Temporal single cell profiling:
Sequence your cells while keeping them alive.
With cytoplasmic biopsies, retrieved on the FluidFM OMNIUM® Platform, perform temporal single-cell profiling.
The combination of high throughput single-cell RNA sequencing and advanced bioinformatics reveals the challenge of cellular heterogeneity and cancer plasticity. Live-seq with FluidFM (Chen, et al., Nature, 2022) preserves cell viability, allowing direct correlation between gene expression and cell fate.
This method not only provides valuable insights into cellular behaviors and their dynamic changes within diverse microenvironments but also enhances in vitro modeling of cellular responses.
As the cell stays alive, it can be sequenced again.
This means that instead of inferring genetic relationships using pseudo-time predictions, Live-seq can directly connect changes in gene expression over time. This approach opens new avenues for innovative research and therapeutic strategies by offering a direct readout of gene function in live cells.
Pinpoint Drivers of cancer development and treatment resistance
Live-seq with cytoplasmic biopsies help to identify the genetic mutations and aberrations that drive cancer development.
Decipher Cancer Heterogeneity Researching the Cancer Microenvironment
By selecting specific cells for analysis, researchers can uncover the heterogeneity within tumors, leading to a better understanding of treatment resistance and disease progression.
Researching the Cancer Microenvironment
Study the interactions between cancer cells and their surrounding environment in 2D with full context preservation and visual control.
Related Resources
Publications
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.
[1] W. Chen, O. Guillaume-Gentil, P. Yde Rainer, C. G. Gäbelein, W. Saelens, V. Gardeaux, A. Klaeger, R. Dainese, M. Zachara, T. Zambelli, J. A. Vorholt & B. Deplancke. Live-seq enables temporal transcriptomic recording of single cells. (Aug 2022) Nature, doi:10.1038/s41586-022-05046-9
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.
[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
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.
[3] 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.
Stories
Mitochondria Transplantation with FluidFM - Story featuring Dr. Christoph Gäbelein.
Temporal transcriptomics recording in single cells with FluidFM - Story featuring Dr. Orane Guillaume-Gentil.
Educational
- Temporal single-cell profiling on biopsies taken from living cells
- Biopsies for Temporal Transcriptome Analysis
- In Vitro Disease Modeling with FluidFM
- Next Challenges in Single Cell Lineage Tracing
- An Overview of Transcriptomics
- Evolution of single-cell RNA sequencing: from scRNA-seq to Live-seq
- An introduction to a novel single-cell analysis method: single-cell biopsy
- An overview of single-cell manipulation techniques
- An overview of single-cell extraction
- An overview of single-cell injection
- Cell fate trajectories inference methods, Pseudotime analysis and RNA velocity in the age of single cell omics.
References
Chen W, Guillaume-Gentil O, Rainer PY, Gabelein CG, Saelens W, Gardeux V, Klaeger A, Dainese R, Zachara M, Zambelli T, et al. Live-seq enables temporal transcriptomic recording of single cells. Nature 2022, 608:733-740.