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Single-cell sequencing technologies are important hot tools for decoding the heterogeneity of tissues, organs, cells and molecules, mainly based on the next-generation sequencing technology. It mainly includes single-cell genome sequencing, single-cell epigenome sequencing and single-cell transcriptome sequencing, along with the multi-omics single-cell sequencing technology. Epigenetics is an important regulatory link between genomics and cell phenotype. It plays a role in transcriptional regulation through chromatin accessibility, DNA and histone modification, nucleosome arrangement and three-dimensional conformation of chromatin. At present, researchers have developed a variety of single-cell sequencing techniques at epigenetic level, plotted multiple heterogeneity atlases at epigenetic level for several tissues, organs and cells, and have also primarily illuminated the determinant mechanisms for the heterogeneity of cell transcription at epigenetic level. In the future, with the applications of new single-cell sequencing technologies and new algorithms in life science and medical sicences, it is expected that the heterogeneity and the underlying molecular mechanisms of tissues, organs, cells and molecules will be decoded deeply.

Nucleosome positioning is critical to chromatin accessibility and is associated with gene expression programs in cells.sup.1-3. Previous nucleosome mapping methods assemble profiles from cell populations and reveal a cell-averaged pattern: nucleosomes are positioned and form a phased array that surrounds the transcription start sites of active genes.sup.3-6 and DNase I hypersensitive sites.sup.7. However, even in a homogenous population of cells, cells exhibit heterogeneity in expression in response to active signalling.sup.8,9 that may be related to heterogeneity in chromatin accessibility.sup.10-12. Here we report a technique, termed single-cell micrococcal nuclease sequencing (scMNase-seq), that can be used to simultaneously measure genome-wide nucleosome positioning and chromatin accessibility in single cells. Application of scMNase-seq to NIH3T3 cells, mouse primary naive CD4 T cells and mouse embryonic stem cells reveals two principles of nucleosome organization: first, nucleosomes in heterochromatin regions, or that surround the transcription start sites of silent genes, show large variation in positioning across different cells but are highly uniformly spaced along the nucleosome array; and second, nucleosomes that surround the transcription start sites of active genes and DNase I hypersensitive sites show little variation in positioning across different cells but are relatively heterogeneously spaced along the nucleosome array. We found a bimodal distribution of nucleosome spacing at DNase I hypersensitive sites, which corresponds to inaccessible and accessible states and is associated with nucleosome variation and variation in accessibility across cells. Nucleosome variation is smaller within single cells than across cells, and smaller within the same cell type than across cell types. A large fraction of naive CD4 T cells and mouse embryonic stem cells shows depleted nucleosome occupancy at the de novo enhancers detected in their respective differentiated lineages, revealing the existence of cells primed for differentiation to specific lineages in undifferentiated cell populations.Single-cell micrococcal nuclease sequencing simultaneously measures chromatin accessibility and genome-wide nucleosome positioning in single cells to reveal principles of nucleosome organization., Author(s): Binbin Lai [sup.1] , Weiwu Gao [sup.1] [sup.2] , Kairong Cui [sup.1] , Wanli Xie [sup.1] [sup.3] , Qingsong Tang [sup.1] , Wenfei Jin [sup.4] , Gangqing Hu [sup.1] [...]

Programmed death-1 (PD-1), a key immune checkpoint molecule, has been developed as an oncotherapy target for various carcinomas. However, treatment with anti-PD-1 elicited only a minimal effect in pancreatic ductal adenocarcinoma (PDAC). Subsequent studies revealed the existence of a subset of PD-1+ T cells coexpressing CD38 and CD101, representing a fixed dysfunctional subpopulation that are not able to be rescued by anti-PD-1 immunotherapy. However, whether this subpopulation of PD-1 expressing CD8+ T cells could be useful in predicting PDAC stage or prognosing survival is unknown. In this study, we used flow cytometry and immunofluorescence assay to analyze the expression of CD38 and CD101 in 183 clinical PDAC samples, including 84 of peripheral blood and 99 of surgical tissues. High coexpression of CD38/CD101 on peripheral PD-1+CD8+ T cells or tumor-infiltrating lymphocytes (TILs) was found to be most significantly correlated with Tumor/Node/Metastasis (T/N/M) classification and clinical stage, in contrast PD-1+CD8+ T cells could not correlate with T classification. CD38/CD101 co-repression on TILs also correlated with the poor survival in these PDAC patient samples. Our data suggest that CD38/CD101 might represent a more helpful biomarker than PD-1 alone for diagnosis and prognosis of PDAC. [ABSTRACT FROM AUTHOR]

Through positive selection, double-positive cells in the thymus differentiate into CD4+ or CD8+ T single-positive cells that subsequently develop into different types of effective T cells, such as T-helper and cytotoxic T lymphocyte cells, that play distinctive roles in the immune system. Development, differentiation, and function of thymocytes and CD4+ and CD8+ T cells are controlled by a multitude of secreted and intracellular factors, ranging from cytokine signaling modules to transcription factors and epigenetic modifiers. Members of the E26 transformation specific (Ets) family of transcription factors, in particular, are potent regulators of these CD4+ or CD8+ T-cell processes. In this review, we summarize and discuss the functions and underlying mechanisms of the Ets family members that have been characterized as involved in these processes. Ongoing research of these factors is expected to identify practical applications for the Ets family members as novel therapeutic targets for inflammation-related diseases. [ABSTRACT FROM AUTHOR]

T helper 17 (Th17) cells have been identified as a distinct T helper lineage that mediates tissue inflammation. Retinoic acid receptor-related orphan receptor (ROR) γt has been identified as the master transcription factor (TF) required for Th17 cell lineage commitment. There is an established consensus that TFs never function alone. Thus, RORγt is considered to form protein complexes that mediate Th17 cell differentiation. Given the importance of RORγt complexes in Th17 cell development and function, here, we summarize recent progress in research investigating the interaction of RORγt with potential partners, highlighting detailed mechanisms that direct Th17 cell differentiation and potential therapeutic targets in inflammatory diseases. [ABSTRACT FROM AUTHOR]

Programmed death-1 (PD-1), a key immune checkpoint molecule, has been developed as an oncotherapy target for various carcinomas. However, treatment with anti-PD-1 elicited only a minimal effect in pancreatic ductal adenocarcinoma (PDAC). Subsequent studies revealed the existence of a subset of PD-1 + T cells coexpressing CD38 and CD101, representing a fixed dysfunctional subpopulation that are not able to be rescued by anti-PD-1 immunotherapy. However, whether this subpopulation of PD-1 expressing CD8 + T cells could be useful in predicting PDAC stage or prognosing survival is unknown. In this study, we used flow cytometry and immunofluorescence assay to analyze the expression of CD38 and CD101 in 183 clinical PDAC samples, including 84 of peripheral blood and 99 of surgical tissues. High coexpression of CD38/CD101 on peripheral PD-1 + CD8 + T cells or tumor-infiltrating lymphocytes (TILs) was found to be most significantly correlated with Tumor/Node/Metastasis (T/N/M) classification and clinical stage, in contrast PD-1 + CD8 + T cells could not correlate with T classification. CD38/CD101 co-repression on TILs also correlated with the poor survival in these PDAC patient samples. Our data suggest that CD38/CD101 might represent a more helpful biomarker than PD-1 alone for diagnosis and prognosis of PDAC.