Cited by 114Alzheimer's disease research and treatmentsDementia and Cognitive Impairment ResearchNeuroinflammation and Neurodegeneration Mechanisms

ABI3 and PLCG2 missense variants as risk factors for neurodegenerative diseases in Caucasians and African Americans

Open access
Conway, Olivia J, Carrasquillo, Minerva M, Wang, Xue, Bredenberg, Jenny M, Reddy, Joseph S, Strickland, Samantha L, Younkin, Curtis S, Burgess, Jeremy D +18 more·2018·Molecular Neurodegeneration

Abstract

BACKGROUND: Rare coding variants ABI3_rs616338-T and PLCG2_rs72824905-G were identified as risk or protective factors, respectively, for Alzheimer's disease (AD). METHODS: We tested the association of these variants with five neurodegenerative diseases in Caucasian case-control cohorts: 2742 AD, 231 progressive supranuclear palsy (PSP), 838 Parkinson's disease (PD), 306 dementia with Lewy bodies (DLB) and 150 multiple system atrophy (MSA) vs. 3351 controls; and in an African-American AD case-control cohort (181 AD, 331 controls). 1479 AD and 1491 controls were non-overlapping with a prior report. RESULTS: Using Fisher's exact test, there was significant association of both ABI3_rs616338-T (OR = 1.41, p = 0.044) and PLCG2_rs72824905-G (OR = 0.56, p = 0.008) with AD. These OR estimates were maintained in the non-overlapping replication AD-control analysis, albeit at reduced significance (ABI3_rs616338-T OR = 1.44, p = 0.12; PLCG2_rs72824905-G OR = 0.66, p = 0.19). None of the other cohorts showed significant associations that were concordant with those for AD, although the DLB cohort had suggestive findings (Fisher's test: ABI3_rs616338-T OR = 1.79, p = 0.097; PLCG2_rs72824905-G OR = 0.32, p = 0.124). PLCG2_rs72824905-G showed suggestive association with pathologically-confirmed MSA (OR = 2.39, p = 0.050) and PSP (OR = 1.97, p = 0.061), although in the opposite direction of that for AD. We assessed RNA sequencing data from 238 temporal cortex (TCX) and 224 cerebellum (CER) samples from AD, PSP and control patients and identified co-expression networks, enriched in microglial genes and immune response GO terms, and which harbor PLCG2 and/or ABI3. These networks had higher expression in AD, but not in PSP TCX, compared to controls. This expression association did not survive adjustment for brain cell type population changes. CONCLUSIONS: We validated the associations previously reported with ABI3_rs616338-T and PLCG2_rs72824905-G in a Caucasian AD case-control cohort, and observed a similar direction of effect in DLB. Conversely, PLCG2_rs72824905-G showed suggestive associations with PSP and MSA in the opposite direction. We identified microglial gene-enriched co-expression networks with significantly higher levels in AD TCX, but not in PSP, a primary tauopathy. This co-expression network association appears to be driven by microglial cell population changes in a brain region affected by AD pathology. Although these findings require replication in larger cohorts, they suggest distinct effects of the microglial genes, ABI3 and PLCG2 in neurodegenerative diseases that harbor significant vs. low/no amyloid ß pathology.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1186/s13024-018-0289-x

Cites

57 of 57 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • ABI3 is highly expressed in microglia.

    “Similar to newly identified other AD risk variants (e.g., TREM2, SPI1, and MS4A6A), ABI3 is highly expressed in microglia (8, 9, 11).”

    From Deletion of <i>Abi3</i> gene locus exacerbates neuropathological features of Alzheimer’s disease in a mouse model of Aβ amyloidosis (2021) · cites this paper as [9]

    The Background identifies ABI3-expressing microglial clusters in AD brains, and the Discussion describes ABI3 as part of a co-expressed microglial gene network. The Results report higher expression of that network in AD temporal cortex, but do not establish that ABI3 itself is highly expressed in microglia generally. (LLM, conf=0.82)

    Experimental — accuracy not yet measured
  • The association of the ABI3 variant with LOAD was replicated by independent groups.

    “Subsequently, this association was replicated by independent groups (9, 10).”

    From Deletion of <i>Abi3</i> gene locus exacerbates neuropathological features of Alzheimer’s disease in a mouse model of Aβ amyloidosis (2021) · cites this paper as [9]

    The Results (‘Association of rs616338 and rs72824905 with AD’) say the authors validated the previously reported ABI3 association and found the same direction of effect in a non-overlapping AD replication cohort. That cohort’s result was not statistically significant (OR = 1.44, p = 0.116), and this paper alone does not establish replication by multiple independent groups. (LLM, conf=0.85)

    Experimental — accuracy not yet measured
  • ABI3 has a microglia-specific gene expression pattern.

    “Consistent with its microglia specific gene expression pattern (8, 9, 11), we found that deletion of Abi3 locus altered the expression of genes regulating microglial phagocytosis and immune response.”

    From Deletion of <i>Abi3</i> gene locus exacerbates neuropathological features of Alzheimer’s disease in a mouse model of Aβ amyloidosis (2021) · cites this paper as [9]

    The Results (Brain expression of ABI3 and PLCG2; page unavailable) place ABI3 in co-expression networks highly enriched for microglial genes. The Discussion likewise describes ABI3 as part of a network of co-expressed microglial genes. These passages support an association with microglial expression, but do not establish that ABI3 expression is specific to microglia. (LLM, conf=0.85)

    Experimental — accuracy not yet measured
  • The P522R variant in PLCG2 is protective not only in Alzheimer's disease but also in other neurodegenerative diseases such as frontotemporal dementia and dementia with Lewy bodies.

    “The missense variant P522R in PLCG2 (rs72824905-G, P = 5.38 × 10−10, OR = 0.68) was shown to be protective, not only in the context of AD4,5, but also in other neurodegenerative diseases such as frontotemporal dementia and dementia with Lewy bodies6.”

    From PLCγ2 regulates TREM2 signalling and integrin-mediated adhesion and migration of human iPSC-derived macrophages (2021) · cites this paper as [5]

    The Results report a protective association of PLCG2 P522R with Alzheimer’s disease (OR = 0.56, p = 0.008). For dementia with Lewy bodies, the association was only suggestive, not significant (OR = 0.32, p = 0.124). The paper’s listed disease cohorts do not include frontotemporal dementia, so it does not support that part of the claim. Page numbers are unavailable in our copy. (LLM, conf=0.88)

    Experimental — accuracy not yet measured
  • The P522R variant in PLCG2 confers protection for Alzheimer's disease and results in a subtle increase in enzymatic activity.

    “The P522R variant in PLCG2 has been shown to confer protection for AD and to result in a subtle increase in enzymatic activity.”

    From PLCγ2 regulates TREM2 signalling and integrin-mediated adhesion and migration of human iPSC-derived macrophages (2021) · cites this paper as [5]

    The Conclusions identify PLCG2_rs72824905-G (p.Pro522Arg) as a protective factor for Alzheimer's disease. The Discussion says this variant is expected to increase PLCγ2 signaling activity, but does not report a measured, subtle increase in its enzymatic activity. Page numbers are not available in our copy. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Conway, O. J., Carrasquillo, M. M., Wang, X., Bredenberg, J. M., Reddy, J. S., Strickland, S. L., Younkin, C. S., Burgess, J. D., Allen, M., Lincoln, S. J., Nguyen, T., Malphrus, K. G., Soto, A. I., Walton, R. L., Boeve, B. F., Petersen, R. C., Lucas, J. A., Ferman, T. J., Cheshire, W. P., van Gerpen, J. A., Uitti, R. J., Wszolek, Z. K., Ross, O. A., Dickson, D. W., Graff-Radford, N. R., & Ertekin-Taner, N.
Affiliations
  • Mayo Clinic in Florida (US)
  • Mayo Clinic (US)
Venue
Molecular Neurodegeneration
Published
2018-10-11
Volume
13
Issue
1
Pages
53-53
ISSN
1750-1326 (ISSN-L)
OpenAlex
W2896393831
Cited by
112
References
57
Citations by year
2026: 8 · 2025: 8 · 2024: 13 · 2023: 12 · 2022: 28 · 2021: 17 · 2020: 20 · 2019: 4 · 2018: 2
FWCI
7.39
Type
journal article
Language
en
Open access
Locations
  • Molecular Neurodegeneration (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Institute on Aging (RF AG051504, U01 AG046139)
  • National Institute of Neurological Disorders and Stroke (R01 NS080820, R01 NS078086)
Topics
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
  • Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
Keywords
PLCγ2, missense mutations, Alzheimer's disease, neurodegenerative diseases, progressive supranuclear palsy, Parkinson's disease, dementia with Lewy bodies, multiple system atrophy, genetic risk factors, African Americans, temporal cortex, cerebellum, co-expression network, gene regulatory networks, transcription factor binding sites, protein-protein interaction network
MeSH terms
Aged, Aged, 80 and over, Black or African American, Brain, Female, Humans, Male, Risk Factors, Microglia, Neurodegenerative Diseases, Mutation, Missense, White People, Adaptor Proteins, Signal Transducing, Phospholipase C gamma

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 ›

Are you an author, or do you see a problem with this page? Request a review