UC Santa Cruz researchers have discovered a peptide in human RNA that regulates inflammation and may provide a new avenue for treating diseases such as arthritis and lupus. The team used a screening process based on the powerful gene-editing tool CRISPR to shed light on one of the biggest mysteries about our RNA: the molecule responsible for carrying out the genetic information contained in our DNA.
This peptide originates from a long non-coding RNA (lncRNA) called LOUP. According to the researchers, the human genome encodes more than 20,000 lncRNAs, making it the largest group of genes produced from the genome. But despite this abundance, scientists know little about why lncRNAs exist or what they do. This is why lncRNA is sometimes referred to as the “dark matter of the genome.”
The study, published on May 23 in the proceedings of the National Academy of Sciences (PNAS), is one of the few in the existing literature that reveals the mysteries of lncRNA. It also presents a new strategy for high-throughput screening to rapidly identify functional lncRNAs in immune cells. The pooled screen approach allows researchers to target thousands of genes in a single experiment, which is a much more efficient way to study uncharacterized portions of the genome than traditional experiments that focus on one gene at a time.
The research was led by immunologist Susan Carpenter, professor and Sinsheimer Chair of the Department of Molecular, Cellular and Developmental Biology at UC Santa Cruz. She studies the molecular mechanisms involved in protection against infections. Specifically, it focuses on the processes that lead to inflammation to determine the role that lncRNAs play in these pathways.
“Inflammation is a central feature of almost all diseases,” he said. “In this study, my lab focused on trying to determine which ncRNA genes are involved in regulating inflammation.”
This meant studying lncRNAs in a type of white blood cell known as a monocyte. They used a modification of CRISPR/Cas9 technology, called CRISPR inhibition (CRISPRi), to repress gene transcription and discover which of a monocyte’s lncRNAs play a role in its differentiation into a macrophage, another type of critical white blood cell. to a well-functioning immune response.
Additionally, the researchers used CRISPRi to detect lncRNA from macrophages for involvement in inflammation. Unexpectedly, they located a region that is multifunctional and can function as RNA, in addition to containing an undiscovered peptide that regulates inflammation.
Understanding that this specific peptide regulates inflammation gives drug makers a target to block the molecular interaction behind that response in order to suppress it, Carpenter said. “In an ideal world, a small molecule would be designed to disrupt that specific interaction, rather than, for example, targeting a protein that could be expressed throughout the body,” she explained. “We’re still a long way from addressing these pathways with that level of precision, but that’s definitely the goal. There’s a lot of interest in RNA therapy right now.”
Co-authors of the UC Santa Cruz study include Haley Halasz, Eric Malekos, Sergio Covarrubias, Samira Yitiz, Christy Montano, Lisa Sudek and Sol Katzman, along with researchers from UCSF and MIT. The research was supported by funds from the National Institute of General Medical Sciences (R35GM137801 to Carpenter) and the National Institute of Allergy and Infectious Diseases (F31AI179201 to Malekos).