Proteomic Services: supporting research into cardiac disease
Cardiovascular disease is the leading cause of human death worldwide. Its causes are diverse, but atherosclerosis and/or hypertension are the most common. Ageing brings a number of physiological and morphological changes that alter cardiovascular function and lead to increased risk of cardiovascular disease, even in healthy individuals.
EMBL-EBI's Proteomics Services Team provides a range of resources to help research scientists understand these changes, and to assist in the identification of novel drugs and other therapeutics to maintain the aging heart in prime condition.
To understand how these resources can help clinical research, let's take a look at the potassium channel inward rectifier potassium channel 2 (KCNH2) protein, also known as hERG1 or "Ether-a-go-go" related gene potassium channel 1.
Cellular function of the KCNH2 protein complex
Ion channels are membrane-spanning protein complexes that allow ions to travel across the lipid bilayer. Voltage-gated potassium (Kv) channels are a large family of such proteins that show K+ over Na+ ion selectivity and play a central role in membrane electrical activity. Channel properties are modulated by the cyclic nucleotide, cAMP, and by subunit assembly. KCNH2 is an alpha subunit that complexes to form an inward-rectifying channel, which passes current into the inside of the cell. Beta subunits are auxiliary proteins that associate with alpha subunits in an α4β4 stoichiometry and do not conduct current on their own; rather, they modulate the activity of Kv channels. The sequence and function of the KCNH2 protein is described in full in the UniProtKB database, and its monomeric structure can be accessed via PDBe.
There is experimental evidence that this protein is expressed in the heart to be found by by examining proteomics mass spectrometry data available at the PRIDE database, where it is seen to be present in aortic tissue as well as umbilical vein endothelial cells. PRIDE holds extensive data on the healthy heart, comparative studies pertaining to healthy and diseased tissue and also model organism studes, for example the mouse heart proteome project. In order to assist the cardiovascular researcher find appropriate datasets to download and reanalyse, experiments performed in a relevant tissue type have been tagged to enable filtering, the resulting list of experiments is available here.
Interactions and pathways
However, proteins do not operate in isolation, and to fully understand their behaviour, we need to look at them in the context of the proteins with which they interact. The voltage-gated ion channel complexes (EBI-9511172 and EBI-9511245) which these proteins form are described in greater detail in the Complex Portal, an enyclopedia of macromolecular protein complexes. Placing these complexes into the context of a well studied pathway is the job of the Reactome database, which visually represents well-studied biological pathways in a detailed, computationally accessible format. Embedded toools enable the analysis of transcriptomic, proteomic or metabolomic datasets supplied by the user, assigning the biological molecules in these lists to pathways and then allowing the reseacher to perform over-representation or enrichment analyses.
Researchers may, however, wish to explore novel mechanisms by which these pathways may be externally regulated, and one method to do this is by using the experimental data in the IntAct molecular interaction database and look at additional proteins which may interact with, and modulate the activity of KCNH2.
In order to better serve the cardiac researcher, the IntAct database has curated interactions of a gene list assembled by the Cardiovascular Gene Annotation group at the University College, London (funded by the British Heart Foundation grant RG/13/5/30112) in collaboration with the Cardiac Proteomics and Signalling Laboratory at UCLA (funded by NHLBI Proteomics Center Award HHSN268201000035C). The dataset can be accessed here or included in an advanced search using the following term in the search box: annot:"dataset:Cardiac - Interactions involving cardiac related proteins"
A variety of mutations in KCNH2 have been found to underlie the congenital Long-QT syndrome, LQT2. LQT2 may give rise to severe arrhythmogenic phenotypes leading to sudden cardiac death. Models of wild-type (WT) and mutant channels have been incorporated into a comprehensive model of the cardiac ventricular cell in order to understand the mechanisms by which heterogeneous LQT2 genotypes can lead to prolongation of the action potential duration. In this model, which can be found in the BioModels database, the cell is depolarized to the test potential for 250ms (from 50ms to 300ms) from a holding potential of -40mV and then repolarized to -40mV.
To find a list of models related to cardiac function, a quick search based on GO terms derived from "circulatory system process" (GO:0003013) using the BioModels GO tree currently returns four models:
- Clancy2001_Kchannel (BIOMD0000000121)
- Clancy2002_CardiacSodiumChannel_WT (BIOMD0000000126)
- Cooling2007_IP3transients_CardiacMyocyte (BIOMD0000000400)
- Shi1993_Caffeine_pressor_tolerance (BIOMD0000000241)
Find out more
This quick tour of the Proteomics Services Team resources is designed to give you just a taste of how these can be used as part of your research work. Tutorials on how to use the databases and tools described above can be found on the EBI Train Online resources or feel free to use the 'Contact Us' button on any database page to contact us directly.
Resource enhancements specifically for cardiovascular research are supported by NHLBI Contract 268201000035C: Proteome Biology of Cardiovascular Disease. The Proteomics Services resources are supported by EMBL core funding and multiple grants from the US NIH, UK BBSRC, and the European Commission, as documented for each resource.