title: Selective local lysis and sampling of live cells for nucleic acid analysis using a microfluidic probe.
abstract: Heterogeneity is inherent to biology, thus it is imperative to realize methods capable of obtaining spatially-resolved genomic and transcriptomic profiles of heterogeneous biological samples. Here, we present a new method for local lysis of live adherent cells for nucleic acid analyses. This method addresses bottlenecks in current approaches, such as dilution of analytes, one-sample-one-test, and incompatibility to adherent cells. We make use of a scanning probe technology - a microfluidic probe - and implement hierarchical hydrodynamic flow confinement (hHFC) to localize multiple biochemicals on a biological substrate in a non-contact, non-destructive manner. hHFC enables rapid recovery of nucleic acids by coupling cell lysis and lysate collection. We locally lysed ~300 cells with chemical systems adapted for DNA or RNA and obtained lysates of ~70 cells/μL for DNA analysis and ~15 cells/μL for mRNA analysis. The lysates were introduced into PCR-based workflows for genomic and transcriptomic analysis. This strategy further enabled selective local lysis of subpopulations in a co-culture of MCF7 and MDA-MB-231 cells, validated by characteristic E-cadherin gene expression in individually extracted cell types. The developed strategy can be applied to study cell-cell, cell-matrix interactions locally, with implications in understanding growth, progression and drug response of a tumor.
authors.affiliation: IBM Research - Zurich, Säumerstrasse 4, 8803 Rüschlikon, Switzerland.
authors.forename: Aditya
authors.initials: A
authors.lastname: Kashyap
authors.affiliation: IBM Research - Zurich, Säumerstrasse 4, 8803 Rüschlikon, Switzerland.
authors.forename: Julien
authors.initials: J
authors.lastname: Autebert
authors.affiliation: IBM Research - Zurich, Säumerstrasse 4, 8803 Rüschlikon, Switzerland.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Delamarche
authors.affiliation: IBM Research - Zurich, Säumerstrasse 4, 8803 Rüschlikon, Switzerland.
authors.forename: Govind V
authors.initials: GV
authors.lastname: Kaigala
mesh_terms: D045744:Cell Line, Tumor; D002477:Cells / Q000737:chemistry; D018920:Coculture Techniques; D004247:DNA / Q000302:isolation & purification*; D006801:Humans; D057446:Hydrodynamics; D046210:Microfluidic Analytical Techniques; D044085:Microfluidics; D016133:Polymerase Chain Reaction; D012313:RNA / Q000302:isolation & purification*
chemical_list: D012313:RNA; D004247:DNA