Overview | Research directions | Group members | Collaborations | Selected Publications | Funding

Overview

RNA impacts nearly every aspect of gene expression and it is now clear that the majority of human genetic diseases are caused by mistakes in RNA metabolism. It has become progressively evident that RNA is not just a carrier of genetic information, but also a catalyst and a guide for sequence-specific recognition and processing of other RNA molecules. Progress in our understanding of RNA biology has made it possible to identify RNA molecules as targets of therapeutic intervention and to use RNA as a tool for functional studies and as a novel therapeutic molecule to treat human disease. Since a few years, RNA-based techniques (RNA interference, antisense RNA etc.) are becoming more and more useful in therapy and applied research. 

Professor Denti described her research on RNA Therapies for neurodegenerative disease in an interview by Osservatorio Terapie Avanzate (in italian).

A recent interview with Prof. Michela A. Denti on advantages and pitfalls of RNA-based therapeutics can be found here (in italian).

Details of the recent participation of the laboratory in the miRNADisEasy consortium, studying microRNAs as lung cancer biomarkers, can be found here (in six languages)

A description of the laboratory ongoing research, its significance and potential applications can be found here.

Simone Detassis talks about "Pitfalls and problems of miRNA expression analysis" in a webinar for the Oligonucleotide Therapeutics Society on February 12, 2019

The laboratory participates in COST Action 17103 "Delivery of Antisense RNA Therapeutics" https://antisenserna.eu

MiRNAQCD: MiRNA Quality Control and Diagnosis
A downloadable R-package to carry out quality control, training and classification analyses on datasets containing MiRNA multiplets.

Research directions

  • microRNAs (miRNAs). These are ca. 21 nt regulatory RNAs that control development and differentiation acting as post-transcriptional negative regulators of the expression of key target genes. Recent studies have demonstrated that there is altered expression of miRNA genes in several human malignancies and that miRNAs may act as oncogenes or tumour suppressors. MiRNAs are now also exploited as diagnostic and prognostic biomarkers. We carry out a functional analysis of the miRNAs specifically over- or under-expressed in lung cancers, melanoma, epithelial ovarian cancers and neurodegenerative diseases (e.g. Frontotemporal dementia) search for their target genes and investigate their role in pathogenesis;
  • Antisense RNA-induced exon skipping in gene therapy. The importance of alternative splicingfor the diversity of the proteome and the large number of genetic diseases that are due to splicing defects call for methods to modulate alternative splicing decisions. Although splicing can be modulated by antisense oligonucleotides, this approach is confronted with problems of efficient delivery and the need for repeated administrations of large amounts of oligonucleotides. Therefore, we developed a method to induce the efficient and specific skipping of an exon with the help of the U1 small nuclear RNA involved in pre-messenger RNA splicing in the nucleus. Antisense U1 snRNA-induced exon skipping has been successfully employed to devise a therapeutic strategy for Duchenne Muscular Dystrophy. We are now exploring the possibility to apply antisense U1 snRNA-induced exon skipping to other genetic disorders, such as Frontotemporal dementia, retinal dystrophies and metabolic diseases.

Group members

  • Michela A. Denti, PI
  • Francesca Precazzini, PostDoc 

Selected publications

Articles

Castelluzzo M, Perinelli A, Detassis S, Denti MA, Ricci L 2020 MiRNA-QC-and-Diagnosis: An R package for diagnosis based on MiRNA expression.
SoftwareX https://doi.org/10.1016/j.softx.2020.100569.

Detassis S, Del Vescovo V, Grasso M, Masella S, Cantaloni C, Cima L, Cavazza A, Graziano P, Rossi G, Barbareschi M, Ricci L, Denti MA. 2020 miR375-3p distinguishes low-grade neuroendocrine from non-neuroendocrine lung tumors in FFPE samples. Front. Mol. Biosci. 7:86. doi: 10.3389/fmolb.2020.00086

Masè M, Grasso M, Avogaro L, Nicolussi Giacomaz N, D’Amato E, Tessarolo F, Graffigna A, Denti MA*, Ravelli F*. Upregulation of miR-133b and miR-328 in Patients With Atrial Dilatation: Implications for Stretch-Induced Atrial Fibrillation. Front Physiol 10:1133 2019 doi: 10.3389/fphys.2019.01133 *equally contributing

Detassis S, Grasso M, Tabraue-Chávez M, Marin Romero A, Ilyine H, Ress C, Ceriani S, Erspan M, Maglione A, Díaz-Mochón J, Pernagallo S*, Denti MA* 2019 “A new platform for the direct profiling of microRNAs in biofluids.” Analytical Chemistry. 91 (9), 5874-5880 DOI: 10.1021/acs.analchem.9b00213. *equally contributing

Grasso M, Piscopo P, Talarico G, Ricci L, Crestini A, Tosto G, Gasparini M, Bruno G, Denti MA*, Confaloni A*. Plasma microRNAs profiling distinguishes patients with frontotemporal dementia from healthy subjects. 2019 Neurobiology of Aging. DOI: 10.1016/j.neurobiolaging.2019.01.024 In press. *equally contributing 

Piscopo P, Grasso M, Puopolo M, D’Acunto E, Talarico G, Crestini A, Gasparini M, Campopiano R, Gambardella S, Castellano AE, Bruno G, Denti MA*, Confaloni A*. “Circulating miR-127-3p as a biomarker for differential diagnosis in Frontotemporal Dementia.” 2018 Journal of Alzheimer’s Disease, 65: 455-464  *equally contributing 

Pistore C, Giannoni E, Colangelo T, Rizzo F, Magnani E, Muccillo L, Giurato G, Mancini M, Rizzo S, Riccardi M, Sahnane N, Del Vescovo V, Kishore K, Mandruzzato M, Macchi F, Pelizzola M, Denti MA, Furlan D, Weisz A, Colantuoni V, Chiarugi P, Bonapace IM “DNA methylation variations are required for epithelial-to-mesenchimal transition induced by cancer associate fibroblasts in prostate cancer cells” 2017 Oncogene doi:10.1038/onc.2017.159 

Masè M, Grasso M, Avogaro L, D'Amato E, Tessarolo F, Graffigna A, Denti MA*, Ravelli F*. “Selection of reference genes is critical for miRNA expression analysis in human cardiac tissue. A focus on atrial fibrillation.” 2017 Scientific Reports 7:41127 | DOI: 10.1038/srep41127 *equally contributing 

Ferri L, Covello G, Caciotti A, Guerrini R, Denti MA*, Morrone A* "Double-target antisense U1snRNAs correct mis-splicing due to GLA deep intronic mutations in Fabry Disease" 2016 Molecular Therapy Nucleic Acids 5, e380; doi:10.1038/mtna.2016.88 *equally contributing

Moncini M, Lunghi M Valmadre A, Grasso M, Del Vescovo V, Riva P, Denti MA, Venturin M “The miR-15/107 family of microRNA genes regulates CDK5R1/p35 with implications for Alzheimer’s disease pathogenesis" 2016 Mol Neurobiol. doi:10.1007/s12035-016-0002-4 

Piscopo P, Grasso M, Fontana F, Crestini A, Puopolo M, Del Vescovo V, Venerosi A, Calamandrei G, Vencken SF, Greene CM, Confaloni A, Denti MA "Reduced miR-659-3p levels correlate with progranulin increase in hypoxic conditions: implications for frontotemporal dementia" 2016 Front Mol Neurosci 9:31 doi: 10.3389/fnmol.2016.00031 

Ricci L, Del Vescovo V, Cantaloni C, Grasso M, Barbareschi M, Denti MA “Statistical analysis of a Bayesian classifier based on the expression of miRNAs” 2015 BMC Bioinformatics. 16(1):287. doi: 10.1186/s12859-015-0715-9.

Bacchi N, Messina A, Burtscher V, Dassi E, Provenzano G, Bozzi Y, Demontis GC, Koschak A*, Denti MA*, Casarosa S* “A new splicing isoform of Cacna2d4 mimicking the effects of c.2451insC mutation in the retina. Novel molecular and electrophysiological insights.” 2015 Invest Ophthalmol Vis Sci. 56(8):4846-56. doi: 10.1167/iovs.15-16410. *equally contributing

Covello G, Siva K, Adami V, Denti MA “An electroporation protocol for efficient DNA transfection in PC12 cells.” Cytotechnology 2014 66(4):543-553 DOI: 10.1007/s10616-013-9608-9

Bisio A, De Sanctis V, Del Vescovo V, Denti MA, Jegga AG, Inga A, Ciribilli Y  “Identification of new p53 target microRNAs by bioinformatics and functional analysis” BMC Cancer 2013 13:552

Del Vescovo V, Meier T, Inga A, Denti MA*, Borlak J* “A Cross-Platform Comparison of Affymetrix and Agilent Microarrays Reveals Discordant miRNA Expression in Lung Tumors of c-Raf Transgenic Mice”. PLoS ONE  2013 8(11): e78870. doi:10.1371/journal.pone.0078870 * equally contributing

Barbareschi M, Cantaloni C, Del Vescovo V, Cavazza A, Monica V, Carella R, Rossi G, Morelli L, Cucino A, Silvestri M, Tirone G, Pelosi G, Graziano P, Papotti M, Dalla Palma P, Doglioni C, Denti MA.“Heterogeneity of large cell carcinoma of the lung: an immunophenotypic and miRNA based analysis”. Am. J. Clin. Pathol. 2011 136:773-782. 

Del Vescovo V, Cantaloni C, Cucino A, Girlando S, Silvestri M, Bragantini E, Fasanella S, Cuorvo LV, Dalla Palma P, Rossi G, Papotti M, Pelosi G, Graziano P, Cavazza A, Denti MA, Barbareschi M.  "miR-205 expression levels in non-small cell lung cancer do not always distinguish adenocarcinomas from squamous cell carcinomas." Am. J. Surg. Pathol. 2011 35:268-275.

Reviewes

Detassis S, Grasso M, Del Vescovo V, Denti MA “microRNAs Make the Call in Cancer Personalized Medicine” 2017 Front. Cell Dev. Biol. 5:86 doi: 10.3389/fcell.2017.00086 

Godfrey C, Desviat LR, Smedsrod B, Piétri-Rouxel F, Denti MA, Disterer P, Lorain S, Nogales-Gadea G, Sardone V, Anwar R, El Andaloussi S, Lehto T, Khoo B, Brolin Hjortkjaer C, van Roon-Mom WMC, Goyenvalle A, Aartsma-Rus A, Arechavala-Gomeza V “Delivery is key: lessons learnt from developing splice switching antisense therapy” 2017 EMBO Molecular Medicine doi: 10.15252/emmm.201607199 

Fontana F, Siva K, Denti MA “A network in Fronto Temporal Dementia - an RNA perspective” 2015 Front Mol Neurosci 8:9 doi: 10.3389/fnmol.2015.00009.

Grasso M, Piscopo P, Confaloni A, Denti MA “Circulating miRNAs as biomakers for neurodegenerative diseases”. 2014 Molecules 19:6891-6910. doi:10.3390/molecules19056891 

Bacchi N, Casarosa S*, Denti MA* “Splicing-correcting therapeutic approaches for retinal dystrophies: where endogenous gene regulation and specificity matter.” 2014 Invest Ophthalmol Visual Sci. 55(5):3285-94. doi: 10.1167/iovs.14-14544.  *equally contributing

Del Vescovo V, Grasso M, Barbareschi M, Denti MA, "microRNAs as lung cancer biomarkers" World Journal Clinical Oncology 2014 5(4):604-620; doi:10.5306/wjco.v5.i4.604

Siva K, Covello G, Denti MA “Exon-skipping Antisense Oligonucleotides to Correct Missplicing in Neurogenetic Diseases” Nucl. Acids Therap. 2014 24(1): 69-86. doi:10.1089/nat.2013.0461 

Book chapters

Denti MA and Covello G  “Oligonucleotide therapy” in “Safety and Efficacy of Gene-Based Therapeutics for Inherited Disorders” 2017 Nicola Brunetti-Pierri (Ed.) Springer ISBN 978-3-319-53455-8 DOI 10.1007/978-3-319-53457-2_8 

Del Vescovo V, Denti MA “microRNA and lung cancer” in “microRNA: Cancer. From molecular biology to clinical practice”  2015 Gaetano Santulli (Ed.) Springer ISBN 978-3-319-23729-9 

Grasso M, Piscopo P, Crestini A, Confaloni A, Denti MA  “Circulating microRNAs in neurodegenerative diseases” in “Circulating microRNAs in disease diagnostics and their potential biological relevance” 2015 Peter Igaz (Ed.) Springer ISBN 978-3-0348-0953-5

Grasso M, Fontana F, Denti MA  “Circulating cell-free microRNAs as biomarkers for neurodegenerative diseases” in “Frontiers in Neurotherapeutics: Mapping Nervous System Diseases via microRNAs”.  2015 Christian Barbato and Francesca Ruberti (Eds.) CRC Press-Taylor & Francis Group (Boca Raton FL, USA) ISBN 9781482263527.

 

Funding

European Commission, Marie Skłodowska-Curie Actions - Reasearch and Innovation Staff Exchange“miRNA-DisEASY:microRNA biomarkers in an innovative biophotonic sensor kit for high-specific diagnosis”

Fondazione Cassa di Risparmio di Trento e Rovereto, Bando Ricerca e Sviluppo 2019 Un dispositivo diagnostico innovativo per la misurazione di microRNA in biopsie liquide