Vision of the infrastructure activity/group
Cancer incidence continues to rise annually. Despite modern approaches to treatment, many patients still die. This is why continuous cancer research using state-of-the-art approaches and methods is still urgently needed. A multidisciplinary approach combining modern molecular methods, such as next-generation sequencing (NGS), with more traditional ones, such as standard pathological histological examination of tissue using immunohistochemical methods, is increasingly important in cancer research, both pre-clinical and clinical. However, in vitro studies in cell culture and in vivo studies in laboratory animals are also often necessary. This is particularly important in the investigation of new therapies, such as gene and cell therapies, and therapies involving new delivery systems, where pre-clinical research is necessary before clinical trials can begin. Such an integrated approach also ensures international comparability of research, as well as the possibility of international networking and involvement in international clinical studies.
The rapid development of science, and in particular of new techniques and advanced research equipment, requires research institutions to continuously upgrade their own research facilities and to provide continuous training, both for specialized staff operating research equipment and for researchers. At the same time, modern research equipment also requires highly qualified staff who can ensure its optimal functioning and assist researchers in carrying out their research.
The Institute of Oncology Ljubljana has for this reason set up the Infrastructure group whose task is to:
(a) to integrate the current research facilities into a coherent whole,
b) to provide professionally qualified staff to take care of the research equipment,
c) provide assistance to users in the use of the equipment and in the conduct of research,
d) to ensure the strategic development of the research infrastructure to ensure the future international competitiveness of the Institute.
Areas of activity of the Infrastructure Group
Molecular and microbiology Core
The use of gene therapy is currently on the rise worldwide, mainly due to DNA vaccines and gene therapies for the treatment of diseases such as lymphoma or spinal muscular atrophy. New therapeutic plasmids with tissue specificity and without antibiotic resistance genes are under development. There are many options for targeted gene therapy for cancer - the genes selected can be immunomodulatory, anti-angiogenic or encode antibodies against immune checkpoints. The aim of this Core will be to provide researchers with all the necessary equipment and expertise to prepare a variety of plasmids with species specificity, tissue specificity, codon optimization, nuclear localization sequence and different therapeutic genes. Plasmids prepared in this way represent the first step in the development of such therapies, enabling researchers at the Institute of Oncology Ljubljana to develop their own therapies from plasmid construction, through pre-clinical testing and finally to translation into the clinic. This also includes a strong emphasis on collaboration with industry, as the plasmids produced in this way represent intellectual property that can also be patented. Currently, the Institute of Oncology Ljubljana is already collaborating with Jafral d.o.o., a Slovenian company that produces plasmid DNA developed at the Ljubljana Institute of Oncology, to conduct the first human clinical trial in Europe for intratumoral therapy with the IL-12 gene.
Cell Culture Core
Through multidisciplinary research in the field of cell and tumor biology, the Institute of Oncology Ljubljana has acquired knowledge that gives us a good basis for studying the efficacy of various anti-tumor therapies at the cellular level, as well as for studying the changes in cell function induced by these therapies. The Department of Experimental Oncology has also been involved for more than 30 years in the development of a delivery system based on a physical method called electroporation. This type of delivery system is useful for targeted delivery of cytostatics or non-viral gene therapy. The former approach is called electrochemotherapy and the latter gene delivery. Today, electrochemotherapy is already used in 170 cancer treatment centers worldwide. Gene electrotransfer technology is already being used in clinical trials in the US, but due to strict European Medicines Agency (EMA) regulations on advanced therapy medicines, it is still at the research stage in Europe. In the course of research into electroporation, the Institute of Oncology Ljubljana has acquired the necessary knowledge to work on all levels of cell culture, from 2D cell cultures of tumor and normal cells, primary cell cultures isolated from blood and patient tumors, to more advanced 3D cell cultures such as spheroids and organoids. The existing cell bank, which will be further expanded, provides a source of cells for most of the research carried out at the Institute and ensures the development of standards and positive controls needed by cytology and pathology laboratories for their research work. The Cell culture laboratory at the Institute of Oncology Ljubljana also provides all the necessary equipment to grow 2D and 3D cell cultures, both in normoxia and hypoxia, and to perform various assays of cell viability, proliferation, apoptosis, necrosis and various cell function assays.
Animal colony Core
One of the most important steps in translating therapies into the clinic is to test them in animal tumor models in vivo. Animal models are essential in studies of the tumor microenvironment, the interaction of the immune system with tumor cells and its response to therapy, and the processes of metastasis. Currently, in vitro models do not allow such studies. The Department of Experimental Oncology of the Ljubljana Institute of Oncology currently conducts more than 60% of all research in Slovenia performed in laboratory animals. The Department collaborates with other Research programmes within the Institute of Oncology Ljubljana as well as with other institutions such as the Faculty of Medicine, the Veterinary Faculty, the Faculty of Electrical Engineering, the University Medical Centre Ljubljana, the Biotechnical Faculty, the Faculty of Chemistry and Chemical Technology and the Faculty of Pharmacy.
The research group of the Department of Experimental Oncology at the Oncology Institute of Ljubljana is the group with the longest tradition of research in the field of experimental and translational oncology in Slovenia. The animal colony is equipped with all the necessary facilities for working with laboratory animals, namely for working with laboratory mice. It allows working with both immunocompromised and immunocompetent mice. It also allows work with subcutaneously induced tumor xenografts as well as orthotopic tumor models. The equipment in the animal colony also allows monitoring the response to therapies, both by measuring the size of tumors and by various non-invasive imaging methods such as ultrasound, IVIS, and macroscopy using a fluorescent stereo-microscope. In addition, researchers at the Department of Experimental Oncology are also trained to perform various types of surgical procedures, such as the insertion of osmotic pumps or pellets containing therapeutic agents, lymph node exposure, and the placement of a model of a dorsal or abdominal window to allow microscopic observation of the tumor or tissue.
Radiobiology Core
Nowadays, radiation therapy is still one of the most important treatments for cancer, being used in more than 50% of patients. Basic and clinical radiobiological research is therefore still extremely important. New approaches to cancer treatment most often combine radiation therapy with immune checkpoint inhibitors or other immunomodulatory therapies. However, how the characteristics of tumors and their microenvironment influence the response to radiation and the potential for modifying them to improve radiotherapy remains unexplored. The irradiation facility at the Institute of Oncology Ljubljana, which is dedicated to research work, is the only one in the wider region that allows irradiation of both cell cultures in vitro and tumors in mice in vivo. Additionally, more than 20 researchers are trained to work in the irradiation facility. In collaboration with radiotherapists at the Institute of Oncology Ljubljana, this represents a direct communication between clinical and pre-clinical research, allowing for a faster translation of findings into clinical practice.
Advanced microscopy, histopathology and flow cytometry Core
The use of different types of microscopy has become standard in modern oncology research. Recently, flow cytometry has played an increasingly important role. Approaches that allow monitoring of the same cell or the same animal/tumor over time are increasingly being used at the level of cells and tumor models. In combination with fluorescent proteins or fluorochrome-labelled antibodies, various processes in cells or tumors can be monitored, the composition of the tumor microenvironment can be determined or changes in the function and permeability of the tumor vasculature in living animals can be monitored. The use of advanced confocal microscopes also allows 3D image capture, which can be used to more precisely determine the localization of the observed events/objects. On the other hand, at the level of clinical research, classical light-field microscopy in combination with various histopathological and immunohistopathological stains is still the most important. In combination with flow cytometry, it is also possible to obtain information on the presence of different immune cells or markers in the blood of patients or mice, as well as information on the presence of different cell types in the tumor tissue itself.
Next generation sequencing Core
The field of next-generation sequencing (NGS) has seen remarkable developments in the last few years. In the field of oncology, this is particularly important as it is oncogenic mutations that are most often responsible for tumor initiation and development. Knowledge of these mutations enables the development of better, more targeted therapies. With the advent of NGS, the search for new mutations and changes in the transcriptome of cancer cells has become an important part of both clinical and pre-clinical research. At the Institute of Oncology Ljubljana, we have therefore made NGS facilities and bioinformatics data analysis experts available to researchers as part of our infrastructure group.
Registers and records Core
The effectiveness and efficiency of cancer control efforts by the medical profession, health policy and researchers can only be objectively evaluated with good quality, reliable and complete data. In oncological epidemiology, data on patients, their disease and their treatment, collected in population-based cancer registries, form the basis of all research. The Institute of Oncology Ljubljana manages one of the oldest health databases in the world, the Cancer Registry of the Republic of Slovenia, which contains data on all cancer patients in Slovenia since 1950. As part of the general Cancer Registry, we are also setting up national clinical registries, which provide more data on the diagnosis and treatment of cancer patients and serve as a basis for assessing the quality of patient care and the burden of late sequelae. Data on screening programs are available in the national screening registries, as well as in a separate registry on people with a family history of hereditary cancer. We provide modern IT support for all national health registries as well as for other registries, using both traditional and emerging (artificial intelligence, machine learning) methods for data analysis. The databases also provide a unique basis for the development of a biobank, which is planned at the Institute of Oncology Ljubljana in the near future.