Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063249/Farah_Random_D2_2000nuul_03102024_Lib1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063249/Farah_Random_D1_2000nuul_04102024_Lib2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063249/Farah_Random_D3_2000nuul_03102024_Lib1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063249/Farah_B2M_D1_2000nuul_03102024_Lib1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063249/Farah_B2M_D2_2000nuul_03102024_Lib1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063249/Farah_B2M_D3_2000nuul_03102024_Lib1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063249/FilePeack.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063249/FileRaw.zipprimaryOK200marcello.manfredi@uniupo.itMarcello ManfrediMass SpectrometryData-independent acquisitionIn vitro models3d arc hitectureSensory neuronsScaffold-free assemblyInterneurons cross-talkhttps://www.ebi.ac.uk/pride/archive/projects/PXD063249Sensory NeuronCell CultureDRG explants were collected from local abattoir. Briefly, 10~12 DRG explants were dissected from cervical spine of freshly slaughtered cattle. These DRG explants were transferred and dissected in an ice-cold buffer containing sucrose 238 mM, KCl 2.5 mM, NaH2PO4 1.0 mM, MgCl2 3.8 mM, HEPES 20 mM, D-glucose 11.0 mM, ascorbic acid 0.4 mM and 1% (v/v) penicillin / streptomycin (P/S, 15140-122, Gibco, UK). The dissection of DRG explant was performed in a Petri-dish on ice. After removing connective tissue and nerve root, DRG explant was sliced using a surgery scalpel. Then, the tissue was transferred to 5 mL collagenase P solution (4 mg/mL, COLLP-RO, Roche, DE) and enzymatically digested in a 15 mL centrifuge tube placed on a tilting shaker. The digestion was 2 hours at 37 °C. The digested suspension passed through a 100 μm cell strainer (Falcon, Corning, US), and was diluted in 10 mL DRG culture medium. The bDRG culture medium was composed of DMEM/F12 (50% v/v, DMEM, 52100-021, Gibco, UK and F-12 Ham, N6760, Sigma, UK), 10% (v/v) fetal calf serum (FCS, 35-010-CV, Corning, CA, US), 1% (v/v) P/S, 0.11 g/L sodium pyruvate (P5280; Sigma, JP), 20 mM HEPES (15630122, ThermoFisher, US) and 1% (v/v) ITS universal culture supplement (354352, Sigma, US). This was followed by a density centrifuge above 12% (v/v) bovine serum albumin (BSA, A3294, Sigma, DE). The centrifuge was 600 g for 7 min. The pellet was resuspended in 500 ~ 1000 μL (volume around twice of the pellet size) DRG culture medium. 10 μL cell suspension was taken out and mixed with 10 μL trypan blue solution (0.4%, T8154, Sigma) for neuron counting. In the counting, viable cells were not stained by trypan blue, and neurons can be easily identified for a larger size than glia. [5] The DRG cell was seeded at a density of 5000 neurons / cm2. The DRG culture surface was sequentially pre-coated with Poly-D-lysine (100 μg/mL, P6407, Sigma, US) and laminin (2 μg/mL, L2020, Sigma, US). The cells are cultured in a 37 °C incubator supplied with 90% humidity and 5% CO2. Half medium was changed once per 2 days. The viability of neuron and glia was evaluated using the previously published method. [11] Briefly, the cells were incubated with 10 μM ethidium homodimer (46043, Sigma, DE) for 20 minutes at 37 °C. Then, the cells were fixed using 4% formalin for 1 hour. Necrosis was identified by an ethidium homodimer-stained nucleus. Apoptosis was recognized based on nuclei morphology under Hoechst staining (2 μM, 14530, Sigma, US). An immunofluorescent labelling of neurons assisted differentiation between the cell death of neuron and glia.PrideFor proteomic analysis, cells were lysed with RIPA buffer and ultrasonication. Proteins were then precipitated with cold acetone and resuspended. Proteins were then reduced in 25 µL of 100 mM NH4HCO3 with 2.5 μL of 200 mM DTT (Merck) at 60°C for 45 min and next alkylated with 10 μL 200 mM iodoacetamide (Merck) for 1 hour at RT in dark conditions. Iodoacetamide excess was removed by the addition of 200 mM DTT. Proteins were then digested with trypsin. The digests were dried by Speed Vacuum and then desalted. Digested peptides were analyzed on an Ultimate 3000 RSLC nano coupled directly to an Orbitrap Exploris 480 with a High-Field Asymmetric Waveform Ion Mobility Spectrometry System (FAIMS) (all Thermo Fisher Scientific). Samples were injected onto a reversed-phase C18 column (15 cm × 75 µm i.d., Thermo Fisher Scientific) and eluted with a gradient of 6% to 95% mobile phase B over 41 min by applying a flow rate of 500 nL/min, followed by an equilibration with 6% mobile phase B for 1 min. The acquisition time of one sample was 41 min and the total recording of the MS spectra was carried out in positive resolution with a high voltage of 2500 V and the FAIMS interface in standard resolution, with a CV of -45V. The acquisition was performed in data-independent mode (DIA): precursor mass range was set between 400 and 900, isolation window of 8 m/z, window overlap of 1 m/z, HCD collision energy of 27%, orbitrap resolution of 30000 and RF Lens at 50%. The normalized AGC target was set to 1000, the maximum injection time was 25 ms, and microscan was 1. For DIA data processing, DIA-NN (version 1.8.1) was used: the identification was performed with “library-free search” and “deep learning-based spectra, RTs and IMs prediction” enabled, database: bos taurus reviewed (Uniprot, downloaded on 20-03-2025). Enzyme was set to Trypsin/P, precursors of charge state 1–4, peptide lengths 7–30 and precursor m/z 400–900 were considered with maximum two missed cleavages. Carbamidomethylation on C was set as fixed modification and Oxidation on M was set as variable modification, using a maximum of two variable modifications per peptide. FDR was set to 1%.ProteomicsMarcello ManfrediUniversity of Piemonte OrientalePARTIALBos Taurus (bovine)10.1016/J.CELBIO.2026.100489marcello.manfredi@uniupo.itUniversity of Eastern PiedmontItalyfalseHydrodynamically-Assembled Multicellular System towards structural self-organization and functional crosstalkIn vitro models are widely used in fundamental research and high-throughput drug discovery. Particularly the sensory neurons dissociated from dorsal root ganglion (DRG) are cultured in monolayer to study the pain associated biology. The problem of monolayer culture is that the naïve multicellular architecture is deprived. The impact of multicellular assembly on biology remains elusive. Also, biofabrication of multicellular system usually depends on a complex scaffold design to support the aggregate which is difficult to scale up. The scaffold-cell interaction may confound the in vitro testing result. Here, we present a scaffold-free assembly using hydrodynamic forces. Cells are assembled in normal culture medium into a precise geometry within two minutes. During culture, the DRG cells self-organize into a 2.5 ~ 3-dimensional architecture. Cells binds to each other to maintain their shape and mechanobiology. We demonstrate interneuron crosstalk in the multicellular system via the synchronization of calcium signals and the cluster-wise expression of neuronal activation markers. Thus, multicellular architecture determines the cell shape and functional crosstalk. This evidence pinpoints the multicellular principle of in vitro models. The scaffold-free assembling is a simple tool to improve the robustness of in vitro model in predicting in vivo biology, which may benefit the innovation in pain 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