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Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-cell Levels

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE143647 | GEO | 2020/01/15

REPOSITORIES: GEO

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Joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels.

Project description:Chimeric antigen receptor (CAR)-T immunotherapy has yielded impressive results in several B cell malignancies, establishing itself as a powerful means to redirect the natural properties of T lymphocytes. In this strategy, the T cell genome is modified by the integration of lentiviral vectors encoding CAR that direct tumor cell killing. However, this therapeutic approach is often limited by the extent of CAR-T cell expansion in vivo. A major outstanding question is whether or not CAR-T integration itself enhances the proliferative competence of individual T cells by rewiring their regulatory landscape. To address this question, it is critical to define the identity of an individual CAR-T cell and simultaneously chart where the CAR-T vector integrates into the genome. Here, we report the development of a method called EpiVIA (https://github.com/VahediLab/epiVIA) for the joint profiling of the chromatin accessibility and lentiviral integration site analysis at the population and single-cell levels. We validate our technique in clonal cells with previously defined integration sites and further demonstrate the ability to measure lentiviral integration sites and chromatin accessibility of host and viral genomes at the single-cell resolution in CAR-T cells. We anticipate that EpiVIA will enable the single-cell deconstruction of gene regulation during CAR-T therapy, leading to the discovery of cellular factors associated with durable treatment.

| S-EPMC7071901 | biostudies-literature

Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-cell Levels I

Project description:We report the development of a novel method called EpiVIA (https://github.com/VahediLab/epiVIA) for the joint profiling of the chromatin accessibility and lentiviral integration site analysis at the population and single-cell levels. We validate our technique in clonal cells with previously defined integration sites and further demonstrate the ability to measure lentiviral integration sites and chromatin accessibility of host and viral genomes at the single-cell resolution in CAR-T cells. We anticipate that EpiVIA will enable the single-cell deconstruction of gene regulation during CAR-T therapy, leading to the discovery of cellular factors associated with durable treatment.

2020-01-15 | GSE143645 | GEO

Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-cell Levels II

2020-01-15 | GSE143646 | GEO

Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-cell Levels

Project description:Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-cell Levels

| PRJNA601172 | ENA

Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-cell Levels II

Project description:Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-cell Levels II

| PRJNA601177 | ENA

Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-cell Levels I

Project description:Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-cell Levels I

| PRJNA601178 | ENA

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.

Project description:Although we can increasingly measure transcription, chromatin, methylation, and other aspects of molecular biology at single-cell resolution, most assays survey only one aspect of cellular biology. Here we describe sci-CAR, a combinatorial indexing-based coassay that jointly profiles chromatin accessibility and mRNA (CAR) in each of thousands of single cells. As a proof of concept, we apply sci-CAR to 4825 cells, including a time series of dexamethasone treatment, as well as to 11,296 cells from the adult mouse kidney. With the resulting data, we compare the pseudotemporal dynamics of chromatin accessibility and gene expression, reconstruct the chromatin accessibility profiles of cell types defined by RNA profiles, and link cis-regulatory sites to their target genes on the basis of the covariance of chromatin accessibility and transcription across large numbers of single cells.

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scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.

Project description:Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.

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Profiling Chromatin Accessibility at Single-cell Resolution.

Project description:How distinct transcriptional programs are enacted to generate cellular heterogeneity and plasticity, and enable complex fate decisions are important open questions. One key regulator is the cell's epigenome state that drives distinct transcriptional programs by regulating chromatin accessibility. Genome-wide chromatin accessibility measurements can impart insights into regulatory sequences (in)accessible to DNA-binding proteins at a single-cell resolution. This review outlines molecular methods and bioinformatic tools for capturing cell-to-cell chromatin variation using single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) in a scalable fashion. It also covers joint profiling of chromatin with transcriptome/proteome measurements, computational strategies to integrate multi-omic measurements, and predictive bioinformatic tools to infer chromatin accessibility from single-cell transcriptomic datasets. Methodological refinements that increase power for cell discovery through robust chromatin coverage and integrate measurements from multiple modalities will further expand our understanding of gene regulation during homeostasis and disease.

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Profiling single-cell chromatin accessibility in plants.

Project description:Coupling assay for transposase-accessible chromatin sequencing (ATAC-seq) with microfluidic separation and cellular barcoding has emerged as a powerful approach to investigate chromatin accessibility of individual cells. Here, we define a protocol for constructing single-cell ATAC-seq libraries from maize seedling nuclei and the preliminary computational steps for assessing data quality. This protocol can be readily adapted to other plant species or tissues with minor changes to reveal chromatin accessibility variation among individual cells. For complete details on the use and execution of this protocol, please refer to Marand et al. (2021).

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