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Related Concept Videos

MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...

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Updated: May 10, 2026

Mosaic Zebrafish Transgenesis for Functional Genomic Analysis of Candidate Cooperative Genes in Tumor Pathogenesis
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Mosaic Zebrafish Transgenesis for Functional Genomic Analysis of Candidate Cooperative Genes in Tumor Pathogenesis

Published on: March 31, 2015

Multicolor microRNA FISH effectively differentiates tumor types.

Neil Renwick1, Pavol Cekan, Paul A Masry

  • 1Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA.

The Journal of Clinical Investigation
|June 4, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces multicolor miRNA FISH for visualizing microRNAs in formalin-fixed paraffin-embedded tissues. The new method accurately distinguishes between basal cell carcinoma and Merkel cell carcinoma using specific microRNA biomarkers.

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MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as a Novel Detection and Quantification Method

Published on: October 7, 2025

Area of Science:

  • Oncology
  • Molecular Biology
  • Biochemistry

Background:

  • MicroRNAs (miRNAs) are valuable tumor biomarkers due to their cell-type specificity and abundance.
  • Current detection methods like real-time PCR destroy crucial visuospatial information in tissue samples.
  • There is a need for techniques that allow miRNA visualization directly within preserved tissue specimens.

Purpose of the Study:

  • To develop and validate a multicolor fluorescence in situ hybridization (FISH) method for visualizing microRNAs in formalin-fixed paraffin-embedded (FFPE) tissues.
  • To differentiate between basal cell carcinoma (BCC) and Merkel cell carcinoma (MCC), two skin tumors with similar histology but different origins.
  • To identify and utilize specific microRNAs as biomarkers for accurate tumor classification.

Main Methods:

  • Developed multicolor miRNA FISH optimized for fixation and ribosomal RNA (rRNA) retention.
  • Enhanced signal amplification and detection through increased probe-hapten linker lengths.
  • Improved probe specificity by using shortened probes with minimal rRNA complementarity.
  • Validated the method on 4 BCC and 12 MCC FFPE tissue samples.
  • Used sequencing-based miRNA profiling and discriminant analysis to identify tumor-specific miRNAs (miR-205 in BCC, miR-375 in MCC).

Main Results:

  • Successfully visualized and differentiated between BCC and MCC using the developed miRNA FISH technique.
  • Identified miR-205 as a specific biomarker for BCC and miR-375 for MCC.
  • Achieved accurate classification of all tested tumors in a blinded analysis.
  • Demonstrated reliable normalization of miRNA signals against reference rRNA signals.

Conclusions:

  • Established a reliable multicolor miRNA FISH technique for parallel visualization of differentially expressed miRNAs in FFPE tumor tissues.
  • The developed method overcomes limitations of existing techniques by preserving visuospatial information.
  • This technique offers a powerful tool for cancer diagnostics and research, enabling precise tumor subtyping based on miRNA expression profiles.