FuseFISH: robust detection of transcribed gene fusions in single cells

TY - JOUR

T1 - FuseFISH

T2 - robust detection of transcribed gene fusions in single cells

AU - Semrau, Stefan

AU - Crosetto, Nicola

AU - Bienko, Magda

AU - Boni, Marina

AU - Bernasconi, Paolo

AU - Chiarle, Roberto

AU - van Oudenaarden, Alexander

N1 - Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

PY - 2014/1/16

Y1 - 2014/1/16

N2 - Transcribed gene fusions are key biomarkers in many hematologic and solid tumors, often representing the primary oncogenic driver mutation. Here, we report an experimental and computational pipeline for detecting fusion transcripts using single-molecule RNA FISH and unbiased correlation analysis (FuseFISH). We constructed a genome-wide database of optimal oligonucleotide sequences, enabling quick design of FuseFISH probes against known and novel fusions. We implemented FuseFISH in cell lines, tissue sections, and purified RNA, reliably detecting one BCR-ABL1 positive in 10,000 negative cells. In 34 hematologic samples, we detected BCR-ABL1 transcripts with high specificity and sensitivity. Finally, we measured BCR-ABL1 expression heterogeneity and dynamics in single CML cells exposed to the kinase inhibitor Nilotinib. Our resource and methods are ideal for streamlined validation of fusions newly identified by next-generation sequencing, and they pave the way to studying the impact of fusion expression variability on clinical outcome.

AB - Transcribed gene fusions are key biomarkers in many hematologic and solid tumors, often representing the primary oncogenic driver mutation. Here, we report an experimental and computational pipeline for detecting fusion transcripts using single-molecule RNA FISH and unbiased correlation analysis (FuseFISH). We constructed a genome-wide database of optimal oligonucleotide sequences, enabling quick design of FuseFISH probes against known and novel fusions. We implemented FuseFISH in cell lines, tissue sections, and purified RNA, reliably detecting one BCR-ABL1 positive in 10,000 negative cells. In 34 hematologic samples, we detected BCR-ABL1 transcripts with high specificity and sensitivity. Finally, we measured BCR-ABL1 expression heterogeneity and dynamics in single CML cells exposed to the kinase inhibitor Nilotinib. Our resource and methods are ideal for streamlined validation of fusions newly identified by next-generation sequencing, and they pave the way to studying the impact of fusion expression variability on clinical outcome.

KW - Cell Line, Tumor

KW - Computational Biology

KW - Databases, Nucleic Acid

KW - Fusion Proteins, bcr-abl

KW - Genome, Human

KW - Humans

KW - In Situ Hybridization, Fluorescence

KW - RNA, Messenger

KW - Transcription, Genetic

U2 - 10.1016/j.celrep.2013.12.002

DO - 10.1016/j.celrep.2013.12.002

M3 - Article

C2 - 24373969

SN - 2211-1247

VL - 6

SP - 18

EP - 23

JO - Cell Reports

JF - Cell Reports

IS - 1

ER -