Table 1

Phenotypic and functional complexity of tumor-immune landscapes revealed by high-dimensional and single-cell analysis technologies

Cancer type	High dimensional technologies	Key observations	References
Clear cell renal cell carcinoma	CyTOF, mIHC	Broad expression of PD1 on T cells with heterogeneous expression of TIM3, CTLA4 and 4-1BB. CD38⁺ CD204⁺ CD206^- TAMs colocalized with CD8⁺ T cells and is correlated with immunosuppression in tumor tissue.	Chevrier et al, 201837
Hepatocellular carcinoma	CyTOF, mIHC	Differential enrichment of various immune subsets in the TME vs the non-TME and PBMC. Tregs and exhausted CD8⁺ T cells were particularly enriched in the TME. TRMs (CD103⁺ CD45RO⁺ CD8⁺) and TEMs (CD45RO⁺ CCR7^- CD8⁺) that had higher expression of exhaustion markers (PD1, CTLA4 and Lag3) were more abundant in advanced-stage tumors, implicating their roles in tumor progression.	Chew et al, 201738
Hepatocellular carcinoma	scRNA-Seq, mIHC	Differential enrichment of immune subsets such as exhausted CD8⁺ T cells, MAIT cells and Tregs in tumor vs adjacent normal tissue. Association of LAYN expression with Tregs and exhausted CD8⁺ T cells. Novel CD8⁺ FoxP3⁺ regulatory-like cells were present in the HCC TME. Greater clonal expansion indicating tumor reactivity of CD8⁺ T cells and Tregs within the TME as compared with non-TME and PBMC.	Zheng et al, 201739
Breast carcinoma	scRNA-Seq	Greater heterogeneity in T cell and myeloid cell types in the TME, with genes related to signaling pathways like inflammation and hypoxia. Phenotypic states of T cells were affected by both TCR stimulation and the signals from the TME. Findings support the continuous T cell activation but not macrophage polarization model in cancer.	Azizi et al, 201840
Basal cell carcinoma	scATAC-Seq	Exhausted CD8⁺ T cells and T follicular helper cells were expanded post-anti-PD1 immunotherapy. These cells potentially share a common gene regulatory program which drives their development post-immunotherapy.	Satpathy et al, 201942
Triple-negative breast cancer	MIBI	Tumor tissue architectures are correlated with expression of PD1, PD-L1 and IDO. Compartmentalized tumors, that is, ordered immune structures along with tumor border, is associated with superior survival of the patients.	Keren et al, 201843
Colorectal cancer	scRNA-Seq, mIHC	Tumor tissue was enriched with T cells with more exhausted, clonally expanded and less mobile phenotypes while the normal tissue and PB was associated with a more naive or recently activated phenotype. CXCL13⁺ BHLHE40⁺ IFNG⁺ Th1-like cells were clonally expanded and enriched in tumors that displayed microsatellite instability, providing a possible explanation for their response to checkpoint blockade therapy.	Zhang et al, 201841
Lung adenocarcinoma	CyTOF, scRNA-Seq, mIHC	Reduced T effector/Treg ratio and NK cell and CD16⁺ monocyte numbers in tumor tissue. Reduced CD141⁺ DCs and increased PPARγ^hi macrophages in tumor CD141⁺ DCs were implicated in formation of TLS. Targeting tumor-infiltrating myeloid subsets could potentially enhance T cells response.	Lavin et al, 201744

CyTOF, cytometry by time of flight; DC, dendritic cell; HCC, hepatocellular carcinoma; IDO, indoleamine-pyrrole 2,3-dioxygenase; MAIT cells, mucosal-associated invariant T cells; MIBI, multiplexed ion beam imaging; mIHC, multiplex immunohistochemistry; NK, natural killer; PBMC, peripheral blood mononuclear cell; scATAC-Seq, single-cell assay for transposase-accessible chromatin sequencing; TAM, tumor-associated macrophage; TCR, T cell receptor; TLS, tertiary lymphoid structures; TME, tumor microenvironment.