CIC bioGUNE. Platform for Genomics, Proteomics, Metabolomics and Gene Silencing

CIC bioGUNE is a non-profit-making association set up under the auspices of the Basque Authority according to the directives of the Decree for creation of CIC (BOPV – Basque Country Gazette - 7/10/2002), which was got under way in January 2005 with the aim of generating new knowledge, technology transfer, high-level training and the exploitation of results in the area of biomedicine. From the start, four technology platforms were set up (analysis of genomes, proteomics, metabolomics and structural biology) with the intention of allowing researchers from the institution and the Basque Country in general to use new technologies in those areas. The CIC bioGUNE technology platforms have formed part of the CIBEREHD since its creation in 2007, as integrated platforms, providing services and advice in the design and interpretation of results in the aforementioned areas. Until 2014 102 services coming to a net worth of 727,000€ were supplied, taking part in the publication of 107 articles with other members of the CIBEREHD.

As regards metabolomics, both our own platform at CIC bioGUNE, and OWL metabolomics, a spin-off of CIC bioGUNE working in metabolomics, have helped to further the use of metabolomics as a research tool. As a result of this we could mention the granting of the INTERCIBERS project “Understanding obesity (Ob), metabolic syndrome (MetS), type 2 diabetes (T2DM) and fatty liver disease (FL): a multidisciplinary approach”, in which CIBERSAM, CIBEROBN and CIBERDEM also participated, the LIVERBIOMARK project or the marketing of the OWLliver, a metabolomic test for non-invasive diagnosis of non-alcoholic fatty liver disease (NAFLD), which is already being used at different hospitals and institutions attached to the CIBEREHD.

Platforms:

 

Through its UPLC-MS system, the metabolomics platform of CIC bioGUNE makes a quantitative and highly sensitive analysis of low molecular weight (under 1500 Da) metabolites, which includes over 30,000 different molecules such as, for example, sugars, amino acids, fatty acids, lipids and nucleotides. In cooperation with OWL metabolomics and different CIBEREHD groups, the CIC bioGUNE platform has specialised in the directed analysis of polar chemical metabolites with affinity for HILIC or AMIDE chromatography columns. It currently provides services for determining the main metabolites of the metabolism of methionine, of pyrimidines and folates. The metabolomics platform has coordinated the LIVERBIOMARK project at CIC bioGUNE, undertaken in cooperation with OWL metabolomics and the Hospital Clinic de Barcelona in order to find non-invasive markers of cirrhosis. In cooperation with Dr Jesús Bañales it carries out molecular characterisation of exosomes secreted by cholangiocytes with special interest in models of cholangioma. In cooperation with groups from the Hospital Universitario de San Sebastián and OWL metabolomics it is characterising the metabolome of stools in order to identify new non-invasive markers of colorectal cancer. Thanks to these cooperation schemes it has also developed tools based on the metabolomic analysis of serum to determine hepatic toxicity. The platform has highly qualified personnel with experience in the extraction of metabolites in different cell cultures, samples of  tissues (liver, brain, hippocampus, sciatic nerve) as well as in samples of stools, urine and blood, in both experimental models and in human samples. This accumulated experience means that the platform can provide support in experimental design for companies and research laboratories interested in applying this technology in their research. There is growing interest in developing metabolomic applications for a better understanding on the molecular level of pathologies as well as for developing innovative tools for early diagnosis. In this respect, the metabolomic analysis of samples by NMR spectroscopy at the CIC bioGUNE will also enable the integration of two major research strategies: biomedical research in cell biology (which contributes the biomedical problem and has access to the samples) and structural biology (which provides the methodology and technology).

The proteomics platform has given technological scientific support to different CIBEREHD laboratories of the CIC bioGUNE as well as outside laboratories. Some of the internal ones that could be mentioned are the cooperation with groups in the context of liver diseases, in exosomes or the analysis of post-translational modifications and glycomics. As regards outside users we could mention groups like the one at the Hospital Clinic: urine peptidomics of cirrhotic patients; (IGTP): proteomic analysis of infantile hepatoblastomes; (BioDonostia), proteomic analysis of cholangiocarcinoma. The proteomics platform has published 18 articles in international journals in which its attachment to the CIBEREHD network is cited.

The genome analysis platform has made all the technologies developed available to the CIBEREHD groups, as well as its cooperation during experimental designs especially of genome or full transcriptome studies. Thanks to this interaction the head of the platform is participating as both coIP (co-chief researcher) in an FIS project with a CIBEREHD group and in other cases, as well as carrying out the required laboratory experimentation to generate the data requested, it is also involved in the analysis of data, generation of specific graphics and interpretation of results. This is vouched for by several joint publications with these groups and other works currently being prepared.