Dispatches from ARVO 2014, Day 2: Crowdsourcing Science

May 6, 2014

By Jennifer Phillips, Ph.D.

Another day of scientific discovery has come and gone here at ARVO. Continuing with yesterday’s inspirations from Chris Anderson’s book “Makers”, the theme of today was Crowdsourcing. This concept of putting complex questions to a large and diverse group of people with different areas of expertise has been used effectively in the business world, but it’s also a tactic that comes into play at scientific conferences like this one, where there is certainly no shortage of complex questions to address. Large interdisciplinary meetings like this, where clinicians and scientists with a wide range of training and interests, is a perfect environment in which to generate interest and momentum in a project that’s just too big or multifaceted for a single research group to tackle. With the recent advances in molecular techniques and the ability to process vast amounts of genetic sequence information, you might surmise that identifying the genetic basis of disease has gotten easier. In fact, although these tools have indeed allowed us to learn a great deal about inherited forms of RP and other diseases, they’ve also revealed how much more there is to the genome than previously understood.

We’ve known for a while that the human genome contains tens of thousands of genes that supply the code for making proteins, and that a substantial number of those genes can be alternately spliced to generate a variety of similar, but distinct, proteins. We’ve also known that there are certain ‘non-coding’ portions of the genome, that is, parts that don’t correspond to a protein. Some of these act as recognition sequences—cellular traffic signals, if you will—to coordinate the activation of a nearby gene that does code for a functional protein. Additionally, while genes encoding proteins are built from an RNA transcript, there are also genes whose RNA transcripts don’t serve as templates for protein at all, but instead perform certain cellular functions in their own right. It’s this last group of molecules that has become a lot more prominent in recent years, as new sequencing techniques allow us to detect how many different non-coding RNAs—many of them specific to a particular tissue or cell type—are in play. This is an important undertaking because we don’t have a good grasp of how many genetic problems might be caused by mutations in non-coding regions of the genome. Given the number of people who have inherited conditions and no genetic diagnosis, it wouldn’t be surprising to find that mutations in some of these non-coding RNAs contribute to human disease.

One of the talks I heard today was by Eric Pierce, describing his research group’s efforts to understand the role of RNAs in retinal cell function. Pierce’s team conducted a large scale sequencing project to identify all of the distinct RNA molecules present in retinal cells and found literally thousands of new non-coding transcripts that are likely to play important roles in regulating other retinal genes that do code for proteins. Knowing that there are that many more molecules in play in a tissue (the retina) that was already known to be very complicated is a step in the right direction, and we can make some guesses about the functions of each of those molecules, but the staggering number of them identified in this and other studies make it a daunting task, quite impossible for a single research team to manage. This is where the crowdsourcing bit comes in. Although he didn’t use that term, Dr. Pierce advocated for a community effort in investigating these RNAs. What would this involve? In addition to studying the consequence of removing or inhibiting their function in retinal cells, there is a great need for developing new sequence analysis software to help to organize and analyze the incredible volume of information we can now obtain from the genome.

I heard some more from Budd Tucker and David Gamm, whose work using patient-derived retinal cell cultures impressed me so much at last year’s meeting, and I’m planning to write about the latest stem cell research later this week. Stay tuned!

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