Genes & genomics最新文献

{"title":"From bacterial to microbiome-derived vesicles: genome-informed identity, source qualification, and translational quality for skin-directed cosmetics.","authors":"Hyewon Pak, Taeyoon Park, Myoung Jin Ho","doi":"10.1007/s13258-026-01803-6","DOIUrl":"10.1007/s13258-026-01803-6","url":null,"abstract":"<p><p>Bacterial extracellular vesicles (BEVs) are increasingly proposed as materials for skin-directed cosmetics, yet rapid adoption of \"exosome\" terminology has outpaced clarity on their origin, composition, and manufacturing quality. This review argues that the value of BEVs depends on scientific discipline rather than marketing appeal, and that they are promising because they are biologically potent, not because they are intrinsically benign. We retain BEVs as the scientific umbrella term for vesicles released by bacteria and we propose the term microbiome-derived vesicles (MDVs) as the consumer-facing designation for qualified commensal BEVs - a surface term that avoids the difficulty of \"bacterial\" while its definition preserves bacterial provenance. We develop a three-axis framework for BEV identity that integrates compositional analysis, producer-strain genomics, and functional or safety profiling, and we position whole-genome sequencing (WGS) as decisive for source qualification and mechanistic interpretation but insufficient to prove the efficacy of a purified preparation. Building on this framework, we summarize isolation, purification, and analytical characterization requirements; interpret current skin-efficacy evidence in light of its methodological limits; and discuss formulation, cosmetic application, regulatory positioning, and manufacturable quality. We conclude that transparent bacterial provenance, reproducible preparation, and evidence proportionate to the claims made are prerequisites for evaluating commensal BEVs, described for skin applications as MDVs, as a scientifically defined cosmetic platform.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1247-1263"},"PeriodicalIF":2.0,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148919561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cisplatin-induced oxidative stress and ferroptosis-associated injury in retinal pigment epithelial cells attenuated by Toxoplasma gondii infection.","authors":"Xin-Cheng Wang, Yu-Sun Yun, In-Wook Choi, Wei Zhou, Jaemin Yuk, Guang-Ho Cha","doi":"10.1007/s13258-026-01806-3","DOIUrl":"https://doi.org/10.1007/s13258-026-01806-3","url":null,"abstract":"<p><strong>Background: </strong>Cisplatin causes oxidative and iron-dependent injury, but whether it induces ferroptosis-associated damage in retinal pigment epithelial cells and how Toxoplasma gondii (T. gondii) can modify this response remain unclear.</p><p><strong>Objective: </strong>This study investigated cisplatin-induced oxidative stress, apoptosis, ferroptosis-associated changes, and iron dysregulation in ARPE-19 cells and evaluated the effects of acute T. gondii infection.</p><p><strong>Methods: </strong>ARPE-19 cells were exposed to increasing concentrations of cisplatin for 24 h. Cell viability, oxidative stress, antioxidant capacity, apoptosis-related proteins, ferroptosis-defense molecules, and intracellular iron were assessed using biochemical assays, fluorescence staining, reverse-transcription polymerase chain reaction, and western blotting. Cells treated with 20 μM cisplatin were additionally infected with T. gondii at a multiplicity of infection of 5 or treated with ferrostatin-1, deferoxamine, or Z-VAD-FMK.</p><p><strong>Results: </strong>Cisplatin reduced cell viability in a concentration-dependent manner, with a half-maximal inhibitory concentration of 20.37 μM, and increased reactive oxygen species, malondialdehyde, cleaved caspase-3, and Bax while decreasing superoxide dismutase, glutathione, and Bcl-xL. It also reduced GPX4 and SLC7A11 protein expression and FSP1 mRNA levels, while increasing FTH1 and SLC11A2 protein expression and intracellular Fe²⁺ and total iron. T. gondii infection improved viability, reduced oxidative stress and cleaved caspase-3, restored antioxidant capacity and GPX4/SLC7A11 expression, and limited iron accumulation. Ferrostatin-1 and deferoxamine did not markedly suppress apoptotic proteins, whereas Z-VAD-FMK inhibited apoptotic signaling without restoring GPX4 or SLC7A11.</p><p><strong>Conclusions: </strong>Cisplatin induces concurrent oxidative stress, apoptosis, impairment of ferroptotic defense, and iron accumulation in ARPE-19 cells. Acute T. gondii infection attenuates these alterations by preserving redox balance, ferroptosis-defense pathways, and iron homeostasis.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149108456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete chloroplast-based analysis reveals the emergence of candidate new species and revised divergence time in Vincetoxicum.","authors":"Bumjin Jang, Byung Jun Jin, Yun Ji Park, Sumin Jeong, Yeseul Kim, Thi Tuyen Cu, Bo-Mi Nam, Inkyu Park","doi":"10.1007/s13258-026-01808-1","DOIUrl":"https://doi.org/10.1007/s13258-026-01808-1","url":null,"abstract":"<p><strong>Background: </strong>The taxonomic understanding of Vincetoxicum remains unresolved due to the lack of genetic information for Vincetoxicum inamoenum. Vincetoxicum sp. was recently identified as a morphologically distinct putative new species related to V. inamoenum, increasing the necessity for a more accurate reconstruction of the taxonomic history of Vincetoxicum based on molecular and phylogenetic evidence from V. inamoenum and V. sp.</p><p><strong>Objective: </strong>To assemble the complete chloroplast genomes of V. inamoenum and V. sp., elucidate their genetic divergence from 12 Vincetoxicum species, and determine the phylogenetic relationship and divergence time of the candidate new species of Vincetoxicum.</p><p><strong>Methods: </strong>Complete chloroplast genomes of V. inamoenum and V. sp. were assembled. Repeat sequences, nucleotide diversity, and selective pressure between V. inamoenum and V. sp. were analyzed using 12 previously reported Vincetoxicum species. Phylogenetic analysis was performed to determine the phylogenetic position and divergence time.</p><p><strong>Results: </strong>The chloroplast genomes of V. inamoenum and V. sp. were 160,787 and 160,849 base pairs long, respectively. Highly variable regions were identified between the two Vincetoxicum species (accD-psaI) and among the 14 Vincetoxicum species (trnH-psbA). The psaI, rpl33 and ycf2 genes exhibited positive selection. The phylogenetic tree showed that V. inamoenum and V. sp. formed a sister group and reconstructed the phylogenetic relationships within Vincetoxicum. Divergence time estimation indicated that V. inamoenum and V. sp. diverged approximately 1.182 million years ago (95% Highest Posterior Density: 0.181-2.751).</p><p><strong>Conclusions: </strong>Distinct genetic differences and divergence time indicate that V. sp. is a putative new species and provide a more comprehensive and accurate understanding of the genomic diversity and phylogenetic insight into Vincetoxicum.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149073959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"KIF18A knockdown enhances oxidative phosphorylation, suggesting a metabolic basis for antiviral activity against influenza A virus.","authors":"Hyeong-Rae Kim, Jiwon Kim, Dongju Han, In-Gu Lee, Younghyun Lim, Jeonghyeon Lee, Seungyeon Lee, So-Hee Hong, Young-Jin Seo","doi":"10.1007/s13258-026-01810-7","DOIUrl":"https://doi.org/10.1007/s13258-026-01810-7","url":null,"abstract":"<p><strong>Background: </strong>Influenza A virus (IAV) infection remains a major global health burden, underscoring the need to identify novel host-directed antiviral mechanisms. KIF18A, a kinesin-8 family motor protein, has emerged as a proviral host factor that supports IAV replication, and its pharmacological inhibition suppresses viral infection. However, the transcriptional and metabolic processes underlying this antiviral effect remain incompletely understood.</p><p><strong>Objective: </strong>We aimed to characterize the transcriptional consequences of KIF18A knockdown in IAV-infected cells and identify metabolic pathways potentially associated with its antiviral activity.</p><p><strong>Methods: </strong>KIF18A expression was silenced in HEK293T cells by transfection with KIF18A-targeting small interfering RNA. Transcriptomic profiling was performed by RNA sequencing, followed by differential expression and gene set enrichment analyses. Mitochondrial respiratory function was evaluated using the Seahorse XFp Mito Stress assay.</p><p><strong>Results: </strong>KIF18A knockdown induced extensive transcriptomic remodeling in IAV-infected cells without activating canonical antiviral gene programs. Gene set enrichment analysis of the MSigDB Hallmark collection identified oxidative phosphorylation as the second most significantly enriched pathway. This enrichment was evident in both IAV-infected and non-infected cells, indicating that oxidative phosphorylation upregulation is an intrinsic response to KIF18A depletion rather than a virus-specific effect. Among electron transport chain components, genes encoding Complex Ⅴ ATP synthase subunits exhibited the most consistent upregulation. Concordantly, Seahorse analysis showed significant increases in basal and ATP-linked respiration in siKIF18A cells, without a corresponding increase in proton leak.</p><p><strong>Conclusion: </strong>KIF18A knockdown intrinsically upregulates oxidative phosphorylation and enhances mitochondrial ATP-coupled respiration at both the transcriptional and functional levels, implicating metabolic reprogramming as a candidate mechanism contributing to KIF18A knockdown-mediated antiviral activity against IAV.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149074138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-nucleus RNA sequencing reveals excitatory and inhibitory neuronal subtype imbalance and its potential regulatory mechanisms in GM1 gangliosidosis.","authors":"Sichi Liu, Ting Xie, Yonglan Huang","doi":"10.1007/s13258-026-01804-5","DOIUrl":"https://doi.org/10.1007/s13258-026-01804-5","url":null,"abstract":"<p><strong>Background: </strong>GM1 gangliosidosis is a rare lysosomal storage disorder caused by biallelic mutations in GLB1, leading to progressive neurodegeneration. The cellular and molecular mechanisms, particularly at the neuronal subtype level, remain incompletely understood.</p><p><strong>Objective: </strong>The research employed single-nucleus transcription sequencing to explore neuropathological mechanisms associated with GM1 Gangliosidosis systematically.</p><p><strong>Methods: </strong>High-quality single-nucleus data obtained from GM1 gangliosidosis model mice and wild-type mice underwent comprehensive quality control and dimensionality reduction processing, and extensive clustering and annotation were performed. Subsequently, the neurons were re-annotated, and the differentiation trajectories of different subtypes of neurons were analyzed through temporal sequence modeling, as well as the key communication pathways between them and other cells, as well as the ligand pairs.</p><p><strong>Results: </strong>The main classes of neural cells (neurons, microglia, and astrocytes) could be recognized well. On targeting the neurons alone through focused approach, another round of secondary clustering followed by the labeling of subpopulations showed there are two subgroups within the populatio, excitatory and inhibitory neurons. The results of functional enrichment analysis indicate that the relatively enhanced functions in the GM1 group mainly involve processes such as lytic vacuole organization, ceramide and sphingolipid metabolism, and glycosphingolipid breakdown. The GO analysis of inhibitory neurons shows that processes such as cytoplasmic translation, oxidative phosphorylation, and ATP synthesis are relatively enhanced in the Wildtype group. Pseudo-time analysis further revealed the developmental trajectories of neuronal subpopulations on the pseudo-time axis and the dynamic changes in gene expression. The analysis of intercellular communication revealed that ExNs mainly communicate with OPCs through the Nrg3-Erbb4 pair, while Neutrophils mainly interact with InNs via the Nrg1-Erbb4 pair.</p><p><strong>Conclusion: </strong>This study, through a comprehensive analysis of single-nucleus sequencing data of GM1 gangliosidosis, has revealed the key cell subpopulations and their related functions in these diseases, providing a theoretical basis for the mechanism of disease occurrence and possible treatment strategies.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149038152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exome-wide screening discovers novel pathogenic variants in Vietnamese primary congenital glaucoma patients.","authors":"Thi Mai Anh Dao, Van Khanh Tran, Phuoc-Dung Nguyen, Ngoc Lan Nguyen, Quoc Tung Mai, Le Thi Phuong, Tran Thi Quynh Trang, Trong Van Pham, Hung M Vu, Thi Anh Van Bui, Thanh Van Ta, Thinh Huy Tran, Ji-Hwan Park, Minjae Kim, Huy Nguyen Van","doi":"10.1007/s13258-026-01805-4","DOIUrl":"https://doi.org/10.1007/s13258-026-01805-4","url":null,"abstract":"<p><strong>Background: </strong>Primary congenital glaucoma (PCG), the most prevalent pediatric variant, is a major contributor of childhood blindness globally. Traditional diagnosis relies on clinical features such as the classic triad (epiphora, photophobia, and blepharospasm), elevated intraocular pressure (IOP), corneal enlargement and optic disc cupping. Early diagnosis remains challenging as the conventional diagnosis often requires cooperation from pediatric patients.</p><p><strong>Objective: </strong>To identify the genetic etiology and underlying variants in a cohort of Vietnamese patients diagnosed with PCG using WES.</p><p><strong>Methods: </strong>A cohort of 32 Vietnamese patients with clinically diagnosed PCG was subjected to Whole-Exome Sequencing (WES) for genetic etiology identification. Validation of candidate variants was achieved using Sanger sequencing, with pathogenicity classification following ACMG/AMP guideline.</p><p><strong>Results: </strong>Genetic examination revealed pathogenic/likely pathogenic variants in 18.75% of the cohort (6/32 probands), involving in three genes: CYP1B1, TEK, FOXC1; and VUS in 6.25% (2/32 probands) spanning the gene LTBP2, FBN1. Three novel point variants in glaucoma-assiciated genes were identified, including a frameshift in FOXC1 (p.Tyr5fs*40), a stop-gained variant in TEK (p.Trp216*), and a missense variant in FBN1 (p.Lys54Glu). Additionally, a new putative large chromosomal deletion was identified on FOXC1 gene. While CYP1B1 remains a primary driver of PCG, finding alterations in FOXC1 and FBN1-typically associated with Axenfeld-Rieger and Marfan syndromes-underscores the clinical overlap between PCG and other developmental or systemic disorders.</p><p><strong>Conclusion: </strong>Achieving a 25% diagnostic rate, the study suggests that broader genetic testing by WES would greatly beneficial in the identification and categorization of glaucoma. The data suggest that WES is a powerful diagnostic resource, particularly when corneal clouding impedes fundus examination, and can provide essential insights into systemic syndromic risks.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149001687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic and network analyses identify epigenetic regulators of drug-tolerant persister (DTP) subsets in EGFR-mutant HCC827 non-small cell lung cancer.","authors":"JuneKyu Han, Euitaek Jung, Soon Young Shin","doi":"10.1007/s13258-026-01801-8","DOIUrl":"https://doi.org/10.1007/s13258-026-01801-8","url":null,"abstract":"<p><strong>Background: </strong>The clinical efficacy of osimertinib, a third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI), in EGFR-mutant non-small cell lung cancer (NSCLC) is limited by the inevitable acquired resistance. Drug-tolerant persister (DTP) cells, which survive initial therapy, are considered a key reservoir for this resistance. Understanding the molecular characteristics of DTPs is essential for developing strategies to prevent relapse.</p><p><strong>Objective: </strong>This study aimed to characterize the transcriptomic landscape of osimertinib-tolerant DTP cells and identify key epigenetic regulators associated with the DTP phenotype in EGFR-mutant HCC827 NSCLC cells through integrated transcriptomic and network analyses.</p><p><strong>Methods: </strong>We established an in vitro model of osimertinib tolerance using an EGFR-mutant (exon 19 deletion) HCC827 NSCLC cell line. Parental HCC827 cells and DTP subsets were subjected to transcriptomic analysis by RNA sequencing (RNA-seq). Differentially expressed genes were identified, followed by bioinformatics analyses, including Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction (PPI) network analyses to identify key biological processes driving the DTP phenotype. Key findings were validated using quantitative real-time PCR (qPCR).</p><p><strong>Results: </strong>Osimertinib treatment induced a morphologically distinct DTP population. Transcriptomic profiling revealed a marked shift in gene expression compared to parental cells. Functional enrichment analysis showed significant upregulation of epigenetic pathways. PPI network analysis identified a core module of eight hub genes, including histone deacetylases (HDAC5, HDAC9), sirtuins (SIRT1, SIRT2), and histone acetyltransferase (KAT2B). qPCR confirmed increased expression of HDAC5, HDAC9, and SIRT1.</p><p><strong>Conclusion: </strong>Epigenetic reprogramming accompanies the transition to an osimertinib-tolerant state in EGFR-mutant HCC827 cells. Targeting HDACs and sirtuins may represent a promising strategy to eliminate DTP subpopulations and delay or prevent acquired resistance.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148976723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RUNX3: a regulator of macrophage apoptosis with positive prognostic impact in sepsis.","authors":"Yanyan Sun, Zhen Yang, Xiaoxiang Jin, Ying Guo, Huifeng Wang","doi":"10.1007/s13258-026-01797-1","DOIUrl":"https://doi.org/10.1007/s13258-026-01797-1","url":null,"abstract":"<p><strong>Background: </strong>Sepsis, a life-threatening condition, remains a leading cause of mortality globally. Transcription factors (TFs) play a pivotal role in its pathogenesis. RUNX3, a member of the RUNX family, has been implicated in immune regulation, but its function in sepsis remains unclear.</p><p><strong>Objective: </strong>To determine whether RUNX3 expression is altered in sepsis and associated with patient prognosis, and to investigate its function and potential transcriptional regulatory targets in macrophages.</p><p><strong>Methods: </strong>We analyzed RNA-seq data from sepsis patients to identify differentially expressed TFs and examined the prognostic impact of RUNX3 by Kaplan-Meier survival analysis. RUNX3 was stably overexpressed in RAW264.7 macrophages, and cell proliferation and apoptosis were assessed by EdU and flow cytometry assays. RNA-seq of RUNX3-overexpressing cells was performed to identify potential transcriptional regulatory targets, a subset of which was validated by RT-qPCR.</p><p><strong>Results: </strong>RUNX3 expression was downregulated in sepsis patients, and low RUNX3 expression was associated with poor prognosis. RUNX3 overexpression promoted proliferation and inhibited apoptosis in RAW264.7 cells. Integrating RNA-seq with public RUNX3 binding data identified 89 potential transcriptional regulatory targets, among which Tgfbr3, Tgfbi, Il2rb, Gbp2, Gzmb, and Ptgds were confirmed as RUNX3-responsive by RT-qPCR. High expression of these targets was associated with favorable prognosis in sepsis patients.</p><p><strong>Conclusion: </strong>RUNX3 is closely associated with the prognosis of sepsis, and its overexpression promotes proliferation and suppresses apoptosis in macrophages, potentially by regulating downstream target genes, providing a novel perspective on sepsis pathogenesis.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148976683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Subtype-specific clinical significance of RRM1 and RRM2 expression in non-small cell lung cancer: a TCGA-based analysis.","authors":"Se-Young Yun, Yunha Lee, Junchae Lee, Hyowon Hong, Jae-Ho Lee","doi":"10.1007/s13258-026-01788-2","DOIUrl":"10.1007/s13258-026-01788-2","url":null,"abstract":"<p><strong>Background: </strong>Non-small cell lung cancer (NSCLC), including lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), exhibits significant molecular heterogeneity. Ribonucleotide reductase (RNR), composed of RRM1 and RRM2, is essential for DNA synthesis and repair, but its subtype-specific clinical significance in NSCLC remains unclear.</p><p><strong>Objective: </strong>To investigate the clinical and prognostic significance of RRM1 and RRM2 expression in NSCLC, with a focus on subtype-specific differences between LUAD and LUSC.</p><p><strong>Methods: </strong>We analyzed RNA expression and clinical data from 980 NSCLC patients in The Cancer Genome Atlas (TCGA). Associations with clinicopathologic characteristics, overall survival, and oncogenic driver alterations were assessed.</p><p><strong>Results: </strong>In LUAD, high RRM2 expression was significantly associated with advanced pathologic stage (p = 0.004), nodal involvement (p = 0.005), higher T stage (p = 0.030), and gender (p = 0.046). In LUSC, RRM2 was associated with age (p = 0.008), pathologic stage (p = 0.006), and N stage (p = 0.001). RRM1 showed no significant associations with stage-related parameters in either subtype. Correlation analyses revealed modest associations between RRM1 and multiple oncogenic drivers, whereas RRM2 showed stronger subtype-specific correlations, particularly with KRAS/BRAF in LUAD and CDKN2A/SOX2 in LUSC. Kaplan-Meier analysis demonstrated that high expression of both RRM1 and RRM2 was associated with poorer overall survival in LUAD, but not in LUSC. However, neither marker remained significant after adjustment for clinicopathological variables in multivariate analysis.</p><p><strong>Conclusion: </strong>RRM2 is associated with tumor progression in both NSCLC subtypes, while the prognostic associations of RRM1 and RRM2 are confined to LUAD. Although neither marker demonstrated independent prognostic significance in multivariate analysis, the findings support subtype-dependent roles of RNR components and highlight the potential biological and therapeutic relevance of nucleotide metabolism pathways in LUAD.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1223-1231"},"PeriodicalIF":2.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148396506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A digital PCR-based platform for rapid assessment of chloroplast stress adaptation in microalgal metabolic engineering.","authors":"Jinuk Jeong, Seohyun Park, Kornsorn Srikulnath, Byung Sun Yu, Kyudong Han","doi":"10.1007/s13258-026-01794-4","DOIUrl":"10.1007/s13258-026-01794-4","url":null,"abstract":"<p><p>Microalgae rapidly adjust their chloroplast physiology in response to environmental stress, and these adaptive responses are closely associated with cellular fitness and metabolic performance. However, conventional assessments of stress adaptation primarily rely on growth characteristics, pigment accumulation, or physiological measurements, which often require extended cultivation periods and may not capture early molecular responses. In this study, we introduce a digital PCR (dPCR)-based platform for rapid assessment of chloroplast stress adaptation in microalgae. The platform quantifies the chloroplast-to-nuclear genome copy number ratio (C/N ratio) using multiplex dPCR and utilizes this metric as a molecular indicator of chloroplast acclimation. As a proof-of-concept, the assay was applied to the halotolerant microalga Dunaliella salina cultivated under different salinity stress conditions. Distinct temporal changes in the C/N ratio were observed across salinity treatments, indicating dynamic chloroplast genome remodeling during stress adaptation. The assay enabled sensitive detection of chloroplast responses at early cultivation stages, prior to the appearance of clear phenotypic differences. These findings demonstrate that chloroplast-to-nuclear genome quantification by dPCR provides a rapid and reproducible approach for monitoring chloroplast stress adaptation in microalgae. The proposed platform offers a practical molecular tool for strain evaluation, cultivation optimization, and stress-response studies, and may support future applications in microalgal biotechnology and industrial production systems.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1177-1182"},"PeriodicalIF":2.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148548699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}