Current Issues in Molecular Biology最新文献

Small for gestational age (SGA) is often used as a proxy for fetal growth restriction (FGR), yet not all FGR fetuses are born SGA. SGA individuals, particularly those with catch-up growth, have increased cardiometabolic risk. We therefore studied infants and children from pregnancies at increased FGR risk, irrespective of birthweight. Two cohorts enriched for suboptimal fetal growth were recruited: an infant cohort (N = 80) to examine relationships between fetal weight trajectory and postnatal growth and a cohort of children aged 3-7 years (N = 80), 31 of whom provided blood samples for transcriptome and metabolome analyses. In infants, fetal weight trajectory correlated negatively with BMI change from birth to three months (R = -0.40, p = 0.004) and six months (R = -0.38, p = 0.012), as well as with skinfold, abdominal and arm circumferences. In children, supervised transcriptome analysis highlighted a pathway including ARG1. Unsupervised analysis had previously identified two SBP-differentiated groups; novel findings include LATS1, implicated in SBP GWAS, as the most significant gene, and GHRL, suggesting appetite-regulation mechanisms underlie SBP differences. Ornithine, a differentially expressed metabolite between fetal and childhood weight trajectory quartiles, together with ARG1, suggested involvement of the arginine-nitric oxide pathway. Early life indicators of cardiometabolic risk have been elucidated, highlighting pathways to inform future prevention.

Renal cell carcinoma (RCC) is a common and deadly urological cancer, for which there are no robust prognostic biomarkers or personalized treatment strategies. Paraptosis, a distinct form of regulated cell death marked by cytoplasmic vacuolization, is being increasingly recognized for its roles in tumorigenesis and therapy responses, yet its functional implications in RCC remain poorly defined. Transcriptomic profiles and corresponding clinical metadata from the TCGA-KIRC and GSE33371 datasets were systematically analyzed to characterize the paraptosis-related gene (PaRG) expression profile in renal cell carcinoma (RCC). Patients were categorized into two subtypes via consensus clustering, 574 overlapping differentially expressed genes (DEGs) were identified, and a four-gene (COL7A1, RNASE2, SLC10A2, and APOLD1) prognostic signature was constructed using LASSO and multivariate Cox regression. We analyzed the signature's associations with tumor microenvironment (TME) features, cancer stem cell (CSC) indices, and tumor mutation burden (TMB), and validated the expression of the signature genes in RCC cell lines via qRT-PCR and Western blot. The four-gene signature showed robust prognostic performance (1-, 3-, and 5-year AUC: 0.751, 0.735, and 0.733 in the total cohort; 0.735, 0.731, and 0.767 in the training cohort), with high-risk patients having significantly poorer overall survival than the low-risk group. The low-risk group exhibited higher Stromal, Immune, and ESTIMATE scores (enriched immune/stromal infiltration), while the high-risk group had elevated CSC content and TMB, and the signature correlated with differential sensitivity to multiple chemotherapeutics. Both qRT-PCR and Western blot confirmed upregulation of COL7A1 and RNASE2 and downregulation of SLC10A2 and APOLD1 in RCC cell lines. Our study establishes a paraptosis-based two-subtype classification and four-gene prognostic signature for RCC that can reliably predicting patient survival, delineate TME characteristics, and guide personalized therapy, with COL7A1 emerging as a potential therapeutic target for advancing our understanding of paraptosis in RCC pathogenesis and optimizing treatment.

Paired box (PAX) genes encode a family of nine transcription factors that function as master regulators of embryogenesis, organogenesis, and lineage specification. Their tightly regulated spatial and temporal expression is essential for the development of multiple organ systems, including the central nervous system, eyes, kidneys, immune system, musculoskeletal system, and endocrine organs. Germline mutations of PAX genes result in a broad and often pleiotropic spectrum of human disease, reflecting the developmental programs governed by each family member. Pathogenic variants in PAX genes underlie diverse congenital disorders such as aniridia (PAX6), renal coloboma syndrome (PAX2), otofaciocervical syndrome with immunodeficiency (PAX1), Waardenburg syndrome (PAX3), maturity-onset diabetes of the young (PAX4), and tooth agenesis (PAX9). These conditions frequently demonstrate variable expressivity, incomplete penetrance, and overlapping phenotypes, which make it challenging to be clinically recognized. Beyond embryogenesis and embryologic development, emerging evidence indicates that several PAX proteins remain active in postnatal tissue maintenance, adult stem cell regulation, immune function, and regenerative responses (particularly PAX7 in skeletal muscle satellite cells and PAX5 in B-cell homeostasis), further expanding their clinical relevance. This review provides a synopsis of the major, clinically relevant, germline PAX gene mutations, emphasizing genotype-phenotype correlations, developmental mechanisms, and disease classification across the organ systems. By integrating molecular genetics with human pathology, we highlight the diagnostic implications of PAX genes as central determinants of congenital disease and provide a framework for understanding how alterations in the developmental transcriptional networks translate into human pathology.

Background/Objectives: Cervical cancer is a prominent source of morbidity and mortality among women, particularly in low- and middle-income nations. Neutrophil Gelatinase-Associated Lipocalin (NGAL), a glycoprotein involved in cancer-related activities, has been proposed as a biomarker; however, its involvement in cervical cancer remains unknown. The study aim is to evaluate the prognostic significance of serum NGAL levels in cervical cancer patients in relation to International Federation of Gynecology and Obstetrics (FIGO) stage, operability, and HPV subtype distribution before and after treatment. Methods: The study involved 130 women, 100 with histologically proven cervical cancer and 30 healthy controls. The serum NGAL levels were determined before and after treatment using an ELISA test. HPV genotyping was carried out using real-time PCR on 21 high- and low-risk subtypes. Results: NGAL levels increased marginally during therapy (from 134 to 144 ng/mL; p = 0.28), but the rise was significant in inoperable patients (p = 0.02) and increased with advanced FIGO stage, although this did not reach statistical significance (p = 0.07). HPV 16 was the most common subtype (26.0%), while women aged 51-60 had the highest overall HPV positive rate (72.7%). There was no significant association between NGAL levels and HPV subtypes (p = 0.17). Conclusion: NGAL does not appear to be an accurate short-term indicator of therapy response. However, increased levels in advanced-stage and inoperable instances indicate prognostic significance. NGAL most likely represents tumor-associated inflammation rather than HPV subtype. These findings support its possible inclusion in future biomarker panels, subject to validation in bigger investigations. Persistent HPV infection in midlife women highlights the significance of ongoing screening.

Recent advances in molecular genetics, nucleic acid synthesis, and bioinformatics have provided novel opportunities for plants' protection against insect pests. Currently, both DNA and RNA serve as active insecticidal ingredients, transcending their traditional role as carriers of genetic information. This novel activity is achieved through two fundamentally distinct mechanisms. The first one is DNA containment (DNAc), employing oligonucleotide insecticides based on contact unmodified antisense DNA biotechnology (CUADb), also known as 'genetic zipper' technology. The second one is RNA interference (RNAi), employing RNA biocontrols based on double-stranded RNA (dsRNA) technology. The investigation of the molecular mechanism underlying the antisense activity of nucleic acids emerged in the early 1960s. While the antisense effects of RNA in gene silencing through interference (RNAi) was documented in the late 1990s as antiviral immune responses in nematodes, the CUADb antisense approach initially emerged as a powerful strategy for pest control against lepidopterans in 2008. The CUADb approach relies on disrupting rRNA biogenesis and ribosome production, while RNAi shows the best results in mRNA degradation and no efficient result is known for rRNA. The efficacy of these approaches appears to be species dependent. For example, CUADb demonstrates optimal activity against Sternorrhyncha (e.g., aphids, mealybugs, psyllids, and scale insects), thrips, and mites. In turn, the RNAi strategy shows a strong insecticidal potential against beetles from the Tenebrionidae and Chrysomelidae families. Here, we will review the differences between the two technologies, their mechanisms of action and the current challenges facing their adoption.

The recognition of microRNAs as components of animal-source foods (ASFs) with epigenetic characteristics and regulation has spurred research in an interesting direction, particularly in understanding their microRNAs (miRNAs) fraction. Thus, a constant supply of them through food intake, with equally conserved targets, may facilitate their accumulation in tissues rich in their targets. Here, we consider the potentially dominant miRNAs in animal-source foods (ASFs) documented in the literature, identified through a frequency-weighted ordinal recurrence approach. let-7d-5p, miR-101-3p, and miR-133b consistently showed dominant rankings in a product-specific manner in lean meat. In meat fat, let-7i-5p, miR-30c-5p, and miR-23a-3p were highly ranked. Among various types of meat offal, miR-145-5p, miR-92-5p, and miR-24-3p emerged as the predominant miRNAs. Similarly, in dairy products, miR-200a-3p, miR-200c-3p, miR-223-3p, miR-25-3p, miR-29a-3p, and miR-29b-3p were recurrently dominant, whereas miR-17-5p, miR-184, miR-30e-5p, and miR-92b-3p showed a comparable prevalence in seafood. Even though bioinformatic approaches suggest miRNAs from raw ASFs showed major enrichment of processes and pathways culminating in epithelial barrier integrity modulation, such putative functions tend to be equally enriched by predicted targets of the miRNAs in processed products. Product-specific highly ranked miRNAs from food categories stipulate possible preferential enrichment in contexts of cell-cell adhesion, cytoskeletal dynamics, and inflammatory control by meat (lean, fat, offal), immune homeostasis by dairy, and neural signalling by seafood, providing hypotheses for future functional studies. However, a limited understanding of their stability during gastrointestinal transit may present a more immediate limitation to their potential translational applicability.

The growing prevalence of antibiotic-resistant bacterial infections poses a serious burden on healthcare systems worldwide. Endolysins are promising candidates for a new type of antibiotic due to their strong bacteriolytic activity. However, important limitations, including reduced activity and short persistence in the bloodstream, must still be addressed. We evaluated the key physicochemical and biological factors limiting the activity and stability of the endolysins Cpl-1 and Pal in blood. The analysis included ionic composition and strength, pH, bystander proteins, physiological temperature, and proteolytic activity. Our results indicate that the aforementioned factors significantly affect Cpl-1 and Pal, suggesting that physiological conditions in human circulation markedly restrict the anti-bacterial potential of endolysins. To overcome these limitations, we designed a set of Cpl-1 and Pal variants with modified amino acid compositions aimed at increasing their resistance to such physiological constraints. One variant demonstrated improved performance in an ex vivo mouse model and lacked a cleavage site for blood proteases.

Silphium perfoliatum is a promising economic plant rich in bioactive secondary metabolites, yet the molecular regulation of phenylpropanoid biosynthesis across development remains unclear. To elucidate the regulatory networks underlying these metabolic processes, we integrated metabolomic and transcriptomic analyses across six developmental stages, from cotyledon to flowering. LC-MS/MS identified 1964 metabolites, with phenylpropanoids representing the largest class (601 compounds). Differential accumulation analysis showed pronounced temporal dynamics in phenylpropanoid levels, especially chlorogenic acid and its derivatives, with many compounds peaking at the flowering stage. In parallel, RNA-seq revealed 31,624 differentially expressed genes (DEGs). Functional enrichment highlighted phenylpropanoid and flavonoid biosynthetic pathways as major metabolic hubs. Correlation analysis indicated that PAL, 4CL, HCT, F3H, FLS, and F3'H expression was tightly coordinated with the accumulation of phenolic acids and flavonoids, suggesting these gene encoded enzymes may represent rate-limiting steps. Furthermore, weighted gene co-expression network analysis (WGCNA) identified a "blue" module strongly associated with phenylpropanoid accumulation and significantly enriched in pathway-related genes. Together, these results provide a comprehensive regulatory framework for phenylpropanoid biosynthesis in S. perfoliatum and offer valuable genetic targets for metabolic engineering and molecular breeding to enhance bioactive compound production.

Uncontrolled inflammation contributes to the development of neurodegenerative diseases (NDs) like Alzheimer's disease (AD). N-(p-Coumaroyl) serotonin (CS) has demonstrated a significant capacity to modulate hyper-inflammation. We explored whether CS could mitigate inflammatory responses in endotoxin-challenged microglial cells and sought to elucidate the specific molecular mechanisms governing these effects. ELISA, nitric oxide (NO) assays, Western blotting and immunocytochemistry were performed to study inflammatory responses and related signal transduction mechanisms. CS pretreatment effectively attenuated the inflammatory output in endotoxin-primed microglial models. This was evidenced by a significant reduction in key cytokines (such as IL-6, TNF-α, and MCP-1) and a concomitant decrease in the protein levels of iNOS and COX-2. These effects were mediated through the disruption of MAPK/NF-κB signaling cascades and the sequestration of NF-κB within the cytoplasm. Beyond its anti-inflammatory role, CS promoted the HO-1/NQO1 signaling pathway and interfered with the LPS-mediated TLR4/MyD88 cascade. Our collective evidence indicates that the modulation of microglia-mediated inflammation by CS is underpinned by the suppression of MAPK/NF-κB and the induction of antioxidant systems, suggesting that CS may have the potential to improve NDs.

Aril paleness (AP) is a new physiological disorder of pomegranate (Punica granatum L.) characterized by pale, dry and tasteless arils, while the peel remains healthy-looking. Its molecular basis is unknown. We used an integrated metabolomic and targeted gene expression approach on arils from four Iranian cultivars displaying no to severe AP symptoms. LC-MS profiling detected 617 reliable metabolites, with 266 metabolites consistently reduced in all symptomatic samples. Enrichment analysis revealed that arginine biosynthesis, glutathione metabolism and primary amino acid metabolism were the processes most strongly affected by AP. Protein interaction network analysis indicated that the arginine degradation pathway is the primary down-regulated module that interacts with the anthocyanin biosynthetic machinery, primarily through phenylalanine ammonia-lyase (PAL) hubs. Based on this network, seven genes representing both pathways were selected for targeted expression analysis. The qPCR analysis showed strong repression of arginase (PgADS, XM-031537872), aldehyde dehydrogenase (PgAL12A1, XM-031551051) and anthocyanin synthase (PgOXKF, KF841619.1) in the cultivar 'Torud' exhibiting severe AP symptoms compared with the symptom-free cultivar 'Damavand'. In contrast, phenylalanine ammonia-lyase (PgPAL1, KY094504.2) was unexpectedly induced 33-fold in the cultivar 'Torud', while the downstream anthocyanin-related UDP-glucosyltransferase (PgUGT, MK058491.1) remained unchanged. These findings suggest that the collapse of arginine metabolism, combined with the downstream blockage of anthocyanin biosynthesis, underlies AP. These findings provide the first molecular insights into the mechanisms underlying AP, offering a basis for breeding and post-harvest strategies aimed at enhancing pomegranate's AP tolerance.