Selective local lysis and sampling of live cells for nucleic acid analysis using a microfluidic probe

Area of Science:

• Molecular Biology
• Genomics
• Cell Biology

Background:

• Biological samples exhibit inherent heterogeneity, necessitating methods for spatially-resolved genomic and transcriptomic profiling.
• Current approaches for nucleic acid analysis face challenges including analyte dilution, single-sample-per-test limitations, and incompatibility with adherent cells.

Purpose of the Study:

• To present a new non-contact, non-destructive method for local lysis of live adherent cells for nucleic acid analyses.
• To overcome limitations of existing techniques by enabling localized analysis of heterogeneous biological samples.

Main Methods:

• Utilized scanning probe technology, specifically a microfluidic probe, with hierarchical hydrodynamic flow confinement (hHFC).
• hHFC was employed for non-contact, non-destructive localization of biochemicals and coupling of cell lysis with lysate collection.
• Developed chemical lysis systems for DNA and RNA, achieving high cell densities in collected lysates (~70 cells/μL for DNA, ~15 cells/μL for mRNA).

Main Results:

• Successfully performed local lysis of approximately 300 cells, yielding concentrated lysates suitable for downstream analysis.
• Demonstrated selective local lysis of subpopulations within a co-culture of MCF7 and MDA-MB-231 cells, confirmed by E-cadherin gene expression.
• Integrated the collected lysates into PCR-based workflows for both genomic and transcriptomic analysis.

Conclusions:

• The developed microfluidic probe strategy effectively enables localized nucleic acid recovery from adherent cells.
• This method addresses key bottlenecks in spatial profiling, offering improved analyte concentration and compatibility with adherent cell types.
• The technique has significant implications for studying local cell-cell and cell-matrix interactions, crucial for understanding tumor growth, progression, and drug response.