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

G. Ferrero, F. Cordero, S. Tarallo, M. Arigoni, F. Riccardo, G. Gallo, G. Ronco, M. Allasia, N. Kulkarni, G. Matullo, P. Vineis, RA. Calogero, B. Pardini, A. Naccarati,

. 2018 ; 9 (3) : 3097-3111. [pub] 20171214

Language English Country United States

Document type Journal Article

Persistent link   https://www.medvik.cz/link/bmc18010016

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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$a The role of non-coding RNAs in different biological processes and diseases is continuously expanding. Next-generation sequencing together with the parallel improvement of bioinformatics analyses allows the accurate detection and quantification of an increasing number of RNA species. With the aim of exploring new potential biomarkers for disease classification, a clear overview of the expression levels of common/unique small RNA species among different biospecimens is necessary. However, except for miRNAs in plasma, there are no substantial indications about the pattern of expression of various small RNAs in multiple specimens among healthy humans. By analysing small RNA-sequencing data from 243 samples, we have identified and compared the most abundantly and uniformly expressed miRNAs and non-miRNA species of comparable size with the library preparation in four different specimens (plasma exosomes, stool, urine, and cervical scrapes). Eleven miRNAs were commonly detected among all different specimens while 231 miRNAs were globally unique across them. Classification analysis using these miRNAs provided an accuracy of 99.6% to recognize the sample types. piRNAs and tRNAs were the most represented non-miRNA small RNAs detected in all specimen types that were analysed, particularly in urine samples. With the present data, the most uniformly expressed small RNAs in each sample type were also identified. A signature of small RNAs for each specimen could represent a reference gene set in validation studies by RT-qPCR. Overall, the data reported hereby provide an insight of the constitution of the human miRNome and of other small non-coding RNAs in various specimens of healthy individuals.
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$a Cordero, Francesca $u Department of Computer Science, University of Turin, Turin, Italy. Italian Institute for Genomic Medicine, IIGM (formerly Human Genetics Foundation, HuGeF), Turin, Italy.
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$a Tarallo, Sonia $u Italian Institute for Genomic Medicine, IIGM (formerly Human Genetics Foundation, HuGeF), Turin, Italy.
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$a Arigoni, Maddalena $u Molecular Biotechnology Center, Department of Biotechnology and Health Sciences, University of Turin, Turin, Italy.
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$a Riccardo, Federica $u Molecular Biotechnology Center, Department of Biotechnology and Health Sciences, University of Turin, Turin, Italy.
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$a Gallo, Gaetano $u Department of Medical and Surgical Sciences, University of Catanzaro, Catanzaro, Italy. Department of Colorectal Surgery, Clinica S. Rita, Vercelli, Italy.
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$a Ronco, Guglielmo $u Center for Cancer Epidemiology and Prevention, AO City of Health and Science, Turin, Italy.
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$a Allasia, Marco $u Department of Surgical Sciences, University of Turin and Città della Salute e della Scienza, Turin, Italy.
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$a Kulkarni, Neha $u Molecular Biotechnology Center, Department of Biotechnology and Health Sciences, University of Turin, Turin, Italy.
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$a Vineis, Paolo $u Italian Institute for Genomic Medicine, IIGM (formerly Human Genetics Foundation, HuGeF), Turin, Italy. MRC-HPA Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom.
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$a Naccarati, Alessio $u Italian Institute for Genomic Medicine, IIGM (formerly Human Genetics Foundation, HuGeF), Turin, Italy. Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic.
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