The Yeast HMGB Protein Hmo1 Is a Multifaceted Regulator of DNA Damage Tolerance

The Saccharomyces cerevisiae chromosomal architectural protein Hmo1 is categorized as an HMGB protein, as it contains two HMGB motifs that bind DNA in a structure-specific manner. However, Hmo1 has a basic C-terminal domain (CTD) that promotes DNA bending instead of an acidic one found in a canonical HMGB protein. Hmo1 has diverse functions in genome maintenance and gene regulation. It is implicated in DNA damage tolerance (DDT) that enables DNA replication to bypass lesions on the template. Hmo1 is believed to direct DNA lesions to the error-free template switching (TS) pathway of DDT and to aid in the formation of the key TS intermediate sister chromatid junction (SCJ), but the underlying mechanisms have yet to be resolved. In this work, we used genetic and molecular biology approaches to further investigate the role of Hmo1 in DDT. We found extensive functional interactions of Hmo1 with components of the genome integrity network in cellular response to the genotoxin methyl methanesulfonate (MMS), implicating Hmo1 in the execution or regulation of homology-directed DNA repair, replication-coupled chromatin assembly, and the DNA damage checkpoint. Notably, our data pointed to a role for Hmo1 in directing SCJ to the nuclease-mediated resolution pathway instead of the helicase/topoisomerase mediated dissolution pathway for processing/removal. They also suggested that Hmo1 modulates both the recycling of parental histones and the deposition of newly synthesized histones on nascent DNA at the replication fork to ensure proper chromatin formation. We found evidence that Hmo1 counteracts the function of histone H2A variant H2A.Z (Htz1 in yeast) in DDT possibly due to their opposing effects on DNA resection. We showed that Hmo1 promotes DNA negative supercoiling as a proxy of chromatin structure and MMS-induced DNA damage checkpoint signaling, which is independent of the CTD of Hmo1. Moreover, we obtained evidence indicating that whether the CTD of Hmo1 contributes to its function in DDT is dependent on the host's genetic background. Taken together, our findings demonstrated that Hmo1 can contribute to, or regulate, multiple processes of DDT via different mechanisms.

A synthetic heavy chain variable domain antibody library (VHL) provides highly functional antibodies with favorable developability

Synthetic antibody libraries have been developed as an efficient source for the discovery of the heavy chain variable (VH) domain, which exhibits low immunogenicity, high tissue penetration, and diverse binding epitopes in therapeutic biopharmaceuticals. In this study, the human IGHV3-23*04 germline gene was chosen as the scaffold with a high expression level and favorable thermal stability. Amino acid diversity was introduced into the complementarity determining region 3 (CDR3) to exclude potential sequence liabilities. A library containing 2.6 × 1011 independent clones was successfully constructed. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, interleukin-17A (IL17A), B-cell maturation antigen (BCMA), and G-protein coupled receptor family C group 5 member D (GPRC5D) were used as target antigens to screen and identify VHs. In each case, Thirty-one to fifty-five VHs were screened out. The VH-Fc antibodies showed superior affinities (as high as 4.6 nM) to the corresponding antigens but did not bind to antigen-irrelevant cell CHO-S. Furthermore, the anti-RBD and anti-IL17A VH-Fc antibodies showed strong functional activity in the receptor-blocking assays. The VH-Fc antibodies from the synthetic library exhibited favorable developability (thermal stability, colloidal stability, hydrophilicity, anti-aggregation ability, and no interaction with human IgGs). We demonstrated that high-affinity and highly functional VH domain antibodies were generated from the rationally designed library with desired physicochemical properties. This approach is generally universal to target any antigen and has significant potential to accelerate candidate selection.

Regulation of citrinin biosynthesis in Monascus purpureus: Impacts on growth, morphology, and pigments production

Fungal hyphae self-assemble a variety of cellular macrostates, ranging from suspended mycelium to dense pellets, all inextricably linked to their productivity. In this study, using CRISPR/Cas technology, we constructed a ctnA knockout strain (ΔctnA) and an overexpression strain (A2) so as to investigate the effects of interfering with citrinin biosynthesis on the growth, morphology and pigmentation of M.purpureus. Results indicated that deletion of ctnA in M. purpureus RP2 led to increased mycelium length, delayed conidium formation, and a citrinin content of 22% of the wild-type strain. Conversely, ctnA overexpression in strain A2 resulted in delayed mycelial growth, normal conidium formation, and a citrinin content of 120% compared to the wild-type strain, with minimal effects on pigments content. Notably, the ΔctnA strain formed small, tightly structured pellets (mean diameter 1.2 ± 0.06 mm) and exhibited low citrinin content, promoting pigments production. Our findings suggest a complex interplay between citrinin biosynthesis and morphological development, providing insights for optimizing metabolite production in industrial applications.

Lactate controls cancer stemness and plasticity through epigenetic regulation

Tumors arise from uncontrolled cell proliferation driven by mutations in genes that regulate stem cell renewal and differentiation. Intestinal tumors, however, retain some hierarchical organization, maintaining both cancer stem cells (CSCs) and cancer differentiated cells (CDCs). This heterogeneity, coupled with cellular plasticity enabling CDCs to revert to CSCs, contributes to therapy resistance and relapse. Using genetically encoded fluorescent reporters in human tumor organoids, combined with our machine-learning-based cell tracker, CellPhenTracker, we simultaneously traced cell-type specification, metabolic changes, and reconstructed cell lineage trajectories during tumor organoid development. Our findings reveal distinctive metabolic phenotypes in CSCs and CDCs. We find that lactate regulates tumor dynamics, suppressing CSC differentiation and inducing dedifferentiation into a proliferative CSC state. Mechanistically, lactate increases histone acetylation, epigenetically activating MYC. Given that lactate's regulation of MYC depends on the bromodomain-containing protein 4 (BRD4), targeting cancer metabolism and BRD4 inhibitors emerge as a promising strategy to prevent tumor relapse.

miR-484 as an "OncomiR" in Breast Cancer Promotes Tumorigenesis by Suppressing Apoptosis Genes

PURPOSE

Breast cancer (BC) is one of the most common causes of death among females. Cancer cells escape from apoptosis, causing the cells to proliferate uncontrollably. MicroRNAs (miRNAs) are known to regulate apoptosis in cancer cells.

OBJECTIVE

This study aimed to determine the change in miR-484 in different BC cells and its relationship with the apoptosis pathway.

METHODS

In the study, tumor and healthy tissue samples adjacent to the tumor were collected from 42 patients (6 benign, 36 malignant). Tissue samples were classified according to tumor type, tumor histological grade, proliferation index, and molecular subtypes. Gene expression levels were determined by quantitative real-time polymerase chain reaction (qRT-PCR), and protein levels were determined using the Western Blot method. The results were analyzed using the delta-delta Ct method.

RESULTS

Findings showed that miR-484 expression levels were higher in malignant tumors than in benign tumors, and higher in tumor tissues than healthy tissues. Additionally, it was determined that as Ki-67 levels and histological grade and aggressiveness increased, miR-484 expression levels also increased. In tumor tissue compared with healthy adjacent tissue, there was an increase in BCL2 expression and a decrease in Casp3 and Casp9 expression. Therefore, a positive correlation was found between miR-484 expression and BCL2, and a negative correlation was found between CASP3 and CASP9 expression.

CONCLUSION

Our results show that miR-484 may play a roll as an onco-miR in BC. Increased miR-484 and BCL2, and decreased Casp3, in breast tumor tissues suggest that Casp9 expression may increase uncontrolled cell proliferation by suppressing apoptosis in BC cells and may contribute to tumor progression.

Molecular, cellular, and metabolic insights of cinnamon (Cinnamomum zeylanicum) advantages in diabetes and related complications: condiment or medication?

Diabetes mellitus (DM) is a growing concern in public health, which affects about 10% of the population. There are several chronic complications due to DM, including kidney failure, blindness, amputations, myocardial infarction, and stroke. Cinnamon zeylanicum (C. verum, Ceylon cinnamon, or true cinnamon) has been shown to have desirable effects such as anti-obesity, anti-diabetic, anti-dyslipidemia, and anti-inflammatory effects in experimental studies. In this regard, Scopus, PubMed, and Google Scholar databases have been investigated with keywords of "Cinnamon," "Cinnamomum zeylanicum," "diabetes mellitus," "diabetes complication," "hypoglycemic," "anti-hyperglycemic," and "anti-diabetic" from incept to June 2024. This study aimed to review all pharmacological effects and molecular pathways of C. zeylanicum in DM and its complications in vitro, in vivo, and in clinical. Based on these studies, C. zeylanicum has good potential to design human studies for controlling and modifying DM and its related disorders.

Summary of Critical Care Nurses' Understanding, Adherence, and Barriers in Applying Ventilator-Associated Pneumonia Prevention Guidelines: A Narrative Review

Both adults and pediatric patients who are on mechanical ventilation face high rates of mortality and morbidity due to ventilator-associated pneumonia (VAP), which is the most prevalent deadly hospital-acquired infection. Healthcare organizations provide evidence-based guidelines to help nurses decrease VAP in ICUs; however, there are obstacles to putting these guidelines into practice. An extensive investigation was conducted for pertinent English studies published from January 2014 to February 2024 in the databases of Science Direct, Scopus, PubMed, and CINAHL. The study centered on nurses' understanding, adherence, and obstacles regarding introducing VAP prevention guidelines. The majority of ICU nurses have a basic to intermediate understanding of evidence-based methods to reduce VAP. The nurses in the ICUs typically followed the guidelines for preventing VAP about 60% of the time. A basic analysis of descriptive content identified the obstacles preventing critical care nurses (CCNs) from following VAP PGs. The obstacles were separated into 2 groups: barriers related to nurses (such as education, experience, and training) and barriers related to the work environment (such as lack of supplies, staffing shortage, lack of policies, and ineffective supervision). To improve their skills, CCNs should get frequent updates on courses and seminars related to the VAP PG implementation. Healthcare administrators must be aware of these obstacles and implement work procedures that help CCNs overcome them if they want to increase compliance.

Production, characterization and biodistribution of therapeutic high-density lipoprotein-like nanoparticles reconstituted with or without histidine-tagged recombinant ApoA1

High-density lipoproteins (HDLs) are known for their cardiovascular protection due to apolipoprotein A-1 (ApoA1), their primary protein. ApoA1 promotes cholesterol reverse transport and exhibits antioxidant and anti-inflammatory properties. Although increasing HDL levels has not consistently reduced cardiovascular mortality in clinical trials, reconstituted HDL (rHDL) nanoparticles containing ApoA1 show potential in treating acute inflammation, such as in ischemic stroke, sepsis, and even COVID-19. ApoA1 is commonly produced in bacteria due to its simplicity and potential therapeutic optimisation. Addition of a histidine tag to recombinant ApoA1 may improve purification, stability and therapeutic efficacy, although its functional impact remains a subject of debate. In this study, ApoA1 with a poly-histidine tag (His-rApoA1) was produced in a clear coli system for simplified purification, followed by an evaluation of the tag's effects on rHDL nanoparticle properties. rHDL and His-rHDL nanoparticles were prepared using the sodium cholate dialysis method, combining recombinant rApoA1 or His-rApoA1 with phosphatidylcholine at a 1:75 M ratio. Nuclear magnetic resonance confirmed that both forms of rApoA1 structurally resembled plasma ApoA1, whether lipid-free or in nanoparticle form. Dynamic light scattering and electron microscopy revealed nanoparticle sizes around 7 nm with native HDL-like morphology. Testing on endothelial cells (EA.hy926) showed rapid uptake of rHDL and His-rHDL while preserving cell viability. Additionally, both nanoparticles reduced interleukin-6 and ICAM-1 expression in cells, demonstrating their anti-inflammatory and protective effects, unaffected by the poly-histidine tag. Intravenous injection in mice shows homogeneous distribution of His-rHDL in the liver, lungs, and spleen, with no cytotoxicity, indicating potential use for treating inflammatory diseases.

Acid-sensing ion channel 1a promotes alcohol-associated liver disease in mice via regulating endoplasmic reticulum autophagy

Alcohol-associated liver disease (ALD) is a hepatocyte dysfunction disease caused by chronic or excessive alcohol consumption, which can lead to extensive hepatocyte necrosis and even liver failure. Currently, the pathogenesis of ALD and the anti-ALD mechanisms have not been fully elucidated yet. In this study, we investigated the effects of endoplasmic reticulum autophagy (ER-phagy) in ALD and the role of acid-sensing ion channel 1a (ASIC1a) in ER stress-mediated ER-phagy. A mouse model of ALD was established using the Gao-Binge method and the AML12 cell line treated with alcohol was used as an in vitro model. We showed that ASIC1a expression was significantly increased and ER-phagy was activated in both the in vivo and in vitro models. In alcohol-treated AML12 cells, we showed that blockade of ASIC1a with PcTx-1 or knockdown of ASIC1a reduced alcohol-induced intracellular Ca2+ accumulation and ER stress. In addition, inhibition of ER stress with 4-PBA reduced the level of ER-phagy. Furthermore, knockdown of the ER-phagy receptor family with sequence similarity 134 member B (FAM134B) alleviated alcohol-triggered hepatocyte injury and apoptosis. In conclusion, this study demonstrates that alcohol activates ER stress-induced ER-phagy and liver injury by increasing ASIC1a expression and ASIC1a-mediated Ca2+ influx, providing a novel strategy for the treatment of ALD.

The Complex Interactions Between HIV-1 and Human Host Cell Genome: From Molecular Mechanisms to Clinical Practice

Antiretroviral therapy (ART) has significantly improved the prognosis of human immunodeficiency virus type 1 (HIV-1) infection. Although ART can suppress plasma viremia below detectable levels, it cannot eradicate the HIV-1 DNA (provirus) integrated into the host cell genome. This integration often results in unrepaired DNA damage due to the HIV-1-induced inhibition of DNA repair pathways. Furthermore, HIV-1 infection causes telomere attrition in host chromosomes, a critical factor contributing to CD4+ T cell senescence and apoptosis. HIV-1 proteins can induce DNA damage, block DNA replication, and activate DNA damage responses across various organs. In this review, we explore multiple aspects of the intricate interactions between HIV-1 and the host genome involved in CD4+ T cell depletion, inflammaging, the clonal expansion of infected cells in long-term-treated patients, and viral latency. We discuss the molecular mechanisms of DNA damage that contribute to comorbidities in HIV-1-infected individuals and highlight emerging therapeutic strategies targeting the integrated HIV-1 provirus.

Muscle-specific Ryanodine receptor 1 properties underlie limb-girdle muscular dystrophy 2B/R2 progression

Ryanodine receptor 1 Ca2+ leak is a signal in skeletal muscle, but chronic leak can underlie pathology. Here we show that in healthy male mouse, limb-girdle muscle presents higher sympathetic input, elevated ryanodine receptor 1 basal phosphorylation, Ca2+ leak and mitochondrial Ca2+ content compared to distal leg muscles. These regional differences are consistent with heat generation in resting muscle to maintain core temperature. The dysferlin-null mouse develops severe pathology in the limb-girdle but not leg muscles. Absence of dysferlin disrupts dihydropyridine receptors' inhibitory control over ryanodine receptor 1 leak, synergistically increasing leak through the already phosphorylated channel of limb-girdle muscle. This alters Ca2+ handling and distribution leading to reactive oxygen species production prior to disease onset. With age, oxidation of Ca2+ -handling proteins in dysferlin-null limb-girdle muscle alters basal Ca2+ movements. Our results show that muscle-specific pathology in dysferlin-null mice is linked to increased ryanodine receptor 1 Ca2+ leak.

Coenzyme Q10 supplementation affects cellular ionic balance: relevance to aging

Aging results into disruptive physiological functioning and cellular processes that affect the composition and structure of the plasma membrane. The plasma membrane is the major regulator of ionic homeostasis that regulates the functioning of membrane transporters and exchangers. Coenzyme Q10 is a lipid-soluble antioxidant molecule that declines during aging and age-associated diseases. The present study aims to explore the role of Coenzyme Q10 supplementation to rats during aging on membrane transporters and redox biomarkers. The study was conducted on young and old male Wistar rats supplemented with 20 mg/kg b.w. of Coenzyme Q10 per day. After a period of 28 days, rats were sacrificed and erythrocyte membrane was isolated. The result exhibits significant decline in biomarkers of oxidative stress in old control rats when compared with young control. The effect of Coenzyme Q10 supplementation was more pronounced in old rats. The functioning of membrane transporters and Na+/H+ exchanger showed potential return to normal levels in the Coenzyme Q10 treated rats. Overall, the results demonstrate that Coenzyme Q10 plays an important role in maintaining redox balance in cells which interconnects with membrane integrity. Thus, Coenzyme Q10 supplementation may play an important role in protecting age related alterations in erythrocyte membrane physiology.

Airway epithelial cells as drivers of severe asthma pathogenesis

Our understanding of the airway epithelium's role in driving asthma pathogenesis has evolved over time. From being regarded primarily as a physical barrier that could be damaged via inflammation, the epithelium is now known to actively contribute to asthma development through interactions with the immune system. The airway epithelium contains multiple cell types with specialized functions spanning barrier action, mucociliary clearance, immune cell recruitment, and maintenance of tissue homeostasis. Environmental insults may cause direct or indirect injury to the epithelium leading to impaired barrier function, epithelial remodelling, and increased release of inflammatory mediators. In severe asthma, the epithelial barrier repair process is inhibited and the response to insults is exaggerated, driving downstream inflammation. Genetic and epigenetic mechanisms also maintain dysregulation of the epithelial barrier, adding to disease chronicity. Here, we review the role of the airway epithelium in severe asthma and how targeting the epithelium can contribute to asthma treatment.

Identification of Isovitexin as a novel CYP17A1 inhibitor through virtual screening and evaluation of its anti-cancer effects in MCF-7 breast cancer cells

Over 75% of breast cancers are hormone receptor positive and are associated with better prognosis after treatment, when compared to other types of breast cancer. However, discontinuation of treatment due to side effects is common among one-third of the patients, leading to poor outcomes. On long-term treatment, development of resistance to the current therapeutics is common. CYP17A1, a key enzyme in androgen and estrogen synthesis, is associated in the development and progression of breast cancers. Phytochemicals, which are abundant in three traditional medicinal plants, Fenugreek, Ginger, and Basil, generally used in regulating hormonal disorders were screened for potential inhibition of CYP17A1, by molecular docking (Autodock Vina). The binding affinities were compared with standard CYP17A1 inhibitors Abiraterone and Ketoconazole. Docking analysis revealed that Isovitexin (- 9.5 kcal/mol) and Orientin (- 9.4 kcal/mol) showed comparable binding affinities to Abiraterone and Ketoconazole. Molecular Simulations and MM-GBSA were employed to explore the stability of ligand-protein complexes. Isovitexin had stable interactions with the CYP17A1 than Orientin evident from the RMSD, RMSF, Protein-Ligand contacts and MM-GBSA values. In silico ADMET profiles of the phytochemicals and standard breast cancer drugs (Letrozole, Tamoxifen, Paclitaxel, and Docetaxel) were evaluated using Swiss ADME and pkCSM and found to be similar. In in vitro assays, Isovitexin was found to be cytotoxic to MCF-7 cells, causing 46% apoptosis at < 10 nM levels. The study reveals that Isovitexin, with high cytotoxicity, may be effective in the treatment of both ER- and PR-positive (MCF-7) cancers. Overall, the findings have implications for the therapeutic development of hormone receptor-positive breast cancers.

ER nests are specialized ER subdomains in Arabidopsis where peroxisomes and lipid droplets form

Organelles are defining features of eukaryotic cells, yet much remains to be learned about organelle biogenesis. Lipid droplets and peroxisomes, which play opposing roles in storing and catabolizing fats, form from a mysterious domain in the endoplasmic reticulum (ER). We used live-cell fluorescence microscopy to visualize peroxisome and lipid droplet biogenesis in young Arabidopsis seedlings, where lipid catabolism is active, and peroxisomes can be unusually large. We found that the ER domains where these organelles are born, which we term ER nests, are complex, dynamic structures that exclude general ER proteins but accumulate other proteins, including lipid biosynthetic enzymes and the COPII component SAR1. Furthermore, ER nests appear to define peroxisome-lipid droplet contact sites. Our findings provide a framework for understanding how these domains form and sort their protein components, illuminate eukaryotic lipid biosynthesis, and elucidate how distinct organelles arise from the ER.

Deciphering genetic causality between plasma BDNF and 91 circulating inflammatory proteins through bidirectional mendelian randomization

Prior studies reported an association between the levels of brain-derived neurotrophic factor (BDNF) circulating in the bloodstream and those of different inflammatory factors. However, their causal relationship remains unclear. Here, we performed a Mendelian randomization (MR) study to investigate the causal relationships between plasma BDNF levels and 91 circulating inflammatory proteins to shed light on the possible role of BDNF in the pathogenesis and progression of inflammation-related neurological diseases in order to distinguish correlation from possible causal effects. Data for plasma BDNF levels were derived from a genome-wide association study (GWAS) encompassing 3,301 European participants. Genetic association estimates for 91 inflammation proteins were extracted from a GWAS meta-analysis that enrolled 14,824 European participants. The primary MR analysis employed the inverse variance weighted (IVW) method and was corroborated by additional methods including MR-Egger, weighted median, weighted mode, and simple mode. Analyses of sensitivity were performed by evaluating the heterogeneity, horizontal pleiotropy, and robustness of the results. Genetic evidence indicated that elevated plasma BDNF levels possibly contribute to decreased concentrations of 13 inflammation proteins (OR: 0.951-0.977), including beta-nerve growth factor (Beta-NGF), caspase 8 (CASP-8), interleukin-15 receptor subunit alpha (IL-15RA), interleukin-17 A (IL-17 A), interleukin-17 C (IL-17 C), interleukin-2 (IL-2), interleukin-20 (IL-20), interleukin-20 receptor subunit alpha (IL-20RA), interleukin-24 (IL-24), interleukin-33 (IL-33), leukemia inhibitory factor (LIF), neurturin (NRTN), as well as neurotrophin-3 (NT-3). The associations between BDNF and IL-33 remained statistically significant after FDR correction (FDR > 0.05). Furthermore, reverse MR analysis showed that C-C motif chemokine 23 (CCL23), CUB domain-containing protein 1 (CDCP1), and NRTN is suggestive for a positive causal effect on BDNF plasma levels (OR: 1.240-1.422). Moreover, 5 proteins are likely to be associated with lower plasma levels of BDNF (OR: 0.742-0.971), including adenosine deaminase (ADA), cystatin D (CST5), interleukin-13 (IL-13), interleukin-17 A (IL-17 A), and vascular endothelial growth factor A (VEGF-A). Genetically determined plasma BDNF levels influence IL-33 and are possibly associated with 12 circulating inflammatory proteins. The data suggest that 8 inflammatory proteins exhibit either negative or protective roles to BDNF levels, respectively. Of these, 5 are negatively associated with BDNF levels, while 3 play protective roles. These findings may offer new theoretical and empirical insights into the pathogenesis and progression of inflammation-related neurological diseases.

miR-512-3p as a Potential Biomarker of Poor Outcome in Pediatric Medulloblastoma

The tumorigenesis of medulloblastoma (MB), the most frequent malignant brain tumor in children, is not completely known. MicroRNA (miRNA) expression profiles have been associated with human cancers; however, the role played by miRNAs in pediatric MB has been poorly explored. Global miRNA expression in MB and non-neoplastic cerebellum samples was evaluated by microarray assay. Nine miRNAs (miR-31-5p, -329, -383, -433, -485-3p, -485-5p, -491, -512-3p, and 539-5p) in 51 pediatric MB and 7 pediatric non-neoplastic cerebellum samples were chosen for validation by qRT-PCR. The validated miRNAs were less expressed in the MB samples than in the non-neoplastic controls. In our cohort of patients, higher miR-512-3p expression was associated with incomplete degree of resection, classification as high risk, classification as group 4, and poor overall survival. In silico analysis in an independent cohort of MB patients identified that some of the miR-512-3p target genes were also correlated with prognostic features. Our results have shown that miR-512-3p could be associated with poor clinical outcomes in pediatric MB, suggesting that miR-512-3p is a potential biomarker of prognosis.

Advancing Breast Cancer Treatment: The Role of Immunotherapy and Cancer Vaccines in Overcoming Therapeutic Challenges

Breast cancer (BC) remains a significant global health challenge due to its complex biology, which complicates both diagnosis and treatment. Immunotherapy and cancer vaccines have emerged as promising alternatives, harnessing the body's immune system to precisely target and eliminate cancer cells. However, several key factors influence the selection and effectiveness of these therapies, including BC subtype, tumor mutational burden (TMB), tumor-infiltrating lymphocytes (TILs), PD-L1 expression, HER2 resistance, and the tumor microenvironment (TME). BC subtypes play a critical role in shaping treatment responses. Triple-negative breast cancer (TNBC) exhibits the highest sensitivity to immunotherapy, while HER2-positive and hormone receptor-positive (HR+) subtypes often require combination strategies for optimal outcomes. High TMB enhances immune responses by generating neoantigens, making tumors more susceptible to immune checkpoint inhibitors (ICIs); whereas, low TMB may indicate resistance. Similarly, elevated TIL levels are associated with better immunotherapy efficacy, while PD-L1 expression serves as a key predictor of checkpoint inhibitor success. Meanwhile, HER2 resistance and an immunosuppressive TME contribute to immune evasion, highlighting the need for multi-faceted treatment approaches. Current breast cancer immunotherapies encompass a range of targeted treatments. HER2-directed therapies, such as trastuzumab and pertuzumab, block HER2 dimerization and enhance antibody-dependent cellular cytotoxicity (ADCC), while small-molecule inhibitors, like lapatinib and tucatinib, suppress HER2 signaling to curb tumor growth. Antibody-drug conjugates (ADCs) improve tumor targeting by coupling monoclonal antibodies with cytotoxic agents, minimizing off-target effects. Meanwhile, ICIs, including pembrolizumab, restore T-cell function, and CAR-macrophage (CAR-M) therapy leverages macrophages to reshape the TME and overcome immunotherapy resistance. While immunotherapy, particularly in TNBC, has demonstrated promise by eliciting durable immune responses, its efficacy varies across subtypes. Challenges such as immune-related adverse events, resistance mechanisms, high costs, and delayed responses remain barriers to widespread success. Breast cancer vaccines-including protein-based, whole-cell, mRNA, dendritic cell, and epitope-based vaccines-aim to stimulate tumor-specific immunity. Though clinical success has been limited, ongoing research is refining vaccine formulations, integrating combination therapies, and identifying biomarkers for improved patient stratification. Future advancements in BC treatment will depend on optimizing immunotherapy through biomarker-driven approaches, addressing tumor heterogeneity, and developing innovative combination therapies to overcome resistance. By leveraging these strategies, researchers aim to enhance treatment efficacy and ultimately improve patient outcomes.

Design and Synthesis of Bis-Chalcones as Curcumin Simplified Analogs and Assessment of Their Antiproliferative Activities Against Human Lung Cancer Cells and Trypanosoma cruzi Amastigotes

Background: Anticancer therapies represent the primary treatment option for a significant number of cancer patients globally; however, many of these treatments are associated with severe side effects as they target molecular structures present in both cancerous and healthy cells. In a similar context, the treatment of Chagas disease, a neglected tropical illness, is hindered by the high toxicity of the currently available drugs. Researchers are increasingly focusing on the development of safer and more selective alternatives, with natural compounds being studied as potential starting points for the creation of more effective drug candidates with a favorable therapeutic index. Objectives: The aim of this study was to design simplified curcumin-derived structures that preserved or enhanced their therapeutic activity against human lung cancer cell lines and T. cruzi, while also improving bioavailability and minimizing toxicity. Methods: In this study, curcumin and two natural curcuminoids inspired the synthesis of a chalcone and a set of bis-chalcones, compound classes known for their enhanced stability compared with their natural parent derivatives. The synthetic strategy used was the acid-catalyzed aldol condensation reaction. The stability profiles, IC50 values against A549 and H460 tumor cell lines, and trypanocidal activity against T. cruzi amastigotes of these derivatives were assessed. Results: The synthesized derivatives exhibited improved stability compared with the parent compounds, along with lower IC50 values in both A549 and H460 tumor cell lines. Additionally, one of the new analogs showed promising trypanocidal activity against T. cruzi amastigotes. Conclusions: This study provides a potential pathway toward the development of more effective and less toxic treatments for both cancer and Chagas disease. The simplified curcumin derivatives represent a promising foundation for designing new therapeutic agents with improved bioavailability and efficacy.

Caveolae-Mediated Transcytosis and Its Role in Neurological Disorders

The blood-brain barrier (BBB) controls the flow of substances to maintain a homeostatic environment in the brain, which is highly regulated and crucial for the normal function of the central nervous system (CNS). Brain endothelial cells (bECs), which are directly exposed to blood, play the most important role in maintaining the integrity of the BBB. Unlike endothelial cells in other tissues, bECs have two unique features: specialized endothelial tight junctions and actively suppressed transcellular vesicle trafficking (transcytosis). These features help to maintain the relatively low permeability of the CNS barrier. In addition to the predominant role of tight junctions in the BBB, caveolae-mediated adsorptive transcytosis has attracted much interest in recent years. The active suppression of transcytosis is dynamically regulated during development and in response to diseases. Altered caveolae-mediated transcytosis of bECs has been reported in several neurological diseases, but the understanding of this process in bECs is limited. Here, we review the process of caveolae-mediated transcytosis based on previous studies and discuss its function in the breakdown of the BBB in neurological disorders.

Diet-Induced Proteomic and Metabolomic Signatures in Chronic Kidney Disease: A Precision Nutrition Approach

Background: Diet is a key modifiable factor that can either support renal health or accelerate the onset and progression of chronic kidney disease (CKD). Recent advances in multiomics, particularly proteomics and metabolomics, significantly enhanced our understanding of the molecular mechanisms linking diet to CKD risk. Proteomics offers a comprehensive analysis of protein expression, structure, and interactions, revealing how dietary components regulate cellular processes and signaling pathways. Meanwhile, metabolomics provides a detailed profile of low-molecular-weight compounds, including endogenous metabolites and diet-derived molecules, offering insights into the metabolic states that influence kidney function. Methods: We have conducted a narrative review of key papers from databases such as PubMed, Scopus, and Web of Science to explore the potential of proteomic and metabolomic analysis in identifying molecular signatures associated with diet in human and animal biological samples, such as blood plasma, urine, and in kidney tissues. These signatures help elucidate how specific foods, food groups, and overall dietary patterns may either contribute to or mitigate CKD risk. Results: Recent studies the impact of high-fat diets on protein expression involved in energy metabolism, inflammation, and fibrosis, identifying early biomarkers of kidney injury. Metabolic, including disruptions in in fatty acid metabolism, glucose regulation, and amino acid pathways, have been recognized as key indicators of CKD risk. Additionally, several studies explore specific metabolites found in biological fluids and renal tissue in response to protein-rich foods, assessing their potential roles in a progressive loss of kidney function. Emerging evidence also suggests that dietary interventions targeting the gut microbiota may help alleviate inflammation, oxidative stress, and toxin accumulation in chronic kidney disease. Notably, recent findings highlight metabolomic signatures linked to beneficial shifts in gut microbial metabolism, particularly in the context of prebiotic supplementation. Conclusions: By integrating proteomics and metabolomics, future research can refine precision nutrition strategies, helping mitigate CKD progression. Expanding large-scale studies and clinical trials will be essential in translating these molecular insights into actionable dietary guidelines.

Daxx and HIRA go viral - How chromatin remodeling complexes affect DNA virus infection

Daxx and HIRA are key proteins in the host response to DNA virus infections. Daxx is involved in apoptosis, transcription regulation, and stress responses. During DNA virus infections, Daxx helps modulate the immune response and viral progression. Viruses like adenoviruses and herpesviruses can exploit Daxx to evade immune detection, either by targeting it for degradation or inhibiting its function. Daxx also interacts with chromatin to regulate transcription, which viruses can manipulate to enhance their own gene expression and replication. HIRA is a histone chaperone and reported to be essential for chromatin assembly and gene regulation. It plays a critical role in maintaining chromatin structure and modulating gene accessibility. During DNA virus infection, HIRA influences chromatin remodeling, affecting both viral and host DNA accessibility, which impacts viral replication and gene expression. Additionally, the histone variant H3.3 is crucial for maintaining active chromatin states. It is incorporated into chromatin independently of DNA replication and is associated with active gene regions. During viral infections, H3.3 dynamics can be altered, affecting viral genome accessibility and replication efficiency. Overall, Daxx and HIRA are integral to orchestrating viral infection programs, maintaining latency and/or persistence, and influencing virus-induced transformation by modulating chromatin dynamics and host immune responses, making them significant targets for therapeutic strategies once fully understood. Here, we summarize various DNA viruses and their crosstalk with Daxx and HIRA.

circ-1584 selectively promotes the antitumor activity of the oncolytic virus M1 on pancreatic cancer

Pancreatic cancer is among the most challenging tumors to treat, and due to its immune tolerance characteristics, existing immunotherapy methods are not effective in alleviating the disease. Oncolytic virus therapy, a potential new strategy for treating pancreatic cancer, also faces the limitation of being ineffective when used alone. Elucidating the key host endogenous circular RNAs (circRNAs) involved in M1 virus-mediated killing of pancreatic ductal adenocarcinoma (PDAC) cells may help overcome this limitation. Here, we report that the oncolytic virus M1, a nonpathogenic alphavirus, exhibits different cell viability-inhibitory effects on different pancreatic cancer cells in the clinical stage. Through high-throughput circRNA sequencing, we found that circRNA expression varies among these cells. Further gain-of-function and loss-of-function experiments have shown that circ-1584 can selectively enhance the anti-pancreatic cancer effects of the M1 virus in vitro and in vivo. Additionally, circ-1584 may negatively regulate miR-578 to modulate the anti-pancreatic cancer effects of the M1 virus. Our findings lay the foundation for using circRNA as an adjuvant to enhance the M1 virus efficacy against pancreatic cancer.

A New Perspective on the Role of Alterations in Mitochondrial Proteins Involved in ATP Synthesis and Mobilization in Cardiomyopathies

The heart requires a continuous energy supply to sustain its unceasing contraction-relaxation cycle. Mitochondria, a double-membrane organelle, generate approximately 90% of cellular energy as adenosine triphosphate (ATP) through oxidative phosphorylation, utilizing the electrochemical gradient established by the respiratory chain. Mitochondrial function is compromised by damage to mitochondrial DNA, including point mutations, deletions, duplications, or inversions. Additionally, disruptions to proteins associated with mitochondrial membranes regulating metabolic homeostasis can impair the respiratory chain's efficiency. This results in diminished ATP production and increased generation of reactive oxygen species. This review provides an overview of mutations affecting mitochondrial transporters and proteins involved in mitochondrial energy synthesis, particularly those involved in ATP synthesis and mobilization, and it examines their role in the pathogenesis of specific cardiomyopathies.

Plasma N-Glycoproteomics in monozygotic twin pairs discordant for body mass index reveals an obesity signature related to inflammation and iron metabolism

BACKGROUND

N-glycosylation is a complex, post-translational modification which influences protein function and is sensitive to physiological changes. Obesity is associated with alterations in protein function; however, little is known about the glycoproteome in obesity beyond observations of association with types and structures of selected glycopeptides. Most often, due to technical challenges, glycan composition and structure information are missing. Here, we combined label-free data-independent proteomics and targeted quantitative glycoproteomics to study N-glycosylation of plasma proteins in obesity. Using a monozygotic twin study design, we controlled for genetic variation and focused only on the acquired effects of obesity.

METHODS

Using plasma samples of 48 monozygotic twin pairs discordant for BMI (intrapair difference > 2.5 kg/m2), we identified using mass spectrometry, differential protein and glycopeptide levels between heavier and leaner co-twins. We used a within-twin paired analysis model and considered p < 0.05 as significant.

RESULTS

We identified 48 protein and 33 N-glycosylation expression differences (p < 0.05) between co-twins. These differences occurred either both in the protein expression and glycoprotein (sometimes in opposing directions) or independently from each other. Haptoglobin protein was upregulated (Fold Change = 1.10, p = 0.001) in heavier co-twins along with seven upregulated glycan compositions at N-glycosylation site Asn241. The complement protein C3 was upregulated (Fold Change = 1.08, p = 0.014) along with one upregulated glycopeptide at Asn85. Additionally, many glycopeptides were upregulated despite non-significant differences in protein-backbone plasma levels.

CONCLUSION

Differential protein expression related to cholesterol biosynthesis and acute phase signalling as well as N-glycosylation of proteins related to iron metabolism and inflammation can be linked to acquired obesity.

Genes as Genome Stabilizers in Pluripotent Stem Cells

Pluripotent stem cells, comprising embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), are characterized by their self-renewal capacity and the ability to differentiate into cells of all three germ layers of an adult animal. Out of the two, iPSCs are generated through the reprogramming of somatic cells by inducing a pluripotency-specific transcriptional program. This process requires a resetting of the somatic cell genome to a pluripotent cell-specific genome, resulting in cellular stress at genomic, epigenetic, and transcriptional levels. Notably, in contrast to the predominant compact and inactive organization of chromatin in somatic cells, the chromatin in ESCs and iPSCs is open. Furthermore, maintaining a pluripotent state needs a plethora of changes in the genetic landscape of the cells. Here, we attempt to elucidate how certain genes safeguard genomic stability in ESCs and iPSCs, aiding in the complex cellular mechanisms that regulate self-renewal, pluripotency, and somatic reprogramming.

Synthesis, Characterization, and DFT Studies of NHC-Derived Amide-Functionalized Organoselenium Compounds

The NHC-Se scaffold has emerged as an intriguing target, opening new avenues for discovering compounds that could significantly improve public health. Recently, extensive efforts have been made to synthesize NHC-Se-based organic compounds for various biomedical applications. Herein, we disclose a straightforward method to access a series of new N-heterocyclic carbene (NHC)-derived organoselenium molecules functionalized with an amide moiety. The parent NHC-Se adduct with a pendent ester moiety is sufficiently activated to facilitate a base- and additive-free ester-to-amide bond transformation. Furthermore, the use of PEG 3550, a biocompatible solvent, enhances reaction efficiency and simplifies the workup. This approach employs a broad spectrum of aliphatic amines with good functional group tolerance, offering a versatile and ecofriendly method for extending chemical space around organoselenium compounds. Additionally, density functional theory (DFT) calculations provide insights into the electronic properties, stability, and reactivity profiles of the synthesized compounds, suggesting their promising potential for applications in biomedical fields.

Research progress on ferroptosis in head and neck squamous cell carcinoma

Ferroptosis, a regulated iron-dependent cell death pathway driven by lipid peroxidation and mitochondrial dysfunction, has emerged as a critical player in diseases characterized by dysregulated iron metabolism and redox imbalance. In recent years, its therapeutic potential has garnered significant attention in head and neck squamous cell carcinoma (HNSCC), a malignancy notorious for its high incidence, frequent recurrence, and poor prognosis. This review systematically delineates the molecular underpinnings of ferroptosis in HNSCC pathogenesis and therapy, focusing on four interconnected axes: (1) iron homeostasis disruption, exemplified by dysregulation of the iron efflux channel ferroportin (FPN); (2) lipid peroxidation dynamics, mediated through key regulators such as SLC7A11; (3) mitochondrial remodeling, including structural and functional alterations during ferroptosis execution; and (4) critical signaling cascades, notably the PI3K-AKT-mTOR pathway, which orchestrates cellular survival and death decisions. Therapeutic exploration has identified ferroptosis inducers (e.g., erastin) as promising agents to disrupt redox equilibrium in HNSCC cells, while pharmacological inhibitors offer potential for mitigating off-target toxicity. Notably, combination strategies integrating ferroptosis modulation with conventional therapies or other programmed cell death mechanisms demonstrate synergistic efficacy, highlighting a paradigm shift in precision oncology. This study aims to provide a mechanistic framework for ferroptosis in HNSCC, bridging preclinical insights with translational opportunities. By elucidating context-dependent regulatory networks and optimizing therapeutic targeting, we propose novel strategies to overcome treatment resistance, ultimately improving clinical outcomes and quality of life for HNSCC patients.

Comprehensive review of the expanding roles of the carnitine pool in metabolic physiology: beyond fatty acid oxidation

Traditionally, the carnitine pool is closely related to fatty acid metabolism. However, with increasing research, the pleiotropic effects of the carnitine pool have gradually emerged. The purpose of this review is to comprehensively investigate of the emerging understanding of the pleiotropic role of the carnitine pool, carnitine/acylcarnitines are not only auxiliaries or metabolites of fatty acid oxidation, but also play more complex and diverse roles, including energy metabolism, mitochondrial homeostasis, epigenetic regulation, regulation of inflammation and the immune system, tumor biology, signal transduction, and neuroprotection. This review provides an overview of the complex network of carnitine synthesis, transport, shuttle, and regulation, carnitine/acylcarnitines have the potential to be used as communication molecules, biomarkers and therapeutic targets for multiple diseases, with profound effects on intercellular communication, metabolic interactions between organs and overall metabolic health. The purpose of this review is to comprehensively summarize the multidimensional biological effects of the carnitine pool beyond its traditional role in fatty acid oxidation and to summarize the systemic effects mediated by carnitine/acylcarnitine to provide new perspectives for pharmacological research and treatment innovation and new strategies for the prevention and treatment of a variety of diseases.

Innovations in Snake Venom-Derived Therapeutics: A Systematic Review of Global Patents and Their Pharmacological Applications

Active compounds from natural sources, particularly snake venoms, are crucial for pharmaceutical development despite challenges in drug discovery. Snake venoms, historically used for medicinal purposes, contain bioactive peptides and enzymes that show therapeutic potential for conditions such as arthritis, asthma, cancer, chronic pain, infections and cardiovascular diseases. The objective of this study was to examine pharmacological and biomedical innovations by identifying the key research trends, the most studied snake species, and their therapeutic applications. A systematic review of patents related to snake venoms was conducted using the European Patent Office database, Espacenet, covering 2014 to mid-2024. The search employed the keyword "venom," applying IPC classification A61K38/00, resulting in 31 patents after screening. A PubMed survey on "snake venom derivatives innovations" was conducted to compare the scientific literature volume with the identified patents. This review highlights the therapeutic potential of snake venom-derived products for coagulation disorders, cancer, inflammation, and pain management. Despite challenges in pharmacokinetics and venom variability, advancements in biotechnology offer promise for personalized therapies. The future of snake venom-based treatments appears promising for addressing complex medical conditions.

Delta-catenin is required for cell proliferation in virus positive Merkel cell carcinoma cell lines but not in human fibroblasts

Merkel cell carcinoma (MCC) is a highly aggressive neuroendocrine skin cancer often driven by the integration of Merkel cell polyomavirus (MCPyV) into the host genome and the persistent expression of its viral oncoproteins, small tumor (ST) antigen and truncated large tumor (t-LT) antigen. While human fibroblasts support MCPyV replication, the cell of origin for MCC remains unknown. We hypothesized that MCPyV initially replicates in fibroblasts but, in rare cases, infects Merkel cell progenitors, contributing to MCC development. Using TurboID mass spectrometry, we identified δ-catenin as a novel ST interactor in fibroblasts. However, while ST binds δ-catenin in fibroblasts, this interaction is absent in virus-positive (VP)-MCC cell lines. Despite this, δ-catenin is essential for VP-MCC, but not for fibroblast, cell proliferation. We found that fibroblasts predominantly express δ-catenin isoform 1, whereas VP-MCC cells mainly express isoform 3. Overexpression of isoform 1 in VP-MCC failed to restore ST binding. δ-catenin promotes VP-MCC proliferation by regulating cell cycle gene expression through its interaction with Kaiso, a transcriptional repressor. Additionally, we found that LSD1 (KDM1A) regulates δ-catenin isoform 3 expression by modulating ESRP1, a δ-catenin splicing factor. Our findings reveal novel host factors involved in MCPyV infection and MCC tumorigenesis, suggesting that the host cell supporting viral replication and the MCC cell of origin may be distinct cell types.

Discovery of Potent and Selective MNK Kinase Inhibitors for the Treatment of Leukemia

MNK activity is regulated by the p38 and Erk MAPK pathways. Phosphorylation of MNK leads to its activation and binding to the eIF4G/eIF4E complex. MNK then phosphorylates eIF4E at Ser209, whose activation is associated with oncogene translation, leading to tumorigenesis. Given this important role for eIF4E in tumorigenesis, MNK inhibition with novel small molecule inhibitors could be a promising strategy to combat AML, which continues to be an area of unmet medical need. Here, we report the medicinal optimization of a series of novel inhibitors and their evaluation of their effects on eIF4E and leukemia cell viability. We discovered a class of ether-containing compounds with a high MNK1/2 selectivity. These MNK inhibitors show good potency in reducing cell viability and colony formation and have desirable pharmacokinetic properties. X-ray cocrystallization was accomplished to confirm the binding mode of our inhibitors and aid in future optimization.

Harnessing bee venom for inflammatory diseases management: from traditional medicine to nanotechnology

This review investigates the anti-inflammatory potential of bee venom, a natural compound comprising peptides, enzymes, biogenic amines other bioactive amines, and other bioactive components. It aims to elucidate how bee venom mitigates inflammatory responses caused by tissue injury, infections, and trauma. This study also explores the advancements in nanotechnology to enhance bee venom's therapeutic effects. A systematic review of studies from Google Scholar and PubMed, up to 2025, was conducted. Both in vitro and in vivo research focusing on bee venom's effects on proinflammatory mediators were analyzed. Specific attention was given to its molecular mechanisms, therapeutic impact on inflammatory conditions, and the role of nanotechnology in improving drug delivery and stability. Bee venom and its components, including melittin, apamin, and phospholipase A2 demonstrate robust anti-inflammatory properties by inhibiting key proinflammatory mediators. These effects have been observed in the treatment of chronic inflammatory conditions such as rheumatoid arthritis and skin disorders. Studies show bee venom's capacity to reduce excessive inflammatory responses effectively. Moreover, incorporating nanotechnology significantly enhances its therapeutic benefits by improving delivery, stability, and bioavailability, paving the way for advanced applications. Bee venom offers a natural, powerful approach to combating the inflammation and related chromic disorders. Its ability to regulate inflammatory pathways is promising for therapeutic use. The integration of nanotechnology further amplifies its potential, providing innovative solutions for efficient and targeted treatments. This study also highlights the need for more clinical trials to establish bee venom as a mainstream therapeutic agent in modern medicine.

Posttranslational Regulation of Mammalian Sulfur Amino Acid Metabolism

Metabolism of the mammalian proteinogenic sulfur amino acids methionine and cysteine includes the methionine cycle and reverse transsulfuration pathway, establishing many connections with other important metabolic routes. The main source of these amino acids is the diet, which also provides B vitamins required as cofactors for several enzymes of the metabolism of these amino acids. While methionine is considered an essential amino acid, cysteine can be produced from methionine in a series of reactions that also generate homocysteine, a non-proteinogenic amino acid linking reverse transsulfuration with the methionine and folate cycles. These pathways produce key metabolites that participate in synthesizing a large variety of compounds and important regulatory processes (e.g., epigenetic methylations). The impairment of sulfur amino acid metabolism manifests in many pathological processes, mostly correlated with oxidative stress and alterations in glutathione levels that also depend on this part of the cellular metabolism. This review analyzes the current knowledge on the posttranslational regulation of mammalian sulfur amino acid metabolism, highlighting the large number of modification sites reported through high-throughput studies and the surprisingly limited knowledge of their functional impact.

EGFR-induced lncRNA TRIDENT promotes drug resistance in non-small cell lung cancer via phospho-TRIM28-mediated DNA damage repair

Long noncoding RNAs (lncRNAs) play numerous roles in cellular biology and alterations in lncRNA expression profiles have been implicated in a variety of cancers. Here, we identify and characterize a lncRNA, TRIM28 Interacting DNA damage repair Enhancing Noncoding Transcript (TRIDENT), whose expression is induced upon epithelial growth factor receptor (EGFR) activation, and which exerts pro-oncogenic functions in EGFR-driven non-small cell lung cancer. Knocking down TRIDENT leads to decreased tumor-cell proliferation in both in vitro and in vivo model systems and induces sensitization to chemotherapeutic drugs. Using ChIRP-MS analysis we identified TRIM28 as a protein interactor of TRIDENT. TRIDENT promotes phosphorylation of TRIM28 and knocking down TRIDENT leads to accumulation of DNA damage in cancer cells via decreased TRIM28 phosphorylation. Altogether, our results reveal a molecular pathway in which TRIDENT regulates TRIM28 phosphorylation to promote tumor cell growth and drug resistance. Our findings suggest that TRIDENT can be developed as a biomarker or therapeutic target for EGFR mutant non-small cell lung cancer.

Polyphenol Intake in Elderly Patients: A Novel Approach to Counteract Colorectal Cancer Risk?

Colorectal cancer (CRC) accounts for approximately 10% of all cancers worldwide with an incidence of approximately 60% in patients older than 70 years. In the elderly, the definition of a better therapeutic strategy depends on several factors including the patient's frailty and comorbidity status, life expectancy, and chemotherapy tolerance. In older patients, adverse drug reactions require a reduction in the dose of treatment, resulting in worse oncologic outcomes. In recent years, an increasing number of studies have focused on the potential effects of polyphenols on human health and their use in cancer therapy. In this comprehensive review, we searched the major databases and summarized experimental data of the most important polyphenols in the CRC chemoprevention, with a focus on the molecular mechanisms involved and the antitumor effects in the elderly population. In vitro and in vivo studies have shown that polyphenols exert chemopreventive activity by modulating cell signaling, resulting in the inhibition of cancer development or progression. However, the efficacy seen in experimental studies has not been confirmed in clinical trials, mainly due to their low bioavailability and non-toxic doses. Further research is needed to increase polyphenol bioavailability and reduce side effects in order to suggest their possible use to increase the efficacy of chemotherapeutic treatment.

Comparison of Deep Learning and Traditional Machine Learning Models for Predicting Mild Cognitive Impairment Using Plasma Proteomic Biomarkers

Mild cognitive impairment (MCI) is a clinical condition characterized by a decline in cognitive ability and progression of cognitive impairment. It is often considered a transitional stage between normal aging and Alzheimer's disease (AD). This study aimed to compare deep learning (DL) and traditional machine learning (ML) methods in predicting MCI using plasma proteomic biomarkers. A total of 239 adults were selected from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort along with a pool of 146 plasma proteomic biomarkers. We evaluated seven traditional ML models (support vector machines (SVMs), logistic regression (LR), naïve Bayes (NB), random forest (RF), k-nearest neighbor (KNN), gradient boosting machine (GBM), and extreme gradient boosting (XGBoost)) and six variations of a deep neural network (DNN) model-the DL model in the H2O package. Least Absolute Shrinkage and Selection Operator (LASSO) selected 35 proteomic biomarkers from the pool. Based on grid search, the DNN model with an activation function of "Rectifier With Dropout" with 2 layers and 32 of 35 selected proteomic biomarkers revealed the best model with the highest accuracy of 0.995 and an F1 Score of 0.996, while among seven traditional ML methods, XGBoost was the best with an accuracy of 0.986 and an F1 Score of 0.985. Several biomarkers were correlated with the APOE-ε4 genotype, polygenic hazard score (PHS), and three clinical cerebrospinal fluid biomarkers (Aβ42, tTau, and pTau). Bioinformatics analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed several molecular functions and pathways associated with the selected biomarkers, including cytokine-cytokine receptor interaction, cholesterol metabolism, and regulation of lipid localization. The results showed that the DL model may represent a promising tool in the prediction of MCI. These plasma proteomic biomarkers may help with early diagnosis, prognostic risk stratification, and early treatment interventions for individuals at risk for MCI.

TIMS2Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS2Rescore

The high throughput analysis of proteins with mass spectrometry (MS) is highly valuable for understanding human biology, discovering disease biomarkers, identifying therapeutic targets, and exploring pathogen interactions. To achieve these goals, specialized proteomics subfields, including plasma proteomics, immunopeptidomics, and metaproteomics, must tackle specific analytical challenges, such as an increased identification ambiguity compared to routine proteomics experiments. Technical advancements in MS instrumentation can mitigate these issues by acquiring more discerning information at higher sensitivity levels. This is exemplified by the incorporation of ion mobility and parallel accumulation and serial fragmentation (PASEF) technologies in timsTOF instruments. In addition, AI-based bioinformatics solutions can help overcome ambiguity issues by integrating more data into the identification workflow. Here, we introduce TIMS2Rescore, a data-driven rescoring workflow optimized for DDA-PASEF data from timsTOF instruments. This platform includes new timsTOF MS2PIP spectrum prediction models and IM2Deep, a new deep learning-based peptide ion mobility predictor. Furthermore, to fully streamline data throughput, TIMS2Rescore directly accepts Bruker raw mass spectrometry data and search results from ProteoScape and many other search engines, including Sage and PEAKS. We showcase TIMS2Rescore performance on plasma proteomics, immunopeptidomics (HLA class I and II), and metaproteomics data sets. TIMS2Rescore is open-source and freely available at https://github.com/compomics/tims2rescore.

A Comprehensive Review of Metabolic Dysfunction-Associated Steatotic Liver Disease: Its Mechanistic Development Focusing on Methylglyoxal and Counterbalancing Treatment Strategies

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a multifactorial disorder characterized by excessive lipid accumulation in the liver which dysregulates the organ's function. The key contributor to MASLD development is insulin resistance (IR) which affects many organs (including adipose tissue, skeletal muscles, and the liver), whereas the molecular background is associated with oxidative, nitrosative, and carbonyl stress. Among molecules responsible for carbonyl stress effects, methylglyoxal (MGO) seems to play a major pathological function. MGO-a by-product of glycolysis, fructolysis, and lipolysis (from glycerol and fatty acids-derived ketone bodies)-is implicated in hyperglycemia, hyperlipidemia, obesity, type 2 diabetes, hypertension, and cardiovascular diseases. Its causative effect in the stimulation of prooxidative and proinflammatory pathways has been well documented. Since metabolic dysregulation leading to these pathologies promotes MASLD, the role of MGO in MASLD is addressed in this review. Potential MGO participation in the mechanism of MASLD development is discussed in regard to its role in different signaling routes leading to pathological events accelerating the disorder. Moreover, treatment strategies including approved and potential therapies in MASLD are overviewed and discussed in this review. Among them, medications aimed at attenuating MGO-induced pathological processes are addressed.

Oxidative stress in a cellular model of alcohol-related liver disease: protection using curcumin nanoformulations

Alcohol-related liver disease (ARLD) is a global health issue causing significant morbidity and mortality, due to lack of suitable therapeutic options. ARLD induces a spectrum of biochemical and cellular alterations, including chronic oxidative stress, mitochondrial dysfunction, and cell death, resulting in hepatic injury. Natural antioxidant compounds such as curcumin have generated interest in ARLD due to their ability to scavenge reactive oxygen species (ROS), however, therapy using these compounds is limited due to poor bioavailability and stability. Therefore, the aim of this study was to assess the antioxidant potential of free antioxidants and curcumin entrapped formulations against oxidative damage in an ARLD cell model. HepG2 (VL-17A) cells were treated with varying concentrations of alcohol (from 200 to 350 mM) and parameters of oxidative stress and mitochondrial function were assessed over 72 h. Data indicated 350 mM of ethanol led to a significant decrease in cell viability at 72 h, and a significant increase in ROS at 30 min. A substantial number of cells were in late apoptosis at 72 h, and a reduction in the mitochondrial membrane potential was also found. Pre-treatment with curcumin nanoformulations increased viability, as well as, reducing ROS at 2 h, 48 h and 72 h. In summary, antioxidants and entrapped nanoformulations of curcumin were able to ameliorate reduced cell viability and increased ROS caused by ethanol treatment. This demonstrates their potential at mitigating oxidative damage and warrants further investigation to evaluate their efficacy for ARLD therapy.

Dynamic In Vivo Mapping of the Methylproteome Using a Chemoenzymatic Approach

Dynamic protein post-translational methylation is essential for cellular function, highlighted by the essential role of methylation in transcriptional regulation and its aberrant dysregulation in diseases, including cancer. This underscores the importance of cataloging the cellular methylproteome. However, comprehensive analysis of the methylproteome remains elusive due to limitations in current enrichment and analysis pipelines. Here, we employ an l-methionine analogue, ProSeMet, that is chemoenzymatically converted to the SAM analogue ProSeAM in cells and in vivo to tag proteins with a biorthogonal alkyne that can be directly detected via liquid chromatography and tandem mass spectrometry (LC-MS/MS), or functionalized for subsequent selective enrichment and LC-MS/MS identification. Without enrichment, we identify known and novel lysine mono-, di-, and tripargylation, histidine propargylation, and arginine propargylation with site-specific resolution on proteins including heat shock protein HSPA8, the translational elongation factor eEF1A1, and the metabolic enzyme phosphoglycerate mutase 1, or PGAM1, for which methylation has been implicated in human disease. With enrichment, we identify 486 proteins known to be methylated and 221 proteins with novel propargylation sites encompassing diverse cellular functions. Systemic ProSeMet delivery in mice propargylates proteins across organ systems with blood-brain barrier penetrance and identifies site-specific propargylation in vivo with LC-MS/MS. Leveraging these pipelines to define the cellular methylproteome may have broad applications for understanding the methylproteome in the context of disease.

Antagonizing the S1P-S1P3 Axis as a Promising Anti-Angiogenic Strategy

BACKGROUND

Angiogenesis, the process of new blood vessel formation, is critically regulated by a balance of pro- and anti-angiogenic factors. This process plays a central role in tumor progression and is modulated by tumor cells. Sphingosine-1-phosphate (S1P), a bioactive lipid signaling molecule acting via G-protein-coupled receptors (S1PR1-5), has emerged as a key mediator of vascular development and pathological angiogenesis in cancer. Consequently, targeting the S1P-S1PRs axis represents a promising strategy for antiangiogenic therapies. This study explores S1PR3 as a potential therapeutic target in osteosarcoma, the most common primary bone malignancy, which we have previously demonstrated to secrete S1P within the acidic tumor microenvironment.

METHODS

The effects of KRX-725-II and its derivatives, Tic-4-KRX-725-II and [D-Tic]4-KRX-725-II-pepducins acting as S1PR3 antagonists as allosteric modulators of GPCR activity-were tested on metastatic osteosarcoma cells (143B) for proliferation and migration inhibition. Anti-angiogenic activity was assessed using endothelial cells (HUVEC) through proliferation and tubulogenesis assays in 2D, alongside sprouting and migration analyses in a 3D passively perfused microfluidic chip.

RESULTS

S1PR3 inhibition did not alter osteosarcoma cell growth or migration. However, it impaired endothelial cell tubulogenesis up to 75% and sprouting up to 30% in respect to controls. Conventional 2D assays revealed reduced tubule nodes and length, while 3D microfluidic models demonstrated diminished sprouting area and maximum migration distance, indicating S1PR3's role in driving endothelial cell differentiation.

CONCLUSIONS

These findings highlight S1PR3 as a critical regulator of angiogenesis and posit its targeting as a novel anti-angiogenic strategy, particularly for aggressive, S1P-secreting tumors with pronounced metastatic potential and an acidic microenvironment.

Development of Biphasic Culture System for an Entomopathogenic Fungus Beauveria bassiana PfBb Strain and Its Virulence on a Defoliating Moth Phauda flammans (Walker)

Beauveria bassiana PfBb is a new strain with high host specificity to the target pest Phauda flammans. We conducted a series of experiments to optimize the biphasic fermentation system of B. bassiana PfBb by screening the medium compositions and fermentation environmental conditions in both liquid and solid fermentations. In the liquid fermentation, glucose and yeast extract with a C:N ratio of 17:1 were the optimal carbon and nitrogen sources, respectively, for B. bassiana PfBb mycelium growth and blastospore production, and liquid fermentation with an inoculation concentration of 1 × 108/mL and an inoculum content of 50 mL conidial suspension, at 180 rpm/min rotation speed, pH 7 and 26 °C, favored mycelium growth. However, additional trace elements did not significantly improve liquid fermentation. In the solid fermentation, wheat bran and chaff at a ratio of 8:2 were identified as the best substrates that facilitated B. bassiana PfBb sporulation and conidial germination, and optimal substrates with 20% inoculum content, 50% water content, and 3-day fermentation in darkness had the highest conidia yield. The resulting conidia, stored at -20, 4, and 20 °C for one year, did not significantly change the water content, and with prolonged storage duration, conidial germination was significantly higher at -20 and 4 °C. Moreover, conidia stored at 4 °C for one year maintained its validity and virulence, which were toxic to all instar larvae of P. flammans. Our results provide essential support for the commercial production of B. bassiana PfBb-based biopesticides.

Platelets and mitochondria: the calcium connection

Calcium signaling has a fundamental importance in maintaining various platelet functions, such as those involved in hemostasis and thrombosis. Agonist-induced mobilization of calcium (Ca2+) from intracellular stores coupled with activation of store-operated calcium entry (SOCE) and non-SOCE or receptor-operated calcium entry (ROCE) regulates platelet degranulation, integrin activation, shape change, generation of thromboxane A2, and aggregation or procoagulant function. Platelet mitochondria also take up a small amount of cytosolic Ca2+ that contributes to bioenergetics, cytosolic Ca2+ buffering, cell signaling and death. Voltage-dependent anion channels (VDAC) in the outer mitochondrial membrane and mitochondrial Ca2+ uniporter complex (MCUC) in the inner mitochondrial membrane (IMM) are pivotal for transporting Ca2+ into the mitochondrial matrix. On the other hand, matrix Ca2+ efflux is dependent on the IMM localized sodium/calcium exchanger (NCLX). Despite the well-established role of cytosolic Ca2+, the participation of mitochondrial Ca2+ homeostasis in platelet physiology remains unknown. This mini-review summarizes the recent developments in the field of mitochondrial Ca2+ transport in platelet physiology.

J-shaped association of neutrophil-to-lymphocyte ratio with all-cause mortality and linear association with cardiovascular mortality in stroke survivors

Background

The correlation between systemic inflammation and stroke has been well-established. Notably, the neutrophil-to-lymphocyte ratio (NLR) has been linked to poor outcomes and increased short-term mortality in acute ischemic stroke (AIS). This study aims to explore the association between NLR and long-term mortality among stroke survivors.

Methods

This study analyzed data from 1,229 stroke survivors enrolled in the National Health and Nutrition Examination Survey (NHANES) from 2001 to 2018. The participants were categorized according to quartiles of NLR level. Multivariate Cox regression and restricted cubic splines (RCS) were applied to evaluate the relationship between NLR and all-cause and cardiovascular disease (CVD) mortality.

Results

Over a median follow-up of 6.41 years, 485 deaths were recorded. After multivariate adjustment, individuals in the highest NLR quartile (Q4) demonstrated significantly higher risks of all-cause mortality (hazard ratio [HR] = 1.58, 95% confidence interval [CI]: 1.06-2.34) and CVD mortality (HR = 1.90, 95% CI: 1.07-3.37) compared to those in the lowest quartile (Q1). RCS analysis revealed a J-shaped relationship between NLR and all-cause mortality and a linear relationship with CVD mortality.

Conclusion

These findings suggest a J-shaped association between NLR and all-cause mortality, along with a linear relationship between NLR and CVD mortality in stroke survivors.

Sexual dimorphism in right ventricular adaptation to pressure overload involves differential angiogenic response

This study investigated the sexual dimorphism in right ventricle (RV) remodeling in right heart failure susceptible Fischer CDF rats using the pulmonary artery banding (PAB) model. Echocardiography and hemodynamic measurements were performed in adult male and female Fischer CDF rats at 1- or 2-wk post-PAB. RV systolic pressure and RV hypertrophy were significantly elevated in PAB rats compared with sham control at 1- and 2-wk post-PAB; however, no differences were observed between male and female rats. Increase in cardiomyocyte cross-sectional area and RV end-diastolic diameter was observed in male rats compared with female rats at 2-wk post-PAB. Conversely, higher fractional area change and cardiac index were observed in female rats compared with male rats at 2-wk post-PAB. To explore the mechanisms, a focused PCR array was performed and higher expression of angiogenic genes, including sphingosine kinase-1 (Sphk1), was observed in the RV of female rats compared with male rats. Consistent with the higher angiogenic gene expression, female rats had a higher RV vascular density at 2-wk post-PAB compared with male rats. Female RV endothelial cells (RVECs) had better angiogenic ability compared with male cells that was potentiated by estradiol. Furthermore, effect of estradiol on RVECs was inhibited by Sphk1 inhibitor (PF-543). Together, female Fischer CDF rats develop adaptive RV remodeling post-PAB compared with maladaptive remodeling in male rats. Moreover, the adaptive remodeling in female rats is associated with better RV angiogenic response that may result from better angiogenic ability of female RVECs and proangiogenic effects of estradiol through Sphk1.NEW & NOTEWORTHY Female patients with pulmonary hypertension have better right ventricular adaptation compared with male. These sex differences were modeled in right heart failure susceptible Fischer CDF rat using pulmonary artery banding model. Preservation of right ventricular function in female rats is linked to better right ventricular angiogenic response that involves higher intrinsic angiogenic ability of female right ventricular endothelial cells together with the proangiogenic effects of female sex hormone estradiol through sphingosine kinase-1.

Aberrant miRNA expression and protein arginine methyltransferase 5 (PRMT5) in cancer: A review

The search for important factors involved in triggering and promoting cancer cell growth and survival has led to the identification of key players, including transcription factors, chromatin remodelers, epigenetic modifying enzymes, signaling molecules, and miRNAs. However, the interplay and crosstalk between some of these factors and the impact they have on tumorigenesis remains largely unexplored. In this review, we focus on type II protein arginine methyltransferase 5 (PRMT5)-mediated epigenetic silencing and its regulatory tumor suppressor miRNAs, as well as the mechanisms by which circular PRMT5 RNA (circ-PRMT5) promotes cancer cell proliferation and survival.

EpiBrCan-Lite: A lightweight deep learning model for breast cancer subtype classification using epigenomic data

BACKGROUND AND OBJECTIVES

Early breast cancer subtypes classification improves the survival rate as it facilitates prognosis of the patient. In literature this problem was prominently solved by various Machine Learning and Deep Learning techniques. However, these studies have three major shortcomings: huge Trainable Weight Parameters (TWP), suffer from low performance and class imbalance problem.

METHODS

This paper proposes a lightweight model named EpiBrCan-Lite for classifying breast cancer subtypes using DNA methylation data. This model encompasses three blocks namely Data Encoding, TransGRU, and Classification blocks. In Data Encoding block, the input features are encoded into equal sized chunks and then passed down to TransGRU block which is a modified version of traditional Transformer Encoder (TE). In TransGRU block, MLP module of traditional TE is replaced by GRU module, consisting of two GRU layers to reduce TWP and capture the long-range dependencies of input feature data. Furthermore, output of TransGRU block is passed to Classification block for classifying breast cancer into their subtypes.

RESULTS

The proposed model is validated using Accuracy, Precision, Recall, F1-score, FPR, and FNR metrics on TCGA breast cancer dataset. This dataset suffers from the class imbalance problem which is mitigated using Synthetic Minority Oversampling Technique (SMOTE). Experimentation results demonstrate that EpiBrCan-Lite model attained 95.85 % accuracy, 95.96 % recall, 95.85 % precision, 95.90 % F1-score, 1.03 % FPR, and 4.12 % FNR despite of utilizing only 1/1500 of TWP than other state-of-the-art models.

CONCLUSION

EpiBrCan-Lite model is efficiently classifying breast cancer subtypes, and being lightweight, it is suitable to be deployed on low computational powered devices.

Impact of binge drinking on alcoholic liver disease

Numerous studies have examined the pathophysiological changes induced by chronic alcohol (ethanol) consumption and the underlying mechanisms, while much less attention has been devoted to understanding the health impacts of binge drinking. Binge drinking is defined as the excessive consumption of alcohol within a single drinking episode, and is the typical consumption pattern among young people in Western countries. While most young binge drinkers are not clinically alcohol dependent, binge drinking has emerged as a significant social and public health concern. The circulating alcohol consumed during binge episodes permeates cellular membranes throughout the body, exerting profound effects on multiple organs, and signaling pathways. Regular binge drinking eventually induces hepatic steatosis (fatty liver), initiates acute inflammation, and accelerates neutrophil infiltration, de novo lipogenesis, adipocyte death/lipolysis, and the production of nonoxidative alcohol metabolites, processes that synergize to damage liver tissue and impair liver function. Metabolic abnormalities such as diabetes and obesity can also exacerbate the progression of alcohol-related liver disease among binge drinkers. Several animal models have been developed to evaluate the pathophysiological changes resulting from binge drinking; however, the pathogenesis of binge drinking is not fully understood due to differences in alcohol metabolism between animal models and humans. Thus, given the high prevalence and severe health implications of binge drinking, there is an urgent need for comprehensive experimental and clinical investigations to unravel the associated pathophysiological changes. This review summarizes recent research findings on the impact of binge drinking, specifically focusing on its contributions to alcoholic liver injury.

Exploring Epigenetic and Genetic Modulation in Animal Responses to Thermal Stress

There is increasing evidence indicating that global temperatures are rising significantly, a phenomenon commonly referred to as 'global warming', which in turn is believed to be causing drastic changes to the global climate. Global warming (GW) directly impacts animal health, reproduction, production, and welfare, presenting several challenges to livestock enterprises. Thermal stress (TS) is one of the key consequences of GW, and all animal species, including livestock, have diverse physiological, epigenetic and genetic mechanisms to respond to TS. As a result, TS can significantly affect an animals' health, immune responsiveness, metabolic pathways etc. which can also influence the productivity, performance, and welfare of animals. Moreover, prolonged exposure to TS can lead to transgenerational and intergenerational changes that are mediated by epigenetic changes. For example, in several animal species, the effects of TS are encoded epigenetically during the animals' growth or productive stage, and these epigenetic changes can be transmitted intergenerationally. Such epigenetic changes can affect animal productivity by changing the phenotype so that it aligns with its ancestors' environment, irrespective of its immediate environment. Furthermore, epigenetic and genetic changes can also help protect cells from the adverse effects of TS by modulating the transcriptional status of heat-responsive genes in animals. This review focuses on the genetic and epigenetic modulation and regulation that occurs in TS conditions via HSPs, histone alterations and DNA methylation.