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Deep single-cell RNA sequencing data for 11138 T cells from tumour, adjacent normal tissue and peripheral blood of treatment-naive CRC patients. The DATA ACCESS AGREEMENT is provided at Applicants can request access to the data by directly downloading it or by sending an email to The process that is used to approve an application includes verifying the institution, participants and research purposes of the application. In general this process will take about two weeks. In principal, any scientific research program complying with the laws and bioethic regulation policies of China will be approved.

T cells are central players in cancer immunotherapy1, yet some of their fundamental properties such as development and migration within tumours remain elusive. The enormous T cell receptor (TCR) repertoire, required for recognising foreign and self-antigens2,3, could serve as lineage tags to track these T cells in tumours4. Here, we obtained transcriptomes of 11,138 single T cells from 12 colorectal cancer (CRC) patients and developed STARTRAC (Single T-cell Analysis by Rna-seq and Tcr TRACking) indices to quantitatively analyse dynamic relationships among 20 identified T cell subsets with distinct functions and clonalities. While both CD8+ effector and “exhausted” T cells exhibited high clonal expansion, they were independently connected with tumour-resident CD8+ effector memory cells, implicating a TCR-based fate decision. Of the CD4+ T cells, the majority of tumour-infiltrating Tregs showed clonal exclusivity, whereas certain Treg clones were developmentally linked to multiple TH clones. Notably, we identified two IFNG+ TH1-like clusters in tumours, the GZMK+ TEM and CXCL13+ TH1-like clusters, which were associated with distinct IFN-γ-regulating transcription factors, EOMES/RUNX3 and BHLHE40, respectively. Only CXCL13+BHLHE40+ TH1-like cells were preferentially enriched in tumours of microsatellite-instable (MSI) patients, which might explain their favourable response rates to immune-checkpoint blockade. Furthermore, we found IGFLR1 to be highly expressed in both CXCL13+BHLHE40+ TH1-like and CD8+ exhausted T cells and possessed co-stimulatory functions. Our integrated STARTRAC analyses provides a powerful avenue to comprehensively dissect the T cell properties in CRC, which could shed new insights into the dynamic relationships of T cells in other cancers

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001003910 Illumina HiSeq 4000 11138
Publications Citations
Deep single-cell RNA sequencing data of individual T cells from treatment-naïve colorectal cancer patients.
Sci Data 6: 2019 131
The Transcription Factor Bhlhe40 Programs Mitochondrial Regulation of Resident CD8<sup>+</sup> T Cell Fitness and Functionality.
Immunity 51: 2019 491-507.e7
A dynamic CD2-rich compartment at the outer edge of the immunological synapse boosts and integrates signals.
Nat Immunol 21: 2020 1232-1243
Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics.
Nat Methods 18: 2021 92-99
Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.
Front Immunol 11: 2020 620196
Single-cell differential splicing analysis reveals high heterogeneity of liver tumor-infiltrating T cells.
Sci Rep 11: 2021 5325
Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity.
Genomics Proteomics Bioinformatics 19: 2021 377-393
CD161 expression and regulation defines rapidly responding effector CD4+ T cells associated with improved survival in HPV16-associated tumors.
J Immunother Cancer 10: 2022 e003995
Intestinal cellular heterogeneity and disease development revealed by single-cell technology.
Cell Regen 11: 2022 26