Biology subjects

Malatesta, P.

Publications and source records attributed to Malatesta, P..

4 recordsLinked to original sources

bioRxiv2026

Chronic Proliferation and Glia Heterogeneity in CMT1A: Involvement of RUNX2-Positive Schwann Cells and Endoneurial Fibroblasts

Charcot Marie Tooth type 1A (CMT1A) is the most common inherited peripheral neuropathy, caused by duplication of the peripheral myelin protein 22 (PMP22) gene and characterized by dysmyelination and defects in myelin maturation. Hypercellularity is a prominent feature of the disease, although its origin, persistence, and underlying mechanisms remain controversial. Here, we performed a longitudinal analysis of sciatic nerves from wild-type (WT) and CMT1A rats between 2 and 12 months of age. We demonstrated that CMT1A nerves exhibit persistent cellular proliferation extending into adulthood. This phenotype is confirmed by bulk RNA-seq data showing sustained enrichment of proliferation-associated gene signatures. Cell type signature analysis identifies overrepresentation of immature, neural crest related, and epithelial mesenchymal transitional (EMT) transcriptional programs in CMT1A nerves. Among the most upregulated genes, RUNX2 showed strong and prolonged expression at both transcript and protein levels. Consistently with the key role of RUNX2 in the activation of the injury response, CMT1A nerves also showed a marked enrichment in SOX10+JUN+ cells, that only partially overlap with SOX10+RUNX2+ cells, indicating a maladaptive activation of the injury-like Schwann cell (SC) program. Interestingly, we detected robust upregulation of SMOC2, an extracellular matrix protein selectively expressed by endoneurial fibroblasts, pointing to activation of non-canonical cell types and altered extracellular matrix remodeling. Together, these data demonstrate that CMT1A peripheral nerves are characterized by chronic hypercellularity driven by persistent proliferation, EMT, and dysregulated injury transcriptional programs, collectively pointing at progressive and multicellular nerve remodeling as a relevant pathomechanism in the disease.

neuroscience↗

bioRxiv2026

Entanglement-based continuum conformational landscape of proteins

MotivationWith the rapid development of AI methods that predict protein structures from sequence, understanding the structure-function relation increasingly depends on quantitative structural descriptors that are both biologically meaningful and scalable to large datasets. Here, we introduce mathematical topology metrics that quantify the entanglement complexity of a tertiary protein structure while respecting uncrossability constraints. ResultsBy employing only three such metrics across all protein structures in the Protein Data Bank, we represent the proteome structural space in a continuous three-dimensional space. Distances within this space capture structural similarity and correlate with functional similarity. We find that the mathematical entanglement based landscape of protein structural space diversifies with the evolutionary expansion of protein function across species. Moreover, this continuous representation reproduces CATH classifications with high accuracy for major structural classes. These results indicate that these metrics efficiently encode structural features linked to protein function and provide a more informative description than conventional metrics. AvailabilityData used in this study are available in the Protein Data Bank. Details of the machine learning model used can be found in https://github.com/roshitac/CATH_Classification-. ContactBanu.Ozkan@asu.edu, Eleni.Panagiotou@asu.edu Supplementary informationSupplementary data are available at Journal Name online.

molecular biology↗

bioRxiv2020

An Eutherian-Specific microRNA Controls the Translation of Satb2 in a Model of Cortical Differentiation

Cerebral cortical development is controlled by key transcription factors that specify the neuronal identities in the different cortical layers. These transcription factors are crucial for the identity of the different neurons, but the mechanisms controlling their expression in distinct cells are only partially known. Here we investigate the expression and stability of the mRNAs of Tbr1, Bcl11b, Fezf2, Satb2 and Cux1 in single developing mouse cortical cells. We focus on Satb2 and find that its mRNA expression occurs much earlier than its protein synthesis and in a set of cells broader than expected, suggesting an initially tight control of its translation, which is subsequently de-repressed at late developmental stages. Mechanistically, Satb2 3UTR modulates protein translation of GFP reporters during mouse corticogenesis. By in vitro pull-down of Satb2 3UTR-associated miRNAs, we select putative miRNAs responsible for SATB2 inhibition, focusing on those strongly expressed in early progenitor cells and reduced in late cells. miR-541, an Eutherian-specific miRNA, and miR-92a/b are the best candidates and their inactivation triggers robust and premature SATB2 translation in both mouse and human cortical cells. Our findings indicate that RNA interference plays a major role in the timing of cortical cell identity and may be part of the toolkit involved in specifying supra-granular projection neurons.

developmental biology↗

bioRxiv2020

Sox2-dependent maintenance of mouse oligodendroglioma involves the Sox2-mediated downregulation of Cdkn2b, Ebf1, Zfp423 and Hey2

Cancer stem cells (CSC) are essential for tumorigenesis. The transcription factor Sox2 is overexpressed in brain tumors. In gliomas, Sox2 is essential to maintain CSC. In mouse high-grade glioma pHGG, Sox2 deletion causes cell proliferation arrest and inability to reform tumors in vivo; 134 genes are significantly derepressed. To identify genes mediating the effects of Sox2 deletion, we overexpressed into pHGG cells nine among the most derepressed genes, and identified four genes, Cdkn2b, Ebf1, Zfp423 and Hey2, that strongly reduced cell proliferation in vitro and brain tumorigenesis in vivo. CRISPR/Cas9 mutagenesis, or pharmacological inactivation, of each of these genes, individually, showed that their activity is essential for the proliferation arrest caused by Sox2 deletion. These Sox2-inhibited antioncogenes also inhibited clonogenicity in primary human glioblastoma-derived cancer stem-like cell lines. These experiments identify critical anti-oncogenic factors whose inhibition by Sox2 is involved in CSC maintenance, defining new potential therapeutic targets for gliomas. Table of Contents Image O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/976811v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@1c42c8forg.highwire.dtl.DTLVardef@496b73org.highwire.dtl.DTLVardef@2d4c31org.highwire.dtl.DTLVardef@1e5367e_HPS_FORMAT_FIGEXP M_FIG C_FIG Main PointsSox2 maintains glioma tumorigenicity by repressing the antioncogenic activity of a regulatory network involving the Ebf1, Hey2, Cdkn2b and Zfp423 genes. Mutation of these genes prevents the cell proliferation arrest of Sox2-deleted glioma cells.

cancer biology↗