Canadian researchers have identified a "silent" mutation of a gene that contributes to shorter survival in patients with mantle cell lymphoma (MCL), a subgroup of non-Hodgkin lymphoma that, despite new therapies, is considered incurable.
In research presented during a virtual meeting on Advances in Malignant Lymphoma held by the American Association for Cancer Research (AACR), the research team described how silent or non-coding mutations in the gene-a novel oncogene called HNRNPH1 (heterogenous nuclear ribonucleoprotein H1)-triggers the runaway production of a protein that can serve as a potential driver of MCL tumor formation.
"Mutations that don't alter peptide sequences or protein function are often dismissed," said Krysta Coyle, PhD, a postdoctoral fellow in molecular biology and biochemistry at Simon Fraser University in Burnaby, British Columbia, Canada. "This study indicates that non-coding and silent mutations can be relevant to cancer biology and patient outcomes."
Coyle added that the identification of the functional role played by this mutated gene ultimately could illuminate a path leading to new targeted therapies against this aggressive lymphoma.
"Identifying the functional role of this oncoprotein may indicate novel therapeutic targets," she noted in an interview.
Research on Mutations
As outlined in her talk, Coyle and colleagues recently published a study in Blood showing that HNRNPH1 mutations were found in about 10 percent of MCL tumors, as revealed by a combination of exome and genome sequencing (2020; https://doi.org/10.1182/blood.2019002385). As such, the research team concluded that HNRNPH1 was one of the most common mutated genes found in MCL, which accounts for 4-9 percent of all non-Hodgkin lymphoma diagnoses worldwide.
Among other things, the team discovered that HNRNPH1 is a splicing factor of mantle cell lymphoma that helps regulate growth and maturation of RNA. In recent years, researchers have focused on the role of splicing factors and their crucial role in the process whereby genes give rise to proteins. Here, splicing factors edit the coded message copied from genes. These copies of a gene's message, called transcripts, are made of RNA. Splicing snips out part of the message, called introns, that don't encode protein, and paste together the remaining portion of message, the exons, that do encode protein.
In essence, splicing factors are somewhat akin to film editors, but instead of splicing together movie scenes, the splicing factor cuts away introns to assemble exons that instruct a cell's ribosomes to make proteins. If the splicing goes awry, the result can lead to an overexpression of a protein that can drive cancer formation.
In their most recent study, Coyle reported how the team examined RNA sequencing data from 103 MCL tumors and identified two variants of HNRNPH1. The first, termed canonical, produces a productive transcript that encodes a functional HNRNPH1 protein. The alternative excludes or skips over a particular exon-exon 4-resulting in a nonsense message.
"We found that tumors with mutations in HNRNPH1 had a lower exon skipping ratio, which corresponds to a higher proportion of canonical transcripts, and likely would result in a higher abundance of HNRNPH1 protein," said Coyle. "When exon 4 is skipped, the messenger RNA is subject to nonsense-mediated decay.
"Normally, an excess of HNRNPH1 would bind to its own RNA, force exon skipping, and create a non-productive transcript which limits further protein production," she added. "When the HNRNPH1 gene is mutated, the sequence alteration prevents HNRNPH1 protein from binding its own RNA and thus an overexpression of HNRNPH1 can occur."
Given this information, Coyle and colleagues hypothesized that HNRNPH1 regulated its own splicing, implying that mutations inhibit a negative feedback loop that otherwise would put a brake on its production and limit protein formation. Their hypothesis was validated using a variety of experimental models, including analysis of a tissue microarray of 72 MCL tumors.
The team further reviewed and analyzed RNA sequencing data that resulted in the identification of 155 splicing events associated with alterations of HNRNPH1 splicing.
"The genes identified as differentially spliced cover all aspects of RNA maturation," Coyle said, "suggesting that while HNRNPH1 is certainly involved in regulating specific target genes, it contributes to a network of additional RNA regulators that overall can affect the pathobiology of mantle cell lymphoma."
As for next steps, Coyle said the team already is conducting additional studies into the altered splicing program that results in HNRNPH1 overexpression to identify functional and targetable events for MCL therapy. The researchers also are exploring how HNRNPH1 specifically contributes to the etiology of MCL, and whether HNRNPH1 splicing could serve as useful biomarker for survival of MCL patients.
"Our work contributes to a growing field exploring alternative splicing in cancer," she said. "Whole transcriptome analyses of splicing events will provide important information about splicing as a hallmark of cancer."
Warren Froelich is a contributing writer.