An integrated bioinformatics strategy to elucidate the function of hub genes linked to Alzheimer's disease

Epigenetic Modifications Associated With Wildland-Urban Interface (WUI) Firefighting

Wildland-urban interface (WUI) firefighting involves exposure to burning vegetation, structures, and other human-made hazards, often without respiratory protection. Response activities can last for long periods of time, spanning multiple days or weeks. Epigenetic modifications, including microRNA (miRNA) expression and DNA methylation, are responsive to toxicant exposures and are part of the development of cancers and other diseases. Epigenetic modifications have not been studied in relation to WUI fires. Firefighters (n = 99) from southern California, including 79 firefighters who responded to at least one WUI fire, provided blood samples at baseline and approximately 10 months later. We quantified the relative abundance of 800 miRNAs in blood samples using the nCounter Human v3 miRNA expression panel and blood leukocyte DNA methylation throughout the genome via the Infinium EPIC array. We used linear mixed models to compare the expression of each miRNA across time and DNA methylation at each locus, adjusting for potential confounders. In the miRNA analysis among all firefighters, 65 miRNAs were significantly different at follow-up compared to baseline at a false discovery rate of 5%. Results were similar when restricted to firefighters with a recorded WUI fire exposure during the interim period, although only 50 were significant. Expression of miRNA hsa-miR-518c-3p, a tumor suppressor, was significantly associated with WUI fire response (fold change 0.77, 95% CI = [0.69, 0.87]). In the DNA methylation analysis, no statistically significant changes over time were identified. In summary, WUI fire exposures over a wildfire season altered miRNA expression but did not substantially impact DNA methylation.

Investigating gene expression datasets of hippocampus tissue to discover Alzheimer's disease-associated molecular markers

BACKGROUND

Alzheimer's disease (AD) is an advancing neurodegenerative disorder distinguished by the formation of amyloid plaques and neurofibrillary tangles in the human brain. Nevertheless, the lack of peripheral biomarkers that can detect the development of AD remains a significant limitation.

OBJECTIVE

The main aim of this work was to discover the molecular markers associated with AD.

METHODS

We conducted a comprehensive microarray analysis of gene expression data from hippocampus tissue in AD patients and control samples using three microarray datasets (GSE1297, GSE28146, and GSE29378) collected from Gene Expression Omnibus (GEO). The datasets were pre-processed and normalized, revealing 346 significant genes, 103 of which were upregulated and 243 downregulated. The PPI network of significant genes was constructed to detect the top 50 hub genes, which were then further analyzed using Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes pathway (KEGG), and GSEA, revealing 47 key genes involved in AD-related pathways. These key genes were then subjected to feed forward loop (FFL) motif analysis for the prediction of transcriptional factors (TFs) and microRNAs (miRNAs) mediated gene regulatory networks.

RESULTS

The interaction of AD-associated TFs HNF4A, SPI1, EGR1, STAT3, and MYC and miRNAs hsa-miR-155-5p and hsa-miR-16-5p in the transcriptional and post-transcriptional events of 3 upregulated and 10 downregulated genes: H2AFZ, MCM3, MYO1C, AXIN1, CCND1, ETS2, MYH9, RELA, RHEB, SOCS3, TBL1X, TBP, TXNIP, and YWHAZ, respectively, has been identified. The miRNA/TF-mediated three types of the FFL motifs, i.e., miRNA-FFL, TF-FFL, and composite-FFL, were constructed, and seven common genes among these FFL were identified: CCND1, MYH9, SOCS3, RHEB, MYO1C, TXNIP, AXIN1, and TXNIP.

CONCLUSIONS

These findings may provide insights into the development of potential molecular markers for therapeutic management of AD.

Recent advancement in understanding of Alzheimer's disease: Risk factors, subtypes, and drug targets and potential therapeutics

Alzheimer's disease (AD) is a significant neocortical degenerative disorder characterized by the progressive loss of neurons and secondary alterations in white matter tracts. Understanding the risk factors and mechanisms underlying AD is crucial for developing effective treatments. The risk factors associated with AD encompass a wide range of variables, including gender differences, family history, and genetic predispositions. Additionally, environmental factors such as air pollution and lifestyle-related conditions like cardiovascular disease, gut pathogens, and liver pathology contribute substantially to the development and progression of AD and its subtypes. This review provides current update and deeper insights into the role of diverse risk factors, categorizing AD into its distinct subtypes and elucidating their specific pathophysiological mechanisms. Unlike previous studies that often focus on isolated aspects of AD, our review integrates these factors to offer a comprehensive understanding of the disease. Furthermore, the review explores a variety of drug targets linked to the neuropathology of different AD subtypes, highlighting the potential for targeted therapeutic interventions. We further discussed the novel therapeutic options and categorized them according to their targets. The roles of different drug targets were comprehensively studied, and the mechanism of action of their inhibitors was discussed in detail. By comprehensively covering the interplay of risk factors, subtype differentiation, and drug targets, this review provides a deeper understanding of AD and suggests directions for future research and therapeutic strategies.

Network Pharmacology Reveals Key Targets and Pathways of Madhuca longifolia for Potential Alzheimer's Disease Treatment

Madhuca longifolia, commonly known as the mahua tree, has been traditionally used in medicine due to its anti-inflammatory, anti-diabetic, and antimicrobial properties. Its active compounds help in managing diabetes, alleviating cognitive impairment associated with Alzheimer's disease. Nonetheless, the exact neuroprotective mechanism of Madhuca longifolia against Alzheimer's disease remains unclear. This study looked into possible methods by which Madhuca longifolia protects against Alzheimer's disease using network pharmacology, molecular docking and molecular dynamic simulations studies. By applying pre-screening of active constituents, target prediction, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analysis, our study found that Madhuca longifolia is related to eight active ingredients (Ascorbic acid, Riboflavin, Pantothenic acid, (4 R)-2beta,3beta,23-trihydroxy-oleana-5,12-dien-28-oic acid, Quercetin, Nicotinic acid, Bassiaic acid Thiamine) and 272 common gene targets, with significant involvement in pathways such as PI3K-Akt signaling and neuroactive ligand-receptor interaction. Network analysis demonstrated how Madhuca longifolia can prevent AD by modifying important signalling networks, which may be one of the molecular mechanisms driving the plant's effectiveness against the disease. Molecular docking studies revealed that there were robust binding abilities of Quercetin, Riboflavin and Pantothenic acid to key target proteins AKT1, JUN, and STAT3. Later, molecular dynamic simulations was done to examine the successful activity of the active compounds against potential targets, and it was found that AKT1 and AKT1-Quercetin complex became stable at 260 ps. It may be seen through the study that quercetin may act as a good inhibitor for treatment. This thorough investigation provides a strong basis for future research and development efforts by advancing our understanding of Madhuca longifolia medicinal potential in Alzheimer's disease.

Abnormalities in sex hormones and sexual dysfunction in males with diabetes mellitus: A mechanistic insight

Diabetes is a considerate metabolic disorder that can lead to a series of complications, involving the malfunctioning of the reproductive system of males. It has been observed that there is a gradual rise in male diabetic patients and almost half of the diabetic males have low semen quality and decrease reproductive function. In diabetic conditions, prolonged hyperglycemia leads to oxidative stress, diabetic neuropathy, and insulin resistance. Insulin resistance and its deficiency can impair the hypothalamus, pituitary gland, gonads, and perigonads. This causes a decrease in the secretion of gonadal steroids such as GnRH (gonadotropin-releasing hormone), FSH (follicle-stimulating hormone), LH (luteinizing hormone), and Testosterone. Moreover, it also causes damage to the testicles, spermatogenic and stromal cells, seminiferous tubules, and various structural injuries to male reproductive organs. During spermatogenesis, glucose metabolism plays an important role, because the fundamental activities of cells and their specific features, such as motility and mature sperm fertilization activity, are maintained by glucose metabolism. All these activities can influence the fertility and reproductive health of males. But the glucose metabolism is primarily disrupted in diabetic conditions. Until now, there has been no medicine focusing on the reproductive health of diabetic people. In this chapter, we review the consequences of diabetes on the reproductive system of males and all the pathways involved in the dysfunction of the reproductive system. This will help interpret the effects of DM on male reproductive health.

Modulation of Small RNA Signatures by Astrocytes on Early Neurodegeneration Stages; Implications for Biomarker Discovery

Diagnosis of neurodegenerative disease (NDD) is complex, therefore simpler, less invasive, more accurate biomarkers are needed. small non-coding RNA (sncRNA) dysregulates in NDDs and sncRNA signatures have been explored for the diagnosis of NDDs, however, the performance of previous biomarkers is still better. Astrocyte dysfunction promotes neurodegeneration and thus derived scnRNA signatures could provide a more precise way to identify of changes related to NDD course and pathogenesis, and it could be useful for the dissection of mechanistic insights operating in NDD. Often sncRNA are transported outside the cell by the action of secreted particles such as extracellular vesicles (EV), which protect sncRNA from degradation. Furthermore, EV associated sncRNA can cross the BBB to be found in easier to obtain peripheral samples, EVs also inherit cell-specific surface markers that can be used for the identification of Astrocyte Derived Extracellular Vesicles (ADEVs) in a peripheral sample. By the study of the sncRNA transported in ADEVs it is possible to identify astrocyte specific sncRNA signatures that could show astrocyte dysfunction in a more simpler manner than previous methods. However, sncRNA signatures in ADEV are not a copy of intracellular transcriptome and methodological aspects such as the yield of sncRNA produced in ADEV or the variable amount of ADEV captured after separation protocols must be considered. Here we review the role as signaling molecules of ADEV derived sncRNA dysregulated in conditions associated with risk of neurodegeneration, providing an explanation of why to choose ADEV for the identification of astrocyte-specific transcriptome. Finally, we discuss possible limitations of this approach and the need to improve the detection limits of sncRNA for the use of ADEV derived sncRNA signatures.

History in Perspective: The Prime Pathological Players and Role of Phytochemicals in Alzheimer’s Disease

Alzheimer's disease is a steadily progressive, irreversible neurological disorder that is most frequently categorized under the umbrella term "neurodegeneration". Several attempts are underway to clarify the pathogenic mechanisms, identify the aetiologies, and determine a pathway by which the therapeutic steps can be implemented. Oxidative stress is one of the pathogenic processes, which is commonly believed to be associated with neurodegenerative diseases. Accumulation of extracellular amyloid-β protein (Aβ), hyperphosphorylation of tau, initiation of neurometabolic reactions characterized by the loss of neuronal function and synaptic failure, and decreased or lost learning capability and memory function are the most central neuropathological characteristics of AD. According to the amyloid cascade hypothesis, the enhanced deposition of Aβ deposits and neurofibrillary tangles due to hyperphosphorylation of Tau activates the cascade reactions in the brain. These reactions affect the synaptic activity and activation of microglia, which results in neuroinflammation due to enhanced immune function. Plant-based phytochemicals have also been used long ago against several diseases. Phytoconstituents play a significant neuroprotective property by preventing the pathophysiology of the disease. In this review, we have discussed the formation and crosstalk between amyloid and tau pathologies as well as the effect of neuroinflammation on the progression of AD. We have specifically focused on the formation of NFT, β-amyloids, inflammation, and pathophysiology of AD and the role of phytochemicals in the prevention of AD.

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AD is an insidious, slowly progressive, and neurodegenerative disorder.

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Common symptoms are memory loss, difficulty in recalling, and understanding.

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β-amyloids and Neurofibrillary tangles are the main factors in AD pathogenesis.

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Activated microglia and oxidative stress have different effects on AD progression.

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Phytochemicals show a key role against AD by inhibiting several pathways.