((Commentary on pmic.202400385 - title of the Commentary t.b.a.)) Extracellular Origins of Cognition: Lessons from Primate Neocortical ECM

((Commentary on pmic.202400385 - title of the Commentary t.b.a.)) Extracellular Origins of Cognition: Lessons from Primate Neocortical ECM | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL PROTEOMICS This is a preprint and has not been peer reviewed. Data may be preliminary. 22 May 2025 V1 Latest version Share on ((Commentary on pmic.202400385 - title of the Commentary t.b.a.)) Extracellular Origins of Cognition: Lessons from Primate Neocortical ECM Author : Shani Stern 0000-0002-2644-7068 [email protected] Authors Info & Affiliations https://doi.org/10.22541/au.174792832.29560731/v1 258 views 206 downloads Contents Abstract Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract The brain’s extracellular matrix (ECM) is an intricate and dynamic network that plays essential roles in neurodevelopment, synaptic plasticity, and circuit stability. Despite its importance, the molecular composition and spatial organization of the developing brain ECM remain poorly characterized. In this commentary, we highlight the recent study by Vilicich et al., which employs a multi-modal approach, integrating single-cell transcriptomics, proteomics, and immunohistofluorescence, to construct a map of the ECM in the developing neocortex of humans and non-human primates. By curating a comprehensive list of extracellular proteins termed the ”Exomatrix” and analyzing their distribution across cortical layers and developmental stages, the authors reveal layer-specific and evolutionarily conserved ECM features. These findings not only expand our understanding of ECM’s role in shaping the brain during early development but also emphasize its potential involvement in the pathogenesis of neurodevelopmental disorders, urging further research into ECM biology as a frontier in neuroscience. Abstract The brain’s extracellular matrix (ECM) is an intricate and dynamic network that plays essential roles in neurodevelopment, synaptic plasticity, and circuit stability. Despite its importance, the molecular composition and spatial organization of the developing brain ECM remain poorly characterized. In this commentary, we highlight the recent study by Vilicich et al., which employs a multi-modal approach, integrating single-cell transcriptomics, proteomics, and immunohistofluorescence, to construct a map of the ECM in the developing neocortex of humans and non-human primates. By curating a comprehensive list of extracellular proteins termed the ”Exomatrix” and analyzing their distribution across cortical layers and developmental stages, the authors reveal layer-specific and evolutionarily conserved ECM features. These findings not only expand our understanding of ECM’s role in shaping the brain during early development but also emphasize its potential involvement in the pathogenesis of neurodevelopmental disorders, urging further research into ECM biology as a frontier in neuroscience. The brain ECM is a complex and dynamic network of molecules. It includes proteins like laminins, collagens, and glycoproteins, as well as polysaccharides such as glycosaminoglycans. It surrounds and supports neurons and glial cells and occupies approximately 20% of the brain volume ( 1 ). Unlike in other tissues, the brain ECM is uniquely enriched with molecules like hyaluronan and chondroitin sulfate proteoglycans, forming specialized structures such as perineuronal nets ( 2 ). Far from being just structural scaffolding, we now realize that the brain ECM plays essential role in neural development, synaptic plasticity, and circuit stability ( 3 ). It guides processes such as neuronal migration, axon pathfinding, and synapse formation during development; In adulthood, it helps regulate learning, memory, and repair after injury ( 4 ). Disruptions or alterations in the ECM are increasingly linked to neurological and psychiatric disorders, including epilepsy, schizophrenia, and autism spectrum disorder (ASD) ( 5 ). In recent years, we are just starting to understand its profound roles in the brain. However, while neurons are the most studied cells of the brain and research on glial cells is now rapidly catching up ( 6, 7 ), the research on the brain ECM is still lagging. During early development, the ECM generates a variety of molecular cues that direct neuronal growth and function, and it actively contributes to the formation of key CNS structures such as the neural tube and neocortex ( 8 ). These functions influence essential developmental processes, including neurogenesis, neuronal migration and differentiation, and axon guidance. In the mature CNS, the ECM plays vital roles by maintaining neural stability and enabling synaptic remodeling and plasticity ( 9, 10 ). The significant role that the ECM displays in regulating synaptic connections and plasticity has been recently fully recognized; It is now considered a part of the tetrapartite synapse consisting of the pre-synaptic and post-synaptic neurons, glia, and the ECM ( 9 ). Accumulating data support the roles of the interactions between presynaptic and postsynaptic neuronal elements with glia and the ECM for the formation and plasticity of chemical synapses ( 10 ), with neural ECM formed and destroyed in an activity-dependent manner ( 11, 12 ). In the adult brain, lattices of the ECM tightly enwrap the synapses. These lattices stabilize synapses, preventing them from undergoing structural or morphological changes; These are also needed to permit the events of synaptic plasticity ( 13 ). The dysregulation of synaptic ECM has been linked to synaptopathies in a long list of brain disorders ( 10, 14-16 ). A new study by Vilicich et al. reveals new findings about the development of brain ECM in using post-mortem tissues of fetuses. The knowledge of the developing neocortex in mammals historically comes from histological and transcriptomics experiments in mice models and to a lesser extent in humans. Using these approaches, cellular components have been characterized but the extracellular environment characterization has not been thoroughly studied. Vilicich et al. used a combination of single-cell transcriptomic analyses from published datasets, and their proteomics and immunohistofluorescence analyses, to seek to understand the extracellular environment of the developing cortex. Importantly, their work concentrates on human and non-human primates’ (NHPs) brains, showing both differences and similarities. As a first step of their analysis, the authors derived from five existing databases an integrated database of human genes that encode putative extracellular proteins. They filtered out genes that appeared in other databases as coding for intracellular, transmembrane proteins, or subcellular localization of proteins and named the remaining genes the Exomatrix. This curated list of 809 genes was termed the ‘Exomatrix’. Among this list of 809 genes that are predicted to encode extracellular proteins in the brain, they have subcategorized 233 proteins according to the literature ( 17 ), remaining with 576 genes that did not fit into any known matrisome category. The authors next used rhesus macaque cortices fetuses at day 51-52 post conception (corresponding to 90-day post conception in human fetuses (Barry et al. 2006)) and human fetuses at week 16 of pregnancy. Proteome analysis was performed on the samples and the genes in the Exomatrix were considered. A correlation of 0.72 (with 168 common genes) was observed between the human and non-human primate (NHP) genes. Next, they micro-dissected the sample into 3 layers; germinal zones (the subplate and intermediate zone (the next ~900 µm thick layer), and the cortical plate and marginal zone (the outermost three layers. However, some proteins were specific for each layer. For example, osteopontin (encoded by the SPP1 gene) was present in the cortical plate and subplate and was absent from the germinal zone. In contrast, the laminin subunits LAMB1 and LAMB2 were specific to the germinal zone, where laminins play essential roles in radial glial stem cell behavior ( 18 ). The authors additionally compared their Exomatrix proteome analysis to several transcriptomic databases and found similarities and correlations. While over 90% of proteins had a matching mRNA, only explained by the higher sensitivity of detecting mRNAs compared to the proteomics analysis. Additionally, post-transcriptional regulation, translation efficiency, and protein degradation dynamics may contribute to the limited mRNA-to-protein overlap observed. Similarly, when comparing early embryonic stages (human pial sample week 6.8) to single-cell transcriptomic databases, all proteins from the Exomatrix had matching mRNAs. Here, as with 16 weeks post conception tissue, most protein hits were present in the RNA data, while the opposite was not the case. Vilicich et al.’s study offers valuable insights into the extracellular composition of the developing neocortex. Their integrative approach, combining transcriptomic, proteomic, and immunohistofluorescence data, highlights the complexity and dynamic nature of the brain’s ECM. By comparing human and non-human primate tissues across developmental layers, they identify conserved and distinct molecular features, underscoring the need for further cross-species analyses with larger datasets. It is important to consider that our superior brain abilities are due to evolutionary developments in the extracellular matrix and not only in the cellular components of our brains. Recent studies ( 16, 19-23 ) show that changes in the brain ECM occur in multiple neurological disorders, sometimes years before the patients show any symptoms. These may occur early at the prodromal stages of these disorders. This highlights the importance of further studies of ECM structures of our brain \RL and lays the foundation for a new generation of studies on how ECM sculpts the developing brain. References: 1. D. Sood et al. , Fetal brain extracellular matrix boosts neuronal network formation in 3D bioengineered model of cortical brain tissue. ACS Biomater Sci Eng 2 , 131-140 (2016).2. J. W. Fawcett, T. Oohashi, T. Pizzorusso, The roles of perineuronal nets and the perinodal extracellular matrix in neuronal function. Nat Rev Neurosci 20 , 451-465 (2019).3. K. R. Long, W. B. Huttner, How the extracellular matrix shapes neural development. Open Biol 9 , 180216 (2019).4. N. George, H. M. Geller, Extracellular matrix and traumatic brain injury. J Neurosci Res 96 , 573-588 (2018).5. A. Dityatev, C. Seidenbecher, M. Morawski, Brain extracellular matrix: An upcoming target in neurological and psychiatric disorders. Eur J Neurosci 53 , 3807-3810 (2021).6. A. Doron et al. , Hippocampal astrocytes encode reward location. Nature 609 , 772-778 (2022).7. I. Fischer et al. , Shank3 mutation impairs glutamate signaling and myelination in ASD mouse model and human iPSC-derived OPCs. Sci Adv 10 , eadl4573 (2024).8. S. Amin, V. Borrell, The Extracellular Matrix in the Evolution of Cortical Development and Folding. Front Cell Dev Biol 8 , 604448 (2020).9. A. Dityatev, D. A. Rusakov, Molecular signals of plasticity at the tetrapartite synapse. Curr Opin Neurobiol 21 , 353-359 (2011).10. M. Ferrer-Ferrer, A. Dityatev, Shaping Synapses by the Neural Extracellular Matrix. Front Neuroanat 12 , 40 (2018).11. A. Dityatev et al. , Activity-dependent formation and functions of chondroitin sulfate-rich extracellular matrix of perineuronal nets. Dev Neurobiol 67 , 570-588 (2007).12. G. Bruckner, J. Grosche, M. Hartlage-Rubsamen, S. Schmidt, M. Schachner, Region and lamina-specific distribution of extracellular matrix proteoglycans, hyaluronan and tenascin-R in the mouse hippocampal formation. J Chem Neuroanat 26 , 37-50 (2003).13. T. M. Dankovich, S. O. Rizzoli, The Synaptic Extracellular Matrix: Long-Lived, Stable, and Still Remarkably Dynamic. Front Synaptic Neurosci 14 , 854956 (2022).14. D. Bonneh-Barkay, C. A. Wiley, Brain extracellular matrix in neurodegeneration. Brain Pathol 19 , 573-585 (2009).15. H. Pantazopoulos, S. Berretta, In Sickness and in Health: Perineuronal Nets and Synaptic Plasticity in Psychiatric Disorders. Neural Plast 2016 , 9847696 (2016).16. D. Cordeiro, T. Stern, S. Stern, Focusing on the tetra-partite synapse in Parkinson’s disease research using human patient-derived neurons. Neural Regen Res 19 , 979-981 (2024).17. A. Naba et al. , The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices. Mol Cell Proteomics 11 , M111 014647 (2012).18. S. Radner et al. , beta2 and gamma3 laminins are critical cortical basement membrane components: ablation of Lamb2 and Lamc3 genes disrupts cortical lamination and produces dysplasia. Dev Neurobiol 73 , 209-229 (2013).19. I. Rosh et al. , Synaptic dysfunction and extracellular matrix dysregulation in dopaminergic neurons from sporadic and E326K-GBA1 Parkinson’s disease patients. NPJ Parkinsons Dis 10 , 38 (2024).20. U. Tripathi et al. , Upregulated ECM genes and increased synaptic activity in Parkinson’s human DA neurons with PINK1/ PRKN mutations. NPJ Parkinsons Dis 10 , 103 (2024).21. W. A. Rike, S. Stern, Proteins and Transcriptional Dysregulation of the Brain Extracellular Matrix in Parkinson’s Disease: A Systematic Review. Int J Mol Sci 24 , (2023).22. M. Karlinski Zur et al. , Altered extracellular matrix structure and elevated stiffness in a brain organoid model for disease. Nat Commun 16 , 4094 (2025).23. B. Brant et al. , IQSEC2 mutation associated with epilepsy, intellectual disability, and autism results in hyperexcitability of patient-derived neurons and deficient synaptic transmission. Mol Psychiatry 26 , 7498-7508 (2021). Information & Authors Information Version history V1 Version 1 22 May 2025 Copyright This work is licensed under a Non Exclusive No Reuse License. Collection PROTEOMICS Keywords brain cortex extracellular matrix primate Authors Affiliations Shani Stern 0000-0002-2644-7068 [email protected] University of Haifa View all articles by this author Metrics & Citations Metrics Article Usage 258 views 206 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Shani Stern. ((Commentary on pmic.202400385 - title of the Commentary t.b.a.)) Extracellular Origins of Cognition: Lessons from Primate Neocortical ECM. Authorea . 22 May 2025. DOI: https://doi.org/10.22541/au.174792832.29560731/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . 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