An Alzheimer’s disease pathway uncovered by functional omics: the risk gene CELF1 regulates KLC1 splice variant E expression, which drives Aβ pathology

In an era when numerous disease-associated genes have been identified, determining the molecular mechanisms of complex diseases is still difficult. The CELF1 region was identified by genome-wide association studies as an Alzheimer’s disease (AD) risk locus. Using transcriptomics and cross-linking and immunoprecipitation sequencing (CLIP-seq), we found that CELF1, an RNA-binding protein, binds to KLC1 RNA and regulates its splicing. Analysis of two brain banks revealed that CELF1 expression is correlated with inclusion of KLC1 exons downstream of the CELF1-binding region identified by CLIP-seq. In AD, low CELF1 levels result in high levels of KLC1 splice variant E ( KLC1\_vE ), an amyloid-β (Aβ) pathology-driving gene product. Cell culture experiments confirmed regulation of KLC1\_vE by CELF1. Analysis of mouse strains with different propensities for Aβ accumulation confirmed that Klc1_vE drives Aβ pathology. Using omics methods, we revealedthe molecular pathway of a complex disease supported by human and mouse genetics. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Strategic Research Program for Brain Sciences (to T.M.), KAKENHI (C) (23591706 and 26461747 to T.M.), Takeda Science Foundation (to T.M.), SENSHIN Medical Research Foundation (to T.M.), Restar Communications Corporation (to M.I. and T.M.), the departmental committees of the Ligue Contre le Cancer du Grand Ouest 22, 29, 35 (to L.P.), the Japanese Brain Bank Network for Neuroscience Research (to H.A.), and the Natural Sciences and Engineering Research Council of Canada (2018-03945 to M.A.S.). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committees/IRBs of Osaka University and Fukushimura Hospital gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The CELF1 CLIP-seq data have been published (Genom Data. 2016 Apr 19;8:97-103. doi:10.1016/j.gdata.2016.04.009). The exon array experiments are available as a preprint (https://doi.org/10.1101/373704), and the raw microarray data are available in GEO as data set GSE11898