PROBE participates in a long list of research projects every year, both as a service provider and as a research partner. In addition, the main researchers at PROBE all head their own projects. Below you find a list of the most prominent projects PROBE is currently involved in.
The Multiple Sclerosis Biomarker Project
Multiple sclerosis is a chronic inflammatory disabling disease of the central nervous system with largely unknown cause and pathogenesis. There is a general lack of available biomarkers for diagnosis, prognosis and treatment prediction. Early diagnosis and treatment is essential to slow down progressive deterioration and accumulation of disability, and biological markers for early detection of the disease are much needed. In our multiple sclerosis biomarker discovery project, we are using state-of-the-art quantitative proteomics methods to discover and verify disease specific protein biomarkers for multiple sclerosis with potential diagnostic or prognostic value, or biomarkers that can be used to follow treatment efficiency. The proteomics methods that we use in this project are: label-free and iTRAQ semi-quantitative shotgun approaches for biomarker discovery, and selected reaction monitoring for biomarker verification.
Project leader: Frode Berven
HPP: Chromosome 19 Proteomics Consortium
The HPP is a world wide spanning project, organized by the Human Proteome Organisation (HUPO). Some major goals for this project are to a) develop quantitative protein assays for all 20 300 known human proteins and to map their most common modifications and isoforms b) measure their concentrations in major normal human tissues/organs/body fluids c) monitor the effect of various diseases on these proteins to reveal novel biomarker candidates. The work has been divided worldwide and a consortium has been established for each of the 23 chromosomes. PROBE has joined the consortium assigned chromosome 19, together with 15 laboratories from Spain, 5 laboratories in Sweden and one laboratory in India. PROBE will be involved in mass spectrometry based proteomics in this project to identify and quantify a portion of proteins from chromosome 19 and their modifications and isoforms, to make quantitative SRM-assays for these proteins and to use the developed assays to measure disease specific effects for several diseases. The diseases that will be the main focus for the Chromosome 19 Consortium are: prostate cancer, brain cancer, lung cancer, diabetes, cardiovascular diseases and reumatoid arthritis & osteo arthritis.
PROBE's Contact Person: Frode Berven
Quantitative Proteomics Analysis of Epac
Quantitative proteomic analysis of Epac induced differentiation in human SH-SY5Y neuroblastoma cells. Neuroblastoma is a pediatric solid tumor, which is derived from precursor or immature cells of the sympathetic nervous system (SNS), and primary tumours can be found at any location of SNS structures. Mutations in the receptor tyrosine kinase ALK (anaplastic lymphoma kinase) are the main cause of familial neuroblastoma. Moreover, oncogenic mutations of ALK are also found in primary tumours and in the human neuroblastoma cell line SH-SY5Y. Despite that the noradrenergic SH-SY5Y cell line originates from a highly malignant tumour it has maintained the capacity to undergo neuronal differentiation under proper growth conditions. These characteristics together with a distinct sensitivity to oxidative stress makes the neuroblastoma SH-SY5Y cell line an excellent model system to study neuronal differentiation and neuroblastoma tumourigenesis, as well as several aspects of neuronal degenerative diseases.
In this project we investigate the role of the exchange protein directly activated by cAMP (Epac) in SH-SY5Y neuroblastoma cells. Using both morphological studies and quantitative proteomics, we have found that Epac induces differentiation of human SH-SY5Y cells into a neuronal phenotype.
PROBE's Contact Person: Frode Selheim
Development of Bioinformatics Tools and Infrastructure for Quantitative Proteomics
The primary objective of this project is the development of novel robust and flexible bioinformatics tools and algorithms for analyzing quantitative proteomics data. This includes the development of an integrated suite of bioinformatics tools for improving, simplifying and automating the currently often manual and work-intensive labor of analyzing proteomics data.
The secondary objective is to develop and improve much needed systems for efficient storing and sharing of proteomics data, thus creating a better framework for the further analysis of the data.
PROBE's Contact Person: Harald Barsnes
The project is funded by the The Research Counsil of Norway.