IRCCS San Raffaele Scientific Institute Showcase

Obesity and frailty are prevalent geriatric conditions that share some pathophysiological mechanisms and are associated with adverse clinical outcomes. The relationship between frailty, obesity, and polymorphism remains inadequately explored. Single nucleotide polymorphisms (SNPs) offer insights into genetic predispositions that may influence the development of both frailty and obesity. SNPs related to frailty and linked to the renin–angiotensin system (CYP11B2 rs1799998, AGT rs5051, and AGTR1 rs2131127), apoptosis pathways (CASP8 rs6747918), growth hormone signaling (GHR rs6180), inflammation (TLR4 rs5030717, CD33 rs3865444, and sFN1 rs7567647), adducin (ADD3 rs3731566), and the 9p21–23 region (rs518054) were found to be associated with various measures of obesity in community-dwelling older adults.

The reported raw data are about i) characterization of gold nanorods and ii) hyperthermia experiments carried out in the absence and presence of GNRs as well as well as in the absence and presence of bladder tumor. These data can be used together with those summarized in the supplementary Table S1 and S2 present in the manuscript.

This large dataset includes raw clinical data of patients with Parkinson's disease and healthy controls recruited and analyzed for the project Grant RF-2018-12366746 that was funded by the Italian Ministry of Health.

This dataset includes raw data analyzed and published in the following paper: Sarasso E, Gardoni A, Marelli S, Balestrino R, Zenere L, Castelnuovo A, Malcangi M, Basaia S, Grassi A, Tettamanti A, Canu E, Ferini-Strambi L, Filippi M, Agosta F. Gait Analysis and Magnetic Resonance Imaging Characteristics in Patients with Isolated Rapid Eye Movement Sleep Behavior Disorder. Mov Disord. 2024 Jul 4. doi: 10.1002/mds.29911. Epub ahead of print. PMID: 38962883 This publication was funded by the Italian Ministry of Health, Grant RF-2018-12366746

Images and dataset of densitometric analysis used for the generation of the figure 1 of the paper by Ravasi G, Pelucchi S, Canonico F, Mariani R, Piperno A. Atypical phenotype in a patient with ceruloplasmin mutations in the compound heterozygous state. Meta Gene. 2021, 29: 100905. doi.org/10.1016/j.mgene.2021.100905. This paper is associated to the project "Blood-cerebrospinal fluid-barrie defect as gate for targeting by liver-directed ceruloplasmin gene replacement therapy in the rare disease aceruloplasminemia" supported by Italian Ministry of Health, with the grant RF-2018-1236671 to Massimo ALESSIO as principal investigator at the IRCCS-San Raffaele Hospital, Milano, Italy.

Raw images and dataset of densitometric analysis used for the generation of the figure 1 of the paper by Pelucchi S, Ravasi G, Piperno A. Ceruloplasmin variants might have different effects in different iron overload disorders. J Hepatol. 2021, 75:1003-1004. doi: 10.1016/j.jhep.2021.05.005. This paper is associated to the project "Blood-cerebrospinal fluid-barrie defect as gate for targeting by liver-directed ceruloplasmin gene replacement therapy in the rare disease aceruloplasminemia" supported by Italian Ministry of Health, with the grant RF-2018-1236671 to Massimo ALESSIO as principal investigator at the IRCCS-San Raffaele Hospital, Milano, Italy.

The dataset includes 172 subjects for a total of 519 fetal rs-fMRI scans with respective brain segmentations. Brain segmentations were obtained with the RS-FetMRI package (https://github.com/NicoloPecco/RS-FetMRI). For each subject the gestational week at scan is reported as the last two digits of the file name. The RF-2016-02364081 DL dataset has been used to train and test deep learning architectures (i.e. Swin-UNETR, UNTER, CNN, GAN) on a fetal brain extraction task for the study titled ‘Optimizing performance of transformer-based models for fetal brain MR image segmentation’. Pretrain weights of Swin-UNETR best model can be found on the ‘weight’ folder (Fetal_pretrain.pth).

Preliminary data for the selection of housekeeping genes suitable for our cells to be used as normaliser for the full experiment that will allow us to identify genes potentially modified by the infection with ZIKV and counteracted with the heparin treatment. Instead of performing RNAseq analyses, we decided to opt for QuantiGene Plex (Thermofisher). This test incorporate branched DNA technology for accurate gene expression profiling. Branched DNA assays allow direct measurement of RNA transcripts using signal amplification (Luminex 200 technology) rather than target amplification. We decided to include 4 conditions: uninfected, uninfected + heparin, ZIKV and ZIKV + heparin, and three time points: 4, 24, 48 h post infection, for a total of 12 samples. We performed three 1:4 serial dilutions of all samples. Then, we load the plate with all undiluted samples + all dilutions made. We performed the experiment according to the manufacturer’s instructions (Thermofisher). Thanks to the Thermofisher free online software, we performed the analyses of the data we obtained from the Luminex reading. From the analyses file, we highlighted the data that were saturated (over 20000 reads), then we remove data from "uninfected + heparin 4h" and "ZIKV 4h" since the preparation was not perfect and the data were not reliable (incorrect serial dilution). We selected the samples in which genes are not saturated (dilution 1:64), and we performed the geometric mean (GEOMEAN) of all genes expressed by the same sample. We divided each values by its GEOMEAN and we calculated the standard deviation (SD). We selected the genes with the lower SD. This experiment allowed us to identify the best 4 housekeeping genes: the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase 1 (PGK1), ubiquitin C (UBC) and the ATPase H+ transporting the A subunit V1 (ATP6V1A) .

Preliminary data of ZIKV infection in brain organoids. We perform immunostaining to characterise organoids grown in culture for 5 weeks. We identified neurons (MAP2) and astrocytes (GFAP). We tested the cytopathic effect of ZIKV in this 3D-system after infection with 1.000.000 infectious particles. We took pictures every 3 days post-infection by optic microscope and collected the supernatant for the retrotitration through plaque forming assay to check viral replication.

Raw data of the figures reported in the published related article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10609960/