Project (Eugenio Fornasiero)

Synapses are hotspots of local protein synthesis and turnover, where precise regulation of mRNAs and their binding proteins determines neuronal function. While we know a lot about synapse structure under normal conditions, we still lack a detailed understanding of how synaptic compartments control protein turnover and RNA localization, especially during synaptic activity and aging.

In this project, you will investigate how mRNA-binding proteins orchestrate synaptic vesicle cluster stability, protein turnover and RNA localization. Using multi-omics approaches (including spatial transcriptomics, proteomics, and imaging datasets) you will integrate data to uncover how mRNA regulation shapes synaptic function. Your analyses will combine quantitative modeling, network analysis, and spatial transcriptomics to identify regulatory relationships, generating computational predictions that guide functional experiments in neuronal cultures and brain slices.

This is a unique opportunity to explore fundamental questions in neuroscience while applying cutting-edge bioinformatics and systems biology approaches, bridging molecular datasets with cellular function.

Desired skills:

• Strong interest in molecular and computational biology
  
• Experience with one or more of: RNA-seq, proteomics, or other omics datasets
  
• Proficiency in data analysis, scripting (Python, R, or similar), and statistical modeling
  
• Ability to integrate computational analyses with experimental datasets
  
• Willingness to learn wet-lab approaches
  
• Collaborative mindset for multidisciplinary, international research

• Turnover atlas of proteome and phosphoproteome across mouse tissues and brain regions. Li W, Dasgupta A, Yang K, Wang S, Hemandhar-Kumar N, Chepyala SR, Yarbro JM, Hu Z, Salovska B, Fornasiero EF*, Peng J*, Liu Y*. Cell. 2025
  *Co-corresponding authors. https://www.ncbi.nlm.nih.gov/pubmed/40118046


• DELTA: a method for brain-wide measurement of synaptic protein turnover reveals localized plasticity during learning. Mohar B, Michel G, Wang YZ, Hernandez V, Grimm JB, Park JY, Patel R, Clarke M, Brown TA, Bergmann C, Gebis KK, Wilen AP, Liu B, Johnson R, Graves A, Tchumatchenko T, Savas JN, Fornasiero EF, Huganir RL, Tillberg PW, Lavis LD, Svoboda K, Spruston N. Nat Neurosci. 2025
  https://www.ncbi.nlm.nih.gov/pubmed/40164741
  


• Spatial proteomics in neurons at single-protein resolution. Unterauer EM, Shetab Boushehri S, Jevdokimenko K, Masullo LA, Ganji M, Sograte-Idrissi S, Kowalewski R, Strauss S, Reinhardt SCM, Perovic A, Marr C, Opazo F, Fornasiero EF*, Jungmann R*. Cell. 2024
  *Co-corresponding authors.
  https://www.ncbi.nlm.nih.gov/pubmed/38552614
  


• The DNA-PAINT palette: a comprehensive performance analysis of fluorescent dyes. Steen PR, Unterauer EM, Masullo LA, Kwon J, Perovic A, Jevdokimenko K, Opazo F, Fornasiero EF, Jungmann R. Nat Methods. 2024
  https://www.ncbi.nlm.nih.gov/pubmed/39112798
  


• Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain. Kumar NH, Kluever V, Barth E, Krautwurst S, Furlan M, Pelizzola M, Marz M, Fornasiero EF. Nucleic Acids Res. 2024
  https://www.ncbi.nlm.nih.gov/pubmed/38471806
  


• A Versatile Synaptotagmin-1 Nanobody Provides Perturbation-Free Live Synaptic Imaging And Low Linkage-Error in Super-Resolution Microscopy. Queiroz Zetune Villa Real K, Mougios N, Rehm R, Sograte-Idrissi S, Albert L, Rahimi AM, Maidorn M, Hentze J, Martínez-Carranza M, Hosseini H, Saal KA, Oleksiievets N, Prigge M, Tsukanov R, Stenmark P, Fornasiero EF*, Opazo F*. Small Methods. 2023
  * Co-corresponding authors.
  https://www.ncbi.nlm.nih.gov/pubmed/37421204
  


• Protein lifetimes in aged brains reveal a proteostatic adaptation linking physiological aging to neurodegeneration. Kluever V, Russo B, Mandad S, Kumar NH, Alevra M, Ori A, Rizzoli SO, Urlaub H, Schneider A, Fornasiero EF. Sci Adv. 2022
  https://www.ncbi.nlm.nih.gov/pubmed/35594347
  

For a complete list: https://pubmed.ncbi.nlm.nih.gov/?term=Fornasiero+EF&sort=date