Amyotrophic Lateral Sclerosis Protective Variants Proposed in Untranslated Gene Region

Using whole-genome sequence data for more than 76,500 amyotrophic lateral sclerosis (ALS) cases or controls, an international team has focused in on apparent ALS modifiers in the 3' untranslated region of the interleukin 18 receptor accessory protein gene IL18RAP.

As they reported in Nature Neuroscience on Thursday, researchers from the Weizmann Institute of Science, the New York Genome Center's ALS Consortium, Project MinE ALS Sequencing Consortium, and elsewhere analyzed whole-genome sequences from 3,955 individuals with ALS and more than 1,800 unaffected control individuals, focusing on tens of thousands of variants falling in untranslated regions of the genome.

"The noncoding genome is substantially larger than the protein-coding genome but has been largely unexplored by genetic association studies," senior and corresponding author Eran Hornstein, a molecular genetics and molecular neuroscience researcher at the Weizmann Institute of Science, and his coauthors wrote, noting that the new study "emphasizes the importance of noncoding genetic association studies."

The team narrowed in on a region from the IL18RAP 3' UTR containing rare variants that were overrepresented in control individuals who did not develop the neurodegenerative condition, pointing to an ALS protective effect for the UTR.

The investigators estimated that ALS risk is ramped down roughly fivefold in individuals with the newly described IL18RAP 3' UTR variants, consistent with ties between ALS and IL-18, a cytokine that contributes to neuroinflammation by activating NF-kappa B transcription factors and other signaling pathways.

Past research suggests that the 3' UTR variants "reduce IL18RAP [messenger RNA] association with RNA-binding proteins, destabilize the mRNA, and further downregulate IL18RAP-NF-kappa B signaling in microglia," the authors explained, noting that the microglia central nervous system cells "induce motor neuron death in ALS, which is mediated, in part, via triggering the IL-18 and NF-kappa B signaling pathway."

After validating the IL18RAP 3' UTR association in another 2,184 individuals with ALS and 68,584 without, the researchers performed a series of follow-up experiments digging into the functional consequences of IL18RAP 3' UTR variants — from impacts on messenger RNA stability or double-stranded RNA-binding protein activity to motor neuron survival.

With the help of CRISPR-Cas9-based gene editing, the team saw signs that the potentially protective version of the IL18RAP 3' UTR buffered against the effects of an ALS-related C9orf72 expansion in microglia cells developed from human induced pluripotent stem cells via effects on the activity of immune system-related NF-kappa B transcription factors and the effector genes they regulate.

"[W]e demonstrate that the variant IL18RAP 3' UTR dampens neurotoxicity of human iPSC-derived microglia bearing an ALS-associated expansion in C9orf72 (C9-ALS microglia) in an NF-kappa B-dependent manner," the authors wrote, noting that "noncoding variant analysis reveals a genetic and mechanistic link for the IL-18 pathway in ALS and encourages systematic exploration of noncoding regions to uncover genetic mechanisms of disease."