KAP1/TRIM28 - antiviral and proviral protagonist of herpesvirus biology

Dysregulation of the constitutive heterochromatin machinery (HCM) that silences pericentromeric regions and endogenous retroviral elements in the human genome has consequences for aging and cancer. By recruiting epigenetic regulators, Krüppel-associated box (KRAB)-associated protein 1 (KAP1/TRIM28/TIF1β) is integral to the function of the HCM. Epigenetically silencing DNA genomes of incoming herpesviruses to enforce latency, KAP1 and HCM also serve in an antiviral capacity. In addition to gene silencing, newer reports highlight KAP1's ability to directly activate cellular gene transcription. Here, we discuss the many facets of KAP1, including recent findings that unexpectedly connect KAP1 to the inflammasome, reveal KAP1 cleavage as a novel mode of regulation, and argue for a pro-herpesviral KAP1 function that ensures transition from transcription to replication of the herpesvirus genome.

eIF4E orchestrates mRNA processing, RNA export and translation to modify specific protein production

The eukaryotic translation initiation factor eIF4E acts as a multifunctional factor that simultaneously influences mRNA processing, export, and translation in many organisms. Its multifactorial effects are derived from its capacity to bind to the methyl-7-guanosine cap on the 5'end of mRNAs and thus can act as a cap chaperone for transcripts in the nucleus and cytoplasm. In this review, we describe the multifactorial roles of eIF4E in major mRNA-processing events including capping, splicing, cleavage and polyadenylation, nuclear export and translation. We discuss the evidence that eIF4E acts at two levels to generate widescale changes to processing, export and ultimately the protein produced. First, eIF4E alters the production of components of the mRNA processing machinery, supporting a widescale reprogramming of multiple mRNA processing events. In this way, eIF4E can modulate mRNA processing without physically interacting with target transcripts. Second, eIF4E also physically interacts with both capped mRNAs and components of the RNA processing or translation machineries. Further, specific mRNAs are sensitive to eIF4E only in particular mRNA processing events. This selectivity is governed by the presence of cis-acting elements within mRNAs known as USER codes that recruit relevant co-factors engaging the appropriate machinery. In all, we describe the molecular bases for eIF4E's multifactorial function and relevant regulatory pathways, discuss the basis for selectivity, present a compendium of ~80 eIF4E-interacting factors which play roles in these activities and provide an overview of the relevance of its functions to its oncogenic potential. Finally, we summarize early-stage clinical studies targeting eIF4E in cancer.

Neoadjuvant immunotherapy for dMMR and pMMR colorectal cancers: therapeutic strategies and putative biomarkers of response

Approximately 15% of locally advanced colorectal cancers (CRC) have DNA mismatch repair deficiency (dMMR), resulting in high microsatellite instability and a high tumour mutational burden. These cancers are frequently sensitive to therapy with immune-checkpoint inhibitors (ICIs) in the metastatic setting. This sensitivity seems to be even more pronounced in locally advanced disease, and organ preservation has become a realistic aim in ongoing clinical trials involving patients with dMMR rectal cancer. By contrast, metastatic CRCs with proficient DNA mismatch repair (pMMR) are generally resistant to ICIs, although a proportion of locally advanced pMMR tumours seem to have a high degree of sensitivity to ICIs. In this Review, we describe the current and emerging clinical evidence supporting the use of neoadjuvant ICIs in patients with dMMR and pMMR CRC, and the potential advantages (based on a biological rationale) of such an approach. We discuss how neoadjuvant 'window-of-opportunity' trials are being leveraged to progress biomarker discovery and we provide an overview of potential predictive biomarkers of response to ICIs, exploring the challenges faced when evaluating such biomarkers in biopsy-derived samples. Lastly, we describe how these discoveries might be used to drive a rational approach to trialling novel immunotherapeutic strategies in patients with pMMR CRC, with the ultimate aim of disease eradication and the generation of long-term immunosurveillance.

IKZF1 gene deletions drive resistance to cytarabine in B-cell precursor acute lymphoblastic leukemia

IKZF1 deletions occur in 10-15% of patients with B-cell precursor acute lymphoblastic leukemia (BCP-ALL) and predict a poor outcome. However, the impact of IKZF1 loss on sensitivity to drugs used in contemporary treatment protocols has remained underexplored. Here we show in experimental models and in patients that loss of IKZF1 promotes resistance to cytarabine (AraC), a key component of both upfront and relapsed treatment protocols. We attribute this resistance, in part, to diminished import and incorporation of AraC due to reduced expression of the solute carrier hENT1. Moreover, we found elevated mRNA expression of Evi1, a known driver of therapy resistance in myeloid malignancies. Finally, a kinase directed CRISPR/Cas9-screen identified that inhibition of either mediator kinases CDK8/19 or casein kinase 2 can restore response to AraC. We conclude that this high-risk group of patients could benefit from alternative antimetabolites, or targeted therapies that re-sensitize leukemic cells to AraC.

In vitro and in vivo investigation of antibacterial silver nanoparticles functionalized bone grafting substitutes

Infection is a major concern in surgery involving grafting and should be considered thoroughly when designing biomaterials. There is considerable renewed interest in silver nanoparticles (AgNPs) owing to their ability to potentiate antibacterial properties against multiple bacterial strains. This study aimed to develop two antibacterial bone regenerative scaffolds by integrating AgNPs in bovine bone particles (BBX) (Product 1), and a light cross-linked hydrogel GelMA (Product 2). The constructs were characterized using scanning electron microscopy. Metabolic activity of osteoblasts and osteoclasts on the constructs was investigated using PrestoBlue™. Disk diffusion assay was conducted to test the antibacterial properties. The regenerative capacity of the optimized AgNP functionalized BBX and GelMA were tested in a rabbit cranial 6 mm defect model. The presence of AgNPs appears to enhance proliferation of osteoblasts compared to AgNP free controls in vitro. We established that AgNPs can be used at a 100 μg dose that inhibits bacteria, with minimal adverse effects on the bone cells. Our rabbit model revealed that both the BBX and GelMA hydrogels loaded AgNPs were biocompatible with no signs of necrosis or inflammatory response. Grafts functionalized with AgNPs can provide antibacterial protection and simultaneously act as a scaffold for attachment of bone cells.

Pathogenicity and virulence of Yersinia

The genus Yersinia includes human, animal, insect, and plant pathogens as well as many symbionts and harmless bacteria. Within this genus are Yersinia enterocolitica and the Yersinia pseudotuberculosis complex, with four human pathogenic species that are highly related at the genomic level including the causative agent of plague, Yersinia pestis. Extensive laboratory, field work, and clinical research have been conducted to understand the underlying pathogenesis and zoonotic transmission of these pathogens. There are presently more than 500 whole genome sequences from which an evolutionary footprint can be developed that details shared and unique virulence properties. Whereas the virulence of Y. pestis now seems in apparent homoeostasis within its flea transmission cycle, substantial evolutionary changes that affect transmission and disease severity continue to ndergo apparent selective pressure within the other Yersiniae that cause intestinal diseases. In this review, we will summarize the present understanding of the virulence and pathogenesis of Yersinia, highlighting shared mechanisms of virulence and the differences that determine the infection niche and disease severity.

A multi-omics approach reveals a link between ribosomal protein alterations and proteome rebalancing in Arabidopsis thaliana seeds

The ability of seeds to restore their amino acid content and composition after the elimination of the most abundant seed storage proteins (SSPs) is well-documented, yet the underlying mechanisms remain unclear. To better understand how seeds compensate for major proteomic disruptions, we conducted a comprehensive analysis on an Arabidopsis mutant lacking the three most abundant SSPs, the cruciferins. Our initial findings indicated that carbon, nitrogen, and sulfur levels, as well as total protein and oil content, remained unchanged in these mutants suggesting rebalanced seeds. Transcriptomics and proteomics performed during seed maturation of Col-0 and the triple mutant revealed significant modulation in many components of the translational machinery, especially ribosomal proteins (RPs), and in the antioxidation response in the mutant. These findings suggest that RPs play a critical role in facilitating proteomic homeostasis during seed maturation when proteomic perturbation occurs. Biochemical and metabolic analyses of the triple mutant dry seeds revealed increased protein carbonylation and elevated glutathione levels further supporting the link between SSP accumulation and seed redox homeostasis. Overall, we propose that in response to significant proteomic perturbations, changes in the proteome and amino acid composition of seeds are accompanied by a broad remodeling of the translation apparatus. We postulate that these alterations are key elements in seed adaptability and robustness to large proteomic perturbations during seed maturation.

Functional links between the microbiome and the molecular pathways of colorectal carcinogenesis

Colorectal cancer (CRC) is a common cancer, with a concerning rise in early-onset CRC cases, signalling a shift in disease epidemiology. Whilst our understanding of the molecular underpinnings of CRC has expanded, the complexities underlying its initiation remain elusive, with emerging evidence implicating the microbiome in CRC pathogenesis. This review synthesizes current knowledge on the intricate interplay between the microbiome, tumour microenvironment (TME), and molecular pathways driving CRC carcinogenesis. Recent studies have reported how the microbiome may modulate the TME and tumour immune responses, consequently influencing cancer progression, and whilst specific bacteria have been linked with CRC, the underlying mechanisms remains poorly understood. By elucidating the functional links between microbial landscapes and carcinogenesis pathways, this review offers insights into how bacteria orchestrate diverse pathways of CRC development, shedding light on potential therapeutic targets and personalized intervention strategies.

Preparation and preliminary evaluation of a tritium-labeled allosteric P2X4 receptor antagonist

P2X4 receptors are ATP-gated cation channels that were proposed as novel drug targets due to their role in inflammation and neuropathic pain. Only few potent and selective P2X4 receptor antagonists have been described to date. Labeled tool compounds suitable for P2X4 receptor binding studies are lacking. Here, we present a novel allosteric P2X4 receptor antagonist possessing high potency in the low nanomolar range. We describe its tritium-labeling resulting in the P2X4-selective radiotracer [3H]PSB-OR-2020 with high specific activity (45 Ci/mmol; 1.67 TBq/mmol). A radioligand binding assay was developed using human embryonic kidney (HEK293) cell membranes recombinantly expressing the human P2X4 receptor. Competition binding studies with structurally diverse P2X4 receptor antagonists revealed different allosteric binding sites indicating that the new class of P2X4 receptor antagonists, to which PSB-OR-2020 belongs, interacts with an unprecedented allosteric site. [3H]PSB-OR-2020 may become a useful tool for research on P2X4 receptors and for promoting drug development.

α-Tocopherol Long-Chain Metabolite α-T-13'-COOH Exhibits Biphasic Effects on Cell Viability, Induces ROS-Dependent DNA Damage, and Modulates Redox Status in Murine RAW264.7 Macrophages

SCOPE

The α-tocopherol long-chain metabolite α-tocopherol-13'-hydroxy-chromanol (α-T-13'-COOH) is a proposed regulatory intermediate of endogenous vitamin E metabolism. Effects of α-T-13'-COOH on cell viability and adaptive stress response are not well understood. The present study aims to investigate the concentration-dependent effects of α-T-13'-COOH on cellular redox homeostasis, genotoxicity, and cytotoxicity in murine RAW264.7 macrophages as a model system.

METHODS AND RESULTS

Murine RAW264.7 macrophages are exposed to various dosages of α-T-13'-COOH to determine its regulatory effects on reactive oxygen species (ROS) production, DNA damage, expression of stress-related markers, and the activity of ROS scavenging enzymes including superoxide dismutases, catalase, and glutathione-S-transferases. The impact on cell viability is assessed by analyzing cell proliferation, cell cycle arrest, and cell apoptosis.

CONCLUSION

α-T-13'-COOH influences ROS production and induces DNA damage in a dose-dependent manner. The metabolite modulates the activity of ROS-scavenging enzymes, with significant changes observed in the activities of antioxidant enzymes. A biphasic response affecting cell viability is noted: sub-micromolar doses of α-T-13'-COOH promote cell proliferation and enhance DNA synthesis, whereas supraphysiological doses lead to DNA damage and cytotoxicity. It hypothesizes an adaptive stress response, characterized by upregulation of ROS detoxification mechanisms, enhanced cell cycle arrest, and increased apoptosis, indicating a correlation with oxidative stress and subsequent cellular damage.

3D confinement alters smooth muscle cell responses to chemical and mechanical cues

Smooth muscle cell (SMC) phenotypic switching is a hallmark of many vascular diseases. Although prior work has established that chemical and mechanical cues contribute to SMC phenotypic switching, the impact of three-dimensional (3D) confinement on this process remains elusive. Yet, in vivo, arterial SMCs reside within confined environments. In this study, we designed a microfluidic assay to investigate the interplay between 3D confinement and different environmental stimuli in SMC function. Our results show that tightly, but not moderately, confined SMCs acquire a contractile phenotype when exposed to collagen I. Elevated compressive forces induced by hydrostatic pressure abolish this upregulation of the contractile phenotype and compromise SMC survival, particularly in tightly confined spaces. Transforming growth factor beta 1, which promotes the contractile state in moderate confinement, fails to enhance the contractility of tightly confined cells. Fibronectin and engagement of cadherin 2 suppress the contractile phenotype of SMCs regardless of the degree of confinement. In contrast, homophilic engagement of cadherin 11 upregulates SMC-specific genes and enhances contractility in both moderately and tightly confined cells. Overall, our work introduces 3D confinement as a regulator of SMC phenotypic responses to chemical and mechanical signals.

Investigation of Long Noncoding RNA-NRAV and Long Noncoding RNA-Lethe Expression in Crimean-Congo Hemorrhagic Fever

Crimean-Congo hemorrhagic fever (CCHF) is a zoonotic infectious disease caused by the CCHF virus, a member of the Bunyavirales order and the Orthonairoviridae family. The exact pathogenesis is not fully understood. Long noncoding RNAs (lncRNAs) are RNAs that are shown to play a role in various pathological processes of viral diseases. NRAV and Lethe are two well-known lncRNAs. Although previous studies have shown that NRAV and Lethe play important roles in the pathogenesis of viral infections, their role in CCHF is unknown. This study aimed to evaluate the expression levels of NRAV and Lethe in patients with CCHFV. Eighty patients diagnosed with CCHF were included, and RNA was extracted from their blood samples. The expression of NRAV and Lethe was measured using quantitative real-time polymerase chain reaction (qPCR). Patients were divided into three groups based on severity score, which was mild, moderate, and severe, and into two groups (survivors and non-survivors). The expression levels of NRAV and Lethe were compared between these groups. Of the patients, 49 (61.25%) were male, 31 (38.75%) were female, and the mean age was 38.62 ± 19.28 years. No differences in age or gender were found between the groups. It was shown that NRAV expression was 21.86 times higher in the severe patient group compared to the moderate group and 22.74 times higher than in the mild group, statistically significant. When comparing fatal cases with survivors, NRAV expression levels were found to be 9.2 times higher in fatal cases. Lethe levels were 3 times lower in moderately severe cases compared to mild cases, but this difference was not statistically significant. In conclusion, our study suggests that NRAV may be a lncRNA involved in the pathogenesis of CCHFV.

Exploring acetylation-related gene markers in polycystic ovary syndrome: insights into pathogenesis and diagnostic potential using machine learning

OBJECTIVE

Polycystic ovary syndrome (PCOS) is a prevalent cause of menstrual irregularities and infertility in women, impacting quality of life. Despite advancements, current understanding of PCOS pathogenesis and treatment remains limited. This study uses machine learning-based data mining to identify acetylation-related genetic markers associated with PCOS, aiming to enhance diagnostic precision and therapeutic efficacy.

METHODS

Advanced machine learning techniques were used to improve the precision of key gene identification and reveal their biological mechanisms. Validation on an independent dataset (GSE48301) confirmed their diagnostic value, assessed through ROC curves and nomograms for PCOS risk prediction. Molecular mechanisms of acetylation-related gene regulation in PCOS were further examined through clustering, immune-environmental, and gene network analyses.

RESULTS

Our analysis identified 15 key acetylation-regulated genes differentially expressed in PCOS, including SGF29, NOL6, KLF15, and INO80D, which are relevant to PCOS pathogenesis. ROC curve analyses on training and validation datasets confirmed the model's high diagnostic accuracy. Additionally, these genes were associated with immune cell infiltration, offering insights into the inflammatory aspect of PCOS.

CONCLUSION

The identified acetylation gene markers offer novel insights into the molecular mechanisms underlying PCOS and hold promise for enhancing the development of precise diagnostic and therapeutic strategies.

Valsartan: An Angiotensin Receptor Blocker Modulates BDNF Expression and Provides Neuroprotection Against Cerebral Ischemic Reperfusion Injury

AT1 receptor blockers (ARBs) are commonly used drugs to treat cardiovascular disease and hypertension, but research on their impact on brain disorders is unattainable. Valsartan (VAL) is a drug that specifically blocks AT1 receptor. Despite the previous evidence for VAL to provide neuroprotection in case of ischemic reperfusion injury, evaluation of their potential in mitigating mitochondrial dysfunction that causes neuronal cell death and neurobehavioral impairment remains unknown. The aim of this study was to evaluate the therapeutic effect of repurposed drug VAL against ischemic reperfusion injury-induced neuronal alternation. tMCAO surgery was performed to induce focal cerebral ischemic reperfusion injury. Following ischemic reperfusion injury, we analyzed the therapeutic efficacy of VAL by measuring the infarct volume, brain water content, mitochondrial oxidative stress, mitochondrial membrane potential, histopathological architecture, and apoptotic marker protein. Our results showed that VAL administrations (5 and 10 mg/kg b.wt.) mitigated the brain damage, enhanced neurobehavioral outcomes, and alleviated mitochondrial-mediated oxidative damage. In addition to this, our findings demonstrated that VAL administration inhibits neuronal apoptosis by restoring the mitochondrial membrane potential. A follow-up investigation demonstrated that VAL induces BDNF expression and promoted ischemic tolerance via modulating the Akt/p-Creb signaling pathway. In summary, our results suggested that VAL administration provided neuroprotection, ameliorated mitochondrial dysfunction, preserved the integrity of neurons, and lead to functional improvement after ischemic reperfusion injury.

Electroactive Nanomaterials for the Prevention and Treatment of Heart Failure: From Materials and Mechanisms to Applications

Heart failure (HF) represents a cardiovascular disease that significantly threatens global well-being and quality of life. Electroactive nanomaterials, characterized by their distinctive physical and chemical properties, emerge as promising candidates for HF prevention and management. This review comprehensively examines electroactive nanomaterials and their applications in HF intervention. It presents the definition, classification, and intrinsic characteristics of conductive, piezoelectric, and triboelectric nanomaterials, emphasizing their mechanical robustness, electrical conductivity, and piezoelectric coefficients. The review elucidates their applications and mechanisms: 1) early detection and diagnosis, employing nanomaterial-based sensors for real-time cardiac health monitoring; 2) cardiac tissue repair and regeneration, providing mechanical, chemical, and electrical stimuli for tissue restoration; 3) localized administration of bioactive biomolecules, genes, or pharmacotherapeutic agents, using nanomaterials as advanced drug delivery systems; and 4) electrical stimulation therapies, leveraging their properties for innovative pacemaker and neurostimulation technologies. Challenges in clinical translation, such as biocompatibility, stability, and scalability, are discussed, along with future prospects and potential innovations, including multifunctional and stimuli-responsive nanomaterials for precise HF therapies. This review encapsulates current research and future directions concerning the use of electroactive nanomaterials in HF prevention and management, highlighting their potential to innovating in cardiovascular medicine.

Nano-medicine therapy reprogramming metabolic network of tumour microenvironment: new opportunity for cancer therapies

Metabolic heterogeneity is one of the characteristics of tumour cells. In order to adapt to the tumour microenvironment of hypoxia, acidity and nutritional deficiency, tumour cells have undergone extensive metabolic reprogramming. Metabolites involved in tumour cell metabolism are also very different from normal cells, such as a large number of lactate and adenosine. Metabolites play an important role in regulating the whole tumour microenvironment. Taking metabolites as the target, it aims to change the metabolic pattern of tumour cells again, destroy the energy balance it maintains, activate the immune system, and finally kill tumour cells. In this paper, the regulatory effects of metabolites such as lactate, glutamine, arginine, tryptophan, fatty acids and adenosine were reviewed, and the related targeting strategies of nano-medicines were summarised, and the future therapeutic strategies of nano-drugs were discussed. The abnormality of tumour metabolites caused by tumour metabolic remodelling not only changes the energy and material supply of tumour, but also participates in the regulation of tumour-related signal pathways, which plays an important role in the survival, proliferation, invasion and metastasis of tumour cells. Regulating the availability of local metabolites is a new aspect that affects tumour progress. (The graphical abstract is by Figdraw).

Overweight Leads to an Increase in Vitamin E Absorption and Status in Mice

SCOPE

This study investigates whether vitamin E (VE) deficiency in subjects with obesity could, at least partly, be due to a defect in VE intestinal absorption.

METHODS AND RESULTS

Mice follow either a high-fat (HF) or a control (CTL) diet for 12 weeks. The study evaluates their VE status, the expression of genes encoding proteins involved in lipid and fat-soluble vitamin intestinal absorption, and VE absorption using a γ-tocopherol-rich emulsion. HF mice have a weight (+23.0%) and an adiposity index (AI, +157.0) superior to CTL mice (p < 0.05). α-Tocopherol concentrations are higher in both plasma (+45.0%) and liver (+116.9%) of HF mice compared to CTL mice (p < 0.05). α-Tocopherol concentration in the adipose tissue of HF mice is higher than that of CTL mice after correction by the AI (+72.4%, p < 0.05). No difference is found in the expression of genes coding for proteins involved in intestinal lipid metabolism in fasting mice. After force-feeding, γ-tocopherol plasma concentration is higher in HF mice compared to CTL mice (+181.5% at 1.5 h after force-feeding, p < 0.05).

CONCLUSION

HF mice display higher status and more efficient absorption of VE than CTL mice. VE absorption is thus likely not impaired in the early stages of obesity.

Induction of cardiac alternans in human iPS-derived cardiomyocytes through β-adrenergic receptor stimulation

Cardiac alternans (C-ALT) is a phenomenon of alternating strong and weak contractions in the heart and is considered a risk factor for the development of heart failure and arrhythmias. However, no model has been reported that can induce C-ALT in vitro using human cells, and the developmental mechanism of C-ALT has not been studied using human cells. In this study, we successfully induced C-ALT in vitro using human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). By stimulating β-adrenergic receptor with isoproterenol on hiPSC-CMs cultured in atmospheric condition (with ~0.04% CO2), contractility and calcium transient were observed to alternately increase and decrease with each beat. In contrast, C-ALT was not induced in hiPSC-CMs cultured at 5% CO2 concentration. Since previous studies have linked C-ALT to problems with calcium regulation in the sarcoplasmic reticulum (SR), we exposed hiPSC-CMs to compounds that alter SR Ca2+ loading and analyzed their contractile responses. The results showed that exposure to verapamil, thapsigargin, and ryanodine either suppressed or eliminated C-ALT. In contrast, omecamtiv mecarbil and blebbistatin, which alter contractility without SR Ca2+ loading, did not induce or suppress C-ALT. These results suggest that C-ALT in hiPSC-CMs induced by isoproterenol may be due to abnormal regulation of the ryanodine receptor's opening and closing caused by excessive Ca2+ load in the SR from β-adrenergic receptor stimulation.

Homology-based identification and structural analysis of Pangasius hypophthalmus Annexins and Serine proteases to search molecules for wound healing applications

Chronic wounds and burns are a worldwide healthcare problem that erodes patients' well-being and healthcare systems. This silent and costly epidemic requires new, cost-efficient solutions to improve patients' physical and economic welfare. Eschar-degrading vegetal and bacterial proteases have been utilized as a solution. However, these proteins are evolutionarily far from those present in human wound healing. Serine protease (SP) and annexin (ANX) proteins interact within the skin healing process. A homology-based identification pipeline can help in discovering selective human SP and ANX analogs in the epithelial tissue of the fast-healing species, Pangasius hypophthalmus. In the present work, we found 14 candidates for RT-PCR in P. hypophthalmus using homology inference. The genetically detected candidates were then structurally and sequentially analyzed to understand their possible relation to SPs and ANXs involved in human wound healing. A total of six TBLASTN/BLASTX candidates (four SPs and two ANXs) were detected in P. hypophthalmus skin. Structural analysis revealed that all SP candidates resembled human KLK4, KLK5, KLK6, and KLK8, whereas all ANX only resembled human ANXA4. Structure and sequence analysis revealed high conservation of ANX Ca2+ binding sites (GDXD) and SP catalytic triad (HDS) motifs. In addition, structural analysis revealed that SP substrate selectivity position 186 was the main difference between human KLK5 and P. hypophthalmus SPs. These findings may allow the proposal and testing of more selective formulations, broadening treatments beyond debridement.

Granzyme mRNA-miRNA interaction and its implication to functional impact

BACKGROUND

Granzyme activity can affect the processing and stability of miRNAs within target cells. They also could induce changes in miRNA expression that impact apoptotic signaling. Granzyme-induced apoptosis might result in changes to the miRNA profile, which can further influence the apoptosis and inflammation processes.

OBJECTIVE

The aim of this study was to bioinformatically analyze which miRNAs and transcription factors bind to the CDS and UTR regions of the granzyme family to regulate gene expression in relation to granzyme evolution and their association with human cancer diseases.

METHODS

The expression patterns of granzyme genes were analyzed in various human tissues. MiRNAs binding to the CDS and UTR of the granzyme family were examined, and the transcription factors binding to these miRNAs binding sites were also analyzed. Cytoscape program was used to visualize and analyze the networks of interactions between granzyme mRNA and miRNAs. Additionally, the evolutionary patterns of the granzyme family in relation to miRNAs and transcription factors binding were investigated.

RESULTS

Analysis of the expression patterns of the granzyme family in various human tissues shows that GZMA and GZMK are strongly expressed in lymph nodes. GZMB exhibits strong expression in the bone marrow, while GZMA is prominently expressed in the spleen. Twenty-two miRNAs bind to both GZMK and GZMB mRNA, while six miRNAs bind to both GZMK and GZMM mRNA. The only miRNA that binds to GZMK, GZMB, GZMM, and GZMA mRNA is hsa-miR-146a-5p. Transcription factors JUND, FOS, and JUN are distinctly interconnected with has-miR-5696 and GZMK. Association data between the granzyme family and cancers showed that various miRNAs were consistently implicated and exhibited either upregulation or downregulation.

CONCLUSION

Although the granzyme family possesses distinct genetic information, it shows relatively high expression levels in the lymph node, spleen, and bone marrow. Many miRNAs specifically regulate granzyme gene expression, and various transcription factors are involved. Analyzing the granzyme genes-miRNAs-transcription factors-related network will provide crucial insights into the mechanisms of cancer development and suppression.

Reduced insulin/IGF-1 signalling upregulates two anti-viral immune pathways, decreases viral load and increases survival under viral infection in C. elegans

Reduced insulin/IGF-1 signalling (rIIS) improves survival across diverse taxa and there is a growing interest in its role in regulating immune function. Whilst rIIS can improve anti-bacterial resistance, the consequences for anti-viral immunity are yet to be systematically examined. Here, we show that rIIS in adult Caenorhabditis elegans increases the expression of key genes in two different anti-viral immunity pathways, whilst reducing viral load in old age, increasing survival and reducing rate-of-senescence under infection by naturally occurring positive-sense single-stranded RNA Orsay virus. We found that both drh-1 in the anti-viral RNA interference (RNAi) pathway and cde-1 in the terminal uridylation-based degradation of viral RNA pathway were upregulated in early adulthood under rIIS and increased anti-viral resistance was not associated with reproductive costs. Remarkably, rIIS increased anti-viral gene expression only in infected worms, potentially to curb the costs of constitutively upregulated immunity. RNA viruses are found across taxa from plants to mammals and we demonstrate a novel role for rIIS in regulating resistance to viral infection. We therefore highlight this evolutionarily conserved signalling pathway as a promising therapeutic target to improve anti-viral immunity.

Integrating epigenetic modification and stem cell therapy strategies: A novel approach for advancing Alzheimer's disease treatment - A literature review

Alzheimer's disease (AD) is the most frequent form of dementia and represents an increasing global burden, particularly in countries like Indonesia, where the population has begun to age significantly. Current medications, including cholinesterase inhibitors and NMDA receptor antagonists, have modest effects on clinical symptoms in the early to middle stages, but there is no curative treatment available so far despite progress. Activating or repressing epigenetic modifications, including DNA methylation, histone modification and microRNA regulation, appears to play an important role in AD development. These alterations further enact transcriptional changes relevant to the signature AD pathologies of amyloid-β deposition, tau protein malfunctioning, neuroinflammation, and neuronal death. Here, we discuss the feasibility of targeting these epigenetic alterations as a new treatment strategy due to the reversibility of epigenetics and their ability to correct faulty gene expression. We also review the combined promise of stem cell therapies and epigenetic modulation in neurodegeneration, inflammation and cognitive decline. This combined approach may provide a multifaceted strategy to slow disease progression, replace lost neurons, and restore neural function. Despite challenges, including ethical, financial, and methodological barriers, ongoing research in epigenetic modulation and stem cell therapy holds promise for pioneering therapies in AD.

Decoding early-onset of colorectal cancer: Insights into SERPINA3 expression patterns

Early-onset colorectal cancer (EOCRC), recognized as a distinct subgroup with an increased incidence over the past two decades, characterized by its aggressive nature and potentially unique molecular factors that differentiate it from traditional colorectal cancer (CRC). In this study, we investigated differentially expressed genes in a young-CRC patient using paired-end mRNA-sequencing. Validation of target genes through qRT-PCR highlighted a significant increase in SERPINA3 levels in EOCRC, representing a novel finding. Epithelial expression of SERPINA3 demonstrated a strong association with disease progression, whereas stromal expression showed a negative correlation. Our findings reveal the distinct expression patterns and potential involvement of SERPINA3 in both the initiation and progression of CRC, suggesting that SERPINA3 could serve as a marker for distinguishing early-onset from late-onset cases.

Prenatal Perfluoroalkyl Substance Exposure in Association with Global Histone Post-Translational Methylation in 2-Year-Old Children

Perfluoroalkyl substances (PFASs) have elimination half-lives in years in humans and are persistent in the environment. PFASs can cross the placenta and impact fetal development. Exposure to PFASs may lead to adverse effects through epigenetic mechanisms. This study aimed to investigate whether prenatal exposure to perfluorooctyl sulfonate (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), and perfluoroundecanoic acid (PFUA) was associated with global histone methylation level changes among the 130 2-year-old children followed-up in a birth cohort study in Taiwan. PFOS, PFOA, PFNA, and PFUA were measured by UHPLC/MS/MS in cord blood. Global histone methylation levels were measured from the blood leukocytes of 2-year-old children by Western blotting. Multivariable regression analyses were applied to adjust for potential confounding effects. Among the 2-year-old children, an IQR increase in the natural log-transformed PFUA exposure was associated with an increased H3K4me3 level by 2.76-fold (95%CI = (0.79, 4.73), p = 0.007). PFOA and PFNA exposures was associated with a decreased H3K27me3 level by 2.35-fold (95%CI = (-4.29, -0.41), p = 0.01) and 2.01-fold (95%CI = (-4.00, -0.03), p = 0.04), respectively. Our findings suggest that prenatal PFAS exposure affected histone post-translational modifications.

Mesenchymal stem cell transplantation plays a role in relieving cancer pain

Tumors can invade, compress, and damage nerves, leading to persistent pain and seriously affecting the quality of life of patients. However, their treatment is challenging. Sensitization of peripheral receptors, abnormal activity of primary sensory neurons, activation of glial cells, enhanced inflammatory responses, and sensory information transmission contribute towards cancer pain. Therefore, considerable attention has been paid to exploring prospective methods to inhibit the occurrence of these factors and relieve cancer pain. Studies on different types of pains have revealed that the transplantation of functionally active cells into the host has the pharmacological effect of producing analgesia. Mesenchymal stem cells (MSCs) can act as small active pumps to reduce the expression of pain-related molecules and produce analgesic effects. Moreover, MSCs can establish complex communication networks with non-tumor and cancer cells in the microenvironment, interact with each other, and can be used as destinations for inflammation and tumor sites, affecting their potential for invasion and metastasis. This emphasizes the key role of MSCs in cancer and pain management. The pain relief mechanisms of MSCs include neuronutrition, neural protection, neural network reconstruction, immune regulation, and improvement of the inflammatory microenvironment around the nerve injury. All of these are beneficial for the recovery of injured or stimulated nerves and the reconstruction of neural function, and play a role in relieving pain. The pain treatment strategy of cell transplantation is to repair injured nerves and produce analgesic pharmacological properties that are different from those of painkillers and other physiotherapies. Although the therapeutic role of MSCs in cancer and pain is in its early stages, the therapeutic value of MSCs for cancer pain has great prospects. Therefore, in this study, we explored the possible mechanism between MSCs and cancer pain, the potential therapeutic role of therapeutic cells in cancer pain, and some problems and challenges.

Exploring Molecular Alterations in Breast Cancer Among Indian Women Using Label-Free Quantitative Serum Proteomics

The clinical data indicate that diverse parameters characterize breast cancer patients in India, including age at presentation, risk factors, outcomes, and behavior. Alarming incidence and mortality rates emphasize the crucial need for early screening measures to combat breast cancer-related deaths effectively. Quantitative proteomic approaches prove pivotal in predicting cancer prognosis, analyzing protein expression patterns tied to disease aggressiveness and metastatic potential, and facilitating conversant therapy selection. Thus, this study was envisioned with the goal of identifying protein markers associated with breast cancer in Indian women, which could potentially be developed as diagnostic tools and therapeutic targets in the future. Applying label-free proteomic quantitation method and statistical analysis, several differentially expressed proteins (DEPs) were identified in the serum of breast cancer patients compared to controls, including SBSN, ANG, PCOLCE, and WFDC3 (upregulated), and PFN1, FLNA, and DSG2 (downregulated). The expression of SBSN was also validated by western blotting. Statistical methods were employed to proteomic expression data, which highlighted the ability of DEPs to distinguish between breast cancer and control samples. Conclusively, this study recognizes prospective biomarkers for breast cancer among Indian women and highlights the requisite of in-depth functional studies to elucidate their precise roles in breast cancer development. We particularly emphasize on SBSN and PFN1, as these proteins were observed to be progressively overexpressed and under expressed, respectively, in breast cancer samples compared to control samples, ranging from early-stage to metastatic cases.

Evaluating the Efficacy of Irisin Injection in Mimicking the Molecular Responses Induced by Endurance Exercise in Mouse Liver Tissue

Background

Physical activity has been found to improve liver health by reducing oxidative stress (OS), possibly through the protein irisin. Heat shock proteins (HSPs) and microRNAs (miRNAs) help regulate the body's response to stress and maintain cellular health. This study aimed to investigate the expression of the HSP70 gene and protein, miR-223a, and serum irisin levels in the liver after 8 weeks of endurance exercise or irisin injection.

Methods

Twenty-one mice were randomly assigned to a control group, an endurance training group, and an irisin injection group. The expression of the HSP70 gene and miR-223a was analyzed using real-time polymerase chain reaction (PCR), while HSP70 protein levels were measured using immunohistochemistry (IHC) and Western blot analysis. The concentration of irisin in the mouse serum was evaluated using the enzyme-linked immunosorbent assay (ELISA) method.

Results

The endurance training and irisin injection groups exhibited a significant increase in the HSP70 gene (405.30% and 816.03%, respectively) and protein expression (173.89% in IHC, 36.76% in Western blot for endurance training; 206.73% in IHC, 59.80% in Western blot for irisin injection) as well as elevated serum irisin levels (49.75% for endurance training and 60.65% for irisin injection) compared with the control group. In contrast, miR-223a expression decreased in both the endurance training (21.37%) and irisin injection (52.80%) groups (P < 0.05 in all cases). Mice in the irisin injection group demonstrated higher levels of the HSP70 gene (81.28%) and protein expression (11.99% in IHC and 16.84% in Western blot) and lower miR-223a levels (39.97%) than those in the endurance training group (P < 0.05).

Conclusions

The study concludes that irisin administration can replicate the effects of long-term endurance exercise on HSP70 and miR-223a and may have a more significant impact on their production than exercise training alone.

Exploring the Venom Gland Transcriptome of Bothrops asper and Bothrops jararaca: De Novo Assembly and Analysis of Novel Toxic Proteins

Previous proteomic studies of viperid venom revealed that it is mainly composed of metalloproteinases (SVMPs), serine proteinases (SVSPs), phospholipase A2 (PLA2), and C-type lectins (CTLs). However, other proteins appear in minor amounts that affect prey and need to be identified. This study aimed to identify novel toxic proteins in the venom gland transcriptome of Bothrops asper and Bothrops jararaca, using data from NCBI. Bioinformatics tools were used to assemble, identify, and compare potentially novel proteins in both species, and we performed functional annotation with BLASTX against the NR database. While previous assemblies have been performed for B. jararaca, this is the first assembly of the B. asper venom gland transcriptome. Proteins with potentially novel functions were identified, including arylsulfatase and dihydroorotate dehydrogenase, among others, that could have implications for venom toxicity. These results suggest that the identified proteins may contribute to venom toxic variation and provide new opportunities for antivenom research. The study improves the understanding of the protein composition of Bothrops venom and suggests new possibilities for the development of treatments and antivenoms.

The Warburg Effect: Is it Always an Enemy?

The Warburg effect, also known as 'aerobic' glycolysis, describes the preference of cancer cells to favor glycolysis over oxidative phosphorylation for energy (adenosine triphosphate-ATP) production, despite having high amounts of oxygen and fully active mitochondria, a phenomenon first identified by Otto Warburg. This metabolic pathway is traditionally viewed as a hallmark of cancer, supporting rapid growth and proliferation by supplying energy and biosynthetic precursors. However, emerging research indicates that the Warburg effect is not just a strategy for cancer cells to proliferate at higher rates compared to normal cells; thus, it should not be considered an 'enemy' since it also plays complex roles in normal cellular functions and/or under stress conditions, prompting a reconsideration of its purely detrimental characterization. Moreover, this review highlights that distinguishing glycolysis as 'aerobic' and 'anaerobic' should not exist, as lactate is likely the final product of glycolysis, regardless of the presence of oxygen. Finally, this review explores the nuanced contributions of the Warburg effect beyond oncology, including its regulatory roles in various cellular environments and the potential effects on systemic physiological processes. By expanding our understanding of these mechanisms, we can uncover novel therapeutic strategies that target metabolic reprogramming, offering new avenues for treating cancer and other diseases characterized by metabolic dysregulation. This comprehensive reevaluation not only challenges traditional views but also enhances our understanding of cellular metabolism's adaptability and its implications in health and disease.

Investigating the Presence of Selenoneine, Ergothioneine, and Selenium-Containing Biomolecules in Fish and Fish-Derived Commercial Products

Two potent antioxidants, selenoneine and ergothioneine, have been determined simultaneously for the first time in the muscle of highly consumed fish and in fish-derived products. The extraction methods were optimized, and their subsequent analysis was performed by HPLC-ESI-MS/MS. Best extraction efficiency (106 ± 3 and 104 ± 5%) was attained by performing a simple aqueous extraction containing 100 mmol L-1 ammonium acetate or ammonium formate as extractants. Selenoneine and ergothioneine were simultaneously detected in tuna (0.306 ± 0.006 and 3.5 ± 0.2 μg g-1) and swordfish (0.14 ± 0.02 and 1.1 ± 0.4 μg g-1) muscle tissues, while in fish roe and in farmed salmon, only ergothioneine was detected (with contents ranging 0.03-3.3 μg g-1). Moreover, the presence of their respective methylated forms was also considered. Additionally, Se-containing biomolecule profiles from water-soluble proteins were obtained by SEC-ICP-MS analysis. Results revealed similar profiles between fish and fish roe, whereas for ultraprocessed fish products, Se seems to be mostly associated with low-molecular-weight biomolecules. The results included in this work may contribute to a better understanding of the relations between selenoneine and ergothioneine in fishery products as well as their fate and potential modifications of Se-containing biomolecule profiles during fish processing.

Interleukin-33 mediated regulation of microRNAs in human cord blood-derived mast cells: Implications for infection, immunity, and inflammation

Mast cell (MCs) activation is the driving force of immune responses in several inflammatory diseases, including asthma and allergies. MCs are immune cells found throughout the body and are equipped with numerous surface receptors that allow them to respond to external signals from parasites and bacteria as well as to intrinsic signals such as cytokines. Upon activation, MCs release various mediators and proteases that contribute to inflammation. This study aimed to identify microRNAs (miRNAs) that regulate MC response to interleukin-33 and their target genes using a model of human cord blood-derived mast cells (hCBMCs). hCBMCs were induced with 10 and 20 ng of recombinant human interleukin-33 (rhIL-33) for 6 and 24 h, respectively. Total RNA was extracted from these cells and miRNA profiling was performed using high-throughput microarrays. Differential expression of miRNAs and target analysis were performed using Transcriptome Analysis Console and Ingenuity Pathway Analysis. The most significant miRNAs in each condition were miR-6836-5p (fold change = 1.76, p = 3E-03), miR-6883-5p (fold change = -2.13, p = 7E-05), miR-1229-5p (fold change = 2.46, p = 8E-04), and miR-3613-5p (fold change = 66.7, p = 1E-06). Target analysis revealed that these miRNAs regulate mast cell responsiveness and degranulation by modulating the expression of surface receptors, adaptors, and signaling molecules in response to rhIL-33 stimulation. This study is the first miRNA profiling and target analysis of hCBMCs that will further enhance our understanding of the role of miRNAs in the immune response in a timely manner and their relevance for the development of a new therapeutic target for inflammatory disorders.

The interaction of BDNF with estrogen in the development of hypertension and obesity, particularly during menopause

The expression of BDNF in both neuronal and non-neuronal cells is influenced by various stimuli, including prenatal developmental factors and postnatal conditions such as estrogens, dietary habits, and lifestyle factors like obesity, blood pressure, and aging. Central BDNF plays a crucial role in modulating how target tissues respond to these stimuli, influencing the pathogenesis of hypertension, mitigating obesity, and protecting neurons from aging. Thus, BDNF serves as a dynamic mediator of environmental influences, reflecting an individual's unique history of exposure. Estrogens, on the other hand, regulate various processes to maintain overall physiological well-being. Through nuclear estrogen receptors (ERα, ERβ) and the membrane estrogen receptor (GPER1), estrogens modulate transcriptional processes and signaling events that regulate the expression of target genes, such as ERα, components of the renin-angiotensin system (RAS), and hormone-sensitive lipase. Estrogens are instrumental in maintaining the set point for blood pressure and energy balance. BDNF and estrogens work cooperatively to prevent obesity by favoring lipolysis, and counteractively regulate blood pressure to adapt to the environment. Estrogen deficiency leads to menopause in women with low central BDNF level. This review delves into the complex mechanisms involving BDNF and estrogen, especially in the context of hypertension and obesity, particularly among postmenopausal women. The insights gained aim to inform the development of comprehensive therapeutic strategies for these prevalent syndromes affecting approximately 68% of adults.

Activation of BDNF-TrkB Signaling in Specific Structures of the Sheep Brain by Kynurenic Acid

Fluctuations in kynurenic acid (KYNA) and brain-derived neurotrophic factor (BDNF) levels in the brain reflect its neurological status. The aim of the study was to investigate the effect of transiently elevated KYNA concentrations in the cerebroventricular circulation on the expression of BDNF and its high-affinity tropomyosin-related kinase receptor B (TrkB) in specific structures of the sheep brain. Intracerebroventricularly cannulated anestrous sheep were subjected to a series of four 30 min infusions of KYNA: 4 × 5 μg/60 μL/30 min (KYNA20, n = 6) and 4 × 25 μg/60 μL/30 min (KYNA100, n = 6) or a control infusion (n = 6), at 30 min intervals. Sections of the hippocampal CA3 field, amygdala (AMG), prefrontal cortex (PCx), and the hypothalamic medial-basal (MBH) and preoptic (POA) areas were dissected from the brain immediately after the experiment. The highest concentration of BDNF protein was found in the CA3 field (p < 0.001), which was 8-fold higher than in the AMG and 12-fold higher than that in the PCx (MBH and POA were not analyzed). The most pronounced BDNF mRNA expression was observed in the MBH, followed by the PCx, POA, AMG and CA3, while the highest abundance of TrkB mRNA was recorded in the AMG, followed by the MBH, PCx, CA3, and POA. KYNA increased (p < 0.05-p < 0.01) BDNF protein levels and the expression of its gene in the brain structures were examined, with the effect varying by dose and brain region. KYNA, particularly at the KYNA100 dose, also increased (p < 0.01) TrkB gene expression, except for the AMG, where the lower KYNA20 dose was more effective (p < 0.01). These findings suggest a positive relationship between KYNA levels in the cerebroventricular circulation and BDNF-TrkB expression in specific brain regions in a sheep model. This indicates that a transient increase in the CSF KYNA concentration can potentially restore BDNF production, for which deficiency underlies numerous neurological disorders.

Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution

Transcription and translation are intertwined processes in which mRNA isoforms are crucial intermediaries. However, methodological limitations in analyzing translation at the mRNA isoform level have left gaps in our understanding of critical biological processes. To address these gaps, we developed an integrated computational and experimental framework called long-read Ribo-STAMP (LR-Ribo-STAMP) that capitalizes on advancements in long-read sequencing and RNA-base editing-mediated technologies to simultaneously profile translation and transcription at both the gene and mRNA isoform levels. We also developed the EditsC metric to quantify editing and leverage the single-molecule, full-length transcript information provided by long-read sequencing. Here, we report concordance between gene-level translation profiles obtained with long-read and short-read Ribo-STAMP. We show that LR-Ribo-STAMP successfully profiles translation of mRNA isoforms and links regulatory features, such as upstream open reading frames (uORFs), to translation measurements. We apply LR-Ribo-STAMP to discovering translational differences at both the gene and isoform levels in a triple-negative breast cancer cell line under normoxia and hypoxia and find that LR-Ribo-STAMP effectively delineates orthogonal transcriptional and translation shifts between conditions. We also discover regulatory elements that distinguish translational differences at the isoform level. We highlight GRK6, in which hypoxia is observed to increase expression and translation of a shorter mRNA isoform, giving rise to a truncated protein without the AGC Kinase domain. Overall, LR-Ribo-STAMP is an important advance in our repertoire of methods that measures mRNA translation with isoform sensitivity.

Rapid FEV1 decline and the effects of both FEV1 and FVC on cardiovascular disease: A UK biobank cohort analysis

BACKGROUND

The relationship between lung function and cardiovascular disease (CVD) has emerged as a significant research focus in recent years, but studies on the effects of both forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) remain limited.

METHODS

Among 29,662 participants in the UK Biobank study free of CVD, rapid lung function decline was defined as the decline in either FEV1 (greatest quartile), FVC (greatest quartile), or both (when both FEV1 and FVC exceeded the greatest quartile). CVDs include coronary heart disease (CHD), arrhythmias, heart failure (HF), peripheral arterial disease (PAD), and other CVDs (including endocarditis, stroke, and myocardial diseases). Cox proportional hazards models were used to explore the associations between lung function and CVD incidence. Fine‒Gray models were used to account for the competing risk of death.

RESULTS

Among 29,662 participants in the UK Biobank study free of CVD, the adjusted hazard ratios (HRs) for FEV1 rapid decline were 1.150 (95% CI: 1.009-1.311) for CHD, 1.307 (95% CI: 1.167-1.465) for arrhythmias, 1.406 (95% CI: 1.084-1.822) for HF, 1.287 (95% CI: 1.047-1.582) for PAD, 1.170 (95% CI: 1.022-1.340) for other CVDs, and 1.216 (95% CI: 1.124-1.315) for composite CVD. The adjusted HRs for the impact of both rapid decreases in FEV1 and FVC were 1.386 (95% CI: 1.226-1.567) for arrhythmias, 1.390 (95% CI: 1.041-1.833) for HF, 1.222 (95% CI: 1.054-1.417) for other CVDs, and 1.230 (95% CI: 1.128-1.340) for composite CVD.

CONCLUSIONS

The rapid decline in FEV1 and the impact of both FEV1 and FVC are closely associated with the subsequent incidence of various CVDs and composite CVD.

Decoding the Challenges: navigating Intact Peptide Mass Spectrometry-Based Analysis for Biological Applications

Quantitative analysis of peptides in biological fluids offers a high diagnostic and prognostic tool to reflect the pathophysiological condition of the patient. Recently, methods based on liquid chromatography coupled with mass spectrometry (LC-MS) for the quantitative determination of intact peptides have been replacing traditionally used ligand-binding assays, which suffer from cross-reactivity issues. The use of "top-down" analysis of peptides is rapidly increasing since it does not undergo incomplete or non-reproducible digestion like "bottom-up" approaches. However, the low abundance of peptides and their peculiar characteristics, as well as the complexity of biological fluids, make their quantification challenging. Herein, the analytical pitfalls that may be encountered during the development of an LC-MS method for the analysis of intact peptides in biological fluids are discussed. Challenges in the pre-analytical phase, stability after sampling and sample processing, significantly impact the accuracy of peptide quantification. Emerging techniques, such as microextractions, are becoming crucial for improved sample cleanup and enrichment of target analytes. A comparison between the roles of high-resolution and low-resolution mass spectrometry in the quantification of intact peptides, as well as the introduction of supercharging reagents to enhance ionization, will be discussed.

Co-exposure effect of different colour of LED lights and increasing temperature on zebrafish larvae (Danio rerio): Immunohistochemical, metabolomics, molecular and behaviour approaches

Although there are studies in the literature on the effects of different coloured light-emitting diodes (LEDs) on different organisms, there is limited information on how these effects change with temperature increase. In this study, the effects of blue, green, red and white LED lights on the early development process of zebrafish (Danio rerio (Hamilton, 1822)) were comprehensively investigated. In addition, to simulate global warming, it was examined how a one-degree temperature increase affects this process. For this purpose, zebrafish embryos, which were placed at 4 hpf (hours post fertilization) in an incubator whose interior was divided into four areas, were kept at three different temperatures (28, 29 and 30 °C) for 120 h. The group kept in a dark environment was chosen as the control. The temperature of the control group was also increased at the same rate as the other groups. The results showed that at the end of the exposure period, temperature and light colour caused an increase in body malformations. Histopathological damage and immunopositive signals of HSP 70 and 8-OHdG biomarkers in larval brains, increase in free oxygen radicals, apoptotic cells and lipid accumulation throughout the body, increase in locomotor activity, decrease in heart rate and blood flow, and significant changes in more than thirty metabolite levels were detected. In addition, it has been determined that many metabolic pathways are affected, especially glutathione, vitamin B6 and pyrimidine metabolism. Moreover, it has been observed that a one-degree temperature increase worsens this negative effect. It was concluded that blue light was the closest light to the control group and was less harmful than other light colours. The study revealed that blue light produced results that were most similar to those seen in the control group.

Lactate and lysine lactylation of histone regulate transcription in cancer

Histone lysine modifications were well-established epigenetic markers, with many types identified and extensively studied. The discovery of histone lysine lactylation had revealed a new form of epigenetic modification. The intensification of this modification was associated with glycolysis and elevated intracellular lactate levels, both of which were closely linked to cellular metabolism. Histone lactylation plays a crucial role in multiple cellular homeostasis, including immune regulation and cancer progression, thereby significantly influencing cell fate. Lactylation can modify both histone and non-histone proteins. This paper provided a comprehensive review of the typical epigenetic effects and lactylation on classical transcription-related lysine sites and summarized the known enzymes involved in histone lactylation and delactylation. Additionally, some discoveries of histone lactylation in tumor biology were also discussed, and some prospects for this field were put forward.

Associations Between Urinary Phthalate Metabolites and Decreased Serum α-Klotho Level: A Cross-Sectional Study Among US Adults in Middle and Old Age

Phthalates are widely used chemicals with ubiquitous human exposure. Evidence indicated that phthalate exposure was associated with an increased risk of aging-related diseases. Klotho is a transmembrane protein with anti-aging functions, and its association with phthalates remains unknown. To find the association between phthalate exposure and serum α-Klotho, a cross-sectional study was performed in 4482 adults (40-79 years old) who completed the National Health and Nutrition Examination Survey (NHANES) (2007-2016). As shown in the results of multivariable linear regression analyses, mono(carboxynonyl) phthalate (MCNP) and mono-n-butyl phthalate (MBP) were inversely associated with α-Klotho, and the regression coefficients of MCNP and MBP were -1.14 (95% confidence interval (CI): -2.00, -0.27) and -0.08 (95% CI: -0.14, -0.02). Subgroup analyses based on the quartiles of each phthalate metabolite showed that both MCNP and MBP were only inversely associated with α-Klotho in the subgroups of the highest levels. For mono-isobutyl phthalate (MIBP), the inverse association with α-Klotho was only statistically significant in the subgroup of the lowest level, and the regression coefficient was -26.87 (95% CI: -52.53, -1.21). Our findings suggest that α-Klotho might be involved in the association of phthalate exposure with aging-related diseases. Future research investigating the causality between phthalates and α-Klotho and its underlying mechanisms is encouraged.

Vibrio alginolyticus Reprograms CIK Cell Metabolism via T3SS Effector VopS to Promote Host Cell Ferroptosis

Vibrio alginolyticus is a Gram-negative pathogen of both marine animals and humans, resulting in significant losses for the aquaculture industry. Emerging evidence indicates that V. alginolyticus manipulates cell death for its pathogenicity, but the underlying molecular mechanisms remain unclear. Here, a gene designated vopS in V. alginolyticus HY9901 was identified, which was predicted to encode the T3SS effector protein. To determine whether VopS contributes to the pathogenesis of V. alginolyticus, the ΔvopS mutant strain was constructed and phenotypically characterized. The deletion of VopS not only reduced the ability to secrete extracellular proteases and virulence but also affected the expression of the T3SS genes. Furthermore, VopS was cytotoxic and induced apoptosis, as confirmed by elevated LDH and the activation of caspase-3. Metabolomic analysis revealed considerable metabolomic disruptions upon V. alginolyticus infection. The VopS effector induced host cell ferroptosis by promoting the synthesis of adrenic acid, depleting cellular glutathione, and subsequently increasing the accumulation of ferrous (Fe2+). Taken together, our findings provide that the VopS effector is an essential virulence factor of V. alginolyticus, which can lead to ferroptosis.

The economic burden of nosocomial infections for hospitals: evidence from Germany

BACKGROUND

Nosocomial infections (NI) significantly worsen patient outcomes, resulting in higher mortality rates and reduced health-related quality of life. Furthermore, they pose substantial economic strain on healthcare systems and hospitals. For instance, patients with nosocomial infections (NIs) experience prolonged hospital stays compared to those without NIs. These extended stays result in occupied bed-days, leading to opportunity costs for hospitals. This study aimed to estimate the opportunity costs for a German hospital based on hospital stays, daily revenue, and occupancy rates (OCR).

METHODS

We analysed cost data obtained from routine records maintained by the accounting department of a German hospital's surgical and orthopedic units from 2018 to 2019 for the "HygArzt" research project. To ensure balance, we employed genetic matching. We estimated the differences in length of stay (LOS) and daily revenue between patients with and without nosocomial infections (NI) using linear regression. Finally, we calculated the opportunity cost borne by the hospital by treating NI patients instead of non-NI patients. All costs are reported in 2018 Euros.

RESULTS

The final sample included 81 patients with NI matched with 207 patients without NI. The majority of the NI patients (77.0%) had surgical site infection (SSI). Compared to non-NI patients, we observed that NI patients had a longer LOS (10 days, p < 0.001) and lower daily revenue (€400, p < 0.001). We also found that comorbidities and the frequency of operations had significant impact on the LOS. Using a baseline 30 to 50% preventable NIs, successful prevention of a single NI could potentially reduce the length of hospital stay by 3 to 5 days and increase hospital revenue by approximately €120 to €200 per day per prevented NI. Consequently, the hospital saves 3 to 5 more bed-days to backfill and generate more revenue, and/or make more efficient resource allocation by changing bed-capacity and staffing. The resulting opportunity costs can potentially exceed €1,000 per preventable case.

CONCLUSION

NIs pose a substantial economic burden for hospitals. From a health economics' perspective, there are strong economic incentives for hospitals to implement infection control interventions, such as the involvement of a prevention link physician/nurse.

Clinical Evidence Regarding Spermidine-Hyaluronate Gel as a Novel Therapeutic Strategy in Vestibulodynia Management

Background: Vestibulodynia (VBD) represents a summation and overlapping of trigger factors (infections, hormonal disturbances, allergies, genetic aspects, psychological vulnerability, and others) with broad individual variability. As there are no standard treatment options for VBD, the disease is still in need of appropriate therapeutic tools. Objectives: A prospective observational trial was performed to confirm the efficacy of a topical gel containing a spermidine-hyaluronate complex (UBIGEL donna™) as either a stand-alone or companion treatment through a multicenter study on a large sample population. Methods: For women with VBD (n = 154), the treatment consisted of approximately two months (4 + 4 weeks) of applications according to the posology of UBIGEL. Evaluation of symptoms was performed on relevant clinical endpoints: dyspareunia and vulvovaginal pain/burning by a visual scale (VAS); vestibular trophism by a vestibular trophic health (VeTH) score; vulvoscopy through a cotton swab test; and the level of hypertonic pelvic floor by a physical graded assessment of levator ani hypertonus. Results: A total of 154 patients treated with UBIGEL donna™ showed significant improvements across all five evaluated parameters, including pain, dyspareunia, swab test results, muscle hypertonicity, and vestibular trophism. Pain and dyspareunia scores decreased by 46.5% and 33.5%, respectively, while significant improvements were also observed in the other parameters (p < 0.0001). These improvements were consistent across various stratifications, including age and disease duration. Conclusions: The findings of the present study suggest that UBIGEL donna™ is effective in alleviating pain and dyspareunia, as well as reducing vestibular hypersensitivity in women with VBD. Although UBIGEL donna™ alone cannot serve as a comprehensive substitute for all recommended therapies, we suggest that multimodal therapy strategies may be crucial for attaining substantial improvement in any aspect of the condition.

From gene to therapy: a review of deciphering the role of ABCD1 in combating X-Linked adrenoleukodystrophy

X-linked adrenoleukodystrophy (X-ALD) is a severe genetic disorder caused by ABCD1 mutations, resulting in the buildup of very-long-chain fatty acids, leading to significant neurological decline and adrenal insufficiency. Despite advancements in understanding the mechanisms of X-ALD, its pathophysiology remains incompletely understood, complicating the development of effective treatments. This review provides a comprehensive overview of X-ALD, with a focus on the genetic and biochemical roles of ABCD1 and the impacts of its mutations. Current therapeutic approaches are evaluated, discussing their limitations, and emphasizing the need to fully elucidate the pathogenesis of X-ALD. Additionally, this review highlights the importance of international collaboration to enhance systematic data collection and advance biomarker discovery, ultimately improving patient outcomes with X-ALD.

Generation of a novel constitutive smooth muscle cell-specific Myh11 -driven Cre mouse model

Dysfunction in either embryonic or postnatal vascular smooth muscle cells (SMCs) significantly contributes to the progression of various cardiovascular diseases. Therefore, elucidating the molecular mechanisms governing VSMC development and homeostasis is crucial. MYH11 is the most reliable lineage gene for SMCs and has been utilized to develop tamoxifen-inducible Cre driver lines for achieving SMC-specific gene manipulation by crossing with mice carrying the lox P -flanked gene, particularly in adult mice. For studies involving SMCs during embryogenesis, the commonly used constitutive Cre driver is controlled by the Tagln ( Sm22α ) promoter. However, this Cre driver exhibits activity in multiple non-SMC populations, including cardiomyocytes and skeletal muscle precursors, introducing confounding effects. Additionally, most existing SMC-specific Cre drivers are generated using a transgenic approach, raising concerns about random site integration and variable gene copy numbers. To address these limitations, we report a novel Cre mouse model generated by knock-in (KI) of a nuclear-localized Cre recombinase into the Myh11 gene locus using homologous recombination. We confirmed that the Cre activity precisely recapitulates endogenous Myh11 expression by crossing with Rosa26 mTmG or tdTomato reporter mice. Moreover, Myh11 -driven Cre can efficiently delete the floxed allele of the transcription factor Tead1 specifically in SMCs. The Tead1 SMC-specific knockout mice did not exhibit an overt phenotype, thereby circumventing the embryonic lethal phenotype mediated by Tagln -driven Cre, as we previously reported. These findings establish this novel Cre driver line as a robust tool for tracing the Myh11 -positive SMC lineage and manipulating gene function specifically in SMCs during embryonic development in mice.

Trypsin in pancreatitis: The culprit, a mediator, or epiphenomenon?

Pancreatitis is a common, life-threatening inflammatory disease of the exocrine pancreas. Its pathogenesis remains obscure, and no specific or effective treatment is available. Gallstones and alcohol excess are major etiologies of pancreatitis; in a small portion of patients the disease is hereditary. Pancreatitis is believed to be initiated by injured acinar cells (the main exocrine pancreas cell type), leading to parenchymal necrosis and local and systemic inflammation. The primary function of these cells is to produce, store, and secrete a variety of enzymes that break down all categories of nutrients. Most digestive enzymes, including all proteases, are secreted by acinar cells as inactive proforms (zymogens) and in physiological conditions are only activated when reaching the intestine. The generation of trypsin from inactive trypsinogen in the intestine plays a critical role in physiological activation of other zymogens. It was proposed that pancreatitis results from proteolytic autodigestion of the gland, mediated by premature/inappropriate trypsinogen activation within acinar cells. The intra-acinar trypsinogen activation is observed in experimental models of acute and chronic pancreatitis, and in human disease. On the basis of these observations, it has been considered the central pathogenic mechanism of pancreatitis - a concept with a century-old history. This review summarizes the data on trypsinogen activation in experimental and genetic rodent models of pancreatitis, particularly the more recent genetically engineered mouse models that mimic mutations associated with hereditary pancreatitis; analyzes the mechanisms mediating trypsinogen activation and protecting the pancreas against its' damaging effects; discusses the gaps in our knowledge, potential therapeutic approaches, and directions for future research. We conclude that trypsin is not the culprit in the disease pathogenesis but, at most, a mediator of some pancreatitis responses. Therefore, the search for effective therapies should focus on approaches to prevent or normalize other intra-acinar pathologic processes, such as defective autophagy leading to parenchymal cell death and unrelenting inflammation.

NEK2 is a potential pan-cancer biomarker and immunotherapy target

BACKGROUND

NEK2 is a member of the NEKs family and plays an important role in cell mitosis. Increasing evidence suggests that NEK2 is associated with the development of multiple tumors, but systematic studies of NEK2 in cancer are still lacking. Therefore, we evaluated the prognostic value of NEK2 in 33 cancers to elucidate the potential function of NEK2 in pan-cancers.

METHODS

We investigated the role of NEK2 in pan-cancers utilizing The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database. Additionally, we analyzed the association between NEK2 gene expression across various cancers, protein expression, the tumor microenvironment (TME), and drug sensitivity using several software and web platforms.The potential oncogenic role of NEK2 was initially explored using bioinformatics methods. Furthermore, we conducted in vitro experiments to preliminarily validate the function of NEK2 in cervical cancer.

RESULTS

NEK2 is overexpressed in almost all tumors, and mutation of NEK2 are associated with a poorer tumor prognosis. In addition, the correlation between NEK2 and immune features such as immune cell infiltration, immune checkpoint genes, tumor mutational burden (TMB), Microsatellite instability(MSI) etc. suggest that NEK2 could potentially be applied in the immunotherapy of tumors.

CONCLUSION

NEK2 may be a potential pan-cancer biomarker and immunotherapeutic target for improving the efficacy of tumor therapy.

Deciphering toxico-proteomics of Asiatic medically significant venomous snake species: A systematic review and interactive data dashboard

Snakebite envenomation (SBE) is a neglected tropical disease (NTD) with an approximate 1.8 million cases annually. The tremendous figure is concerning, and the currently available treatment for snakebite envenomation is antivenom. However, the current antivenom has limited cross-neutralisation activity due to the variations in snake venom composition across species and geographical locations. The proteomics of medically important venomous species is essential as they study the venom compositions within and among different species. The advancement of sophisticated proteomic approaches allows intensive investigation of snake venoms. Nevertheless, there is a need to consolidate the venom proteomics profiles and distribution analysis to examine their variability patterns. This review systematically analysed the proteomics and toxicity profiles of medically important venomous species from Asia across different geographical locations. An interactive dashboard - Asiatic Proteomics Interactive Datasets was curated to consolidate the distribution patterns of the venom compositions, serve as a comprehensive directory for large-scale comparative meta-analyses. The population proteomics demonstrate higher diversities in the predominant venom toxins. Besides, inter-regional differences were also observed in Bungarus sp., Naja sp., Calliophis sp., and Ophiophagus hannah venoms. The elapid venoms are predominated with three-finger toxins (3FTXs) and phospholipase A2 (PLA2). Intra-regional variation is only significantly observed in Naja naja venoms. Proteomics diversity is more prominent in viper venoms, with widespread dominance observed in snake venom metalloproteinase (SVMP) and snake venom serine protease (SVSP). Correlations exist between the proteomics profiles and the toxicity (LD50) of the medically important venomous species. Additionally, the predominant toxins, alongside their pathophysiological effects, were highlighted and discussed as well. The insights of interactive toxico-proteomics datasets provide comprehensive frameworks of venom dynamics and contribute to developing antivenoms for snakebite envenomation. This could reduce misdiagnosis of SBE and accelerate the researchers' data mining process.

Transforming Cardiotoxicity Detection in Cancer Therapies: The Promise of MicroRNAs as Precision Biomarkers

Cardiotoxicity (CDTX) is a critical side effect of many cancer therapies, leading to increased morbidity and mortality if not addressed. Early detection of CDTX is essential, and while echocardiographic measures like global longitudinal strain offer promise in identifying early myocardial dysfunction, the search for reliable biomarkers continues. MicroRNAs (miRNAs) are emerging as important non-coding RNA molecules that regulate gene expression post-transcriptionally, influencing key biological processes such as the cell cycle, apoptosis, and stress responses. In cardiovascular diseases, miRNAs have demonstrated potential as biomarkers due to their stability in circulation and specific expression patterns that reflect pathological changes. Certain miRNAs have been linked to CDTX and hold promise for early detection, prognosis, and therapeutic targeting. These miRNAs not only assist in identifying early cardiac injury, but also offer opportunities for personalized interventions by modulating their expression to influence disease progression. As research advances, integrating miRNA profiling with traditional diagnostic methods could enhance the management of CDTX in cancer patients, paving the way for improved patient outcomes and more tailored therapeutic strategies. Further clinical studies are essential to validate the clinical utility of miRNAs in managing CDTX.

Alzheimer's Disease: Exploring the Landscape of Cognitive Decline

Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline, memory loss, and impaired daily functioning. The pathology of AD is marked by the accumulation of amyloid beta plaques and tau protein tangles in the brain, along with neuroinflammation and synaptic dysfunction. Genetic factors, such as mutations in APP, PSEN1, and PSEN2 genes, as well as the APOE ε4 allele, contribute to increased risk of acquiring AD. Currently available treatments provide symptomatic relief but do not halt disease progression. Research efforts are focused on developing disease-modifying therapies that target the underlying pathological mechanisms of AD. Advances in identification and validation of reliable biomarkers for AD hold great promise for enhancing early diagnosis, monitoring disease progression, and assessing treatment response in clinical practice in effort to alleviate the burden of this devastating disease. In this paper, we analyze data from the CAS Content Collection to summarize the research progress in Alzheimer's disease. We examine the publication landscape in effort to provide insights into current knowledge advances and developments. We also review the most discussed and emerging concepts and assess the strategies to combat the disease. We explore the genetic risk factors, pharmacological targets, and comorbid diseases. Finally, we inspect clinical applications of products against AD with their development pipelines and efforts for drug repurposing. The objective of this review is to provide a broad overview of the evolving landscape of current knowledge regarding AD, to outline challenges, and to evaluate growth opportunities to further efforts in combating the disease.

Precise regulating the specific oxygen consumption rate to strengthen the CoQ10 biosynthesis by Rhodobater sphaeroides

Coenzyme Q10 (CoQ10) is the most consumed dietary supplement and mainly biosynthesized by aerobic fermentation of Rhodobacter sphaeroides (R. sphaeroides). Oxygen supply was identified as a bottleneck for improving CoQ10 yield in R. sphaeroides. In this study, a precise regulation strategy based on dielectric spectroscopy (DS) was applied to further improve CoQ10 biosynthesis by R. sphaeroide. First, a quantitative response model among viable cells, cell morphology, and oxygen uptake rate (OUR) was established. DS could be used to detect viable R. sphaeroides cells, and the relationship among cell morphology, CoQ10 biosynthesis, and OUR was found to be significant. Based on this model, the online specific oxygen consumption rate (QO2) control strategy was successfully applied to the CoQ10 fermentation process. QO2 controlled at 0.07 ± 0.01 × 10- 7mmol/cell/h was most favorable for CoQ10 biosynthesis, resulting in a 28.3% increase in CoQ10 production. Based on the multi-parameters analysis and online QO2 control, a precise online nutrient feeding strategy was established using conductivity detected by DS. CoQ10 production was improved by 35%, reaching 3384 mg/L in 50 L bioreactors. This online control strategy would be effectively applied for improving industrial CoQ10 production, and the precise fermentation control strategy could also be applied to other fermentation process.