A novel single-cell analysis method - single-cell biopsy with FluidFM®  

This short note aims to provide the reader with an overview of a novel and non-invasive single-cell analysis method suited for a broad range of Life Sciences and biological applications - the single-cell biopsy.


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Single-cell biopsy - The definition

Single cell analysis biopsy FluidFM Cytosurge

 The origin of the term "Single-cell biopsy" by Cytosurge

Do you know what biopsy means?


The term biopsy was coined from Greek bios ‘life’ + opsis ‘sight’. It's an extraction of sample cells or tissues for examination - it implies that the patient stays alive. 


Bringing biopsy down to the single cell


The term "single-cell biopsy" describes a single-cell analysis method that relies on the use of the FluidFM OMNIUM system to collect sub-cellular amounts of RNA without disrupting cellular viability or physiology. Then, a highly sensitive low-input RNA-seq protocol created by Chen et al. (2022) provides a downstream analysis of the transcriptome. [1,2] Researchers demonstrated that the gene expression profiles obtained from single-cell biopsies are suitable representations of lysed cell transcriptomes. [3]

Single-cell biopsy

A novel method to perform a continuous and non-destructive single-cell analysis based on the FluidFM technology.


Non-destructive extraction

Gently extract from cytoplasm while keeping the cell alive and fully viable.

Save the physiological context

During extraction, keep the targeted cell in its context next to its neighboring cells and conserve established cell-cell interactions.

Continuous analysis

Semi-automated repetition of the gentle extraction several times on the same cell, e.g. before and after stimulation by a specific drug.

Discuss your single-cell analysis experiment with our experts! 

A system designed for its users - The FluidFM OMNIUM

Schematics of the single-cell biopsy analysis method with FluidFM

Stand-alone - User-friendly and semi-automated FluidFM technology supporting the single-cell biopsy analysis method

The FluidFM OMNIUM technology has been designed as a stand-alone, easy-to-use, and semi-automated system. The system works with our patented, hollow, force-controlled FluidFM probes that exist in a variety of tip shapes, aperture sizes and mechanical specifications. 


The process is simple - after you set your parameters and hit start, the system does the rest. It also automatically washes and cleans the probes, so even if you use the same probe on different cells, there is no cross contamination.

The precision of a unique technology - the probes


The FluidFM Nanosyringe is specifically designed for gentle injection into and extraction from single cells. It is the tiniest syringe, so small that it can be inserted into a cell without causing harm.


The selection of our unique hollow FluidFM probes have apertures as small as 300 nm, enabling sub-picoliters of liquids to be delivered or withdrawn through the probe’s microchannel in the most accurate and smoothest manner.

FluidFM probes suited for single-cell analysis

An example of FluidFM probes suited for single-cell analysis

Applications of the single-cell biopsy

 
 

Single-cell biopsies represent a new method to perform non-invasively, continuously and in a controlled manner, single-cell analysis by single-cell extraction.


The method has encountered a growing interest in various fields of research, from neurosciences, virology or transcriptomics. More specifically, this method has found a perfect fit in the field of single-cell omics. Single-cell omics addresses cellular heterogeneity head on by isolating and analyzing molecular components from individual cells.


On the left hand-side, discover how the FluidFM technology can be employed to perform a gentle, accurate and direct extraction of cellular content.

Empower your single-cell research with FluidFM

Recommended readings

Genome-wide molecular recording using Live-seq

Chen et al. show the establishment of Live-seq, an approach for single-cell transcriptome profiling that preserves cell viability during RNA extraction using FluidFM. By using a model involving exposure of macrophages with lipopolysaccharide (LPS), they were able to apply a genome-wide ranking of genes based on their ability to impact macrophage LPS response heterogeneity.  Furthermore, they show that Live-seq can be used to sequentially profile the transcriptomes of individual macrophages before and after stimulation with LPS. This enables the direct mapping of a cell’s trajectory and transforms scRNA-seq from an end-point to a temporal analysis approach.


W. Chen, O. Guillaume-Gentil, R. Dainese, P. Yde Rainer, M. Zachara, C. G. Gäbelein, J. A. Vorholt & B. Deplancke. Genome-wide molecular recording using Live-seq. (March 2021) bioRxiv 2021.03.24.436752



Single-Cell Mass Spectrometry

In this publication Guillaume-Gentil et al. show non-destructive and quantitative withdrawal of intracellular fluid with sub-picoliter resolution using FluidFM, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. By this method they detected and identified several metabolites from the cytoplasm of individual HeLa cells. Validated by 13C-Glucose feeding experiments, this showed that metabolite sampling combined with mass spectrometry analysis was possible while preserving the physiological context and the viability of the analyzed cell. Thus, enabling complementary analysis of the cell. 


O. Guillaume-Gentil, T. Rey, P. Kiefer, A.J. Ibáñez, R. Steinhoff, R. Brönnimann, L. Dorwling-Carter, T. Zambelli, R. Zenobi & J.A. Vorholt. Single-Cell Mass Spectrometry of Metabolites Extracted from Live Cells by Fluidic Force Microscopy. (May 2017) Anal Chem., 89(9), 5017-5023. doi:10.1021/acs.analchem.7b00367



Tunable Single-Cell Extraction for Molecular Analyses

Guillaume-Gentil et al. demonstrate the use of FluidFM for quantitative sampling of cytoplasmic and nucleoplasmic fractions from single cells at a sub-picoliter resolution followed by a comprehensive analysis of the soluble molecules withdrawn from the cytoplasm or the nucleus and dispensed adaptable to a broad range of analytical methods, including the detection of enzyme activities and transcript abundances.


O. Guillaume-Gentil, R.V. Grindberg, R. Kooger, L. Dorwling-Carter, V. Martinez, D. Ossola, M. Pilhofer, T. Zambelli & J.A. Vorholt. Tunable Single-Cell Extraction for Molecular Analyses. (Jul 2016) Cell, 166(2), 506-516. doi: 10.1016/j.cell.2016.06.025.

80+ publications with FluidFM

References

[1] W. Chen, O. Guillaume-Gentil, R. Dainese, P. Yde Rainer, M. Zachara, C. G. Gäbelein, J. A. Vorholt & B. Deplancke. Genome-wide molecular recording using Live-seq. (March 2021) bioRxiv 2021.03.24.436752

[2] O. Guillaume-Gentil, T. Rey, P. Kiefer, A.J. Ibáñez, R. Steinhoff, R. Brönnimann, L. Dorwling-Carter, T. Zambelli, R. Zenobi & J.A. Vorholt. Single-Cell Mass Spectrometry of Metabolites Extracted from Live Cells by Fluidic Force Microscopy. (May 2017) Anal Chem., 89(9), 5017-5023. doi:10.1021/acs.analchem.7b00367

[3] Chen, W., Guillaume-Gentil, O., Rainer, P.Y. et al. Live-seq enables temporal transcriptomic recording of single cells. Nature 608, 733–740 (2022). https://doi.org/10.1038/s41586-022-05046-9