Current Applied Sciences
Interdisciplinary Journal

Comparison and Optimization of RNA Extraction from Formalin-Fixed Paraffin-Embedded Tissues of Hepatocellular Carcinoma

Document Type : Original Article

Authors

Nasim Hafezi 1
Seyedeh Maryam Hosseini-khah 2
Zahra Hosseini-khah 3
Alireza Rafiei 4

1 Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran

2 Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad 91886-17871, Iran

3 Diabetes Research Center, Mazandaran University of Medical Sciences, Sari, Iran

4 Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Mazandaran, Iran

https://doi.org/10.22034/cas.2021.144303
Abstract
Detection of a new molecular marker for diagnosis and treatment of cancer is a growing field of recent research. The main challenge for molecular investigation is nucleic acid extraction from formalin-fixed, paraffin-embedded tissue (FFPE) of fine-needle aspiration (FNA) samples. In this research, we have compared four different commercially available RNA isolation kits by evaluating the quality and quantity of total RNA. RNA extraction of 10 FNA-FFPE of hepatocellular carcinoma and 10 normal tissue samples were compared and optimized using four commercially available kits: Isol-RNA lysis Reagent (5-PRIME), Cinna Pure RNA kit (SinaClon BioScience), Denazist RNA extraction kit (DENAzist Asia Biotechnology), and RNeasy FFPE Kit (Qiagen) to use in downstream applications. Evaluation of RNA extracting was done by spectrophotometer and electrophoresis. Also, quantitative reverse-transcription PCR was used for assessing the expression of SOX2. RNeasy FFPE Kit had the highest concentration of RNA between the four commercial kits (106.2 ± 17.15) and also, the highest RNA integrity with some modification. The most preferred kit for RNA extraction based on gene amplification was the RNeasy FFPE Kit, which has the lowest CT due to the high quality and integrity of RNA compared to the other three kits with the same modification. Our results suggested that RNeasy FFPE Kit with some modifications in temperature and incubation time was the best kit for RNA extraction from FNA-FFPE issues to a considerable extent with high purity and maintaining the integrity of RNA.

Graphical Abstract

Comparison and Optimization of RNA Extraction from Formalin-Fixed Paraffin-Embedded Tissues of Hepatocellular Carcinoma

Keywords

Comparison
Optimization
FFPE
RNA isolation
HCC

  • Receive Date 30 November 2022
  • Revise Date 26 December 2022
  • Accept Date 07 January 2023

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