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We are analyzing https://www.nature.com/articles/s41591-018-0045-3.

Title:
Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing | Nature Medicine
Description:
Cancer immunotherapies have shown sustained clinical responses in treating non-small-cell lung cancer1–3, but efficacy varies and depends in part on the amount and properties of tumor infiltrating lymphocytes4–6. To depict the baseline landscape of the composition, lineage and functional states of tumor infiltrating lymphocytes, here we performed deep single-cell RNA sequencing for 12,346 T cells from 14 treatment-naïve non-small-cell lung cancer patients. Combined expression and T cell antigen receptor based lineage tracking revealed a significant proportion of inter-tissue effector T cells with a highly migratory nature. As well as tumor-infiltrating CD8+ T cells undergoing exhaustion, we observed two clusters of cells exhibiting states preceding exhaustion, and a high ratio of “pre-exhausted” to exhausted T cells was associated with better prognosis of lung adenocarcinoma. Additionally, we observed further heterogeneity within the tumor regulatory T cells (Tregs), characterized by the bimodal distribution of TNFRSF9, an activation marker for antigen-specific Tregs. The gene signature of those activated tumor Tregs, which included IL1R2, correlated with poor prognosis in lung adenocarcinoma. Our study provides a new approach for patient stratification and will help further understand the functional states and dynamics of T cells in lung cancer. Deep single-cell RNA sequencing of tumor-infiltrating T cells in non-small-cell lung cancer identifies features associated with functional states and clinical outcome
Website Age:
30 years and 10 months (reg. 1994-08-11).

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pubmed, article, google, scholar, cas, central, nature, cells, cancer, cell, lung, zhang, singlecell, sequencing, tumor, access, nat, zheng, supplementary, content, immune, data, medicine, science, beijing, peking, university, cookies, information, landscape, regulatory, med, blockade, immunity, centre, china, table, privacy, published, nonsmallcell, lymphocytes, expression, advanced, molecular, authors, journal, guo, zemin, infiltrating, rna,

Topics {✒️}

nature portfolio journals permissions reprints nature portfolio privacy policy advertising open-label highly migratory nature content single-cell profiling cd4–c9–ctla4 rights social media single-cell rna-seq full-length rna-seq single-cell sequencing exploration small-cell lung cancer1 small-cell lung cancer nf-κb c-rel peking university–tsinghua university nature+ nature 515 nature 545 nature 511 nature 401 nature article originally published helge gottfried roider tissue-resident memory features tissue-resident memory subset anti–pd-l1 antibody anti-pd-1 checkpoint blockade comprehensive molecular profiling single-cell sequencing genes specifically expressed springerlink instant access sequencing data permissions tiansheng yan rna-sequencing single-cell transcriptomes human lung cancer cell immune checkpoint tissue expression profiles liang jin immune cell populations anti–pd-1 antibody cell receptor heterogeneity personal data activated tumor tregs privacy tumor infiltrating lymphocytes4 tumor infiltrating lymphocytes

Questions {❓}

  • Ward’s hierarchical agglomerative clustering method: which algorithms implement Ward’s criterion?

Schema {🗺️}

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