Cluster analysis of risk factor genetic polymorphisms in Alzheimer's disease

Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation

Anatomically modern humans arose in Africa ∼300,000 years ago, but the demographic and adaptive histories of African populations are not well-characterized. Here, we have generated a genome-wide dataset from 840 Africans, residing in western, eastern, southern, and northern Africa, belonging to 50 ethnicities, and speaking languages belonging to four language families. In addition to agriculturalists and pastoralists, our study includes 16 populations that practice, or until recently have practiced, a hunting-gathering (HG) lifestyle. We observe that genetic structure in Africa is broadly correlated not only with geography, but to a lesser extent, with linguistic affiliation and subsistence strategy. Four East African HG (EHG) populations that are geographically distant from each other show evidence of common ancestry: the Hadza and Sandawe in Tanzania, who speak languages with clicks classified as Khoisan; the Dahalo in Kenya, whose language has remnant clicks; and the Sabue in Ethiopia, who speak an unclassified language. Additionally, we observed common ancestry between central African rainforest HGs and southern African San, the latter of whom speak languages with clicks classified as Khoisan. With the exception of the EHG, central African rainforest HGs, and San, other HG groups in Africa appear genetically similar to neighboring agriculturalist or pastoralist populations. We additionally demonstrate that infectious disease, immune response, and diet have played important roles in the adaptive landscape of African history. However, while the broad biological processes involved in recent human adaptation in Africa are often consistent across populations, the specific loci affected by selective pressures more often vary across populations.

TFCP2 activates beta-catenin/TCF signaling in the progression of pancreatic cancer

Aberrant activation of beta-catenin/TCF (T-cell factor) signaling is frequently observed in the pancreatic cancer. However, the regulation of nuclear beta-catenin/TCF transcription machinery remains largely unknown. In this study, TFCP2 (transcriptional factor CP2) expression in pancreatic cancer was detected by qPCR, immunohistochemistry and western blot. Western blot, colony formation assay, migration and invasion experiment were performed to investigate the effects of TFCP2 on the growth and migration of pancreatic cancer cells. In vivo, mouse metastasis models were utilized to determine metastasis ability. Western blots were used to evaluate the related protein expression. Luciferase reporter assay was used to explore the role of TFCP2 on beta-catenin/TCF signaling. We have shown that the transcription factor TFCP2 was up-regulated in the pancreatic cancer. Over-expression of TFCP2 promoted the growth, migration, invasion and colony formation of pancreatic cancer cells, while knocking down the expression of TFCP2 inhibited the growth, migration, invasion, colony formation and metastasis of pancreatic cancer cells. The mechanism study revealed that TFCP2 interacted beta-catenin, enhanced the interaction between beta-catenin and TCF4, and activated beta-catenin/TCF signaling. Taken together, our study demonstrated the oncogenic roles of TFCP2 in pancreatic cancer, and suggested that TFCP2 might be a target for the treatment of pancreatic cancer.

Relationship between the polymorphism in exon 5 of BACE1 gene and Alzheimer's disease

BACKGROUND AND AIMS

The β-Site APP-cleaving enzyme 1 (BACE1) gene polymorphism (rs638405) has been extensively investigated for association to Alzheimer's disease (AD). However, results of different studies have been contradictory. The aim of this meta-analysis was to evaluate the association between BACE1 gene polymorphism (rs638405) and AD.

METHODS

All eligible studies were searched in PubMed, Cochrane Library, Embase, SinoMed, and the China Knowledge Resource Integrated Database. Pooled odds ratios (ORs) and 95 % confidence intervals (95 % CIs) were used to evaluate the strength of the association between BACE1 gene polymorphism and AD.

RESULTS

Twenty studies in 19 papers containing 4377 AD patients and 4563 controls were included for rs638405 polymorphism. The results suggested that rs638405 in BACE1 was not associated with the risk of AD. Stratification analyses indicated rs638405 decreased the risk of apolipoprotein-E ε4 (APOE4) positive AD patients. Furthermore, we found rs638405 also decreased the risk of Asian AD patients. By exclusion of three studies that did not conform to Hardy-Weinberg equilibrium (HWE), our data suggested rs638405 in BACE1 was a protective factor of AD.

CONCLUSIONS

To sum up, our data indicated that BACE1 gene polymorphism in exon 5 might decrease the risk of Asian AD and APOE4 positive patients.

Genetic Factors Affecting Late-Onset Alzheimer's Disease Susceptibility

Alzheimer's disease is considered a progressive brain disease in the older population. Late-onset Alzheimer's disease (LOAD) as a multifactorial dementia has a polygenic inheritance. Age, environment, and lifestyle along with a growing number of genetic factors have been reported as risk factors for LOAD. Our aim was to present results of LOAD association studies that have been done in northwestern Iran, and we also explored possible interactions with apolipoprotein E (APOE) status. We re-evaluated the association of these markers in dominant, recessive, and additive models. In all, 160 LOAD and 163 healthy control subjects of Azeri Turkish ethnicity were studied. The Chi-square test with Yates' correction and Fisher's exact test were used for statistical analysis. A Bonferroni-corrected p value, based on the number of statistical tests, was considered significant. Our results confirmed that chemokine receptor type 2 (CCR2), estrogen receptor 1 (ESR1), toll-like receptor 2 (TLR2), tumor necrosis factor alpha (TNF α), APOE, bridging integrator 1 (BIN1), and phosphatidylinositol-binding clathrin assembly protein (PICALM) are LOAD susceptibility loci in Azeri Turk ancestry populations. Among them, variants of CCR2, ESR1, TNF α, and APOE revealed associations in three different genetic models. After adjusting for APOE, the association (both allelic and genotypic) with CCR2, BIN1, and ESRα (PvuII) was evident only among subjects without the APOE ε4, whereas the association with CCR5, without Bonferroni correction, was significant only among subjects carrying the APOE ε4 allele. This result is an evidence of a synergistic and antagonistic effect of APOE on variant associations with LOAD.

TNF-alpha G308A polymorphism and the susceptibility to Alzheimer's disease: an updated meta-analysis

BACKGROUND AND AIMS

Tumor necrosis factor (TNF)-alpha G308A polymorphism has been reported in the association with susceptibility to Alzheimer's disease (AD); however, results have been contradictory. We conducted an updated meta-analysis to evaluate the role of TNF-alpha G308A in the occurrence of AD.

METHODS

Relevant articles were retrieved from online databases. The combined odds ratio, odds ratio in different genetic models, and the related 95% confidence intervals were calculated. Publication bias and homogeneity among individual studies were estimated. Subgroup analyses and sensitivity analyses were also performed.

RESULTS

In overall analyses, no risk of AD was associated with TNF-alpha G308A under different genetic models. However, in the subgroup analyses, a significant association between TNF-alpha G308A and AD risk was observed in Chinese. In addition, a significant protective effect of TNF-alpha -308A was found in the occurrence of AD among North European populations under a dominant model.

CONCLUSIONS

The result of this meta-analysis suggests that TNF-alpha G308A polymorphism may be associated with the increased risk of AD in Chinese and decreased risk of AD in northern European populations.

BioAge: toward a multi-determined, mechanistic account of cognitive aging

The search for reliable early indicators of age-related cognitive decline represents a critical avenue for progress in aging research. Chronological age is a commonly used developmental index; however, it offers little insight into the mechanisms underlying cognitive decline. In contrast, biological age (BioAge), reflecting the vitality of essential biological systems, represents a promising operationalization of developmental time. Current BioAge models have successfully predicted age-related cognitive deficits. Research on aging-related cognitive function indicates that the interaction of multiple risk and protective factors across the human lifespan confers individual risk for late-life cognitive decline, implicating a multi-causal explanation. In this review, we explore current BioAge models, describe three broad yet pathologically relevant biological processes linked to cognitive decline, and propose a novel operationalization of BioAge accounting for both moderating and causal mechanisms of cognitive decline and dementia. We argue that a multivariate and mechanistic BioAge approach will lead to a greater understanding of disease pathology as well as more accurate prediction and early identification of late-life cognitive decline.

Multiple mechanisms of iron-induced amyloid beta-peptide accumulation in SHSY5Y cells: protective action of negletein

The increased accumulation of iron in the brain in Alzheimer's disease (AD) is well documented, and excess iron is strongly implicated in the pathogenesis of the disease. The adverse effects of accumulated iron in AD brain may include the oxidative stress, altered amyloid beta-metabolism and the augmented toxicity of metal-bound amyloid beta 42. In this study, we have shown that exogenously added iron in the form of ferric ammonium citrate (FAC) leads to considerable accumulation of amyloid precursor protein (APP) without a corresponding change in the concerned gene expression in cultured SHSY5Y cells during exposure up to 48 h. This phenomenon is also associated with increased β-secretase activity and augmented release of amyloid beta 42 in the medium. Further, the increase in β-secretase activity, in SHSY5Y cells, upon exposure to iron apparently involves reactive oxygen species (ROS) and NF-κB activation. The synthetic flavone negletein (5,6-dihydroxy-7-methoxyflavone), which is a known chelator for iron, can significantly prevent the effects of FAC on APP metabolism in SHSY5Y cells. Further, this compound inhibits the iron-dependent formation of ROS and also blocks the iron-induced oligomerization of amyloid beta 42 in vitro. In concentrations used in this study, negletein alone appears to have only marginal toxic effects on cell viability, but, on the other hand, the drug is capable of ameliorating the iron-induced loss of cell viability considerably. Our results provide the initial evidence of potential therapeutic effects of negletein, which should be explored in suitable animal models of AD.

Genetics of late-onset Alzheimer's disease: update from the alzgene database and analysis of shared pathways

The genetics of late-onset Alzheimer's disease (LOAD) has taken impressive steps forwards in the last few years. To date, more than six-hundred genes have been linked to the disorder. However, only a minority of them are supported by a sufficient level of evidence. This review focused on such genes and analyzed shared biological pathways. Genetic markers were selected from a web-based collection (Alzgene). For each SNP in the database, it was possible to perform a meta-analysis. The quality of studies was assessed using criteria such as size of research samples, heterogeneity across studies, and protection from publication bias. This produced a list of 15 top-rated genes: APOE, CLU, PICALM, EXOC3L2, BIN1, CR1, SORL1, TNK1, IL8, LDLR, CST3, CHRNB2, SORCS1, TNF, and CCR2. A systematic analysis of gene ontology terms associated with each marker showed that most genes were implicated in cholesterol metabolism, intracellular transport of beta-amyloid precursor, and autophagy of damaged organelles. Moreover, the impact of these genes on complement cascade and cytokine production highlights the role of inflammatory response in AD pathogenesis. Gene-gene and gene-environment interactions are prominent issues in AD genetics, but they are not specifically featured in the Alzgene database.

The frequency of the TRPC4AP haplotype in Alzheimer's patients

A haplotype in the gene for transient receptor potential cation channel, subfamily C, member 4 associated protein (TRPC4AP), has been identified in two extended pedigrees with late-onset Alzheimer's disease. Nine of the SNPs in the haplotype were analyzed in our unrelated Alzheimer's patients and controls. The H1 haplotype was found in 36% of the patients (199 patients) and in 26% of the controls (85 controls) (P=0.0282; OR=1.56; 95%CI=1.05-2.32). The latent classification method of analysis showed that the H1 haplotype was characteristic of Alzheimer's patients, with ages-of-onset between 66 and 80 years. When clinical phenotypes were analyzed, there was a suggestion that the patients with this haplotype may have more behavioral changes and hallucinations. Moreover, both the latent classification analysis and logistic regression analysis indicated that there was no association of the haplotype with either APOE status or gender. The gene is part of a superfamily of cation channels that are involved with calcium entry into cells.