identifying cancerous and non-cancerous components. 56,58 In this study, we implemented two alternative strategies, one focusing on scRNA integration bulk and the other on flow-sorted epithelial profile. Li et al showed co-expression of lineage, however, bronchioid became overwhelmingly dominant and did not determine the lineage classification of patients.…”

The dynamic dysregulated network identifies stage-specific markers during lung adenocarcinoma malignant progression and metastasis

“…For example, single-cell transcriptomic studies revealed substantial heterogeneity in cellular composition of the tumor microenvironment 8 , 46 , 47 and molecular properties in primary and metastatic LUAD. 48 , 49 Liu et al. demonstrated intra-patient and intra-tumor heterogeneity in the regulation of pathways related to LUAD tumor progression.…”

Artificial Intelligence-Assisted Transcriptomic Analysis to Advance Cancer Immunotherapy

“…Lineage plasticity, enabling the switch of cells from one phenotypic state to another, has been proposed as a source of ITH in cancer [ 48 ]. In primary NSCLC, both CNV and mitochondrial mutation-based lineage tracking analyses based on scRNA-seq data clearly showed that mixed-lineage and single-lineage tumor cells in the same patient originated from common tumor ancestors rather than from different origins [ 49 ]. Moreover, patients harboring high mixed-lineage features of different cancer subtypes had shorter survival.…”