RNA‐seq study on the effect of MAPT rs242557 deletion in HMC3 cells

Abstract

AbstractBackgroundMicrotubule associated protein tau (MAPT) is associated with neurodegenerative diseases including Frontotemporal dementia (FTD), Progressive supranuclear palsy (PSP), Corticobasal degeneration (CBD), Alzheimer’s disease (AD) and Parkinson’s disease (PD). Multiple GWAS on AD, PD, PSP and CBD have identified strong signal in MAPT intronic region (SNP, rs242557). Being part of FANTOM5 enhancer in eye and brain, we are interested in the effect of this region in HMC3 (human microglial clone 3) cell line.MethodUsing CRISPR‐Cas9 genome editing, a clone was isolated having homozygous 309 bp deletion encompassing rs242557 and its flanking sequences in HMC3. Sanger sequencing confirmed the deletion while whole genome sequencing corroborated the same and also confirmed no off‐target effects. To identify gene transcripts whose expression was altered due to the deletion, paired‐end RNA‐seq was performed using total RNA extracted from rs242557 KO and wild type (WT) clones.ResultThere were 272 up‐ and 861 down‐regulated transcripts (p< = 0.01) between WT and KO cells. Down‐regulated transcripts include AD risk genes ICA1, EPDR1, PTK2B, SORL1, DOC2A, and TSPOAP1, and PD candidate gene, SNCA. Notable among up‐regulated transcripts was AD risk gene, CASS4. Enrichment analyses revealed biological processes and pathways that are related to structural constituents and organization of neurons and synapses. Currently, we are validating the transcript data.ConclusionOur preliminary data suggests that the genomic region encompassing rs242557 might affect multiple AD risk genes.