Table 3 Key findings related to characterizing TME among various tumors using scRNA-seq
From: Advances in single-cell RNA sequencing and its applications in cancer research
Tumor | Year | Species | Protocol | Accession number (custom database if available) | Key findings | References |
|---|---|---|---|---|---|---|
Lung cancer | 2022 | Human | 10 × Genomics | Identified a novel lymphocyte-related Mφ cluster named SELENOP-Mφ; a comprehensive depiction of the immune heterogeneity and definition of Mφ clusters could help design personalized treatment for lung cancer patients | [101] | |
Colorectal Cancer | 2022 | Human | DNBelab C4 platform | Correspondence with authors | Revealed significant differences in the TME between yCRC and oCRC; the TME of yCRC was more immunosuppressive than that of oCRC | [243] |
|  | 2022 | Human | 10 × Genomics | OEP001756 | Generated a single-cell and spatial atlas of colorectal liver metastasis and found highly metabolically activated MRC1+ CCL18+ M2-like macrophages in metastatic sites. Efficient neoadjuvant chemotherapy can slow down such metabolic activation, suggesting that it may be possible to target metabolism pathways to prevent metastasis | [167] |
Gastric cancer | 2020 | Human | 10 × Genomics | Correspondence with authors | Identified different immune cell subtypes and their specific transcription factors. The IRF8 transcription factor was downregulated in CD8+ TILs from gastric cancer tissues compared to control tissues | [244] |
|  | 2020 | Human | 10 × Genomics | Correspondence with authors | Revealed widespread reprogramming across multiple cellular elements in the gastric cancer TME. Cellular remodeling was delineated by changes in cell numbers, transcriptional states, and intercellular interactions | [100] |
|  | 2023 | Human | 10 × Genomics | GSE212212 | Provided a comprehensive molecular portrait of the immune cell composition and cell states in advanced gastric cancer patients, highlighting adaptive immune irresponsiveness in GSRCC and a mediator role of CXCL13 in the TIME | [83] |
|  | 2023 | Human | 10 × Genomics | HRA002108 | Signature genes of PDGC were strongly enriched for the EMT program. DGC tended to be immune-rich type, whereas PDGC tended to be immune-poor (defined according to the density of tumor-infiltrating CD8+ T cells) | [143] |
Liver cancer | 2020 | Human | 10 × Genomics | CRA002308 | Identified a subset of M2 macrophage with high expression of CCL18 and the transcription factor CREM that potentially participate in tumor progression and a new subset of activated CD8+ T cells highly expressing XCL1 that were correlated with better patient survival rates | [176] |
|  | 2022 | Human | 10 × Genomics | EGAC00001001616, GSE149614 | Identified MMP9+ macrophages to be terminally differentiated TAMs and PPARγ to be the pivotal transcription factor driving their differentiation. Characterized heterogeneous subpopulations of malignant hepatocytes and their multifaceted functions in shaping the immune microenvironment of HCC | [177] |
|  | 2023 | Human | 10 × Genomics | Mendeley Data (skrx2fz79n) | Identified a TIB structure that was formed by the interaction of SPP1+ macrophages and CAFs, and this structure was related to immunotherapy efficacy. Blockade of SPP1 or macrophage-specific deletion of Spp1 in mice destroyed the TIB structure and sensitized HCC cells to immunotherapy | [102] |
|  | 2023 | Human | 10 × Genomics | PRJNA793914 | TREM2+ TAMs played an important role in suppressing CD8+ T cells. TREM2 deficiency increased the therapeutic effect of anti-PD-L1 blockade by enhancing the antitumor activity of CD8+ T cells | [104] |
Breast cancer | 2018 | Human | 10 × Genomics | GSE113197 | Revealed the existence of three distinct epithelial cell populations, one basal, and two luminal (secretory L1 and hormone-responsive L2) cell types, laying a foundation for understanding how the system goes awry during breast cancer | [245] |
|  | 2021 | Human | 10 × Genomics | HRA000477 | Revealed significant heterogeneity in tumor-infiltrating B-cell subgroups and suggested local differentiation of infiltrating memory B cells within breast tumors | [97] |
Esophageal cancer | 2020 | Human | 10 × Genomics | GSE145370 | Exhausted T and NK cells, Tregs, alternatively activated macrophages, and tolerogenic DCs were dominant in the TME. The crosstalk between macrophages and Tregs contributes to potential immunosuppression in the TME | [246] |
|  | 2021 | Human | 10 × Genomics | Correspondence with authors | Significant differences were found in stromal and immune cells between the esophagus normal and tumor tissues. LAG3 and HAVCR2 might be targets for immunotherapy in ESCC | [186] |
|  | 2022 | Human | 10 × Genomics | Correspondence with authors | Nonimmune stromal cells were significantly enriched in the TME. Most subsets of epithelial cells were enriched in the cancer regions, whereas inflammatory CAFs were enriched in the stromal regions | [247] |
Ovarian cancer | 2020 | Human | Modified Smart-seq2 | GSE146026 | Significant interpatient variability in the composition and functional programs of ascites cells was found. Malignant cell variability was partly explained by differences in copy number alteration patterns and stemness program expression | [188] |
|  | 2022 | Human | 10 × Genomics | PRJNA784961; GSE189889 | Acral melanoma had a suppressed immune environment compared with cutaneous melanoma from nonacral skin. Expression of multiple, therapeutically tractable immune checkpoints was observed, including PD-1, LAG-3, CTLA-4, VISTA, TIGIT, and ADORA2 | [195] |
Acute lymphoblastic leukemia | 2021 | Human | 10 × Genomics | GSE172158 | Two exhausted T-cell populations, characterized by upregulation of TIGIT, PDCD1, HLADRA, LAG3, and CTLA4, were discovered in B-ALL patients. Clonally expanded exhausted T cells were found to be likely to originate from CD8+ effector memory/terminal effector cells | [248] |
Diffuse large B cell lymphoma | 2021 | Human | 10 × Genomics | GEO: GSE182436 | Resolved the DLBCL microenvironment at systems-level resolution and identified opportunities for therapeutic targeting | [214] |
Follicular lymphoma | 2019 | Human | 10 × Genomics | Correspondence with authors | Parallel measurement of single-cell expression in thousands of tumor cells and tumor-infiltrating lymphocytes can be used to obtain a systems-level view of the tumor microenvironment and identify new avenues for therapeutic development | [249] |
|  | 2022 | Human | 10 × Genomics | https://cellxgene.cziscience. com/collections/968834a0–1895–40df-8720–666029b3bbac | Follicular lymphoma microenvironment characteristics were associated with tumor cell mutations and MHC II expression | [250] |
Angioimmunoblastic T cell lymphoma | 2022 | Human | 10 × Genomics | Correspondence with authors | B cells within the AITL TME featured decreased expression of key markers such as CD73 and CXCR5. There was an expansion of distinct CD8+ T-cell populations with an exhausted phenotype and an expression profile indicative of dysfunction, impaired cytotoxicity, and upregulation of the chemokines XCL2 and XCL1 | [251] |
Classic Hodgkin lymphoma | 2020 | Human | 10 × Genomics | EGA: EGAS00001004085 | Provided detailed functional and spatial characteristics of immune cells in classic Hodgkin lymphoma at single-cell resolution. Identified a regulatory T-cell-like immunosuppressive subset of LAG3+ T cells contributing to the immune-escape phenotype | [93] |