Single-nucleotide polymorphisms of GSK3B, GAB2 and SORL1 in late-onset Alzheimer's disease: interactions with the APOE genotype

AD-Syn-Net: systematic identification of Alzheimer's disease-associated mutation and co-mutation vulnerabilities via deep learning

Alzheimer's disease (AD) is one of the most challenging neurodegenerative diseases because of its complicated and progressive mechanisms, and multiple risk factors. Increasing research evidence demonstrates that genetics may be a key factor responsible for the occurrence of the disease. Although previous reports identified quite a few AD-associated genes, they were mostly limited owing to patient sample size and selection bias. There is a lack of comprehensive research aimed to identify AD-associated risk mutations systematically. To address this challenge, we hereby construct a large-scale AD mutation and co-mutation framework ('AD-Syn-Net'), and propose deep learning models named Deep-SMCI and Deep-CMCI configured with fully connected layers that are capable of predicting cognitive impairment of subjects effectively based on genetic mutation and co-mutation profiles. Next, we apply the customized frameworks to data sets to evaluate the importance scores of the mutations and identified mutation effectors and co-mutation combination vulnerabilities contributing to cognitive impairment. Furthermore, we evaluate the influence of mutation pairs on the network architecture to dissect the genetic organization of AD and identify novel co-mutations that could be responsible for dementia, laying a solid foundation for proposing future targeted therapy for AD precision medicine. Our deep learning model codes are available open access here: https://github.com/Pan-Bio/AD-mutation-effectors.

SORL1 Polymorphisms in Mexican Patients with Alzheimer’s Disease

The present study evaluated the risk effect of 12 Single Nucleotide Polymorphisms in the SORL1 gene in the Mexican population using Late-Onset Alzheimer’s Disease (LOAD) and control subjects. Considering APOE as the strongest genetic risk factor for LOAD, we conducted interaction analyses between single nucleotide polymorphisms (SNPs) and the APOE genotype. Methods: Patients were interviewed during their scheduled visits at neurologic and geriatric clinics from different institutions. The LOAD diagnosis included neurological, geriatric, and psychiatric examinations, as well as the medical history and neuroimaging. Polymorphisms in SORL1 were genotyped by real-time PCR in 156 subjects with LOAD and 221 controls. APOE genotype was determined in each study subject. Allelic, genotypic, and haplotypic frequencies were analyzed; an ancestry analysis was also performed. Results: The A/A genotype in rs1784933 might be associated with an increased LOAD risk. Two blocks with high degree linkage disequilibrium (LD) were identified. The first block composed by the genetic variants rs668387, rs689021 and rs641120 showed a positive interaction (mainly the rs689021) with rs1784933 polymorphism. Moreover, we found a significant association between the APOE ε4 allele carriers and the variant rs2070045 located in the second LD block. Conclusion: The rs1784933 polymorphism is associated with LOAD in Mexican patients. In addition, the presence of APOE ε4 allele and SORL1 variants could represent a genetic interaction effect that favors LOAD risk in the Mexican population. SNPs have been proposed as genetic markers associated with the development of LOAD that can support the clinical diagnosis. Future molecular studies could help understand sporadic Alzheimer’s Disease (AD) among the Mexican population, where currently there is a sub-estimate number in terms of disease frequency and incidence.

Genetics of dementia: insights from Latin America

Alzheimer’s disease (AD) and frontotemporal dementia (FTD) are neurodegenerative disorders that result in a significant burden to both patients and caregivers. By 2050, the number of people with dementia in Latin America will increase 4-fold. A deep understanding of the relevant genetic factors of AD and FTD is fundamental to tackle this reality through prevention. A review of different genetic variants that cause AD or FTD in Latin America was conducted. We searched Medline and PubMed databases using the keywords “Alzheimer’s disease,” “frontotemporal dementia,” “mutation,” “America,” and “Latin America,” besides specific Latin American countries. Forty-five items were chosen and analyzed. PSEN1 mutations are the commonest cause of genetic early-onset Alzheimer’s disease (EOAD), followed by PSEN2 and APP mutations. Genetic FTD can be mainly explained by GRN and MAPT mutations, as well as C9orf72 G4C2 repeat expansion. APOE ε4 can modify the prevalence and incidence of late-onset Alzheimer’s disease (LOAD), in addition to the cognitive performance in affected carriers.

The impact of GAB2 genetic variations on cerebrospinal fluid markers in Alzheimer's disease

BACKGROUND

Growth factor receptor-bound protein-associated binding protein 2 gene (GAB2) has been regarded as one of the susceptibility gene associated with Alzheimer's disease (AD). However, the role of GAB2 polymorphisms on cerebrospinal fluid (CSF) proteins in AD continuum remains unclear.

METHODS

We evaluated the connection between four single nucleotide polymorphisms (SNPs) of GAB2 and AD-related CSF biomarkers including amyloid β (Aβ), total tau (T-tau) and phosphorylated tau (P-tau) level in 627 Alzheimer's Disease Neuroimaging Initiative (ADNI) subjects.

RESULTS

rs1385600 and rs1007837 were significantly associated with all the three biomarkers in CSF (rs1385600: Aβ Pc =0.0112, T-tau Pc =0.0356, P-tau Pc =0.0116; rs1007837: Aβ Pc =0.0058, T-tau Pc =0.0278, P-tau Pc =0.0231). rs2373115 only showed significant association with Aβ and P-tau (Aβ, Pc=0.0398, P-tau, Pc=0.0329). rs10793294 showed no significant association with all the three biomarkers.

CONCLUSIONS

Our study suggested that GAB2 variants were significantly associated with the level of the three CSF biomarkers, which further supported that GAB2 genetic variation modulates AD risk via the alteration of both Aβ and tau pathology.

Genome-wide association and interaction studies of CSF T-tau/Aβ42 ratio in ADNI cohort

The pathogenic relevance in Alzheimer's disease (AD) presents a decrease of cerebrospinal fluid amyloid-ß₄₂ (Aß₄₂) burden and an increase in cerebrospinal fluid total tau (T-tau) levels. In this work, we performed genome-wide association study (GWAS) and genome-wide interaction study of T-tau/Aß₄₂ ratio as an AD imaging quantitative trait on 843 subjects and 563,980 single-nucleotide polymorphisms (SNPs) in ADNI cohort. We aim to identify not only SNPs with significant main effects but also SNPs with interaction effects to help explain "missing heritability". Linear regression method was used to detect SNP-SNP interactions among SNPs with uncorrected p-value ≤0.01 from the GWAS. Age, gender, and diagnosis were considered as covariates in both studies. The GWAS results replicated the previously reported AD-related genes APOE, APOC1, and TOMM40, as well as identified 14 novel genes, which showed genome-wide statistical significance. Genome-wide interaction study revealed 7 pairs of SNPs meeting the cell-size criteria and with bonferroni-corrected p-value ≤0.05. As we expect, these interaction pairs all had marginal main effects but explained a relatively high-level variance of T-tau/Aß₄₂, demonstrating their potential association with AD pathology.

Associations of rs3740677 within GAB2 Gene with LOAD in Chinese Han Population

GRB2-associated binding protein 2 (GAB2) has been identified as a crucial factor in Alzheimer's disease (AD), and ten common variants within GAB2 have been detected to be associated with AD onset risk in genome-wide association studies (GWAS). Here, we first screened a common locus (rs3740677) in 3' UTR of GAB2 sequence which is targeted by the miRNA-185 and initiatively explored the probable associations of rs3740677 with risk for late-onset AD (LOAD) in a large scale case-control study from Chinese Han populations (992 LOAD patients and 1358 healthy subjects). Eventually, the genotype (P = 0.024) and allele (P = 0.008) distribution of rs3740677 showed significant difference between LOAD and control group, and we observed a significant association of T allele in rs3740677 with LOAD risk in multivariate analysis and it decreased the risk for LOAD (dominant: OR = 0.831, 95 % CI = 0.702-0.983, P = 0.031; additive: OR = 0.855, 95 % CI = 0.745-0.983, P = 0.027) adjusted for age, gender, and APOE ε4 status. Our study further confirmed the association of GAB2 and AD. However, the absolute and correct association of rs3740677 with AD still required more investigations in diverse regions and ethnics.

Meta-analysis of the Association between Alzheimer Disease and Variants in GAB2, PICALM, and SORL1

The genetic variants play a crucial role in the pathogenesis of Alzheimer's disease (AD), while the relationships of specific single nucleotide polymorphisms (SNPs) with AD are still controversial. We performed the meta-analysis to obtain a more precise estimation of whether growth factor receptor-bound protein-associated binding protein 2 (GAB2), phosphatidylinositol binding clathrin assembly protein (PICALM), and sortilin-related receptor (SORL1) variants are associated with AD. Databases including PubMed, Embase, and Cochrane Library were searched to find relevant studies. Cochran's Q-statistic and I ² were used to assess the heterogeneity among the included studies. Odds ratios (OR) and 95 % confidence intervals (95 % CIs) were conducted to evaluate the association between the SNP and the susceptibility to AD. Publication bias was estimated by funnel plots. All of the statistical analyses were implemented using R Version 3.2.1 software. A total of 35 case-control studies involving 15 SNPs were included. There was no significant association between SNPs of GAB2 rs2373115 (G > T) and PICALM rs541458 (C > T) and AD. The allele T of rs3851179 in PICALM was associated with a 13 % increase in the risk of AD. Seven SNPs on SORL1 were significantly associated with AD. Four SNPs, including rs1010159*T, rs641120*A, rs668387*T, and rs689021*A, were associated with a decreased risk of AD, while the other three SNPs, including rs12285364*T, rs2070045*G, and rs2282649*T, were all associated with an increased risk of AD. The results of the present study suggested that multiple gene variants were associated with AD. The SNP of rs3851179 (PICALM), rs12285364 (SORL1), rs2070045 (SORL1), and rs2282649 (SORL1) was associated with an increased risk of AD, whereas SORL1 rs1010159, rs641120, rs668387, and rs689021 were associated with a decreased risk of AD.

Meta-analysis of association between the genetic polymorphisms on chromosome 11q and Alzheimer's disease susceptibility

Alzheimer's disease (AD) is a neurodegenerative disease mostly occurred in the elderly. Genetic mutation is one of well-established risk factors for AD. Several polymorphisms on chromosome 11q were reported to be associated with AD susceptibility. Hence we performed a meta-analysis to systematically assess the association between the most-reported polymorphisms on chromosome 11q (rs10793294, rs7115850, rs7101429, rs4945261, rs2373115, rs670142, rs610932, rs541458 and rs3851179) and AD risk. A comprehensive literature search in the electronic databases was performed to identify all eligible studies. The pooled odds ratios (OR) and 95% confidence intervals (95% CI) were calculated to evaluate the association between 11q variants and AD risk by using the allelic model. Sensitivity analysis was carried out to analyze the influence of single study on the overall results. Begg's funnel plots and Egger's test were used to assess the publication biases among studies. All the statistical analyses were conducted by using STATA 12.0 Software (Stata Corp, College Station, TX, USA). A total of 35 eligible articles were included in our meta-analysis. Our data showed that the polymorphism of rs610932 were significantly associated with lower AD risk with a pooled OR of 0.88 (95% CI: 0.84-0.92, P=0.005). The other SNPs of rs494526 (OR=0.83, 95% CI: 0.65-1.00, P<0.001), rs2373115 (OR=0.85, 95% CI: 0.75-0.95, P<0.001) and rs670139 (OR=1.09, 95% CI: 1.05-1.12, P=0.554) were shown to be correlated with lower AD risk. Subgroup analysis revealed a similar result in Caucasians. But only the rs610932 polymorphism was found to be associated with lower AD risk in Asians. The polymorphism of rs610932 was shown to be a risk factor for AD while the other three genetic variants (rs494526, rs2373115 and rs610932) may act as protective factors against AD.

Common Polymorphisms in the GSK3β Gene May Contribute to the Pathogenesis of Alzheimer Disease: A Meta-Analysis

OBJECTIVE

Although it is well known that GSK3β participates in the proliferation and survival of various tumor cells, its role in diseases of the central nervous system has been sparsely documented. In the past few years, studies regarding the relationship between GSK3β rs334558 T>C and rs6438552 C>T polymorphisms and Alzheimer disease (AD) risk have yielded contradictory results. As such, this meta-analysis seeks to satisfy the need to further investigate this relationship.

METHODS

In this research, published studies regarding the association of GSK3β rs6438552 and rs334558 mutation with AD risk was systematically assessed. Studies were retrieved from MEDLINE, Science Citation Index, the Cochrane Library, PubMed, Embase, CINAHL, Current Contents Index, Chinese Biomedical, Chinese Journal Full-Text, and Weipu Journal. Pooled odds ratios and 95% confidence intervals were calculated for allele contrast and homozygous, heterozygous, dominant, and recessive genetic model comparisons.

RESULTS

It was found that GSK3β rs334558 T>C and rs6438552 C>T polymorphisms were correlated with susceptibility to AD under 4 genetic models (all P<.05). In country-stratified subgroups, the results showed increased risk of developing AD in rs334558 T>C polymorphism among Chinese and Spain populations in majority groups. GSK3β rs6438552 C>T polymorphism was correlated with increased the risk of developing AD only in Australian populations.

CONCLUSION

Our findings suggest that there exists a significant association between GSK3β rs334558 T>C polymorphism and increased susceptibility of AD. Moreover, future updated studies with stratified case-control population are warranted for validation studies.

The role of the retromer complex in aging-related neurodegeneration: a molecular and genomic review

The retromer coat complex is a vital component of the intracellular trafficking mechanism sorting cargo from the endosomes to the trans-Golgi network or to the cell surface. In recent years, genes encoding components of the retromer coat complex and members of the vacuolar protein sorting 10 (Vps10) family of receptors, which play pleiotropic functions in protein trafficking and intracellular/intercellular signaling in neuronal and non-neuronal cells and are primary cargos of the retromer complex, have been implicated as genetic risk factors for sporadic and autosomal dominant forms of several neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease and frontotemporal lobar degeneration. In addition to their functions in protein trafficking, the members of the Vps10 receptor family (sortilin, SorL1, SorCS1, SorCS2, and SorCS3) modulate neurotrophic signaling pathways. Both sortilin and SorCS2 act as cell surface receptors to mediate acute responses to proneurotrophins. In addition, sortilin can modulate the intracellular response to brain-derived neurotrophic factor (BDNF) by direct control of BDNF levels and regulating anterograde trafficking of Trk receptors to the synapse. This review article summarizes the emerging data from this rapidly growing field of intracellular trafficking signaling in the pathogenesis of neurodegeneration.

Common polymorphism in the MMP-13 gene may contribute to the risk of human cancers: a meta-analysis

Cancer was viewed to be driven by accumulating genetic abnormalities that generally include chromosomal abnormalities, mutations in tumor-suppressor genes, and oncogenes. The aim of this meta-analysis was to systematically summarize the possible associations between MMP-13 rs2252070 A>G variant and cancer risks. We systematically reviewed studies focusing on MMP-13 polymorphisms with human cancer susceptibility that were published before April 30, 2014. Relevant articles were identified through research of PubMed, Embase, Web of Science, Cochrane Library, CISCOM, CINAHL, Google Scholar, CBM, and CNKI databases. All analyses were calculated using the Version 12.0 STATA software. Odds ratios (OR) and 95 % confidence interval (95 % CI) were calculated. Eleven independent case-control studies were included in the meta-analysis, which involved 3,465 patients with cancers and 4,073 healthy controls. The results identified a positive association between rs2252070 A>G polymorphism and susceptibility to cancer under five genetic models (all P < 0.05). Ethnicity subgroup analysis implied that significant difference was detected for rs2252070 A>G polymorphism with increased risk of cancers among Asians and Caucasians in majority of the groups. Our findings suggest significant association for MMP-13 rs2252070 A>G to increased susceptibility to human cancer, especially in the progression of lung carcinoma.

The Role of SORL1 in Alzheimer's Disease

Genetic variation in SORL1 gene, also known as LR11, has been identified to associate with Alzheimer's disease (AD) through replicated genetic studies. As a type I transmembrane protein, SORL1 is composed of several distinct domains and belongs to both the low-density lipoprotein receptor (LDLR) family and the vacuolar protein sorting 10 (VPS10) domain receptor family. The level of SORL1 was found to be decreased in the AD brain which positively correlated with β-amyloid (Aβ) accumulation. Emerging data suggests that SORL1 contributes to AD through various pathways, including emerging as a central regulator of the trafficking and processing of amyloid precursor protein (APP), involvement in Aβ destruction, and interaction with ApoE and tau protein. Primarily, SORL1 interacts with distinct sets of cytosolic adaptors for anterograde and retrograde movement of APP between the trans-Golgi network (TGN) and early endosomes, thereby restricting the delivery of the precursor to endocytic compartments that favor amyloidogenic breakdown. In this article, we review recent epidemiological and genetical findings of SORL1 that related with AD and speculate the possible roles of SORL1 in the progression of this disease. Finally, given the potential contributions of SORL1 to AD pathogenesis, targeting SORL1 might present novel opportunities for AD therapy.

Comparable autoantibody serum levels against amyloid- and inflammation-associated proteins in Parkinson's disease patients and controls

Naturally occurring autoantibodies (NAbs) against a number of potentially disease-associated cellular proteins, including Amyloid-beta_1–42 (Abeta_1–42), Alpha-synuclein (Asyn), myelin basic protein (MBP), myelin oligodendrocyte glycoprotein (MOG), and S100 calcium binding protein B (S100B) have been suggested to be associated with neurodegenerative disorders, in particular Alzheimer’s (AD) and Parkinson’s disease (PD). Whereas the (reduced) occurrence of specific NAbs in AD is widely accepted, previous literature examining the relation of these NAb titres between PD patients and controls, as well as comparing these levels with demographic and clinical parameters in PD patients have produced inconsistent findings. We therefore aimed, in a cross-sectional approach, to determine serum titres of the above NAbs in a cohort of 93 PD patients (31 of them demented) and 194 controls. Levels were correlated with demographic and clinical variables, cerebrospinal fluid Abeta_1–42, total tau and phospho-tau levels, as well as with single nucleotide polymorphisms (SNPs) of genes which either have been reported to influence the immune system, the amyloid cascade or the occurrence of PD (ApoE, GSK3B, HLA-DRA, HSPA5, SNCA, and STK39). The investigated NAb titres were neither significantly associated with the occurrence of PD, nor with demographic and clinical parameters, neurodegenerative markers or genetic variables. These results argue against a major potential of blood-borne parameters of the adaptive immune system to serve as trait or state markers in PD.

Association between the SORL1 rs2070045 polymorphism and late-onset Alzheimer's disease: interaction with the ApoE genotype in the Chinese Han population

Late-onset Alzheimer's Disease (LOAD) is a common neurodegenerative disease [1], and the two well identified pathological hallmarks of LOAD are senile plaques formed from amyloid β peptides (Aβ) and neurofibrillary tangles (NFTs) consisting of hyperphorylated tau protein [2]. The neuronal Sortilin-related receptor (SORL1) is involved in the processing and trafficking of amyloid precursor protein (APP) into recycling pathways, thus influencing Aβ generation and by this AD pathology [3]. To explore the relationship between the single nucleotide polymorphism (SNP) of the SORL1 SNP 19 rs2070045 and LOAD, a case-control study was conducted in a Chinese Han cohort including 77 LOAD patients and 100 control participants. This SNP 19 rs2070045 was genotyped with a polymerase chain reaction-restriction fragment length polymorphism, (PCR-RFLP) method. The association was revealed between the polymorphism of SNP 19 rs2070045 (T/T, T/G, G/G) and the risk of LOAD. The results of this study indicated that the T allele (T/G+T/T) of SNP 19 rs2070045 was successful in exerting obvious influence in LOAD patients (χ(2)=4.884, P=0.027<0.05). However, there is no sufficient evidence to prove that the T allele of SNP 19 rs2070045 is associated with ɛ4 allele of ApoE gene in LOAD patients (χ(2)=0.771, P=0.380>0.05).