Table 2.
Summary of advantages and disadvantages of current single-cell sequencing platforms in studying the evolution of early-stage LUAD.
| Molecular level | mRNA | mRNA+ Protemoics | Genome | Epigenome | |
|---|---|---|---|---|---|
| Method | Smart-seq2 | Droplet-based scRNA-seq | CITE-seq, Mars-seq | SNS, SCI-seq | sciATAC-seq; scATAC-seq |
| Indications | Alternative splicing of genes | Differential gene expression calling | Analysis of targeted populations;phenotypic classifications based on surface protein and transcriptomic | Recording of the interaction between mutant tumor cells and the immune cells’ behaviors | Epigenetic biomarkers for early cancer diagonstic and epigentic regulation of genes |
| Allelic expression of genes | |||||
| Gene regulatory network reconstruction dynamic changes and heterogeneity cell percentage and subtypes | |||||
| The cell clonal evolution | |||||
| Cell trajectory inference | |||||
| Advantages | Full-length transrcpit to find the mutation and splicing alteration of tumor cell | Available commercial kits | Rare cell-type dicovery and more presice in cell phenotype identification | Genetic deterministic genes in governing the emergence and maintenance of heterogeneity and colonel evolution | Investigation of regulatory state transitions and chromatin- modifying proteins in malignant transformation |
| High content to identify different types and heterogeneity | |||||
| Sufficient quantity and quality of gene detections | |||||
| Disadvantages | Pathology misdiagnosis in early stage of lung cancer | High cost; difficult to standarized in different labs | Missing information about transcriptional heterogeneity during tumor progression | Difficult to determine how cells navigate these regulatory transitions toward malignant | |
| Hard to identify the lineage tracing of cell phenotypes and rare cell types | |||||
| Hard to characterize the clonality, inter-patient ITH, and initiation tumor site | |||||
| Require live cells and high sample quality | |||||
| Reference | Marjanovic, N.D., et al. (36) | (33, 43, 45, 47, 62) | Lavin, Y., et al. (35); LaFave, L.M., et al. (42); Leader, Grout et al. (62) | Rooney, Shukla et al. (63) | LaFave, L.M., et al. (35); Marjanovic, N.D., et al. (36) |
NSCLC, non-small cell lung cancer; Smart-seq2, Switching Mechanism At the end of the 5’-end of the RNA Transcript; scRNA, single-cell RNA sequencing; SNS, single-nucleus sequencing; SCI-seq, single-cell combinatorial indexed sequencing; scATAC-seq, Single-cell sequencing assay for transposase- accessible chromatin; ITH, intratumor heterogeneity; CITE-seq, cellular Indexing of Transcriptomes and Epitopes by Sequencing; Mars-seq, massively parallel single-cell RNA-Seq.