Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on 5,063 single T cells isolated from peripheral blood, tumor, and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional profiles of these individual cells, coupled with assembled T cell receptor (TCR) sequences, enable us to identify 11 T cell subsets based on their molecular and functional properties and delineate their developmental trajectory. Specific subsets such as exhausted CD8 T cells and Tregs are preferentially enriched and potentially clonally expanded in hepatocellular carcinoma (HCC), and we identified signature genes for each subset. One of the genes, layilin, is upregulated on activated CD8 T cells and Tregs and represses the CD8 T cell functions in vitro. This compendium of transcriptome data provides valuable insights and a rich resource for understanding the immune landscape in cancers.

Cancer immunotherapies have shown sustained clinical responses in treating non-small-cell lung cancer, but efficacy varies and depends in part on the amount and properties of tumor infiltrating lymphocytes. 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.

No abstract

The core histone tail domains are known to be key regulators of chromatin structure and function. The tails are required for condensation of nucleosome arrays into secondary and tertiary chromatin structures, yet little is known regarding tail structures or sites of tail interactions in chromatin. We have developed a system to test the hypothesis that the tails participate in internucleosomal interactions during salt-dependent chromatin condensation, and here we used it to examine interactions of the H3 tail domain. We found that the H3 tail participates primarily in intranucleosome interactions when the nucleosome array exists in an extended "beads-ona-string" conformation and that tail interactions reorganize to engage in primarily internucleosome interactions as the array successively undergoes salt-dependent folding and oligomerization. These results indicated that the location and interactions of the H3 tail domain are dependent upon the degree of condensation of the nucleosomal array, suggesting a mechanism by which alterations in tail interactions may elaborate different structural and functional states of chromatin.The eukaryotic genome is assembled into vast arrays of nucleosomes, which are in turn condensed into 30-nm chromatin fibers and other secondary chromatin structures (1-3). In vitro evidence indicates that the folding of nucleosome arrays into secondary structures is strongly favored at physiological concentrations of mono-and divalent salts, as is the oligomerization of arrays into higher order, tertiary chromatin structures (2, 4, 5). The stability of secondary and tertiary chromatin structures is influenced by the incorporation of specific non-allelic variants of the core histone proteins, the binding of linker histones, and association of ancillary chromatin proteins (2, 3). It is generally believed that for genomic DNA to be accessible to various enzymatic machineries, the chromatin fiber has to undergo transient decondensation, facilitated by specific posttranslational modifications such as lysine acetylation within the histone tail domains or ATP-dependent chromatin remodeling (6, 7).The core histone tail domains are essential for compaction of oligonucleosome arrays into secondary chromatin structures and for efficient assembly of oligomeric tertiary structures (1, 2, 8 -10). However, the structures and interactions of the histone tail domains and the molecular mechanisms by which they facilitate chromatin compaction remain largely uncharacterized. Evidence indicates that these highly basic domains interact with both protein and DNA targets within chromatin (11-15), and it is generally assumed that the core histone tail domains participate in internucleosomal as well as intranucleosome interactions within condensed chromatin. Indeed, several crystal structures of nucleosome core particles indicate that the tails project away from the main body of the nucleosome to potentially mediate internucleosomal interactions (2,16,17). These interactions may occur in cis, between nucleosomes within...

No abstract