Rapid micro fluorescence in situ hybridization in tissue sections

TL;DR

This paper introduces a rapid microfluidic FISH technique using a non-contact probe for fast, efficient detection of biomarkers like HER2 in tissue sections, significantly reducing hybridization time and probe consumption.

Contribution

The study presents a novel microfluidic FISH method that accelerates hybridization, reduces reagent use, and enables sequential testing on FFPE tissue sections.

Findings

Hybridization time reduced to under 15 minutes.

Probe consumption decreased by approximately 100-fold.

Assay turnaround time less than 3 hours.

Abstract

This paper describes a micro fluorescence in situ hybridization ({\mu}FISH)-based rapid detection of cytogenetic biomarkers on formalin-fixed paraffin embedded (FFPE) tissue sections. We demonstrated this method in the context of detecting human epidermal growth factor 2 (HER2) in breast tissue sections. This method uses a non-contact microfluidic scanning probe (MFP), which localizes FISH probes at the micrometer length-scale to selected cells of the tissue section. The scanning ability of the MFP allows for a versatile implementation of FISH on tissue sections. We demonstrated the use of oligonucleotide FISH probes in ethylene carbonate-based buffer enabling rapid hybridization within < 1 min for chromosome enumeration and 10-15 min for assessment of the HER2 status in FFPE sections. We further demonstrated recycling of FISH probes for multiple sequential tests using a defined volume of probes by forming hierarchical hydrodynamic flow confinements. This microscale method is compatible with the standard FISH protocols and with the Instant Quality (IQ) FISH assay, reduces the FISH probe consumption ~100-fold and the hybridization time 4-fold, resulting in an assay turnaround time of < 3 h. We believe rapid {\mu}FISH has the potential of being used in pathology workflows as a standalone method or in combination with other molecular methods for diagnostic and prognostic analysis of FFPE sections.