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Article ; Online: Limbic-predominant age-related TDP-43 encephalopathy (LATE-NC): Co-pathologies and genetic risk factors provide clues about pathogenesis.

Nelson, Peter T / Fardo, David W / Wu, Xian / Aung, Khine Zin / Cykowski, Matthew D / Katsumata, Yuriko

Journal of neuropathology and experimental neurology

2024

Abstract: Limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) is detectable at autopsy in more than one-third of people beyond age 85 years and is robustly associated with dementia independent of other pathologies. Although LATE- ... ...

Abstract	Limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) is detectable at autopsy in more than one-third of people beyond age 85 years and is robustly associated with dementia independent of other pathologies. Although LATE-NC has a large impact on public health, there remain uncertainties about the underlying biologic mechanisms. Here, we review the literature from human studies that may shed light on pathogenetic mechanisms. It is increasingly clear that certain combinations of pathologic changes tend to coexist in aging brains. Although "pure" LATE-NC is not rare, LATE-NC often coexists in the same brains with Alzheimer disease neuropathologic change, brain arteriolosclerosis, hippocampal sclerosis of aging, and/or age-related tau astrogliopathy (ARTAG). The patterns of pathologic comorbidities provide circumstantial evidence of mechanistic interactions ("synergies") between the pathologies, and also suggest common upstream influences. As to primary mediators of vulnerability to neuropathologic changes, genetics may play key roles. Genes associated with LATE-NC include TMEM106B, GRN, APOE, SORL1, ABCC9, and others. Although the anatomic distribution of TDP-43 pathology defines the condition, important cofactors for LATE-NC may include Tau pathology, endolysosomal pathways, and blood-brain barrier dysfunction. A review of the human phenomenology offers insights into disease-driving mechanisms, and may provide clues for diagnostic and therapeutic targets.
Language	English
Publishing date	2024-04-13
Publishing country	England
Document type	Journal Article
ZDB-ID	3088-0
ISSN	1554-6578 ; 0022-3069
ISSN (online)	1554-6578
ISSN	0022-3069
DOI	10.1093/jnen/nlae032
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Article ; Online: LATE-NC risk alleles (in TMEM106B, GRN, and ABCC9 genes) among persons with African ancestry.

Katsumata, Yuriko / Fardo, David W / Shade, Lincoln M P / Nelson, Peter T

Journal of neuropathology and experimental neurology

2023 Volume 82, Issue 9, Page(s) 760–768

Abstract: Limbic-predominant age-related TDP-43 encephalopathy (LATE) affects approximately one-third of older individuals and is associated with cognitive impairment. However, there is a highly incomplete understanding of the genetic determinants of LATE ... ...

Abstract	Limbic-predominant age-related TDP-43 encephalopathy (LATE) affects approximately one-third of older individuals and is associated with cognitive impairment. However, there is a highly incomplete understanding of the genetic determinants of LATE neuropathologic changes (LATE-NC) in diverse populations. The defining neuropathologic feature of LATE-NC is TDP-43 proteinopathy, often with comorbid hippocampal sclerosis (HS). In terms of genetic risk factors, LATE-NC and/or HS are associated with single nucleotide variants (SNVs) in 3 genes-TMEM106B (rs1990622), GRN (rs5848), and ABCC9 (rs1914361 and rs701478). We evaluated these 3 genes in convenience samples of individuals of African ancestry. The allele frequencies of the LATE-associated alleles were significantly different between persons of primarily African (versus European) ancestry: In persons of African ancestry, the risk-associated alleles for TMEM106B and ABCC9 were less frequent, whereas the risk allele in GRN was more frequent. We performed an exploratory analysis of data from African-American subjects processed by the Alzheimer's Disease Genomics Consortium, with a subset of African-American participants (n = 166) having corroborating neuropathologic data through the National Alzheimer's Coordinating Center (NACC). In this limited-size sample, the ABCC9/rs1914361 SNV was associated with HS pathology. More work is required concerning the genetic factors influencing non-Alzheimer disease pathology such as LATE-NC in diverse cohorts.
MeSH term(s)	Humans ; Alleles ; Aging/pathology ; Polymorphism, Single Nucleotide/genetics ; Alzheimer Disease/genetics ; Alzheimer Disease/pathology ; TDP-43 Proteinopathies/pathology ; Progranulins/genetics ; Membrane Proteins/genetics ; Nerve Tissue Proteins/genetics ; Sulfonylurea Receptors/genetics
Chemical Substances	GRN protein, human ; Progranulins ; TMEM106B protein, human ; Membrane Proteins ; Nerve Tissue Proteins ; ABCC9 protein, human ; Sulfonylurea Receptors
Language	English
Publishing date	2023-08-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	3088-0
ISSN	1554-6578 ; 0022-3069
ISSN (online)	1554-6578
ISSN	0022-3069
DOI	10.1093/jnen/nlad059
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Article ; Online: Quantitative phenotype scan statistic (QPSS) reveals rare variant associations with Alzheimer's disease endophenotypes.

Katsumata, Yuriko / Fardo, David W

BMC medical genetics

2020 Volume 21, Issue 1, Page(s) 106

Abstract: Background: Current sequencing technologies have provided for a more comprehensive genome-wide assessment and have increased genotyping accuracy of rare variants. Scan statistic approaches have previously been adapted to genetic sequencing data. Unlike ... ...

Abstract	Background: Current sequencing technologies have provided for a more comprehensive genome-wide assessment and have increased genotyping accuracy of rare variants. Scan statistic approaches have previously been adapted to genetic sequencing data. Unlike currently-employed association tests, scan-statistic-based approaches can both localize clusters of disease-related variants and, subsequently, examine the phenotype association within the resulting cluster. In this study, we present a novel Quantitative Phenotype Scan Statistic (QPSS) that extends an approach for dichotomous phenotypes to continuous outcomes in order to identify genomic regions where rare quantitative-phenotype-associated variants cluster. Results: We demonstrate the performance and practicality of QPSS with extensive simulations and an application to a whole-genome sequencing (WGS) study of cerebrospinal fluid (CSF) biomarkers from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Using QPSS, we identify regions of rare variant enrichment associated with levels of AD-related proteins, CSF Aβ Conclusions: QPSS is implemented under the assumption that causal variants within a window have the same direction of effect. Typical self-contained tests employ a null hypothesis of no association between the target variant set and the phenotype. Therefore, an advantage of the proposed competitive test is that it is possible to refine a known region of interest to localize disease-associated clusters. The definition of clusters can be easily adapted based on variant function or annotation.
MeSH term(s)	Algorithms ; Alleles ; Alzheimer Disease/diagnosis ; Alzheimer Disease/genetics ; Alzheimer Disease/metabolism ; Biomarkers ; Genetic Association Studies/methods ; Genetic Predisposition to Disease ; Genetic Variation ; Humans ; Linkage Disequilibrium ; Models, Genetic ; Models, Statistical ; Neuroimaging/methods ; Phenotype ; Reproducibility of Results
Chemical Substances	Biomarkers
Language	English
Publishing date	2020-05-15
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2041359-2
ISSN	1471-2350 ; 1471-2350
ISSN (online)	1471-2350
ISSN	1471-2350
DOI	10.1186/s12881-020-01046-6
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Article: The association of gabapentin initiation and neurocognitive changes in older adults with normal cognition.

Oh, GYeon / Moga, Daniela C / Fardo, David W / Abner, Erin L

Frontiers in pharmacology

2022 Volume 13, Page(s) 910719

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2022-11-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2022.910719
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Article ; Online: Association analyses of repeated measures on triglyceride and high-density lipoprotein levels: insights from GAW20.

Ghosh, Saurabh / Fardo, David W

BMC genetics

2018 Volume 19, Issue Suppl 1, Page(s) 73

Abstract: Background: The GAW20 group formed on the theme of methods for association analyses of repeated measures comprised 4sets of investigators. The provided "real" data set included genotypes obtained from a human whole-genome association study based on ... ...

Abstract	Background: The GAW20 group formed on the theme of methods for association analyses of repeated measures comprised 4sets of investigators. The provided "real" data set included genotypes obtained from a human whole-genome association study based on longitudinal measurements of triglycerides (TGs) and high-density lipoprotein in addition to methylation levels before and after administration of fenofibrate. The simulated data set contained 200 replications of methylation levels and posttreatment TGs, mimicking the real data set. Results: The different investigators in the group focused on the statistical challenges unique to family-based association analyses of phenotypes measured longitudinally and applied a wide spectrum of statistical methods such as linear mixed models, generalized estimating equations, and quasi-likelihood-based regression models. This article discusses the varying strategies explored by the group's investigators with the common goal of improving the power to detect association with repeated measures of a phenotype. Conclusions: Although it is difficult to identify a common message emanating from the different contributions because of the diversity in the issues addressed, the unifying theme of the contributions lie in the search for novel analytic strategies to circumvent the limitations of existing methodologies to detect genetic association.
MeSH term(s)	Genome-Wide Association Study ; Humans ; Hypertriglyceridemia/drug therapy ; Hypertriglyceridemia/genetics ; Hypoglycemic Agents/therapeutic use ; Likelihood Functions ; Linear Models ; Lipoproteins, HDL/blood ; Longitudinal Studies ; Phenotype ; Polymorphism, Single Nucleotide ; Triglycerides/blood
Chemical Substances	Hypoglycemic Agents ; Lipoproteins, HDL ; Triglycerides
Language	English
Publishing date	2018-09-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2041497-3
ISSN	1471-2156 ; 1471-2156
ISSN (online)	1471-2156
ISSN	1471-2156
DOI	10.1186/s12863-018-0651-6
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Article ; Online: The MUC6/AP2A2 Locus and Its Relevance to Alzheimer's Disease: A Review.

Nelson, Peter T / Fardo, David W / Katsumata, Yuriko

Journal of neuropathology and experimental neurology

2020 Volume 79, Issue 6, Page(s) 568–584

Abstract: We recently reported evidence of Alzheimer's disease (AD)-linked genetic variation within the mucin 6 (MUC6) gene on chromosome 11p, nearby the adaptor-related protein complex 2 subunit alpha 2 (AP2A2) gene. This locus has interesting features related to ...

Abstract	We recently reported evidence of Alzheimer's disease (AD)-linked genetic variation within the mucin 6 (MUC6) gene on chromosome 11p, nearby the adaptor-related protein complex 2 subunit alpha 2 (AP2A2) gene. This locus has interesting features related to human genomics and clinical research. MUC6 gene variants have been reported to potentially influence viral-including herpesvirus-immunity and the gut microbiome. Within the MUC6 gene is a unique variable number of tandem repeat (VNTR) region. We discovered an association between MUC6 VNTR repeat expansion and AD pathologic severity, particularly tau proteinopathy. Here, we review the relevant literature. The AD-linked VNTR polymorphism may also influence AP2A2 gene expression. AP2A2 encodes a polypeptide component of the adaptor protein complex, AP-2, which is involved in clathrin-coated vesicle function and was previously implicated in AD pathogenesis. To provide background information, we describe some key knowledge gaps in AD genetics research. The "missing/hidden heritability problem" of AD is highlighted. Extensive portions of the human genome, including the MUC6 VNTR, have not been thoroughly evaluated due to limitations of existing high-throughput sequencing technology. We present and discuss additional data, along with cautionary considerations, relevant to the hypothesis that MUC6 repeat expansion influences AD pathogenesis.
MeSH term(s)	Adaptor Protein Complex 2/genetics ; Adaptor Protein Complex alpha Subunits/genetics ; Alzheimer Disease/genetics ; Alzheimer Disease/pathology ; DNA Copy Number Variations ; Genetic Predisposition to Disease ; Humans ; Mucin-6/genetics ; Polymorphism, Single Nucleotide
Chemical Substances	Adaptor Protein Complex 2 ; Adaptor Protein Complex alpha Subunits ; MUC6 protein, human ; Mucin-6 ; adaptor protein complex 2, alpha 2 subunit
Language	English
Publishing date	2020-04-26
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	3088-0
ISSN	1554-6578 ; 0022-3069
ISSN (online)	1554-6578
ISSN	0022-3069
DOI	10.1093/jnen/nlaa024
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Article: Association analyses of repeated measures on triglyceride and high-density lipoprotein levels: insights from GAW20

Ghosh, Saurabh / Fardo, David W

BMC genetics. 2018 Sept., v. 19, no. Supplement 1

2018

Abstract: BACKGROUND: The GAW20 group formed on the theme of methods for association analyses of repeated measures comprised 4sets of investigators. The provided “real” data set included genotypes obtained from a human whole-genome association study based on ... ...

Abstract	BACKGROUND: The GAW20 group formed on the theme of methods for association analyses of repeated measures comprised 4sets of investigators. The provided “real” data set included genotypes obtained from a human whole-genome association study based on longitudinal measurements of triglycerides (TGs) and high-density lipoprotein in addition to methylation levels before and after administration of fenofibrate. The simulated data set contained 200 replications of methylation levels and posttreatment TGs, mimicking the real data set. RESULTS: The different investigators in the group focused on the statistical challenges unique to family-based association analyses of phenotypes measured longitudinally and applied a wide spectrum of statistical methods such as linear mixed models, generalized estimating equations, and quasi-likelihood–based regression models. This article discusses the varying strategies explored by the group’s investigators with the common goal of improving the power to detect association with repeated measures of a phenotype. CONCLUSIONS: Although it is difficult to identify a common message emanating from the different contributions because of the diversity in the issues addressed, the unifying theme of the contributions lie in the search for novel analytic strategies to circumvent the limitations of existing methodologies to detect genetic association.
Keywords	data collection ; equations ; fenofibrate ; genotype ; high density lipoprotein ; humans ; methylation ; phenotype ; regression analysis ; triacylglycerols
Language	English
Dates of publication	2018-09
Size	p. 73.
Publishing place	BioMed Central
Document type	Article
ISSN	1471-2156
DOI	10.1186/s12863-018-0651-6
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Article ; Online: Associations of potential ADRD plasma biomarkers in cognitively normal volunteers.

Estepp, Taylor G / Charnigo, Richard J / Abner, Erin L / Jicha, Gregory A / Sudduth, Tiffany L / Fardo, David W / Wilcock, Donna M

Alzheimer's & dementia : the journal of the Alzheimer's Association

2023 Volume 19, Issue 8, Page(s) 3593–3601

Abstract: Introduction: This study examined the relationships between 13 novel blood-plasma biomarkers and dementia-related demographic and health factors in a cohort of 237 cognitively normal research volunteers whose average age was ≈82 years and who were 63% ... ...

Abstract	Introduction: This study examined the relationships between 13 novel blood-plasma biomarkers and dementia-related demographic and health factors in a cohort of 237 cognitively normal research volunteers whose average age was ≈82 years and who were 63% female. Methods: We regressed each biomarker on selected covariates to explore the associations between the biomarkers and selected factors to assess whether they may contribute to biomarker values. Post hoc sensitivity analyses were done with updated data and consistent variable sets for robustness and batch effects. Results: Biomarker concentrations were largely not associated with demographics or health conditions, but some expected associations (e.g., apolipoprotein E [APOE] status with amyloid beta [Aβ]42/Aβ40) were observed. Post hoc results remained similar to those of the main analysis. Discussion: The absence of strong associations between the biomarkers with age, gender, or medical conditions suggests that changes in these biomarkers, when observed, may be attributable to neuropathological changes. Highlights: Among N = 237 cognitively normal adults, we studied candidate Alzheimer's disease and related dementia (ADRD) plasma biomarkers. Biomarkers were largely not associated with demographic or health factors. Apolipoprotein E (APOE) status was associated with amyloid beta (Aβ)42/Aβ40 ratio. These results support hypotheses that plasma biomarkers are informative for ADRD.
MeSH term(s)	Adult ; Humans ; Female ; Aged, 80 and over ; Male ; Amyloid beta-Peptides ; Healthy Volunteers ; Alzheimer Disease/diagnosis ; Apolipoproteins E/genetics ; Biomarkers
Chemical Substances	Amyloid beta-Peptides ; Apolipoproteins E ; Biomarkers
Language	English
Publishing date	2023-02-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2211627-8
ISSN	1552-5279 ; 1552-5260
ISSN (online)	1552-5279
ISSN	1552-5260
DOI	10.1002/alz.13000
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Article: Detecting novel micro RNAs in rheumatoid arthritis with gene-based association testing.

Lenert, Aleksander / Fardo, David W

Clinical and experimental rheumatology

2017 Volume 35, Issue 4, Page(s) 586–592

Abstract: Objectives: To identify novel risk genes by gene-based association analysis in rheumatoid arthritis (RA).: Methods: We performed gene-based association testing with GATES (Gene-based Association Test using Extended Simes procedure) to augment the ... ...

Abstract	Objectives: To identify novel risk genes by gene-based association analysis in rheumatoid arthritis (RA). Methods: We performed gene-based association testing with GATES (Gene-based Association Test using Extended Simes procedure) to augment the power of genomewide-association study (GWAS) results from the largest meta-GWAS by Okada et al. in 14,361 RA cases and 43,923 controls of European ancestry using 8,694,488 SNPs. Results: We identified 115 genes significantly associated with RA by gene-based association testing corresponding to 43 RA risk loci; 23 risk loci contained a single top risk gene, while 20 risk loci contained two or more risk genes. We replicated 39 of the genomewide significant risk loci identified by Okada et al. in Europeans with RA; we found identical top genes for 26 loci. Our gene-based testing identified 6 new top gene hits for each of the following 6 RA risk loci: RPP14 (for DNASE1L3-ABHD6-PXK), PXT1 (for ETV7), MIR5708 (for TPD52), DDX6 (for CXCR5), SUOX (for CDK2), and PCAT29 (for LOC145837). We also identified a potential novel RA risk locus (11q23.3, start position 118528941 bp) which contains the following 3 genes: TREH-PHLDB1-MIR6716; the locus was not identified previously but may be a proxy for CXCR5. Conclusions: Through novel comprehensive gene-based association testing in >50,000 Europeans with RA using ~8 million SNPs, we confirmed prior RA risk loci and identified novel risk genes including non-coding regulatory miRNAs, providing further insight into the complex genetics of RA.
MeSH term(s)	Arthritis, Rheumatoid/genetics ; Case-Control Studies ; European Continental Ancestry Group/genetics ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; MicroRNAs/genetics
Chemical Substances	MicroRNAs
Language	English
Publishing date	2017-07
Publishing country	Italy
Document type	Journal Article
ZDB-ID	605886-3
ISSN	1593-098X ; 0392-856X
ISSN (online)	1593-098X
ISSN	0392-856X
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Article ; Online: Tau and TDP-43 proteinopathies: kindred pathologic cascades and genetic pleiotropy.

Chornenkyy, Yevgen / Fardo, David W / Nelson, Peter T

Laboratory investigation; a journal of technical methods and pathology

2019 Volume 99, Issue 7, Page(s) 993–1007

Abstract: We review the literature on Tau and TDP-43 proteinopathies in aged human brains and the relevant underlying pathogenetic cascades. Complex interacting pathways are implicated in Alzheimer's disease and related dementias (ADRD), wherein multiple proteins ... ...

Abstract	We review the literature on Tau and TDP-43 proteinopathies in aged human brains and the relevant underlying pathogenetic cascades. Complex interacting pathways are implicated in Alzheimer's disease and related dementias (ADRD), wherein multiple proteins tend to misfold in a manner that is "reactive," but, subsequently, each proteinopathy may contribute strongly to the clinical symptoms. Tau proteinopathy exists in brains of individuals across a broad spectrum of primary underlying conditions-e.g., developmental, traumatic, and inflammatory/infectious diseases. TDP-43 proteinopathy is also expressed in a wide range of clinical disorders. Although TDP-43 proteinopathy was first described in the central nervous system of patients with amyotrophic lateral sclerosis (ALS) and in subtypes of frontotemporal dementia (FTD/FTLD), TDP-43 proteinopathy is also present in chronic traumatic encephalopathy, cognitively impaired persons in advanced age with hippocampal sclerosis, Huntington's disease, and other diseases. We list known Tau and TDP-43 proteinopathies. There is also evidence of cellular co-localization between Tau and TDP-43 misfolded proteins, suggesting common pathways or protein interactions facilitating misfolding in one protein by the other. Multiple pleiotropic gene variants can alter risk for Tau or TDP-43 pathologies, and certain gene variants (e.g., APOE ε4, Huntingtin triplet repeats) are associated with increases of both Tau and TDP-43 proteinopathies. Studies of genetic risk factors have provided insights into multiple nodes of the pathologic cascades involved in Tau and TDP-43 proteinopathies. Variants from a specific gene can be either a low-penetrant risk factor for a group of diseases, or alternatively, a different variant of the same gene may be a disease-driving allele that is associated with a relatively aggressive and early-onset version of a clinically and pathologically specific disease type. Overall, a complex but enlightening paradigm has emerged, wherein both Tau and TDP-43 proteinopathies are linked to numerous overlapping upstream influences, and both are associated with multiple downstream pathologically- and clinically-defined deleterious effects.
MeSH term(s)	Animals ; Genetic Pleiotropy ; Humans ; TDP-43 Proteinopathies/etiology ; Tauopathies/etiology
Language	English
Publishing date	2019-02-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	80178-1
ISSN	1530-0307 ; 0023-6837
ISSN (online)	1530-0307
ISSN	0023-6837
DOI	10.1038/s41374-019-0196-y
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