Cited by 317Genetic Associations and EpidemiologyLipoproteins and Cardiovascular HealthAlzheimer's disease research and treatments

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Apolipoprotein E (APOE) genotype-associated disease risks: a phenome-wide, registry-based, case-control study utilising the UK Biobank

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Lumsden, Amanda L., Mulugeta, Anwar, Zhou, Ang, Hyppönen, Elina·2020·eBioMedicine

DOI 10.1016/j.ebiom.2020.102954PMC PMC7452404

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Abstract

Background The three main alleles of the APOE gene (ε4, ε3 and ε2) carry differential risks for conditions including Alzheimer's disease (AD) and cardiovascular disease. Due to their clinical significance, we explored disease associations of the APOE genotypes using a hypothesis-free, data-driven, phenome-wide association study (PheWAS) approach. Methods We used data from the UK Biobank to screen for associations between APOE genotypes and over 950 disease outcomes using genotype ε3ε3 as a reference. Data was restricted to 337,484 white British participants (aged 37–73 years). Findings After correction for multiple testing, PheWAS analyses identified associations with 37 outcomes, representing 18 distinct diseases. As expected, ε3ε4 and ε4ε4 genotypes associated with increased odds of AD (p ≤ 7.6 × 10 −46 ), hypercholesterolaemia (p ≤ 7.1 × 10 −17 ) and ischaemic heart disease (p ≤ 2.3 × 10 −4 ), while ε2ε3 provided protection for the latter two conditions (p ≤ 3.7 × 10 −10 ) compared to ε3ε3. In contrast, ε4-associated disease protection was seen against obesity, chronic airway obstruction, type 2 diabetes, gallbladder disease, and liver disease (all p ≤ 5.2 × 10 −4 ) while ε2ε2 homozygosity increased risks of peripheral vascular disease, thromboembolism, arterial aneurysm, peptic ulcer, cervical disorders, and hallux valgus (all p ≤ 6.1 × 10 −4 ). Sensitivity analyses using brain neuroimaging, blood biochemistry, anthropometric, and spirometric biomarkers supported the PheWAS findings on APOE associations with respective disease outcomes. Interpretation PheWAS confirms strong associations between APOE and AD, hypercholesterolaemia, and ischaemic heart disease, and suggests potential ε4-associated disease protection and harmful effects of the ε2ε2 genotype, for several conditions. Funding National Health and Medical Research Council of Australia.

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Fig. 1 APOE genotypes and risk of disease. Forest plots depicting the OR (black box symbols) and 95% CI (horizontal lines) for each genotype compared to reference genotype, ε3ε3. Data is presented for representative disease outcomes where at least one genotype showed a signal in the PheWAS. Actual values are shown to the right of each graph. Case and control numbers and p-values (logistic regression) for each comparison group can be found in table S4 (appendix pp 8–32), with further breakdown by genotype shown within figures S3–S7 (appendix pp 36–40). “Other aneurysm” encompasses aortic, and other arterial aneurysms, but not cerebral, or heart aneurysms. “Other cerebral degenerations” includes gangliosidosis, sphingolipidosis, neuronal ceroid lipofuscinosis, Rett syndrome, Reye syndrome, systemic atrophy primarily affecting the central nervous system, and degeneration of the nervous system due to alcohol. “Nutrition, metabolism and development symptoms” pertains to symptoms including severe protein-energy malnutrition, feeding difficulties and mismanagement, and abnormal weight loss.CC BY-NC-ND · PubMed Central

Fig. 2 APOE genotypes and differences in biomarkers Graphs are displayed as standardised mean differences in biomarker levels for each APOE genotype with reference to ε3ε3. The values on the right correspond to absolute mean difference values (β) and 95% CI. *Note that for white matter hyperintensity (WMH) volume (E), the plotted data were inverse normal transformed to approximate normal distribution, while the volume values presented to the right are natural values. The panel includes markers related to brain health (A–E), cardiovascular risk (F–M), diabetes (N–O), obesity (P–R), and lung health (S–U). Population numbers and p-value (linear regression) for each biomarker can be found in table S5 (appendix p 33). APOA: apolipoprotein A. APOB: apolipoprotein B. BMI: Body mass index. CRP: C-reactive protein. FEV1: Forced expiratory volume during one second. FVC: Forced vital capacity. HbA1c: Haemoglobin A1c (glycated haemoglobin). HDL: high density lipoprotein. LDL: low density lipoprotein. Lp(A): lipoprotein A. WC: waist circumference. WHR: waist-hip ratio. WMH: white matter hyperintensity.CC BY-NC-ND · PubMed Central

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The UK Biobank resource with deep phenotyping and genomic data
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“Chronologically, e4 is believed to be the ancestral allele from which the e3 and e2 variants sequentially evolved over 200,000 years ago [1].”
Background
Oxidized LDL triggers changes in oxidative stress and inflammatory biomarkers in human macrophages
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“As is typically reported, e2e3 and e2e4 were protective for hypercholesterolaemia compared to e3e3 (with lower levels of “bad” cholesterol indicators; total cholesterol, LDL and APOB). e2e3 also had increased levels of “good” cholesterol indicators (HDL-cholesterol and APOA) and was associated with reduced risk of IHD…”
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“The APOE ε 4 allele is a well ‐ established risk factor for dementia, particularly AD and VD. APOE ε 4 has also been associated with an atherogenic lipid profile, which increases the risk of cerebrovascular disease, a key contributor to vascular dementia [2].”
The effect of C-reactive protein and interleukin-3 on mild cognitive impairment with APOE ɛ4
Yang, X., Chi, L., Qiao, M., Huang, A. C., Wu, H., Chen, S., Fan, J., Lin, X., Chen, J., & Initiative, A. D. N. (2025) · Journal of Alzheimer s Disease · doi:10.1177/13872877251333149
“Besides, an analysis of APOE polymorphisms 31 showed that APOE ɛ 4 carriers had lower CRP levels, but APOE ɛ 2 carriers had higher CRP levels.”
Emotional stress and cardiovascular health: Impacts on neurodegenerative disease progression
El‐Aziz, M. K. A., Wadan, A. S., Albahttiti, A. T. I., & Moradikor, N. (2025) · Progress in brain research · doi:10.1016/bs.pbr.2025.04.004 · Cited by 1
ApoE, Atherosclerosis, and Hypercholesterolemia
Shi, W. (2025) · Springer eBooks · doi:10.1007/978-3-031-52641-1_26-1
Genomics and Transcriptomics of Alzheimer Disease
Vilor‐Tejedor, N., Rodríguez‐Fernández, B., Genius, P., Luckett, E. S., Anastasi, F., Lorenzini, L., Murray, H., Bull, C. J., Clement, M. H. S., Morris, A., et al. (2025) · Springer eBooks · doi:10.1007/978-3-031-80849-4_13
ApoE Polymorphism Analysis in Health and Disease of South Asian PopulationsPreprint
Paudel, P., Sah, A., & Paudel, P. (2025) · Research Square · doi:10.21203/rs.3.rs-5554316/v1
Phenotypic and Genetic Associations Between Cardiovascular Disease Subtypes and Alzheimer’s DiseasePreprint
Toyli, A., Zhao, C., Su, K.-J., Shen, H., Deng, H., Chen, Q., Sha, Q., & Zhou, W. (2025) · medRxiv · doi:10.1101/2025.08.29.25334750
“32) remains the most prominent shared locus, given its well-established roles in lipid metabolism 27,29 , blood-brain barrier integrity 6,28 , and both cardiovascular and neurodegenerative diseases 27,28,30 .”
An APOE ε4–Uric Acid Axis Underpins Mesoamerican NephropathyPreprint
Landires, I., Courville, K., Cumbrera, R., Bustamante, N., Pimentel-Peralta, G., Velez, J. I., Johnson, R. J., Arcos‐Burgos, M., & Núñez-Samudio, V. (2025) · Research Square · doi:10.21203/rs.3.rs-7880187/v1
Circulating Metabolites are Linked to Dementia and Brain Imaging Phenotypes, and Mediate Modifiable Risk PathwaysPreprint
Liu, Y., Abdolkarimi, D., Gilchrist, L., Calhas, S., Wretlind, A., Velayudhan, L., Ashton, N. J., Zetterberg, H., Waters, S., Legido‐Quigley, C., et al. (2025) · medRxiv · doi:10.1101/2025.10.31.25339240
Quantifying the versatility of routinely measured prognostic factors
Innes, H. A., & Johnson, P. J. (2025) · Diagnostic and Prognostic Research · doi:10.1186/s41512-025-00206-7
“An example of a versatile genetic variant is the APOE genotype, which simultaneously associates with the risk of Alzheimer’s disease, liver cancer, cirrhosis, obesity, ischaemic heart disease, type 2 diabetes, gall-bladder disease and other outcomes [9].”
Apolipoprotein E genotypes are associated with diabetic peripheral neuropathy in Lebanese adults with type 2 diabetes: a case-control study
Nemr, R., Zidi, S., Echtay, A. S., Racoubian, E., Beydoun, N., & Almawi, W. Y. (2025) · Frontiers in Endocrinology · doi:10.3389/fendo.2025.1738873
Additional file 1 of Specification curve analysis to identify heterogeneity in risk factors for dementia: findings from the UK Biobank
Luo, R., Zeraatkar, D., Glymour, M. M., Ellis, R. J., Estiri, H., & Patel, C. J. (2024) · Figshare · doi:10.6084/m9.figshare.25918962
Additional file 5 of Humanized APOE genotypes influence lifespan independently of tau aggregation in the P301S mouse model of tauopathy
Williams, T., Bathe, T., Vo, Q., Sacilotto, P., McFarland, K., Ruiz, A. J., Hery, G. P., Sullivan, P. M., Borchelt, D. R., Prokop, S., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23543276
Additional file 6 of Humanized APOE genotypes influence lifespan independently of tau aggregation in the P301S mouse model of tauopathy
Williams, T., Bathe, T., Vo, Q., Sacilotto, P., McFarland, K., Ruiz, A. J., Hery, G. P., Sullivan, P. M., Borchelt, D. R., Prokop, S., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23543279
Additional file 1 of Proteomic analysis identifies dysregulated proteins and associated molecular pathways in a cohort of gallbladder cancer patients of African ancestry
Baichan, P., Naicker, P., Augustine, T. N., Smith, M., Candy, G. P., Devar, J. W., & Nweke, E. E. (2024) · Figshare · doi:10.6084/m9.figshare.26572009
Additional file 2 of Proteomic analysis identifies dysregulated proteins and associated molecular pathways in a cohort of gallbladder cancer patients of African ancestry
Baichan, P., Naicker, P., Augustine, T. N., Smith, M., Candy, G. P., Devar, J. W., & Nweke, E. E. (2024) · Figshare · doi:10.6084/m9.figshare.26572012
Additional file 1 of APOE ε4 carriage associates with improved myocardial performance from adolescence to older age
Topriceanu, C., Shah, M., Webber, M. R., Chan, F., Shiwani, H., Richards, M., Schott, J. M., Chaturvedi, N., Moon, J., Hughes, A. D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26696055
Additional file 2 of Specification curve analysis to identify heterogeneity in risk factors for dementia: findings from the UK Biobank
Luo, R., Zeraatkar, D., Glymour, M. M., Ellis, R. J., Estiri, H., & Patel, C. J. (2024) · Figshare · doi:10.6084/m9.figshare.25919134
Additional file 4 of Humanized APOE genotypes influence lifespan independently of tau aggregation in the P301S mouse model of tauopathy
Williams, T., Bathe, T., Vo, Q., Sacilotto, P., McFarland, K., Ruiz, A. J., Hery, G. P., Sullivan, P. M., Borchelt, D. R., Prokop, S., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23543273
Additional file 8 of Proteomic analysis identifies dysregulated proteins and associated molecular pathways in a cohort of gallbladder cancer patients of African ancestry
Baichan, P., Naicker, P., Augustine, T. N., Smith, M., Candy, G. P., Devar, J. W., & Nweke, E. E. (2024) · Figshare · doi:10.6084/m9.figshare.26572030
Additional file 2 of Humanized APOE genotypes influence lifespan independently of tau aggregation in the P301S mouse model of tauopathy
Williams, T., Bathe, T., Vo, Q., Sacilotto, P., McFarland, K., Ruiz, A. J., Hery, G. P., Sullivan, P. M., Borchelt, D. R., Prokop, S., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23543264
Additional file 4 of Proteomic analysis identifies dysregulated proteins and associated molecular pathways in a cohort of gallbladder cancer patients of African ancestry
Baichan, P., Naicker, P., Augustine, T. N., Smith, M., Candy, G. P., Devar, J. W., & Nweke, E. E. (2024) · Figshare · doi:10.6084/m9.figshare.26572018
Additional file 3 of Proteomic analysis identifies dysregulated proteins and associated molecular pathways in a cohort of gallbladder cancer patients of African ancestry
Baichan, P., Naicker, P., Augustine, T. N., Smith, M., Candy, G. P., Devar, J. W., & Nweke, E. E. (2024) · Figshare · doi:10.6084/m9.figshare.26572015
Additional file 6 of Proteomic analysis identifies dysregulated proteins and associated molecular pathways in a cohort of gallbladder cancer patients of African ancestry
Baichan, P., Naicker, P., Augustine, T. N., Smith, M., Candy, G. P., Devar, J. W., & Nweke, E. E. (2024) · Figshare · doi:10.6084/m9.figshare.26572024
Additional file 3 of Humanized APOE genotypes influence lifespan independently of tau aggregation in the P301S mouse model of tauopathy
Williams, T., Bathe, T., Vo, Q., Sacilotto, P., McFarland, K., Ruiz, A. J., Hery, G. P., Sullivan, P. M., Borchelt, D. R., Prokop, S., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23543267
Additional file 1 of Sex differences in the association between cardiovascular diseases and dementia subtypes: a prospective analysis of 464,616 UK Biobank participants
Dong, C., Zhou, C., Fu, C., Hao, W., Ozaki, A., Shrestha, N., Virani, S. S., Mishra, S. R., & Zhu, D. (2022) · Figshare · doi:10.6084/m9.figshare.19728635
Additional file 5 of Proteomic analysis identifies dysregulated proteins and associated molecular pathways in a cohort of gallbladder cancer patients of African ancestry
Baichan, P., Naicker, P., Augustine, T. N., Smith, M., Candy, G. P., Devar, J. W., & Nweke, E. E. (2024) · Figshare · doi:10.6084/m9.figshare.26572021
Additional file 1 of Humanized APOE genotypes influence lifespan independently of tau aggregation in the P301S mouse model of tauopathy
Williams, T., Bathe, T., Vo, Q., Sacilotto, P., McFarland, K. N., Ruiz, A. J., Hery, G. P., Sullivan, P. M., Borchelt, D. R., Prokop, S., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23543261
Additional file 7 of Proteomic analysis identifies dysregulated proteins and associated molecular pathways in a cohort of gallbladder cancer patients of African ancestry
Baichan, P., Naicker, P., Augustine, T. N., Smith, M., Candy, G. P., Devar, J. W., & Nweke, E. E. (2024) · Figshare · doi:10.6084/m9.figshare.26572027
Epidemiology of BTCs
Koshiol, J. E., Argirion, I., & Piñeros, M. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-29287-3.00006-4
APOE, Human Ancestry, and Evolution
Smith, C. J., Ashford, J. W., & Perfetti, T. A. (2025) · Springer eBooks · doi:10.1007/978-3-031-52641-1_4-1
Relationship between amyloid burden, cholinergic integrity, and cognitive function
Lee, L., Chou, C., Shih, Y., Fang, Y.-M., Chiu, Y.-L., Chuang, Y., & Liu, Y.-C. (2025) · Journal of Alzheimer s Disease · doi:10.1177/13872877251406620
“71,72 In our study, we observed a signi ﬁ cant association between amyloid burden and global cognition, as measured using MMSE scores, in the early Alzheimer ’ s disease group but not in the control group .”
Cardiometabolic indicators of cognitive impairment in the Cameron County Hispanic Cohort
Musfee, F. I., Agarwal, S., Maroufy, V., Liu, C., McCormick, J. B., FISHER-HOCH, S. P., & Savitz, S. I. (2025) · Journal of Alzheimer s Disease · doi:10.1177/13872877251408098
“22 For the APOE haplotype analyses, we used two imputed SNPs (rs429358 and rs7412) in the APOE region (imputation R 2 > 0.95) to estimate the APOE haplotype in our cohort using PLINK and R. 23”
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“…that the rs429358 mutation augments MDD prevalence by 2.17 times, correlating with elevated hypercholesterolemia and coronary heart disease risks [90–92], potentially due to this locus’s impact on APOE protein structure and function, thus affecting its receptor binding affinity, lipid…”
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Authors: Lumsden, A. L., Mulugeta, A., Zhou, A., & Hyppönen, E.
Affiliations: University of South Australia (AU)
Corresponding author: Hyppönen, Elina
ORCID: Lumsden, Amanda L.
Mulugeta, Anwar
Zhou, Ang
Hyppönen, Elina
Venue: eBioMedicine
Publisher: Elsevier BV
Published: 2020-09
Volume: 59
Pages: 102954
ISSN: 2352-3964 (ISSN-L)
DOI: 10.1016/j.ebiom.2020.102954
PMC: PMC7452404
OpenAlex: W3069395596
Cited by: 317
References: 31
Citations by year: 2026: 54 · 2025: 72 · 2024: 82 · 2023: 59 · 2022: 33 · 2021: 17
FWCI: 3.88
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc-nd
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
creativecommons.org/licenses/by-nc-nd/4.0/ (vor)
Locations: EBioMedicine (publishedVersion, cc-by-nc-nd)
PubMed Central (publishedVersion, cc-by-nc-nd)
PubMed (publishedVersion)
UniSA Research Outputs Repository (University of South Australia) (submittedVersion, other-oa)
Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion, cc-by-nc-nd)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: UK Biobank (GNT1123603)
National Health and Medical Research Council (GNT1157281)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Health Sciences › Medicine › Cardiology and Cardiovascular Medicine › Lipoproteins and Cardiovascular Health
Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Alzheimer's disease research and treatments
Keywords: apolipoprotein E, APOE genotype, APOE ε4, APOE ε2, Alzheimer's disease, hypercholesterolemia, ischemic heart disease, phenome-wide association study, disease risk, obesity, type 2 diabetes, peripheral vascular disease, thromboembolism, arterial aneurysm, peptic ulcer, hallux valgus, cardiovascular disease, genetic risk factors
MeSH terms: Adult, Aged, Alleles, Apolipoproteins E, Female, Genotype, United Kingdom, Humans, Male, Middle Aged, Phenotype, Population Surveillance, Registries, Risk Factors, Case-Control Studies, Biological Specimen Banks, Risk Assessment, Genetic Predisposition to Disease, Genetic Association Studies

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Apolipoprotein E (APOE) genotype-associated disease risks: a phenome-wide, registry-based, case-control study utilising the UK Biobank

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