Transcriptomics and biochemical evidence of trigonelline ameliorating learning and memory decline in the senescence-accelerated mouse prone 8 (SAMP8) model by suppressing proinflammatory cytokines and elevating neurotransmitter release

In recent years, exploring natural compounds with functional properties to ameliorate aging-associated cognitive decline has become a research priority to ensure healthy aging. In the present study, we investigated the effects of Trigonelline (TG), a plant alkaloid, on memory and spatial learning in 16-week-old senescence-accelerated mouse model SAMP8 using an integrated approach for cognitive and molecular biology aspects. After 30 days of oral administration of TG at the dose of 5 mg/kg/day, the mice were trained in Morris Water Maze task. TG-treated SAMP8 mice exhibited significant improvement in the parameters of escape latency, distance moved, and annulus crossing index. Next, we performed a whole-genome transcriptome profiling of the mouse hippocampus using microarrays. Gene ontology analyses showed that a wide range of biological processes, including nervous system development, mitochondrial function, ATP synthesis, and several signaling pathways related to inflammation, autophagy, and neurotransmitter release, were significantly enriched in TG-treated SAMP8 compared to nontreated. Further, a nonlinear dimensionality reduction technique, Uniform Manifold Approximation and Projection (UMAP), was applied to identify clusters of functions that revealed TG primarily regulated pathways related to inflammation, followed by those involved in neurotransmitter release. In addition, a protein-protein interaction network analysis indicated that TG may exert its biological effects through negatively modulating Traf6-mediated NF-κB activation. Finally, ELISA test showed that TG treatment significantly decreased proinflammatory cytokines- TNFα and IL6 and increased neurotransmitters- dopamine, noradrenaline, and serotonin in mouse hippocampus. Altogether, our integrated bio-cognitive approach highlights the potential of TG in alleviating age-related memory and spatial impairment.

An ensemble machine learning model based on multiple filtering and supervised attribute clustering algorithm for classifying cancer samples

BACKGROUND

Machine learning is one kind of machine intelligence technique that learns from data and detects inherent patterns from large, complex datasets. Due to this capability, machine learning techniques are widely used in medical applications, especially where large-scale genomic and proteomic data are used. Cancer classification based on bio-molecular profiling data is a very important topic for medical applications since it improves the diagnostic accuracy of cancer and enables a successful culmination of cancer treatments. Hence, machine learning techniques are widely used in cancer detection and prognosis.

METHODS

In this article, a new ensemble machine learning classification model named Multiple Filtering and Supervised Attribute Clustering algorithm based Ensemble Classification model (MFSAC-EC) is proposed which can handle class imbalance problem and high dimensionality of microarray datasets. This model first generates a number of bootstrapped datasets from the original training data where the oversampling procedure is applied to handle the class imbalance problem. The proposed MFSAC method is then applied to each of these bootstrapped datasets to generate sub-datasets, each of which contains a subset of the most relevant/informative attributes of the original dataset. The MFSAC method is a feature selection technique combining multiple filters with a new supervised attribute clustering algorithm. Then for every sub-dataset, a base classifier is constructed separately, and finally, the predictive accuracy of these base classifiers is combined using the majority voting technique forming the MFSAC-based ensemble classifier. Also, a number of most informative attributes are selected as important features based on their frequency of occurrence in these sub-datasets.

RESULTS

To assess the performance of the proposed MFSAC-EC model, it is applied on different high-dimensional microarray gene expression datasets for cancer sample classification. The proposed model is compared with well-known existing models to establish its effectiveness with respect to other models. From the experimental results, it has been found that the generalization performance/testing accuracy of the proposed classifier is significantly better compared to other well-known existing models. Apart from that, it has been also found that the proposed model can identify many important attributes/biomarker genes.

Dec1 deficiency protects the heart from fibrosis, inflammation, and myocardial cell apoptosis in a mouse model of cardiac hypertrophy

Cardiac inflammation and fibrosis triggered by left ventricular pressure overload are the major causes of heart dysfunction. Differentiated embryonic chondrocyte gene 1 (Dec1) is a basic helix-loop-helix transcription factor that is comprehensively involved in inflammation and tissue fibrosis, but its role in cardiac hypertrophy remains unclear. This study explored the effects of Dec1 on cardiac fibrosis, inflammation, and apoptosis in hypertrophic conditions. Transverse aortic constriction (TAC) was performed to induce cardiac hypertrophy in wild-type (WT) mice and in Dec1 knock out (KO) mice for 4 weeks. Using the TAC mouse model, prominent differences in cardiac hypertrophy at the morphological, functional, and molecular levels were delineated by Masson's Trichrome and TUNEL staining, immunohistochemistry, RT-PCR and Western Blot. DNA microarray and microRNA (miRNA) array analyses were carried out to identify gene and miRNA expression patterns. Dec1KO mice exhibited a more severe hypertrophic heart, whereas WT mice showed a more pronounced perivascular fibrosis after TAC at 4 weeks. The Dec1 deficiency promoted M2 phenotype macrophages. Dec1KO TAC mice showed fewer apoptotic cells than WT TAC mice. APEX1, WNT16, FGF10 and MMP-10 were differentially expressed according to DNA microarray analysis and expression levels of those genes and the corresponding miRNAs (miR-295, miR-200 b, miR-130a, miR-92a) showed the same trends. Furthermore, luciferase reporter assay confirmed that FGF10 is the direct target gene of miR-130. In conclusion, a Dec1 deficiency protects the heart from perivascular fibrosis, regulates M1/M2 macrophage polarization and reduces cell apoptosis, which may provide a novel insight for the treatment of cardiac hypertrophy.

Gene Expression Profiling and Assessment of Vitamin D and Serotonin Pathway Variations in Patients With Irritable Bowel Syndrome

BACKGROUND/AIMS

Irritable bowel syndrome (IBS) is a multifaceted disorder that afflicts millions of individuals worldwide. IBS is currently diagnosed based on the presence/duration of symptoms and systematic exclusion of other conditions. A more direct manner to identify IBS is needed to reduce healthcare costs and the time required for accurate diagnosis. The overarching objective of this work is to identify gene expression-based biological signatures and biomarkers of IBS.

METHODS

Gene transcripts from 24 tissue biopsy samples were hybridized to microarrays for gene expression profiling. A combination of multiple statistical analyses was utilized to narrow the raw microarray data to the top 200 differentially expressed genes between IBS versus control subjects. In addition, quantitative polymerase chain reaction was employed for validation of the DNA microarray data. Gene ontology/pathway enrichment analysis was performed to investigate gene expression patterns in biochemical pathways. Finally, since vitamin D has been shown to modulate serotonin production in some models, the relationship between serum vitamin D and IBS was investigated via 25-hydroxyvitamin D (25[OH]D) chemiluminescence immunoassay.

RESULTS

A total of 858 genetic features were identified with differential expression levels between IBS and asymptomatic populations. Gene ontology enrichment analysis revealed the serotonergic pathway as most prevalent among the differentially expressed genes. Further analysis via real-time polymerase chain reaction suggested that IBS patient-derived RNA exhibited lower levels of tryptophan hydroxylase-1 expression, the enzyme that catalyzes the rate-limiting step in serotonin biosynthesis. Finally, mean values for 25(OH)D were lower in IBS patients relative to non-IBS controls.

CONCLUSIONS

Values for serum 25(OH)D concentrations exhibited a trend towards lower vitamin D levels within the IBS cohort. In addition, the expression of select IBS genetic biomarkers, including tryptophan hydroxylase 1, was modulated by vitamin D. Strikingly, the direction of gene regulation elicited by vitamin D in colonic cells is "opposite" to the gene expression profile observed in IBS patients, suggesting that vitamin D may help "reverse" the pathological direction of biomarker gene expression in IBS. Thus, our results intimate that IBS pathogenesis and pathophysiology may involve dysregulated serotonin production and/or vitamin D insufficiency.

Effect of leucine uptake on hepatic and skeletal muscle gene expression in rats: a microarray analysis

[Purpose]

This study was performed to explore the physiological functions of leucine by exploring genes with leucine-dependent variability using DNA microarray.

[Methods]

Sprague-Dawley rats (n = 20) were separated into a HPD (30% High Protein Diet, n = 10) group and a NPD (0% Non Protein Diet, n = 10) group and fed a protein diet for 2 weeks. At the end of the 2-week period, the rats were fasted for 12-16 hours, further separated into subgroups within the HPD (Saline, n = 5, Leucine, n = 5) and NPD (Saline, n = 5, Leucine, n = 5) groups and administered with a leucine solution. The liver and muscles were harvested after 2 hours for RNA extraction. RNA purification from the isolated muscles and target gene identification using DNA chip were performed. The target gene was determined based on the results of the DNA chip experiment, and mRNA expression of the target gene was analyzed using Real-Time PCR.

[Results]

In the skeletal muscle, 27 genes were upregulated while 52 genes were down regulated after leucine administration in the NPD group. In the liver, 160 genes were up-regulated while 126 were down-regulated. The per2 gene was one of the genes with leucine-dependent induction in muscles and liver.

[Conclusion]

This study was performed to explore the physiological functions of leucine, however, a large number of genes showed variability. Therefore, it was difficult to definitively identify the genes linked with a particular physiological function. Various nutritional effects of leucine were observed. High variability in cytokines, receptors, and various membrane proteins were observed, which suggests that leucine functions as more than a nutrient. The interpretation may depend on investigators’ perspectives, therefore, discussion with relevant experts and the BCAA (Branched-Chain Amino Acids) society may be needed for effective utilization of this data.

Inhalation Anesthesia-Induced Neuronal Damage and Gene Expression Changes in Developing Rat Brain

Nitrous Oxide (N2O), an N-methyl-D-aspartate (NMDA) receptor antagonist, and isoflurane (ISO), which acts on multiple receptors including postsynaptic gamma-aminobutyric acid (GABA) receptors, are frequently used inhalation anesthetics, alone or as a part of a balanced anesthetic regimen administered to pregnant women and to human neonates and infants requiring surgery. The current study investigated histological features and gene expression profiles in response to prolonged exposure to N2O or ISO alone, and their combination in developing rat brains. Postnatal day 7 rats were exposed to clinically-relevant concentrations of N2O (70%), ISO (1.0%) or N2O plus ISO (N2O + ISO) for 6 hours. The neurotoxic effects were evaluated and the brain tissues were harvested for RNA extraction 6 hours after anesthetic administration. The prolonged exposure to N2O + ISO produced elevated neuronal cell death as indicated by an increased number of TUNEL-positive cells in frontal cortical levels compared with control. No significant neurotoxic effects were observed in animals exposed to N2O or ISO alone. DNA microarray analysis revealed gene expression changes after N2O, ISO or N2O + ISO exposure. Differentially expressed genes (DEGs) from the N2O + ISO group were significantly associated with 45 pathways directly related to brain functions. Although the gene expression profiles from animals exposed to N2O or ISO alone were remarkably different from those of the control group, the pathways of these genes involved were not closely associated with neurons. These findings provide novel insights into the mechanisms by which N2O + ISO cause neurotoxicity in the developing brain, suggesting multiple factors are involved in the neuronal cell death-inducing effects (cascades) of N2O + ISO.

Prediction of microbial infection of cultured cells using DNA microarray gene-expression profiles of host responses

Infection by microorganisms may cause fatally erroneous interpretations in the biologic researches based on cell culture. The contamination by microorganism in the cell culture is quite frequent (5% to 35%). However, current approaches to identify the presence of contamination have many limitations such as high cost of time and labor, and difficulty in interpreting the result. In this paper, we propose a model to predict cell infection, using a microarray technique which gives an overview of the whole genome profile. By analysis of 62 microarray expression profiles under various experimental conditions altering cell type, source of infection and collection time, we discovered 5 marker genes, NM_005298, NM_016408, NM_014588, S76389, and NM_001853. In addition, we discovered two of these genes, S76389, and NM_001853, are involved in a Mycolplasma-specific infection process. We also suggest models to predict the source of infection, cell type or time after infection. We implemented a web based prediction tool in microarray data, named Prediction of Microbial Infection (http://www.snubi.org/software/PMI).

Fluorescence lifetime imaging of quantum dot labeled DNA microarrays

Quantum dot (QD) labeling combined with fluorescence lifetime imaging microscopy is proposed as a powerful transduction technique for the detection of DNA hybridization events. Fluorescence lifetime analysis of DNA microarray spots of hybridized QD labeled target indicated a characteristic lifetime value of 18.8 ns, compared to 13.3 ns obtained for spots of free QD solution, revealing that QD labels are sensitive to the spot microenvironment. Additionally, time gated detection was shown to improve the microarray image contrast ratio by 1.8, achieving femtomolar target sensitivity. Finally, lifetime multiplexing based on Qdot525 and Alexa430 was demonstrated using a single excitation-detection readout channel.