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Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer’s disease
Open accessAbstract
Genome-wide association studies (GWAS) have identified several risk variants for late-onset Alzheimer's disease (LOAD). These common variants have replicable but small effects on LOAD risk and generally do not have obvious functional effects. Low-frequency coding variants, not detected by GWAS, are predicted to include functional variants with larger effects on risk. To identify low-frequency coding variants with large effects on LOAD risk, we carried out whole-exome sequencing (WES) in 14 large LOAD families and follow-up analyses of the candidate variants in several large LOAD case-control data sets. A rare variant in PLD3 (phospholipase D3; Val232Met) segregated with disease status in two independent families and doubled risk for Alzheimer's disease in seven independent case-control series with a total of more than 11,000 cases and controls of European descent. Gene-based burden analyses in 4,387 cases and controls of European descent and 302 African American cases and controls, with complete sequence data for PLD3, reveal that several variants in this gene increase risk for Alzheimer's disease in both populations. PLD3 is highly expressed in brain regions that are vulnerable to Alzheimer's disease pathology, including hippocampus and cortex, and is expressed at significantly lower levels in neurons from Alzheimer's disease brains compared to control brains. Overexpression of PLD3 leads to a significant decrease in intracellular amyloid-β precursor protein (APP) and extracellular Aβ42 and Aβ40 (the 42- and 40-residue isoforms of the amyloid-β peptide), and knockdown of PLD3 leads to a significant increase in extracellular Aβ42 and Aβ40. Together, our genetic and functional data indicate that carriers of PLD3 coding variants have a twofold increased risk for LOAD and that PLD3 influences APP processing. This study provides an example of how densely affected families may help to identify rare variants with large effects on risk for disease or other complex traits.
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“Most of the genes associated with the ~40 loci identified by genome-wide association (GWA) analysis or by rare variant sequencing studies are expressed in glial cells (e.g., APOE, TREM2, BIN1, CD33, INPP5D, CTSB, CTSD, and PICALM).”
From The Major Risk Factors for Alzheimer’s Disease: Age, Sex, and Genes Modulate the Microglia Response to Aβ Plaques (2019) · cites this paper as Cruchaga et al., 2014
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“gene enrichment analysis indicates that ARMs, but not IRMs, are enriched for known AD risk genes such as Apoe, Trem2, Tyrobp (DAP12), Ctsb, Ctsd, H2-Eb1, and Pld3”
From The Major Risk Factors for Alzheimer’s Disease: Age, Sex, and Genes Modulate the Microglia Response to Aβ Plaques (2019) · cites this paper as Cruchaga et al., 2014
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“whereas the PLD3 variant, V232M, was identified using a family-based study design [13].”
From Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer’s disease resilience (2017) · cites this paper as [13]
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“Recently, several possibly functional, rare variants with large protective [9, 10] and risk effects [11–13] have been identified for AD in APP, APOE, PLD3, and TREM2 using novel study designs.”
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“We also found that LECs isolated from the meninges of 6-month-old 5xFAD mice showed significant changes in the expression of genes involved in processes such as exocytosis, phospholipase D signaling, and response to low-density lipoprotein (Extended Data Fig. 1f–k), suggesting that meningeal Aβ deposition might affect meningeal LECs early on through deleterious processes previously implicated in”
From Meningeal lymphatics affect microglia responses and anti-Aβ immunotherapy (2021) · cites this paper as [14]
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“For example, rare variants in SORL1 and ABCA7 have been identified in family-based studies of LOAD [147–150], each of which have been associated with alterations in APP processing.”
From Genetic architecture of Alzheimer's disease (2020) · cites this paper as [149]
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Metadata
- Authors
- Cruchaga, C., Karch, C. M., Jin, S. C., Benitez, B. A., Cai, Y., Guerreiro, R., Harari, O., Norton, J., Budde, J., Bertelsen, S., Jeng, A. T., Cooper, B., Skorupa, T., Carrell, D., Levitch, D., Hsu, S., Choi, J., Ryten, M., UK Brain Expression Consortium (UKBEC), Hardy, J., Ryten, M., Trabzuni, D., Weale, M. E., Ramasamy, A., Smith, C., Sassi, C., Bras, J., Gibbs, J. R., Hernandez, D. G., Lupton, M. K., Powell, J., Forabosco, P., Ridge, P. G., Corcoran, C. D., Tschanz, J. T., Norton, M. C., Munger, R. G., Schmutz, C., Leary, M., Demirci, F. Y., Bamne, M. N., Wang, X., Lopez, O. L., Ganguli, M., Medway, C., Turton, J., Lord, J., Braae, A., Barber, I., Brown, K., The Alzheimer’s Research UK (ARUK) Consortium, Passmore, P., Craig, D., Johnston, J., McGuinness, B., Todd, S., Heun, R., Kölsch, H., Kehoe, P. G., Hooper, N. M., Vardy, E. R. L. C., Mann, D. M., Pickering-Brown, S., Brown, K., Kalsheker, N., Lowe, J., Morgan, K., David Smith, A., Wilcock, G., Warden, D., Holmes, C., Pastor, P., Lorenzo-Betancor, O., Brkanac, Z., Scott, E., Topol, E., Morgan, K., Rogaeva, E., Singleton, A. B., Hardy, J., Kamboh, M. I., St George-Hyslop, P., Cairns, N., Morris, J. C., Kauwe, J. S. K., & Goate, A. M.
- Affiliations
- Washington University in St. Louis (US)
- National Institutes of Health (US)
- National Hospital for Neurology and Neurosurgery (GB)
- King's College London (GB)
- University of Edinburgh (GB)
- National Research Council (IT)
- Brigham Young University (US)
- Utah State University (US)
- University of Pittsburgh (US)
- University of Nottingham (GB)
- Queen's University Belfast (GB)
- Royal Derby Hospital (GB)
- University of Bonn (DE)
- University of Bristol (GB)
- University of Leeds (GB)
- Newcastle University (GB)
- University of Manchester (GB)
- University of Oxford (GB)
- University of Washington (US)
- Scripps Research Institute (US)
- University of Toronto (CA)
- Corresponding author
- Cruchaga, Carlos
- ORCID
- Cruchaga, Carlos
- Karch, Celeste M.
- Jin, Sheng Chih
- Guerreiro, Rita
- Harari, Oscar
- Budde, John
- Bertelsen, Sarah
- Skorupa, Tara
- Carrell, David
- Hsu, Simon
- Trabzuni, Daniah
- Weale, Michael E.
- Ramasamy, Adaikalavan
- Smith, Colin
- Sassi, Celeste
- Gibbs, J. Raphael
- Hernandez, Dena G.
- Lupton, Michelle K.
- Powell, John
- Forabosco, Paola
- Ridge, Perry G.
- Tschanz, JoAnn T.
- Norton, Maria C.
- Munger, Ronald G.
- Demirci, F. Yesim
- Wang, Xingbin
- Ganguli, Mary
- Turton, James
- Lord, Jenny
- Braae, Anne
- Passmore, Peter
- Craig, David
- McGuinness, Bernadette
- Todd, Stephen
- Heun, Reinhard
- Kehoe, Patrick G.
- Hooper, Nigel M.
- Vardy, Emma R.L.C.
- Mann, David M.
- Pickering-Brown, Stuart
- Kalsheker, Noor
- Lowe, James
- Wilcock, Gordon
- Holmes, Clive
- Scott, Erick
- Topol, Eric
- Rogaeva, Ekaterina
- Singleton, Andrew B.
- Kamboh, M. Ilyas
- Cairns, Nigel
- Morris, John C.
- Goate, Alison M.
- Venue
- Nature
- Published
- 2013-12-11
- Volume
- 505
- Issue
- 7484
- Pages
- 550-554
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4050701
- OpenAlex
- W2099248872
- Cited by
- 461
- References
- 52
- Citations by year
- 2026: 13 · 2025: 17 · 2024: 23 · 2023: 21 · 2022: 22 · 2021: 32 · 2020: 30 · 2019: 37 · 2018: 50 · 2017: 44 · 2016: 50 · 2015: 68 · 2014: 51
- FWCI
- 39.22
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Research Portal (Queen's University Belfast) (submittedVersion)
- Bristol Research (University of Bristol) (submittedVersion)
- Newcastle University ePrints (Newcastle Univesity)
- Funders
- U.S. Department of Health and Human Services
- Pfizer
- BrightFocus Foundation
- Wellcome Trust (100140, 089703, 081864, 089698)
- National Institute for Health and Care Research (ACF-2007-18-011, ACF-2012-17-017)
- National Institutes of Health (5p30ns069329-02)
- Genentech
- U.S. Public Health Service (NIH R01039700)
- Canadian Institutes of Health Research
- Medical Research Council (MR/K01417X/1, MC_G1000735, MR/L016400/1, MC_G1000734)
- National Institute on Aging (R01 AG 11380, R01AG039700, NIH P50AG05681, RF1AG044546, ZIAAG000950, R01AG042611, AG 07562, R01AG041718, AG-005133, P50AG005133, K01AG046374, AG041718, R01AG007562, R01AG030653, ZO1 AG000950-10, R01AG011380, R01AG035083, U24 AG21886, AG023652, R01AG021136, R01AG018712, R01AG041797, R01AG044546, R01 AG18712, ZO1AG000950-11, Z01AG000950, P50AG005681, P01 AG0 3991, P01AG003991, U24AG026395, R01 AG 21136, U24AG056270, P01AG026276, U24AG021886, AG 030653)
- National Institute on Drug Abuse (R25DA027995)
- National Institute of Neurological Disorders and Stroke (P30-NS069329)
- Topics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Alzheimer's disease research and treatments
- Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- late-onset Alzheimer's disease, PLD3, rare coding variants, amyloid-beta processing, amyloid precursor protein, gene burden analysis, familial Alzheimer's disease, African Americans, European ancestry, therapeutic target, genetic risk variants
- MeSH terms
- Aged, Aged, 80 and over, Alzheimer Disease, Black or African American, Brain, Europe, Exodeoxyribonucleases, Female, Humans, Male, Peptide Fragments, Phospholipase D, Protein Processing, Post-Translational, Genetic Variation, Case-Control Studies, Amyloid beta-Peptides, Amyloid beta-Protein Precursor, Age of Onset, Genetic Predisposition to Disease, Exome, Proteolysis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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