Oncotarget

Research Papers:

Small non-coding RNA profiling in human biofluids and surrogate tissues from healthy individuals: description of the diverse and most represented species

Giulio Ferrero, Francesca Cordero, Sonia Tarallo, Maddalena Arigoni, Federica Riccardo, Gaetano Gallo, Guglielmo Ronco, Marco Allasia, Neha Kulkarni, Giuseppe Matullo, Paolo Vineis, Raffaele A. Calogero, Barbara Pardini and Alessio Naccarati _

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Oncotarget. 2018; 9:3097-3111. https://doi.org/10.18632/oncotarget.23203

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Abstract

Giulio Ferrero1,2,*, Francesca Cordero1,3,*, Sonia Tarallo3, Maddalena Arigoni4, Federica Riccardo4, Gaetano Gallo5,6, Guglielmo Ronco7, Marco Allasia8, Neha Kulkarni4, Giuseppe Matullo3,9, Paolo Vineis3,10, Raffaele A. Calogero4, Barbara Pardini3,9,* and Alessio Naccarati3,11,*

1Department of Computer Science, University of Turin, Turin, Italy

2Department of Clinical and Biological Sciences, University of Turin, Turin, Italy

3Italian Institute for Genomic Medicine, IIGM (formerly Human Genetics Foundation, HuGeF), Turin, Italy

4Molecular Biotechnology Center, Department of Biotechnology and Health Sciences, University of Turin, Turin, Italy

5Department of Medical and Surgical Sciences, University of Catanzaro, Catanzaro, Italy

6Department of Colorectal Surgery, Clinica S. Rita, Vercelli, Italy

7Center for Cancer Epidemiology and Prevention, AO City of Health and Science, Turin, Italy

8Department of Surgical Sciences, University of Turin and Città della Salute e della Scienza, Turin, Italy

9Department of Medical Sciences, University of Turin, Turin, Italy

10MRC-HPA Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom

11Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic

*These authors contributed equally to this work

Correspondence to:

Alessio Naccarati, email: [email protected]

Keywords: next-generation sequencing; small non-coding RNA profiling; microRNAs; non-invasive biomarkers; surrogate tissues

Received: September 06, 2017     Accepted: November 15, 2017     Published: December 14, 2017

ABSTRACT

The role of non-coding RNAs in different biological processes and diseases is continuously expanding. Next-generation sequencing together with the parallel improvement of bioinformatics analyses allows the accurate detection and quantification of an increasing number of RNA species. With the aim of exploring new potential biomarkers for disease classification, a clear overview of the expression levels of common/unique small RNA species among different biospecimens is necessary. However, except for miRNAs in plasma, there are no substantial indications about the pattern of expression of various small RNAs in multiple specimens among healthy humans.

By analysing small RNA-sequencing data from 243 samples, we have identified and compared the most abundantly and uniformly expressed miRNAs and non-miRNA species of comparable size with the library preparation in four different specimens (plasma exosomes, stool, urine, and cervical scrapes).

Eleven miRNAs were commonly detected among all different specimens while 231 miRNAs were globally unique across them. Classification analysis using these miRNAs provided an accuracy of 99.6% to recognize the sample types. piRNAs and tRNAs were the most represented non-miRNA small RNAs detected in all specimen types that were analysed, particularly in urine samples. With the present data, the most uniformly expressed small RNAs in each sample type were also identified. A signature of small RNAs for each specimen could represent a reference gene set in validation studies by RT-qPCR.

Overall, the data reported hereby provide an insight of the constitution of the human miRNome and of other small non-coding RNAs in various specimens of healthy individuals.


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