title: An intronic PICALM polymorphism, rs588076, is associated with allelic expression of a PICALM isoform.
abstract: BACKGROUND
  Although genome wide studies have associated single nucleotide polymorphisms (SNP)s near PICALM with Alzheimer's disease (AD), the mechanism underlying this association is unclear. PICALM is involved in clathrin-mediated endocytosis and modulates Aß clearance in vitro. Comparing allelic expression provides the means to detect cis-acting regulatory polymorphisms. Thus, we evaluated whether PICALM showed allele expression imbalance (AEI) and whether this imbalance was associated with the AD-associated polymorphism, rs3851179.
  
  
  RESULTS
  We measured PICALM allelic expression in 42 human brain samples by using next-generation sequencing. Overall, PICALM demonstrated equal allelic expression with no detectable influence by rs3851179. A single sample demonstrated robust global PICALM allelic expression imbalance (AEI), i.e., each of the measured isoforms showed AEI. Moreover, the PICALM isoform lacking exons 18 and 19 (D18-19 PICALM) showed significant AEI in a subset of individuals. Sequencing these individuals and subsequent genotyping revealed that rs588076, located in PICALM intron 17, was robustly associated with this imbalance in D18-19 PICALM allelic expression (p = 9.54 x 10-5). This polymorphism has been associated previously with systolic blood pressure response to calcium channel blocking agents. To evaluate whether this polymorphism was associated with AD, we genotyped 3269 individuals and found that rs588076 was modestly associated with AD. However, when both the primary AD SNP rs3851179 was added to the logistic regression model, only rs3851179 was significantly associated with AD.
  
  
  CONCLUSIONS
  PICALM expression shows no evidence of AEI associated with rs3851179. Robust global AEI was detected in one sample, suggesting the existence of a rare SNP that strongly modulates PICALM expression. AEI was detected for the D18-19 PICALM isoform, and rs588076 was associated with this AEI pattern. Conditional on rs3851179, rs588076 was not associated with AD risk, suggesting that D18-19 PICALM is not critical in AD. In summary, this analysis of PICALM allelic expression provides novel insights into the genetics of PICALM expression and AD risk.
authors.forename: Ishita
authors.initials: I
authors.lastname: Parikh
authors.forename: Christopher
authors.initials: C
authors.lastname: Medway
authors.forename: Steven
authors.initials: S
authors.lastname: Younkin
authors.forename: David W
authors.initials: DW
authors.lastname: Fardo
authors.affiliation: Departments of Physiology, Sanders-Brown Center on Aging, University of Kentucky, 800 S, Limestone St,, Lexington, KY 40536, USA. Steve.estus@uky.edu.
authors.forename: Steven
authors.initials: S
authors.lastname: Estus
mesh_terms: D000369:Aged, 80 and over; D000483:Alleles; D022981:Allelic Imbalance / Q000235:genetics; D000544:Alzheimer Disease / Q000235:genetics*; D005260:Female; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D055106:Genome-Wide Association Study; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007438:Introns / Q000235:genetics*; D008297:Male; D034041:Monomeric Clathrin Assembly Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D020033:Protein Isoforms / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D034041:Monomeric Clathrin Assembly Proteins; C439003:PICALM protein, human; D020033:Protein Isoforms