Table 2.

Establishment of the Cancer Cell Atlas by single-cell sequencing technologies

The atlas		Methodology	Key findings	References
Cancer specific	Spatial atlas of LUAD evolution	Single-cell RNA sequencing	Deciphered the geospatial evolution of cellular lineages, states and transcriptional features from normal tissue to LUAD. They also found that CD24 can mediate protumor phenotypes	[201]
	Ecosystem atlas in breast cancer	Single-cell RNA sequencing	Constructed the transcriptional atlas of the evolution trajectory from normal breast and preneoplastic BRCA1( ±) tissue to various subtypes of breast cancer, highlighting the significant heterogeneity in microenvironment	[202, 203]
	Infiltrated B cells in TNBC	Single-cell RNA sequencing and antigen receptor profiling	The presence of infiltrated B lymphocytes indicated the local differentiation within breast tumors and revealed the positive correlation between B cells and survival via potential immunosurveillance	[204]
	T cell atlas in gliomas	Single-cell RNA sequencing	Provided the landscape of tumor-infiltrating T cells of IDH wild-type and mutation glioma and identified CD161 as an immunotherapy target	[205]
	Immune cell atlas in PDAC	Single-cell RNA sequencing	Established the immune cell atlas in PDAC, which acts as a reference to evaluate the immune landscape and potential effect of immunotherapy	[71]
	Immune cell atlas in ESCC	Single-cell RNA sequencing and TCR sequencing	Demonstrated the dynamics of various immune cells along tumor progression and indicated several immunosuppressive mechanisms	[206]
	Cellular hierarchy atlas in AML	Microwell-Seq and SMRT-seq	Revealed the AML landscape and proposed a ‘cancer attractor’ phenotype, which may help define the AML progenitor cell associated with prognosis	[69]
Pancancer atlas	CancerSEA	Single-cell RNA sequencing	Provided a user-friendly database of 14 functional states of tumor cells (including stemness, invasion and EMT). It also provided the functional states associated PCG/lncRNA repertoires among cancers	[207]
	CD8 + T cell atlas	Transposase-accessible chromatin sequencing, RNA sequencing	Defined the differentiation trajectory of CD8 + T cells toward dysfunction and revealed the underlying transcriptional drivers across various tumors, including melanoma and HCC	[208]
	TIM atlas	Single-cell RNA sequencing	Revealed the similarity and distinction of TIMs, including mast cells, DCs and TAMs, across 15 tumors and revealed the association with somatic mutations and gene expression	[209]
	HLA atlas	Immunoaffinity purification and liquid chromatography mass spectrometry	Delineated the HLA-I and HLA-II immunopeptidomes from tumor and benign human tissue samples, enabling the balanced comparison of HLA ligand levels and thus facilitating immunotherapy	[210]
	Fibroblast atlas	Single-cell RNA sequencing	Demonstrated that fibroblast transcriptional states are conservative across species and in different diseases	[211]

LUAD: lung adenocarcinoma; IDH: isocitrate dehydrogenase; TIM: tumor-infiltrating myeloid cells; TAM: tumor-infiltrating macrophages; HLA: human leucocyte antigen; PDAC: pancreatic ductal adenocarcinoma; TNBC: triple-negative breast cancer; ESCC: esophageal squamous cell carcinoma; AML: acute myeloid leukemia; SMRT-seq: single-cell single-molecule real-time sequencing