HDAC1/2 inhibitor therapy improves multiple organ systems in aged mice

Identifying Age-Modulating Compounds Using a Novel Computational Framework for Evaluating Transcriptional Age

The differentiation of human pluripotent stem cells (hPSCs) provides access to a wide range of cell types and tissues. However, hPSC-derived lineages typically represent a fetal stage of development, and methods to expedite the transition to an aged identity to improve modeling of late-onset disease are limited. In this study, we introduce RNAge, a transcriptome-based computational platform designed to enable the evaluation of an induced aging or a rejuvenated state. We validated this approach across independent datasets spanning different tissues and species, and show that it can be used to evaluate the effectiveness of existing age-retaining or age-modulating interventions. We also used RNAge to perform an in silico compound screen using the LINCS L1000 dataset. This approach led to the identification and experimental confirmation of several novel compounds capable of inducing aging or rejuvenation in primary fibroblasts or hPSC-derived neurons. Additionally, we observed that applying this novel induced aging strategy to an hPSC model of Alzheimer's disease (AD) accelerated neurodegeneration in a genotype-specific manner. Our study offers a robust method for quantifying age-related manipulations and unveils compounds that significantly broaden the toolkit for age-modifying strategies in hPSC-derived lineages.

Histone deacetylases and their inhibitors in kidney diseases

Histone deacetylases (HDACs) have emerged as key regulators in the pathogenesis of various kidney diseases. This review explores recent advancements in HDAC research, focusing on their role in kidney development and their critical involvement in the progression of chronic kidney disease (CKD), acute kidney injury (AKI), autosomal dominant polycystic kidney disease (ADPKD), and diabetic kidney disease (DKD). It also discusses the therapeutic potential of HDAC inhibitors in treating these conditions. Various HDAC inhibitors have shown promise by targeting specific HDAC isoforms and modulating a range of biological pathways. Their protective effects include modulation of apoptosis, autophagy, inflammation, and fibrosis, underscoring their broad therapeutic potential for kidney diseases. However, further research is essential to improve the selectivity of HDAC inhibitors, minimize toxicity, overcome drug resistance, and enhance their pharmacokinetic properties. This review offers insights to guide future research and prevention strategies for kidney disease management.

A new Similarity Based Adapted Louvain Algorithm (SIMBA) for active module identification in p-value attributed biological networks

Real-world networks, such as biological networks, often exhibit complex structures and have attributes associated with nodes, which leads to significant challenges for analysis and modeling. Community detection algorithms can help identify groups of nodes of particular importance. However, traditional methods focus primarily on topological information, overlooking the importance of attribute-based similarities. This limitation hinders their ability to identify functionally coherent subnetworks. To address this, we propose a new scoring method for graph partitioning on the basis of a novel similarity function between node attributes. We then adapt the Louvain algorithm to optimize this scoring function, enabling the identification of communities that are both densely connected and functionally coherent. Extensive experiments on diverse biological networks, including artificial and real-world datasets, demonstrate the superiority of our approach over state-of-the-art methods. By leveraging both topological and attribute-based information, our approach provides a powerful tool for uncovering biologically meaningful modules and gaining deeper insights into complex biological processes.

Aging and tumors: a dynamic interaction

Aging is an inevitable physiological process in organisms, and the development of tumors is closely associated with cellular senescence. This article initially examines the role of cellular senescence in tumorigenesis, emphasizing the correlation between telomere length-a marker of cellular senescence-and tumor risk. Concurrently, the study explores the expression levels of senescence-associated markers, such as p16, p53, and mTOR, in the context of tumor development. Additionally, the study investigates the impact of tumors on cellular and organismal senescence, including the effects on immune system function and metabolic processes. Ultimately, the discussion explores the potential application of anti-aging strategies in tumor therapy and considers the possibility of utilizing senescence mechanisms as a novel therapeutic approach for tumors. This research provides novel insights into the complex interplay between senescence and tumor development, suggesting potential strategies for future preventative measures and therapeutic interventions.

Epigenetic modifications and emerging therapeutic targets in cardiovascular aging and diseases

The complex mechanisms underlying the development of cardiovascular diseases remain not fully elucidated. Epigenetics, which modulates gene expression without DNA sequence changes, is shedding light on these mechanisms and their heritable effects. This review focus on epigenetic regulation in cardiovascular aging and diseases, detailing specific epigenetic enzymes such as DNA methyltransferases (DNMTs), histone acetyltransferases (HATs), and histone deacetylases (HDACs), which serve as writers or erasers that modify the epigenetic landscape. We also discuss the readers of these modifications, such as the 5-methylcytosine binding domain proteins, and the erasers ten-eleven translocation (TET) proteins. The emerging role of RNA methylation, particularly N6-methyladenosine (m6A), in cardiovascular pathogenesis is also discussed. We summarize potential therapeutic targets, such as key enzymes and their inhibitors, including DNMT inhibitors like 5-azacytidine and decitabine, HDAC inhibitors like belinostat and givinotide, some of which have been approved by the FDA for various malignancies, suggesting their potential in treating cardiovascular diseases. Furthermore, we highlight the role of novel histone modifications and their associated enzymes, which are emerging as potential therapeutic targets in cardiovascular diseases. Thus, by incorporating the recent studies involving patients with cardiovascular aging and diseases, we aim to provide a more detailed and updated review that reflects the advancements in the field of epigenetic modification in cardiovascular diseases.

Chromatin accessibility: biological functions, molecular mechanisms and therapeutic application

The dynamic regulation of chromatin accessibility is one of the prominent characteristics of eukaryotic genome. The inaccessible regions are mainly located in heterochromatin, which is multilevel compressed and access restricted. The remaining accessible loci are generally located in the euchromatin, which have less nucleosome occupancy and higher regulatory activity. The opening of chromatin is the most important prerequisite for DNA transcription, replication, and damage repair, which is regulated by genetic, epigenetic, environmental, and other factors, playing a vital role in multiple biological progresses. Currently, based on the susceptibility difference of occupied or free DNA to enzymatic cleavage, solubility, methylation, and transposition, there are many methods to detect chromatin accessibility both in bulk and single-cell level. Through combining with high-throughput sequencing, the genome-wide chromatin accessibility landscape of many tissues and cells types also have been constructed. The chromatin accessibility feature is distinct in different tissues and biological states. Research on the regulation network of chromatin accessibility is crucial for uncovering the secret of various biological processes. In this review, we comprehensively introduced the major functions and mechanisms of chromatin accessibility variation in different physiological and pathological processes, meanwhile, the targeted therapies based on chromatin dynamics regulation are also summarized.

Amide Alkaloids as Privileged Sources of Senomodulators for Therapeutic Purposes in Age-Related Diseases

Nature is an important source of bioactive compounds and has continuously made a large contribution to the discovery of new drug leads. Particularly, plant-derived compounds have long been identified as highly interesting in the field of aging research and senescence. Many plants contain bioactive compounds that have the potential to influence cellular processes and provide health benefits. Among them, Piper alkaloids have emerged as interesting candidates in the context of age-related diseases and particularly senescence. These compounds have been shown to display a variety of features, including antioxidant, anti-inflammatory, neuroprotective, and other bioactive properties that may help counteracting the effects of cellular aging processes. In the review, we will put the emphasis on piperlongumine and other related derivatives, which belong to the Piper alkaloids, and whose senomodulating potential has emerged during the last several years. We will also provide a survey on their potential in therapeutic perspectives of age-related diseases.

Protective Effect of Que Zui Tea on d-Galactose-Induced Oxidative Stress Damage in Mice via Regulating SIRT1/Nrf2 Signaling Pathway

Que Zui tea (QT) is an important herbal tea in the diet of the 'Yi' people, an ethnic group in China, and it has shown significant antioxidant, anti-inflammatory, and hepatoprotective effects in vitro. This study aims to explore the protective effects of the aqueous-ethanol extract (QE) taken from QT against ᴅ-galactose (ᴅ-gal)-induced oxidative stress damage in mice and its potential mechanisms. QE was identified as UHPLC-HRMS/MS for its chemical composition and possible bioactive substances. Thus, QE is rich in phenolic and flavonoid compounds. Twelve compounds were identified, the main components of which were chlorogenic acid, quinic acid, and 6'-O-caffeoylarbutin. Histopathological and biochemical analysis revealed that QE significantly alleviated brain, liver, and kidney damage in ᴅ-gal-treated mice. Moreover, QE remarkably attenuated oxidative stress by activating the Nrf2/HO-1 pathway to increase the expression of antioxidant indexes, including GSH, GSH-Px, CAT, SOD, and T-AOC. In addition, QE administration could inhibit the IL-1β and IL-6 levels, which suppress the inflammatory response. QE could noticeably alleviate apoptosis by inhibiting the expressions of Caspase-3 and Bax proteins in the brains, livers, and kidneys of mice. The anti-apoptosis mechanism may be related to the upregulation of the SIRT1 protein and the downregulation of the p53 protein induced by QE in the brain, liver, and kidney tissues of mice. Molecular docking analysis demonstrated that the main components of QE, 6'-O-caffeoylarbutin, chlorogenic acid, quinic acid, and robustaside A, had good binding ability with Nrf2 and SIRT1 proteins. The present study indicated that QE could alleviate ᴅ-gal-induced brain, liver and kidney damage in mice by inhibiting the oxidative stress and cell apoptosis; additionally, the potential mechanism may be associated with the SIRT1/Nrf2 signaling pathway.