Ramp sequence may explain synonymous variant association with Alzheimer’s disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA)

BACKGROUND Synonymous variant NC_000007.14:g.100373690T>C ( rs2405442:T>C ) in the Paired Immunoglobulin-like Type 2 Receptor Alpha ( PILRA ) gene was previously associated with decreased risk for Alzheimer’s disease (AD) in genome-wide association studies, but its biological impact is largely unknown. OBJECTIVE We hypothesized that rs2405442:T>C decreases mRNA and protein levels by destroying a ramp of slowly translated codons at the 5’ end of PILRA . METHODS We assessed rs2405442:T>C predicted effects on PILRA through quantitative polymerase chain reactions (qPCR) and enzyme-linked immunosorbent assays (ELISA) using Chinese hamster ovary (CHO) cells. RESULTS Both mRNA ( P =1.9184 × 10 −13 ) and protein ( P =0.01296) levels significantly decreased in the mutant versus the wildtype in the direction that we predicted based on destroying a ramp sequence. CONCLUSIONS We show that rs2405442:T>C alone directly impacts PILRA mRNA and protein expression, and ramp sequences may play a role in regulating AD-associated genes without modifying the protein product. Research in Context Systematic review: Genetic variants identified through genome-wide association studies often lack biological support for their association with Alzheimer’s disease. Although synonymous variant rs2405442:T>C in PILRA was previously reported as protective against Alzheimer’s disease, its effects have generally been attributed to linkage with missense variant, rs1859788:A>G . Interpretation: We show that rs2405442:T>C alone decreases mRNA and protein levels by destroying a ramp of slowly translated codons at the beginning of PILRA . We also show that a ramp sequence is present in PILRA and likely regulates mRNA and protein levels, thus offering a plausible biological mechanism explaining rs2405442:T>C association with Alzheimer’s disease independent of rs1859788:A>G . Future directions: We provide the first protocol to evaluate how disease-associated variants impact ramp sequences, which could explain why some genetic variants are reported by genome-wide association studies. Future studies might examine if the ramp sequence could be therapeutically targeted to regulate PILRA expression without changing the protein product.