Table 3 Summary of single-cell sequencing studies on primary tumors from a variety of human cancers
From: Single-cell sequencing and tumorigenesis: improved understanding of tumor evolution and metastasis
| Tumor | Tissue source (number of cells, patients/cell lines) | Data type | Results | Reference |
|---|---|---|---|---|
| Breast | ||||
| TNBC (200, 2) | CNV | TNBC displays punctuated clonal evolution where CNVs are shared across single cells | [6] | |
| TNBC (66, 1), ER + HER2- (113, 1) | CNV and SNV | TNBC has a higher mutation rate than ER + HER2- tumors or normal cells; CNVs are an early event in tumorigenesis | [39] | |
| TNBC (1000, 12) | CNV | Supports theory of punctuated clonal evolution | [40] | |
| ER + (332, 2) | CNV | Supports theory of punctuated clonal evolution | [41] | |
| MDA-MB-231 and CN34 cell lines (44, 2) | RNA-seq | Rare cell populations with highly variable gene expression differences have increased metastatic capacity and ability to survive treatment | [42] | |
| MDA-MB-231 cell line (15, 1) | RNA-seq | Development of drug-resistance to paclitaxel is associated with unique mutations; gene expression changes not detectable in bulk tumors | [43] | |
| HER2 + (8, 2)a | RNA-seq | 404 genes differentially expressed in breast cancer stem cells, including CA12 which may be prognostic | [37] | |
| Lung | ||||
| Lung adenocarcinoma PDX (34, 1) | RNA-seq | Gene expression profiling identifies a subpopulation of PDX cells with poor prognosis | [44] | |
| Lung adenocarcinoma PDX (34, 1) | RNA-seq and WES | Identification of a subpopulation of KRAS+/low risk cells that were drug resistant | [45] | |
| LC2/ad and LC2/ad-R lung cancer cell lines (336, 7) | RNA-seq | Increased plasticity in gene expression among cells is associated with vandetanib resistance | [46] | |
| Brain | ||||
| EGFR amplified glioblastomas (50-60, 2) | CNV | Patterns of EGFR mutations differ among cells; heterogeneity may contribute to therapy resistance | [48] | |
| Glioblastomas (430, 5)a | RNA-seq | Variable EGFR CNVs and cells reflecting different subtypes are present in primary glioblastomas | [38] | |
| Colon | ||||
| Colon tumor and normal adjacent cells (63, 1) | SNV | Different mutational profiles found in two sub-clonal populations of cells may suggest bi-clonal origins | [49] | |
| HCT116 cell line (96, 1) | RNA-seq | SCS reveals cryptic mutations not detected in bulk tumor | [50] | |
| Bladder | ||||
| Muscle-invasive bladder transitional-cell carcinoma (66, 1) | SNV | Cell-lineage-specific mutations may initiate carcinogenesis and drive cancer progression | [51] | |
| Squamous cell carcinoma of the bladder (75, 1) | RNA-seq | Cell-to-cell heterogeneity in the expression of genes within cancer-related pathways may affect outcomes | [52] | |
| Kidney | ||||
| Clear cell renal cell carcinoma (20, 1) | SNV | ccRCC more genetically complex than predicted based on whole-tumor sequencing | [53] | |
| ccRCC primary carcinoma and paired metastasis propagated in PDX model (116, 1) | RNA-seq | Differential expression of targetable genes between cells supports multi-agent treatment strategy | [54] | |
| Blood | ||||
| Secondary AML (36, 3) | SNV | SCS identifies genomic complexity not seen in whole-tumor analysis and resolves clonal relationships | [55] | |
| Pediatric ALL (1479, 6) | SNV | CNVs precede somatic mutations; diversity of driver mutations affects clonal fitness | [56] | |
| B-cell ALL (276, 3) | CNV | CNVs not detected in bulk tumors are observed in single cells; CNVs develop in response to environmental stressors | [57] | |
| JAK2-negative myeloproliferative neoplasm (58, 1) | SNV | Lack of identifiable sub-clones suggests tumor is monoclonal, but large genetic distances exist between cells | [58] | |