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Differential Expression of Hippocampal Circular RNAs in the BTBR Mouse Model for Autism Spectrum Disorder

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Abstract

Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition with unknown etiology. Recent experimental evidences suggest the contribution of non-coding RNAs (ncRNAs) in the pathophysiology of ASD. In this work, we aimed to investigate the expression profile of the ncRNA class of circular RNAs (circRNAs) in the hippocampus of the BTBR T + tf/J (BTBR) mouse model and age-matched C57BL/6J (B6) mice. Alongside, we analyzed BTBR hippocampal gene expression profile to evaluate possible correlations between the differential abundance of circular and linear gene products. From RNA sequencing data, we identified circRNAs highly modulated in BTBR mice. Thirteen circRNAs and their corresponding linear isoforms were validated by RT-qPCR analysis. The BTBR-regulated circCdh9 was better characterized in terms of molecular structure and expression, highlighting altered levels not only in the hippocampus, but also in the cerebellum, prefrontal cortex, and amygdala. Finally, gene expression analysis of the BTBR hippocampus pinpointed altered biological and molecular pathways relevant for the ASD phenotype. By comparison of circRNA and gene expression profiles, we identified 6 genes significantly regulated at either circRNA or mRNA gene products, suggesting low overall correlation between circRNA and host gene expression. In conclusion, our results indicate a consistent deregulation of circRNA expression in the hippocampus of BTBR mice. ASD-related circRNAs should be considered in functional studies to identify their contribution to the etiology of the disorder. In addition, as abundant and highly stable molecules, circRNAs represent interesting potential biomarkers for autism.

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Abbreviations

ASD:

Autism spectrum disorder

ncRNAs:

Non-coding RNAs

circRNAs:

Circular RNAs

BTBR:

BTBR T + tf/J

B6:

C57BL/6J

lncRNAs:

Long non-coding RNAs

DEC:

Differentially expressed circRNA

DEG:

Differentially expressed gene

miscRNA:

Miscellaneous RNA

Cb:

Cerebellum

VS:

Ventral striatum

Pfx:

Prefrontal cortex

Amy:

Amygdala

HS:

Heparan sulfate

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Acknowledgements

We thank the Institute of Applied Genomics for sequencing and Bio-Fab Research for helpful technical support.

Funding

This work was supported by 2018-LIFE2020-REG LAZIO to C.P.; and ELIXIR-IIB and Cineca, Call HPC@Cineca, to C.M.

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Authors and Affiliations

  1. Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy

    Silvia Gasparini, Giorgia Del Vecchio, Ivano Legnini, Valerio Licursi, Arianna Rinaldi & Carlo Presutti

  2. SCAI-Super Computing Applications and Innovation Department, CINECA, Rome, Italy

    Silvia Gioiosa, Tiziano Flati & Tiziana Castrignano

  3. Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, National Research Council, Bari, Italy

    Silvia Gioiosa & Tiziano Flati

  4. Department of Ecological and Biological, Sciences University of Tuscia, Viterbo, Italy

    Tiziana Castrignano

  5. National Institute of Health, Rome, Italy

    Laura Ricceri & Maria Luisa Scattoni

  6. Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy

    Cecilia Mannironi

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  1. Silvia Gasparini
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  2. Giorgia Del Vecchio
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Correspondence to Carlo Presutti or Cecilia Mannironi.

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All experiments were conducted in strict accordance with the European Community and Italian Nation regulation of animal use in research, and following NIH guidelines on animal care. The authors declare that they have no competing interests.

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Fig. S1

Pearson’s correlation between RNA-seq and RT-qPCR data. The analysis was done on 12 circRNAs. (a) Pearson’s correlation graph. R2 and p are indicated. (b) RNA-seq and RT-qPCR data are expressed as log2FC. Dots in black (panel a) and characters in bold (panel b) highlight circRNAs with a Pearson’s significant correlation (see Fig. 2b in the main manuscript). (PNG 31 kb)

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Gasparini, S., Del Vecchio, G., Gioiosa, S. et al. Differential Expression of Hippocampal Circular RNAs in the BTBR Mouse Model for Autism Spectrum Disorder. Mol Neurobiol 57, 2301–2313 (2020). https://doi.org/10.1007/s12035-020-01878-6

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