New look inside cell nucleus could improve cancer diagnostics

Dec 23, 2013 by Daniel Stolte Thanks to a special imaging technique, the nucleus is visible here in green inside a plant cell. Credit: David Galbraith/BIO5

Researchers have successfully isolated and sequenced the entire messenger RNA the "genetic photocopies" contained in the nucleus of a single brain cell. This research, published in the journal Proceedings of the National Academy of Sciences, will help researchers better understand how organs function in health and disease and provide another stepping stone toward personalized medicine.

Most cells in animals and plants contain a nucleus, which stores the cell's DNA. Since the DNA never leaves the nucleus, the information stored in the genetic material has to be copied before it can serve in its role as a blueprint for protein synthesis, which happens outside the nucleus. This is accomplished by transcribing sequences of the DNA code into strands of so-called "messenger" RNA. The entirety of messenger RNA at any given time is called the transcriptome; the entirety of DNA inside the nucleus is referred to as the genome.

Transcriptomes tell researchers which genes are being actively transcribed at any given time, and therefore are indicative of a cell's identity and condition.

A team of researchers led by David Galbraith, a professor of plant sciences in the University of Arizona's BIO5 Institute, and Roger Lasken, a professor at the J. Craig Venter Institute in San Diego managed to isolate the transcriptome from the single nucleus of a rat brain cell and decipher the genetic information encoded in it.

By analyzing the transcriptomes of individual cells, researchers hope to better understand the processes that turn, say, a normal cell into a tumor cell. Analyses of single cells have only recently become possible; previously, scientists could only average patterns across many cells, hiding potentially important variation occurring in individual cells.

"The organs and tissues in our body are composed of many different cells, and in order to understand how the organ functions, we have to find out how the individual cells function and disentangle what each of them contributes," Galbraith said. "Further, we need to know how much variation is found in these individual cells."

Previous efforts had shown it was possible to sequence the genetic information encoded in a transcriptome taken from a single cell, but Galbraith's group wanted to know whether it was possible to do the same with just the nucleus since, being copied in the nucleus, that is where the transcriptome originates.

To test their approach, Galbraith and his collaborators isolated the messenger RNA from the nucleus of a mouse brain cell, amplified the number of copies, deciphered the genetic information using high-throughput next generation sequencing, then mapped it back onto the DNA of the known mouse genome sequence.

The method achieved almost the same coverage when applied to single nuclei versus single cells, Galbraith said.

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New look inside cell nucleus could improve cancer diagnostics