Table 5.

Studies that use single-cell sequencing to characterize human tumors

Study	Malignancy	Single-cell Technology	Key Findings
Puram et al 2017	HNSCC	scRNA-seq	• Classified HNSCC to 3 subtypes: basal-mesenchymal, classical, atypical • p-EMT program at tumor edge with CAF-TGFβ signaling • p-EMT program recapitulated in LNs • Higher p-EMT score associated with worse prognosis
Cyril Neftel et al 2019	GBM	scRNA-seq	• Four cellular states drive glioblastoma malignant cells heterogeneity • In vivo single-cell lineage tracing supports plasticity between these four states • Genetics and the microenvironment influence the frequency of cells in each state • TCGA subtypes reflect the highest-frequency malignant states and the microenvironment
Mariella G. Filbin et al 2018	GBM	scRNA-seq	• Gliomas with histone H3 lysine27-to-methionine mutations primarily contain cells that resemble oligodendrocyte precursor cells (OPC-like), whereas more differentiated malignant cells are a minority • OPC-like cells exhibit greater proliferation and tumor-propagating potential than their more differentiated counterparts and are at least in part sustained by PDGFRA signaling.
Andrew S Venteicher at al 2017	GBM	scRNA-seq	• differences in bulk expression profiles between IDH-A and IDH-O are primarily explained by the impact of signature genetic events and TME composition, but not by distinct expression programs of glial lineages in the malignant cells. • higher-grade tumors present enhanced proliferation, larger pools of undifferentiated glioma cells, and an increase in macrophage over microglia programs in the TME
Patel et al 2014	GBM	scRNA-seq	• Each tumor expressed at least 2 signatures of subtypes previously believed to be exclusive based on WES
Casasent et al 2018	BrCa	scDNA-seq TSCS	• Genome evolution occurred in ducts prior to invasion from single clone(s) • Multiple clones able to invade independently
Kim et al 2018	TNBC	scDNA-seq scRNA-seq	• Treatment-resistant tumors harbored resistant clones that were undetectable with WES but detectable on single-cell level prior to initiation of chemotherapy • Transcriptional changes within treatment resistant samples identified throughout course of treatment
Guo et al 2018	Lung	scRNA-seq	• Identified “pre-exhausted” T cells • Patients with high ratio of “pre-exhausted” to exhausted T cells had improved prognosis
Yost et al 2019	BCC/cuSCC	scRNA-seq TCR-seq	• Included patients before/after anti-PD-1 therapy • Clonal expansion of CD8+ T cells with novel clonotypes not present in pre-treatment tissue samples
Jerby-Arnon et al 2018	Melanoma	scRNA-seq	• Identified ICI resistance program associated with T cell exclusion and immune evasion • Resistance program predicted clinical response to anti-PD-1 therapy in independent 112 patient cohort
Sade-Feldman et al 2018	Melanaoma	scRNA-seq	• Two distinct states of CD8+ T cells were identified and relative proportion of each was linked to regression or progression after ICI • TCF7 expression in CD8+ T cells predictive of ICI response in independent cohort
Peter van Glen et al 2019	AML	scRNA-seq	• Variable cell-type composition of AML correlates to genetics and outcome • Primitive AML cells aberrantly co-express stemness and myeloid priming genes • Differentiated AML cells express immunomodulatory factors and suppress T cells
Li et al 2017	CRC	scRNA-seq	• Defined 2 subtypes of CAFs in tumor samples • EMT-related genes upregulated in CAF subpopulations • Improved prognostication based on single-cell expression compared to subtypes based on bulk transcriptomics
Leung et al 2017	CRC	scDNA-seq	• Supported linear theory of metastases in progression toward liver metastasis • One patient with two distinct metastatic sites able to be traced to separate mutation events in primary tumor through phylogenetic analysis

BCC: basal cell carcinoma; BrCa: breast cancer; CAF: cancer-associated fibroblast; CRC: colorectal carcinoma; cuSCC: cutaneous squamous cell carcinoma; GBM: glioblastoma multiforme; HNSCC: head and neck squamous cell carcinoma; ICI: immune checkpoint inhibition; LN: lymph node; p-EMT: partial epithelial-to-mesenchymal transition; scDNA-seq: single cell DNA sequencing; scRNA-seq: single cell RNA sequencing; TCR-seq: T cell receptor sequencing; TNBC: triple negative breast cancer; TSCS: topographic single cell sequencing; WES: whole exome sequencing.