Multiscale modeling uncovers 7q11.23 copy number variation–dependent changes in ribosomal biogenesis and neuronal maturation and excitability
Marija Mihailovich, Pierre-Luc Germain, Reinald Shyti, Davide Pozzi, Roberta Noberini, Yansheng Liu, Davide Aprile, Erika Tenderini, Flavia Troglio, Sebastiano Trattaro, Sonia Fabris, Ummi Ciptasari, Marco Tullio Rigoli, Nicolò Caporale, Giuseppe D’Agostino, Filippo Mirabella, Alessandro Vitriolo, Daniele Capocefalo, Adrianos Skaros, Agnese Virginia Franchini, Sara Ricciardi, Ida Biunno, Antonino Neri, Nael Nadif Kasri, Tiziana Bonaldi, Rudolf Aebersold, Michela Matteoli, Giuseppe Testa
Marija Mihailovich, Pierre-Luc Germain, Reinald Shyti, Davide Pozzi, Roberta Noberini, Yansheng Liu, Davide Aprile, Erika Tenderini, Flavia Troglio, Sebastiano Trattaro, Sonia Fabris, Ummi Ciptasari, Marco Tullio Rigoli, Nicolò Caporale, Giuseppe D’Agostino, Filippo Mirabella, Alessandro Vitriolo, Daniele Capocefalo, Adrianos Skaros, Agnese Virginia Franchini, Sara Ricciardi, Ida Biunno, Antonino Neri, Nael Nadif Kasri, Tiziana Bonaldi, Rudolf Aebersold, Michela Matteoli, Giuseppe Testa
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Research Article Neuroscience

Multiscale modeling uncovers 7q11.23 copy number variation–dependent changes in ribosomal biogenesis and neuronal maturation and excitability

Abstract

Copy number variation (CNV) at 7q11.23 causes Williams-Beuren syndrome (WBS) and 7q microduplication syndrome (7Dup), neurodevelopmental disorders (NDDs) featuring intellectual disability accompanied by symmetrically opposite neurocognitive features. Although significant progress has been made in understanding the molecular mechanisms underlying 7q11.23-related pathophysiology, the propagation of CNV dosage across gene expression layers and their interplay remains elusive. Here we uncovered 7q11.23 dosage–dependent symmetrically opposite dynamics in neuronal differentiation and intrinsic excitability. By integrating transcriptomics, translatomics, and proteomics of patient-derived and isogenic induced neurons, we found that genes related to neuronal transmission follow 7q11.23 dosage and are transcriptionally controlled, while translational factors and ribosomal genes are posttranscriptionally buffered. Consistently, we found phosphorylated RPS6 (p-RPS6) downregulated in WBS and upregulated in 7Dup. Surprisingly, p-4EBP was changed in the opposite direction, reflecting dosage-specific changes in total 4EBP levels. This highlights different dosage-sensitive dyregulations of the mTOR pathway as well as distinct roles of p-RPS6 and p-4EBP during neurogenesis. Our work demonstrates the importance of multiscale disease modeling across molecular and functional layers, uncovers the pathophysiological relevance of ribosomal biogenesis in a paradigmatic pair of NDDs, and uncouples the roles of p-RPS6 and p-4EBP as mechanistically actionable relays in NDDs.

Authors

Marija Mihailovich, Pierre-Luc Germain, Reinald Shyti, Davide Pozzi, Roberta Noberini, Yansheng Liu, Davide Aprile, Erika Tenderini, Flavia Troglio, Sebastiano Trattaro, Sonia Fabris, Ummi Ciptasari, Marco Tullio Rigoli, Nicolò Caporale, Giuseppe D’Agostino, Filippo Mirabella, Alessandro Vitriolo, Daniele Capocefalo, Adrianos Skaros, Agnese Virginia Franchini, Sara Ricciardi, Ida Biunno, Antonino Neri, Nael Nadif Kasri, Tiziana Bonaldi, Rudolf Aebersold, Michela Matteoli, Giuseppe Testa

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Figure 7

REST mediates WBS pathophysiological phenotypes.

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REST mediates WBS pathophysiological phenotypes. (A) Master regulator an...
(A) Master regulator analysis of the 7q11.23 dosage–dependent genes based on transcription factor–curated targets. The x and y axes respectively indicate the magnitude and significance of the inferred changes in the activity, while the color and size respectively indicate the magnitude and significance of the change in expression of the factor at the RNA level. Factors in a box are consistent and statistically significant in both activity and expression. nES, normalized enrichment score. (B) The genes altered in WBS versus control and rescued by REST inhibition in isoWBS iNeurons are especially associated with potassium ion transmembrane transport and extracellular structural organization. (C) Heatmap showing potassium transport and translation-related genes that were consistently differentially expressed in WBS iNeurons and were rescued by REST inhibitor (RESTi) in isogenic lines. Note that for ease of comparison between the inhibition experiment and 7q11.23 CNV, the fold changes are shown relative to WBS.