1
|
Kulminski AM, Philipp I, Shu L, Culminskaya I. Definitive roles of TOMM40-APOE-APOC1 variants in the Alzheimer's risk. Neurobiol Aging 2022; 110:122-131. [PMID: 34625307 PMCID: PMC8758518 DOI: 10.1016/j.neurobiolaging.2021.09.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 02/03/2023]
Abstract
Despite advances, the roles of genetic variants from the APOE-harboring 19q13.32 region in Alzheimer's disease (AD) remain controversial. We leverage a comprehensive approach to gain insights into a more homogeneous genetic architecture of AD in this region. We use a sample of 2,673 AD-affected and 16,246 unaffected subjects from 4 studies and validate our main findings in the landmark Alzheimer's Disease Genetics Consortium cohort (3,662 AD-cases and 1,541 controls). We report the remarkably high excesses of the AD risk for carriers of the ε4 allele who also carry minor alleles of rs2075650 (TOMM40) and rs12721046 (APOC1) polymorphisms compared to carriers of their major alleles. The exceptionally high 4.37-fold (p=1.34 × 10-3) excess was particularly identified for the minor allele homozygotes. The beneficial and adverse variants were significantly depleted and enriched, respectively, in the AD-affected families. This study provides compelling evidence for the definitive roles of the APOE-TOMM40-APOC1 variants in the AD risk.
Collapse
Affiliation(s)
- Alexander M. Kulminski
- Corresponding Author: Alexander M. Kulminski, Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA,
| | | | | | | |
Collapse
|
2
|
Kulminski AM, Philipp I, Loika Y, He L, Culminskaya I. Protective association of the ε2/ε3 heterozygote with Alzheimer's disease is strengthened by TOMM40-APOE variants in men. Alzheimers Dement 2021; 17:1779-1787. [PMID: 34310032 DOI: 10.1002/alz.12413] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/07/2021] [Accepted: 05/25/2021] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Despite advances, understanding the protective role of the apolipoprotein E (APOE) ε2 allele in Alzheimer's disease (AD) remains elusive. METHODS We examined associations of variants comprised of the TOMM40 rs8106922 and APOE rs405509, rs440446, and ε2-encoding rs7412 polymorphisms with AD in a sample of 2862 AD-affected and 169,516 AD-unaffected non-carriers of the ε4 allele. RESULTS Association of the ε2/ε3 heterozygote of men with AD is 38% (P = 1.65 × 10-2 ) more beneficial when it is accompanied by rs8106922 major allele homozygote and rs405509 and rs440446 heterozygotes than by rs8106922 heterozygote and rs405509 and rs440446 major allele homozygotes. No difference in the beneficial associations of these two most common ε2/ε3-bearing variants with AD was identified in women. The role of ε2/ε3 heterozygote may be affected by different immunomodulation functions of rs8106922, rs405509, and rs440446 variants in a sex-specific manner. DISCUSSION Combination of TOMM40 and APOE variants defines a more homogeneous AD-protective ε2/ε3-bearing profile in men.
Collapse
Affiliation(s)
- Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina, USA
| | - Ian Philipp
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina, USA
| | - Yury Loika
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina, USA
| | - Liang He
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina, USA
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina, USA
| |
Collapse
|
3
|
He L, Loika Y, Park Y, Bennett DA, Kellis M, Kulminski AM. Exome-wide age-of-onset analysis reveals exonic variants in ERN1 and SPPL2C associated with Alzheimer's disease. Transl Psychiatry 2021; 11:146. [PMID: 33637690 PMCID: PMC7910483 DOI: 10.1038/s41398-021-01263-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/07/2021] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
Despite recent discoveries in genome-wide association studies (GWAS) of genomic variants associated with Alzheimer's disease (AD), its underlying biological mechanisms are still elusive. The discovery of novel AD-associated genetic variants, particularly in coding regions and from APOE ε4 non-carriers, is critical for understanding the pathology of AD. In this study, we carried out an exome-wide association analysis of age-of-onset of AD with ~20,000 subjects and placed more emphasis on APOE ε4 non-carriers. Using Cox mixed-effects models, we find that age-of-onset shows a stronger genetic signal than AD case-control status, capturing many known variants with stronger significance, and also revealing new variants. We identified two novel variants, rs56201815, a rare synonymous variant in ERN1, and rs12373123, a common missense variant in SPPL2C in the MAPT region in APOE ε4 non-carriers. Besides, a rare missense variant rs144292455 in TACR3 showed the consistent direction of effect sizes across all studies with a suggestive significant level. In an attempt to unravel their regulatory and biological functions, we found that the minor allele of rs56201815 was associated with lower average FDG uptake across five brain regions in ADNI. Our eQTL analyses based on 6198 gene expression samples from ROSMAP and GTEx revealed that the minor allele of rs56201815 was potentially associated with elevated expression of ERN1, a key gene triggering unfolded protein response (UPR), in multiple brain regions, including the posterior cingulate cortex and nucleus accumbens. Our cell-type-specific eQTL analysis using ~80,000 single nuclei in the prefrontal cortex revealed that the protective minor allele of rs12373123 significantly increased the expression of GRN in microglia, and was associated with MAPT expression in astrocytes. These findings provide novel evidence supporting the hypothesis of the potential involvement of the UPR to ER stress in the pathological pathway of AD, and also give more insights into underlying regulatory mechanisms behind the pleiotropic effects of rs12373123 in multiple degenerative diseases including AD and Parkinson's disease.
Collapse
Affiliation(s)
- Liang He
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA.
| | - Yury Loika
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Yongjin Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA.
| |
Collapse
|
4
|
Genetic Association Studies of Age-Related Traits: New Perspectives. ACTA ACUST UNITED AC 2021; 3. [PMID: 33511377 PMCID: PMC7839997 DOI: 10.20900/agmr20210003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Understanding the role of genetic factors in non-Mendelian traits characteristic for post-reproductive life, herein referred to as age-related traits, is lagged behind the understanding of the genetic architecture of Mendelian traits. This lag calls for new, more comprehensive approaches in the analyses of age-related traits leveraging their characteristic features. This paper discusses the role of the inherent heterogeneity in genetic predisposition to age-related traits and pleiotropy. It shows that the comprehensive analyses leveraging such heterogeneity can substantially increase the efficiency and accelerate the progress in uncovering genetic predisposition to such traits.
Collapse
|
5
|
Loika Y, Irincheeva I, Culminskaya I, Nazarian A, Kulminski AM. Polygenic risk scores: pleiotropy and the effect of environment. GeroScience 2020; 42:1635-1647. [PMID: 32488673 DOI: 10.1007/s11357-020-00203-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/08/2020] [Indexed: 10/24/2022] Open
Abstract
Polygenic risk scores (PRSs) discriminate trait risks better than single genetic markers because they aggregate the effects of risk alleles from multiple genetic loci. Constructing pleiotropic PRSs and understanding heterogeneity, and the replication of PRS-trait associations can strengthen its applications. By using variational Bayesian multivariate high-dimensional regression, we constructed pleiotropic PRSs jointly associated with body mass index, systolic and diastolic blood pressure, total and high-density lipoprotein cholesterol in a sample of 18,108 Caucasians from three independent cohorts. We found that dissecting heterogeneity associated with birth year, which is a proxy of exogenous exposures, improved the replication of significant PRS-trait associations from 37.5% (6 of 16) in the entire sample to 90% (18 of 20) in the more homogeneous sample of individuals born before the year 1925. Our findings suggest that secular changes in exogenous exposures may substantially modify pleiotropic risk profiles affecting translation of genetic discoveries into health care.
Collapse
Affiliation(s)
- Yury Loika
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708-0408, USA.
| | - Irina Irincheeva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708-0408, USA.
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708-0408, USA
| | - Alireza Nazarian
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708-0408, USA
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708-0408, USA.
| |
Collapse
|
6
|
Kulminski AM, Shu L, Loika Y, Nazarian A, Arbeev K, Ukraintseva S, Yashin A, Culminskaya I. APOE region molecular signatures of Alzheimer's disease across races/ethnicities. Neurobiol Aging 2020; 87:141.e1-141.e8. [PMID: 31813627 PMCID: PMC7064423 DOI: 10.1016/j.neurobiolaging.2019.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 08/19/2019] [Accepted: 11/06/2019] [Indexed: 11/20/2022]
Abstract
The role of even the strongest genetic risk factor for Alzheimer's disease (AD), the apolipoprotein E (APOE) ε4 allele, in its etiology remains poorly understood. We examined molecular signatures of AD defined as differences in linkage disequilibrium patterns between AD-affected and -unaffected whites (2673/16,246), Hispanics (392/867), and African Americans (285/1789), separately. We focused on 29 polymorphisms from 5 genes in the APOE region emphasizing beneficial and adverse effects of the APOE ε2- and ε4-coding single-nucleotide polymorphisms, respectively, and the differences in the linkage disequilibrium structures involving these alleles between AD-affected and -unaffected subjects. Susceptibility to AD is likely the result of complex interactions of the ε2 and ε4 alleles with other polymorphisms in the APOE region, and these interactions differ across races/ethnicities corroborating differences in the adverse and beneficial effects of the ε4 and ε2 alleles. Our findings support complex race/ethnicity-specific haplotypes promoting and protecting against AD in this region. They contribute to better understanding of polygenic and resilient mechanisms, which can explain why even homozygous ε4 carriers may not develop AD.
Collapse
Affiliation(s)
- Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA.
| | - Leonardo Shu
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Yury Loika
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Alireza Nazarian
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Konstantin Arbeev
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Svetlana Ukraintseva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Anatoliy Yashin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| |
Collapse
|
7
|
Kulminski AM, Shu L, Loika Y, He L, Nazarian A, Arbeev K, Ukraintseva S, Yashin A, Culminskaya I. Genetic and regulatory architecture of Alzheimer's disease in the APOE region. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2020; 12:e12008. [PMID: 32211503 PMCID: PMC7085286 DOI: 10.1002/dad2.12008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/07/2019] [Accepted: 11/20/2019] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Apolipoprotein E (APOE) ε2 and ε4 alleles encoded by rs7412 and rs429358 polymorphisms, respectively, are landmark contra and pro "risk" factors for Alzheimer's disease (AD). METHODS We examined differences in linkage disequilibrium (LD) structures between (1) AD-affected and unaffected subjects and (2) older AD-unaffected and younger subjects in the 19q13.3 region harboring rs7412 and rs429358. RESULTS AD is associated with sex-nonspecific heterogeneous patterns of decreased and increased LD of rs7412 and rs429358, respectively, with other polymorphisms from five genes in this region in AD-affected subjects. The LD patterns in older AD-unaffected subjects resembled those in younger individuals. Polarization of the ε4- and ε2 allele-related heterogeneous LD clusters differentiated cell types and implicated specific tissues in AD pathogenesis. DISCUSSION Protection and predisposition to AD is characterized by an interplay of rs7412 and rs429358, with multiple polymorphisms in the 19q13.3 region in a tissue-specific manner, which is not driven by common evolutionary forces.
Collapse
Affiliation(s)
- Alexander M. Kulminski
- Biodemography of Aging Research UnitSocial Science Research InstituteDuke UniversityDurhamNorth Carolina
| | - Leonardo Shu
- Biodemography of Aging Research UnitSocial Science Research InstituteDuke UniversityDurhamNorth Carolina
| | - Yury Loika
- Biodemography of Aging Research UnitSocial Science Research InstituteDuke UniversityDurhamNorth Carolina
| | - Liang He
- Biodemography of Aging Research UnitSocial Science Research InstituteDuke UniversityDurhamNorth Carolina
| | - Alireza Nazarian
- Biodemography of Aging Research UnitSocial Science Research InstituteDuke UniversityDurhamNorth Carolina
| | - Konstantin Arbeev
- Biodemography of Aging Research UnitSocial Science Research InstituteDuke UniversityDurhamNorth Carolina
| | - Svetlana Ukraintseva
- Biodemography of Aging Research UnitSocial Science Research InstituteDuke UniversityDurhamNorth Carolina
| | - Anatoliy Yashin
- Biodemography of Aging Research UnitSocial Science Research InstituteDuke UniversityDurhamNorth Carolina
| | - Irina Culminskaya
- Biodemography of Aging Research UnitSocial Science Research InstituteDuke UniversityDurhamNorth Carolina
| |
Collapse
|
8
|
Finch CE, Kulminski AM. The Alzheimer's Disease Exposome. Alzheimers Dement 2019; 15:1123-1132. [PMID: 31519494 PMCID: PMC6788638 DOI: 10.1016/j.jalz.2019.06.3914] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Environmental factors are poorly understood in the etiology of Alzheimer's disease (AD) and related dementias. The importance of environmental factors in gene environment interactions (GxE) is suggested by wide individual differences in cognitive loss, even for carriers of AD-risk genetic variants. RESULTS AND DISCUSSION We propose the "AD exposome" to comprehensively assess the modifiable environmental factors relevant to genetic underpinnings of cognitive aging and AD. Analysis of endogenous and exogenous environmental factors requires multi-generational consideration of these interactions over age and time (GxExT). New computational approaches to the multi-level complexities may identify accessible interventions for individual brain aging. International collaborations on diverse populations are needed to identify the most relevant exposures over the life course for GxE interactions.
Collapse
Affiliation(s)
- Caleb E Finch
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA.
| |
Collapse
|
9
|
Kulminski AM, Huang J, Loika Y, Arbeev KG, Bagley O, Yashkin A, Duan M, Culminskaya I. Strong impact of natural-selection-free heterogeneity in genetics of age-related phenotypes. Aging (Albany NY) 2019; 10:492-514. [PMID: 29615537 PMCID: PMC5892700 DOI: 10.18632/aging.101407] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/24/2018] [Indexed: 11/25/2022]
Abstract
A conceptual difficulty in genetics of age-related phenotypes that make individuals vulnerable to disease in post-reproductive life is genetic heterogeneity attributed to an undefined role of evolution in establishing their molecular mechanisms. Here, we performed univariate and pleiotropic genome-wide meta-analyses of 20 age-related phenotypes leveraging longitudinal information in a sample of 33,431 individuals and dealing with the natural-selection-free genetic heterogeneity. We identified 142 non-proxy single nucleotide polymorphisms (SNPs) with phenotype-specific (18 SNPs) and pleiotropic (124 SNPs) associations at genome-wide level. Univariate meta-analysis identified two novel (11.1%) and replicated 16 SNPs whereas pleiotropic meta-analysis identified 115 novel (92.7%) and nine replicated SNPs. Pleiotropic associations for most novel (93.9%) and all replicated SNPs were strongly impacted by the natural-selection-free genetic heterogeneity in its unconventional form of antagonistic heterogeneity, implying antagonistic directions of genetic effects for directly correlated phenotypes. Our results show that the common genome-wide approach is well adapted to handle homogeneous univariate associations within Mendelian framework whereas most associations with age-related phenotypes are more complex and well beyond that framework. Dissecting the natural-selection-free genetic heterogeneity is critical for gaining insights into genetics of age-related phenotypes and has substantial and unexplored yet potential for improving efficiency of genome-wide analysis.
Collapse
Affiliation(s)
- Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Jian Huang
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Yury Loika
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Konstantin G Arbeev
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Olivia Bagley
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Arseniy Yashkin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Matt Duan
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| |
Collapse
|
10
|
Kulminski AM, Huang J, Wang J, He L, Loika Y, Culminskaya I. Apolipoprotein E region molecular signatures of Alzheimer's disease. Aging Cell 2018; 17:e12779. [PMID: 29797398 PMCID: PMC6052488 DOI: 10.1111/acel.12779] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2018] [Indexed: 01/01/2023] Open
Abstract
Although the APOE region is the strongest genetic risk factor for Alzheimer's diseases (ADs), its pathogenic role remains poorly understood. Elucidating genetic predisposition to ADs, a subset of age-related diseases characteristic for postreproductive period, is hampered by the undefined role of evolution in establishing molecular mechanisms of such diseases. This uncertainty is inevitable source of natural-selection-free genetic heterogeneity in predisposition to ADs. We performed first large-scale analysis of linkage disequilibrium (LD) structures characterized by 30 polymorphisms from five genes in the APOE 19q13.3 region (BCAM, NECTIN2, TOMM40, APOE, and APOC1) in 2,673 AD-affected and 16,246 unaffected individuals from five cohorts. Consistent with the undefined role of evolution in age-related diseases, we found that these structures, being highly heterogeneous, are significantly different in subjects with and without ADs. The pattern of the difference represents molecular signature of AD comprised of single nucleotide polymorphisms (SNPs) from all five genes in the APOE region. Significant differences in LD in subjects with and without ADs indicate SNPs from different genes likely involved in AD pathogenesis. Significant and highly heterogeneous molecular signatures of ADs provide unprecedented insight into complex polygenetic predisposition to ADs in the APOE region. These findings are more consistent with a complex haplotype than with a single genetic variant origin of ADs in this region.
Collapse
Affiliation(s)
- Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
| | - Jian Huang
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
| | - Jiayi Wang
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
| | - Liang He
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
| | - Yury Loika
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina
| |
Collapse
|
11
|
Doherty A, Kernogitski Y, Kulminski AM, Pedro de Magalhães J. Identification of polymorphisms in cancer patients that differentially affect survival with age. Aging (Albany NY) 2017; 9:2117-2136. [PMID: 29064820 PMCID: PMC5680559 DOI: 10.18632/aging.101305] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/06/2017] [Indexed: 01/08/2023]
Abstract
The World Health Organization predicts that the proportion of the world's population over 60 will almost double from 12% to 22% between 2015 and 2050. Ageing is the biggest risk factor for cancer, which is a leading cause of deaths worldwide. Unfortunately, research describing how genetic variants affect cancer progression commonly neglects to account for the ageing process. Herein is the first systematic analysis that combines a large longitudinal data set with a targeted candidate gene approach to examine the effect of genetic variation on survival as a function of age in cancer patients. Survival was significantly decreased in individuals with heterozygote or rare homozygote (i.e. variant) genotypes compared to those with a common homozygote genotype (i.e. wild type) for two single nucleotide polymorphisms (rs11574358 and rs4147918), one gene (SIRT3) and one pathway (FoxO signalling) in an age-dependent manner. All identified genes and pathways have previously been associated with ageing and cancer. These observations demonstrate that there are ageing-related genetic elements that differentially affect mortality in cancer patients in an age-dependent manner. Understanding the genetic determinants affecting prognosis differently with age will be invaluable to develop age-specific prognostic biomarkers and personalized therapies that may improve clinical outcomes for older individuals.
Collapse
Affiliation(s)
- Aoife Doherty
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, United Kingdom
| | - Yelena Kernogitski
- Biodemography of Aging Research Unit (BARU), Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit (BARU), Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, United Kingdom
| |
Collapse
|
12
|
Kulminski AM, Kernogitski Y, Culminskaya I, Loika Y, Arbeev KG, Bagley O, Duan M, Arbeeva L, Ukraintseva SV, Wu D, Stallard E, Yashin AI. Uncoupling associations of risk alleles with endophenotypes and phenotypes: insights from the ApoB locus and heart-related traits. Aging Cell 2017; 16:61-72. [PMID: 27683205 PMCID: PMC5242299 DOI: 10.1111/acel.12526] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2016] [Indexed: 12/04/2022] Open
Abstract
Traditionally, genomewide association studies (GWAS) have emphasized the benefits of large samples in the analyses of age‐related traits rather than their specific properties. We adopted a realistic concept of genetic susceptibility to inherently heterogeneous, age‐related traits driven by the elusive role of evolution in their properties. We analyzed in detail the associations of rs693 and rs562338 polymorphisms representing the Apolipoprotein B locus with endophenotypes (total cholesterol [TC] and high‐density lipoprotein cholesterol) and phenotypes (myocardial infarction [MI] and survival) in four large‐scale studies, which include 20 748 individuals with 2357 MI events. We showed that a strong, robust predisposition of rs693 and rs562338 to TC (β = 0.72, P = 7.7 × 10−30 for rs693 and β = −1.08, P = 9.8 × 10−42 for rs562338) is not translated into a predisposition to MI and survival. The rs693_A allele influences risks of MI and mortality after MI additively with lipids. This allele shows antagonistic effects—protecting against MI risks (β = −0.18, P = 1.1 × 10−5) or increasing MI risks (β = 0.15, P = 2.8 × 10−3) and mortality after MI, in different populations. Paradoxically, increased TC concentrations can be protective against MI for the rs693_A allele carriers. Our results uncouple the influences of the same alleles on endophenotypes and phenotypes despite potential causal relationships among the latter. Our strategy reveals virtually genomewide significance for the associations of rs693 with MI (P = 5.5 × 10−8) that is contrasted with a weak estimate following the traditional, sample‐size‐centered GWAS strategy (P = 0.16) in the same sample. These results caution against the use of the traditional GWAS strategy for gaining profound insights into genetic predisposition to healthspan and lifespan.
Collapse
Affiliation(s)
- Alexander M. Kulminski
- Biodemography of Aging Research Unit; Social Science Research Institute; Duke University; Durham NC 27708-0408 USA
| | - Yelena Kernogitski
- Biodemography of Aging Research Unit; Social Science Research Institute; Duke University; Durham NC 27708-0408 USA
| | - Irina Culminskaya
- Biodemography of Aging Research Unit; Social Science Research Institute; Duke University; Durham NC 27708-0408 USA
| | - Yury Loika
- Biodemography of Aging Research Unit; Social Science Research Institute; Duke University; Durham NC 27708-0408 USA
| | - Konstantin G. Arbeev
- Biodemography of Aging Research Unit; Social Science Research Institute; Duke University; Durham NC 27708-0408 USA
| | - Olivia Bagley
- Biodemography of Aging Research Unit; Social Science Research Institute; Duke University; Durham NC 27708-0408 USA
| | - Matt Duan
- Biodemography of Aging Research Unit; Social Science Research Institute; Duke University; Durham NC 27708-0408 USA
| | - Liubov Arbeeva
- Biodemography of Aging Research Unit; Social Science Research Institute; Duke University; Durham NC 27708-0408 USA
| | - Svetlana V. Ukraintseva
- Biodemography of Aging Research Unit; Social Science Research Institute; Duke University; Durham NC 27708-0408 USA
| | - Deqing Wu
- Biodemography of Aging Research Unit; Social Science Research Institute; Duke University; Durham NC 27708-0408 USA
| | - Eric Stallard
- Biodemography of Aging Research Unit; Social Science Research Institute; Duke University; Durham NC 27708-0408 USA
| | - Anatoliy I. Yashin
- Biodemography of Aging Research Unit; Social Science Research Institute; Duke University; Durham NC 27708-0408 USA
| |
Collapse
|
13
|
Kulminski AM, He L, Culminskaya I, Loika Y, Kernogitski Y, Arbeev KG, Loiko E, Arbeeva L, Bagley O, Duan M, Yashkin A, Fang F, Kovtun M, Ukraintseva SV, Wu D, Yashin AI. Pleiotropic Associations of Allelic Variants in a 2q22 Region with Risks of Major Human Diseases and Mortality. PLoS Genet 2016; 12:e1006314. [PMID: 27832070 PMCID: PMC5104356 DOI: 10.1371/journal.pgen.1006314] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/22/2016] [Indexed: 11/21/2022] Open
Abstract
Gaining insights into genetic predisposition to age-related diseases and lifespan is a challenging task complicated by the elusive role of evolution in these phenotypes. To gain more insights, we combined methods of genome-wide and candidate-gene studies. Genome-wide scan in the Atherosclerosis Risk in Communities (ARIC) Study (N = 9,573) was used to pre-select promising loci. Candidate-gene methods were used to comprehensively analyze associations of novel uncommon variants in Caucasians (minor allele frequency~2.5%) located in band 2q22.3 with risks of coronary heart disease (CHD), heart failure (HF), stroke, diabetes, cancer, neurodegenerative diseases (ND), and mortality in the ARIC study, the Framingham Heart Study (N = 4,434), and the Health and Retirement Study (N = 9,676). We leveraged the analyses of pleiotropy, age-related heterogeneity, and causal inferences. Meta-analysis of the results from these comprehensive analyses shows that the minor allele increases risks of death by about 50% (p = 4.6×10−9), CHD by 35% (p = 8.9×10−6), HF by 55% (p = 9.7×10−5), stroke by 25% (p = 4.0×10−2), and ND by 100% (p = 1.3×10−3). This allele also significantly influences each of two diseases, diabetes and cancer, in antagonistic fashion in different populations. Combined significance of the pleiotropic effects was p = 6.6×10−21. Causal mediation analyses show that endophenotypes explained only small fractions of these effects. This locus harbors an evolutionary conserved gene-desert region with non-coding intergenic sequences likely involved in regulation of protein-coding flanking genes ZEB2 and ACVR2A. This region is intensively studied for mutations causing severe developmental/genetic disorders. Our analyses indicate a promising target region for interventions aimed to reduce risks of many major human diseases and mortality. Biomedical research and medical care are traditionally focused on individual health conditions in order to postpone, ameliorate, or prevent the accumulation of morbidities in late life. An attractive idea is to find factors, which could reduce burden of not just one disease but a major subset of them to efficiently extend healthy lifespan. Here we focus on the analyses of genetic predisposition to risks of major human age-related diseases and mortality. The analyses highlight a locus in band 2q22.3 associated with risks of coronary heart disease, heart failure, stroke, diabetes, cancer, neurodegenerative diseases, and death. Our analyses indicate a promising target region for interventions aimed to reduce risks of many major human diseases and mortality.
Collapse
Affiliation(s)
- Alexander M. Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
- * E-mail:
| | - Liang He
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Yury Loika
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Yelena Kernogitski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Konstantin G. Arbeev
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Elena Loiko
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Liubov Arbeeva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Olivia Bagley
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Matt Duan
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Arseniy Yashkin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Fang Fang
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Mikhail Kovtun
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Svetlana V. Ukraintseva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Deqing Wu
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| | - Anatoliy I. Yashin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC United States of America
| |
Collapse
|
14
|
Explicating heterogeneity of complex traits has strong potential for improving GWAS efficiency. Sci Rep 2016; 6:35390. [PMID: 27739495 PMCID: PMC5064392 DOI: 10.1038/srep35390] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 09/28/2016] [Indexed: 12/11/2022] Open
Abstract
Common strategy of genome-wide association studies (GWAS) relying on large samples faces difficulties, which raise concerns that GWAS have exhausted their potential, particularly for complex traits. Here, we examine the efficiency of the traditional sample-size-centered strategy in GWAS of these traits, and its potential for improvement. The paper focuses on the results of the four largest GWAS meta-analyses of body mass index (BMI) and lipids. We show that just increasing sample size may not make p-values of genetic effects in large (N > 100,000) samples smaller but can make them larger. The efficiency of these GWAS, defined as ratio of the log-transformed p-value to the sample size, in larger samples was larger than in smaller samples for a small fraction of loci. These results emphasize the important role of heterogeneity in genetic associations with complex traits such as BMI and lipids. They highlight the substantial potential for improving GWAS by explicating this role (affecting 11–79% of loci in the selected GWAS), especially the effects of biodemographic processes, which are heavily underexplored in current GWAS and which are important sources of heterogeneity in the various study populations. Further progress in this direction is crucial for efficient use of genetic discoveries in health care.
Collapse
|
15
|
He L, Kernogitski Y, Kulminskaya I, Loika Y, Arbeev KG, Loiko E, Bagley O, Duan M, Yashkin A, Ukraintseva SV, Kovtun M, Yashin AI, Kulminski AM. Pleiotropic Meta-Analyses of Longitudinal Studies Discover Novel Genetic Variants Associated with Age-Related Diseases. Front Genet 2016; 7:179. [PMID: 27790247 PMCID: PMC5061751 DOI: 10.3389/fgene.2016.00179] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/21/2016] [Indexed: 01/31/2023] Open
Abstract
Age-related diseases may result from shared biological mechanisms in intrinsic processes of aging. Genetic effects on age-related diseases are often modulated by environmental factors due to their little contribution to fitness or are mediated through certain endophenotypes. Identification of genetic variants with pleiotropic effects on both common complex diseases and endophenotypes may reveal potential conflicting evolutionary pressures and deliver new insights into shared genetic contribution to healthspan and lifespan. Here, we performed pleiotropic meta-analyses of genetic variants using five NIH-funded datasets by integrating univariate summary statistics for age-related diseases and endophenotypes. We investigated three groups of traits: (1) endophenotypes such as blood glucose, blood pressure, lipids, hematocrit, and body mass index, (2) time-to-event outcomes such as the age-at-onset of diabetes mellitus (DM), cancer, cardiovascular diseases (CVDs) and neurodegenerative diseases (NDs), and (3) both combined. In addition to replicating previous findings, we identify seven novel genome-wide significant loci (< 5e-08), out of which five are low-frequency variants. Specifically, from Group 2, we find rs7632505 on 3q21.1 in SEMA5B, rs460976 on 21q22.3 (1 kb from TMPRSS2) and rs12420422 on 11q24.1 predominantly associated with a variety of CVDs, rs4905014 in ITPK1 associated with stroke and heart failure, rs7081476 on 10p12.1 in ANKRD26 associated with multiple diseases including DM, CVDs, and NDs. From Group 3, we find rs8082812 on 18p11.22 and rs1869717 on 4q31.3 associated with both endophenotypes and CVDs. Our follow-up analyses show that rs7632505, rs4905014, and rs8082812 have age-dependent effects on coronary heart disease or stroke. Functional annotation suggests that most of these SNPs are within regulatory regions or DNase clusters and in linkage disequilibrium with expression quantitative trait loci, implying their potential regulatory influence on the expression of nearby genes. Our mediation analyses suggest that the effects of some SNPs are mediated by specific endophenotypes. In conclusion, these findings indicate that loci with pleiotropic effects on age-related disorders tend to be enriched in genes involved in underlying mechanisms potentially related to nervous, cardiovascular and immune system functions, stress resistance, inflammation, ion channels and hematopoiesis, supporting the hypothesis of shared pathological role of infection, and inflammation in chronic age-related diseases.
Collapse
Affiliation(s)
- Liang He
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke UniversityDurham, NC, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Alexander M. Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke UniversityDurham, NC, USA
| |
Collapse
|
16
|
Kulminski AM, Raghavachari N, Arbeev KG, Culminskaya I, Arbeeva L, Wu D, Ukraintseva SV, Christensen K, Yashin AI. Protective role of the apolipoprotein E2 allele in age-related disease traits and survival: evidence from the Long Life Family Study. Biogerontology 2016; 17:893-905. [PMID: 27447179 DOI: 10.1007/s10522-016-9659-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 07/16/2016] [Indexed: 01/12/2023]
Abstract
The apolipoprotein E (apoE) is a classic example of a gene exhibiting pleiotropism. We examine potential pleiotropic associations of the apoE2 allele in three biodemographic cohorts of long-living individuals, offspring, and spouses from the Long Life Family Study, and intermediate mechanisms, which can link this allele with age-related phenotypes. We focused on age-related macular degeneration, bronchitis, asthma, pneumonia, stroke, creatinine, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol, diseases of heart (HD), cancer, and survival. Our analysis detected favorable associations of the ε2 allele with lower LDL-C levels, lower risks of HD, and better survival. The ε2 allele was associated with LDL-C in each gender and biodemographic cohort, including long-living individuals, offspring, and spouses, resulting in highly significant association in the entire sample (β = -7.1, p = 6.6 × 10-44). This allele was significantly associated with HD in long-living individuals and offspring (relative risk [RR] = 0.60, p = 3.1 × 10-6) but this association was not mediated by LDL-C. The protective effect on survival was specific for long-living women but it was not explained by LDL-C and HD in the adjusted model (RR = 0.70, p = 2.1 × 10-2). These results show that ε2 allele may favorably influence LDL-C, HD, and survival through three mechanisms. Two of them (HD- and survival-related) are pronounced in the long-living parents and their offspring; the survival-related mechanism is also sensitive to gender. The LDL-C-related mechanism appears to be independent of these factors. Insights into mechanisms linking ε2 allele with age-related phenotypes given biodemographic structure of the population studied may benefit translation of genetic discoveries to health care and personalized medicine.
Collapse
Affiliation(s)
- Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708-0408, USA.
| | - Nalini Raghavachari
- National Institute on Aging, 31 Center Drive, MSC 2292, Bethesda, MD, 20892, USA
| | - Konstantin G Arbeev
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708-0408, USA
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708-0408, USA
| | - Liubov Arbeeva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708-0408, USA
| | - Deqing Wu
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708-0408, USA
| | - Svetlana V Ukraintseva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708-0408, USA
| | - Kaare Christensen
- The Danish Aging Research Center, University of Southern Denmark, 5000, Odense C, Denmark
- Department of Clinical Genetics and Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000, Odense C, Denmark
| | - Anatoliy I Yashin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708-0408, USA
| |
Collapse
|
17
|
Kulminski AM, Arbeev KG, Culminskaya I, Ukraintseva SV, Stallard E, Province MA, Yashin AI. Trade-offs in the effects of the apolipoprotein E polymorphism on risks of diseases of the heart, cancer, and neurodegenerative disorders: insights on mechanisms from the Long Life Family Study. Rejuvenation Res 2016; 18:128-35. [PMID: 25482294 DOI: 10.1089/rej.2014.1616] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The lack of evolutionary established mechanisms linking genes to age-related traits makes the problem of genetic susceptibility to health span inherently complex. One complicating factor is genetic trade-off. Here we focused on long-living participants of the Long Life Family Study (LLFS), their offspring, and spouses to: (1) Elucidate whether trade-offs in the effect of the apolipoprotein E e4 allele documented in the Framingham Heart Study (FHS) are a more general phenomenon, and (2) explore potential mechanisms generating age- and gender-specific trade-offs in the effect of the e4 allele on cancer, diseases of the heart, and neurodegenerative disorders assessed retrospectively in the LLFS populations. The e4 allele can diminish risks of cancer and diseases of the heart and confer risks of diseases of the heart in a sex-, age-, and LLFS-population-specific manner. A protective effect against cancer is seen in older long-living men and, potentially, their sons (>75 years, relative risk [RR]>75=0.48, p=0.086), which resembles our findings in the FHS. The protective effect against diseases of the heart is limited to long-living older men (RR>76=0.50, p=0.016), as well. A detrimental effect against diseases of the heart is characteristic for a normal LLFS population of male spouses and is specific for myocardial infarction (RR=3.07, p=2.1×10(-3)). These trade-offs are likely associated with two inherently different mechanisms, including disease-specific (detrimental; characteristic for a normal male population) and systemic, aging-related (protective; characteristic for older long-living men) mechanisms. The e4 allele confers risks of neurological disorders in men and women (RR=1.98, p=0.046). The results highlight the complex role of the e4 allele in genetic susceptibility to health span.
Collapse
|
18
|
Kulminski AM, Culminskaya I, Arbeev KG, Arbeeva L, Ukraintseva SV, Stallard E, Wu D, Yashin AI. Birth Cohort, Age, and Sex Strongly Modulate Effects of Lipid Risk Alleles Identified in Genome-Wide Association Studies. PLoS One 2015; 10:e0136319. [PMID: 26295473 PMCID: PMC4546650 DOI: 10.1371/journal.pone.0136319] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 08/02/2015] [Indexed: 02/07/2023] Open
Abstract
Insights into genetic origin of diseases and related traits could substantially impact strategies for improving human health. The results of genome-wide association studies (GWAS) are often positioned as discoveries of unconditional risk alleles of complex health traits. We re-analyzed the associations of single nucleotide polymorphisms (SNPs) associated with total cholesterol (TC) in a large-scale GWAS meta-analysis. We focused on three generations of genotyped participants of the Framingham Heart Study (FHS). We show that the effects of all ten directly-genotyped SNPs were clustered in different FHS generations and/or birth cohorts in a sex-specific or sex-unspecific manner. The sample size and procedure-therapeutic issues play, at most, a minor role in this clustering. An important result was clustering of significant associations with the strongest effects in the youngest, or 3rd Generation, cohort. These results imply that an assumption of unconditional connections of these SNPs with TC is generally implausible and that a demographic perspective can substantially improve GWAS efficiency. The analyses of genetic effects in age-matched samples suggest a role of environmental and age-related mechanisms in the associations of different SNPs with TC. Analysis of the literature supports systemic roles for genes for these SNPs beyond those related to lipid metabolism. Our analyses reveal strong antagonistic effects of rs2479409 (the PCSK9 gene) that cautions strategies aimed at targeting this gene in the next generation of lipid drugs. Our results suggest that standard GWAS strategies need to be advanced in order to appropriately address the problem of genetic susceptibility to complex traits that is imperative for translation to health care.
Collapse
Affiliation(s)
- Alexander M. Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
- * E-mail:
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
| | - Konstantin G. Arbeev
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
| | - Liubov Arbeeva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
| | - Svetlana V. Ukraintseva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
| | - Eric Stallard
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
| | - Deqing Wu
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
| | - Anatoliy I. Yashin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
| |
Collapse
|
19
|
Cohen AA, Milot E, Li Q, Bergeron P, Poirier R, Dusseault-Bélanger F, Fülöp T, Leroux M, Legault V, Metter EJ, Fried LP, Ferrucci L. Detection of a novel, integrative aging process suggests complex physiological integration. PLoS One 2015; 10:e0116489. [PMID: 25761112 PMCID: PMC4356614 DOI: 10.1371/journal.pone.0116489] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 12/10/2014] [Indexed: 12/21/2022] Open
Abstract
Many studies of aging examine biomarkers one at a time, but complex systems theory and network theory suggest that interpretations of individual markers may be context-dependent. Here, we attempted to detect underlying processes governing the levels of many biomarkers simultaneously by applying principal components analysis to 43 common clinical biomarkers measured longitudinally in 3694 humans from three longitudinal cohort studies on two continents (Women's Health and Aging I & II, InCHIANTI, and the Baltimore Longitudinal Study on Aging). The first axis was associated with anemia, inflammation, and low levels of calcium and albumin. The axis structure was precisely reproduced in all three populations and in all demographic sub-populations (by sex, race, etc.); we call the process represented by the axis "integrated albunemia." Integrated albunemia increases and accelerates with age in all populations, and predicts mortality and frailty--but not chronic disease--even after controlling for age. This suggests a role in the aging process, though causality is not yet clear. Integrated albunemia behaves more stably across populations than its component biomarkers, and thus appears to represent a higher-order physiological process emerging from the structure of underlying regulatory networks. If this is correct, detection of this process has substantial implications for physiological organization more generally.
Collapse
Affiliation(s)
- Alan A. Cohen
- Groupe de recherche PRIMUS, Department of Family Medicine, University of Sherbrooke, 3001 12e Ave N, Sherbrooke, QC, J1H 5N4, Canada
| | - Emmanuel Milot
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351, boul. des Forges, C.P. 500, Trois-Rivières, QC, G9A 5H7, Canada
| | - Qing Li
- Groupe de recherche PRIMUS, Department of Family Medicine, University of Sherbrooke, 3001 12e Ave N, Sherbrooke, QC, J1H 5N4, Canada
| | - Patrick Bergeron
- Groupe de recherche PRIMUS, Department of Family Medicine, University of Sherbrooke, 3001 12e Ave N, Sherbrooke, QC, J1H 5N4, Canada
| | - Roxane Poirier
- Department of Biology, University of Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, QC, J1K 2R1, Canada
| | - Francis Dusseault-Bélanger
- Department of Mathematics, University of Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, QC, J1K 2R1, Canada
| | - Tamàs Fülöp
- Department of Geriatrics, University of Sherbrooke, 3001 12e Ave N, Sherbrooke, QC, J1H 5N4, Canada
| | - Maxime Leroux
- Economics Department, ESG, Université du Québec à Montréal, 315 rue Sainte-Catherine Est, Montréal, QC, H2X 3X2, Canada
| | - Véronique Legault
- Groupe de recherche PRIMUS, Department of Family Medicine, University of Sherbrooke, 3001 12e Ave N, Sherbrooke, QC, J1H 5N4, Canada
| | - E. Jeffrey Metter
- Translational Gerontology Branch, Longitudinal Studies Section, National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital, 3001 S. Hanover Street, Baltimore, Maryland 21225, United States of America
| | - Linda P. Fried
- Mailman School of Public Health, Columbia University, 722 W. 168th Street, R1408, New York, New York 10032, United States of America
| | - Luigi Ferrucci
- Translational Gerontology Branch, Longitudinal Studies Section, National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital, 3001 S. Hanover Street, Baltimore, Maryland 21225, United States of America
| |
Collapse
|
20
|
Corella D, Ordovás JM. Aging and cardiovascular diseases: the role of gene-diet interactions. Ageing Res Rev 2014; 18:53-73. [PMID: 25159268 DOI: 10.1016/j.arr.2014.08.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 08/15/2014] [Accepted: 08/18/2014] [Indexed: 12/21/2022]
Abstract
In the study of longevity, increasing importance is being placed on the concept of healthy aging rather than considering the total number of years lived. Although the concept of healthy lifespan needs to be defined better, we know that cardiovascular diseases (CVDs) are the main age-related diseases. Thus, controlling risk factors will contribute to reducing their incidence, leading to healthy lifespan. CVDs are complex diseases influenced by numerous genetic and environmental factors. Numerous gene variants that are associated with a greater or lesser risk of the different types of CVD and of intermediate phenotypes (i.e., hypercholesterolemia, hypertension, diabetes) have been successfully identified. However, despite the close link between aging and CVD, studies analyzing the genes related to human longevity have not obtained consistent results and there has been little coincidence in the genes identified in both fields. The APOE gene stands out as an exception, given that it has been identified as being relevant in CVD and longevity. This review analyzes the genomic and epigenomic factors that may contribute to this, ranging from identifying longevity genes in model organisms to the importance of gene-diet interactions (outstanding among which is the case of the TCF7L2 gene).
Collapse
|
21
|
Kulminski AM, Arbeev KG, Culminskaya I, Arbeeva L, Ukraintseva SV, Stallard E, Christensen K, Schupf N, Province MA, Yashin AI. Age, gender, and cancer but not neurodegenerative and cardiovascular diseases strongly modulate systemic effect of the Apolipoprotein E4 allele on lifespan. PLoS Genet 2014; 10:e1004141. [PMID: 24497847 PMCID: PMC3907310 DOI: 10.1371/journal.pgen.1004141] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/06/2013] [Indexed: 02/04/2023] Open
Abstract
Enduring interest in the Apolipoprotein E (ApoE) polymorphism is ensured by its evolutionary-driven uniqueness in humans and its prominent role in geriatrics and gerontology. We use large samples of longitudinally followed populations from the Framingham Heart Study (FHS) original and offspring cohorts and the Long Life Family Study (LLFS) to investigate gender-specific effects of the ApoE4 allele on human survival in a wide range of ages from midlife to extreme old ages, and the sensitivity of these effects to cardiovascular disease (CVD), cancer, and neurodegenerative disorders (ND). The analyses show that women's lifespan is more sensitive to the e4 allele than men's in all these populations. A highly significant adverse effect of the e4 allele is limited to women with moderate lifespan of about 70 to 95 years in two FHS cohorts and the LLFS with relative risk of death RR = 1.48 (p = 3.6×10−6) in the FHS cohorts. Major human diseases including CVD, ND, and cancer, whose risks can be sensitive to the e4 allele, do not mediate the association of this allele with lifespan in large FHS samples. Non-skin cancer non-additively increases mortality of the FHS women with moderate lifespans increasing the risks of death of the e4 carriers with cancer two-fold compared to the non-e4 carriers, i.e., RR = 2.07 (p = 5.0×10−7). The results suggest a pivotal role of non-sex-specific cancer as a nonlinear modulator of survival in this sample that increases the risk of death of the ApoE4 carriers by 150% (p = 5.3×10−8) compared to the non-carriers. This risk explains the 4.2 year shorter life expectancy of the e4 carriers compared to the non-carriers in this sample. The analyses suggest the existence of age- and gender-sensitive systemic mechanisms linking the e4 allele to lifespan which can non-additively interfere with cancer-related mechanisms. Discovering genetic origins of healthspan and lifespan could lead to breakthroughs in increasing the years of healthy and long life. In this paper we characterize the association of the e4 allele of the well-studied ApoE gene with lifespan in two generations of participants of large longitudinal studies, the Framingham Heart Study and the Long Life Family Study, and investigate the role of major human diseases such as cardiovascular disease, cancer, and neurodegenerative disorders in this association. This wide range of systemic analyses is possible given the large sample with directly genotyped ApoE polymorphism available from these studies (N = 9841, with 2557 deaths). The analyses show that women's lifespan is more sensitive to the e4 allele than men's in these populations. However, the strongly adverse effect of the e4 allele is not observed for all women, but only for those 70 to 95 years old. Cardiovascular disease, cancer, and neurodegenerative disorders do not mediate the association of the e4 allele with lifespan. However, cancer, but not cardiovascular and neurodegenerative diseases, non-additively enhances this effect resulting in 4.2 years of difference in mean lifespan for the e4 allele carriers compared to the non-carriers.
Collapse
Affiliation(s)
- Alexander M. Kulminski
- Center for Population Health and Aging, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Science and Policy, Duke University, Durham, North Carolina, United States of America
- Social Science Research Institute, Duke University, Durham, North Carolina, United States of America
- * E-mail:
| | - Konstantin G. Arbeev
- Center for Population Health and Aging, Duke University, Durham, North Carolina, United States of America
- Social Science Research Institute, Duke University, Durham, North Carolina, United States of America
| | - Irina Culminskaya
- Center for Population Health and Aging, Duke University, Durham, North Carolina, United States of America
- Social Science Research Institute, Duke University, Durham, North Carolina, United States of America
| | - Liubov Arbeeva
- Center for Population Health and Aging, Duke University, Durham, North Carolina, United States of America
| | - Svetlana V. Ukraintseva
- Center for Population Health and Aging, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Science and Policy, Duke University, Durham, North Carolina, United States of America
- Social Science Research Institute, Duke University, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University, Durham, North Carolina, United States of America
| | - Eric Stallard
- Center for Population Health and Aging, Duke University, Durham, North Carolina, United States of America
- Social Science Research Institute, Duke University, Durham, North Carolina, United States of America
| | - Kaare Christensen
- The Danish Aging Research Center, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics and Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, New York, United States of America
| | - Michael A. Province
- Washington University School of Medicine, Division of Statistical Genomics, St. Louis, Missouri, United States of America
| | - Anatoli I. Yashin
- Center for Population Health and Aging, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Science and Policy, Duke University, Durham, North Carolina, United States of America
- Social Science Research Institute, Duke University, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University, Durham, North Carolina, United States of America
| |
Collapse
|