LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue
Poorna Manasa Bhamidimarri,
Laila Salameh,
Amena Mahdami,
Hanan Wael Abdullah,
Bassam Mahboub,
Rifat Hamoudi
Affiliations
Poorna Manasa Bhamidimarri
Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
Laila Salameh
Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates
Amena Mahdami
Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
Hanan Wael Abdullah
Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
Bassam Mahboub
Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates; Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
Rifat Hamoudi
Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates; Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates; Division of Surgery and Interventional Sciences, University College London, London, United Kingdom; BIMAI-Lab, Biomedically Informed Artificial Inelligence Laboratory, University of Sharjah, Sharjah, 27272, United Arab Emirates; Centre of Excelence for Precision Medicine, Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates; Corresponding author. College of Medicine, University of Sharjah, Sharjah, PO Box 27272, United Arab Emirates.
Whole transcriptome analysis (WTA) using RNA extracted from Formalin Fixed Paraffin Embedded (FFPE) tissue is an invaluable tool to understand the molecular pathology of disease. RNA extracted from FFPE tissue is either degraded and/or in very low quantities hampering gene expression analysis. Earlier studies described protocols applied for cellular RNA using poly-A primer-based linear amplification. The current study describes a method, LINCATRA (LINear amplifiCAtion of RNA for whole TRAnscriptome analysis). It employs random nonamer primer based method which can amplify short, fragmented RNA with high fidelity from as low as 5 ng to obtain enough material for WTA. The two-cycle method significantly amplified RNA at ∼1000 folds (p 2, p < 0.05) identified between lung cancer and asthma cohorts validating the method developed. This method is applicable in clinical molecular pathology field for both diagnostics and elucidation of disease mechanisms.
