A Selection of Important Genes and Their Correlated Behavior in Alzheimer's Disease

Pathogenic tau induces an adaptive elevation in mRNA translation rate at early stages of disease

Alterations in the rate and accuracy of messenger RNA (mRNA) translation are associated with aging and several neurodegenerative disorders, including Alzheimer's disease and related tauopathies. We previously reported that error-containing RNA that are normally cleared via nonsense-mediated mRNA decay (NMD), a key RNA surveillance mechanism, are translated in the adult brain of a Drosophila model of tauopathy. In the current study, we find that newly-synthesized peptides and translation machinery accumulate within nuclear envelope invaginations that occur as a consequence of tau pathology, and that the rate of mRNA translation is globally elevated in early stages of disease in adult brains of Drosophila models of tauopathy. Polysome profiling from adult heads of tau transgenic Drosophila reveals the preferential translation of specific mRNA that have been previously linked to neurodegeneration. Unexpectedly, we find that panneuronal elevation of NMD further elevates the global translation rate in tau transgenic Drosophila, as does treatment with rapamycin. As NMD activation and rapamycin both suppress tau-induced neurodegeneration, their shared effect on translation suggests that elevated rates of mRNA translation are an early adaptive mechanism to limit neurodegeneration. Our work provides compelling evidence that tau-induced deficits in NMD reshape the tau translatome by increasing translation of RNA that are normally repressed in healthy cells.

Small but mighty: the rise of microprotein biology in neuroscience

The mammalian central nervous system coordinates a network of signaling pathways and cellular interactions, which enable a myriad of complex cognitive and physiological functions. While traditional efforts to understand the molecular basis of brain function have focused on well-characterized proteins, recent advances in high-throughput translatome profiling have revealed a staggering number of proteins translated from non-canonical open reading frames (ncORFs) such as 5' and 3' untranslated regions of annotated proteins, out-of-frame internal ORFs, and previously annotated non-coding RNAs. Of note, microproteins < 100 amino acids (AA) that are translated from such ncORFs have often been neglected due to computational and biochemical challenges. Thousands of putative microproteins have been identified in cell lines and tissues including the brain, with some serving critical biological functions. In this perspective, we highlight the recent discovery of microproteins in the brain and describe several hypotheses that have emerged concerning microprotein function in the developing and mature nervous system.

Periodic heat waves-induced neuronal etiology in the elderly is mediated by gut-liver-brain axis: a transcriptome profiling approach

Heat stress exposure in intermittent heat waves and subsequent exposure during war theaters pose a clinical challenge that can lead to multi-organ dysfunction and long-term complications in the elderly. Using an aged mouse model and high-throughput sequencing, this study investigated the molecular dynamics of the liver-brain connection during heat stress exposure. Distinctive gene expression patterns induced by periodic heat stress emerged in both brain and liver tissues. An altered transcriptome profile showed heat stress-induced altered acute phase response pathways, causing neural, hepatic, and systemic inflammation and impaired synaptic plasticity. Results also demonstrated that proinflammatory molecules such as S100B, IL-17, IL-33, and neurological disease signaling pathways were upregulated, while protective pathways like aryl hydrocarbon receptor signaling were downregulated. In parallel, Rantes, IRF7, NOD1/2, TREM1, and hepatic injury signaling pathways were upregulated. Furthermore, current research identified Orosomucoid 2 (ORM2) in the liver as one of the mediators of the liver-brain axis due to heat exposure. In conclusion, the transcriptome profiling in elderly heat-stressed mice revealed a coordinated network of liver-brain axis pathways with increased hepatic ORM2 secretion, possibly due to gut inflammation and dysbiosis. The above secretion of ORM2 may impact the brain through a leaky blood-brain barrier, thus emphasizing intricate multi-organ crosstalk.

Transcriptome analysis of the cerebral cortex of acrylamide-exposed wild-type and IL-1β-knockout mice

Acrylamide is an environmental electrophile that has been produced in large amounts for many years. There is concern about the adverse health effects of acrylamide exposure due to its widespread industrial use and also presence in commonly consumed foods and others. IL-1β is a key cytokine that protects the brain from inflammatory insults, but its role in acrylamide-induced neurotoxicity remains unknown. We reported recently that deletion of IL-1β gene exacerbates ACR-induced neurotoxicity in mice. The aim of this study was to identify genes or signaling pathway(s) involved in enhancement of ACR-induced neurotoxicity by IL-1β gene deletion or ACR-induced neurotoxicity to generate a hypothesis mechanism explaining ACR-induced neurotoxicity. C57BL/6 J wild-type and IL-1β KO mice were exposed to ACR at 0, 12.5, 25 mg/kg by oral gavage for 7 days/week for 4 weeks, followed by extraction of mRNA from mice cerebral cortex for RNA sequence analysis. IL-1β deletion altered the expression of genes involved in extracellular region, including upregulation of PFN1 gene related to amyotrophic lateral sclerosis and increased the expression of the opposite strand of IL-1β. Acrylamide exposure enhanced mitochondria oxidative phosphorylation, synapse and ribosome pathways, and activated various pathways of different neurodegenerative diseases, such as Alzheimer disease, Parkinson disease, Huntington disease, and prion disease. Protein network analysis suggested the involvement of different proteins in related to learning and cognitive function, such as Egr1, Egr2, Fos, Nr4a1, and Btg2. Our results identified possible pathways involved in IL-1β deletion-potentiated and ACR-induced neurotoxicity in mice.

The Construction of a Multidomain Risk Model of Alzheimer's Disease and Related Dementias

BACKGROUND

Alzheimer's disease (AD) and related dementia (ADRD) risk is affected by multiple dependent risk factors; however, there is no consensus about their relative impact in the development of these disorders.

OBJECTIVE

To rank the effects of potentially dependent risk factors and identify an optimal parsimonious set of measures for predicting AD/ADRD risk from a larger pool of potentially correlated predictors.

METHODS

We used diagnosis record, survey, and genetic data from the Health and Retirement Study to assess the relative predictive strength of AD/ADRD risk factors spanning several domains: comorbidities, demographics/socioeconomics, health-related behavior, genetics, and environmental exposure. A modified stepwise-AIC-best-subset blanket algorithm was then used to select an optimal set of predictors.

RESULTS

The final predictive model was reduced to 10 features for AD and 19 for ADRD; concordance statistics were about 0.85 for one-year and 0.70 for ten-year follow-up. Depression, arterial hypertension, traumatic brain injury, cerebrovascular diseases, and the APOE4 proxy SNP rs769449 had the strongest individual associations with AD/ADRD risk. AD/ADRD risk-related co-morbidities provide predictive power on par with key genetic vulnerabilities.

CONCLUSION

Results confirm the consensus that circulatory diseases are the main comorbidities associated with AD/ADRD risk and show that clinical diagnosis records outperform comparable self-reported measures in predicting AD/ADRD risk. Model construction algorithms combined with modern data allows researchers to conserve power (especially in the study of disparities where disadvantaged groups are often grossly underrepresented) while accounting for a high proportion of AD/ADRD-risk-related population heterogeneity stemming from multiple domains.

Metabolomics Study Suggests the Mechanism of Different Types of Tieguanyin (Oolong) Tea in Alleviating Alzheimer’s Disease in APP/PS1 Transgenic Mice

Previously, we found that three types of Tieguanyin tea (Tgy-Q, Tgy-N and Tgy-C) extracts could alleviate Alzheimer’s disease (AD) in a mouse model among which Tgy-C was more effective. In this study, APP/PS1 transgenic mice were used to investigate the metabolomic changes in the feces of mice treated with Tieguanyin tea extracts. Results showed that the profile of fecal metabolites was obviously changed in AD mice. Metabolomics analysis found the effects of Tgy-C, especially its decreasing effect on the fecal metabolites in AD mice—132 of the 155 differential metabolites were decreased. KEGG enrichment revealed that differential metabolites could participate in functional pathways including protein digestion and absorption, biosynthesis of amino acids and ABC transporters. Further comparisons of the metabolites between groups showed that although Tgy-N and Tgy-Q exerted a decreasing effect on the fecal metabolites, Tgy-C was more effective. Moreover, correlation analysis found that the levels of the fecal metabolites were highly correlated with the contents of functional components in tea extracts. Finally, 16S rDNA sequencing presented that Tieguanyin extracts modified the gut microbiota by targeting diverse bacteria. In this study, we investigated the differences of three types of Tieguanyin tea extracts on the fecal metabolites as well as the bacterial community of the gut microbiota in AD mice. The identified differential metabolites and the changed intestinal bacteria might provide potential diagnostic biomarkers for the occurrence and progression of AD.

Multiple Criteria Optimization (MCO): A gene selection deterministic tool in RStudio

Identifying genes with the largest expression changes (gene selection) to characterize a given condition is a popular first step to drive exploration into molecular mechanisms and is, therefore, paramount for therapeutic development. Reproducibility in the sciences makes it necessary to emphasize objectivity and systematic repeatability in biological and informatics analyses, including gene selection. With these two characteristics in mind, in previous works our research team has proposed using multiple criteria optimization (MCO) in gene selection to analyze microarray datasets. The result of this effort is the MCO algorithm, which selects genes with the largest expression changes without user manipulation of neither informatics nor statistical parameters. Furthermore, the user is not required to choose either a preference structure among multiple measures or a predetermined quantity of genes to be deemed significant a priori. This implies that using the same datasets and performance measures (PMs), the method will converge to the same set of selected differentially expressed genes (repeatability) despite who carries out the analysis (objectivity). The present work describes the development of an open-source tool in RStudio to enable both: (1) individual analysis of single datasets with two or three PMs and (2) meta-analysis with up to five microarray datasets, using one PM from each dataset. The capabilities afforded by the code include license-free portability and the possibility to carry out analyses via modest computer hardware, such as personal laptops. The code provides affordable, repeatable, and objective detection of differentially expressed genes from microarrays. It can be used to analyze other experiments with similar experimental comparative layouts, such as microRNA arrays and protein arrays, among others. As a demonstration of the capabilities of the code, the analysis of four publicly-available microarray datasets related to Parkinson´s Disease (PD) is presented here, treating each dataset individually or as a four-way meta-analysis. These MCO-supported analyses made it possible to identify MMP9 and TUBB2A as potential PD genetic biomarkers based on their persistent appearance across each of the case studies. A literature search confirmed the importance of these genes in PD and indeed as PD biomarkers, which evidences the code´s potential.

Integration of Imaging Genomics Data for the Study of Alzheimer's Disease Using Joint-Connectivity-Based Sparse Nonnegative Matrix Factorization

Imaging genetics reveals the connection between microscopic genetics and macroscopic imaging, enabling the identification of disease biomarkers. In this work, we make full use of prior knowledge that has significant reference value for investigating the correlation between the brain and genetics to explore more biologically substantial biomarkers. In this paper, we propose joint-connectivity-based sparse nonnegative matrix factorization (JCB-SNMF). The algorithm simultaneously projects structural magnetic resonance imaging (sMRI), single-nucleotide polymorphism sites (SNPs), and gene expression data onto a common feature space, where heterogeneous variables with large coefficients in the same projection direction form a common module. In addition, the connectivity information for each region of the brain and genetic data are added as prior knowledge to identify regions of interest (ROIs), SNPs, and gene-related risks related to Alzheimer's disease (AD) patients. GraphNet regularization increases the anti-noise performance of the algorithm and the biological interpretability of the results. The simulation results show that compared with other NMF-based algorithms (JNMF, JSNMNMF), JCB-SNMF has better anti-noise performance and can identify and predict biomarkers closely related to AD from significant modules. By constructing a protein-protein interaction (PPI) network, we identified SF3B1, RPS20, and RBM14 as potential biomarkers of AD. We also found some significant SNP-ROI and gene-ROI pairs. Among them, two SNPs rs4472239 and rs11918049 and three genes KLHL8, ZC3H11A, and OSGEPL1 may have effects on the gray matter volume of multiple brain regions. This model provides a new way to further integrate multimodal impact genetic data to identify complex disease association patterns.

Nucks1 gene polymorphism rs823114 is associated with the positive symptoms and neurocognitive function of patients with schizophrenia in parts of southern China

Nuclear casein kinase and cyclin-dependent kinase substrate 1 (nucks1) are considered a potential susceptibility gene for certain neurological diseases, such as Parkinson's disease (PD). In our study, we genotyped three single nucleotide polymorphisms (SNPs) (rs4951261, rs823114 and rs951366) of the nucks1 gene in 774 schizophrenic patients and 819 healthy controls using the improved multiplex ligation detection reaction (imLDR) technique. Furthermore, we also studied the relationship between the above SNPs and the clinical psychiatric symptoms and neurocognitive function of the patients. Genotype distributions and allele frequencies of these SNPs showed no significant differences and were found between patients and healthy controls. However, in an analysis of the positive symptom score of rs823114 among male patients, we found that the score of the A/A genotype was lower than that of the G/A+G/G genotypes (P = 0.001, P(corr) = 0.003]. Additionally, we also found that among the female patients, G allele carriers with rs823114 had lower semantic fluency scores than subjects with the A/A genotype (P = 0.010, P(corr) = 0.030]. Our data show for the first time that rs823114 polymorphism of nucks1 may affect positive symptoms and neurocognitive function in patients with schizophrenia in parts of southern China.

Stachydrine Inhibits PC12 Cell Apoptosis Induced by Aβ25-35 in an in vitro Cell Model of Neurocognitive Disorders

Background:

Abnormal deposition of amyloid beta (Aβ) is considered the primary cause of neurocognitive disorders (NCDs). Inhibiting cytotoxicity is an important aspect of the treatment of NCDs. Stachydrine (STA) has been widely used for gynecological and cardiovascular disorders. However, whether STA has protective functions in PC12 cells treated with Aβ25-35 remains unclear.

Introduction:

Traditional Chinese Medicine, stachydrine (STA), is a water-soluble alkaloid of Leonurus heterophyllus, which can inhibit cell apoptosis, suppress tumor growth, maintain homeostasis of myocardial cells, and alleviate endothelial dysfunction. This study will investigate the effect of STA on inhibiting PC12 cell apoptosis induced by Aβ25-35 in an in vitro cell model of neurocognitive disorders.

Methods:

The differentially expressed genes (DEGs) in cells treated with STA were analyzed according to the Gene Expression Omnibus (GSE) 85871 data, and the STITCH database was used to identify the target genes of STA. PC12 cells were treated with Aβ25-35 and/or STA, 3-(4,5- dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was performed and lactate dehydrogenase (LDH) activity was determined. The cell cycle distribution was detected by flow cytometry, and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) or Western blotting were used to detect the expression of genes or proteins.

Results:

GSE85871 data showed 37 upregulated and 48 downregulated genes among the DEGs affected by STA. The results from the STITCH database showed that RPS8 and EED were target genes of STA. GSE1297 analysis showed the 13 most significantly upregulated genes. STA might affect the occurrence of NCDs through the interaction of TP53 with EED and RPS8. Finally, Aβ25-35 promoted apoptosis and LDH release of PC-12 cells, arrested the cell cycle in the G2/M phase, and inhibited the expression of the RPS8, EED, Bcl-2 and P53 genes. STA could reverse the effect of Aβ25-35.

Conclusion:

STA may play an important role in inhibiting apoptosis induced by Aβ25-35 by targeting the RPS8 and EED genes in the NCDs model in vitro.

RPL41 sensitizes retinoblastoma cells to chemotherapeutic drugs via ATF4 degradation

Retinoblastoma is the most common intraocular cancer with metastatic potential affecting infants and children. Although chemotherapy is available for retinoblastoma, side effects and drug resistance are frequent. Rpl41, encoding ribosomal protein L41 (RPL41), has been identified as a tumor suppressor gene, and its targeted degradation of activating transcription factor 4 (ATF4) produces an antitumor effect. The goal of the present study is to provide experimental evidence for the clinical application of a small peptide regimen in combination with chemotherapy for the treatment of retinoblastoma and to investigate the mechanism of their combined cytotoxicity. It was observed that treatment with the RPL41 peptide alone decreased the viability, migration, and invasion of retinoblastoma Y79 and Weri-Rb1 cells, in addition to promoting cell apoptosis and cell cycle arrest. Furthermore, RPL41 protein levels showed a significantly decreased trend in retinoblastoma specimens, whereas ATF4 protein levels tended to be increased. Mechanistically, ATF4 degradation as a result of RPL41 peptide treatment was observed in retinoblastoma Y79 and Weri-Rb1 cells. Most important, low-dose administration of the RPL41 peptide significantly enhanced the antitumor effect of carboplatin, and further analysis confirmed their synergistic effect as anti-retinoblastoma therapy, indicating that RPL41 sensitized Y79 and Weri-Rb1 retinoblastoma cells to carboplatin. Thus, our data provide a preclinical rationale for the exploration of the RPL41 peptide as a potential adjuvant to carboplatin treatment in retinoblastoma.

[Effects of stachyine on apoptosis in an Aβ25-35-induced PC12 cell model of Alzheimer's disease]

OBJECTIVE

To investigate the effects of stachydrine (STA) on apoptosis of Aβ25-35-induced PC12 cells mimicking Alzheimer's disease and explore the mechanisms.

METHODS

The differential genes of STA were analyzed based on GSE85871 data, and the target genes of STA were identified using STITCH database. PC12 cells were treated with Aβ25-35 to establish a cell model of Alzheimer's disease, and the changes in cell viability and cell cycle in response to STA treatment were assessed using MTT assay and flow cytometry, respectively. RT-PCR and Western blotting were used to detect the relevant gene or protein expressions in the treated cells.

RESULTS

GSE85871 data showed 37 up-regulated genes and 48 down-regulated genes in cells following treatment with STA. Analysis of the data from the STITCH database indicated that RPS8 and EED were the target genes of STA. Treatment of PC12 cells with Aβ25-35 significantly lowered the cell viability (P < 0.05) and the expressions of RPS8 and EED at both the mRNA and protein levels (P < 0.05), and obviously inhibited the expression of apoptosis-related proteins Bcl-2 and p53 (P < 0.05). STA treatment of the cells significantly reversed the effect of Aβ25-35 and induced cell cycle arrest in G2/M phase, causing also significantly increases in the expression levels of RPS8, EED, Bcl-2 and p53 (P < 0.05).

CONCLUSIONS

STA plays an important role in inhibiting the apoptosis of PC12 cells induced by Aβ25-35 possibly by regulating RPS8 and EED expression to promote the expressions of Bcl-2 and p53.

Polyphenols in Alzheimer's Disease and in the Gut-Brain Axis

Polyphenolic antioxidants, including dietary plant lignans, modulate the gut-brain axis, which involves transformation of these polyphenolic compounds into physiologically active and neuroprotector compounds (called human lignans) through gut bacterial metabolism. These gut bacterial metabolites exert their neuroprotective effects in various neurodegenerative diseases, such as Alzheimer's disease (AD) and Parkinson's disease (PD), and also have protective effects against other diseases, such as cardiovascular diseases, cancer, and diabetes. For example, enterolactone and enterodiol, the therapeutically relevant polyphenols, are formed as the secondary gut bacterial metabolites of lignans, the non-flavonoid polyphenolic compounds found in plant-based foods. These compounds are also acetylcholinesterase inhibitors, and thereby have potential applications as therapeutics in AD and other neurological diseases. Polyphenols are also advanced glycation end product (AGE) inhibitors (antiglycating agents), and thereby exert neuroprotective effects in cases of AD. Thus, gut bacterial metabolism of lignans and other dietary polyphenolic compounds results in the formation of neuroprotective polyphenols-some of which have enhanced blood-brain barrier permeability. It is hypothesized that gut bacterial metabolism-derived polyphenols, when combined with the nanoparticle-based blood-brain barrier (BBB)-targeted drug delivery, may prove to be effective therapeutics for various neurological disorders, including traumatic brain injury (TBI), AD, and PD. This mini-review addresses the role of polyphenolic compounds in the gut-brain axis, focusing on AD.