Mendelian randomization identifies blood metabolites previously linked to midlife cognition as causal candidates in Alzheimer’s disease

There are currently no disease-modifying treatments for Alzheimer’s disease (AD), and an understanding of preclinical causal biomarkers to help target disease pathogenesis in the earliest phases remains elusive. Here, we investigated whether 19 metabolites previously associated with midlife cognition—a preclinical predictor of AD—translate to later clinical risk, using Mendelian randomization (MR) to tease out AD-specific causal relationships. Summary statistics from the largest genome-wide association studies (GWASs) for AD and metabolites were used to perform bidirectional univariable MR. Bayesian model averaging (BMA) was additionally performed to address high correlation between metabolites and identify metabolite combinations that may be on the AD causal pathway. Univariable MR indicated four extra-large high-density lipoproteins (XL.HDL) on the causal pathway to AD: free cholesterol (XL.HDL.FC: 95% CI = 0.78 to 0.94), total lipids (XL.HDL.L: 95% CI = 0.80 to 0.97), phospholipids (XL.HDL.PL: 95% CI = 0.81 to 0.97), and concentration of XL.HDL particles (95% CI = 0.79 to 0.96), significant at an adjusted P < 0.009. MR–BMA corroborated XL.HDL.FC to be among the top three causal metabolites, in addition to total cholesterol in XL.HDL (XL.HDL.C) and glycoprotein acetyls (GP). Both XL.HDL.C and GP demonstrated suggestive univariable evidence of causality (P < 0.05), and GP successfully replicated within an independent dataset. This study offers insight into the causal relationship between metabolites demonstrating association with midlife cognition and AD. It highlights GP in addition to several XL.HDLs—particularly XL.HDL.FC—as causal candidates warranting further investigation. As AD pathology is thought to develop decades prior to symptom onset, expanding on these findings could inform risk reduction strategies.

More than 50 million people worldwide currently live with dementia, and with an aging world population, this figure is expected to increase to more than 152 million by 2050 (World Alzheimer Report 2018). The most common dementia type is Alzheimer’s disease (AD), characterized by impaired everyday function, severe cognitive decline—particularly working, episodic, and declarative memory (1)—and a range of neuropsychiatric symptoms (2). It represents a major source of global morbidity and mortality and poses significant human and economic costs (3).Disappointingly, AD drug development has proven difficult, with a 99.6% failure rate in the decade of 2002 to 2012, and this rate continues at the same low level today (4). Numerous reasons have been proposed as to why such clinical trials have failed, including incomplete understanding of true causal mechanisms and a failure to intervene early enough in the pathological cascade. It is therefore necessary to discover biomarkers that can identify individuals at high risk of developing AD and at the earliest possible stages of pathology onset. Moreover, it is important for these to be potentially modifiable so as to offer targets for preventative or therapeutic strategies.Metabolomics represents one avenue that may give a deeper insight into AD etiology. Metabolites are small molecules (<1,500 atomic mass units) with a role in metabolism (5). As the products of many biological processes, they sit at the end of the systems biology pathway and therefore represent effective intermediate phenotypes to a given disease because of their proximity to the clinical endpoint (6, 7). Due to 1) their noninvasive nature of measurement, 2) the fact that they are potentially modifiable through diet and lifestyle, and 3) the ability of many to cross the blood brain barrier, blood metabolites are both practical and valuable markers of biological processes and disease states in dementia (8).Markers of lipid metabolism have received particular attention in this context, as the impairment of lipid metabolism has been associated with AD (5, 8–11) and beta-amyloid (Aβ) burden (12, 13). Relevant to early intervention, they have also been associated with cognitive performance and brain function during normal aging (14, 15). Recently, using a large British population-based birth cohort, we investigated associations between 233 blood metabolites and both memory and processing speed at 60 to 64 y of age as well as changes in these cognitive domains from 60 to 64 to 69 y old. Associations with several metabolite classes were observed, including fatty acids (FAs), various compositions of high-density lipoproteins (HDLs), and glycoprotein acetyls (GP) (16).However, it is not yet established whether these metabolites are causally associated with dementia and AD. Using knowledge from these preclinical associations to investigate translatability to later AD risk could hold special utility in informing early treatment intervention, particularly if a causal relationship can be shown. This study therefore aims to expand our observational findings and assess whether 19 blood metabolites previously associated with late midlife cognition causally associate with later clinical AD status. Both univariable and Bayesian multivariable Mendelian randomization (MR) approaches are harnessed to interrogate independent as well as group associations, and a range of sensitivity analyses are performed to further scrutinize results. Identifying candidate blood metabolites, which are detectable preclinically and on the causal pathway to later AD diagnosis, will aid in facilitating further research into early intervention strategies and more targeted therapeutics.     

Cross-region reduction in 5-hydroxymethylcytosine in Alzheimer's disease brain

Epigenetic processes play a key role in the central nervous system and altered levels of 5-methylcytosine have been associated with a number of neurologic phenotypes, including Alzheimer's disease (AD). Recently, 3 additional cytosine modifications have been identified (5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine), which are thought to be intermediate steps in the demethylation of 5-methylcytosine to unmodified cytosine. Little is known about the frequency of these modifications in the human brain during health or disease. In this study, we used immunofluorescence to confirm the presence of each modification in human brain and investigate their cross-tissue abundance in AD patients and elderly control samples. We identify a significant AD-associated decrease in global 5-hydroxymethylcytosine in entorhinal cortex and cerebellum, and differences in 5-formylcytosine levels between brain regions. Our study further implicates a role for epigenetic alterations in AD.     

A Multiple Indicators Multiple Causes (MIMIC) model of Behavioural and Psychological Symptoms in Dementia (BPSD)

Introduction

Although there is evidence for distinct behavioural sub-phenotypes in Alzheimer's disease (AD), their inter-relationships and the effect of clinical variables on their expression have been little investigated.

Methods

We have analysed a sample of 1850 probable AD patients from the UK and Greece with 10 item Neuropsychiatric Inventory (NPI) data. We applied a Multiple Indicators Multiple Causes (MIMIC) approach to investigate the effect of MMSE, disease duration, gender, age and age of onset on the structure of a four-factor model consisting of “psychosis”, “moods”, “agitation” and “behavioural dyscontrol”.

Results

Specific clinical variables predicted the expression of individual factors. When the inter-relationship of factors is modelled, some previously significant associations are lost. For example, lower MMSE scores predict psychosis, agitation and behavioural dyscontrol factors, but psychosis and mood predict the agitation factor. Taking these associations into account MMSE scores did not predict agitation.

Conclusions

The complexity of the inter-relations between symptoms, factors and clinical variables is efficiently captured by this MIMIC model.     

A functional polymorphism of the brain derived neurotrophic factor gene and cortical anatomy in autism spectrum disorder

Autism Spectrum Disorder (ASD) is associated with both (i) post-mortem and neuroimaging evidence of abnormal cortical development, and (ii) altered signalling in Brain Derived Neurotrophic Factor (BDNF) pathways - which regulate neuroproliferative and neuroplastic processes. In healthy controls genotype at a single nucleotide polymorphism that alters BDNF signalling (Val66met) has been related to regional cortical volume. It is not known however if this influence on brain development is intact in ASD. Therefore we compared the relationship between genotype and cortical anatomy (as measured using in vivo Magnetic Resonance Imaging) in 41 people with ASD and 30 healthy controls. We measured cortical volume, and its two sole determinants - cortical thickness and surface area - which reflect differing neurodevelopmental processes. We found "Group-by-Genotype" interactions for cortical volume in medial (caudal anterior cingulate, posterior cingulate) and lateral (rostral middle, lateral orbitofrontal, pars orbitalis and pars triangularis) frontal cortices. Furthermore, within (only) these regions "Group-by-Genotype" interactions were also found for surface area. No effects were found for cortical thickness in any region. Our preliminary findings suggest that people with ASD have differences from controls in the relationship between BDNF val66met genotype and regional (especially frontal) cortical volume and surface area, but not cortical thickness. Therefore alterations in the relationship between BDNF val66met genotype and surface area in ASD may drive the findings for volume. If correct, this suggests ASD is associated with a distorted relationship between BDNF val66met genotype and the determinants of regional cortical surface area - gyrification and/or sulcal positioning.     

Her2 negative luminal breast carcinoma and Ki-67 evaluation

AimTo determine the degree of inter-observer variability in defining the percentage of Ki-67 immunohistochemical expression in breast carcinoma cases and to investigate the validity of using the cut-point of 14% for the administration of adjuvant treatment in luminal B (Her2 negative) carcinomas.Materials and methods99 ER, PR positive, Her2 negative breast carcinomas were consecutively selected from the Pathology files of “IASO” Women's Hospital. Ki-67 immunostaining was evaluated by four pathologists from four different institutions.ResultsConcerning the whole study group, the inter-observer agreement was substantial. Subgroup analysis upon the cases were at least one observer evaluated Ki-67 as being less than 14% showed that the inter-observer agreement was reduced to fair. Further analysis revealed that both below and above the clinicopathological limit of 14%, stands a “grey zone” of about ±7%, in which inter-observer agreement is weak.ConclusionThe administration of cytotoxic therapy in ER, PR positive, Her2 negative breast carcinomas featuring a Ki-67 labeling index of around 14, should be considered with caution. Probably decision-making should also take under consideration the whole morphological and biological profile of each tumor.     

Identification of cis-regulatory variation influencing protein abundance levels in human plasma

Proteins are central to almost all cellular processes, and dysregulation of expression and function is associated with a range of disorders. A number of studies in human have recently shown that genetic factors significantly contribute gene expression variation. In contrast, very little is known about the genetic basis of variation in protein abundance in man. Here, we assayed the abundance levels of proteins in plasma from 96 elderly Europeans using a new aptamer-based proteomic technology and performed genome-wide local (cis-) regulatory association analysis to identify protein quantitative trait loci (pQTL). We detected robust cis-associations for 60 proteins at a false discovery rate of 5%. The most highly significant single nucleotide polymorphism detected was rs7021589 (false discovery rate, 2.5 × 10(-12)), mapped within the gene coding sequence of Tenascin C (TNC). Importantly, we identified evidence of cis-regulatory variation for 20 previously disease-associated genes encoding protein, including variants with strong evidence of disease association show significant association with protein abundance levels. These results demonstrate that common genetic variants contribute to the differences in protein abundance levels in human plasma. Identification of pQTLs will significantly enhance our ability to discover and comprehend the biological and functional consequences of loci identified from genome-wide association study of complex traits. This is the first large-scale genetic association study of proteins in plasma measured using a novel, highly multiplexed slow off-rate modified aptamer (SOMAmer) proteomic platform.     

Association of serotonin and dopamine gene pathways with behavioral subphenotypes in dementia

Genetic association studies investigating the association between genes of serotonergic and dopaminergic systems and behavioral and psychological symptoms in dementia (BPSD) are contradictory. We have utilized 1008 probable Alzheimer's disease (AD) patients from the UK and used the 12-item Neuropsychiatric Inventory. We applied a multiple indicators-multiple causes (MIMIC) approach to investigate the effect of 11 polymorphisms on the 4 behavioral subphenotypes “psychosis”, “moods”, “agitation”, and “behavioural dyscontrol”. Significant associations were observed between the serotonin transporter gene (SERT) polymorphism STin2 and “psychosis”; the dopamine transporter gene (DAT) 3′ variable number tandem repeats (VNTR) and “agitation”; and the dopamine receptor 4 (DRD4) VNTR and “moods” factors. Direct associations were identified between the dopamine receptor 3 (DRD3) BalI polymorphism and depression; the dopamine receptor 1 (DRD1) and dopamine transporter gene 3′ VNTR polymorphisms and aberrant motor behavior; the DRD4 VNTR and sleep disturbances; and the SERT gene VNTR 5HTTLPR and apathy items. Significant interactions observed between polymorphisms suggested epistatic effects and interactions between polymorphisms and medications highlighted potential treatment response. This multiple indicators multiple causes (MIMIC) model efficiently captured the complexity of the interrelations between genetic variation, behavioral symptoms, and clinical variables.     

Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease

Alzheimer's disease (AD) is a progressive neurodegenerative disorder with considerable evidence suggesting an initiation of disease in the entorhinal cortex and hippocampus and spreading thereafter to the rest of the brain. In this study, we combine genetics and imaging data obtained from the Alzheimer's Disease Neuroimaging Initiative and the AddNeuroMed study. To identify genetic susceptibility loci for AD, we conducted a genome-wide study of atrophy in regions associated with neurodegeneration in this condition. We identified one single-nucleotide polymorphism (SNP) with a disease-specific effect associated with entorhinal cortical volume in an intron of the ZNF292 gene (rs1925690; P-value=2.6 × 10(-8); corrected P-value for equivalent number of independent quantitative traits=7.7 × 10(-8)) and an intergenic SNP, flanking the ARPP-21 gene, with an overall effect on entorhinal cortical thickness (rs11129640; P-value=5.6 × 10(-8); corrected P-value=1.7 × 10(-7)). Gene-wide scoring also highlighted PICALM as the most significant gene associated with entorhinal cortical thickness (P-value=6.7 × 10(-6)).     

Variation in DRD2 dopamine gene predicts Extraverted personality

Quantitative geneticists estimate the heritability of Extraverted personality to be around 40–60%. Theory and research which links Extraversion with variation in dopaminergic function suggests that dopaminergic genes should be a start-point for molecular genetic investigations of this trait. Recent endeavours in this area have met with some encouragement but also setbacks. In this study, we investigate the relationship between Extraversion and the DRD2 TaqIA/ANKK1 polymorphism in 224 university students. Presence of at least one copy of the A1 allele was associated with significantly higher Extraversion. The robustness of this finding was confirmed through bootstrap analysis. Findings are discussed in relation to the broader literature, in particular, methodological issues which may have obscured this finding in previous research.