Publications
2024
- Celebrating the Birthday of AMPA Receptor Nanodomains: Illuminating the Nanoscale Organization of Excitatory Synapses with 10 NanocandlesFukata Y, Fukata M, MacGillavry H D, Nair D and Hosy EJournal of Neuroscience 5 June 2024, 44 (23) e2104232024doi: https://doi.org/10.1523/JNEUROSCI.2104-23.2024
Summary
A decade ago, in 2013, and over the course of 4 summer months, three separate observations were reported that each shed light independently on a new molecular organization that fundamentally reshaped our perception of excitatory synaptic transmission (Fukata et al., 2013; MacGillavry et al., 2013; Nair et al., 2013). This discovery unveiled an intricate arrangement of AMPA-type glutamate receptors and their principal scaffolding protein PSD-95, at synapses. This breakthrough was made possible, thanks to advanced super-resolution imaging techniques. It fundamentally changed our understanding of excitatory synaptic architecture and paved the way for a brand-new area of research. In this Progressions article, the primary investigators of the nanoscale organization of synapses have come together to chronicle the tale of their discovery. We recount the initial inquiry that prompted our research, the preceding studies that inspired our work, the technical obstacles that were encountered, and the breakthroughs that were made in the subsequent decade in the realm of nanoscale synaptic transmission. We review the new discoveries made possible by the democratization of super-resolution imaging techniques in the field of excitatory synaptic physiology and architecture, first by the extension to other glutamate receptors and to presynaptic proteins and then by the notion of trans-synaptic organization. After describing the organizational modifications occurring in various pathologies, we discuss briefly the latest technical developments made possible by super-resolution imaging and emerging concepts in synaptic physiology.
- Cytokine profiling and transcriptomics in mononuclear cells define immune variants in Meniere DiseaseFlook M, Rojano E, Gallego-Martinez A, Escalera-Balsera A, Perez-Carpena P, Del Carmen Moleon M, Gonzalez-Aguado R, Rivero de Jesus V, Domínguez-Durán E, Frejo L, Ranea J A G, Lopez-Escamez J AGenes Immun 25, 124–131 (2024)doi: 10.1038/s41435-024-00260-z
Summary
Meniere Disease (MD) is a chronic inner ear disorder characterized by vertigo attacks, sensorineural hearing loss, tinnitus, and aural fullness. Extensive evidence supporting the inflammatory etiology of MD has been found, therefore, by using transcriptome analysis, we aim to describe the inflammatory variants of MD. We performed Bulk RNAseq on 45 patients with definite MD and 15 healthy controls. MD patients were classified according to their basal levels of IL-1β into 2 groups: high and low. Differentially expression analysis was performed using the ExpHunter Suite, and cell type proportion was evaluated using the estimation algorithms xCell, ABIS, and CIBERSORTx. MD patients showed 15 differentially expressed genes (DEG) compared to controls. The top DEGs include IGHG1 (p = 1.64 × 10−6) and IGLV3-21 (p = 6.28 × 10−3), supporting a role in the adaptative immune response. Cytokine profiling defines a subgroup of patients with high levels of IL-1β with up-regulation of IL6 (p = 7.65 × 10−8) and INHBA (p = 3.39 × 10−7) genes. Transcriptomic data from peripheral blood mononuclear cells support a proinflammatory subgroup of MD patients with high levels of IL6 and an increase in naïve B-cells, and memory CD8+ T cells.
- Developmental effect of RASopathy mutations on neuronal network activity on a chipWeiss E-M, Guhathakurta D, Petrušková A, Hundrup V, Zenker M and Fejtová AFront. Cell. Neurosci. 18:1388409.(2024)doi: 10.3389/fncel.2024.1388409
Summary
In this study, we explored how RASopathy mutations affect the development and function of neuronal networks. We cultured cortical neurons form RASopathy mouse models on multielectrode arrays and recorded their activity over time.
We developed MATLAB-based tools to handle the large data sets from these recordings and applied machine-learning methods.
Our analysis showed that neurons with Noonan syndrome-related mutations displayed a common developmental pattern. This pattern was more noticeable early on and diminished over time, indicating possible compensatory mechanisms during network maturation. Despite this, mature networks still showed differences on excitatory/inhibitory balance and network excitability.
This research enhances our understanding of how genetic mutations in RASopathies translate to clinical symptoms by shedding light on the underlying functional network processes. - Exploring miRNA–target gene pair detection in disease with coRmiTCordoba-Caballero J, Perkins J R, García-Criado F, Gallego D, Navarro-Sánchez A, Moreno-Estellés M, Garcés A, Bonet F, Romá-Mateo C, Toro R, Perez B, Sanz P, Kohl M, Rojano E, Seoane P, Ranea J A GBriefings in Bioinformatics, Volume 25, Issue 2, March 2024, bbae060doi: 10.1093/bib/bbae060
Summary
A wide range of approaches can be used to detect micro RNA (miRNA)–target gene pairs (mTPs) from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus on which is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinct rare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related to the disease pathology. All datasets were preprocessed using a standardized, freely available computational workflow, DEG_workflow. This workflow includes coRmiT, a method to compare multiple strategies for mTP detection. We used it to investigate the overlap of the detected mTPs with predicted and validated mTPs from 11 different databases. Results show that there is no clear best strategy for mTP detection applicable to all situations. We therefore propose the integration of the results of the different strategies by selecting the one with the highest odds ratio for each miRNA, as the optimal way to integrate the results. We applied this selection-integration method to the datasets and showed it to be robust to changes in the predicted and validated mTP databases. Our findings have important implications for miRNA analysis. coRmiT is implemented as part of the ExpHunterSuite Bioconductor package available from https://bioconductor.org/packages/ExpHunterSuite.
- Rasopathy-Associated Mutation Ptpn11 has Age-Dependent Effect on Synaptic Vesicle RecyclingGuhathakurta D, Selzam F, Petrušková A, Weiss E-M, Yağız Akdaş E, Montenegro-Venegas C, Zenker M, Fejtová ACell Mol Neurobiol . 2024 Nov 21;44(1):77.doi: 10.1007/s10571-024-01505-1.
Summary
Rasopathies are genetic disorders often associated with developmental delay and intellectual disability. Noonan syndrome (NS) is one of the most common Rasopathies, caused by mutations in PTPN11 in more than 50% of cases. In mammalian neurons, PTPN11 controls the trafficking of postsynaptic glutamate receptors. This process is disrupted in neurons expressing PTPN11 variants associated with Rasopathies and is thought to contribute to the cognitive impairments in Noonan syndrome. Recent work revealed presynaptic impairments upon expression of RASopathy-linked PTPN11 variants in Drosophila. However, the presynaptic role of PTPN11 has not yet been addressed in mammals. Here, we investigated membrane trafficking of synaptic vesicles in cultured mouse cortical neurons expressing Rasopathy-associated PTPN11D61Y variant. We observed a significantly smaller readily releasable and total recycling pool of synaptic vesicles. The drop in synaptic vesicle release competence was accompanied by a decreased rate of SV retrieval. Interestingly, the presynaptic phenotype was evident in mature (DIV21) but not in immature (DIV12) neurons. Thus, our data reveal importance of balanced PTPN11 activity for normal trafficking of neurotransmitter-filled synaptic vesicles in the presynaptic ending of mature neurons.
- Transcriptomic analysis identifies dysregulated pathways and therapeutic targets in PMM2-CDGGallego D, Serrano M, Cordoba-Caballero J, Gámez A, Seoane P, Perkins J R, Ranea J A G, Pérez BBiochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Volume 1870, Issue 5, 2024, 167163doi: 10.1016/j.bbadis.2024.167163
Summary
PMM2-CDG (MIM # 212065), the most common congenital disorder of glycosylation, is caused by the deficiency of phosphomannomutase 2 (PMM2). It is a multisystemic disease of variable severity that particularly affects the nervous system; however, its molecular pathophysiology remains poorly understood. Currently, there is no effective treatment. We performed an RNA-seq based transcriptomic study using patient-derived fibroblasts to gain insight into the mechanisms underlying the clinical symptomatology and to identify druggable targets. Systems biology methods were used to identify cellular pathways potentially affected by PMM2 deficiency, including Senescence, Bone regulation, Cell adhesion and Extracellular Matrix (ECM) and Response to cytokines. Functional validation assays using patients' fibroblasts revealed defects related to cell proliferation, cell cycle, the composition of the ECM and cell migration, and showed a potential role of the inflammatory response in the pathophysiology of the disease. Furthermore, treatment with a previously described pharmacological chaperone reverted the differential expression of some of the dysregulated genes. The results presented from transcriptomic data might serve as a platform for identifying therapeutic targets for PMM2-CDG, as well as for monitoring the effectiveness of therapeutic strategies, including pharmacological candidates and mannose-1-P, drug repurposing