Table 2 Establishment of the Cancer Cell Atlas by single-cell sequencing technologies

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]