Numerous genetic and environmental factors contribute to neurodegenerative diseases characterized by damage to the DNA and changes in the chromatin structure. Many studies have shown that DNA damage and chromatin organization are closely linked, but more research is needed to fully understand this connection, especially in neurodegenerative diseases. Important proteins implicated in neurodegenerative disorders have been linked to chromatin reconfiguration and DNA damage, according to recent research. Epigenetic interventions such as HDAC inhibitors approved for cancer therapy, can be repurposed for neurodegenerative diseases. Furthermore, microRNAs, often dysregulated in neurodegenerative conditions, could be targeted to restore normal gene regulation. Exploring these strategies could lead to more effective treatments by addressing the fundamental epigenetic and chromatin-related mechanisms involved in neurodegeneration. This review discusses the relationship between the contributing proteins and various neurodegenerative diseases, with particular attention to key proteins like tau, which is associated with microtubules, superoxide dismutase 1, huntingtin, α-synuclein, β-amyloid precursor protein and TAR DNA/RNA binding protein 43 and their role in DNA protection and damage repair.
Hypertrophic cardiomyopathy (HCM) is a monogenic cardiovascular disorder that has been poorly studied at the molecular, genetic, and computational levels. Here, we examined the genetic map of HCM polymorphic targets using a computational approach to identify new phytochemicals with potential therapeutic properties. We demonstrate the range of mutations associated with cardiomyopathies, and identify new associations between genes and phenotypes in this disease category. Specifically, our findings suggest that several genes associated with channelopathies might serve as genetic modifiers, altering the clinical features and severity of cardiomyopathic phenotypes, thus likely impacting disease manifestation.
To study the potential molecular mechanism of chrysin in treating HSV-1 based on network pharmacology.
The targets of chrysin were predicted using the SEA, Swiss, and PharmMapper databases, and HSV-1 infection-related genes were identified from the NCBI and Genecard databases. A protein-protein interaction (PPI) network was constructed using Cytoscape 3.9.1 with these genes, followed by GO enrichment and KEGG pathway analyses. Molecular docking was employed to analyze the interaction sites using the AutoDock Vina algorithm.
Network pharmacology analysis identified 178 potential targets associated with chrysin treatment of HSV. Moreover, 2029 HSV-1-related genes were identified, 43 of which were overlapped with chrysin treatment targets. Additionally, 358 GO entries were identified, encompassing 255 biological processes (BP), 38 molecular functions (MF), and 65 cell components (CC). Molecular docking simulations were conducted to assess the binding affinity between chrysin and the predicted hub genes (SRC, VEGFA, EGFR, PTGS2, CDK1, AR, PARP1, and ABL1).
In this study, a potential molecular target of chrysin action in combating HSV-1 infection was identified, offering a novel approach to enhancing the antiviral effectiveness in patients with HSV-1 infection.
The article titled “The Complete telomere-to-telomere Sequence of a Mouse Genome” provides a significant advancement in the field of genomics by completing the telomere-to-telomere (T2T) sequencing of the mouse genome, a task that had previously been hindered by gaps, particularly in regions rich in repetitive sequences. Their work addresses long-standing limitations in the current mouse genome assembly, GRCm39, which, despite being the most widely used reference, left over about 8% of the genome unsequenced. These previously inaccessible regions include crucial areas such as ribosomal DNA arrays, pericentromeric regions, and subtelomeric regions, as well as additional protein-coding genes.
The DNA damage response (DDR) network comprises a range of protein factors and post-translational modifications (PTMs) that cooperate to maintain genomic stability following DNA damage. Lysine crotonylation (Kcr) is an emerging PTM, though its role in the DDR has not been thoroughly explored. We used quantitative proteomics to identify global Kcr substrates and assess their changes in response to DNA damage. Our results revealed 593 Kcr sites on 360 proteins that increased by more than 1.5-fold, while 331 Kcr sites on 233 proteins decreased by more than 0.67-fold following etoposide-induced DNA damage. Alterations in Kcr levels particularly in RNA splicing factors were most markedly pronounced before and after DNA damage. This study presents the first Kcr proteome regulated during the DDR and highlights the potential critical role of RNA-related factors in this process.
Cancer cells often remodel their catabolic processes to support proliferation, growth, survival, and progression. This study investigated the transcriptional dysregulation of choline catabolism genes in pan-cancer, using TCGA and mRNA expression profiles from liver cancer cohorts. The studies revealed that choline catabolic genes, including choline kinase A, choline kinase B, choline dehydrogenase, and choline phosphotransferase, were prominently activated in stage-specific hepatocellular carcinoma (HCC) liver tumors with significant p-values (p < 0.0001). Additionally, these genes were further analyzed for their ontological functionality, showing that they play a crucial role in the biosynthesis of phosphatidylcholine, essential for membrane synthesis during cell proliferation and survival. Furthermore, ROC curve analysis demonstrated greater specificity and sensitivity for these genes in stage-specific HCC tumors with significant area under the curve values. Overall survival studies also confirmed that these genes were associated with poor survival in HCC patients with significant p-values (p < 0.05). Gene effect score analysis revealed higher negative scores for choline catabolic genes in liver tumor cell lines. Moreover, integrative genomic drug sensitivity studies identified a negative correlation with this catabolism, highlighting potential therapeutic targets such as Bryostatin1, Amuvatinib, FH535, Linsitinib, and DMOG. These findings could pave the way for the use of targeted therapies that focus on choline catabolic dysregulation in HCC treatment.
Berberine, a traditional Chinese herbal compound, is known for its broad range of biological activities, including anticancer and phototoxic effects. However, the precise mechanisms underlying its phototoxicity in liver cancer cells remain unclear. In this study, we investigated the potential of berberine as a photosensitizer for photodynamic therapy (PDT) by examining its phototoxic effects under blue light irradiation (488 nm). The results showed that berberine rapidly translocated from the mitochondria to the nucleus upon light exposure, ultimately inducing cell death in SNU449 and Huh7 cells. Additionally, we observed a significant increase in reactive oxygen species, linking the phototoxic effects to oxidative stress. EdU/DAPI staining further revealed a marked reduction in DNA replication, with a complete absence of SNU449 cells in the S phase, indicating cell cycle arrest following treatment with berberine and PDT. Transcriptomic analysis also showed extensive gene expression changes, with GO enrichment indicating altered chromatin accessibility and cellular stress response following berberine and PDT combination therapy. qPCR and Western blotting confirmed that ER stress was significantly induced, triggering the activation of the pro-apoptotic protein DDIT3, which contributes to berberine-PDT-induced cell death. These findings underscore the potential of berberine as a photosensitizer and provide a promising approach for enhancing liver cancer treatment using PDT.