Versatile, facile and low-cost single-cell isolation, culture and sequencing by optical tweezer-assisted pool-screening

Xu, Teng; Li, Yuandong; Han, Xiao; Kan, Lingyan; Ren, Jing; Sun, Luyang; Diao, Zhidian; Ji, Yicai; Zhu, Pengfei; Xu, Jian; Ma, Bo

doi:10.1039/d2lc00888b

Cited by 23 publications

(13 citation statements)

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“…By adopting the Raman flow cytometry mode in FlowRACS [43,44], new clinical or scientific applications such as high-throughput, label-free metabolic profiling of live microbial cells will emerge, which are highly valuable to resolve the long-standing challenge of detecting and quantifying hetero-resistance [49]. At the one-cell RACS-seq or RACS-culture step, new designs of the RAGE chip that improve the precision of cell capture, such as optical tweezer-assisted pool screening [50] or the use of artificial intelligence for automated sorting of cells [50,51], can greatly enhance the throughput, while the automation of SCRS acquisition, sorting, and one cell-one well disposition would ensure downstream single cell genome extraction, amplification and sequencing or cultivation can proceed without human intervention. Notably, in circumstances when costefficient sequencing of a larger number of RACS-sorted microbial cells are important, barcoded single cell genome sequencing that is directly coupled to indexed, low-throughput RACS-seq or unindexed, highthroughput FlowRACS should be established [39].…”

Section: Future Directionsmentioning

confidence: 99%

Single cell metabolic phenome and genome via the ramanome technology platform: Precision medicine of infectious diseases at the ultimate precision?

Zhang

et al. 2023

iLABMED

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Due to the limitations of existing approaches, a rapid, sensitive, accurate, comprehensive, and generally applicable strategy to diagnose and treat bacterial and fungal infections remains a major challenge. Here, based on the ramanome technology platform, we propose a culture‐free, one cell resolution, phenome‐genome‐combined strategy called single‐cell identification, viability and vitality tests and source tracking (SCIVVS). For each cell directly extracted from a clinical specimen, the fingerprint region of the D2O‐probed single cell Raman spectrum (SCRS) enables species‐level identification based on a reference SCRS database of pathogen species, whereas the C‐D band accurately quantifies viability, metabolic vitality, phenotypic susceptibility to antimicrobials, and their intercellular heterogeneity. Moreover, to source track a cell, Raman‐activated cell sorting followed by sequencing or cultivation proceeds, producinging an indexed, high coverage genome assembly or a pure culture from precisely one pathogenic cell. Finally, an integrated SCIVVS workflow that features automated profiling and sorting of metabolic and morphological phenomes can complete the entire process in only a few hours. Because it resolves heterogeneity for both the metabolic phenome and genome, targets functions, can be automated, and is orders‐of‐magnitude faster while cost‐effective, SCIVVS is a new technological and data framework to diagnose and treat bacterial and fungal infections in various clinical and disease control settings.

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Section: Future Directionsmentioning

confidence: 99%

Single cell metabolic phenome and genome via the ramanome technology platform: Precision medicine of infectious diseases at the ultimate precision?

Zhang

et al. 2023

iLABMED

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“…Microfluidic chips allow for accurate manipulation of single cells, such as trapping, releasing, and moving of cells by electrical, mechanical, or optical means . In recent years, there have been significant advances in innovative strategies for both cell isolation and related biomarker analysis at the single-cell level. − For example, Li et al introduced a revolutionary label-free optofluidic nanoplasmonic biosensor, capable of real-time single-cell analysis .…”

Section: Introductionmentioning

confidence: 99%

Electrochemiluminescence Analysis of Multiple Glycans on Single Living Cell with a Closed Bipolar Electrode Array Chip

Wu,

Gu,

Wang

et al. 2024

Anal. Chem.

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The profiling of multiple glycans on a single cell is important for elucidating glycosylation mechanisms and accurately identifying disease states. Herein, we developed a closed bipolar electrode (BPE) array chip for live single-cell trapping and in situ galactose and sialic acid detection with the electrochemiluminescence (ECL) method. Methylene blue-DNA (MB-DNA) as well as biotin-DNA (Bio-DNA) codecorated AuNPs were prepared as nanoprobes, which were selectively labeled on the cell surface through chemoselective labeling techniques. The individual cell was captured and labeled in the microtrap of the cathodic chamber, under an appropriate potential, MB molecules on the cellular membrane underwent oxidation, triggering the reduction of [Ru(bpy) 3 ] 2+ /TPA and consequently generating ECL signals in the anodic chamber. The abundance of MB groups on the single cell enabled selective monitoring of both sialic acid and galactosyl groups with high sensitivity using ECL. The sialic acid and galactosyl content per HepG2 cell were detected to be 0.66 and 0.82 fmol, respectively. Through comprehensive evaluation of these two types of glycans on a single cell, tumor cells, and normal cells could be effectively discriminated and the accuracy of single-cell heterogeneous analysis was improved. Additionally, dynamic monitoring of variations in galactosyl groups on the surface of the single cell was also achieved. This work introduced a straightforward and convenient approach for heterogeneity analysis among single cells.

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“…Microfluidics is an extremely powerful technique with the features of low‐reagent consumption, cost‐effectiveness, miniaturization, automation and high‐throughput capabilities. [ 9,10 ] Microfluidic chip can be flexibly designed into various structures to simulate physiological and pathological conditions, [ 11,12 ] as well as to enable a range of single‐cell operations, such as manipulation, [ 13 ] isolation, [ 14,15 ] sorting, [ 16 ] screening, [ 17 ] and lysis. [ 18,19 ] Additionally, microfluidics can swiftly analyze a vast number of cells, meeting the demands for statistically significant population cell behavior studies while also capturing insights into cellular heterogeneity.…”

Section: Introductionmentioning

confidence: 99%

Microfluidics Coupled Mass Spectrometry for Single Cell Multi‐Omics

Zhang,

Qiao

2023

Small Methods

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Population‐level analysis masks significant heterogeneity between individual cells, making it difficult to accurately reflect the true intricacies of life activities. Microfluidics is a technique that can manipulate individual cells effectively and is commonly coupled with a variety of analytical methods for single‐cell analysis. Single‐cell omics provides abundant molecular information at the single‐cell level, fundamentally revealing differences in cell types and biological states among cell individuals, leading to a deeper understanding of cellular phenotypes and life activities. Herein, this work summarizes the microfluidic chips designed for single‐cell isolation, manipulation, trapping, screening, and sorting, including droplet microfluidic chips, microwell arrays, hydrodynamic microfluidic chips, and microchips with microvalves. This work further reviews the studies on single‐cell proteomics, metabolomics, lipidomics, and multi‐omics based on microfluidics and mass spectrometry. Finally, the challenges and future application of single‐cell multi‐omics are discussed.

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Versatile, facile and low-cost single-cell isolation, culture and sequencing by optical tweezer-assisted pool-screening

Abstract: Real-time image-based sorting of target cells in a precisely indexed manner is desirable for sequencing or cultivating individual human or microbial cells directly from clinical or environmental samples, however versatility...

Cited by 23 publications

References 50 publications

Single cell metabolic phenome and genome via the ramanome technology platform: Precision medicine of infectious diseases at the ultimate precision?

Single cell metabolic phenome and genome via the ramanome technology platform: Precision medicine of infectious diseases at the ultimate precision?

Electrochemiluminescence Analysis of Multiple Glycans on Single Living Cell with a Closed Bipolar Electrode Array Chip

Microfluidics Coupled Mass Spectrometry for Single Cell Multi‐Omics

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