Diet as a risk factor for Alzheimer's disease / Dieta jako czynnik ryzyka choroby Alzheimera.

Chronic exposure to an unhealthy diet is one of the causes of civilization diseases and significantly affects the average longevity. The impact of diet on health is extremely complicated due to the chemical diversity of its composition. The diet provides over 26,000 biochemicals and even more of their metabolites. Among this diversity, three macronutrients: proteins, carbohydrates and fats can be identified that provide energy, and in addition providing their metabolites. According to the latest concepts of the impact of macronutrients in diet on human health, their mutual proportions and not solely absolute quantities are of great importance. In our article we present a short discussion of our own research on this problem in relation to the incidence of Alzheimer's disease against the background of contemporary biochemical and epidemiological literature.

Proportions of macronutrients, including specific dietary fats, in prospective anti-Alzheimer's diet.

Here we present a novel life-long whole-population study, which enabled us to predict a diet that, in terms of macronutrient proportions, may be prophylactic against Alzheimer's Disease (AD). The method is based on the existence of oscillations in the correlation between historical per capita personal income (PCPI) and age-adjusted death rates (AADR) for AD for each state of the USA in 2005. These oscillations can be explained by changing proportions of macronutrients in the average American diet between 1929 and 2005. We assumed that reducing future correlation of PCPI with AADR will reduce the population's susceptibility to AD. Based on the results of fitting macronutrient availabilities to the variability of Roriginal, using Generalized Additive Models (GAM) analysis, we constructed four "Calculator" equations. The Calculator allowed for prediction of an optimal diet characterized by low correlation of PCPI with AADR (Rpredicted) and minimum energy difference from the historical average macronutrient consumption for each corresponding period of life. We predict that protein consumption should be reduced by half in early middle age and late middle age, whereas in late age it should increase. Our predictions are in line with results on humans and simpler organisms in the context of prolonging life.

Open chromatin landscape of rat microglia upon proinvasive or inflammatory polarization.

Microglia are brain-resident, myeloid cells that play important roles in health and brain pathologies. Herein, we report a comprehensive, replicated, false discovery rate-controlled dataset of DNase-hypersensitive (DHS) open chromatin regions for rat microglia. We compared the open chromatin landscapes in untreated primary microglial cultures and cultures stimulated for 6 hr with either glioma-conditioned medium (GCM) or lipopolysaccharide (LPS). Glioma-secreted factors induce proinvasive and immunosuppressive activation of microglia, and these cells then promote tumor growth. The open chromatin landscape of the rat microglia consisted of 126,640 reproducible DHS regions, among which 2,303 and 12,357 showed a significant change in openness following stimulation with GCM or LPS, respectively. Active genes exhibited constitutively open promoters, but there was no direct dependence between the aggregated openness of DHS regions near a gene and its expression. Individual regions mapped to the same gene often presented different patterns of openness changes. GCM-regulated DHS regions were more frequent in areas away from gene bodies, while LPS-regulated regions were more frequent in introns. GCM and LPS differentially affected the openness of regions mapped to immune checkpoint genes. The two treatments differentially affected the aggregated openness of regions mapped to genes in the Toll-like receptor signaling and axon guidance pathways, suggesting that the molecular machinery used by migrating microglia is similar to that of growing axons and that modulation of these pathways is instrumental in the induction of proinvasive polarization of microglia by glioma. Our dataset of open chromatin regions paves the way for studies of gene regulation in rat microglia.

Global pentapeptide statistics are far away from expected distributions.

The relationships between polypeptide composition, sequence, structure and function have been puzzling biologists ever since first protein sequences were determined. Here, we study the statistics of occurrence of all possible pentapeptide sequences in known proteins. To compensate for the non-uniform distribution of individual amino acid residues in protein sequences, we investigate separately all possible permutations of every given amino acid composition. For the majority of permutation groups we find that pentapeptide occurrences deviate strongly from the expected binomial distributions, and that the observed distributions are also characterized by high numbers of outlier sequences. An analysis of identified outliers shows they often contain known motifs and rare amino acids, suggesting that they represent important functional elements. We further compare the pentapeptide composition of regions known to correspond to protein domains with that of non-domain regions. We find that a substantial number of pentapeptides is clearly strongly favored in protein domains. Finally, we show that over-represented pentapeptides are significantly related to known functional motifs and to predicted ancient structural peptides.

Transcriptional regulation of CacyBP/SIP gene and the influence of increased CacyBP/SIP level on gene expression pattern in colorectal cancer HCT116 cells.

The CacyBP/SIP protein is expressed at a particularly high level in brain, spleen, and various tumors. In this work, we have studied transcriptional regulation of the CacyBP/SIP gene and the influence of increased CacyBP/SIP level on gene expression in colorectal cancer HCT116 cells. We have shown that E2F1, EGR1, and CREB transcription factors bind to the CacyBP/SIP gene promoter and stimulate transcription of CacyBP/SIP gene. The role of CREB was further confirmed by the observation that forskolin, a strong activator of CREB phosphorylation/activity, increased CacyBP/SIP gene promoter activity. Moreover, we have shown that CREB dominant negative mutants, CREB133 and KCREB, inhibits CacyBP/SIP promoter activity. To check the biological significance of increased CacyBP/SIP expression/level we have applied RNA microarray analysis and have found that upregulation of CacyBP/SIP entails changes in mRNA level of many genes involved, among others, in immune processes. © 2017 IUBMB Life, 70(1):50-59, 2018.

CI Thermometer: Visualizing Confidence Intervals in Correlation Analysis.

Correlation analysis is one of the most popular statistical methods. Despite that, the way research reports correlation is often misleading. The difficulty increases with the amount of information that must be read and interpreted. The proposed CI thermometer makes correlation matrices much easier to read and provides information that would be difficult to interpret when presented in another way.

Chronically dysregulated NOTCH1 interactome in the dentate gyrus after traumatic brain injury.

Traumatic brain injury (TBI) can result in several dentate gyrus-regulated disabilities. Almost nothing is known about the chronic molecular changes after TBI, and their potential as treatment targets. We hypothesized that chronic transcriptional alterations after TBI are under microRNA (miRNA) control. Expression of miRNAs and their targets in the dentate gyrus was analyzed using microarrays at 3 months after experimental TBI. Of 305 miRNAs present on the miRNA-array, 12 were downregulated (p<0.05). In parallel, 75 of their target genes were upregulated (p<0.05). A bioinformatics analysis of miRNA targets highlighted the dysregulation of the transcription factor NOTCH1 and 39 of its target genes (NOTCH1 interactome). Validation assays confirmed downregulation of miR-139-5p, upregulation of Notch1 and its activated protein, and positive enrichment of NOTCH1 target gene expression. These findings demonstrate that miRNA-based transcriptional regulation can be present at chronic time points after TBI, and highlight the NOTCH1 interactome as one of the mechanisms behind the dentate gyrus pathology-related morbidities.

Profile of 6 microRNA in blood plasma distinguish early stage Alzheimer's disease patients from non-demented subjects.

Alzheimer's disease (AD) is the most common age-related dementia. Among its major challenges is identifying molecular signatures characteristic for the early AD stage in patients with Mild Cognitive Impairment (MCI-AD), which could serve for deciphering the AD pathomechanism and also as non-invasive, easy-to-access biomarkers. Using qRT-PCR we compared the microRNA (miRNA) profiles in blood plasma of 15 MCI-AD patients, whose diagnoses were confirmed by cerebrospinal fluid (CSF) biomarkers, with 20 AD patients and 15 non-demented, age-matched individuals (CTR).To minimize methodological variability, we adhered to standardization of blood and CSF assays recommended by the international Joint Programming for Neurodegenerative Diseases (JPND) BIOMARKAPD consortium, and we employed commercially available Exiqon qRT-PCR-assays. In the first screening, we assessed 179 miRNAs of plasma. We confirmed 23 miRNAs reported earlier as AD biomarker candidates in blood and found 26 novel differential miRNAs between AD and control subjects. For representative 15 differential miRNAs, the TargetScan, MirTarBase and KEGG database analysis indicated putative protein targets among such AD hallmarks as MAPT (Tau), proteins involved in amyloidogenic proteolysis, and in apoptosis. These 15 miRNAs were verified in separate, subsequent subject groups. Finally, 6 miRNAs (3 not yet reported in AD context and 3 reported in AD blood) were selected as the most promising biomarker candidates differentiating early AD from controls with the highest fold changes (from 1.32 to 14.72), consistent significance, specificities from 0.78 to 1 and sensitivities from 0.75 to 1. (patent pending, PCT/IB2016/052440).

MBD3 expression and DNA binding patterns are altered in a rat model of temporal lobe epilepsy.

The aim of the present study was to examine involvement of MBD3 (methyl-CpG-binding domain protein 3), a protein involved in reading DNA methylation patterns, in epileptogenesis and epilepsy. We used a well-characterized rat model of temporal lobe epilepsy that is triggered by status epilepticus, evoked by electrical stimulation of the amygdala. Stimulated and sham-operated animals were sacrificed 14 days after stimulation. We found that MBD3 transcript was present in neurons, oligodendrocytes, and astrocytes in both control and epileptic animals. We detected the nuclear localization of MBD3 protein in neurons, mature oligodendrocytes, and a subpopulation of astrocytes but not in microglia. Amygdala stimulation significantly increased the level of MBD3 immunofluorescence. Immunoprecipitation followed by mass spectrometry and Western blot revealed that MBD3 in the adult brain assembles the NuRD complex, which also contains MTA2, HDAC2, and GATAD2B. Using chromatin immunoprecipitation combined with deep sequencing, we observed differences in the occupancy of DNA regions by MBD3 protein between control and stimulated animals. This was not followed by subsequent changes in the mRNA expression levels of selected MBD3 targets. Our data demonstrate for the first time alterations in the MBD3 expression and DNA occupancy in the experimental model of epilepsy.

Gene set enrichment analysis and ingenuity pathway analysis of metastatic clear cell renal cell carcinoma cell line.

In recent years, genome-wide RNA expression analysis has become a routine tool that offers a great opportunity to study and understand the key role of genes that contribute to carcinogenesis. Various microarray platforms and statistical approaches can be used to identify genes that might serve as prognostic biomarkers and be developed as antitumor therapies in the future. Metastatic renal cell carcinoma (mRCC) is a serious, life-threatening disease, and there are few treatment options for patients. In this study, we performed one-color microarray gene expression (4×44K) analysis of the mRCC cell line Caki-1 and the healthy kidney cell line ASE-5063. A total of 1,921 genes were differentially expressed in the Caki-1 cell line (1,023 upregulated and 898 downregulated). Gene Set Enrichment Analysis (GSEA) and Ingenuity Pathway Analysis (IPA) approaches were used to analyze the differential-expression data. The objective of this research was to identify complex biological changes that occur during metastatic development using Caki-1 as a model mRCC cell line. Our data suggest that there are multiple deregulated pathways associated with metastatic clear cell renal cell carcinoma (mccRCC), including integrin-linked kinase (ILK) signaling, leukocyte extravasation signaling, IGF-I signaling, CXCR4 signaling, and phosphoinositol 3-kinase/AKT/mammalian target of rapamycin signaling. The IPA upstream analysis predicted top transcriptional regulators that are either activated or inhibited, such as estrogen receptors, TP53, KDM5B, SPDEF, and CDKN1A. The GSEA approach was used to further confirm enriched pathway data following IPA.

Etiology matters - Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy.

This study tested the hypothesis that acquired epileptogenesis is accompanied by DNA methylation changes independent of etiology. We investigated DNA methylation and gene expression in the hippocampal CA3/dentate gyrus fields at 3 months following epileptogenic injury in three experimental models of epilepsy: focal amygdala stimulation, systemic pilocarpine injection, or lateral fluid-percussion induced traumatic brain injury (TBI) in rats. In the models studies, DNA methylation and gene expression profiles distinguished controls from injured animals. We observed consistent increased methylation in gene bodies and hypomethylation at non-genic regions. We did not find a common methylation signature in all three different models and few regions common to any two models. Our data provide evidence that genome-wide alteration of DNA methylation signatures is a general pathomechanism associated with epileptogenesis and epilepsy in experimental animal models, but the broad pathophysiological differences between models (i.e. pilocarpine, amygdala stimulation, and post-TBI) are reflected in distinct etiology-dependent DNA methylation patterns.

Traumatic Brain Injury Increases the Expression of Nos1, Aß Clearance, and Epileptogenesis in APP/PS1 Mouse Model of Alzheimer's Disease.

To test the hypothesis that an amyloidogenic genetic background predisposes to worsening of post-TBI outcome, we investigated whether traumatic brain injury (TBI) in amyloid precursor protein (APP)/PS1 mice aggravates epileptogenesis and/or enhances somatomotor and cognitive impairment. To elaborate the mechanisms of worsening outcomes, we studied changes in the expression of genes involved in APP processing and Tau pathways in the perilesional cortex, ipsilateral thalamus, and ipsilateral hippocampus 16 weeks post-TBI. Mild (mTBI) or severe TBI (sTBI) was triggered using controlled cortical impact in 3-month-old APP/PS1 mice and wild-type (Wt) littermates. Morris water-maze revealed a genotype effect on spatial learning and memory as APP/PS1-sTBI mice performed more poorly than Wt-sTBI mice (p < 0.05). Epileptogenesis was affected by genotype and TBI as 88 % of APP/PS1-sTBI mice had epilepsy compared to 11 % in Wt-sTBI (genotype effect p < 0.01) or 50 % in APP/PS1-sham groups (TBI effect p < 0.05). The higher the seizure frequency, the higher the cortical expression of Nos1 (r = 0.83, p < 0.001) and Mapk3 (r = 0.67, p < 0.001). Immunohistochemical analysis confirmed increased amount of NOS1 protein in neuronal somata and processes in the perilesional cortex in APP/PS1-sTBI mice compared to APP/PS1-sham (p < 0.05) or Wt-sTBI mice (p < 0.01). Motor impairment correlated (p < 0.001) with the increased cortical expression of genes encoding proteins related to ß-amyloid (Aß) clearance, including Clu (r = 0.83), Abca1 (r = 0.78), A2m (r = 0.76), Apoe (r = 0.70), and Ctsd (r = 0.63). Immunohistochemical analysis revealed a focal reduction in Aß load lateral to lesion core in APP/PS1-sTBI mice compared to APP/PS1-sham mice (p < 0.05). The present study provides the first comprehensive evidence of exacerbated epileptogenesis and its molecular mechanisms in Alzheimer's disease (AD)-related genetic background after TBI.

Alterations in miRNA levels in the dentate gyrus in epileptic rats.

The aim of this study was to characterize changes in miRNA expression in the epileptic dentate gyrus. Status epilepticus evoked by amygdala stimulation was used to induce epilepsy in rats. The dentate gyri were isolated at 7 d, 14 d, 30 d and 90 d after stimulation (n=5). Sham-operated time-matched controls were prepared for each time point (n=5). The miRNA expression was evaluated using Exiqon microarrays. Additionally, mRNA from the same animals was profiled using Affymetrix microarrays. We detected miRNA expression signatures that differentiate between control and epileptic animals. Significant changes in miRNA expression between stimulated and sham operated animals were observed at 7 and 30 d following stimulation. Moreover, we found that there are ensembles of miRNAs that change expression levels over time. Analysis of the mRNA expression from the same animals revealed that the expression of several mRNAs that are potential targets for miRNA with altered expression level is regulated in the expected direction. The functional characterization of miRNAs and their potential mRNA targets indicate that miRNA can participate in several molecular events that occur in epileptic tissue, including immune response and neuronal plasticity. This is the first report on changes in the expression of miRNA and the potential functional impact of these changes in the dentate gyrus of epileptic animals. Complex changes in the expression of miRNAs suggest an important role for miRNA in the molecular mechanisms of epilepsy.

Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs.

We present the Nencki Genomics Database, which extends the functionality of Ensembl Regulatory Build (funcgen) for the three species: human, mouse and rat. The key enhancements over Ensembl funcgen include the following: (i) a user can add private data, analyze them alongside the public data and manage access rights; (ii) inside the database, we provide efficient procedures for computing intersections between regulatory features and for mapping them to the genes. To Ensembl funcgen-derived data, which include data from ENCODE, we add information on conserved non-coding (putative regulatory) sequences, and on genome-wide occurrence of transcription factor binding site motifs from the current versions of two major motif libraries, namely, Jaspar and Transfac. The intersections and mapping to the genes are pre-computed for the public data, and the result of any procedure run on the data added by the users is stored back into the database, thus incrementally increasing the body of pre-computed data. As the Ensembl funcgen schema for the rat is currently not populated, our database is the first database of regulatory features for this frequently used laboratory animal. The database is accessible without registration using the mysql client: mysql -h database.nencki-genomics.org -u public. Registration is required only to add or access private data. A WSDL webservice provides access to the database from any SOAP client, including the Taverna Workbench with a graphical user interface.