Olfactory function is affected by demographic, cognitive, and genetic factors. In the present thesis, three empirical studies investigated individual differences in olfactory ability. Study I explored demographic and cognitive correlates in common olfactory tasks; odor detection, odor discrimination, and odor identification. The results indicated that old age influenced performance negatively in all tasks, and that semantic memory proficiency and executive functioning were related to odor discrimination and odor identification performance. No cognitive influence was observed for measurements of olfactory threshold. Using population-based data, Study II investigated a potential influence of the ApoE gene on olfactory identification after controlling for health status, semantic memory, and preclinical and clinical dementia. The main finding was that the ApoE- ɛ4 allele interacted with age, such that older ɛ4-carriers had an impaired odor identification performance relative to older non-carriers. Importantly, the negative ApoE- ɛ4 effect on olfactory proficiency was independent of clinical dementia conversion within five years. Study III investigated the effects of the BDNF val66met polymorphism on olfactory change over a five-year interval, in a community dwelling sample of young and old age cohorts. The results showed that age-related decline in olfactory identification was influenced by the BDNF val66met. In middle-aged subjects, no effect of BDNF val66met was observed although older val homozygote carriers showed a selectively larger olfactory decline than the older met carriers. Overall, results suggest that the relative influence of demographic and cognitive factors vary across different olfactory tasks and that two genes (ApoE and BDNF) impact age-related deficits in odor identification. Potential theoretical and practical implications of the findings are discussed as well as potential limitations of association studies in genomics research.

abstract: The apolipoprotein E (APOE) e4 genotype is the most prevalent known genetic risk factor for Alzheimer's disease (AD). In this paper, we examined the longitudinal effect of APOE e4 on hippocampal morphometry in Alzheimer's Disease Neuroimaging Initiative (ADNI). Generally, atrophy of hippocampus has more chance occurs in AD patients who carrying the APOE e4 allele than those who are APOE e4 noncarriers. Also, brain structure and function depend on APOE genotype not just for Alzheimer's disease patients but also in health elderly individuals, so APOE genotyping is considered critical in clinical trials of Alzheimer's disease. We used a large sample of elderly participants, with the help of a new automated surface registration system based on surface conformal parameterization with holomorphic 1-forms and surface fluid registration. In this system, we automatically segmented and constructed hippocampal surfaces from MR images at many different time points, such as 6 months, 1- and 2-year follow up. Between the two different hippocampal surfaces, we did the high-order correspondences, using a novel inverse consistent surface fluid registration method. At each time point, using Hotelling's T^2 test, we found significant morphological deformation in APOE e4 carriers relative to noncarriers in the entire cohort as well as in the non-demented (pooled MCI and control) subjects, affecting the left hippocampus more than the right, and this effect was more pronounced in e4 homozygotes than heterozygotes. / Dissertation/Thesis / Masters Thesis Computer Science 2015

abstract: Alzheimer’s disease (AD), despite over a century of research, does not have a clearly defined pathogenesis for the sporadic form that makes up the majority of disease incidence. A variety of correlative risk factors have been identified, including the three isoforms of apolipoprotein E (ApoE), a cholesterol transport protein in the central nervous system. ApoE ε3 is the wild-type variant with no effect on risk. ApoE ε2, the protective and most rare variant, reduces risk of developing AD by 40%. ApoE ε4, the risk variant, increases risk by 3.2-fold and 14.9-fold for heterozygous and homozygous representation respectively. Study of these isoforms has been historically complex, but the advent of human induced pluripotent stem cells (hiPSC) provides the means for highly controlled, longitudinal in vitro study. The effect of ApoE variants can be further elucidated using this platform by generating isogenic hiPSC lines through precise genetic modification, the objective of this research. As the difference between alleles is determined by two cytosine-thymine polymorphisms, a specialized CRISPR/Cas9 system for direct base conversion was able to be successfully employed. The base conversion method for transitioning from the ε3 to ε2 allele was first verified using the HEK293 cell line as a model with delivery via electroporation. Following this verification, the transfection method was optimized using two hiPSC lines derived from ε4/ε4 patients, with a lipofection technique ultimately resulting in successful base conversion at the same site verified in the HEK293 model. Additional research performed included characterization of the pre-modification genotype with respect to likely off-target sites and methods of isolating clonal variants. / Dissertation/Thesis / Masters Thesis Bioengineering 2017

Introduction: Spontaneous abortion (SA) is the most common complication in pregnancy. The aim of the study was to investigate the causality of selected genetic factors - Apolipoprotein E (Apo E) gene polymorphisms, factor V Leiden (FVL), Prothrombin (PT G20210A) and nongenetics factors - Thyroid stimulating hormone (TSH), free thyroxine (fT4), antibodies against thyroid peroxidase (a-TPO) in the role of early SA. Materials and methods: For genotyping of APO E polymorphism was used PCR-RFLP. The detection of mutations in genes FV and FII was performed using by HRM. Laboratory markers of thyroid (TSH, a-TPO and fT4) were determined by an automated analyzer using chemiluminescent immunoassay. Results: APOE genotypes of investigated group of 410 samples abortioned embryonic/ fetal tissues were not significantly different from 2 606 adult controls (P = 0.653). In observed infertile group of 75 women with isolated SA was FVL detected in heterozygous constitution with a prevalence of 12 %. The prevalence of FVL in a group of women with early insulated SA was significantly higher than 76 controls (12 % vs. 2.6 %, P = 0.031). The difference of PTG20210A prevalence between women with isolated SA and controls was not significant (4 % vs. 5.3 %, P = 1). The prevalence of elevated TSH levels (higher than 2.5...

Objective To assess potential effects of variants in six lipid modulating genes (SORT1, HMGCR, MLXIPL, FADS2, APOE and MAFB) on early development of dyslipidemia independent of the degree of obesity in children, we investigated their association with total (TC), low density lipoprotein (LDL-C), high density lipoprotein (HDL-C) cholesterol and triglyceride (TG) levels in 594 children. Furthermore, we evaluated the expression profile of the candidate genes during human adipocyte differentiation. Results Expression of selected genes increased 101 to >104 fold during human adipocyte differentiation, suggesting a potential link with adipogenesis. In genetic association studies adjusted for age, BMI SDS and sex, we identified significant associations for rs599839 near SORT1 with TC and LDL-C and for rs4420638 near APOE with TC and LDL-C. We performed Bayesian modelling of the combined lipid phenotype of HDL-C, LDL-C and TG to identify potentially causal polygenic effects on this multi-dimensional phenotype and considering obesity, age and sex as a-priori modulating factors. This analysis confirmed that rs599839 and rs4420638 affect LDL-C. Conclusion We show that lipid modulating genes are dynamically regulated during adipogenesis and that variants near SORT1 and APOE influence lipid levels independent of obesity in children. Bayesian modelling suggests causal effects of these variants.

No study has focussed on the longitudinal effect of APOE-ε4 genotype on the logical memory delayed recall total (LDELTOTAL) score in late-onset Alzheimer’s disease (AD). The LDELTOTAL scores were collected at baseline, 12, 24, 36 and 48 months from 382 participants with AD, 503 with cognitive normal (CN), 1293 with mild cognitive impairment (MCI) in the Alzheimer's Disease Neuroimaging Initiative (ADNI). A linear mixed model (LMM) was used to investigate the effect of APOE-ε4 on the longitudinal changes in the LDELTOTAL scores adjusted for age, gender, education and baseline Mini Mental State Examination score. There were significant differences in LDELTOTAL scores among AD, CN, and MCI (P < 0.0001) and among APOE-ε4 alleles at baseline (P < 0.0001). In the multivariable LMM, elders with 75+ years (P = 0.0051), females (P < 0.0001), lower education (P < 0.0001), AD and MCI (both P values < 0.0001) were associated with decreased LDELTOTAL values, while the individuals with 1 or 2 APOE-ε4 allele revealed significantly lower LDELTOTAL scores (both P values <0.0001) compared with individuals without APOE-ε4 allele. Further, APOE-ε4 alleles had significant interactions with four follow-up visits, where all follow-up visits showed significantly higher LDELTOTAL score. In addition, gender showed interaction with age, education and APOE-ε4 with follow-up visits. Our findings provide the first evidence of the effect of APOE-ε4 genotype on the logical memory declines related to AD. Further, APOE-ε4 alleles showed interactions with gender and follow-up visits.

Although multiple susceptibility loci for late-onset Alzheimer's disease (LOAD) have been identified, a large portion of the genetic risk for this disease remains unexplained. LOAD risk may be associated with single-nucleotide polymorphisms responsible for changes in gene expression (eSNPs). To detect eSNPs associated with LOAD, we integrated data from LOAD genome-wide association studies and expression quantitative trait loci using Sherlock (a Bayesian statistical method). We identified a cis-regulatory eSNP (rs2927438) located on chromosome 19q13.32, for which subsequent analyses confirmed the association with both LOAD risk and the expression level of several nearby genes. Importantly, rs2927438 may represent an APOE-independent LOAD eSNP according to the weak linkage disequilibrium of rs2927438 with the 2 polymorphisms (rs7412 and rs429358) defining the APOE-ε2, -ε3, and -ε4 alleles. Furthermore, rs2927438 does not influence chromatin interaction events at the APOE locus or cis-regulation of APOE expression. Further exploratory analysis revealed that rs2927438 is significantly associated with tau levels in the cerebrospinal fluid. Our findings suggest that rs2927438 may confer APOE-independent risk for LOAD.

Genome-wide association studies (GWASs) have reported numerous associations between risk variants and Alzheimer’s disease (AD). However, these associations do not necessarily indicate a causal relationship. If the risk variants can be demonstrated to be biologically functional, the possibility of a causal relationship would be increased. In this article, we reviewed all of the published GWASs to extract the genome-wide significant (p < 5×10−8) and replicated associations between risk variants and AD or AD-biomarkers. The regulatory effects of these risk variants on the expression of a novel class of non-coding RNAs (piRNAs) and protein-coding RNAs (mRNAs), the alteration of proteins caused by these variants, the associations between AD and these variants in our own sample, the expression of piRNAs, mRNAs and proteins in human brains targeted by these variants, the expression correlations between the risk genes and APOE, the pathways and networks that the risk genes belonged to, and the possible long non-coding RNAs (LncRNAs) that might regulate the risk genes were analyzed, to investigate the potential biological functions of the risk variants and explore the potential mechanisms underlying the SNP-AD associations. We found replicated and significant associations for AD or AD-biomarkers, surprisingly, only at 17 SNPs located in 11 genes/snRNAs/LncRNAs in eight genomic regions. Most of these 17 SNPs enriched some AD-related pathways or networks, and were potentially functional in regulating piRNAs and mRNAs; some SNPs were associated with AD in our sample, and some SNPs altered protein structures. Most of the protein-coding genes regulated by the risk SNPs were expressed in human brain and correlated with APOE expression. We conclude that these variants were most robust risk markers for AD, and their contributions to AD risk was likely to be causal. As expected, APOE and the lipoprotein metabolism pathway possess the highest weight among these contributions.

Among many putative genetic risk variations reported to date, the ApoE4 allele remains the most common genetic risk factor for late-onset AD, and is associated with both an increase in incidence and a decrease in age of clinical onset. The majority of ApoE is produced in the: 1) central nervous system (CNS) by astrocytes to transport lipids between cells and modulate the inflammatory response; and 2) liver, where it facilitates lipid uptake into peripheral tissues via low-density lipoprotein (LDL) receptors. Consistent with its dual roles, genetic knockout of ApoE increases the risk for atherosclerosis, but it also dramatically improves AD phenotypes in mouse models. Antisense oligonucleotide (ASO) based modulation of CNS ApoE has only marginal effects on AD phenotypes, suggesting that post-embryonic silencing of ApoE is not a viable therapeutic strategy. However, the recent development of novel CNS siRNA chemical structures enables widespread distribution and potent target silencing throughout the brain. Using this technology, we demonstrate that liver and brain ApoE pools are spatially and functionally distinct, and that complete silencing of brain, not liver, ApoE results in robust reduction of amyloid plaque formation, without impacting systemic cholesterol. Furthermore, RNAseq analysis shows minimal off target effects of the siRNAs and identifies immune modulation and metabolic alterations as potential mechanisms behind ApoE’s role in plaque formation and clearance. Moving forward, these results build upon the rationale to modulate ApoE expression and provide the technology necessary to further evaluate the impact ApoE silencing in AD and other neurodegenerative diseases

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