Archival skin biopsy specimens as a tool for miRNA-based diagnosis: Technical and post-analytical considerations

Mirna Andelic; Margherita Marchi; Stefania Marcuzzo; Raffaella Lombardi; Catharina G Faber; Giuseppe Lauria; Erika Salvi

doi:10.1016/j.omtm.2023.101116

Archival skin biopsy specimens as a tool for miRNA-based diagnosis: Technical and post-analytical considerations

Mol Ther Methods Clin Dev. 2023 Sep 16:31:101116. doi: 10.1016/j.omtm.2023.101116. eCollection 2023 Dec 14.

Authors

Mirna Andelic^{1

2}, Margherita Marchi¹, Stefania Marcuzzo³, Raffaella Lombardi¹, Catharina G Faber⁴, Giuseppe Lauria^{1

5}, Erika Salvi^{1

6}

Affiliations

¹ Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy.
² School of Mental Health and Neuroscience, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ Maastricht, the Netherlands.
³ Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy.
⁴ Department of Neurology and School for Mental Health and Neuroscience, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ Maastricht, the Netherlands.
⁵ Department of Medical Biotechnology and Translational Medicine, University of Milan, 20133 Milan, Italy.
⁶ Data Science Center, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy.

Abstract

Archived specimens, taken by standardized procedures in clinical practice, represent a valuable resource in translational medicine. Their use in retrospective molecular-based studies could provide disease and therapy predictors. Microfluidic array is a user-friendly and cost-effective method allowing profiling of hundreds of microRNAs (miRNAs) from a low amount of RNA. However, even though tissue miRNAs may include potentially robust biomarkers, non-uniformed post-analytical pipelines could hinder translation into clinics. In this study, epidermal RNA from archival skin biopsy specimens was isolated from patients with peripheral neuropathy and healthy individuals. Unbiased miRNA profiling was performed using RT-qPCR-based microfluidic array. We demonstrated that RNA obtained from archival tissue is appropriate for miRNA profiling, providing evidence that different practices in threshold selection could significantly influence the final results. We showed the utility of software-based quality control for amplification curves. We revealed that selection of the most stable reference and the calculation of geometric mean are suitable when utilizing microfluidic arrays without known references. By applying appropriate post-analytical settings, we obtained miRNA profile of human epidermis associated with biological processes and a list of suitable references. Our results, which outline technical and post-analytical considerations, support the broad use of archived specimens for miRNA analysis to unravel disease-specific molecular signatures.

Keywords: RT-qPCR post-analysis settings; archival specimens; epidermal miRNA reference; fixed skin biopsy; miRNA profiling; microfluidic card; post-analytical settings.