Search Results (1,740)

Background/Objectives: Triple-negative breast cancer (TNBC) is enriched for germline pathogenic variants in BRCA1/2 and other DNA repair genes, but the additional value of extended germline profiling beyond BRCA1/2 remains insufficiently characterized in Russian patients. We aimed to characterize germline pathogenic/likely pathogenic variants (GPV/LPVs) and variants of uncertain significance (VUSes) in cancer predisposition and homologous recombination repair (HRR)-related genes in Russian TNBC patients and to assess the additional yield of extended germline profiling beyond BRCA1/2. Methods: We retrospectively analyzed germline DNA from 275 patients with histologically confirmed TNBC. Exome sequencing was performed for 204 patients and focused HRR-panel testing for 71 patients on the MGISEQ-G400 platform. Results: Overall, 114 patients (41.5%) harbored at least one germline GPV/LPV. BRCA1/2 GPV/LPVs were detected in 53 patients (19.3%), with BRCA1 predominating over BRCA2 (48 vs. 5 carriers) and the recurrent BRCA1 c.5329dup variant accounting for 23 cases. In the exome subset, 79 of 204 patients (38.7%) carried a GPV/LPV in Groups 1–3, including 48 (23.5%) with BC-related GPV/LPVs; non-BRCA Group 1 genes contributed seven additional carriers beyond BRCA1/2-only analysis. The expanded HRR set identified 52 GPV/LPV carriers (25.5%) versus 45 (22.1%) in the reference HRR panel, while the common HRR gene set identified 68 carriers (24.7%) in the full cohort. In addition, 183 unique VUSes were found in Groups 1–3 in the exome subset, affecting 128 patients (62.7%). Conclusions: Russian TNBC patients show a substantial germline GPV/LPV burden dominated by BRCA1/2 alterations and the recurrent BRCA1 c.5329dup founder variant. Extended germline profiling identified additional non-BRCA and HRR-related findings beyond BRCA1/2, but the incremental yield was moderate and accompanied by a considerable VUS burden. Broader germline testing may therefore support hereditary risk assessment and exploratory HRR-focused stratification, but non-BRCA HRR findings should not be considered sufficient for therapy selection without additional tumor-level or clinical evidence. Full article

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies because of aggressive tumor biology, pervasive therapeutic resistance, rapid adaptive reprogramming, and a profoundly immunosuppressive tumor microenvironment. This review summarizes recent advances in KRAS-targeted therapies, DNA damage response (DDR)-directed strategies, immune-redirection platforms, and tumor microenvironment modulation. Methods: We conducted a narrative review of peer-reviewed publications, clinical trial reports, trial registries, and selected conference data addressing emerging therapeutic strategies for PDAC. Results: KRAS-targeted therapies, including KRAS G12D-selective and multi-selective RAS(ON) inhibitors, have demonstrated substantial preclinical and emerging clinical activity while revealing diverse mechanisms of adaptive resistance. DDR-directed approaches are expanding beyond BRCA-mutated disease toward functional homologous recombination deficiency, replication stress, and synthetic lethality. In parallel, bispecific antibodies, T-cell engagers, and CAR-T-cell therapies have generated preliminary evidence of antitumor activity, although stromal exclusion, antigen heterogeneity, and immune suppression remain major barriers. These advances indicate that therapeutic resistance in PDAC is a dynamic process involving interconnected oncogenic, genomic, stromal, metabolic, and immune mechanisms. Conclusions: Future progress will require biologically informed treatment frameworks integrating complementary therapeutic modalities according to baseline tumor biology and treatment-induced adaptive states, supported by longitudinal biomarkers and rational clinical trial design. Full article

Vaccination remains the primary strategy for poliomyelitis prevention. The D-antigen of poliovirus is a critical component of inactivated polio vaccines, as it induces the production of neutralizing antibodies and provides protective immunity. Therefore, the development of quantitative immunoassays for monitoring D-antigen content during vaccine production is an important task. In this study, we generated recombinant camelid single-domain antibodies (VHHs) specific for the D-antigen of Sabin poliovirus type 1 and evaluated their antigen specificity. The obtained VHH antibodies demonstrated strong binding to the native D-antigen of Sabin type 1 poliovirus. Furthermore, the use of clone S1-C7 as a capture antibody in combination with Sabin type 1-specific polyclonal antibodies for detection revealed differential recognition of the vaccine-derived Sabin type 1 and homologous wild-type Mahoney strains. Notably, such discrimination was not observed when polyclonal antibodies were used alone, indicating that incorporation of VHH S1-C7 into the assay enhances strain-specific antigen recognition. In a neutralization assay, clone S1-C7 exhibited in vitro neutralizing activity against Sabin type 1 poliovirus. One clone, S1-D9, demonstrated cross-reactivity with all three poliovirus serotypes, suggesting recognition of a conserved epitope in the capsid and potential utility as a universal detection antibody. The generated VHH antibodies represent promising analytical tools for poliovirus antigen characterization. Together with S1-C7, they enable the discrimination of both D- and C-antigen forms as well as vaccine-derived and wild-type strains. Full article

Serotonin N-acetyltransferase (SNAT) is pivotal to melatonin biosynthesis, catalyzing either serotonin into N-acetylserotonin or 5-methoxytryptamine (5-MT) into melatonin. Many SNAT genes have been cloned from a wide range of organisms, including animals and plants, but none has been reported in the model streptophyte green alga Chara braunii. Here, we found one archaeal CbSNAT homologue in the C. braunii genome, which showed 28% and 27% amino acid homology with human Naa50 and rice SNAT3, respectively. The CbSNAT gene, encoding a 172-amino acid protein, was expressed and purified in Escherichia coli. The recombinant CbSNAT protein exhibited SNAT enzyme activity toward serotonin (K_m = 293 μM) and 5-MT (K_m = 28 μM), and was located in the cytoplasm of tobacco cells, similar to other archaeal SNAT homolog proteins. To assess whether CbSNAT was functionally coupled to melatonin biosynthesis, CbSNAT was overexpressed in rice. Transgenic CbSNAT-overexpressing rice seedlings showed enhanced melatonin synthesis and resistance to both cadmium and the herbicide butafenacil. The cadmium resistance was due to the increased expression of chaperone genes such as BIP3, BIP4, and BIP5, whereas the butafenacil resistance resulted from increased expression of protoporphyrinogen oxidase 1, a target gene of butafenacil, via the transcriptional regulatory effects of melatonin. The discovery of a CbSNAT gene in C. braunii opens a new avenue for its use as a genetic resource in the development of crops exhibiting stress resistance to toxic compounds found in modern agriculture. Full article

Fanconi anemia (FA) is a rare disease with a deficient homologous recombination DNA repair pathway and high sensitivity to mitomycin C (MMC). In FA cells, hydroxyurea (HU), when applied in the G2 phase of the cell cycle, exacerbates the chromosomal aberrations (CAs) induced by MMC. Here, we study how exposure to HU in the G2 phase results in an increased CAs frequency in FA cells with or without prior treatment with MMC. We performed chromosome aberration analysis, flow cytometry, and mRNA and protein expression in lymphoblastoid cell lines. We found that HU alone induces post-replicative DNA damage in the form of DNA double-strand breaks (DSBs) in both wild-type and FA cells and a similar increase in the activation of DSBs marker ɣH2AX. HU potentiates the amount of CAs only in MMC-treated FA cells by multiple mechanisms, including (1) hindering the ɣH2AX signal, (2) impairing the translocation of ribonucleotide reductase (RNR) into the cell nucleus, and (3) promoting the activity of WIP1 phosphatase. Concomitantly, increased levels of cell death were observed in FA cell cultures. HU induces DNA damage and potentiates pre-existent damage in FA cells by preventing the translocation of the RNR component p53R2 into the nucleus and activating checkpoint recovery, thus allowing the survival of a proportion of FA cells that have adapted to DNA damage. Full article

Background/Objectives: High-grade serous ovarian cancer (HGSOC) shows variable response to platinum-based neoadjuvant chemotherapy (NACT), with outcomes strongly linked to upfront treatment sensitivity. We evaluated whether oxidative DNA damage in pathologic samples is associated with improved clinical outcomes and reflects tumor–immune interactions. Methods: We analyzed matched pre- and post-NACT tumors from patients with stage III–IV HGSOC using Repair Assisted Damage Detection (RADD) to quantify total and oxidative DNA lesions (oxRADD). Gene expression profiling was performed on a subset of tumors using the NanoString PanCancer I/O 360. Associations with homologous recombination status, platinum sensitivity, recurrence, and survival were assessed. Results: Higher pre-NACT oxidative DNA damage was observed in tumors from patients who later recurred. Among recurrent tumors, elevated oxidative lesions were associated with improved overall survival (61.8 vs. 35.0 months; HR = 0.42, p = 0.037). Oxidative damage predicted recurrence (AUC = 0.71), supporting its utility in risk stratification. Tumors with serious oxidative damage showed reduced IDO1 and TGFβ signaling signatures, along with decreased B cell- and T cell-associated TIGIT signatures after NACT. Conclusions: These findings identify oxidative DNA damage as a potential pretreatment biomarker associated with recurrence, survival, and tumor–immune state, supporting its potential to impact therapeutic decision-making in HGSOC. Full article

Poly(ADP-ribose) polymerase inhibitors (PARPis) have demonstrated remarkable efficacy in tumors carrying BRCA1/2 pathogenic variants (PVs) through the mechanism of synthetic lethality. PVs in other homologous recombination (HR) genes may also impair homologous recombination repair and confer sensitivity to PARPis; however, their predictive value remains uncertain and appears to vary according to the affected gene and tumor type. We review and critically discuss the current evidence regarding the predictive value of non-BRCA HR gene pathogenic variants as biomarkers of PARPi sensitivity across ovarian, breast, prostate, and pancreatic cancers. A narrative review was conducted between October 2023 and December 2025, first identifying pivotal clinical trials of PARP inhibitors across ovarian, breast, prostate, and pancreatic cancers, followed by a targeted search of PubMed, Embase, Web of Science, and Google Scholar for relevant preclinical and clinical studies. Seventeen clinical studies and multiple preclinical reports were analyzed regarding genomic frequency, HRD association, and treatment response. Preclinical studies consistently demonstrated increased PARPi sensitivity in models with alterations in several non-BRCA HR genes. Clinical evidence, however, was heterogeneous. PALB2 demonstrated the strongest and most consistent association with PARPi benefit across tumor types, while RAD51C and RAD51D also showed clinically meaningful activity, particularly in ovarian cancer. In contrast, evidence supporting PARPi sensitivity in tumors harboring ATM, CHEK2, CDK12, and several other HR gene alterations remained limited or inconsistent. Differences in gene function, biallelic inactivation, variant type, and current limitations of HRD companion diagnostic assays likely contribute to the observed variability in clinical response. Non-BRCA HR gene alterations represent promising predictive biomarkers for PARPi therapy but should not be considered a homogeneous group. Future biomarker-driven studies integrating comprehensive genomic profiling and functional assessment of homologous recombination deficiency are needed to refine patient selection and optimize the clinical application of PARPis beyond BRCA1/2-associated cancers. Full article

Extracellular traps (ETs) are a novel host defense mechanism used to immobilize and eliminate invading microorganisms, and their formation depends on the recognition of foreign pathogens by membrane receptors. Previous studies have demonstrated that Vibrio splendidus flagellin can induce the release of ETs in coelomocytes of the sea cucumber Apostichopus japonicus, yet the underlying regulatory mechanism remains unclear. Here, we identify another Toll-like receptor (TLR) homolog, AjTLR2, in Apostichopus japonicus, which is composed of an extracellular LRR domain, a transmembrane domain, and an intracellular TIR domain. As a membrane receptor, AjTLR2 is upregulated upon infection with Vibrio splendidus AJ01, which is isolated from diseased Apostichopus japonicus. The extracellular LRR domain exhibits binding activity toward LPS, PGN, and MAN. In addition to these ligands, AjTLR2 recognizes flagellin C of AJ01 (AJ01-FliC), whereas other AjTLRs, such as AjToll and AjTLR3, do not. Further functional analysis reveals that knockdown of AjTLR2 results in a reduction in the typical weblike DNA structures of ETs, accompanied by a significant decrease in the expression of the ET-associated antimicrobial proteins H2A, H2B, and lysozyme. Furthermore, AjTLR2 knockdown similarly inhibits ET formation induced by recombinant AJ01-FliC protein. Mechanistically, the Apostichopus japonicus proto-oncogene tyrosine-protein kinase Src homolog (AjSRC), previously identified in our laboratory, is a downstream signaling molecule of AjTLR2 and is recruited via the TIR domain of AjTLR2. Knockdown of AjSRC also suppresses AJ01-FliC-induced ET formation. Collectively, our results indicate that the recruitment of AjSRC by AjTLR2 represents a potential regulatory pathway for AJ01-FliC induced ET generation. Full article

Glutaredoxins (GRXs) are small oxidoreductases involved in redox regulation, but the biochemical properties of plant-specific CC-type GRXs remain poorly understood, particularly in legumes. In a previous transcriptomic analysis, two CC-type glutaredoxins from Lotus japonicus, LjGRX460 and LjGRX569, were identified as differentially expressed during symbiosis with nitrogen-fixing rhizobia. Here, both proteins were produced recombinantly and characterized by sequence analysis, structural modelling and in vitro biochemical assays. Phylogenetic and sequence studies confirmed that both proteins belong to the plant-specific CC-type GRX class but differ in active site composition and overall sequence organization. Homology modelling and molecular dynamics simulations revealed distinct conformational properties, including differences in active site accessibility, electrostatic surface distribution and putative oxidation-dependent structural rearrangements. Comparative analyses with representative class I and II GRXs supported substantial structural divergence, suggesting functional specialization. Optimized expression and purification protocols yielded soluble recombinant proteins. Both LjGRX460 and LjGRX569 displayed a strong tendency to form soluble high molecular weight aggregates, similar to the class I control GRX. Enzymatic assays showed low oxidoreductase activity towards classical disulfide substrates compared with class I GRXs, while molecular docking suggested reduced affinity for bis(2-hydroxyethyl) disulfide (HEDS) and preferential interaction with L-cystine. These results indicate that LjGRX460 and LjGRX569 are unlikely to function as classical oxidoreductases and may instead perform specialized regulatory functions. Full article

BRCA1/2 alterations have emerged as clinically relevant biomarkers in prostate cancer because of their prognostic significance and predictive value for response to poly(ADP-ribose) polymerase inhibitors. As indications for molecular testing expand, histopathologists play a pivotal role in ensuring the quality and reliability of somatic BRCA testing. This narrative review provides a histopathologist-oriented overview of the principal pre-analytical, technical, and morphological issues influencing BRCA testing in PC, with emphasis on tissue selection, specimen processing, nucleic acid preservation, and genotype–phenotype correlations. The success of somatic BRCA testing depends on several pre-analytical variables, including fixation, storage time, tumor cellularity (generally ≥10–20% neoplastic cells for reliable NGS analysis), specimen type, and DNA quality. Bone metastasis specimens require special attention because decalcification procedures may compromise nucleic acid integrity and molecular testing performance. From a morphological perspective, BRCA-associated PCs, especially those harboring BRCA2 alterations, are characterized by adverse clinicopathological features, including a higher grade and stage at diagnosis. Although intraductal carcinoma of the prostate and cribriform architecture are associated with genomic instability and poor prognosis, their value as surrogate markers of BRCA1/2 alterations remains uncertain. Histopathologists play a central role in optimizing BRCA testing through appropriate specimen selection, tissue handling, and multidisciplinary collaboration, thereby supporting precision medicine in prostate cancer. Full article

Triple-negative breast cancer (TNBC) lacking androgen receptor (AR) expression defines quadruple-negative breast cancer (QNBC), which is characterized by younger age at diagnosis, high Ki-67 index, and high genomic instability, however a comprehensive description of the genomic characteristics remains poorly defined. A total of 54 TNBC cases were categorized as TNBC with 100% AR expression (TNBC AR-100%) or QNBC, TNBC with 0% AR expression (TNBC AR-0%). Clinical, molecular, and genomic parameters, specifically pathogenic/likely pathogenic (P/LP) variants in homologous recombination repair (HRR) and cancer-related pathways were measured and analyzed. The QNBC cohort exhibited a high homologous recombination deficiency (HRD) score and a greater overall incidence of copy number variants (CNVs). QNBC harbored a higher mutation rate in TP53 and MYC signaling pathway than TNBC AR-100% tumors. P/LP variants corresponding to the HRR, PI3K/AKT, and RTK/RAS pathways were exclusively identified in QNBC. These results suggest that, at both molecular and genomic levels, the two groups are distinct, holding QNBC tumors more aggressive characteristics, genomic instability, and particular impairments in HRR and cancer-related pathways. In terms of actionability, these differences could potentially be leveraged through different combinations of therapies. Full article

Cinnamoyl coenzyme A reductase (CCR) is the first rate-limiting enzyme in the monolignol-specific pathway and plays a pivotal role in lignin biosynthesis. However, CCR genes in Pinus yunnanensis remain uncharacterized, and their undefined substrate specificity further impedes mechanistic insights into lignin regulation while restricting strategies for wood property optimization. Using conserved domain and homology analysis, with a focus on the characteristic NAD(P)-binding motif (KNWYCYGK), we identified 12 CCR family members from the transcriptome data of P. yunnanensis. Phylogenetic analysis clustered the PyCCRs into two distinct clades: PyCCR1~6 fall into the CCR clade, while the remaining members form a CCR-like clade. In this study, twelve ORF regions of the P. yunnanensis CCR genes were cloned, and nine purified recombinant PyCCR proteins were obtained through prokaryotic expression. In vitro enzymatic assays demonstrated that PyCCR1, PyCCR2, PyCCR5, and PyCCR6 catalyzed the conversion of p-coumaroyl-CoA, feruloyl-CoA, and sinapoyl-CoA to p-coumaraldehyde, coniferaldehyde, and sinapaldehyde, respectively. Molecular docking of PyCCR1 to 6 with three substrates identified substrate-binding pocket domains. Within these domains, hydrogen bonds formed between ligands and residues in the R(X)5K motif of PyCCR1 to 6, whereas PyCCRL7 to 12 lacked the complete motif. RT-qPCR analysis showed tissue-specific expression patterns of the 12 genes across buds, stems, leaves, roots, and fruits. Collectively, these findings suggest that the presence of a complete R(X)5K motif may play a crucial role in maintaining the catalytic activity of PyCCRs. Our present study established a mechanistic foundation for elucidating lignin biosynthesis regulation in P. yunnanensis and offer genetic resources for improvement programs. Full article

Fusarium head blight (FHB) caused by Fusarium graminearum leads to huge yield losses and mycotoxin contamination in wheat globally. Paenibacillus polymyxa with strong antagonistic activity was preliminarily identified. To clarify the key antifungal component, an extracellular protein was purified via ammonium sulfate precipitation, DEAE-52 anion-exchange and Sephadex G-75 gel filtration chromatography. SDS-PAGE showed a single band at 76 kDa. liquid chromatography–tandem mass spectrometry (LC-MS/MS) analysis confirmed this protein belongs to glycosyl hydrolase family with 86% sequence coverage. Biochemical characterization showed that the crude protein was stable at 40–90 °C and pH 3.0–9.0, sensitive to proteinase K, trypsin and neutral protease. The purified 76 kDa protein exhibited antifungal activity against F. graminearum. The gene encoding this protein was cloned and expressed in Escherichia coli. The renatured recombinant protein p76kd showed comparable antifungal activity to the native protein. This study purified and characterized a 76 kDa protein annotated as a glycosyl hydrolase via LC-MS/MS peptide matching; its antifungal function is presumed to originate from the conserved glycosyl hydrolase domain according to existing homologous research, which is distinct from previously reported lipopeptides or uncharacterized complexes. This protein provides a promising candidate for the biocontrol of FHB and related fungal diseases in cereal crops. Full article

N-acetylornithine aminotransferase (AcOAT) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that catalyzes a key transamination step in arginine biosynthesis. In cyanobacteria, arginine metabolism is closely associated with nitrogen assimilation and storage, yet biochemical information on cyanobacterial AcOATs remains limited. In this study, the AcOAT encoded by the cce_3094 gene from Crocosphaera subtropica ATCC 51142 (CsAcOAT) was cloned, heterologously expressed, purified, and systematically characterized. Recombinant CsAcOAT was obtained as a soluble protein with an apparent molecular mass of approximately 43 kDa. Steady-state kinetic analysis showed that CsAcOAT catalyzed transamination between N-acetylornithine (AcOrn) and α-ketoglutarate (α-KG), with apparent K_M values of 0.17 ± 0.03 mM for AcOrn and 0.020 ± 0.003 mM for α-KG, indicating a higher affinity for α-KG. The enzyme exhibited optimal activity at pH 8.5 and 30 °C, retained relatively high activity over a broad temperature range of 0–50 °C, and was activated by Zn²⁺ and Co²⁺ but inhibited by Ni²⁺. Structural analysis based on homology modeling, molecular docking, and molecular dynamics simulations suggested a conserved PLP-dependent aminotransferase fold and a stable binding mode for the PLP-AcOrn complex in the active-site pocket. Site-directed mutagenesis further demonstrated that Gly114, Asp239, Lys268, and Thr296 are indispensable for catalytic activity, whereas Ser113, Ala115, and Gln242 make important contributions to catalytic turnover and cofactor-assisted catalysis. These results provide biochemical and structural characterization of CsAcOAT, expand current knowledge of cyanobacterial AcOATs, and offer a useful basis for future studies on arginine metabolism and nitrogen storage in diazotrophic cyanobacteria. Full article

Hippodamia variegata is a key natural enemy of various aphid pests in agricultural ecosystems, and its foraging and oviposition behaviors are strongly dependent on chemical signals from prey aphids and host plants. In this study, we functionally characterized the chemosensory protein HvarCSP8 to elucidate its potential role in mediating olfactory responses to aphid-induced plant volatiles. The expression profiles of HvarCSP8 were examined by quantitative real-time PCR (qRT-PCR) across developmental stages and sexes; the recombinant HvarCSP8 was purified; the potential ligands specificity and affinity were studied using fluorescence-based competitive binding assays; and structural characteristics were obtained via homology modeling and molecular docking simulations. The results demonstrated that HvarCSP8 exhibits pronounced sex- and tissue-specific expression, with significant upregulation in adult antennae, particularly in females. The purified protein exhibited selective binding affinity to multiple aphid-induced plant volatiles, such as α-Farnesene, α-Terpinene, and 2-Ethyl-1-hexanol. Molecular docking revealed that HvarCSP8 interacts with these ligands through multiple amino acid binding sites, among which hydrophobic residues such as VAL29, LEU61, ILE64, and LEU65 frequently occur in binding sites for multiple ligands, suggesting that these residues play important roles in binding. These findings indicate that HvarCSP8 may be involved in the olfactory detection of aphid-induced plant volatiles in H. variegata, providing a candidate target for the development of behavior-based biological control strategies against aphid pests. Full article