Spatially Resolved Genetic Analysis of Tissue Sections Enabled by Microscale Flow Confinement Retrieval and Isotachophoretic Purification

Angew Chem Int Ed Engl. 2019 Oct 21;58(43):15259-15262. doi: 10.1002/anie.201907150. Epub 2019 Sep 16.

Abstract

We have developed a method for spatially resolved genetic analysis of formalin-fixed paraffin-embedded (FFPE) cell block and tissue sections. This method involves local sampling using hydrodynamic flow confinement of a lysis buffer, followed by electrokinetic purification of nucleic acids from the sampled lysate. We characterized the method by locally sampling an array of points with a circa 200 μm diameter footprint, enabling the detection of single KRAS and BRAF point mutations in small populations of RKO and MCF-7 FFPE cell blocks. To illustrate the utility of this approach for genetic analysis, we demonstrate spatially resolved genotyping of FFPE sections of human breast invasive ductal carcinoma.

Keywords: cancer; gene sequencing; isotachophoresis; tissue sections; tumor heterogeneity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breast Neoplasms / genetics*
  • Breast Neoplasms / pathology
  • DNA, Neoplasm / analysis
  • DNA, Neoplasm / metabolism
  • Female
  • Formaldehyde / chemistry
  • Genotype
  • Humans
  • MCF-7 Cells
  • Microscopy, Confocal
  • Paraffin Embedding
  • Point Mutation
  • Proto-Oncogene Proteins B-raf / genetics*
  • Proto-Oncogene Proteins B-raf / metabolism
  • Proto-Oncogene Proteins p21(ras) / genetics*
  • Proto-Oncogene Proteins p21(ras) / metabolism
  • Real-Time Polymerase Chain Reaction
  • Sequence Analysis, DNA

Substances

  • DNA, Neoplasm
  • KRAS protein, human
  • Formaldehyde
  • BRAF protein, human
  • Proto-Oncogene Proteins B-raf
  • Proto-Oncogene Proteins p21(ras)