A new type of CRISPR gene editing that targets noncoding RNAs has revealed the important cellular functions that these perform and could help in the development of personalized cancer treatments.
Unlike traditional CRISPR which uses the Cas9 enzyme as molecular scissors to cut DNA, the new technology deploys the Cas13 enzyme to target RNA without disrupting protein-coding genes or other regulatory elements nearby.
The research, in the journal Cell, revealed nearly 800 RNAs that did not code for proteins—and might once have been considered genetic junk—but were essential for a cell’s survival and growth, with some involved in cell division and development.
Some of the RNAs identified as essential varied by cell type, in contrast to comparable protein-coding genes, making them promising biomarkers and therapeutic targets for bespoke cancer therapies.
“This survey of functional noncoding RNAs advances our understanding of the human genome and demonstrates the potential of CRISPR screens that specifically target RNA—even those that don’t code for proteins,” said senior study author Neville Sanjana, PhD, an associate professor of biology at NYU.
He added: “These noncoding RNAs may yield new biomarkers and therapeutic targets for cancer treatment, a potential opportunity for personalized medicine given their cell type-specific expression.”
The researchers used CRISPR-Cas13 to profile 6199 long noncoding RNAs (lncRNAs) and nearby protein-coding genes across five distinct human cell lines. These included kidney, leukemia, and breast cancer cells.
Using CRISPR to knock down each lncRNA, the team discovered 778 lncRNAs essential for cell function, including a core group of 46 lncRNAs that were universally essential and 732 with functions specific to particular cell types.
Further studies indicated that, if a protein-coding gene was essential to one of the cell lines it was essential to the others. Conversely, the lncRNAs were more specific to different cell types and most operated independently of their nearest protein-coding gene indicating that their function was not purely for the regulation of these.
Essential lncRNAs modulated key pathways for cell proliferation, which plays a role in both human development and cancer, and their loss could impair cell cycle progression and drive programmed cell death.
Many of these essential lncRNAs showed dynamic expression during development that decreased later, indicating an important role for some in the early stages.
Studying approximately 9000 primary tumors from 29 different cancers, Sanjana and the research team found lncRNAs with altered expression in specific types of tumors and identified those whose expression correlated with survival.
“Overall, transcriptome-wide Cas13 pooled transcriptomic screens represent a powerful tool for the systematic investigation of the functional contributions of noncoding transcripts and pave the way to identify functional lncRNAs for any phenotype or disease,” the research team concluded.
