IRCCS San Raffaele Scientific Institute Showcase

Introduction: Autosomal recessive osteopetrosis (ARO) is a rare genetic disease, characterized by increased bone density due to defective osteoclast function. Most of the cases are due to TCIRG1 gene mutation, leading to severe bone phenotype and death in the first years of life. The standard therapy is the hematopoietic stem cell transplantation (HSCT), but its success is limited by several constraints. Conversely, gene therapy (GT) could minimize the immune-mediated complications of allogeneic HSCT and offer a prompt treatment to these patients. Methods: The Tcirg1-defective oc/oc mouse model displays a short lifespan and high bone density, closely mirroring the human condition. In this work, we exploited the oc/oc neonate mice to optimize the critical steps for a successful therapy. Results: First, we showed that lentiviral vector GT can revert the osteopetrotic bone phenotype, allowing long-term survival and reducing extramedullary haematopoiesis. Then, we demonstrated that plerixafor-induced mobilization can further increase the high number of HSPCs circulating in peripheral blood, facilitating the collection of adequate numbers of cells for therapeutic purposes. Finally, pre-transplant non-genotoxic conditioning allowed the stable engraftment of HSPCs, albeit at lower level than conventional total body irradiation, and led to long-term survival and correction of bone phenotype, in the absence of acute toxicity. Conclusion: These results will pave the way to the implementation of an effective GT protocol, reducing the transplant-related complication risks in the very young and severely affected ARO patients.

This paper is associated to the project "Clinical and brain functional MRI effects of a rehabilitative training of upper limb using immersive virtual reality in people with Parkinson's Disease" supported by Italian Ministry of Health, with the grant GR-2018-12366005. In these datasets, data shuffling techniques have been applied to randomize certain data fields to enhance the anonymity of individuals and protect sensitive information. This measure is part of our commitment to data privacy and security, ensuring that personal identification is not possible from the data provided.

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) .