Arpeggio Biosciences is studying “dark DNA”

The human genome is filled with DNA about which we are almost entirely ignorant. Of the 3.2 billion letters that make up our genome, only 1 percent code for proteins—the machinery components of our cells. We used to think that proteins were the only functional output of DNA, so it was a shock to learn that protein-coding genes made up so little of the genome. It was like looking into the night sky for stars—what’s all that blank space doing there?

Scientists have begun to realize that the “blank space” isn’t so useless. Instead of picturing the night sky, picture a trampoline sprinkled with sequins. It might look similar to the night sky—lots of black space with a few sparkles. But if you touch the surface of the trampoline, the sequins move as the trampoline bounces. The trampoline is a better metaphor for all the “junk DNA” in the genome. When that DNA is perturbed, the effects spread and cause visible changes.

Joey Azofeifa, a recent PhD from the computer science program at CU Boulder, studied this “dark portion” of genomes for his graduate work. He was trying to understand a fundamental process of all life: transcription. Before DNA becomes protein, it has to be turned into a molecule similar to DNA, called RNA. This process is called transcription because RNA uses the same biological “language” as DNA (with small differences). When you “read” RNA into protein, it becomes a very different molecule. That process is called translation because you’ve changed the language of the molecule.

Azofeifa studied the phenomenon that transcription is also occurring in regions of our genome that don’t encode proteins. In other words, our cells turn some pieces of DNA into RNA even though that RNA will never become protein through translation. The question is: why would the cell bother doing this?

To study this phenomenon, Joey took advantage of techniques that are able to capture all the RNA being actively transcribed in a population of cells. It can measure this active transcription in a very tight time window, which is an important technological advance. These techniques are relatively new, and distinct from techniques that have been used in the past to study the RNA present in cells at any given time.

Older techniques (such as a method called RNA-seq) measure all the RNA you can isolate from cells. They often require a longer wait between the experimental condition change and the collection of that RNA. This means you would be studying RNA that had been produced long before the experiment but hadn’t yet been degraded. If you want to study the immediate response to a stimulus, these older techniques aren’t as helpful. Azofeifa described why, if you want to understand how a particular drug is changing the RNA landscape of your cells, it’s not as helpful to use these older techniques.

“The problem is that if you wait 12 or 24 hours, a lot of things that have changed are secondary or tertiary and quaternary effects,” said Azofeifa. “So, you’re not really picking up on the immediate primary targets of your drug, you’re picking up on ripples in the pool that were the result of your drug.”

In his graduate work, Azofeifa took advantage of newer techniques, especially a technique called global nuclear run-on sequencing, or GRO-Seq. GRO-Seq allows scientists to study RNA being actively transcribed immediately after a perturbation to cells. He showed that RNA being produced from the “dark regions” of the genome (RNA that never becomes protein) could reveal a lot more about the activity of the cell than we ever suspected.

 

Now, Azofeifa is using GRO-Seq, as well as the related PRO-Seq, in a new initiative: a start-up company located on the CU Boulder campus. Azofeifa, who graduated from Dr. Robin Dowell’s lab from CU, has teamed up with Dowell, as well as another recent Dowell Lab graduate, Tim Read. Together they have launched Arpeggio Biosciences.

Arpeggio is currently studying the effects of drug treatments in different cells, specifically by studying the way that RNA transcription patterns change. Although sequencing RNA from cells after drug treatment is not a new technique in biotechnology, Azofeifa believes that using PRO-Seq, as well as the algorithms that he has developed to analyze the results of these assays, will give Arpeggio the edge.

“Pretty much we’re an RNA-Seq company with a better assay and better algorithms,” laughed Azofeifa.

Arpeggio’s first customer is Forma Therapeutics, an oncology company trying to understand what changes their drugs have on cells. Scientists at Arpeggio will examine where RNA is being transcribed before and after treatment to try and understand how these drugs might be affecting regions of the genome that don’t code for proteins.

Azofeifa has long-term goals for Arpeggio, too.

“These assays are a really awesome magnifying glass,” he said. “And now what we want to do is look through this magnifying glass at a bunch of different tissues.”

Azofeifa argues that in the long run, Arpeggio won’t just be helping us understand how drugs are working—they’ll be helping us understand how diseases are working.

“We can reduce it to a single factor,” said Azofeifa, referring to the ways that a cell’s biochemistry changes during disease states. “And then we have new targets for diseases. Then we can develop new companies around those targets and cure those diseases.”

This ambitious goal may be a while away, but Azofeifa is convinced that Arpeggio is the right company to do it, and that they’re in the right place to do it.

“I feel very grateful to be starting in a place like this,” said Azofeifa. “We’re an RNA company and this is a great place to study RNA. There’s a lot of intellectual support just at CU for us. “

Besides—who wouldn’t want a view of the Front Range?

By Alison Gilchrist (@AlisonAbridged)