Search Results (160)

Metabolic diseases, including type 2 diabetes mellitus (T2DM) and metabolic dysfunction-associated fatty liver disease (MAFLD), are chronic disorders characterized by dysregulated glucose and lipid homeostasis and represent major contributors to insulin resistance, cardiovascular complications, and liver injury. Despite considerable progress in elucidating their pathogenesis, effective preventive and therapeutic strategies remain limited. N6-methyladenosine (m⁶A) RNA demethylase AlkB homolog 5 (ALKBH5), a nuclear epitranscriptomic “eraser,” broadly regulates post-transcriptional gene expression by modulating RNA splicing, nuclear export, stability, and translation. Dysregulation of ALKBH5 has been implicated in tumorigenesis, immune dysfunction, and stress responses, underscoring its wide-ranging biological significance. Emerging evidence further indicates that ALKBH5 plays a pivotal role in maintaining metabolic homeostasis. However, most existing reviews have focused primarily on its roles in cancer, leaving its functions in metabolic diseases relatively unexplored. In this context, this review summarizes the structural characteristics and molecular mechanisms of ALKBH5 and discusses its emerging roles across a spectrum of metabolic diseases, including MAFLD, metabolic complications such as diabetic retinopathy (DR), diabetes-associated cognitive impairment (DACI), atherosclerosis (AS), and diabetic cardiomyopathy (DCM), as well as metabolism-related inflammatory diseases represented by rheumatoid arthritis (RA). Furthermore, recent pharmacological strategies targeting ALKBH5 are discussed, with attention to the challenges posed by its context-dependent, tissue-specific, and disease stage-specific activities. Overall, ALKBH5 emerges as a key epitranscriptomic regulator in metabolic diseases, and advancing therapeutic strategies that account for molecular context and tissue specificity will be critical for achieving safe and effective clinical interventions. Full article

In September 2022, the US Food and Drug Administration (FDA) expanded approval of the legacy Roche monoclonal antibody 4B5-based immunohistochemistry (IHC) assay to identify patients with HER2-low breast cancers predicted to respond to trastuzumab deruxtecan (T-DXd), based on findings from the DESTINY-Breast04 and DESTINY-Breast06 clinical trials. However, this repurposing of a legacy biomarker assay raises significant clinical and technical validation concerns. The legacy HER2 IHC assay was originally developed to identify tumors with HER2 overexpression (3+) resulting from gene amplification, which leads to substantially higher HER2 receptor expression than in low/ultralow expression tumors. The current application to distinguish HER2-low and HER2-ultralow tumors from truly HER2-negative tumors represents a fundamentally different biological and clinical purpose, yet the assay’s analytical and clinical validation for this new purpose remains incomplete. Critical gaps include the lack of established analytical sensitivity and specificity for identifying 1+ HER2 cases, poor reproducibility of pathologist scoring at low HER2 levels, and the absence of alternative methodologies for orthogonal validation. While more sensitive quantitative approaches (such as AQUA) may detect additional low HER2 expression cases missed by conventional IHC, increased analytical sensitivity does not automatically translate to clinical utility. Furthermore, the ASCO/CAP guidelines cutoffs were developed for HER2 overexpression detection and may not be the best choice for HER2-low/ultralow identification without clinical validation and determination of fit-for-purpose analytical specifications. We examine the current challenges of repurposing legacy HER2 IHC biomarker assays for HER2-low detection, evaluating the precedent of other repurposed IHC assays (ALK, CD30, and PD-L1), and emphasizing the necessity for proper technical and clinical validation before widespread implementation. We conclude that prospective clinical trials are essential to establish clinically meaningful cutoffs and analytical specifications appropriate for patient selection in HER2-low disease. Full article

Background: First-line chemoimmunotherapy (I + C) is the standard of care for advanced non-squamous non-small cell lung cancer (NSCLC) without oncogenic mutation. Bevacizumab has been shown to enhance the efficacy of chemotherapy in non-squamous NSCLC, yet its added value when combined with I + C (I + C + B) remains unclear. To address this gap, we conducted a real-world comparative study and a network meta-analysis to evaluate I + C + B versus I + C in this setting. Methods: This retrospective study included patients with advanced EGFR/ALK-negative non-squamous NSCLC treated with first-line I + C + B or I + C. Propensity score matching (PSM) was employed to balance baseline characteristics between groups. Efficacy endpoints were progression-free survival (PFS) and overall survival (OS). Subgroup analyses examined outcomes by PD-L1 expression, age, metastases, and chemotherapy, among other factors. In parallel, a network meta-analysis of four randomized trials (n = 2026) indirectly compared I + C + B against I + C for PFS, OS, and safety outcomes. Results: A total of 277 patients were included, with 167 (60.3%) receiving I + C + B and 110 (39.7%) receiving I + C. Before PSM, the I + C + B regimen significantly prolonged PFS versus I + C (hazard ratio [HR] = 0.69, 95% CI 0.52–0.92, p = 0.010), with this benefit maintaining post-matching (HR = 0.70, 95% CI 0.49–0.99, p = 0.045). However, OS did not differ significantly between groups in either the pre-PSM (HR = 0.93, 95% CI: 0.67–1.30; p = 0.665) or matched analyses (HR = 0.84, 95% CI: 0.54–1.29; p = 0.421). Subgroup analyses suggested greater PFS benefit from I + C + B among PD-L1-negative, older patients, those with brain metastases or multiple metastatic sites, and in patients receiving specific chemotherapy doublets. The network meta-analysis confirmed a PFS advantage for I + C + B over I + C (HR = 0.84, 95% CI: 0.71–0.98) without an OS benefit (HR = 0.95, 95% CI: 0.79–1.14). Toxicity was higher with I + C + B; rates of grade 3–5 adverse events, serious adverse events, and treatment discontinuation were all significantly increased compared to I + C. Conclusions: In the first-line treatment of advanced EGFR/ALK-negative non-squamous NSCLC, adding bevacizumab to I + C improved PFS but did not translate into an OS gain. Although PFS benefits were observed in certain subgroups, these were accompanied by significantly increased treatment-related toxicities. Our findings suggest that no clear subgroup has been identified where the benefit outweighs the risks, necessitating extreme clinical caution. Full article

Background/Objectives: Adenine derivatives are promising anticancer scaffolds, but their cellular mechanisms remain unclear. This study aimed to synthesize adenine–hydrazone hybrids and evaluate their cytotoxic effects in human lung adenocarcinoma (A549) cells. Methods: A series of adenine–hydrazone compounds (3a–r) was synthesized and tested for cytotoxicity in A549 and MRC-5 cells. Selected compounds were further analyzed for LDH release, oxidative stress markers, ROS production, mitochondrial membrane potential, cell-cycle distribution, apoptosis, and in silico docking against VEGFR2, ALK5, and EGFR. Results: Compounds with electron-withdrawing or donor–acceptor substituents showed the highest cytotoxicity, while halogenated and methoxy analogs were moderately active. Among the synthesized derivatives, 4F-substituted derivatives (3c) showed more activity than 2F- and 3F-substituted ones (3a and 3b). 4F- and 3Br-substituted derivatives (3f) showed more activity than only 4F-substituted ones (3c). 4-Nitro-substituted derivative (3i) showed more activity than 4F- (3c), 4Cl- (3d) and 4OMe- (3h) derivatives. Trimethoxy-substituted derivative (3l) showed more activity than di- and mono-substituted methoxy derivatives (3g, 3h, 3j and 3k). Among the salicyl aldehydederivatives (3m–r), 4-N(et)₂-substituted derivative (3r) showed more activity than non-substituted (3m), 5Br-(3n), 5Cl-(3o), 5Me (3p) and 3OCH₃ (3q) derivatives. Treatment induced oxidative stress, mitochondrial depolarization, Sub-G1 cell-cycle accumulation, and apoptosis. Docking studies indicated strong binding to VEGFR2 and ALK5, suggesting dual inhibition as a potential mechanism. Conclusions: Adenine–hydrazone derivatives exert substituent-dependent anticancer effects by inducing redox imbalance-associated mitochondrial dysfunction and regulated cell death. These results highlight their potential as lead structures for lung cancer therapy. Full article

Targeted therapies have revolutionized treatment paradigms for a variety of cancer types; however, challenges including primary and acquired resistance persist, and there remains a high demand for novel treatment options. HER3 (ErbB3), a member of the human epidermal growth factor receptor family of receptor tyrosine kinases, is a target of HER3-DXd, an antibody–drug conjugate currently under clinical investigation. As was previously reported, the cytotoxic activity of HER3-DXd in preclinical models is primarily mediated by the antitumor activity of the released payload. Therefore, we investigated the impact of HER3 expression changes on payload release after HER3-DXd treatment using HER3-positive human cancer cell lines and their xenograft models. In vitro studies showed that the amount of payload released from cells after HER3-DXd treatment was associated with baseline HER3 expression levels, HER3 internalization rate, and turnover rate. In female CAnN.Cg-Foxn1nu/CrlCrlj mouse models, dose and dosing interval influenced membrane HER3 expression levels and tumor payload concentrations. Furthermore, membrane HER3 was upregulated by tyrosine kinase inhibitor treatment in non-small-cell lung cancer cell lines harboring specific driver mutations, including EGFR-activating mutations, ROS1 fusions, and ALK fusions. The increase in HER3 expression induced by osimertinib treatment was associated with increased payload release in PC-9 cells. Our results indicate that HER3 dynamics, as well as baseline HER3 expression, modulate payload release from HER3-DXd and support combination strategies to potentiate the antitumor activity of HER3-DXd. Full article

Petroleum contamination poses a serious threat to human health and ecosystems worldwide, and microbially driven natural attenuation is an effective approach for accelerating hydrocarbon removal. Species of the genus Rhodococcus are recognized for their ability to degrade long chain petroleum hydrocarbons. However, their physiological traits and degradation mechanisms under alkaline conditions remain insufficiently understood. In this study, soil samples were collected from the Dagang oilfield in Tianjin, China, and Rhodococcus sp. A17 was isolated as an active indigenous strain for genomic and physiological characterization under high pH petroleum degradation conditions. The results showed that strain A17 grew optimally at 30 °C, pH 9.0, and 2% salinity. Petroleum hydrocarbon degradation reached 67.8% within 72 h, with a degradation half life of 34.2 h. Genome sequencing identified 18 oxygenase related genes involved in alkane degradation, including alkB, cytochrome P450 monooxygenases, and the long chain alkane monooxygenase ladA, together with four antibiotic resistance genes. Metabolite analysis suggested that alkane degradation might proceed via terminal and subterminal oxidation pathways. Overall, these findings indicate that Rhodococcus sp. A17 exhibits multiple adaptive traits that support its potential application in the bioremediation of petroleum contaminated alkaline environments. Full article

Background: Advances in molecular pathology have transformed NSCLC (Non-Small Cell Lung Cancer) diagnosis, prognosis, and treatment by enabling precise tumor characterization and targeted therapeutic strategies. We review key genomic alterations in NSCLC, including EGFR (epidermal growth factor receptor) mutations, ALK (anaplastic lymphoma kinase) and ROS1 (ROS proto-oncogene 1) rearrangements, BRAF (B-Raf proto-oncogene serine/threonine kinase) mutations, MET (mesenchymal–epithelial transition factor) alterations, KRAS (Kirsten rat sarcoma) mutations, HER2 (human epidermal growth factor receptor 2) alterations and emerging NTRK (neurotrophic receptor tyrosine kinase) fusions and AXL-related pathways. Methods: A total of 48 patients with NSCLC was analyzed, including 22 women and 26 men (mean age 70 years, range 44–86). Tumor specimens were classified histologically as adenocarcinomas (n = 81%) or squamous cell carcinomas (n = 19%). Smoking history, PD-L1 (programmed death-ligand 1) expression, and genetic alterations were assessed. NGS (Next-generation sequencing) identified genomic variants, which were classified according to ACMG (American College of Medical Genetics and Genomics) guidelines. Results: The cohort consisted of 29 former smokers, 13 current smokers, and 5 non-smokers (12%), with a mean smoking burden of 33 pack years. PD-L1 TPS (tumor proportion score) was ≥50% in 10 patients, ≥1–<50% in 22, and <1% in 15 patients. In total, 120 genomic variants were detected (allele frequency ≥ 5%). Of these, 52 (43%) were classified as likely pathogenic or pathogenic, 48 (40%) as variants of unknown significance, and 20 (17%) as benign or likely benign. The most frequently altered genes were TP53 (tumor protein p53) (31%), KRAS and EGFR (15% each), and STK11 (serine/threonine kinase 11) (12%). Adenocarcinomas accounted for 89% of all alterations, with TP53 (21%) and KRAS (15%) being most common, while squamous cell carcinomas predominantly harbored TP53 (38%) and MET (15%) mutations. In patients with PD-L1 TPS ≥ 50%, KRAS mutations were enriched (50%), particularly KRAS G12C and G12D, with frequent co-occurrence of TP53 mutations (20%). No pathogenic EGFR mutations were detected in this subgroup. Conclusions: Comprehensive genomic profiling in NSCLC revealed a high prevalence of clinically relevant mutations, with TP53, KRAS and EGFR as the dominant drivers. The strong association of KRAS mutations with high PD-L1 expression, irrespective of smoking history, highlights the interplay between genetic and immunological pathways in NSCLC. These findings support the routine implementation of broad molecular testing to guide precision oncology approaches in both adenocarcinoma and squamous cell carcinoma patients. Full article

Over the past several decades, rapid advances in molecular genomics have transformed our understanding of thyroid malignancies and are increasingly integrated into international clinical guidelines. Mutational profiles and epigenetic events are now recognized not only as diagnostic and prognostic tools but also as predictors of therapeutic response. Papillary, follicular, oncocytic, medullary, and anaplastic thyroid carcinomas harbor distinct early driver mutations, such as BRAFV600E, RAS, and fusion events (RET, NTRK, and ALK), that cooperate with secondary alterations (TERT promoter, TP53, PIK3CA, and CDKN2A/B loss) to drive dedifferentiation, metastasis, and therapeutic resistance. Insights from The Cancer Genome Atlas (TCGA) and transcriptomic scoring systems (e.g., BRAF–RAS score) now link genotype to tumor morphology, metastatic tropism, and radioactive iodine refractoriness. These molecular insights have been incorporated into updated risk stratification frameworks, preoperative surgical planning, and treatment algorithms, informing the selection of kinase inhibitors, redifferentiation strategies, and enrollment in genotype-directed clinical trials for radioiodine-refractory disease. This review synthesizes recent evidence connecting genomic alterations to clinical behavior and highlights their translation into evolving approaches for thyroid cancer management. Full article

Acrolein, a ubiquitous environmental pollutant, is also formed endogenously as a metabolite under oxidative stress conditions. Its adduct to cytosine, 3,N⁴-α-hydroxypropanocytosine (HPC), has recently been shown to be an in vitro substrate for the AlkB dioxygenase. Using a set of indicator plasmids modified with acrolein, we provide evidence that HPC is a mutagenic non-instructional lesion that predominantly induces C→A transversion, and to a lesser extent C→T and C→G base substitutions. HPC is efficiently repaired in vivo by AlkB, even without induction of the adaptive response. However, the mutation frequency did not differ between the wild-type and AlkA-deficient strains, and AlkA glycosylase fails to excise in vitro the acrolein-modified cytosine from the T₂₂(HPC)₃ oligodeoxynucleotide, both indicating that HPC is not a substrate for AlkA. Based on molecular modeling, we further examined the potential differences in the hydrolytic suspensibility of a known AlkA substrate, the acrolein adduct to adenine (HPA), and the cytosine adduct (HPC) at the glycosylase active site. Analysis of both structural and electrochemical properties indicates that, despite an identical type of modification within an equivalent chemical context, including comparable geometry and topology, the glycosidic bond in HPC is considerably less susceptible to hydrolysis than that in HPA. Full article

N⁶-methyladenosine (m⁶A), the most prevalent internal mRNA modification in eukaryotes, is also present in plants and is known to influence plant–virus interactions. However, its specific role in regulating Potato virus Y (PVY; Potyvirus yituberosi) infection, a major pathogen of potatoes, remains unclear. This study identified 16 potential m⁶A regulator genes in Nicotiana benthamiana through homology screening of Arabidopsis thaliana AlkB family members. Based on expression profiles in leaves at various developmental stages and following PVY infection, NbALKBH1L was selected for further analysis. Enzyme assays confirmed its m⁶A demethylase activity. Experiments with NbALKBH1L mutants, using RT-qPCR and m⁶A-IP-qPCR, demonstrated that it regulates PVY infection via the m⁶A pathway. Further investigation revealed that NbALKBH1L interacts with the PVY-encoded cylindrical inclusion (CI) protein. An interaction network constructed through immunoprecipitation–mass spectrometry (IP-MS) and RNA sequencing (RNA-seq) suggested that NbALKBH1L may serve as a central node in plant antiviral immunity, potentially linking metabolic processes with the regulation of viral infection. In summary, this study advances our understanding of plant m⁶A modifications in antiviral defense and provides valuable insights for future antiviral breeding strategies. Full article

Human DNA dioxygenase ABH2 is a key enzyme of the AlkB family of Fe(II)/α-ketoglutarate-dependent oxygenases, which is specialized in removing alkyl groups from damaged DNA bases in the cell nucleus. At the same time, the occurrence of single-nucleotide polymorphisms (SNPs) in the human ABH2 gene can lead to amino acid substitutions that, in turn, may disrupt the normal functioning of the ABH2 enzyme. Currently, databases contain information about more than 2500 nucleotide substitutions in the ABH2 gene. Using a comprehensive bioinformatics approach, in this review, we analyzed over 200 non-synonymous ABH2 SNPs with eleven prediction programs to identify variants capable of negatively affecting its enzymatic activity. The combination of various programs with different evaluation algorithms and scoring approaches allows us to more reliably identify potentially deleterious amino acid substitutions. Moreover, the differences between the programs used allowed for comparison of their tendency to predict amino acid substitutions as deleterious. Structural analysis of the ABH2-substrate complex showed that selected functionally significant SNPs often affect the organization of the active site, reduce the efficiency of substrate binding, and/or disrupt the coordination of Fe²⁺ and α-ketoglutarate cofactors, leading to changes in catalytic efficiency. The data obtained from the conducted analysis suggest that naturally occurring polymorphisms in the ABH2 gene found in the human population may reduce the repair efficiency of DNA dioxygenase ABH2 and, consequently, modulate susceptibility to oncogenesis and influence the effectiveness of antitumor therapy for carriers of these SNPs. Full article

Next-generation sequencing (NGS) is instrumental for clinical decisions on molecularly targeted therapy (TT). In pediatric oncology, TT is a relatively rare choice administered chiefly on a tumor-agnostic basis. The investigation enrolled 304 pediatric patients with extracranial solid tumors that were diagnosed and treated in 2018–2023. Tumor DNA was sequenced using a customized QiaSeq panel (Qiagen, Hilden, Germany) of genes known to be relevant for pediatric solid tumors, including ALK, BRAF, BRCA1/2, EGFR, FGFR1, KIT, MAP2K1/2, NF1, PDGFRA/B, PIK3CA, PTEN, PTPN11, RAS family genes, etc. The assay allowed detection of nucleotide substitutions and small insertions/deletions, as well as gene copy number alterations. TT sensitivity predictors were identified in 120/304 cases (39.5%): Tier II in 83 patients, Tier IB in 32 patients (almost always ALK in neuroblastoma, n = 31) and Tier IA in 5 patients: BRAF p.V600E (n = 3) and NF1 aberrations (n = 2). TT commenced in 21/304 cases (6.9%), often first-line or as a first relapse therapy (14/21 cases), combined with chemotherapy (TT-CT) in 13 cases. The median of TT duration was 10.9 (range 0.8–43.5) months for single-mode and 12.3 (0.3–61.5) months for TT-CT. Clinical benefit rate was achieved in 14/21 patients (66.7%). At the time of writing, nine patients (42.8%) have no progression and are still on treatment for 30.4 months (range 10.3–40.5) after the start of TT. The median time to the best response to TT was 6 (range 0.8–12.3) months. The tolerance was generally good: the therapy was discontinued for toxicity in only one case. The study provides a TT-focused prospective analysis still rare in pediatric oncology. The outcomes indicate satisfactory tolerance and promising efficacy of TT, prompting an update of current treatment standards for several pediatric cancers. Full article

Brain arteriovenous malformations (bAVMs) consist of a tangled nidus of abnormal dilated vessels characterized by direct connections between arteries and veins that lack an intervening capillary bed, creating a high-to-low flow pressure system that is predisposed to spontaneous hemorrhage with significant associated neurologic morbidity and mortality. Treatment options for bAVMs include the following: surgical resection, intravascular embolization to obliterate blood flow through the AVM, and radiosurgery. Understanding the molecular mechanisms of bAVM formation and factors that predispose it to hemorrhage can lead to novel treatments that can improve the prognosis for patients. This review summarizes emerging insights into the complex and dynamic molecular mechanisms of bAVMs. Dysregulation in key VEGF, TGF-β/BMP9/10–ENG–ALK1–SMAD4, Notch, and MAPK/ERK signaling pathways drive abnormal angiogenesis in both syndromic and sporadic forms, with KRAS/BRAF/MAPK21 mutations specifically linked to the latter. Advances in bAVM-induced animal models have corroborated many of the genetic profiles found in humans, and they continue to provide novel insights into bAVM mechanisms. Collectively, these mechanistic findings are guiding translational advances, with targeted therapies and liquid biopsy approaches emerging as avenues for precision treatment and improved patient outcomes. Full article

Background: Seminoma is a malignant germ cell tumor that most commonly involves the testicles but may involve the mediastinum, the retroperitoneum, and other extra-gonadal sites as well. This study aims to investigate the somatic genomic landscape of seminoma. Methods: Data for a retrospective observational analysis of seminoma was acquired from the American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) with clinical and genomic data from 2017 and beyond. Using the R and R Studio software (R 4.5.0), analyses for common somatic mutations and copy number alterations were run with a statistical significance of p < 0.05. Results: The most mutated genes included KIT (22.6%), KRAS (17.1%), and MTOR (5.1%), with significant copy number alterations in CDKN1B (17.2%), KRAS (14.7%), CCND2 (10.3%), and H3F3C (9.8%). These suggest involvement within the KIT/RAS/MAPK and PI3K/AKT/mTOR (PAM) pathways for seminoma development. A novel finding within comparative evaluation of PMS1 and AMER1 mutations were found in Black individuals. Additionally, our findings were consistent with a lower testicular cancer rate among individuals with African ancestry than European ancestry. BRD4 mutations were found only in metastatic samples while KMT2C, STAG2, ALK, AXL, and EGFR were only found in primary samples, suggesting a possible association. Conclusions: This study provided a comprehensive molecular and genetic profiling of seminoma including key genetic alterations, affected pathways, and potential therapeutic strategies. Moreover, overlap between pathways and gene mutations provides the potential for alternative treatment options for seminoma via multiple pathways. Full article

Improving the quality of oil-contaminated soils remains a critical challenge, and bioaugmentation using allochthonous bacteria offers promising perspectives. This study proposes a framework for exogenous bioaugmentation using a bacterial consortium, composed of strains from diverse climates, immobilized in alginate beads and combined with calcium peroxide as an oxygen-releasing compound. Two conditions were tested: freshly prepared beads (BA) and lyophilized beads (LA). Their performance was compared to natural attenuation (NA) and to landfarming coupled with bioaugmentation using a free autochthonous consortium. Hydrocarbon degradation was assessed through total petroleum hydrocarbon (TPH) and alkane depletion (GC-MS), microbial community dynamics (amplicon sequencing), and abundance of the alkB gene (qPCR). In three months, the BA treatment achieved a 44% TPH reduction, outperforming LA (34%) and NA (10% less than BA). However, LA induced a marked increase in alkB gene copies and microbial biomass at the end of the experiment, suggesting greater long-term potential. Dominant genera varied across treatments: Rhodococcus in NA, Gordonia in BA, and Pseudomonas in LA. In parallel, the autochthonous consortium achieved up to 80% oil degradation. This study demonstrates the viability of lyophilized microbial consortia in scalable, ready-to-use formulations and provides an operational methodology for exogenous bioaugmentation as a tool for the remediation of hydrocarbon-contaminated soils. Full article