Search

The progressive aging of the global population and the high impact of neurodegenerative diseases, such as Alzheimer's disease (AD), underscore the urgent need for innovative diagnostic and therapeutic strategies. AD, the most prevalent neurodegenerative disorder among the elderly, is expected to affect 75 million people in developing countries by 2030. Despite extensive research, the precise etiology of AD remains elusive due to its heterogeneity and complexity. The key pathological features of AD, including amyloid-beta plaques and hyperphosphorylated tau protein, are established years before clinical symptoms appear. Recent studies highlight the pivotal role of neuroinflammation in AD pathogenesis, with the chronic activation of the brain's immune system contributing to the disease's progression. Pro-inflammatory cytokines, such as TNF- α , IL-1 β , and IL-6, are elevated in AD and mild cognitive impairment (MCI) patients, suggesting a strong link between peripheral inflammation and CNS degeneration. There is a pressing need for minimally invasive, cost-effective diagnostic methods. Buccal mucosa cells and saliva, which share an embryological origin with the CNS, show promise for AD diagnosis and prognosis. This study integrates cellular observations with advanced data processing and machine learning to identify significant biomarkers and patterns, aiming to enhance the early diagnosis and prevention strategies for AD. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) is the most common cause of neurodegenerative dementia in the elderly, which is characterized by progressive cognitive impairment. Herein, we undertake a sophisticated computational analysis by integrating single-cell RNA sequencing (scRNA-seq) data from multiple brain regions significantly affected by the disease, including the entorhinal cortex, prefrontal cortex, superior frontal gyrus, and superior parietal lobe. Our pipeline combines datasets derived from the aforementioned tissues into a unified analysis framework, facilitating cross-regional comparisons to provide a holistic view of the impact of the disease on the cellular and molecular landscape of the brain. We employed advanced computational techniques such as batch effect correction, normalization, dimensionality reduction, clustering, and visualization to explore cellular heterogeneity and gene expression patterns across these regions. Our findings suggest that enabling the integration of data from multiple batches can significantly enhance our understanding of AD complexity, thereby identifying key molecular targets for potential therapeutic intervention. This study established a precedent for future research by demonstrating how existing data can be reanalysed in a coherent manner to elucidate the systemic nature of the disease and inform the development of more effective diagnostic tools and targeted therapies. [ABSTRACT FROM AUTHOR]

Analysis of blood-based indicators of brain health could provide an understanding of early disease mechanisms and pinpoint possible intervention strategies. By examining lipid profiles in extracellular vesicles (EVs), secreted particles from all cells, including astrocytes and neurons, and circulating in clinical samples, important insights regarding the brain's composition can be gained. Herein, a targeted lipidomic analysis was carried out in EVs derived from plasma samples after removal of lipoproteins from individuals with Alzheimer's disease (AD) and healthy controls. Differences were observed for selected lipid species of glycerolipids (GLs), glycerophospholipids (GPLs), lysophospholipids (LPLs) and sphingolipids (SLs) across three distinct EV subpopulations (all-cell origin, derived by immunocapture of CD9, CD81 and CD63; neuronal origin, derived by immunocapture of L1CAM; and astrocytic origin, derived by immunocapture of GLAST). The findings provide new insights into the lipid composition of EVs isolated from plasma samples regarding specific lipid families (MG, DG, Cer, PA, PC, PE, PI, LPI, LPE, LPC), as well as differences between AD and control individuals. This study emphasizes the crucial role of plasma EV lipidomics analysis as a comprehensive approach for identifying biomarkers and biological targets in AD and related disorders, facilitating early diagnosis and potentially informing novel interventions. [ABSTRACT FROM AUTHOR]

The central nervous system (CNS) and the immune system collectively coordinate cellular functionalities, sharing common developmental mechanisms. Immunity-related molecules exert an influence on brain development, challenging the conventional view of the brain as immune-privileged. Chronic inflammation emerges as a key player in the pathophysiology of Alzheimer's disease (AD), with increased stress contributing to the disease progression and potentially exacerbating existing symptoms. In this study, the most significant gene signatures from selected RNA-sequencing (RNA-seq) data from AD patients and healthy individuals were obtained and a functional analysis and biological interpretation was conducted, including network and pathway enrichment analysis. Important evidence was reported, such as enrichment in immune system responses and antigen processes, as well as positive regulation of T-cell mediated cytotoxicity and endogenous and exogenous peptide antigen, thus indicating neuroinflammation and immune response participation in disease progression. These findings suggest a disturbance in the immune infiltration of the peripheral immune environment, providing new challenges to explore key biological processes from a molecular perspective that strongly participate in AD development. [ABSTRACT FROM AUTHOR]

(1) Background: Parkinson's disease (PD) is a progressively worsening neurodegenerative disorder affecting movement, mental well-being, sleep, and pain. While no cure exists, treatments like hyperbaric oxygen therapy (HBOT) offer potential relief. However, the molecular biology perspective, especially when intertwined with machine learning dynamics, remains underexplored. (2) Methods: We employed machine learning techniques to analyze single-cell RNA-seq data from human PD cell samples. This approach aimed to identify pivotal genes associated with PD and understand their relationship with HBOT. (3) Results: Our analysis indicated genes such as MAP2, CAP2, and WSB1, among others, as being crucially linked with Parkinson's disease (PD) and showed their significant correlation with Hyperbaric oxygen therapy (HBOT) indicatively. This suggests that certain genomic factors might influence the efficacy of HBOT in PD treatment. (4) Conclusions: HBOT presents promising therapeutic potential for Parkinson's disease, with certain genomic factors playing a pivotal role in its efficacy. Our findings emphasize the need for further machine learning-driven research harnessing diverse omics data to better understand and treat PD. [ABSTRACT FROM AUTHOR]

Alzheimer's disease is one of the leading causes of death globally, significantly impacting countless families and communities. In parallel, recent advancements in molecular biology and network approaches, guided by the Network Medicine perspective, offer promising outcomes for Alzheimer's disease research and treatment. In this study, we aim to discover candidate therapies for AD through drug repurposing. We combined a protein-protein interaction (PPI) network with drug-target interactions. Experimentally validated PPI data were collected from the PICKLE meta-database, while drugs and their protein targets were sourced from the DrugBank database. Then, based on RNA-Seq data, we first assigned weights to edges to indicate co-expression, and secondly, estimated differential gene expression to select a subset of genes potentially related to the disease. Finally, small subgraphs (modules) were extracted from the graph, centered on the genes of interest. The analysis revealed that even if there is no drug targeting several genes of interest directly, an existing drug might target a neighboring node, thus indirectly affecting the aforementioned genes. Our approach offers a promising method for treating various diseases by repurposing existing drugs, thereby reducing the cost and time of experimental procedures and paving the way for more precise Network Medicine strategies. [ABSTRACT FROM AUTHOR]

Accurate protein structure prediction using computational methods remains a challenge in molecular biology. Recent advances in AI-powered algorithms provide a transformative effect in solving this problem. Even though AlphaFold's performance has improved since its release, there are still limitations that apply to its efficacy. In this study, a selection of proteins related to the pathology of Alzheimer's disease was modeled, with Presenilin-1 (PSN1) and its mutated variants in the foreground. Their structural predictions were evaluated using the ColabFold implementation of AlphaFold, which utilizes MMseqs2 for the creation of multiple sequence alignments (MSAs). A higher number of recycles than the one used in the AlphaFold DB was selected, and no templates were used. In addition, prediction by RoseTTAFold was also applied to address how structures from the two deep learning frameworks match reality. The resulting conformations were compared with the corresponding experimental structures, providing potential insights into the predictive ability of this approach in this particular group of proteins. Furthermore, a comprehensive examination was performed on features such as predicted regions of disorder and the potential effect of mutations on PSN1. Our findings consist of highly accurate superpositions with little or no deviation from experimentally determined domain-level models. [ABSTRACT FROM AUTHOR]

Simple Summary: Current global statistics indicate that approximately 1 in 13 individuals will develop post-traumatic stress disorder (PTSD) at some point in their lives. PTSD is a complex psychological disorder that emerges as a result of exposure to traumatic events, and its intricate nature poses challenges for diagnosis. The focus should be directed towards identifying the catalytic factors of PTSD, which can serve as molecular or functional biomarkers. To address this, an extensive review of research sources to compile a comprehensive list of catalytic factors at both the molecular and functional levels was conducted. A mathematical model encompassing all the significant catalytic factors was proposed, with the future aim of developing a holistic model of PTSD that will incorporate a panel of characteristics. Furthermore, the behavior of these factors at the genetic level, considering both ontological and network perspectives was explored, enabling the gain of a deeper understanding of PTSD by capturing their interconnectivity and biological roles. To the best of our knowledge, this study represents the first comprehensive examination and modeling of catalytic factors in PTSD, taking into account their interconnected associations. Post-traumatic stress disorder (PTSD) is a complex psychological disorder that develops following exposure to traumatic events. PTSD is influenced by catalytic factors such as dysregulated hypothalamic-pituitary-adrenal (HPA) axis, neurotransmitter imbalances, and oxidative stress. Genetic variations may act as important catalysts, impacting neurochemical signaling, synaptic plasticity, and stress response systems. Understanding the intricate gene networks and their interactions is vital for comprehending the underlying mechanisms of PTSD. Focusing on the catalytic factors of PTSD is essential because they provide valuable insights into the underlying mechanisms of the disorder. By understanding these factors and their interplay, researchers may uncover potential targets for interventions and therapies, leading to more effective and personalized treatments for individuals with PTSD. The aforementioned gene networks, composed of specific genes associated with the disorder, provide a comprehensive view of the molecular pathways and regulatory mechanisms involved in PTSD. Through this study valuable insights into the disorder's underlying mechanisms and opening avenues for effective treatments, personalized interventions, and the development of biomarkers for early detection and monitoring are provided. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) represents one of the most important healthcare challenges of the current century, characterized as an expanding, "silent pandemic". Recent studies suggest that the peripheral immune system may participate in AD development; however, the molecular components of these cells in AD remain poorly understood. Although single-cell RNA sequencing (scRNA-seq) offers a sufficient exploration of various biological processes at the cellular level, the number of existing works is limited, and no comprehensive machine learning (ML) analysis has yet been conducted to identify effective biomarkers in AD. Herein, we introduced a computational workflow using both deep learning and ML processes examining scRNA-seq data obtained from the peripheral blood of both Alzheimer's disease patients with an amyloid-positive status and healthy controls with an amyloid-negative status, totaling 36,849 cells. The output of our pipeline contained transcripts ranked by their level of significance, which could serve as reliable genetic signatures of AD pathophysiology. The comprehensive functional analysis of the most dominant genes in terms of biological relevance to AD demonstrates that the proposed methodology has great potential for discovering blood-based fingerprints of the disease. Furthermore, the present approach paves the way for the application of ML techniques to scRNA-seq data from complex disorders, providing new challenges to identify key biological processes from a molecular perspective. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) is now classified as a silent pandemic due to concerning current statistics and future predictions. Despite this, no effective treatment or accurate diagnosis currently exists. The negative impacts of invasive techniques and the failure of clinical trials have prompted a shift in research towards non-invasive treatments. In light of this, there is a growing need for early detection of AD through non-invasive approaches. The abundance of data generated by non-invasive techniques such as blood component monitoring, imaging, wearable sensors, and bio-sensors not only offers a platform for more accurate and reliable bio-marker developments but also significantly reduces patient pain, psychological impact, risk of complications, and cost. Nevertheless, there are challenges concerning the computational analysis of the large quantities of data generated, which can provide crucial information for the early diagnosis of AD. Hence, the integration of artificial intelligence and deep learning is critical to addressing these challenges. This work attempts to examine some of the facts and the current situation of these approaches to AD diagnosis by leveraging the potential of these tools and utilizing the vast amount of non-invasive data in order to revolutionize the early detection of AD according to the principles of a new non-invasive medicine era. [ABSTRACT FROM AUTHOR]

Data-driven analysis and characterization of molecular phenotypes comprises an efficient way to decipher complex disease mechanisms. Using emerging next generation sequencing technologies, important disease-relevant outcomes are extracted, offering the potential for precision diagnosis and therapeutics in progressive disorders. Single-cell RNA sequencing (scRNA-seq) allows the inherent heterogeneity between individual cellular environments to be exploited and provides one of the most promising platforms for quantifying cell-to-cell gene expression variability. However, the high-dimensional nature of scRNA-seq data poses a significant challenge for downstream analysis, particularly in identifying genes that are dominant across cell populations. Feature selection is a crucial step in scRNA-seq data analysis, reducing the dimensionality of data and facilitating the identification of genes most relevant to the biological question. Herein, we present a need for an ensemble feature selection methodology for scRNA-seq data, specifically in the context of Alzheimer's disease (AD). We combined various feature selection strategies to obtain the most dominant differentially expressed genes (DEGs) in an AD scRNA-seq dataset, providing a promising approach to identify potential transcriptome biomarkers through scRNA-seq data analysis, which can be applied to other diseases. We anticipate that feature selection techniques, such as our ensemble methodology, will dominate analysis options for transcriptome data, especially as datasets increase in volume and complexity, leading to more accurate classification and the generation of differentially significant features. [ABSTRACT FROM AUTHOR]

The X chromosome gene PLP1 encodes myelin proteolipid protein (PLP), the most prevalent protein in the myelin sheath surrounding the central nervous system. X-linked dysmyelinating disorders such as Pelizaeus–Merzbacher disease (PMD) or spastic paraplegia type 2 (SPG2) are typically caused by point mutations in PLP1. Nevertheless, numerous case reports have shown individuals with PLP1 missense point mutations which also presented clinical symptoms and indications that were consistent with the diagnostic criteria of multiple sclerosis (MS), a disabling disease of the brain and spinal cord with no current cure. Computational structural biology methods were used to assess the impact of these mutations on the stability and flexibility of PLP structure in order to determine the role of PLP1 mutations in MS pathogenicity. The analysis showed that most of the variants can alter the functionality of the protein structure such as R137W variants which results in loss of helix and H140Y which alters the ordered protein interface. In silico genomic methods were also performed to predict the significance of these mutations associated with impairments in protein functionality and could suggest a better definition for therapeutic strategies and clinical application in MS patients. [ABSTRACT FROM AUTHOR]

Mitochondrial (mt) DNA and nuclear (n) DNA have known structures and roles in cells; however, they are rarely compared under specific conditions such as oxidative or degenerative environments that can create damage to the DNA base moieties. Six purine lesions were ascertained in the mtDNA of wild type (wt) CSA (CS3BE–wtCSA) and wtCSB (CS1AN–wtCSB) cells and defective counterparts CS3BE and CS1AN in comparison with the corresponding total (t) DNA (t = n + mt). In particular, the four 5′,8–cyclopurine (cPu) and the two 8–oxo–purine (8–oxo–Pu) lesions were accurately quantified by LC–MS/MS analysis using isotopomeric internal standards after an enzymatic digestion procedure. The 8–oxo–Pu levels were found to be in the range of 25–50 lesions/107 nucleotides in both the mtDNA and tDNA. The four cPu were undetectable in the mtDNA both in defective cells and in the wt counterparts (CSA and CSB), contrary to their detection in tDNA, indicating a nonappearance of hydroxyl radical (HO•) reactivity within the mtDNA. In order to assess the HO• reactivity towards purine nucleobases in the two genetic materials, we performed γ–radiolysis experiments coupled with the 8–oxo–Pu and cPu quantifications on isolated mtDNA and tDNA from wtCSB cells. In the latter experiments, all six purine lesions were detected in both of the DNA, showing a higher resistance to HO• attack in the case of mtDNA compared with tDNA, likely due to their different DNA helical topology influencing the relative abundance of the lesions. [ABSTRACT FROM AUTHOR]

The consequences of aging and disease conditions in tissues involve reactive oxygen species (ROS) and related molecular alterations of different cellular compartments. We compared a murine model of immunodeficient (SCID) xenografted young (4 weeks old) and old (17 weeks old) mice with corresponding controls without tumor implantation and carried out a compositional evaluation of brain tissue for changes in parallel DNA and lipids compartments. DNA damage was measured by four purine 5′,8-cyclo-2′-deoxynucleosides, 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dG), and 8-oxo-7,8-dihydro-2′-deoxyadenosine (8-oxo-dA). In brain lipids, the twelve most representative fatty acid levels, which were mostly obtained from the transformation of glycerophospholipids, were followed up during the aging and disease progressions. The progressive DNA damage due to age and tumoral conditions was confirmed by raised levels of 5′S-cdG and 5′S-cdA. In the brain, the remodeling involved a diminution of palmitic acid accompanied by an increase in arachidonic acid, along both age and tumor progressions, causing increases in the unsaturation index, the peroxidation index, and total TFA as indicators of increased oxidative and free radical reactivity. Our results contribute to the ongoing debate on the central role of DNA and genome instability in the aging process, and on the need for a holistic vision, which implies choosing the best biomarkers for such monitoring. Furthermore, our data highlight brain tissue for its lipid remodeling response and inflammatory signaling, which seem to prevail over the effects of DNA damage. [ABSTRACT FROM AUTHOR]

Oxygen is important for lipid metabolism, being involved in both enzymatic transformations and oxidative reactivity, and is particularly influent when genetic diseases impair the repair machinery of the cells, such as described for Cockayne syndrome (CS). We used two cellular models of transformed fibroblasts defective for CSA and CSB genes and their normal counterparts, grown for 24 h under various oxygen tensions (hyperoxic 21%, physioxic 5% and hypoxic 1%) to examine the fatty acid-based membrane remodeling by GC analysis of fatty acid methyl esters derived from membrane phospholipids. Overall, we first distinguished differences due to oxygen tensions: (a) hyperoxia induced a general boost of desaturase enzymatic activity in both normal and defective CSA and CSB cell lines, increasing monounsaturated fatty acids (MUFA), whereas polyunsaturated fatty acids (PUFA) did not undergo oxidative consumption; (b) hypoxia slowed down desaturase activities, mostly in CSA cell lines and defective CSB, causing saturated fatty acids (SFA) to increase, whereas PUFA levels diminished, suggesting their involvement in hypoxia-related signaling. CSB-deprived cells are the most sensitive to oxidation and CSA-deprived cells are the most sensitive to the radical-based formation of trans fatty acids (TFA). The results point to the need to finely differentiate biological targets connected to genetic impairments and, consequently, suggest the better definition of cell protection and treatments through accurate molecular profiling that includes membrane lipidomes. [ABSTRACT FROM AUTHOR]

A population balance model for the aggregation of iron oxide nanoflowers (IONfs) is presented. The model is based on the fixed pivot technique and is validated successfully for four kinds of aggregation kernels. The extended Derjaguin, Landau, Verwey, and Overbeek (xDLVO) theory is also employed for assessing the collision efficiency of the particles, which is pertinent to the total energy of the interaction. Colloidal stability experiments were conducted on IONfs for two dispersant cases—aqueous phosphate buffered saline solution (PBS) and simulated body fluid (SBF). Dynamic light scattering (DLS) measurements after 24-h of incubation show a significant size increase in plain PBS, whereas the presence of proteins in SBF prevents aggregation by protein corona formation on the IONfs. Subsequent simulations tend to overpredict the aggregation rate, and this can be attributed to the flower-like shape of IONfs, thus allowing patchiness on the surface of the particles that promotes an uneven energy potential and aggregation hindering. In silico parametric study on the effects of the ionic strength shows a prominent dependency of the aggregation rate on the salinity of the dispersant underlying the effect of repulsion forces, which are almost absent in the PBS case, promoting aggregation. In addition, the parametric study on the van der Waals potential energy effect—within common Hamaker-constant values for iron oxides—shows that this is almost absent for high salinity dispersants, whereas low salinity gives a wide range of results, thus underlying the high sensitivity of the model on the potential energy parameters. [ABSTRACT FROM AUTHOR]

Despite the widespread use of silver nanoparticles (AgNPs) in different fields and the amount of investigations available, to date, there are many contradictory results on their potential toxicity. In the present study, extensively characterized 20‐nm AgNPs were investigated using optimized protocols and standardized methods to test several toxicological endpoints in different cell lines. The agglomeration/aggregation state of AgNPs in culture media was measured by dynamic light scattering (DLS). DNA and chromosomal damage on BEAS‐2B and RAW 264.7 cells were evaluated by comet and micronucleus assays, while oxidative DNA damage by modified comet assay and 8‐oxodG/8‐oxodA detection. We also investigated immunotoxicity and immunomodulation by cytokine release and NO production in RAW 264.7 and MH‐S cells, with or without lipopolysaccharide (LPS) stimulus. Transmission electron microscope (TEM) analysis was used to analyze cellular uptake of AgNPs. Our results indicate different values of AgNPs hydrodynamic diameter depending on the medium, some genotoxic effect just on BEAS‐2B and no or slight effects on function of RAW 264.7 and MH‐S in absence or presence of LPS stimulus. This study highlights the relevance of using optimized protocols and multiple endpoints to analyze the potential toxicity of AgNPs and to obtain reliable and comparable results. In this study, optimized protocols and standardized methods were used for evaluating the potential in vitro toxicity of extensively characterized 20‐nm silver nanoparticles (AgNPs). AgNPs dispersions, characterized in culture media, were tested for cytotoxicological, genotoxicological, and immunotoxicological effects on cell lines representative of different route of exposure. Cellular uptake was also investigated. This study highlights the relevance of using optimized protocols and multiple endpoints to investigate the potential toxicity of AgNPs in order to obtain reliable and comparable results. [ABSTRACT FROM AUTHOR]

Hydroxyl radical (HO•) is the most reactive toward DNA among the reactive oxygen species (ROS) generated in aerobic organisms by cellular metabolisms. HO• is generated also by exogenous sources such as ionizing radiations. In this review we focus on the purine DNA damage by HO• radicals. In particular, emphasis is given on mechanistic aspects for the various lesion formation and their interconnections. Although the majority of the purine DNA lesions like 8-oxo-purine (8-oxo-Pu) are generated by various ROS (including HO•), the formation of 5′,8-cyclopurine (cPu) lesions in vitro and in vivo relies exclusively on the HO• attack. Methodologies generally utilized for the purine lesions quantification in biological samples are reported and critically discussed. Recent results on cPu and 8-oxo-Pu lesions quantification in various types of biological specimens associated with the cellular repair efficiency as well as with distinct pathologies are presented, providing some insights on their biological significance. [ABSTRACT FROM AUTHOR]

We report a series of copper(II) artificial metallo‐nucleases (AMNs) and demonstrate their DNA damaging properties and in‐vitro cytotoxicity against human‐derived pancreatic cancer cells. The compounds combine a tris‐chelating polypyridyl ligand, di‐(2‐pycolyl)amine (DPA), and a DNA intercalating phenanthrene unit. Their general formula is Cu‐DPA‐N,N' (where N,N'=1,10‐phenanthroline (Phen), dipyridoquinoxaline (DPQ) or dipyridophenazine (DPPZ)). Characterisation was achieved by X‐ray crystallography and continuous‐wave EPR (cw‐EPR), hyperfine sublevel correlation (HYSCORE) and Davies electron‐nuclear double resonance (ENDOR) spectroscopies. The presence of the DPA ligand enhances solution stability and facilitates enhanced DNA recognition with apparent binding constants (Kapp) rising from 105 to 107 m−1 with increasing extent of planar phenanthrene. Cu‐DPA‐DPPZ, the complex with greatest DNA binding and intercalation effects, recognises the minor groove of guanine–cytosine (G‐C) rich sequences. Oxidative DNA damage also occurs in the minor groove and can be inhibited by superoxide and hydroxyl radical trapping agents. The complexes, particularly Cu‐DPA‐DPPZ, display promising anticancer activity against human pancreatic tumour cells with in‐vitro results surpassing the clinical platinum(II) drug oxaliplatin. [ABSTRACT FROM AUTHOR]

5′,8-Cyclo-2′-deoxyadenosine (cdA) and 5′,8-cyclo-2′-deoxyguanosine (cdG) in their two diastereomeric forms, 5′Sand 5′R, are tandem lesions produced by the attack of hydroxyl radicals to the purine moieties of DNA. Their formation has been found to challenge the cells’ repair machinery, initiating the nucleotide excision repair (NER) for restoring the genome integrity. The involvement of oxidatively induced DNA damage in carcinogenesis and the reduced capacity of some cancer cell lines to repair oxidised DNA base lesions, intrigued us to investigate the implication of these lesions in breast cancer, the most frequently occurring cancer in women. Using liquid chromatography tandem mass spectrometry (LC-MS/MS), we measured the levels of diastereomeric cdA’s and cdG’s in estrogen receptor-alpha positive (ER-α) MCF-7 and triple negative MDA-MB-231 breast cancer cell lines before and after exposure to two different conditions: ionising radiations and hydrogen peroxide, followed by an interval period to allow DNA repair. An increase at the measured levels of all four lesions, i.e. 5′S-cdA, 5′R-cdA, 5′S-cdG and 5′R-cdG, was observed either afterγ-irradiation (5 Gy dose) or hydrogen peroxide treatment (300 μM) compared to the untreated cells (control), independently from the length of the interval period for repair. For comparison reasons, we also measured the levels of 8-oxo-2′-deoxyadenosine (8-oxo-dA), a well-known oxidatively induced DNA damage lesion and base excision repair (BER) substrate. The collected data indicate that MCF-7 and MDA-MB-231 breast cancer cells are highly susceptible to radiation-induced DNA damage, being mainly defective in the repair of these lesions. [ABSTRACT FROM PUBLISHER]

Parkinson's disease (PD) is a progressive neurodegenerative disorder associated with dysfunction of dopaminergic neurons in the brain, lack of dopamine and the formation of abnormal Lewy body protein particles. PD is an idiopathic disease of the nervous system, characterized by motor and nonmotor manifestations without a discrete onset of symptoms until a substantial loss of neurons has already occurred, enabling early diagnosis very challenging. Sensor-based platforms have gained much attention in clinical practice screening various biological signals simultaneously and allowing researchers to quickly receive a huge number of biomarkers for diagnostic and prognostic purposes. The integration of machine learning into medical systems provides the potential for optimization of data collection, disease prediction through classification of symptoms and can strongly support data-driven clinical decisions. This work attempts to examine some of the facts and current situation of sensor-based approaches in PD diagnosis and discusses ensemble techniques using sensor-based data for developing machine learning models for personalized risk prediction. Additionally, a biosensing platform combined with clinical data processing and appropriate software is proposed in order to implement a complete diagnostic system for PD monitoring. [ABSTRACT FROM AUTHOR]

Cover Feature: Polypyridyl-Based Copper Phenanthrene Complexes: Combining Stability with Enhanced DNA Recognition (Chem. Eur. J. 3/2021) Keywords: copper; DNA damage; DNA repair; electrochemistry; EPR spectroscopy EN copper DNA damage DNA repair electrochemistry EPR spectroscopy 828 828 1 01/18/21 20210113 NES 210113 B A new class of DNA intercalating metallodrug is reported b . Copper, DNA damage, DNA repair, electrochemistry, EPR spectroscopy. [Extracted from the article]

Cockayne Syndrome (CS) is an autosomal recessive neurodegenerative premature aging disorder associated with defects in nucleotide excision repair (NER). Cells from CS patients, with mutations in CSA or CSB genes, present elevated levels of reactive oxygen species (ROS) and are defective in the repair of a variety of oxidatively generated DNA lesions. In this study, six purine lesions were ascertained in wild type (wt) CSA, defective CSA, wtCSB and defective CSB-transformed fibroblasts under different oxygen tensions (hyperoxic 21%, physioxic 5% and hypoxic 1%). In particular, the four 5′,8-cyclopurine (cPu) and the two 8-oxo-purine (8-oxo-Pu) lesions were accurately quantified by LC-MS/MS analysis using isotopomeric internal standards after an enzymatic digestion procedure. cPu levels were found comparable to 8-oxo-Pu in all cases (3–6 lesions/106 nucleotides), slightly increasing on going from hyperoxia to physioxia to hypoxia. Moreover, higher levels of four cPu were observed under hypoxia in both CSA and CSB-defective cells as compared to normal counterparts, along with a significant enhancement of 8-oxo-Pu. These findings revealed that exposure to different oxygen tensions induced oxidative DNA damage in CS cells, repairable by NER or base excision repair (BER) pathways. In NER-defective CS patients, these results support the hypothesis that the clinical neurological features might be connected to the accumulation of cPu. Moreover, the elimination of dysfunctional mitochondria in CS cells is associated with a reduction in the oxidative DNA damage. [ABSTRACT FROM AUTHOR]

The reaction of hydroxyl radical (HO•) with DNA produces many primary reactive species and many lesions as final products. In this study, we have examined the optical spectra of intermediate species derived from the reaction of HO• with a variety of single- and double-stranded oligodeoxynucleotides and ct-DNA in the range of 1 μs to 1 ms by pulse radiolysis using an Intensified Charged Coupled Device (ICCD) camera. Moreover, we applied our published analytical protocol based on an LC-MS/MS system with isotopomeric internal standards to enable accurate and precise measurements of purine lesion formation. In particular, the simultaneous measurement of the four purine 5′,8-cyclo-2′-deoxynucleosides (cPu) and two 8-oxo-7,8-dihydro-2′-deoxypurine (8-oxo-Pu) was obtained upon reaction of genetic material with HO• radicals generated either by γ-radiolysis or Fenton-type reactions. Our results contributed to the debate in the literature regarding absolute level of lesions, method of HO• radical generation, 5′R/5′S diastereomeric ratio in cPu, and relative abundance between cPu and 8-oxo-Pu. [ABSTRACT FROM AUTHOR]

Xeroderma Pigmentosum (XP) is a DNA repair disease characterized by nucleotide excision repair (NER) malfunction, leading to photosensitivity and increased incidence of skin malignancies. The role of XP-A in NER pathways has been well studied while discrepancies associated with ROS levels and the role of radical species between normal and deficient XPA cell lines have been observed. Using liquid chromatography tandem mass spectrometry we have determined the four 5',8-cyclopurines (cPu) lesions (i.e., 5′R-cdG, 5′S-cdG, 5′R-cdA and 5′S-cdA), 8-oxo-dA and 8-oxo-dG in wt (EUE-pBD650) and XPA-deficient (EUE-siXPA) human embryonic epithelial cell lines, under different oxygen tension (hyperoxic 21%, physioxic 5% and hypoxic 1%). The levels of Fe and Cu were also measured. The main findings of our study were: (i) the total amount of cPu (1.82–2.52 lesions/106 nucleotides) is the same order of magnitude as 8-oxo-Pu (3.10–4.11 lesions/106 nucleotides) in both cell types, (ii) the four cPu levels are similar in hyperoxic and physioxic conditions for both wt and deficient cell lines, whereas 8-oxo-Pu increases in all cases, (iii) both wt and deficient cell lines accumulated high levels of cPu under hypoxic compared to physioxic conditions, whereas the 8-oxo-Pu levels show an opposite trend, (iv) the diastereoisomeric ratios 5′R/5′S are independent of oxygen concentration being 0.29 for cdG and 2.69 for cdA for EUE-pBD650 (wt) and 0.32 for cdG and 2.94 for cdA for EUE-siXPA (deficient), (v) in deficient cell lines Fe levels were significantly higher. The data show for the first time the connection of oxygen concentration in cells with different DNA repair ability and the levels of different DNA lesions highlighting the significance of cPu. Membrane lipidomic data at 21% O2 indicated differences in the fatty acid contents between wild type and deficient cells, envisaging functional effects on membranes associated with the different repair capabilities, to be further investigated. [ABSTRACT FROM AUTHOR]

The natural peptide somatostatin has hormonal and cytostatic effects exerted by the binding to specific receptors in various tissues. Therapeutic uses are strongly prevented by its very short biological half-life of 1–2 min due to enzymatic hydrolysis, therefore encapsulation methodologies are explored to overcome the need for continuous infusion regimes. Multilamellar liposomes made of natural phosphatidylcholine were used for the incorporation of a mixture of somatostatin and sorbitol dissolved in citrate buffer at pH = 5. Lyophilization and reconstitution of the suspension were carried out, showing the flexibility of this preparation. Full characterization of this suspension was obtained as particle size, encapsulation efficiency and retarded release properties in aqueous medium and human plasma. Liposomal somatostatin incubated at 37 °C in the presence of Fe(II) and (III) salts were used as a biomimetic model of drug-cell membrane interaction, evidencing the free radical processes of peroxidation and isomerization that transform the unsaturated fatty acid moieties of the lipid vesicles. This study offers new insights into a liposomal delivery system and highlights molecular reactivity of sulfur-containing drugs with its carrier or biological membranes for pharmacological applications. [ABSTRACT FROM AUTHOR]

Purine 5′,8-cyclo-2′-deoxynucleosides (cPu) are tandem-type lesions observed among the DNA purine modifications and identified in mammalian cellular DNA in vivo. These lesions can be present in two diasteroisomeric forms, 5′R and 5′S, for each 2′-deoxyadenosine and 2′-deoxyguanosine moiety. They are generated exclusively by hydroxyl radical attack to 2′-deoxyribose units generating C5′ radicals, followed by cyclization with the C8 position of the purine base. This review describes the main recent achievements in the preparation of the cPu molecular library for analytical and DNA synthesis applications for the studies of the enzymatic recognition and repair mechanisms, their impact on transcription and genetic instability, quantitative determination of the levels of lesions in various types of cells and animal model systems, and relationships between the levels of lesions and human health, disease, and aging, as well as the defining of the detection limits and quantification protocols. [ABSTRACT FROM AUTHOR]

The anticancer activity of acridone derivatives has attracted increasing interest, therefore, a variety of substituted analogs belonging to this family have been developed and evaluated for their anti-cancer properties. A series of N-alkyl-acridones 1–6 and N,N′-dialkyl-9,9′-biacridylidenes 7–12 with variable alkyl chains were examined for their topoisomerase I activity at neutral and acidic conditions as well as for their binding capacity to calf thymus and possible radical trapping antioxidant activity. It was found that at a neutral pH, topoisomerase I activity of both classes of compounds was similar, while under acidic conditions, enhanced intercalation was observed. N-alkyl-acridone derivatives 1–6 exhibited stronger, dose-dependent, cytotoxic activity against MCF-7 human breast epithelial cancer cells than N,N′-dialkyl-9,9′-biacridylidenes 7–12, revealing that conjugation of the heteroaromatic system plays a significant role on the effective distribution of the compound in the intracellular environment. Cellular investigation of long alkyl derivatives against cell migration exhibited 40–50% wound healing effects and cytoplasm diffusion, while compounds with shorter alkyl chains were accumulated both in the nucleus and cytoplasm. All N,N′-dialkyl-9,9′-biacridylidenes showed unexpected high scavenging activity towards DPPH or ABTS radicals which may be explained by higher stabilization of radical cations by the extended conjugation of heteroaromatic ring system. [ABSTRACT FROM AUTHOR]

Increased rates of reactive oxygen/nitrogen species (ROS/RNS) are involved in almost all cancer types, associated with tumor development and progression, causing damage to biomolecules such as proteins, nucleic acids and membrane lipids, in different biological compartments. We used a human tumor xenograft mouse model to evaluate for the first time in parallel the remodeling of fatty acid moieties in erythrocyte membrane phospholipids and the level of ROS-induced DNA lesions in liver and kidney tissues. Using liquid chromatography tandem mass spectrometry the 5′R and 5′S diastereoisomers of 5′,8-cyclo-2′-deoxyadenosine and 5′,8-cyclo-2′-deoxyguanosine, together with 8-oxo-7,8-dihydro-2′-deoxyadenosine, were determined in mice at young (4- and 5-weeks) and old (17-weeks) ages and compared with control SCID mice without tumor implantation. Tumor-bearing mice showed a higher level of ROS-damaged nucleosides in genomic DNA as the age and tumor progress, compared to controls (1.07–1.53-fold in liver and 1.1–1.4-fold in kidney, respectively). The parallel fatty acid profile of erythrocyte membranes showed a profound lipid remodeling during tumor and age progression consisting of PUFA consumption and SFA enrichment (ca 28% and 58%, respectively, in late stage tumor-bearing mice), markers of enhanced oxidative and proliferative processes, respectively. Membrane lipid remodeling and ROS-induced DNA lesions may be combined to afford an integrated scenario of cancer progression and ageing, reinforcing a holistic vision among molecular markers rather than the biomarker identification in a single compartment. [ABSTRACT FROM AUTHOR]

5',8-Cyclo-2'-deoxyadenosine (cdA), in the 5'R and 5'Sdiastereomeric forms, are typical non strand-break oxidative DNA lesions, induced by hydroxyl radicals, with emerging importance as a molecular marker. These lesions are exclusively repaired by the nucleotide excision repair (NER) mechanism with a low efficiency, thus readily accumulating in the genome. Poly(ADP-ribose) polymerase1 (PARP1) acts as an early responder to DNA damage and plays a key role as a nick sensor in the maintenance of the integrity of the genome by recognizing nicked DNA. So far, it was unknown whether the two diastereomeric cdA lesions could induce specific PARP1 binding. Here, we provide the first evidence of PARP1 to selectively recognize the diastereomeric lesions of 5'S-cdA and 5'R-cdA in vitro as compared to deoxyadenosine in model DNA substrates (23-mers) by using circular dichroism, fluorescence spectroscopy, immunoblotting analysis, and gel mobility shift assay. Several features of the recognition of the damaged and undamaged oligonucleotides by PARP1 were characterized. Remarkably, PARP1 exhibits different affinities in binding to a double strand (ds) oligonucleotide, which incorporates cdA lesions in R and S diastereomeric form. In particular, PARP1 proved to bind oligonucleotides, including a 5'S-cdA, with a higher affinity constant for the 5'S lesion in a model of ds DNA than 5'R-cdA, showing different recognition patterns, also compared with undamaged dA. This new finding highlights the ability of PARP1 to recognize and differentiate the distorted DNA backbone in a biomimetic system caused by different diastereomeric forms of a cdA lesion. [ABSTRACT FROM AUTHOR]

Herein we report the quantification of purine lesions arising from gamma-radiation sourced hydroxyl radicals (HO•) on tertiary dsDNA helical forms of supercoiled (SC), open circular (OC), and linear (L) conformation, along with single-stranded folded and non-folded sequences of guanine-rich DNA in selected G-quadruplex structures. We identify that DNA helical topology and folding plays major, and unexpected, roles in the formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) and 8-oxo-7,8-dihydro-2'-deoxyadenosine (8-oxo-dA), along with tandem-type purine lesions 5′,8-cyclo-2′-deoxyguanosine (5′,8-cdG) and 5′,8-cyclo-2′-deoxyadenosine (5′,8-cdA). SC, OC, and L dsDNA conformers together with folded and non-folded G-quadruplexes d[TGGGGT]4(TG4T), d[AGGG(TTAGGG)3] (Tel22), and the mutated tel24 d[TTGGG(TTAGGG)3A] (mutTel24) were exposed to HO•radicals and purine lesions were then quantified via stable isotope dilution LC-MS/MS analysis. Purine oxidation in dsDNA follows L > OC ≫ SC indicating greater damage towards the extended B-DNA topology. Conversely, G-quadruplex sequences were significantly more resistant toward purine oxidation in their unfolded states as compared with G-tetrad folded topologies; this effect is confirmed upon comparative analysis of Tel22 (∼50% solution folded) and mutTel24 (∼90% solution folded). In an effort to identify the accessibly of hydroxyl radicals to quadruplex purine nucleobases, G-quadruplex solvent cavities were then modeled at 1.33 Å with evidence suggesting that folded G-tetrads may act as potential oxidant traps to protect against chromosomal DNA damage. [ABSTRACT FROM AUTHOR]