Single-Cell Omics Analyses Enabled by Microchip Technologies

Deng, Yanxiang; Finck, Amanda; Fan, Rong

doi:10.1146/annurev-bioeng-060418-052538

Cited by 52 publications

(35 citation statements)

References 201 publications

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“…Herein, we use high-throughput single-cell 3′ mRNA transcriptome sequencing [14], [15], single-cell multiplex cytokine secretion assay [13], [16], [17], together with live cell imaging of cytotoxic activity to interrogate third-generation anti-CD19/4-1BB/CD28/CD3ζ (CD19-BB-28-3z) CAR-T cells, yielding the first comprehensive portrait of single-cell level transcriptional [18] and cytokine signatures of CAR-T cells upon antigen-specific stimulation. The predominant response is found to be a highly mixed T H 1/T H 2 function with T reg activity emerges from a small fraction of this hybrid T H 1/T H 2 population.…”

Section: Introductionmentioning

confidence: 99%

Single-Cell Analysis of CAR-T Cell Activation Reveals A Mixed TH1/TH2 Response Independent of Differentiation

Xhangolli

Dura

Lee

et al. 2019

Genomics, Proteomics &Amp; Bioinformatics

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The activation mechanism of chimeric antigen receptor (CAR)-engineered T cells may differ substantially from T cells carrying native T cell receptor, but this difference remains poorly understood. We present the first comprehensive portrait of single-cell level transcriptional and cytokine signatures of anti-CD19/4-1BB/CD28/CD3ζ CAR-T cells upon antigen-specific stimulation. Both CD4 + helper T (T H ) cells and CD8 + cytotoxic CAR-T cells are equally effective in directly killing target tumor cells and their cytotoxic activity is associated with the elevation of a range of T H 1 and T H 2 signature cytokines, e.g. , interferon γ, tumor necrotic factor α, interleukin 5 (IL5), and IL13, as confirmed by the expression of master transcription factor genes TBX21 and GATA3 . However, rather than conforming to stringent T H 1 or T H 2 subtypes, single-cell analysis reveals that the predominant response is a highly mixed T H 1/T H 2 function in the same cell. The regulatory T cell activity, although observed in a small fraction of activated cells, emerges from this hybrid T H 1/T H 2 population. Granulocyte-macrophage colony stimulating factor (GM-CSF) is produced from the majority of cells regardless of the polarization states, further contrasting CAR-T to classic T cells. Surprisingly, the cytokine response is minimally associated with differentiation status, although all major differentiation subsets such as naïve, central memory, effector memory, and effector are detected. All these suggest that the activation of CAR-engineered T cells is a canonical process that leads to a highly mixed response combining both type 1 and type 2 cytokines together with GM-CSF, supporting the notion that polyfunctional CAR-T cells correlate with objective response of patients in clinical trials. This work provides new insights into the mechanism of CAR activation and implies the necessity for cellular function assays to characterize the quality of CAR-T infusion products and monitor therapeutic responses in patients.

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Section: Introductionmentioning

confidence: 99%

Single-Cell Analysis of CAR-T Cell Activation Reveals A Mixed TH1/TH2 Response Independent of Differentiation

Xhangolli

Dura

Lee

et al. 2019

Genomics, Proteomics &Amp; Bioinformatics

Self Cite

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“…The most popular are combinations of scRNA-seq with single-cell genomics, DNA methylation or ATAC-seq for regulatory regions. This methodology relies on the different localization patterns of the nucleic acid within a cell, mRNA in the cytosol and DNA in the nucleus [ 107 ]. Selective cell membrane lysis allows the separation of the mRNA from nuclear DNA, which remains intact and can be later isolated by centrifugation or via antibody conjugated magnetic beads, prior to cell lysis [ 108 ].…”

Section: Single-cell Sequencing Technologiesmentioning

confidence: 99%

Applying Single-Cell Analysis to Gonadogenesis and DSDs (Disorders/Differences of Sex Development)

Estermann

Smith

2020

IJMS

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The gonads are unique among the body’s organs in having a developmental choice: testis or ovary formation. Gonadal sex differentiation involves common progenitor cells that form either Sertoli and Leydig cells in the testis or granulosa and thecal cells in the ovary. Single-cell analysis is now shedding new light on how these cell lineages are specified and how they interact with the germline. Such studies are also providing new information on gonadal maturation, ageing and the somatic-germ cell niche. Furthermore, they have the potential to improve our understanding and diagnosis of Disorders/Differences of Sex Development (DSDs). DSDs occur when chromosomal, gonadal or anatomical sex are atypical. Despite major advances in recent years, most cases of DSD still cannot be explained at the molecular level. This presents a major pediatric concern. The emergence of single-cell genomics and transcriptomics now presents a novel avenue for DSD analysis, for both diagnosis and for understanding the molecular genetic etiology. Such -omics datasets have the potential to enhance our understanding of the cellular origins and pathogenesis of DSDs, as well as infertility and gonadal diseases such as cancer.

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“…Specifically, programmable valving systems delivered active manipulation and control of small-scale (~nano/microliter) fluid flow within networks of microfluidic channels, forming separated compartments to perform biochemical reactions in an addressable manner 20 – 22 . Such valving systems were positioned to execute synchronous/asynchronous sequential and parallel fluid manipulation tasks autonomously, leading to the creation of new microfluidic solutions for various applications including diagnostics and -omics 23 , 24 . To date, such programmable valving systems have not been adapted for integration into lab-on-the-body-like wearable platforms, which is primarily due to the bulkiness of the actuation instruments 25 (e.g., external mechanical pumps and optical excitation systems).…”

Section: Introductionmentioning

confidence: 99%

A programmable epidermal microfluidic valving system for wearable biofluid management and contextual biomarker analysis

et al. 2020

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Active biofluid management is central to the realization of wearable bioanalytical platforms that are poised to autonomously provide frequent, real-time, and accurate measures of biomarkers in epidermally-retrievable biofluids (e.g., sweat). Accordingly, here, a programmable epidermal microfluidic valving system is devised, which is capable of biofluid sampling, routing, and compartmentalization for biomarker analysis. At its core, the system is a network of individually-addressable microheater-controlled thermo-responsive hydrogel valves, augmented with a pressure regulation mechanism to accommodate pressure built-up, when interfacing sweat glands. The active biofluid control achieved by this system is harnessed to create unprecedented wearable bioanalytical capabilities at both the sensor level (decoupling the confounding influence of flow rate variability on sensor response) and the system level (facilitating context-based sensor selection/protection). Through integration with a wireless flexible printed circuit board and seamless bilateral communication with consumer electronics (e.g., smartwatch), contextually-relevant (scheduled/on-demand) on-body biomarker data acquisition/display was achieved.

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Single-Cell Omics Analyses Enabled by Microchip Technologies

Cited by 52 publications

References 201 publications

Single-Cell Analysis of CAR-T Cell Activation Reveals A Mixed TH1/TH2 Response Independent of Differentiation

Single-Cell Analysis of CAR-T Cell Activation Reveals A Mixed TH1/TH2 Response Independent of Differentiation

Applying Single-Cell Analysis to Gonadogenesis and DSDs (Disorders/Differences of Sex Development)

A programmable epidermal microfluidic valving system for wearable biofluid management and contextual biomarker analysis

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