Pediatric Surgery International

, Volume 35, Issue 12, pp 1329–1338 | Cite as

First steps in the development of a liquid biopsy in situ hybridization protocol to determine circular RNA biomarkers in rat biofluids

  • Eimear Kirby
  • Wai Hei Tse
  • Daywin Patel
  • Richard KeijzerEmail author
Original Article



Epigenetic factors are involved in the pathogenesis of congenital diaphragmatic hernia (CDH). Circular RNAs (circRNAs) are epigenetic regulators amenable to biomarker profiling. Here, we aimed to develop a liquid biopsy protocol to detect pathognomonic circRNA changes in biofluids.


Our protocol is adapted from the existing BaseScope™ in situ hybridization technique. Rat biofluids were fixed in a gelatin-coated 96-well plate with formalin. Probes were designed to target circRNAs with significant fold change in nitrofen-induced CDH. FastRED fluorescence was assessed using a plate reader and confirmed with confocal microscopy. We tested maternal serum and amniotic fluid samples from control and nitrofen-treated rats.


We detected circRNAs in rat serum and amniotic fluid from control and CDH (nitrofen-treated) rats using fluorescent readout. CircRNA signal was observed in fixed biofluids as fluorescent punctate foci under confocal laser scanning microscopy. This was confirmed by comparison to BaseScope™ lung tissue sections. Signal was concentration dependent and DNase resistant.


We successfully adapted BaseScope™ to detect circRNAs in rat biofluids: serum and amniotic fluid. We detected signal from probes targeted to circRNAs that are dysregulated in rat CDH. This work establishes the preliminary feasibility of circRNA detection in prenatal diagnostics.


Congenital diaphragmatic hernia Circular RNA Biomarker Liquid biopsy BaseScope™ 


Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants performed by any of the authors. All animals were sourced from the University of Manitoba Bannatyne Campus Animal Care and Veterinary Services facility. All procedures performed in studies involving animals were in accordance with the health research ethics board from the University of Manitoba (19–010 (AC11436)). Animal studies were compliant with the ARRIVE guidelines [14].


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Eimear Kirby
    • 1
    • 2
    • 3
  • Wai Hei Tse
    • 2
    • 3
  • Daywin Patel
    • 2
    • 3
  • Richard Keijzer
    • 2
    • 3
    Email author
  1. 1.Trinity Biomedical Sciences InstituteTrinity College Dublin School of MedicineDublinIreland
  2. 2.Division of Pediatric Surgery, Departments of Surgery, Pediatrics & Child Health and Physiology & PathophysiologyUniversity of ManitobaWinnipegCanada
  3. 3.Children’s Hospital Research Institute of ManitobaWinnipegCanada

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