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Editor - Paul Denny
The Parkinson's Disease (PD) Gene Annotation team has had a busy few months; Rebecca annotating key genes involved in the oxidative stress response, and/or regulation of neuron death, including DJ-1 (PARK7) and LRRK2 (PARK8), and Paul focusing on synaptic vesicle transport. As the project progresses, it is becoming clearer how much overlap there is between the proteins involved in the different processes relevant to PD; e.g. LRRK2 regulates synaptic vesicle localization and is also believed to be involved in the response to oxidative stress.
Gene Annotation
Our list of PD risk genes has been growing as a result of the publication of a major new meta-analysis of genome-wide association studies of PD; we have added six genes: SIPA1L2, INPP5F, MIR4697, GCH1, VPS13C and DDRGK1. One of these genes, GCH1, encodes an essential enzyme for dopamine production in nigrostriatal cells and has been shown independently to be associated with an increased risk for PD. Over the next couple of months, we are focusing our annotation efforts on two critical processes associated with PD pathology - the unfolded protein response and mitophagy. Based on the EBI statistics, (30th August 2014), Ruth, Rebecca and Paul have associated 1113 GO terms to 274 proteins, including 171 human proteins.
Gene Ontology
New GO terms are continuing to be created by the GOC editors, based on gaps we have noticed in the ontology that are relevant to PD. This brings the total number of GO terms created through our focused annotation of genes to over 100 - the majority suggested by Rebecca.
Community engagement
Parkinson's UK sends a regular newsletter to their supporters and we were very pleased to hear that this has prompted three local branches, from Cheltenham, Wrexham and North East Wales and Mid-Sussex, to sponsor our project. One other way in which we are planning to communicate directly with a wider audience and stimulate interest in our work here at UCL is to make more use of social media and blogs.
Call for contributions from the Parkinson's Community
Our PD annotations are being improved substantially by contributions from expert scientists and clinicians in our network, but we appreciate more feedback about missing or inaccurate annotations by email. GO annotations can be viewed in QuickGO; e.g the key PD gene PARK2 (parkin) now has over 100 experimentally-supported GO annotations, of which about 30 describe interactions with other proteins.
Meetings Attended
In July Ruth talked about our project to the Mid-Sussex branch of Parkinson's UK and was given a very warm welcome. It was particularly satisfying to get to talk with patients, carers and fund-raisers about our work.
Upcoming events
In October, Ruth will be attending the GO Consortium meeting in Barcelona. Rebecca is participating in the 2nd Workshop on Systematic Curation of Molecular Pathways implicated in Parkinson's Disease, at the Luxembourg Centre for Systems Biomedicine in October. Then both Rebecca and Paul will be presenting at the Parkinson's UK Research Conference, in York in November.
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