Overview

The knowledge of epigenetics mechanisms is crucial not only to better understand normal brain development, plasticity, and function, but also to dissect pathways that are malfunctioning in diseases. Exploring epigenetic mechanisms underlying pathogenic processes thus represents a novel road to identify possible disease modifiers and eventually druggable molecules, which may be targeted or protected during the early phases of the disease progression. Our laboratory aims to investigate the epigenetic basis of complex brain functions, (i.e.: alterations in chromatin remodeling complexes, histone modification patterns and non-coding RNAs) and how it might contribute to neurodevelopmental and neurodegenerative disorders.

The laboratory uses two different paradigms of genetic disorders of the central nervous system, neurodevelopment and neurodegeneration, specifically focusing on AUTISM and HUNTINGTON’S DISEASE.

Research directions

SINEUP RNAs: a new platform for treating haploinsufficiency in Autism Spectrum Disorders (ASD)

Recently funded by: Simons Foundation Autism Research Initiative - Genomics of ASD: Pathways to Biological Convergence and Genetic Therapies (2023-2025).

Autism Spectrum Disorder (ASD) is a highly heterogeneous condition with complex genetic contributions. Most of the currently known high-confidence ASD risk genes harbor de novo disruptive mutations, causing haploinsufficiency. Given that these mutations usually affect only one allele, a potential therapeutic avenue resides in stimulating the expression from the non-mutant allele to restore the protein to physiological levels. 

In this project, we will exploit the modular architecture of SINEUPs, a functional class of non-coding RNAs molecules able to increase target protein levels without altering the expression of their host mRNA.

In our recent investigations, we targeted the chromodomain helicase DNA-binding 8 (CHD8), one of the strongest risk factors for ASD. By employing synthetic SINEUP-CHD8, we efficiently stimulated endogenous CHD8 protein production in human cells and patients’ derived fibroblasts.

Thus, building on these promising results, here, we aim to provide a Proof-of-Concept towards the development of a novel RNA-based therapy for neurodevelopmental syndromes with implications for and beyond CHD8. Particularly, it is relevant to ASDs caused by protein haploinsufficiency. 

• We will provide a deeper analysis of SINEUP efficacy to rescue dysfunctional phenotypes associated to Chd8-suppression in a complex, in vivo mouse preclinical model. 
• We will translate the knowledge gained studying SINEUP-CHD8 - horizontally - to synthesize new active SINEUPs targeting other strong ASD risk factors, caused by gene haploinsufficiency. 

Telomeres dysfunction in Autism Spectrum Disorders

Telomeres are peculiar structures that cap the end of the eukaryotic chromosomes and are crucial for the correct replication of DNA, thus preserving genome integrity. Alteration in telomeres’ length (TL) and integrity are increasingly associated to disease processes, ranging from cancer on one site and extending to several neuropsychiatric disorders on the other site. Specifically, correlative evidence is now emerging reporting alterations in TL in patients with ASD. 

Telomeres integrity is regulated by TERRA, long non-coding RNA transcripts synthetized from sub-telomeric regions and spanning the telomeres. The abundance of TERRA strictly relates to the stability of telomeres and, in turn, to chromosome integrity. Interestingly, chromatin regulators of the chromodomain helicase DNA binding family (CHD8, CHD2, CHD1, CHD3) and RNA binding proteins of the heterogeneous ribonucleoproteins (hnRNPs) family, all prominent risk factors for ASD, were reported to interact with TERRA non-coding RNAs. 

Thus, altogether, these observations suggest a so far unexplored piece of ASD biology: a functional interplay between TERRA, telomeres and strong risk genes in ASD. Alterations in this intrinsic regulatory pathway might correlate to telomeres length maintenance and warrants in depth investigations to understand neglected ASD-relevant mechanisms, thus, possibly illuminating new therapeutic strategies.

Genetic approaches to the study of Huntington’s Disease (HD): morphological studies, transcriptional regulation and single-cell genomics

Recently funded by European Huntington’s Disease Network (EHDN).

This autosomal dominant hereditary neurodegenerative disorder is caused by a CAG trinucleotide repeat expansion in exon 1 of the huntingtin gene, which leads to diffuse neuronal loss in the striatum and cortex and, eventually, death. 

• D1R- and D2R-Medium-Sized Spiny Neurons (MSNs) diversity: insights into striatal vulnerability to Huntington's Disease mutation.
  Although the HTT gene is ubiquitously expressed, the striatum appears to be the most susceptible district to the HD mutation, with MSNs (D1R and D2R) representing 95% of the its neuronal population. Why are striatal MSNs so vulnerable to the HD mutation? Particularly, why do D1R- and D2R-MSNs display different susceptibility to HD? Here, we aim to characterize significant differences between D1R- and D2R-MSNs subpopulations, analysing morphology, transcriptomic and somatic instability in zQ175 knock-in HD mouse model. 
• Enteric Nervous System (ENS) in Huntington’s Disease (HD): neglected phenotypes as possible new disease modifiers- recently funded by the EHDN seed fund.
  While central nervous system phenotypes have been deeply characterized in HD, a number of less described, but strongly disabling peripheral symptoms, including unintended weight loss and gastrointestinal (GI) dysfunction, significantly impact patients’ life quality. Composed by more than a dozen of different neuronal types, the ENS controls GI motility, secretions, digestion, peristalsis, and other functions. Different studies, also in other neurodegenerative diseases, report that alterations in the ENS can lead to GI dysfunction, including dysphagia, the principal cause of fatal pneumonia in HD patients. While experiments on HD mice initially established a correlation between weight loss and GI dysfunction, systematic cellular and molecular studies are still lacking. Here, we propose to characterize the GI changes, ascribable to ENS alterations, taking advantage of wild-type (WT) and Htt knock-in (zQ175, HD) mice, which faithfully mirror the genetics of HD. Specifically, we will conduct:
  • a comprehensive anatomical characterization of possible ENS alterations;
  • an evaluation of GI functionality; 
  • an inclusive single-cell transcriptome analysis of enteric neurons and glia.

CircRNAs alteration in Huntington’s Disease pathogenesis

Recently funded by EMBO postdoctoral fellow (ALTF 897-2021) and Hereditary Disease Foundation (HDF)

Alternative Splicing regulation is crucial not only to the establishment of a repertoire of protein coding RNA isoforms extremely relevant for normal physiology (particularly in neurons), but also to the biogenesis of circular RNAs (circRNAs), a newly re-discovered class of non-coding RNAs. Unusually stable, they are produced by the circularization of exons. Mostly cytosolic in eukaryotic cells, circRNAs are particularly enriched and conserved in neurons. In recent years, the functional relevance of these molecules as novel regulators of cell physiology and during brain development and neurological disorders has become evident. 

The main goal of our research is to discover early alterations in circRNAs globally at genome-wide level. Our hypothesis suggests that huntingtin might directly or indirectly regulate alternative splicing machinery, thus altering global linear splicing, but also exerting a large effect on circRNAs. This highly innovative study will be crucial to the identification of new, key targets for therapeutic intervention as well as new biomarker candidates for the disease.

Recently, we identified and experimentally validated the first brain enriched RNA circle originating from the human HTT locus, circHTT, conserved in mouse, circHtt, and mini-pig. We validated the circularity of the identified molecules by divergent primer amplification, sequencing and RNase R treatment. CircHTT/circHtt expression augments significantly with increasing number of CAG repeats in terminally differentiated cortical neurons, and in brain districts of HD mouse models. Now, our research focuses on characterizing its temporal and spatial expression dynamics in the developing and aging mouse brain, its molecular and cellular function in the nervous system as well as its potential relevance for HD pathophysiology. 

Group members

• Marta Biagioli, Ph.D., Principal Investigator
• Jasmin Morandell, Ph.D., EMBO postdoctoral fellow (ALTF 897-2021)
• Guendalina Bergonzoni, Ph.D Student in Biomolecular Sciences (UNITN)
• Miguel Pellegrini, MsS in Cellular and Molecular Biotechnologies (UNITN)
• Samuele Maturi, Master’s student in Cellular and Molecular Biotechnologies (UNITN)
• Dalia Bortolotti, Master’s student in Cellular and Molecular Biotechnologies (UNITN)
• Lisa Lionello, Bachelors’s student in Biomolecular Sciences and Technologies (UNITN)
• Martina Lazioli, Bachelor’s student in Biomolecular Sciences and Technologies (UNITN)

We are actively looking for highly motivated, competitive postdoctoral fellows, Master’s and Ph.D. students interested in these challenging and charming topics. Please contact the PI (marta.biagioli [at] unitn.it) for inquiries. 

Ongoing collaborations

We are part of TRAIN - TRentino Autism INitiative
Stefano Gustincich, S.I.S.S.A - IIT Genova (Italy)
Stefano Espinoza, Università del Piemonte Orientale (University of Eastern Piedmont) (Italy)
Michael E. Talkowski, Harvard Medical School - Boston (U.S.A.)
Marcy E. MacDonald, Harvard Medical School - Boston (U.S.A.)
IhnSik Seong, Harvard Medical School - Boston (U.S.A.)
Thierry Vöet, Sanger Institute-EBI Single-Cell Genomics Center, Cambridge (UK) 
Emilio Cusanelli, Laboratory of Cell Biology and Molecular Genetics, CIBIO - Trento (Italy)
Toma Tebaldi, Laboratory of RNA and Disease Data Science, CIBIO - Trento (Italy)
Albert Basson, King's College - London (UK)
Christelle Golzio, Department of Translational Medicine and Neurogenetics, Institut de Génétic et de Bioligie Moléculare et Cellulare - IGBMC (France)
Giovanni Provenzano, Laboratory of Molecular and Behavioural Neuroscience, CIBIO – Trento (Italy)
Marco Caprini, Department of Pharmacy and Biotechnology, University of Bologna (Italy)
Ulrika Marklund, Research Division of Molecular Neurobiology - Ulrika Marklund group, Karolinska Instititet (Sweden)
Alessandro Gozzi, IIT Rovereto

Selected publications

Emanuela Kerschbamer, Michele Arnoldi, Takshashila Tripathi, Miguel Pellegrini, Samuele Maturi,Serkan Erdin, Elisa Salviato, Francesca Di Leva, Endre Sebestyén, Erik Dassi, Giulia Zarantonello, Matteo Benelli, Eric Campos, M. Albert Basson, James F. Gusella, Stefano Gustincich, Silvano Piazza, Francesca Demichelis, Michael E. Talkowski, Francesco Ferrari, and Marta Biagioli (2022). CHD8 Suppression Impacts on Histone H3 Lysine 36 Trimethylation and Alters RNA Alternative Splicing. Nucleic Acid Research.

Miguel Pellegrini, Guendalina Bergonzoni, Federica Perroni, Ferdinando Squitieri, Biagioli Marta (2022). Current Diagnostic Methods and Non-Coding RNAs as Possible Biomarkers in Huntington’s Disease. Genes, 13(11), 2017. 

Michele Arnoldi, Giulia Zarantonello, Stefano Espinoza, Stefano Gustincich, Francesca Di Leva, Marta Biagioli (2022). Design and Delivery of SINEUP: A New Modular Tool to Increase Protein Translation. Methods Mol Biol, 2434:63-87.

Giulia Zarantonello, Michele Arnoldi, Michele Filosi, Toma Tebaldi, Giovanni Spirito, Anna Barbieri, Stefano Gustincich, Remo Sanges, Enrico Domenici, Francesca Di Leva, Marta Biagioli (2021). Natural SINEUP RNAs in Autism Spectrum Disorders: RAB11B-AS1 Dysregulation in a Neuronal CHD8 Suppression Model Leads to RAB11B Protein Increase. Frontiers in Genetetics, 12:745229.

Guendalina Bergonzoni, Jessica Döring, Marta Biagioli(*). D1R-and D2R-Medium-Sized Spiny Neurons Diversity: Insights IntoStriatal Vulnerability to Huntington’s Disease Mutation. Frontiers in Cellular Neuroscience 2021. 15, 16. (*) Corresponding author

Vidya Murthy, Toma Tebaldi, Toshimi Yoshida, Serkan Erdin, Teresa Calzonetti, Ravi Vijayvargia, Takshashila Tripathi, Emanuela Kerschbamer, Ihn Sik Seong, Alessandro Quattrone, Michael E. Talkowski, James F. Gusella, Katia Georgopoulos, Marcy E. MacDonald, Marta Biagioli(*). ‘Hypomorphic mutation of the mouse Huntington’s disease gene orthologue’.PLoS Genet 2019 Mar 21;15(3):e1007765. (*) Corresponding author.

Primoz Knap, Toma Tebaldi, Francesca Di Leva, Marta Biagioli, Mauro Dalla Serra, Gabriella Viero. The Unexpected Tuners: Are LncRNAs Regulating Host Translation during Infections? 2017. Toxins9 (11), 357.

The HD iPSC Consortium -Ryan G Lim, Lisa L Salazar, Daniel K Wilton [….Marta Biagioli.....] and Clive N Svendsen. Developmental alterations in Huntington's disease neural cells and pharmacological rescue in cells and mice. Nature Neuroscience, 2017. 20(5):648-660.

Emanuela Kerschbamer and Marta Biagioli. Huntington's Disease as Neurodevelopmental Disorder: Altered Chromatin Regulation, Coding, and Non-Coding RNA Transcription. Frontiers in Neuroscience.2016 Jan 13;9:509.  

For a complete list: https://pubmed.ncbi.nlm.nih.gov/?term=marta%20biagioli&page=3