The effects of environmental stressors on candidate aging associated genes

Targeting TOP2B as a vulnerability in aging and aging-related diseases

The ongoing trend of rapid aging of the global population has unavoidably resulted in an increase in aging-related diseases. There is an immense amount of interest in the scientific community for the identification of molecular targets that may effectively mitigate the process of aging and aging-related diseases. The enzyme Topoisomerase IIβ (TOP2B) plays a crucial role in resolving the topological challenges that occur during DNA-related processes. It is believed that the disruption of TOP2B function contributes to the aging of cells and tissues, as well as the development of age-related diseases. Consequently, targeting TOP2B appears to be a promising approach for interventions aimed at mitigating the effects of aging. This review focuses on recent advancements in the understanding of the role of TOP2B in the processing of aging and aging-related disorders, thus providing a novel avenue for the development of anti-aging strategies.

Dissecting Mitochondrial Mechanisms of Alzheimer's Disease Using Gene Dependency Network and Its Implications for Discovering Nutrients Combatting the Disease

BACKGROUND

Alzheimer's disease (AD) is the leading cause of dementia, with its prevalence increasing as the global population ages. AD is a multifactorial and intricate neurodegenerative disease with pathological changes varying from person to person. Because the mechanism of AD is highly controversial, effective treatments remain a distant prospect. Currently, one of the most promising hypotheses posits mitochondrial dysfunction as an early event in AD diagnosis and a potential therapeutic target.

OBJECTIVE

Here, we adopted a systems medicine strategy to explore the mitochondria-related mechanisms of AD. Then, its implications for discovering nutrients combatting the disease were demonstrated.

METHODS

We employed conditional mutual information (CMI) to construct AD gene dependency networks. Furthermore, the GeneRank algorithm was applied to prioritize the gene importance of AD patients and identify potential anti-AD nutrients targeting crucial genes.

RESULTS

The results suggested that two highly interconnected networks of mitochondrial ribosomal proteins (MRPs) play an important role in the regulation of AD pathology. The close association between mitochondrial ribosome dysfunction and AD was identified. Additionally, we proposed seven nutrients with potential preventive and ameliorative effects on AD, five of which have been supported by experimental reports.

CONCLUSIONS

Our study explored the important regulatory role of MRP genes in AD, which has significant implications for AD prevention and treatment.

scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data

BACKGROUND

Single-cell RNA sequencing (scRNA-seq) methods have been advantageous for quantifying cell-to-cell variation by profiling the transcriptomes of individual cells. For scRNA-seq data, variability in gene expression reflects the degree of variation in gene expression from one cell to another. Analyses that focus on cell-cell variability therefore are useful for going beyond changes based on average expression and, instead, identifying genes with homogeneous expression versus those that vary widely from cell to cell.

RESULTS

We present a novel statistical framework, scShapes, for identifying differential distributions in single-cell RNA-sequencing data using generalized linear models. Most approaches for differential gene expression detect shifts in the mean value. However, as single-cell data are driven by overdispersion and dropouts, moving beyond means and using distributions that can handle excess zeros is critical. scShapes quantifies gene-specific cell-to-cell variability by testing for differences in the expression distribution while flexibly adjusting for covariates if required. We demonstrate that scShapes identifies subtle variations that are independent of altered mean expression and detects biologically relevant genes that were not discovered through standard approaches.

CONCLUSIONS

This analysis also draws attention to genes that switch distribution shapes from a unimodal distribution to a zero-inflated distribution and raises open questions about the plausible biological mechanisms that may give rise to this, such as transcriptional bursting. Overall, the results from scShapes help to expand our understanding of the role that gene expression plays in the transcriptional regulation of a specific perturbation or cellular phenotype. Our framework scShapes is incorporated into a Bioconductor R package (https://www.bioconductor.org/packages/release/bioc/html/scShapes.html).

Abnormal Expression of Mitochondrial Ribosomal Proteins and Their Encoding Genes with Cell Apoptosis and Diseases

Mammalian mitochondrial ribosomes translate 13 proteins encoded by mitochondrial genes, all of which play roles in the mitochondrial respiratory chain. After a long period of reconstruction, mitochondrial ribosomes are the most protein-rich ribosomes. Mitochondrial ribosomal proteins (MRPs) are encoded by nuclear genes, synthesized in the cytoplasm and then, transported to the mitochondria to be assembled into mitochondrial ribosomes. MRPs not only play a role in mitochondrial oxidative phosphorylation (OXPHOS). Moreover, they participate in the regulation of cell state as apoptosis inducing factors. Abnormal expressions of MRPs will lead to mitochondrial metabolism disorder, cell dysfunction, etc. Many researches have demonstrated the abnormal expression of MRPs in various tumors. This paper reviews the basic structure of mitochondrial ribosome, focuses on the structure and function of MRPs, and their relationships with cell apoptosis and diseases. It provides a reference for the study of the function of MRPs and the disease diagnosis and treatment.