Int. J. Mol. Sci., Volume 26, Issue 9 (May-1 2025) – 331 articles

N6-methyladenosine (m⁶A) methylation functions as a vital post-transcriptional and epigenetic modification in higher plants regulated by α-ketoglutarate-dependent dioxygenases (ALKBH). However, the role of ALKBH genes in oriental melon (Cucumis melo L.) fruit ripening has not been explored. Therefore, we treated oriental melon with an exogenous m⁶A demethylase inhibitor (mechlorfenamic acid) then analyzed endogenous ethylene production and ripening-related indicators to explore the effects of m⁶A methylation on ripening. Bioinformatics and real-time quantitative PCR analyses were used to determine the impact of ALKBH genes on key ethylene synthesis gene expression. Treatment effectively inhibited endogenous ethylene production, firmness changes, and soluble solid contents, thereby extending fruit ripening. Eight ALKBH gene family members belonging to five major groups were identified in the melon genome. All members were expressed in ripening fruits, with different expression patterns during ripening. CmALKBH6, CmALKBH7, and CmALKBH8 expression was inhibited by an ethylene inhibitor (1-methylcyclopropene). The transient overexpression (OE) of CmALKBH8 in oriental melon led to the increased expression of the ethylene synthesis genes CmACS1, CmACS2, and CmACO1. In summary, the ethylene-regulated gene CmALKBH8 may participate in oriental melon fruit ripening regulation by modulating the methylation levels of ethylene synthesis-related genes. These findings help us better understand how m⁶A methylation regulates melon ripening. Full article

Prostate cancer (PCa) is a major global health concern, particularly in advanced stages where chemotherapy resistance and androgen-independent tumor growth reduce survival rates to below 30%. Toll-like receptor 3 (TLR3), regulated by tumor suppressor p53, is a promising therapeutic target due to its role in tumor cell apoptosis. However, chronic exposure to inorganic arsenic (iAs), a known carcinogen, has been linked to PCa progression and reduced TLR3 expression and activation by polyinosinic/polycytidylic acid (Poly(I/C)), a synthetic ligand used in PCa immunotherapy. Here, we demonstrate that chronic sodium arsenite (NaAsO) exposure increases p53 transcript and protein levels in immortalized prostate epithelial cells. Despite this, key p53 target genes, including TLR3, CDKN1A, and BAX, were significantly downregulated, indicating a transcriptionally inactive p53. Chromatin immunoprecipitation (ChIP) confirmed diminished p53 binding to TLR3 and CDKN1A promoters, while sequencing ruled out TP53 mutations. A bioinformatic analysis revealed elevated TP53 but reduced TLR3 and CDKN1A in prostate adenocarcinoma, suggesting that iAs-induced oxidative stress disrupts p53 function. These findings reveal a novel mechanism by which iAs promotes PCa progression through impaired p53 activity, highlighting the need to explore post-translational and epigenetic factors affecting p53. Restoring p53 transcriptional activity may offer a therapeutic strategy for PCa patients exposed to NaAsO. Full article

The present Perspective analyzes the remarkable evolution of the Amyloid Cascade Hypothesis 2.0 (ACH2.0) theory of Alzheimer’s disease (AD) since its inception a few years ago, as reflected in the diminishing role of amyloid-beta (Aβ) in the disease. In the initial iteration of the ACH2.0, Aβ-protein-precursor (AβPP)-derived intraneuronal Aβ (iAβ), accumulated to neuronal integrated stress response (ISR)-eliciting levels, triggers AD. The neuronal ISR, in turn, activates the AβPP-independent production of its C99 fragment that is processed into iAβ, which drives the disease. The second iteration of the ACH2.0 stemmed from the realization that AD is, in fact, a disease of the sustained neuronal ISR. It introduced two categories of AD—conventional and unconventional—differing mainly in the manner of their causation. The former is caused by the neuronal ISR triggered by AβPP-derived iAβ, whereas in the latter, the neuronal ISR is elicited by stressors distinct from AβPP-derived iAβ and arising from brain trauma, viral and bacterial infections, and various types of inflammation. Moreover, conventional AD always contains an unconventional component, and in both forms, the disease is driven by iAβ generated independently of AβPP. In its third, the current, iteration, the ACH2.0 posits that proteolytic production of Aβ is suppressed in AD-affected neurons and that the disease is driven by C99 generated independently of AβPP. Suppression of Aβ production in AD seems an oxymoron: Aβ is equated with AD, and the later is inconceivable without the former in an ingrained Amyloid Cascade Hypothesis (ACH)-based notion. But suppression of Aβ production in AD-affected neurons is where the logic leads, and to follow it we only need to overcome the inertia of the preexisting assumptions. Moreover, not only is the generation of Aβ suppressed, so is the production of all components of the AβPP proteolytic pathway. This assertion is not a quantum leap (unless overcoming the inertia counts as such): the global cellular protein synthesis is severely suppressed under the neuronal ISR conditions, and there is no reason for constituents of the AβPP proteolytic pathway to be exempted, and they, apparently, are not, as indicated by the empirical data. In contrast, tau protein translation persists in AD-affected neurons under ISR conditions because the human tau mRNA contains an internal ribosomal entry site in its 5′UTR. In current mouse models, iAβ derived from AβPP expressed exogenously from human transgenes elicits the neuronal ISR and thus suppresses its own production. Its levels cannot principally reach AD pathology-causing levels regardless of the number of transgenes or the types of FAD mutations that they (or additional transgenes) carry. Since the AβPP-independent C99 production pathway is inoperative in mice, the current transgenic models have no potential for developing the full spectrum of AD pathology. What they display are only effects of the AβPP-derived iAβ-elicited neuronal ISR. The paper describes strategies to construct adequate transgenic AD models. It also details the utilization of human neuronal cells as the only adequate model system currently available for conventional and unconventional AD. The final alteration of the ACH2.0, introduced in the present Perspective, is that AβPP, which supports neuronal functionality and viability, is, after all, potentially produced in AD-affected neurons, albeit not conventionally but in an ISR-driven and -compatible process. Thus, the present narrative begins with the “omnipotent” Aβ capable of both triggering and driving the disease and ends up with this peptide largely dislodged from its pedestal and retaining its central role in triggering the disease in only one, although prevalent (conventional), category of AD (and driving it in none). Among interesting inferences of the present Perspective is the determination that “sporadic AD” is not sporadic at all (“non-familial” would be a much better designation). The term has fatalistic connotations, implying that the disease can strike at random. This is patently not the case: The conventional disease affects a distinct subpopulation, and the basis for unconventional AD is well understood. Another conclusion is that, unless prevented, the occurrence of conventional AD is inevitable given a sufficiently long lifespan. This Perspective also defines therapeutic directions not to be taken as well as auspicious ways forward. The former category includes ACH-based drugs (those interfering with the proteolytic production of Aβ and/or depleting extracellular Aβ). They are legitimate (albeit inefficient) preventive agents for conventional AD. There is, however, a proverbial snowball’s chance in hell of them being effective in symptomatic AD, lecanemab, donanemab, and any other “…mab” or “…stat” notwithstanding. They comprise Aβ-specific antibodies, inhibitors of beta- and gamma-secretase, and modulators of the latter. In the latter category, among ways to go are the following: (1) Depletion of iAβ, which, if sufficiently “deep”, opens up a tantalizing possibility of once-in-a-lifetime preventive transient treatment for conventional AD and aging-associated cognitive decline, AACD. (2) Composite therapy comprising the degradation of C99/iAβ and concurrent inhibition of the neuronal ISR. A single transient treatment could be sufficient to arrest the progression of conventional AD and prevent its recurrence for life. Multiple recurrent treatments would achieve the same outcome in unconventional AD. Alternatively, the sustained reduction/removal of unconventional neuronal ISR-eliciting stressors through the elimination of their source would convert unconventional AD into conventional one, preventable/treatable by a single transient administration of the composite C99/iAβ depletion/ISR suppression therapy. Efficient and suitable ISR inhibitors are available, and it is explicitly clear where to look for C99/iAβ-specific targeted degradation agents—activators of BACE1 and, especially, BACE2. Directly acting C99/iAβ-specific degradation agents such as proteolysis-targeting chimeras (PROTACs) and molecular-glue degraders (MGDs) are also viable options. (3) A circumscribed shift (either upstream or downstream) of the position of transcription start site (TSS) of the human AβPP gene, or, alternatively, a gene editing-mediated excision or replacement of a small, defined segment of its portion encoding 5′-untranslated region of AβPP mRNA; targeting AβPP RNA with anti-antisense oligonucleotides is another possibility. If properly executed, these RNA-based strategies would not interfere with the protein-coding potential of AβPP mRNA, and each would be capable of both preventing and stopping the AβPP-independent generation of C99 and thus of either preventing AD or arresting the progression of the disease in its conventional and unconventional forms. The paper is interspersed with “validation” sections: every conceptually significant notion is either validated by the existing data or an experimental procedure validating it is proposed. Full article

Civilization diseases are a growing and global health problem in modern societies. Neurological disorders, cancer, and inflammatory diseases affect a large group of patients around the world. Therefore, it is of utmost importance to search for novel drugs, lifestyle tips, and foods that can help restore balance in the living organism, promote the efficiency of the immune system, and provide satisfactory prophylactic measures. Astragaloside IV (ASIV)—a triterpenoid saponin from Astragalus species, one of the world’s most widely used herbs—has been shown to have a variety of biological properties, including anti-inflammatory, antioxidant, antitumor, and neuroprotective effects. In recent years, the number of in vivo studies on this active ingredient in the scientific literature has increased considerably. The aim of this review was therefore to compile the existing knowledge on the use of this compound in the treatment of selected diseases of civilization—cancer, neurological disorders, and inflammatory diseases—in vivo. Full article

The ALEX²-test (MacroArray Diagnostics, Vienna, Austria) is a diagnostic multiplex IgE-test for the simultaneous detection of IgE to 178 allergens and 117 extracts, in addition to total IgE. Test results from more than 90 countries are stored on a GDPR-compliant cloud server for backup, customer support, and continuous postmarket surveillance. To improve the coverage of exposomes on a global scale and to further increase the sensitivity of the test, the allergen panel was updated from ALEX² to ALEX³. By mid-2023, when ALEX³ was designed, almost 400,000 real-world ALEX² test results were available. Analysing prevalences and average sIgE-levels of individual allergen preparations, coverage of extracts by components, and co-reactivity of members of the same allergen family provided a rationale for updating the array. In parallel, based on the scientific literature and clinical studies, new allergens were selected. On ALEX³, 218 allergens and 82 extracts will be represented, including 52 new allergens. Allergen preparations with low prevalence and clinical relevance, as well as redundant allergens and extracts, were discontinued. New allergens encompass, e.g., cyclophilins, alpha-gal, and additional markers from respiratory and food allergen sources. Using a large dataset of ALEX² test results exemplifies the targeted, data-driven improvement of a diagnostic IgE-macroarray. Full article

The jasmonic acid (JA) signaling pathway has been demonstrated to play a crucial role in plant defense against herbivorous insects. However, the relationship between Ectropis obliqua-induced defensive metabolites and the JA signaling pathway in tea plants remains poorly understood. In this study, we investigated seven key special metabolites, including p-coumaroylputrescine, feruloylputrescine, prunin, naringenin, and three monolignols, to address this knowledge gap. Epicatechin was selected as a positive control based on its well-documented regulation through the JA signaling pathway. Notably, the content of all selected compounds was significantly increased by E. obliqua infestation. Furthermore, exogenous application of high-dose methyl jasmonate (MeJA) induced the accumulation of six of the eight compounds, excluding p-coumaryl alcohol and sinapyl alcohol, whereas low-dose MeJA failed to elicit their accumulation. To confirm the results, we screened two bioactive molecules, D-allose and L-theanine, which significantly increased the endogenous JA levels at low concentrations. Interestingly, neither D-allose nor L-theanine triggered the biosynthesis of these defensive compounds. Additionally, D-allose-treated tea leaves had no significant effect on the performance of E. obliqua larvae. These findings demonstrate that the metabolic accumulation induced by E. obliqua is mediated through a high-threshold JA signaling cascade. This study provides novel insights into the relationship between plant resistance and JA signaling pathway, advancing our understanding of special metabolites mediated plant-insect interactions. Full article

Fetal growth restriction (FGR) is an obstetric condition most frequently caused by placental dysfunction. It is a major cause of perinatal morbidity with limited treatment options, so identifying the underpinning mechanisms is important. Peptidylarginine deiminases (PADs) are calcium-activated enzymes that mediate post-translational citrullination (deimination) of proteins, through conversion of arginine to citrulline. Protein citrullination leads to irreversible changes in protein structure and function and is implicated in many pathobiological processes. Whether placental protein citrullination occurs in FGR is poorly understood. We assessed protein citrullination and PAD isozyme abundance (PAD1, 2, 3, 4 and 6) in human placental samples from pregnancies complicated by early- and late-onset FGR, compared to appropriate-for-gestational-age (AGA) controls. Proteomic mass spectrometry demonstrated that the placental citrullinome profile changed in both early- and late-onset FGR, with 112 and 345 uniquely citrullinated proteins identified in early- and late-onset samples, respectively. Forty-four proteins were citrullinated only in control AGA placentas. The proteins that were uniquely citrullinated in FGR placentas were enriched for gene ontology (GO) terms related to neurological, developmental, immune and metabolic pathways. A greater number of GO and human phenotype pathways were functionally enriched for citrullinated proteins in late- compared with early-onset FGR. Correspondingly, late-onset but not early-onset FGR was associated with significantly increased placental abundance of PAD2 and citrullinated histone H3, determined by Western blotting. PAD3 was downregulated in early-onset FGR while abundance of PAD 1, 4 and 6 was less altered in FGR. Our findings show that placental protein citrullination is altered in FGR placentas, potentially contributing to the pathobiology of placental dysfunction. Full article

Calpains, calcium-dependent cytosolic cysteine proteases, perform controlled proteolysis of their substrates for various cellular and physiological activities. In different cancers, missense mutations accumulate in the genes coding for the calpain cleavage sites in various calpain substrates termed as the calpain cleavage-related mutations (CCRMs). However, the impact of such CCRMs on the calpain–substrate interaction is yet to be explored. This study focuses on the interaction of wild-type and mutant β-integrins with calpain-1 and 2 in uterine corpus endometrial carcinoma (UCEC). A total of 48 calpain substrates with 176 CCRMs were retrieved from different datasets and shortlisted on the basis of their involvement in cancer pathways. Finally, three calpain substrates, ITGB1, ITGB3, and ITGB7, were selected to assess the structural changes due to CCRMs. These CCRMs were observed towards the C-terminal of the cytoplasmic domain within the calpain cleavage site. The wild-type and mutant proteins were docked with calpain-1 and 2, followed by molecular simulation. The interaction between mutant substrates and calpains showcased variations compared to their respective wild-type counterparts. This may be attributed to mutations in the calpain cleavage sites, highlighting the importance of the cytoplasmic domain of β-integrins in the interactions with calpains and subsequent cellular signaling. Highlights: 1. Calpain cleavage-related mutations (CCRMs) can alter cellular signaling. 2. CCRMs impact the structure of C-domains of human integrin-β subunits. 3. Altered structure influences the cleavability of human integrin-β subunits by human calpains. 4. Altered cleavability impacts the cell signaling mediated through calpain–integrin-β axis. 5. Presence of CCRMS may influence the progression of uterine corpus endometrial carcinoma (UCEC). Full article

The cornerstone of first-line treatment in extensive-stage small cell lung cancer (ES-SCLC) is platinum- and etoposide-based chemotherapy. Platinum compounds could immunomodulate the tumor microenvironment in addition to their cytotoxic effect. Genetic variation in immune checkpoint (IC) pathways may predict chemotherapy efficacy. Polymorphisms in the IC genes were determined, and their association with survival was analyzed in 78 patients with ES-SCLC treated with chemotherapy. PD-L1 protein expression in tumor tissue was determined. Three variants in CD274 were associated with better median progression-free survival (mPFS): rs2297136 (hazard ratio [HR] 0.52, 95% CI 0.29–0.93; p = 0.03), rs2282055 (HR 0.23, 95% CI 0.09–0.64; p = 0.005), and rs822336 (HR 0.41, 95% CI 0.23–0.73; p = 0.002). CTLA4 rs231775 was also associated with mPFS (HR 0.30, 95% CI 0.14–0.63; p = 0.002). The variants CD274 rs2297136 and CD274 rs822336 were associated with platinum sensitivity (odds ratio [OR] 0.13, 95% CI 0.02–0.70; p = 0.02, and OR 0.08, 95% CI 0.01–0.46; p = 0.005, respectively). CD274 rs2297136 was also associated with better overall survival (p = 0.02), but not after adjustment for covariates. No association was found between CD274 germline variants and PD-L1 tumor expression. Our results suggest that CD274 and CTLA4 variants may be predictive biomarkers for platinum plus etoposide treatment in ES-SCLC. Full article

This study aimed to determine the microRNA (miRNA) profile extracted from exosomes in plasma samples in pseudoexfoliation (PEX) glaucoma patients compared to controls. A blood sample (10 mL) was obtained after acquiring written informed consent. Exosome was extracted from each plasma sample using an Exoquick-TC kit. RNA sequencing was performed for each exosome sample. A bioinformatics study was conducted for miRNA-related pathways and targets. A total of 14 Korean subjects (7 with PEX glaucoma; 7 age-matched controls) were involved in the final study. In exosomes of PEX glaucoma participants, 330 mature miRNAs were detected. Among these, three miRNAs were significantly upregulated, including hsa-miR-92b-5p (fold change: 24.68), hsa-miR-744-5p (fold change: 2.49), and hsa-miR-148b-3p (fold change: 3.96). Sixty-six miRNAs were significantly downregulated in PEX glaucoma patients compared to the controls (all p < 0.05). These significantly altered miRNAs (both upregulated and downregulated) were associated with the gene ontology (GO) category of neurogenesis (9.41%), which accounted for the largest proportion. The expression of exosomal microRNAs in plasma was significantly different between PEX glaucoma patients and the controls. This suggests their possible roles in the pathogenic mechanism and a good diagnostic marker for PEX glaucoma. Full article

Piwi-interacting RNAs (piRNAs) play a crucial role in silencing transposable elements (TEs) in the germ cells of Metazoa by acting as sequence-specific guides. Originating from distinct genomic loci, called piRNA clusters, piRNA can trigger an epigenetic conversion of TE insertions into piRNA clusters by means of a paramutation-like process. However, the variability in piRNA clusters’ capacity to induce such conversions remains poorly understood. Here, we investigated two Drosophila virilis strains with differing capacities to produce piRNAs from the subtelomeric RhoGEF3 and Adar gene loci. We found that active piRNA generation correlates with high levels of the heterochromatic mark histone 3 lysine 9 trimethylation (H3K9me3) over genomic regions that give rise to piRNAs. Importantly, the maternal transmission of piRNAs drives their production in the progeny, even from homologous loci previously inactive in piRNA biogenesis. The RhoGEF3 locus, once epigenetically converted, maintained enhanced piRNA production in subsequent generations lacking the original allele carrying the active piRNA cluster. In contrast, piRNA expression from the converted Adar locus was lost in offspring lacking the inducer allele. The present findings suggest that the paramutation-like behavior of piRNA clusters may be influenced not only by piRNAs but also by structural features and the chromatin environment in the proximity to telomeres, providing new insights into the epigenetic regulation of the Drosophila genome. Full article

Bone defects caused by various traumas and diseases such as osteoporosis, which affects bone density, and osteosarcoma, which affects the integrity of bone structure, are now well known. Given this situation, several innovative research projects have been reported to improve orthopedic methods and technologies that positively contribute to the regeneration of affected bone tissue, representing a significant advance in regenerative medicine. This review article comprehensively analyzes the transition from existing methods and technologies for implants and bone tissue regeneration to innovative biomaterials. These biomaterials have been of great interest in the last decade due to their physicochemical characteristics, which allow them to overcome the most common limitations of traditional grafting methods, such as the availability of biomaterials and the risk of rejection after their application in regenerative medicine. This could be achieved through an exhaustive study of the applications and properties of various materials with potential applications in regenerative medicine, such as using magnetic nanoparticles and hydrogels sensitive to external stimuli, including pH and temperature. In this regard, this review article describes the most relevant compounds used in bone tissue regeneration, promoting the integration of these biomaterials with the affected area’s bone structure, thereby allowing for regeneration and preventing amputation. Additionally, the types of interactions between biomaterials and mesenchymal stem cells and their effects on bone tissue are discussed, which is critical for developing biomaterials with optimal regenerative properties. Furthermore, the mechanisms of action of the various biomaterials that enhance osteoconduction and osteoinduction, ensuring the success of orthopedic therapies, are analyzed. This enables the treatment of bone defects tailored to each patient’s condition, thereby avoiding limb amputation. Consequently, a promising future for regenerative medicine is emerging, with various therapies that could revolutionize the management of bone defects, offering more efficient and safer solutions. Full article

Overweight and obese individuals show lower mortality rates or better prognoses than those of normal weight in a variety of diseases, a phenomenon called the “obesity paradox”. An inverse association of adiposity with atherosclerosis has been observed in both humans and mice. To dissect phenotypic and genetic connections between the traits, 154 female and 145 male F2 mice were generated from an intercross between BALB/cJ and LP/J apolipoprotein E-deficient mice and fed a Western diet for 12 weeks. Atherosclerotic lesion size in the aortic root, body weight, plasma lipids, and glucose were measured, and genotyping was performed on miniMUGA SNP arrays. Quantitative trait locus (QTL) analyses on all F2 mice with sex as a covariate revealed four significant QTLs on chromosomes (Chr) 3, 6, 13, and 15 for atherosclerosis and three significant QTLs on Chr2, 7, and 15 for body weight. Chr15 QTL for atherosclerosis overlapped with one for body weight near 36 Mb. After adjusting for variation in body weight, Chr15 atherosclerosis QTL was downgraded from significant to suggestive linkage. Body weight was inversely correlated with atherosclerotic lesion sizes and accounted for more variance than a single other risk factor for atherosclerosis among F2 mice. Analysis of public data collected from two backcross cohorts revealed strong correlations between body weight and fat mass in adult mice (r ≥ 0.93; p ≤ 1.6 × 10⁻¹³⁶). Thus, the obesity paradox in atherosclerosis is partially attributable to shared genetic components that have an opposite effect on adiposity and atherosclerosis. Full article

Bile acids and their corresponding intestinal epithelial receptors, the farnesoid X receptor (FXR), the G protein-coupled bile acid receptor (TGR5), play crucial roles in the physiological and pathological processes of intestinal epithelial cells. These acids and receptors are involved in the regulation of intestinal absorption, signal transduction, cellular proliferation and repair, cellular senescence, energy metabolism, and the modulation of gut microbiota. A comprehensive literature search was conducted using PubMed, employing keywords such as bile acid, bile acid receptor, FXR (nr1h4), TGR5 (gpbar1), intestinal epithelial cells, proliferation, differentiation, senescence, energy metabolism, gut microbiota, inflammatory bowel disease (IBD), colorectal cancer (CRC), and irritable bowel syndrome (IBS), with a focus on publications available in English. This review examines the diverse effects of bile acid signaling and bile receptor pathways on the proliferation, differentiation, senescence, and energy metabolism of intestinal epithelial cells. Additionally, it explores the interactions between bile acids, their receptors, and the microbiota, as well as the implications of these interactions for host health, particularly in relation to prevalent intestinal diseases. Finally, the review highlights the importance of developing highly specific ligands for FXR and TGR5 receptors in the context of metabolic and intestinal disorders. Full article

Polycystic ovarian syndrome (PCOS) is a prevalent endocrine condition in women of reproductive age, characterized also by insulin resistance, affecting both obese and non-obese individuals. Hyperprolactinemia in patients with PCOS may additionally aggravate the decline in insulin sensitivity, attributable to prolactin lipogenic effects and influence on metabolic profile. Therefore, this study aimed to investigate the serum levels of prolactin in women with PCOS and their associations with obesity, insulin resistance and prediabetes. A retrospective monocentric study was performed using the electronic database of 157 women diagnosed with PCOS. Serum prolactin, BMI, complete glucose-insulin profile and insulin resistance indices following OGTT were determined. The women with hyperprolactinemia (40.8%) had significantly higher BMI (p = 0.007), fasting glucose (p = 0.003), insulin levels (p < 0.001) and HOMA-IR (p < 0.001). The women with PCOS categorized as overweight/obese (47.1%), insulin resistant (68.8%), having impaired fasting glycaemia (28.7%) and prediabetes (36.3%) showed significantly higher levels of prolactin compared to the respective counterparts. Consequently, higher prolactin levels were significantly associated with an elevated risk of development of overweight/obesity (OR 2.59; 95% CI: 1.34–4.97, p = 0.004), insulin resistance (OR 3.33; 95% CI: 1.54–7.19, p = 0.002) and prediabetes (OR 1.98; 95% CI: 1.02–3.85, p = 0.043) in women with PCOS. Our results suggest that hyperprolactinemia might be a pathophysiological link between obesity, insulin resistance, and carbohydrate metabolism impairments in patients with PCOS. Increased prolactin levels may serve as an additional indicator of insulin resistance and even further exacerbate it in women with PCOS. Full article

New ways of ensuring sustainable development in various areas of life are being intensively researched. One of the key priorities is to maximize the use of invaluable natural ingredients in cosmetic products while minimizing the negative impact on the environment. In this study, a three-component natural composite based on amber, diatomite, and Phytokeratin^TM (hydrolyzed plant protein) was developed using mechanochemical synthesis. The goal was to maximize the release of biologically active substances, such as succinic acid and Phytokeratin^TM, in aqueous solution. The physicochemical properties of the materials were characterized using Scanning Electron Microscopy (SEM), thermogravimetric (TG) and differential thermogravimetric (DTG) analysis, Fourier Transform Infrared (FTIR) spectroscopy, and Ultraviolet–Visible (UV-Vis) spectrophotometry. Additionally, Density Functional Theory (DFT) was used to perform quantum chemical calculations and characterize molecular interactions in the composite. The optimized composite demonstrated favorable release characteristics and structural properties, confirming its suitability for cosmetic applications. DFT calculations revealed the potential molecular-level interactions between the organic components, indicating the stability and functional integration of the composite. The resulting innovative composite was successfully incorporated into eco-friendly cosmetic formulations, including a solid shampoo bar and a nail conditioner. Full article

Kindler Epidermolysis bullosa (KEB; OMIM 173650) is a rare autosomal recessive genodermatosis characterized by bullous poikiloderma and photosensitivity. Additional presentations include blistering, poor wound healing, skin atrophy, and increased risk of skin cancer. Most cases of KEB result from aberrations in the FERMT1 (Fermitin family member 1) gene encoding kindlin-1 and include nonsense, frameshift, splicing, and missense variants. Large deletion variants have been reported in nine cases to date. Most variants are predicted to lead to premature termination of translation and to loss of kindlin-1 function. In this study, we report on a 33-year-old male patient who presented with typical clinical manifestations of KEB. As routine molecular testing failed to obtain a diagnosis, Next Generation Sequencing (NGS) of an Epidermolysis Bullosa (EB)-specific panel was carried out followed by the determination of the deletion breakpoints and verification at the mRNA and protein levels. This approach revealed a new large homozygous deletion of ~9.4 kb in the FERMT1 gene involving exons 7 to 9. Finally, we performed a literature review on large FERMT1 deletions. The deletion is predicted to skip exons 7 to 9 within the mRNA, which results in a frameshift. The patient’s phenotype is likely caused by the resulting truncated and non-functioning protein. Our report further enriches the spectrum of FERMT1 gene variants to improve genotype–phenotype correlations. Full article

Placental development plays a pivotal role in ensuring successful pregnancy outcomes, yet its molecular regulatory mechanisms in sheep remain poorly characterized. This study aimed to systematically investigate stage-specific proteomic dynamics and functional adaptations in ovine placental tissues across gestation to elucidate molecular drivers of placental maturation. Using data-independent acquisition proteomics, we identified 7774 proteins in Hu sheep placental tissues at gestational days 50, 80, and 120. Comparative analysis revealed 1450, 1026, and 1964 differentially expressed proteins (DEPs) in the 50 d vs. 80 d, 80 d vs. 120 d, and 50 d vs. 120 d comparisons, respectively. DEPs were functionally enriched in biological processes including cell proliferation, apoptosis, angiogenesis, nutrient transport, and steroid synthesis, with prominent involvement of the PI3K-Akt, MAPK, and estrogen signaling pathways. Protein interaction networks identified SRC, MAP3K1, KRAS, and TJP1 as central regulators exhibiting dynamic expression patterns across gestation. Temporal expression trends showed progressive upregulation of tight junction, immune response, and glucose metabolism proteins, contrasting with downregulation of endoplasmic reticulum protein processing and proteasome components. Validation experiments confirmed elevated proliferation/transport gene expression at 80 d versus 50 d, followed by increased apoptosis/transport genes and decreased proliferation markers at 120 d. This comprehensive proteomic profiling reveals stage-specific regulatory networks governing placental development in sheep, highlighting coordinated shifts in proliferative, metabolic, and structural remodeling processes. These findings advance our understanding of placental adaptation mechanisms and provide valuable insights for improving reproductive management in livestock species. Full article

Influenza A virus (IAV) infections continue to threaten public health. Current strategies, such as vaccines and antiviral drugs, are limited due to their time-consuming development and drug-resistant strains. Therefore, new effective treatments are needed. Here, virus-supportive cellular factors are promising drug targets, and the encapsulation of candidate substances in poly(D,L-lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) is intended to improve their bioavailability. This study investigates the potential of the indirubin derivative 6-bromoindirubin-3′-glycerol-oxime ether (6BIGOE), a glycogen synthase kinase 3 (GSK-3)β inhibitor, for its potential to regulate IAV replication in vitro. The effects of 6BIGOE-loaded PLGA NPs on cell metabolism were assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and lactate dehydrogenase (LDH) assays in A549 and Calu-3 cells. Viral replication and spread were monitored in various IAV-infected cell lines in the absence and presence of free and 6BIGOE-loaded PLGA NPs via plaque assays and Western blot analysis. The encapsulation of 6BIGOE in PLGA NPs resulted in reduced negative side effects on cell viability while maintaining antiviral efficacy. Both encapsulated and free 6BIGOE exhibited antiviral activity, potentially through GSK-3β inhibition and the disruption of key signaling pathways required for viral replication. The data indicate 6BIGOE, particularly after encapsulation in NPs, as a potential candidate for further investigation and development as an antiviral agent to treat IAV infections. Full article

Transcription factors (TFs) are fundamental regulators of gene expression and perform diverse functions in cellular processes. The management of 3-dimensional (3D) genome conformation and gene expression relies primarily on TFs. TFs are crucial regulators of gene expression, performing various roles in biological processes. They attract transcriptional machinery to the enhancers or promoters of specific genes, thereby activating or inhibiting transcription. Identifying these TFs is a significant step towards understanding cellular gene expression mechanisms. Due to the time-consuming and labor-intensive nature of experimental methods, the development of computational models is essential. In this work, we introduced a two-layer prediction framework based on a support vector machine (SVM) using the latent space representation of a protein language model, ProtBert. The first layer of the method reliably predicts and identifies transcription factors (TFs), and in the second layer, the proposed method predicts and identifies transcription factors that prefer binding to methylated deoxyribonucleic acid (TFPMs). In addition, we also tested the proposed method on an imbalanced database. In detecting TFs and TFPMs, the proposed model consistently outperformed state-of-the-art approaches, as demonstrated by performance comparisons via empirical cross-validation analysis and independent tests. Full article

This study investigated whether ginsenoside Rg₁ (G-Rg₁) alleviated acute gouty arthritis (AGA) in rats by modulating the TLR4/NLRP3 pathway and neutrophil extracellular trap (NET) formation. Rats were orally administered G-Rg₁ or colchicine (Col) for 7 days, and monosodium urate (MSU) was injected into the ankle joints on day 5 to induce AGA. Joint swelling, histopathology (HE staining), and serum markers (MPO, NE, MPO-DNA, IL-6, IL-1β; ELISA) were assessed at the baseline and 6–36 h post-modeling. Western blot and immunofluorescence analyzed the NET-related and TLR4/NLRP3 pathway proteins in synovial tissue. G-Rg₁ significantly reduced ankle swelling and synovial inflammation compared with the AGA group, lowered the serum IL-6, IL-1β, MPO, NE, and MPO-DNA levels, and suppressed NET-associated protein expression. Mechanistically, G-Rg₁ downregulated TLR4/NLRP3 pathway activation in synovial tissue. These findings suggest that G-Rg₁ mitigates AGA by inhibiting TLR4/NLRP3 signaling, thereby reducing inflammatory cytokine release and NET formation. Full article

Ankyrin repeat domain 1 (Ankrd1), a transcriptional target of Yes-associated protein (YAP), is linked to cardiomyopathy. However, its role in cancer, particularly in clear cell renal cell carcinoma (ccRCC), remains vague. In this study, we examined the expression, regulation, and function of Ankrd1 in ccRCC. High Ankrd1 expression was related to poor prognosis in patients with ccRCC in The Cancer Genome Atlas cohort. Ankrd1 expression was regulated by YAP in all ccRCC cell lines examined and also by ERK5 in a subset of ccRCC cell lines. Moreover, silencing of Ankrd1 in ccRCC cell lines resulted in decreased cell motility, whereas its overexpression increased the cell motility. Ankrd1 colocalized with F-actin in lamellipodia upon phorbol ester stimulation. Ankrd1 silencing resulted in alterations in the shape of RCC cells and caused a decrease in lamellipodia formation. Ankrd1 also colocalized with talin-1 in lamellipodia. Ankrd1 depletion repressed talin-1-mediated activation of the integrin pathway. Immunohistochemical examination of surgical specimens revealed high expression of Ankrd1 in metastatic RCC tissues compared with that in primary RCC tissues from the same patients. Collectively, these findings suggest that Ankrd1 plays a critical role in the motility of ccRCC cells through lamellipodia formation. Full article

Grafting is a prevalent horticultural technique that enhances crop yields and stress resilience; nevertheless, compatibility issues frequently constrain its efficacy. This research examined the physiological, hormonal, and transcriptional factors regulating compatibility between the litchi (Litchi chinensis Sonn.) cultivars Feizixiao (FZX) and Ziniangxi (ZNX). The anatomical and growth investigations demonstrated significant disparities between compatible (FZX as scion and ZNX as rootstock) and incompatible (ZNX as scion and FZX as rootstock) grafts, with the latter showing reduced levels of indole acetic acid (IAA). Exogenous 1-naphthalene acetic acid (NAA) application markedly improved the graft survival, shoot development, and hormonal synergy, whereas the auxin inhibitor tri-iodobenzoic acid (TIBA) diminished these parameters. The incompatible grafts showed downregulation of auxin transporter genes, including ATP-binding cassette (ABC) transporter, AUXIN1/LIKE AUX1 (AUX/LAX), and PIN-FORMED (PIN) genes, suggesting impaired vascular tissue growth. Metabolomic profiling revealed dynamic interactions between auxin, salicylic acid, and jasmonic acid, with NAA-treated grafts exhibiting enhanced levels of stress-responsive metabolites. Transcriptome sequencing identified differentially expressed genes (DEGs) linked to auxin signaling (ARF, GH3), seven additional phytohormones, secondary metabolism (terpenoids, anthocyanins, and phenylpropanoids), and ABC transporters. Gene ontology and KEGG analyses highlighted the significance of hormone interactions and the biosynthesis of secondary metabolites in successful grafting. qRT-PCR validation substantiated the veracity of the transcriptome data, emphasizing the significance of auxin transport and signaling in effective graft development. This study provides an in-depth review of the molecular and physiological factors influencing litchi grafting. These findings provide critical insights for enhancing graft success rates in agricultural operations via targeted hormonal and genetic approaches. Full article

While clinical trials have shown the efficacy of using dupilumab and upadacitinib to treat atopic dermatitis (AD), long-term real-world data remain limited. This retrospective cohort study, utilizing data from the Polish National Health Fund Registry, evaluates the long-term effectiveness of dupilumab versus upadacitinib in early treatment responders, focusing on sustained efficacy outcomes and high levels of skin clearance. Data from the Polish National Health Fund Registry were analyzed for 435 patients; 220 were treated with dupilumab and 215 were treated with upadacitinib, each receiving treatment for at least 40 weeks. Upadacitinib had a faster onset of action, leading to significantly higher rates of complete skin clearance compared to dupilumab at weeks 16 and 28 (EASI100 at week 16: 19.5% vs. 7.3%, p < 0.001; week 28: 26.5% vs. 12.7%, p < 0.001). Dupilumab showed continuous efficacy gains, ultimately demonstrating superiority in achieving EASI75 and EASI90 at week 40, though no significant difference was observed in achieving EASI100. Both treatments provided sustained dermatological improvement and enhanced quality of life, achieving high levels of skin clearance over the long term. Full article

Gene-edited cattle overexpressing natural resistance-associated macrophage 1 (NRAMP1) have demonstrated enhanced resistance to tuberculosis (TB). However, introducing synthetic sequences and selection markers may pose potential risks. The endogenous editing of target gene promoters could effectively mitigate these risks. To date, no available mutation sites in the bovine NRAMP1 promoter have been identified to enhance host resistance to TB. In this study, we identified a unique mutation editing site, designated as 2SP, within the bovine NRAMP1 promoter, using bioinformatics analysis and dual luciferase assays. The mutation at the 2SP site specifically increased NRAMP1 promoter activity by 2.3-fold after Mycobacterium tuberculosis H37Ra infection, without modifying promoter activity in non-infected groups. By using base editing techniques, an endogenously edited THP-1 cell line with a mutation at the homologous region of the 2SP site was generated, without introducing screening markers. In H37Ra infection experiments, the edited THP-1 cells specifically upregulated NRAMP1 expression and significantly inhibited H37Ra proliferation, while maintaining baseline NRAMP1 expression levels in the absence of infection. In this research, we identified a novel mutation site and provided a fundamental reference for the development of gene-edited cattle with enhanced resistance to TB. Full article

Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H₂O₂ and O₂. This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1’s mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure’s unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS. Full article

There is an escalating need to comprehend the long-term impacts of nuclear radiation exposure since the permeation of ionizing radiation has been frequent in our current societal framework. A system evaluation of the microbes that reside inside a host’s colon could meet this knowledge gap since the microbes play major roles in a host’s response to stress. Indeed, our past study suggested that these microbes might break their symbiotic association with moribund hosts to form a pro-survival condition exclusive to themselves. In this study, we undertook metagenomics and metabolomics assays regarding the descending colon content (DCC) of adult mice. DCCs were collected 1 month and 6 months after 7 Gy or 7.5 Gy total body irradiation (TBI). The assessment of the metagenomic diversity profile in DCC found a significant sex bias caused by TBI. Six months after 7.5 Gy TBI, decreased Bacteroidetes were replaced by increased Firmicutes in males, and these alterations were reflected in the functional analysis. For instance, a larger number of networks linked to small chain fatty acid (SCFA) synthesis and metabolism were inhibited in males than in females. Additionally, bioenergy networks showed regression dynamics in females at 6 months post-TBI. Increased accumulation of glucose and pyruvate, which are typical precursors of beneficial SCFAs coupled with the activated networks linked to the production of reactive oxygen species, suggest a cross-sex energy-deprived state. Overall, there was a major chronic adverse implication in male mice that supported the previous literature in suggesting females are more radioresistant than males. The sex-biased chronic effects of TBI should be taken into consideration in designing the pertinent therapeutics. Full article

Gestational diabetes mellitus (GDM) requires lifestyle changes that may alter exposure to endocrine-disrupting chemicals (EDCs). This study aimed to assess maternal and fetal exposure to EDCs—including bisphenol-A (BPA), monoethyl phthalate (MEP), and perfluorooctanoic acid (PFOA)—during the COVID-19 pandemic and to evaluate their association with fetal birthweight. Maternal urine (second and third trimester) and paired cord blood samples were analyzed from 58 GDM and 118 non-GDM pregnancies using UPLC-MS/MS. Significant correlations were found between maternal urine and cord blood levels of BPA and MEP. Cord blood BPA levels were significantly lower in GDM mothers (0.35 vs. 0.72 μg/L, p < 0.05), suggesting reduced exposure due to dietary interventions. However, maternal urinary BPA levels in GDM pregnancies were positively associated with fetal birthweight (β = 2.69, p < 0.05), indicating increased susceptibility to obesogenic effects. PFOA was present in all cord blood but only 41% of maternal urine samples. These findings underscore the dual impact of GDM-related lifestyle changes: reduced EDC transfer to the fetus, yet persistent metabolic vulnerability. Full article

Fine-needle aspiration cytology (FNAC) is the gold standard to diagnose thyroid nodules but fails in discriminating the nature of indeterminate lesions. Molecular testing can improve the diagnosis of these nodules and next-generation sequencing (NGS) can be used to test many genes simultaneously. Assess the performance of an NGS 17-gene panel on thyroid indeterminate FNAC. One hundred five indeterminate FNACs, 30.5% high-risk (TIR3B) and 69.5% low-risk (TIR3A), were analyzed by NGS. For TIR3A, the rate of mutated samples was 10.9%, significantly lower (p = 0.0001) compared to TIR3B (63.6%). Twenty-two mutated and fourteen non-mutated samples were submitted to surgery. At histology, the overall malignancy was 85.7% in the indeterminate group that had a positive molecular test and 13.3% in the mutation-negative (p = 0.01). The 17-gene panel had a sensitivity of 90%, specificity of 87%, positive predictive value (PPV) of 91%, and negative predictive value (NPV) of 87%. We reported the utility of Ultrasound Malignancy Risk Stratification of Thyroid Nodules in Adults (EU-TIRADS) in selecting indeterminate nodules for molecular analysis, showing a significant correlation between US score and mutation (p = 0.004). The performance of a 17-gene panel based on NGS technology is promising, allowing the selection of indeterminate nodules to submit to surgery with a great specificity and PPV. Full article

Acute myeloid leukemia (AML) is associated with unfavorable patient outcomes primarily related to disease relapse. Since specific types of leukemic hematopoietic stem and progenitor cells (HSPCs) are suggested to contribute to AML propagation, this study aimed to identify and explore relapse-initiating HSPC subpopulations present at diagnosis, using single-cell analysis (SCA). We developed unique high-resolution techniques capable of tracking single-HSPC-derived subclones during AML evolution. Each subclone was evaluated for chemo-resistance, in vivo leukemogenic potential, mutational profile, and the cell of origin. In BM samples of 15 AML patients, GMP-like and MLP-like HSPC subpopulations were identified as prevalent at relapse, exhibiting chemo-resistance to commonly used chemotherapy agents cytosine arabinoside (Ara-C) and daunorubicin. Reconstruction of phylogenetic lineage trees combined with genetic analysis of single HSPCs and single-HSPC-derived subclones demonstrated two distinct clusters, originating from MLP-like or GMP-like subpopulations, observed both at diagnosis and relapse. These subpopulations induced leukemia development ex vivo and in vivo. Genetic SCA showed that these relapse-related subpopulations harbored mutated EZH2 and TP53, detected already at diagnosis. This study, using combined molecular, functional, and genomic analyses at the level of single cells, identified patient-specific chemo-resistant HSPC subpopulations at the time of diagnosis, promoting AML relapse. Full article