Engineer demonstrates technique for targeting RNA inside living cells

Dave Nelles

When he’s not surfing in Mexico or listening to electronic music, Dave Nelles is busy tinkering – inside living cells!

Growing up, Nelles always knew he wanted to develop technology, but was intrigued by the complexity and diversity of processes in biology.

“Biology is on the verge of becoming a predictive and quantitative pursuit,” says Nelles. “Compared to fields like physics where we have many good models of natural phenomena, biology in general is less mature. One reason for this is a lack of tools to measure and alter specific components of living cells.”

Motivated by this gap, Nelles focused his graduate work in materials science and engineering on technologies to measure and alter a fundamental biological molecule: RNA. Inside cells, DNA is transcribed into messenger RNA (mRNA), which is subsequently translated into protein.

Proteins are the building blocks of life – many functions that take place inside of a cell are made possible by proteins.

“In many diseases, the processing of mRNA is dysfunctional, meaning that the protein that is encoded for by that RNA will not be made correctly, or at all,” said Nelles.

In molecular biology, there’s a technique called CRISPR-Cas9 that is used to modify DNA and has the potential to cure a range of genetic diseases. Nelles and his collaborators have been able to demonstrate that CRISPR-Cas9 can not only bind to DNA, but also to RNA.  This approach is described in a paper published on March 17^th in the journal Cell.

Nelles explains, “Just as CRISPR-Cas9 is making genetic engineering accessible to any scientist with access to basic equipment, RNA-targeted Cas9 may support countless other efforts for studying the role of RNA processing in disease or for identifying drugs that reverse defects in RNA processing.”

In collaboration with Mitchell O’Connell in the lab of Jennifer Doudna at the University of California, Berkeley, Nelles tagged Cas9 with a fluorescent protein and targeted various RNAs to track their movement inside living cells.

“This work is the first example, to our knowledge, of targeting RNA in living cells with CRISPR-Cas9,” said senior author Gene Yeo, PhD, associate professor of Cellular and Molecular Medicine. “Our current work focuses on tracking the movement of RNA inside the cell, but future developments could enable researchers to measure other RNA features or advance therapeutic approaches to correct disease-causing RNA behaviors.”

“For many experiments involving RNA tracking, the cells need to be dead or the targeted RNA must be genetically modified in order for the RNA to be detectable,” said Nelles. “Our experiments were done inside living cells with unmodified RNAs, which has many advantages – for example, we were able to observe RNA being transported to stress granules over time.“

Stress granules are accumulations of RNA and protein in a cell and their formation has been linked to neurodegenerative diseases. Nelles and his team hope that providing a way to track these RNAs will assist with new drug development.

After graduating this Spring, Nelles will be continuing his work as a postdoc at UC San Diego.

Want to learn more about other projects at the Jacobs School? Register to attend Research Expo on April 14, 2016.