Over a million marine species are estimated to inhabit the planet’s oceans, according to the Census of Marine Life. Included in this vast reserve of biodiversity are the echinoderms, with sea urchins, star fish and sea cucumbers among their well known members. Research across biological disciplines has shown that life under the sea can provide significant insights to life on land, with echinoderms increasingly considered valuable for studies into regenerative biology, in light of their extensive capacity to regenerate various body parts. In a study in BMC Genomics, José García-Arrarás, Vladimir Mashanov, and Olga Zueva from the University of Puerto Rico, USA, provide transcriptomic insights to the regulation of central nervous system regeneration, through their analysis of the sea cucumber Holothuria glaberrima. Here García-Arrarás and Mashanov explain how echinoderms can inform our knowledge of human conditions, and what they were able to learn about neural regeneration.
What makes the echinoderm an important system for studies into regeneration? Are they now considered an established model system for such studies?
Echinoderms can be considered ‘masters of regeneration’. They are able to regenerate most of their tissues and organs. This is public knowledge as many non-scientists already know that starfish are capable of regenerating their arms. Nonetheless, starfish are not the only echinoderms that can regenerate body appendages or internal organs, many members of this phylum have amazing regenerative capacities. Sea cucumbers for example, in addition to regenerating their nervous system can regenerate their viscera following a process of evisceration. Several laboratories worldwide use echinoderms to study regeneration; examples include a group in Italy that looks at crinoid arm regeneration, in Russia holothurian muscle regeneration and in Sweden brittle star arm regeneration. However only recently are they being established as model systems. Why has it taken so long? Possibly because it is only now that are we developing the molecular tools to be able to analyse the molecular basis of regeneration.
How can findings in a phylum seemingly far removed from us provide valuable insights into human conditions?
Echinoderms, with their radial body plan might appear to have very little in common with us, but in reality they are much closer to vertebrates (and humans) than other well known model organisms, such as flies (Drosophila) or worms (C. elegans), and thus can provide important insights into human conditions. In fact, we had a common ancestor with echinoderms not so long ago (~500 MYR, compared with ~700 MYR that have passed after separation of fly+worm and human lineages). As a result, there are deep similarities between mammals and echinoderms in certain basic developmental mechanisms, both at the cellular and genetic levels
You employed deep RNA sequencing to analyse the transcriptome of the sea cucumber Holothuria glaberrima during regeneration of its nerve cord. What were the main challenges you faced in assembling and annotating its transcriptome?
For one, as with any other organism whose genome has not been sequenced yet, we had a challenge to assemble relatively long sequences of individual transcripts from a large number of much shorter sequences (reads) without having a reference template. This is very much like assembling a jigsaw puzzle without knowing what the final pattern should look like. De novo assembly software is still relatively young, there are a few competing approaches, and there is no universal protocol that would work for sure in all cases. We had to try various approaches before coming up with an assembly pipeline that yielded acceptable results.
Functional annotation was another challenge. Most of our current knowledge about functions of genes, and interactions between them, comes from research on a few ‘established’ model organisms, such as the mouse, for example. Up to now we have therefore only been able to annotate a fraction of the sea cucumber transcriptome, which represented homologs of well characterised genes in other organisms. Many of the potentially important genes that are unique to sea cucumbers and echinoderms in general still await further analysis.
Your study functionally characterised the genes identified as involved in regeneration. What were the main functional groups you identified?
The study highlighted a number of differentially expressed functional groups of genes, two of them deserve a special mention. First, the transcriptome analysis suggests that extracellular matrix remodeling plays an unexpected role in the regeneration of the central nervous system (CNS). This aspect of echinoderm regeneration has rarely been addressed before, and the unbiased analysis of gene expression data clearly suggests that it is definitely worthwhile studying in the future. Second, our study pointed to a possible mechanism by which post-traumatic neuronal cell death is prevented in the CNS. This mechanism works through the inhibition of the glutamate neuroexcitatory pathway, which is known to cause the death of neurons following injury in the mammalian nervous system.
Several transcription factors were identified in your study as candidates for regulating central nervous system regeneration. Were you surprised by any of them?
We were indeed surprised by the results. First, we expected that many of the known transcription factors that are associated with the induction of stem cell properties would be significantly overexpressed. That was not the case (with one interesting exception), as most of those genes were already expressed in non-injured animals at a certain level. This suggested that the tissues might have been primed for regeneration even before the injury took place. Moreover, we expected those genes associated with the differentiation of neuronal precursors to also significantly increase their expression level over normal conditions and that was not the case either. Again, this is in part due the fact that some of those genes are already expressed in normal, non-injured animals.
What do you think are the most exciting avenues of echinoderm research opened up by your study?
Our study opens up a way to explore the molecular basis of neural regeneration and of other regenerative processes in echinoderms. It provides a list of candidate genes that might be involved in nervous system regeneration. In particular, our study identified eleven putative transcription factors that are predicted to be positioned at or near the top of the regeneration-specific gene regulatory network hierarchy. These ‘master’ genes are the most promising candidates for future functional assays. Moreover, our results may also inform other studies in echinoderm biology, including those of molecular evolution, animal phylogeny and (most important to us) regenerative processes.
What are the next steps for translating these findings in echinoderms to enhance central nervous system regeneration in mammalian systems?
Our study is just one step on the path to understanding the limitations of central nervous system regeneration in mammals. The central question still remains of why can some animals easily regenerate their CNS while others cannot. Sea cucumbers are an example of the former while humans are an example of the latter. As we continue to do comparative studies to determine what are the differences among these animals groups we will approach a better understanding of what can be done to improve CNS regeneration in humans.