​School of Medicine and Surgery

This repository contains MALDI mass spectrometry imaging (MALDI-MSI) data acquired from a clear cell renal cell carcinoma (ccRCC) tissue section. The dataset comprises spatially resolved mass spectra of lipids, N-glycans, and tryptic peptides obtained from the same tissue section using a multi-omics imaging workflow. These complementary molecular layers enable the characterization of distinct histological regions, including healthy renal cortex, renal capsule, and tumor tissue. In particular: FinalMatrix_Coor.RDS contains pixel coordinates. FinalMatrix_Coor_reverseX.RDS contains the same coordinates flipped along the x-axis to match the orientation of the H&E-stained tissue image. FinalMatrix_Lipids.RDS, FinalMatrix_Glycans.RDS, and FinalMatrix_Peptides.RDS contain transformed molecular abundances for each pixel. Each row corresponds to a pixel and each column to an m/z value. list_ind_resolution_4123.RDS and list_ind_resolution_4123_cpp.RDS contain the indices of neighboring pixels for each pixel. The former uses 1-based indexing, whereas the latter uses 0-based indexing. These data were analyzed in the study “Multiomics Tissue Segmentation via Spatially-Informed Nested Biclustering Methods” by Francesco Denti, Cecilia Balocchi, Vanna Denti, and Giulia Capitoli, published in Biometrics. Preprint: https://fradenti.github.io/pdf/Poseidon.pdf Analysis code: https://github.com/Fradenti/poseidon-maldi

Live-cell holotomographic imaging of OHP-induced pathological changes in DRG neurons. These videos show primary adult mouse DRG neuronal cultures exposed to OHP at 7.5 or 25 µM. Refractive index-based imaging captures neurite fragmentation and degeneration, morphological features consistent with necroptosis, and autophagic vacuoles. Images were acquired using a 5 × 5 grid scan, with each grid measuring 90 × 90 µm, every 15 min for 28 h at 7 fps, from 24 to 52 h after OHP incubation.

Final scoring sheet for the cases enrolled in the study

Dataset archives

Here a section of a human papillary thyroid carcinoma, analysed with MALDI-MSI and H&E stained. The dataset includes: -H&E stained WSI (ptc_core_tma_q3.tif); -ROIs (geojson); SCiLS exchange format ROIs (SEF.zip); -imzML of the differnt ROIs (imzML.zip). The ROIs were obtained using the workflow presented in "Improving the annotation for Spatial Proteomics: A computational approach to enhance molecular characterization of Thyroid Nodules" . A detailed description and scripts can be found at https://github.com/Vsc0/msi-enhanced .

Normal human lymph nodes and tonsils, multiplexed with the MILAN technique, analyzed with BRAQUE.

20S proteasome inhibitors have been approved for the treatment of multiple myeloma but induce chemotherapy-related neurotoxicity. Here, we compared the neurotoxicity of bortezomib (BTZ) and carfilzomib (CFZ), a less neurotoxic drug, by investigating preclinical models and dissecting the underlying molecular mechanisms using a multidimensional approach. We developed a new mouse model of CFZ-induced neuropathy and compared it to an established BTZ model using behavioral, morphological/morphometric, and proteomic analyses showing that the more severe neurotoxicity correlated with loss of nerve fibers and protein expression changes. Moreover, mitotoxicity and cytoskeleton alterations were comparatively investigated in terms of onset of altered mitochondrial morphology, functionality, and trafficking, alongside cytoskeletal proteins expression and axonal degeneration in cultured mouse dorsal root ganglion neurons. Both compounds significantly altered mitochondrial network organization and energy production after 24 hours of treatment. However, only BTZ increased microtubule hyper-stabilization by accumulation of tubulin post-translational modifications and induced early axonal degeneration within the first 10 hours, severely impacting mitochondrial trafficking after 24 hours. Taken together, these results point at mitochondrial toxicity as a common downstream effect of both treatments, while BTZ-specific off-target activity on tubulin hyper-stability may initiate early mitochondrial trafficking alterations, a new knowledge helping to inform future mitigation approaches. Data refer to each figure in the article describing the in vivo and in vitro effects of the treatment with proteasome inhibitors Bortezomib and Carfilzomib.

Data refer to the contribute of cytokines and macrophages in two chronic models of chemotherapy-induced peripheral neuropathy (CIPN) comparing paclitaxel (PTX)- and oxaliplatin (OHP)-induced CIPN in rats. Results consists in behavioural, morphological/ morphometrical and neurophysiological assessments, obtained with the administration of PTX 10 mg/kg once a week and OHP 5 mg/kg twice a week.

Results of the pre and post-QuANTUM survey to a panel of 12 international digital and computational pathologists for the assessment of absolute and % tumor cellularity.

Supplementary data for the manuscript "Seeing or believing in hyperplexed spatial proteomics via antibodies." The content of this online repository is explained in the .txt file "FolderContent-ReadMe". Please download and read.