DEO possesses state-of-the-art core technological platforms, run by highly-qualified personnel within dedicated Technological Units. The Technological Units provide cutting-edge technologies (omics, imaging, cell biology, structural biology, computation) and technical assistance to all the scientists of our community. The Directors of the Technological Units are assisted by selected PIs (User Groups) in the strategic decisions and operations of their Units.
Biochemistry and Structural Biology Unit
"Almost all aspect of life are engineered at the molecular level, and without understanding molecules we can only have a sketchy understanding of life itself" Francis Crick, 1988. The Unit supports the Department’s scientists by allowing the investigation of the structure and function of the biological molecules of their interest, and by generating protein tools for their experiments. The Unit provides experienced assistance in biochemistry, a platform for protein and protein complexes expression in insect cells, a wide range of technologies for protein purification and characterisation, as well as for determination of affinities of macromolecular interactions. The Unit manages a technological platform for protein crystallisation, structural determination by X-ray crystallography and preparation of samples and grids for cryo-EM structure determination.
Arnaud Gerard Michel Ceol
The bioinformatics unit works at the interface between the research groups, the technological units and the ICT services. It supports the ICT in the management of the bioinformatics platform, manages the bioinformatics tools, and promotes research and development of bioinformatics resources. We promotes reproducible and traceable data generation and analyses, proposing solutions that gives the groups the possibility to independently manage and share the installation of the bioinformatics software. We also develop and manage integrated systems for the management and analyses of biological and clinical data, in collaboration with the Center of Genomic Science (CGS@SEMM). Our unit participates in national (ACC) and international (EU-life) networks, and is involved in specific research and technological projects.
Cell Culture Unit (CCU)
The main goal of the Cell Culture Unit (CCU) is to provide the scientific groups with the necessary technical support, expertise, and resources for the routine and more specialized culture work. Core members help researchers in: - Setting-up and using gene transfer technologies in primary normal and tumor cells. - Improving the consistency and quality of cell cultures and enhance the abilities of investigators to study biological processes in mechanistic detail. CCU accomplishes its mission by providing: - Physical space, equipment and supplies for cell culture work.
Flow Cytometry Unit
The Flow Cytometry Unit (FCU) offers an efficient and reliable personalized flow cytometric service to researchers. The FCU provides instrumentation, education, and support for flow cytometric analysis and high-speed cell sorting. The unit is equipped with cell analyzers (two FacsCelesta and one MACSQuant) and cell sorters (FACSMelody, FacsAria Fusion and FacsJazz). Flow cytometry is an evolving field with a wide range of applications that includes immunophenotyping, cell division, apoptosis, cell activation, cell cycle analysis, gene reporter assays, single cell cloning. Analytical and sorter applications can be performed directly by the user or, if desired, can be carried out by the unit staff members. Training on various types of applications, as well as software support, is provided to new users. The FCU staff offers assistance with: • Experimental design and sample preparation for specific applications. • Selection and setting up of the required instrument. • Data acquisition, analysis and interpretation. • Basic training, theoretical and practical training courses. • Cell sorting. In order to furnish adapted solutions to specific needs, the unit always collaborates with researchers, providing experimental troubleshooting, scientific advice and personalized instructions and training on flow cytometry and instrument usage.
Genomic Unit was established in 2009 in collaboration with the Center for Genomic Sciences of the Italian Institute of Technology (IIT) hosted at our Campus. The unit is tasked with providing state-of-the-art genomic services to the Department community by implementing the latest sequencing technology. Our equipment include: liquid handling robots to automate pipetting tasks, DNA quantification and quality control instruments, Bioanalyzer, LabChipGX and Tape Station and three next-generation sequencing platforms from Illumina: MiSeq, Hiseq2000 and Novaseq6000, a highly flexible platform performing a broad range of applications for the DNA and RNA analysis also at single-cell level using Chromium system by 10X Genomics. The GU also offers technological support to research groups towards the optimization and development of tailored protocol. A constant technological update and flexibility to the needs is also provided. More than twenty research groups from IEO and IIT institutions are actively using Next Generation Sequencing technologies, with the aim of investigating regulation and structure of human genome in the context of of tumor biology. A highly integrated research community in genomics benefits of technological platforms provided by this Unit, including more than two hundred biologists and approximately thirty computational scientists. Ad hoc User Group Committee, is in charge together with the GU itself of supervising and solving any type of problem and defining new technological investment strategies, management of the access rules and general infrastructure of the unit.
Imaging Development Unit
Mario Romolo Faretta
The Unit has been created to support researchers in the employment of high resolution and content microscopy. Personnel of the unit collaborate and train scientists working on identified projects requiring the provide technologies. The unit does not directly perform single experiments on demand. The existence and structure of the unit will be re-discussed after an initial evaluation phase.
The Imaging Unit supports DEO scientific groups providing state-of-the-art optical imaging platforms and developing on-demand specific imaging and image analysis protocols. It provides its experienced assistance in users’ training to grant direct access to the microscopes, in assisting both microscopy beginners in setting up their experiments and the experienced DEO researchers in pilot experiments or advanced imaging techniques. The available systems cover different microscopy techniques including wide-filed and confocal, total internal reflection (TIRF), high content and time-lapse microscopy and the Unit services include the microscopes’ data back-up and storage and the imaging reagents management.
Mass Spectrometry Unit (MSU)
Over the past decade mass-spectrometry (MS)-based proteomics has proven to be the technology of choice for large-scale protein analysis, to investigate biological processes and disease states. The Proteomics Unit will maintain state-of-the-art MS technological platform to support both the Investigators at the Department of Experimental Oncology (DEO), and the Clinical Research at IEO. Through collaborative projects with internal groups, the Unit provides standard MS-proteomic analyses which includes protein identification, differential quantities proteomic studies (SILAC and label free) and protein-protein interaction analysis. In addition, the Unit is devoted to implement innovative MS-based strategies to enable the in depth proteomic profiling of both clinical patient samples, including both solid tissues (frozen and FFEP) and liquid biopsies. This new set of Clinical Proteomics methods will be developed and optimized in close collaboration with the Bonaldi Group at the DEO.
Molecular and Digital Pathology Unit
The Molecular and Digital Pathology Unit (MDPU) supports research groups at IEO, or in collaborating Institutions, in the execution of large-scale experiments utilizing human pathological material for the identification of novel tumor markers for diagnostic and/or prognostic applications, or of cancer targets for drug discovery efforts. The MDPU provides expertise and specific services for tissue processing (FFPE/fresh/frozen samples), tissue microarray (TMA) construction, tissue sectioning, slide staining and analysis (mostly IHC, ISH), and pathology material storage. The MDPU also supports mouse pathology work, providing a dedicated space and technical assistance to users. In close collaboration with the Pathology Department at IEO, the MDPU has access to tissue archives dating back to 1994, when IEO was established. These archives are an invaluable source of patient material that can be used for the construction and continuous replenishment of ad hocTMAs. Thanks to data stored by the IEO Tumor Registry, all arrayed tissues are linked to complete clinicopathological information and follow-up data. Thus, the MDPU can provide support to large-scale studies that require case collections with high quality follow-up data and/or dedicated TMAs. Through its Bioinformatics experts, the MDPU provides assistance in determining the links between gene expression patterns and clinicopathological parameters or clinical outcome, a necessary step for the validation of new diagnostic and prognostic markers.
Preclinical Drug Testing Unit
The Preclinical Drug Testing Unit (PDTU) is a newly set-up technological unit. Main goal is to set-up and optimize robust and state-of-the art preclinical models for cancer therapy. The working model is based on the strong interaction with the scientific groups of the Department of Experimental Oncology, providing initial input and know-how to help to build-up the models. Our overall objectives are: 1. To set-up models of response to standard therapy. 2. To generate robust models for drug treatment: new drugs and combination therapy. 3. To generate novel models for immunotherapy.