Cancer Organizational Role Established for Non-Coding RNA

This somewhat arbitrary limit distinguishes lncRNAs from small regulatory RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs. LncRNAs have been found to be involved in numerous biological roles including imprinting, epigenetic gene regulation, cell cycle and apoptosis, and metastasis and prognosis in solid tumors. Most lncRNAs are expressed only in a few cells rather than whole tissues, or they are expressed at very low levels, making them difficult to study. Their name notwithstanding, long non-coding RNAs (lncRNAs) have been found to actually encode synthesis of small polypeptides that can fine-tune the activity of critical cellular components.

Investigators at Sanford Burnham Prebys Medical Discovery Institute worked with the lncRNA SPRIGHTLY, which had been previously implicated in colorectal cancer, breast cancer, and melanoma. In the current study, they used a combination of dChIRP (Domain-specific chromatin isolation by RNA purification), which identifies interacting partners of functional regions of long non-coding RNAs, and the CRISPR/Cas9 gene-editing platform.

CRISPRs (clustered regularly interspaced short palindromic repeats) are segments of prokaryotic DNA containing short repetitions of base sequences. Each repetition is followed by short segments of "spacer DNA" from previous exposures to a bacterial virus or plasmid. CRISPRs are found in approximately 40% of sequenced bacteria genomes and 90% of sequenced archaea. CRISPRs are often associated with cas genes that code for proteins related to CRISPRs. Since 2013, the CRISPR/Cas system has been used in research for gene editing (adding, disrupting, or changing the sequence of specific genes) and gene regulation. By delivering the Cas9 enzyme and appropriate guide RNAs into a cell, the organism's genome can be cut at any desired location. The conventional CRISPR/Cas9 system is composed of two parts: the Cas9 enzyme, which cleaves the DNA molecule and specific RNA guides that shepherd the Cas9 protein to the target gene on a DNA strand.

The investigators reported in the May 3, 2017, online edition of the journal Science Advances that that SPRIGHTLY bound to 115 RNA partners that code for proteins, and that six of them (SOX5, SMYD3, SND1, MEOX2, DCTN6, and RASAL2), were major partners with cancer-related functions. Knockout of SPRIGHTLY by CRISPR/Cas9 in melanoma cells significantly decreased SPRIGHTLY lncRNA levels, simultaneously decreasing the levels of its interacting pre-mRNA molecules, and decreasing anchorage-independent growth rate of cells and the rate of in vivo tumor growth in mouse xenografts.

"We show in this study that SPRIGHTLY acts as a hub for organizing cancer-related genes in the nucleus of the cell," said senior author Dr. Ranjan Perera, scientific director of analytical genomics and bioinformatics at Sanford Burnham Prebys Medical Discovery Institute. "These genes may be promising individually or in combination with SPRIGHTLY as therapeutic targets in the fight against cancer."