Expression of INPP5D Isoforms in Human Brain: Impact of Alzheimer’s Disease Neuropathology and Genetics

Abstract

The single nucleotide polymorphisms rs35349669 and rs10933431 within Inositol Polyphosphate-5-Phosphatase D (INPP5D) are strongly associated with Alzheimer’s Disease risk. To better understand INPP5D expression in the brain, we investigated INPP5D isoform expression as a function of rs35349669 and rs10933431, as well as Alzheimer’s disease neuropathology, by qPCR and isoform-specific primers. In addition, INPP5D allelic expression imbalance was evaluated relative to rs1141328 within exon 1. Expression of INPP5D isoforms associated with transcription start sites in exon 1 and intron 14 was increased in individuals with high Alzheimer’s disease neuropathology. In addition, a novel variant with 47bp lacking from exon 12 increased expression in Alzheimer’s Disease brains, accounting for 13% of total INPP5D expression, and was found to undergo nonsense-mediated decay. Although inter-individual variation obscured a possible polymorphism effect on INPP5D isoform expression as measured by qPCR, rs35349669 was associated with rs1141328 allelic expression imbalance, suggesting that rs35349669 is significantly associated with full-length INPP5D isoform expression. In summary, expression of INPP5D isoforms with start sites in exon 1 and intron 14 are increased in brains with high Alzheimer’s Disease neuropathology, a novel isoform lacking the phosphatase domain was significantly increased with the disease, and the polymorphism rs35349669 correlates with allele-specific full-length INPP5D expression.

INPP5D regulates inflammasome activation in human microglia

“…Elevated INPP5D transcripts also were observed in AD brain (Supplementary Fig. 2 ), in line with previous reports 20 , 36 , 37 . When separating microglia based on proximity to Aß plaques (“none” vs “plaque”), this elevation in INPP5D intensity in AD brain tissue is largely driven by plaque-associated microglia (Fig.…”

“…INPP5D encodes a cytosolic protein with a predicted molecular weight in its full-length form of approximately 145 kDa. Multiple isoforms have been reported, some of which encode forms of INPP5D that do not contain the phosphatase domain and are predicted to be inactive 20 , 38 . Medial prefrontal cortex (mPFC) samples from a cohort of 92 individuals (Supplementary Fig.…”

“…2j, k ). A recent study identified significant expression of isoforms of INPP5D in the brain that encode truncated protein that lack the phosphatase domain 20 . This finding may explain the seemingly conflicting results presented herein regarding protein levels of INPP5D in the AD brain: full-length aqueous-soluble INPP5D was dramatically reduced in the AD brain, and the elevation in INPP5D observed by immunostaining may reflect the presence of truncated and functionally inactive INPP5D protein generated from the isoforms lacking the phosphatase domain.…”

“…A recent study revealed that these SNPs are associated with differential promoter utilization and splicing. This results in forms of INPP5D that lack the phosphatase domain 20 . Studies to date have not provided clarity as to whether AD risk SNPs are associated with higher or lower INPP5D activity.…”

Microglial function, INPP5D/SHIP1 signaling, and NLRP3 inflammasome activation: implications for Alzheimer’s disease

“…A recent study investigated RNA expression of the different INPP5D isoforms in the post-mortem brains of AD and non-AD individuals. While they also found an increase in the expression of INPP5D isoforms in the AD brain, the expression of a truncated isoform that lacks the phosphatase domain was increased, suggesting that the increase in INPP5D expression may not necessarily lead to increased SHIP1 activity [ 171 ]. Of note, the investigation of AD-associated SNPs in INPP5D in this study did not reveal a clear SNP effect on overall INPP5D expression [ 171 ].…”