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An intronic PICALM polymorphism, rs588076, is associated with allelic expression of a PICALM isoform.

Parikh I, Medway C, Younkin S, Fardo DW, Estus S - Mol Neurodegener (2014)

Bottom Line: 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.Conditional on rs3851179, rs588076 was not associated with AD risk, suggesting that D18-19 PICALM is not critical in AD.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departments of Physiology, Sanders-Brown Center on Aging, University of Kentucky, 800 S, Limestone St,, Lexington, KY 40536, USA. Steve.estus@uky.edu.

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.

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Evaluation of total PICALM AEI with respect to rs3851179. a-b) Allelic PICALM expression was assessed by rs76719109 or rs592297. Each individual sample was normalized to its gDNA ratio. Rs3861179 was not associated with significant AEI, i.e., only one sample (*) showed significant AEI.
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Figure 4: Evaluation of total PICALM AEI with respect to rs3851179. a-b) Allelic PICALM expression was assessed by rs76719109 or rs592297. Each individual sample was normalized to its gDNA ratio. Rs3861179 was not associated with significant AEI, i.e., only one sample (*) showed significant AEI.

Mentions: To evaluate whether the AD-associated SNP rs3851179 was associated with unequal allelic PICALM expression, we performed AEI analysis with rs76719109 and rs592297on a total of 54 samples. Twelve of these 54 samples were heterozygous for both SNPs. Hence, we analyzed PICALM for AEI in a total of 42 unique individual samples. This effort analyzed 4.2 million sequences for rs76719109 and 1.4 million sequences for rs592297. If rs3851179 modulated total PICALM expression, we expected to see significant AEI in individuals heterozygous for rs3851179, but not in individuals homozygous for rs3851179. When we analyzed the results for the exon 17 SNP, rs76719109, significant AEI was observed in only a single sample, termed AD40 (see below). To evaluate whether a subtle difference in allelic expression may be present and associated with rs3851179, we compared the mean allelic expression between the rs3851179 homozygous and heterozygous groups. This approach did not discern a significant difference between the two groups, i.e., the allelic ratios for rs3851179 homozygous and heterozygous groups was 0.94 ± 0.08 (n = 17) and 0.97 ± 0.06 (n = 18), respectively (Figure 4a, p = 0.24, t-test). Hence, rs3851179 did not appear associated with PICALM AEI. To confirm this finding and extend the analysis to additional samples, we analyzed allelic expression by using the exon 5 SNP, rs592297. Significant AEI was not observed in any sample, noting that the sample with the significant AEI result from the rs76719109 analysis was homozygous for rs592297 and not suitable for evaluation. When the allelic ratios were analyzed by t-test to evaluate whether rs3851179 was associated with allelic expression, the findings confirmed that rs3851179 was not associated with robust AEI; the allelic ratios were 0.93 ± 0.05 (n = 4) for rs3851179 homozygotes and 1.01 ± 0.07 (n = 15) for heterozygotes (Figure 4b, p = 0.06). Hence, we found that the total PICALM allelic ratio for each person was remarkably consistent with both reporter SNPs; rs3851179 is not associated with overall allelic PICALM expression.


An intronic PICALM polymorphism, rs588076, is associated with allelic expression of a PICALM isoform.

Parikh I, Medway C, Younkin S, Fardo DW, Estus S - Mol Neurodegener (2014)

Evaluation of total PICALM AEI with respect to rs3851179. a-b) Allelic PICALM expression was assessed by rs76719109 or rs592297. Each individual sample was normalized to its gDNA ratio. Rs3861179 was not associated with significant AEI, i.e., only one sample (*) showed significant AEI.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4150683&req=5

Figure 4: Evaluation of total PICALM AEI with respect to rs3851179. a-b) Allelic PICALM expression was assessed by rs76719109 or rs592297. Each individual sample was normalized to its gDNA ratio. Rs3861179 was not associated with significant AEI, i.e., only one sample (*) showed significant AEI.
Mentions: To evaluate whether the AD-associated SNP rs3851179 was associated with unequal allelic PICALM expression, we performed AEI analysis with rs76719109 and rs592297on a total of 54 samples. Twelve of these 54 samples were heterozygous for both SNPs. Hence, we analyzed PICALM for AEI in a total of 42 unique individual samples. This effort analyzed 4.2 million sequences for rs76719109 and 1.4 million sequences for rs592297. If rs3851179 modulated total PICALM expression, we expected to see significant AEI in individuals heterozygous for rs3851179, but not in individuals homozygous for rs3851179. When we analyzed the results for the exon 17 SNP, rs76719109, significant AEI was observed in only a single sample, termed AD40 (see below). To evaluate whether a subtle difference in allelic expression may be present and associated with rs3851179, we compared the mean allelic expression between the rs3851179 homozygous and heterozygous groups. This approach did not discern a significant difference between the two groups, i.e., the allelic ratios for rs3851179 homozygous and heterozygous groups was 0.94 ± 0.08 (n = 17) and 0.97 ± 0.06 (n = 18), respectively (Figure 4a, p = 0.24, t-test). Hence, rs3851179 did not appear associated with PICALM AEI. To confirm this finding and extend the analysis to additional samples, we analyzed allelic expression by using the exon 5 SNP, rs592297. Significant AEI was not observed in any sample, noting that the sample with the significant AEI result from the rs76719109 analysis was homozygous for rs592297 and not suitable for evaluation. When the allelic ratios were analyzed by t-test to evaluate whether rs3851179 was associated with allelic expression, the findings confirmed that rs3851179 was not associated with robust AEI; the allelic ratios were 0.93 ± 0.05 (n = 4) for rs3851179 homozygotes and 1.01 ± 0.07 (n = 15) for heterozygotes (Figure 4b, p = 0.06). Hence, we found that the total PICALM allelic ratio for each person was remarkably consistent with both reporter SNPs; rs3851179 is not associated with overall allelic PICALM expression.

Bottom Line: 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.Conditional on rs3851179, rs588076 was not associated with AD risk, suggesting that D18-19 PICALM is not critical in AD.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departments of Physiology, Sanders-Brown Center on Aging, University of Kentucky, 800 S, Limestone St,, Lexington, KY 40536, USA. Steve.estus@uky.edu.

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.

Show MeSH
Related in: MedlinePlus