Diving into Marine Genomes and Regenerative Medicine

From an evolutionary perspective, humans and echinoderms, otherwise known as sea stars and sea urchins, crinoids, brittle stars, and sea cucumbers have common ancestry. But UNC Charlotte Bioinformatics Professor Dan Janies, PhD, is more interested in a particular difference between the species − the ability to regenerate limbs and organs.

“Echinoderms have really interesting properties,” said Janies, who is the Carol Grotnes Belk Distinguished Professor of Bioinformatics and Genomics. “They have a very funny shape. They are five sided rather than bilaterally symmetrical as adults. They also have the ability to regenerate their limbs and some of their organs after injury.”

How echinoderms regenerate is not well understood. To gain that understanding, Janies is working with the Genomics Laboratory at the David H. Murdock Research Institute (DHMRI), located on the NC Research Campus (NCRC), to fully sequence the genomes of sea stars and sea cucumbers.

“We do have some results based on transcriptomes, which are the active genes,” Janies said. “Now we want to sequence whole genomes, and try to figure out the molecular basis of the ability of the animals to regenerate.” He chose to work with the DHMRI Genomics Laboratory because of the quality of the data colleagues at UNCC received from the institute. He also likes their flexibility.

“We have seen the initial quality control results on various organisms,” Janies said, “They’ve been great about rewriting the quotes, and changing the underlying assumptions for us. They are very responsive.”

DHMRI Genomics Group Leader Meredith Bostrom, PhD, added, “We are flexible about giving things a try and altering protocols to do the customized approach that Dr. Janies and other scientists need for their research.”

For DHMRI, this is one of several genomics projects involving marine animals. “We are in an age where humans, mice and other more commonly researched species have been sequenced,” Bostrom said, “Animals like echinoderms have not been sequenced in great depth. We feel very fortunate to help advance this area of genomics and its application to human health.”

Janies’ goal is to “build fundamental knowledge that can be translated to recovery from injury and cancer treatment in humans.”  In research published in the Royal Society of Open Science in 2015, Janies and his colleagues, including members of the UNC Charlotte Bioinformatics Services Division at the NCRC, discovered an abundance of variants in a family of genes called “tissue inhibitors of metalloproteinases (TIMPs)” among echinoderms.

“In humans, TIMP-2 operates in a gene network important for tissue homeostasis. TIMP-2 plays a role in abating the migration of tumor cells and has been proposed as a therapeutic by cancer researchers,” Janies explained.  “What we were able to find out is that these ancient animals that are really good at regeneration, like sea cucumbers, for example, evolved a tremendous array of different variants of these TIMP genes.”

The variations of TIMP genes in sea cucumbers, Janies continued, are not “just the basic set” like those in chordates.

“Sea cucumbers have a vast toolkit of TIMP genes, including Tensilin which participates in what are called mutable collagenous tissues (MCTs) that can stiffen or become fluid under nervous control,” he said.” MCTs and organ regeneration make sea cucumbers a nice point to start from to make a connection to regenerative medicine.”

Janies will use the information generated by the DHMRI Genomics Laboratory as preliminary data for a National Science Foundation Enabling Discovery through Genomic tools (EDGE) grant focused on the development of new model systems for research.

Learn more about genomics capabilities at DHMRI.

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