Research core facilities

ANIMAL WELFARE BODY 

The Animal Welfare Body (Organismo per il benessere animale, OPBA) is the committee responsible to monitor in vivo experiments. OPBA aims to support the scientific activity of researchers by allowing them to carry out in vivo research in compliance with current legislation, according to the international standards of Good Laboratory Practice and in full compliance with the 3Rs principle: Replacement, Reduction, Refinement. The OPBA of our Institute has 5 members: the Animal Welfare Manager, one Veterinarian specialized in laboratory animals, two Scientific Members and a Biostatistician. 

INTERNAL REVIEW BOARD 

The Internal Review Board (IRB) is a Scientific Directorate committee, established in 2018, which supports the Scientific Director to assess the scientific value, design, impact of new proposals for clinical intervention studies, as well as their adherence to good clinical practice, before submission to the Ethics Committee. 

MOLECULAR TUMOR BOARD 

Since 2020, the Molecular Tumor Board (MTB) is a board with a strong multidisciplinary focus, integrating the knowledge and experience of professionals from different fields. It aims to harmonize the access to molecular analyses and help oncologists in the choice of appropriate therapies which take into account the clinical context and tumor biology. The MTB deals with the identification of patients eligible for molecular testing of the most suitable and cost-effective panel of genes. It also deals with the interpretation of data from molecular analysis in order to define the biological meaning and therapeutic actionability of the genetic abnormalities for the identification of potentially active drugs, and discussed patients’ clinical-genomic data to define the optimal treatment.

GRANT OFFICE 

The Grant Office provides timely advice and information to researchers on funding opportunities, coordinates the participation of the research projects to funding programs, provides information on the internal procedures for submissions of project proposals, assists researchers in the submission process and supports financial reports and final audit processes. 

BIOMEDICAL LIBRARY 

The Library is affiliated to the European Association for Health Information and Libraries. It offers a large collection of basic science journals, reference books and electronic access to the full text of scientific and clinical journals, databases and books. 

CLINICAL TRIALS CENTER 

The Clinical Trials Center supports clinical researchers in many aspects of investigational clinical studies, such as feasibility analysis of the study, submission to Ethics Committees/regulatory authorities, budget definition, coordination of the clinical trial in all phases. The organization of the CTC and the presence of dedicated and trained staff (clinical study coordinators and research nurses) allow to conduct the clinical trials in compliance with the good clinical practice (GCP). A special team joining expertise from the Grant Office at the CTC is dedicated to trials with Advanced Therapy Medicinal Products (ATMP), such as gene, cell and CAR-T therapies. 

TECHNOLOGY TRANSFER OFFICE 

The Technology Transfer Office was created in 2009 to valorize research results from a scientific and economic viewpoint, to optimize technology transfer and intellectual property rights management. The TTO offers support for patent activities (from the beginning of a new invention to the filing and maintenance of the correspondent patent), spin-off evaluation and the dissemination of intellectual property culture among researchers

DWH - DATA WAREHOUSE 

The Data warehouse (DWH) is the institutional database where information relating to all the activities that patients carry out at our institution is centralised. It is used for both research and strategic-management purposes, such as monitoring the Operating Theatre performance and the Oncological Outpatient Service performance with a panel of indicators (KPIs). DWH is used also to identify potential patients for clinical trials, to count retrospectively the potential number of patients for new prospective studies, understand the feasibility of retrospective observational studies, extract data for monitoring and benchmarking as well as for accreditation to national and international networks.

FUNCTIONAL AREA: PHASE I PROGRAM 

This is a Cross-Functional Area involving Clinical Departments, the Scientific Directorate (Clinical Trials Center), Laboratories, Diagnostic Facilities, and Administrative Units. The area regulates relationships among the various structures through procedures established within the "Phase I Program," in accordance with the requirements set by AIFA (AIFA Determination 809/2015). Its mission is to ensure a coordinated organization among qualified units for the conduct of Phase I clinical trials, sharing pathways and procedures and achieving positive outcomes in terms of resource optimization, high quality standards and access to new drugs for cancer patients.

WORKING GROUP ON “RESEARCH QUALITY AND INTEGRITY” 

As part of the strategies aimed at promoting a culture of integrity and good scientific conduct within the Institute, the Scientific Directorate has embarked on a process to define lines of action to support researchers in increasing their knowledge and encouraging the implementation of good research conduct practices. The Working Group is tasked with studying and designing specific actions aimed at improving quality and integrity standards and providing researchers with tools and measures that can be applied in their daily activities.

MOLECULAR ANALYSIS PLATFORMS 

Technological innovation and next-generation sequencing (NGS) play a fundamental role in precision medicine. INT is at the forefront for applying NGS technologies in diagnosis and translational research to identify novel biomarkers and therapeutic targets, as well as for patient stratification by mutational analysis. Thanks to cutting-edge instrumentation, INT promotes basic and translational research in the field of precision medicine and supports therapeutic decisions and diagnosis. The following technologies are available at the Department of Advanced Diagnostics: 

• DNA and RNA extraction from fresh/fresh-frozen/FFPE tissue samples, as well as from cell lines and plasma (liquid biopsy) (QIAcube and QIASymphonySP, Qiagen); 
• Quantification and quality assessment of nucleic acids (4200 Tapestation, Agilent, Nanodrop and Qubit, Thermo Fisher); 
• Library preparation, quantification and sequencing for NGS approaches on FFPE/fresh frozen tumor and plasma samples (liquid biopsy), both with ThermoFisher and Illumina solutions; 
• Gene expression profiling analysis, with microarray-based technologies (Gene Chip System 3000, Affymetrix, Thermo Fisher), RNAseq (Illumina, Takara and Lexogen library preparations kits) and NanoString technologies (nCounter, Nanostring); 
• Spatial transcriptomic and proteomic experiments on tumor FFPE and frozen sections (GeoMx DSP, NanoString); 
• Single cell RNAseq profiling (ChromiumX, 10X Genomics); 
• M220 Focused-ultrasonicator (Covaris) for DNA shearing; 
• QuantStudio-Q Real-Time PCR System Digital PCR (Thermo Fisher); 
• QuantStudio 12K Flex Real-Time PCR System with Twister Automation Robot for quantitative real-time PCR (Thermo Fisher); 
• Ion Chef Instrument, Ion PGM and Ion S5XL (Thermo Fisher) and NextSeq 500 (Illumina) for NGS applications; Hamilton Microlab STARlet for liquid handling; 
• NovaSeq 6000 Sequencing System (Illumina); 
• Zephyr G3 NGS workstations (Revvity): a compact, semi-automated solution designed to construct up to 96 NGS libraries per day.

BIOINFORMATICS

The team utilizes advanced computational tools and algorithms to extract insights from complex biological data. The team works closely with researchers across various disciplines, providing support and guidance at every stage of their projects: from experimental design to data analysis (data quality control and pre-processing, sequence alignment, variant calling, functional annotation and downstream analysis) and interpretation. Our activities include data processing and management, developing and implementing algorithms for data analysis, designing and deploying bioinformatics pipelines, developing and maintaining databases and web interfaces for data retrieval, as well as providing training and support to researchers on bioinformatics tools and methodologies.

IMMUNOHISTOCHEMISTRY 

Histological and cytological processing is avaiable through a wide range of histological techniques, immunohistochemistry, in situ hybridization, and autoradiography. The Vectra 3 automated quantitative pathology imaging system performs immuno-profiling and phenotyping of multiple immune cell subsets in situ in FFPE tissue sections (phenoptics), to increase knowledge in prognostic and predicting value of immune contexture in neoplastic regions.

FLOW CYTOMETRY AND CELL SORTING 

In the Department of Experimental Oncology, this facility provides support and advanced equipment to the researchers to analyze and sort the different types of cells constituting the tumor and the tumor-associated microenvironment according to their specific molecular phenotype. The facility is currently equipped with BD FACSAria™ IIu cell sorter and 2 BD FACSCelesta™ flow cytometers. A MALDI imaging is also available. Moreover, several Cytoflex are avaiable in the laboratories of the Department of Experimental Oncology. One MACSQuant Tyto cell sorter is also available in the Medical Oncology Department. Cytek develops advanced spectral flow cytometers using its patented Full Spectrum Profiling™ (FSP®) technology. Instruments like the Cytek Aurora and Northern Lights offer high-resolution, high-content and sensitive cell analysis, enabling deeper biological insights.

CIRCULATING TUMOR CELLS (CTC) CAPTURE

The DEPArray platform (Silicon Biosystem) combines imaging technologies with manipulation and recover of individual, rare cells from a heterogeneous sample. The DEPArray also offers applications at tissue level allowing digital sorting of pure cells derived from FFPE sections that can be used for high resolution molecular analyses. Parsortix (Angle) is a flexible micro-fluidic technology for the enrichment of CTC from whole blood or PBMC, also allowing isolation of CTC clusters for studies of the interaction between CTCs and microenvironment. Samples recovered from Parsortix can be used for subsequent molecular/in vitro/in vivo analyses or in association with DEPArray for isolation of pure CTC. RareCyte provides multiplexed fluorescent imaging systems, and reagents to investigate the spatial context and liquid biopsies.

IMAGING 

The Department of Experimental Oncology is equipped with the BioRad Radiance 2000 and Leica SP8 AFC AOBS WLL HyD laser confocal microscopes for live cell imaging, sequential and simultaneous bright field image collection of up to 8 channels and employment of a wide range of fluorescent dyes. The INCUCYTE SX5 HD/3CLR SYS PKG allows the acquisition of images in High Definition, providing an automated workflow platform for live cellimaging and integrated analysis of cell phenotypes and kinetics. The Azure 600(Biosystems) imaging workstation allows to digitally acquire western blot images developed by chemiluminescence, exploiting NIR, RGB, UV and BLUE fluorescence, imaging of colorimetric and silver stain gels, cell-culture plates and other clear and colorimetric samples. THUNDER Imager (Leica microsystem) is a fluorescence microscope that combines the speed and ease of use of a widefield microscope with the clarity of confocal microscopy, enabling researchers to visualize fine details in thick specimens like cell cultures, tissues and even whole model organisms. 

LABORATORY ANIMAL FACILITY 

Authorized by the Italian Ministry of Health for housing of transgenic and immunodeficient mice under specific pathogen-free conditions (SPF). It is composed of 9 independent rooms that host mice (360 Individually Ventilated Cages (IVC) per room) and 4 fully equipped laboratories. Animal health care is provided by the Animal Welfare Manager and by the veterinarian specialized in laboratory animals. The animal house is equipped with IVIS Spectrum (bioluminescence, fluorescence, 3D images), RS 2000 Small Animal and Cell Irradiator, X-RAD SmART Small Animal Image Guided Irradiator and dedicated micro-PET scanner (GE Healthcare eXplore VISTA).

PROTEOMICS/METABOLOMICS

A fully equipped laboratory (NuMeLab) is dedicated to process biological material and perform analyses in clinical biochemistry, high resolution mass spectrometry for lipidomics, HPLC/mass spectrometry for hormonal and pharmacological analyses, gas chromatography/mass spectrometry for metabolomics analyses, LC Orbitrap, ICP mass spectrometry for elemental analyses. The availability of the dedicated software LipidSearch, together with the skills of laboratory staff, allows lipidomic data processing to help identify etiological, early detection or drug response biomarkers. The NuMeLab also offers innovative applications of mass spectrometry-based breath analysis for a non invasive early diagnosis of head/neck and breast cancers. The NuMeLab also includes a blood bank (about 175.000 samples) of the participants of lifestyle intervention randomized trials (the MeMeMe, DIANA-5, and BRCA trials).

TISSUE AND CELL REPOSITORY The Departments have access to a large bank of frozen and FFPE normal and tumor tissues, and blood/plasma/serum samples, collected and stored within a short time from collection following validated SOPs. All clinical samples are collected following the informed consent of the patients and are linked to dedicated databases of pathological and clinical information. Samples are provided to studies after approval by the Internal Review Board and the Ethical Committee.