The human genome, made up of DNA, consists of three billion building blocks (nucleotides) where some regions (stretches) are complete genes. We all carry variants of the genes and some cause diseases. Here, the goal is to investigate the specific class of genes, the non-coding RNA (ncRNA) genes, in relation to diabetes. The ncRNA genes can be the missing components in diseases that previously have been overlooked.
Our research goal is to develop technologies for ncRNA analysis and to search for functional ncRNAs in relation to diabetes and other (inflammatory) diseases. The central dogma is that a gene encodes for a protein through a step in which it takes an RNA form. However, it has turned out that only 1.2% of the genome encode for proteins, but that there exist numerous non-protein coding (or non-coding) RNA genes. The number of discovered non-coding RNA genes is increasing rapidly. Given the large space in the genome for non-coding RNA genes, this provides a large potential to discover ncRNA which may have many diverse roles.
Diabetes mellitus represents a group of metabolic disorders characterized by chronic hyperglycaemia with or without typical symptoms. These symptoms include thirst, polyuria, fatigue, and sometimes weight loss. The chronic hyperglycaemia results from defects in insulin secretion, insulin action, or both. It is associated with long-term organ damage, particularly in the eyes, kidneys, nerves, heart, and blood vessels. Hence, diabetes is a huge healthcare problem for both the individual affected and the society. Worldwide more than 250 million people are affected - a number predicted to double within the next twenty years. Diabetes-related deaths are likely to increase by more than 50% in the next 10 years without urgent action. Despite considerable knowledge about both type 1 and type 2 diabetes pathogenesis, the co-morbidity and mortality are substantially increased compared to the background population, leaving much room for improvement in translational science within this field. The room for improvement we want to explore is the molecular role of ncRNAs that regulate the complex processes causing inflammation and autoimmunity, including diabetes.
The research strategy is multidisciplinary consisting of a number of specialized areas which are combined to achieve the overall goals. At various levels the areas make use of one another. Below each of these main areas are described in relation to research of the center. A popular description can be found here.
RNA bioinformatics and computational RNA biology includes development and application of computational methods for RNA structure prediction RNA interactions and gene finding of non-coding RNAs (ncRNAs). The development spans from construction of algorithms to pipelines that can handle the processing data and merge with other sources of information such as existing genomic annotations and high-throughput data. The knowledge of RNA structure can be exploited to search for the (structured) ncRNAs in genomic sequence. Recent directions include development of computational methods for predicting RNA interactions to e.g., ncRNAs, protein coding genes (mRNA), and proteins. RNA interactions are also exploited in the design of small interfering RNA, which are utilized to knock down specific genes investigated in relation to specific diseases or phenotypes. In the project we will develop computational methods to search for ncRNA and RNA interactions in genomic sequence and proteins. The search for ncRNAs will include structured as well as unstructed versions. Furthermore, various types of bioinformatics will be employed in combination for general processing of the data generated from the experimental part.
RNA biology covers all aspects of structure and function of RNA molecules. The main topics are the role of RNA in expression of genetic information and regulatory and catalytic functions of non-coding RNA (ncRNA). RNA and disease is an emerging topic, as more and more diseases can be understood in terms of malfunction of RNA molecules, e.g. in splicing of mRNA. The discovery of new ncRNAs and the generation of expression data is presently far ahead of other types of descriptive data and functional studies. In this project, we will establish protocols for high-throughput structure probing and RNA:RNA interaction analyses in order to improve the selection of candidates for functional analysis. The emphasis will be on candidates that have catalytic or regulatory properties whether they are functional as independent molecules or embedded in the context of a larger molecule.
Functional genomics covers the investigation of the genome in relation to phenotypes. Different methodologies and techniques will be employed to study ncRNA structure and function. This includes analyses of gene expression in healthy and diseased tissues at different developmental stages. With the recent advances in throughput in DNA sequencing technologies gene expression analysis can now be studied genome wide without a priori knowledge of gene structure, making this technology ideal for detection of novel ncRNAs. Additionally, ncRNA-RNA and ncRNA-DNA interactions will be investigated by pull-down experiments of ncRNA candidates followed by high throughput sequencing. Finally, in situ hybridizations will be used to detect cellular and sub-cellular location of ncRNA candidates.
Diabetes research at the molecular level involves the study of components which among other things cause defects in insulin secretion. Far most of these studies have so far ignored ncRNAs and only recently, data have indicated that miRNAs play a role in the development of diabetes. Several miRNAs are expressed selectively in pancreatic islets and beta cell lines and studies support that they are involved in regulation of insulin exocytose. A study in miR-375 knockout mice showed that this miRNA is required for normal glucose homeostasis and maintenance of normal alpha and beta-cell mass. Additionally, miRNAs are involved in regulation of the innate immune response and have been coupled to several inflammatory diseases and islet apoptosis mediated by cytokines. In the current project, expression profiling of candidate ncRNA in disease models and patient materials will be studied and the effects of knock-down, over-expression, and different pathogenesis-relevant exposures evaluated. Such an understanding is likely to be helpful in defining new key targets for disease prediction and prevention, for drug development, and for improved therapeutic responsiveness.
Animal models have long been used for clarifying aspects of basic biology and also for more applied research directed at modeling diseases and helping evaluate potential therapies. Among the vertebrate models traditionally the mouse has been the species of choice in many studies. However, it is now also feasible to include domestic animal species as model organisms (e.g. pig and dog) since all tools necessary for molecular genetic studies have become available. These species are closer to humans both in terms of anatomy, physiology and in sequence space than mouse is. Furthermore, their unique population structure ensures that genetic heterogeneity is much lower compared to human populations ensuring an easier access to genetic components underlying specific phenotypic traits (e.g. obesity and diabetes).