Gene Reports最新文献

{"title":"Progress in bioinformatics tools for analysis of metagenomically isolated microbiome: Current status and future prospects","authors":"Deepak Kukkar ,&nbsp;Chahat Chopra ,&nbsp;Ki-Hyun Kim ,&nbsp;Preeti Rajesh","doi":"10.1016/j.genrep.2026.102437","DOIUrl":"10.1016/j.genrep.2026.102437","url":null,"abstract":"<div><div>Recent advances in the metagenomic exploration of non-cultivable microbiota have been achieved with the aid of high-throughput sequencing techniques and related data interpretation methods. The generation of metagenomic data is increasing exponentially, aided by the low cost of next generation sequencing (NGS) analyses. Since the pandemic, demand for bioinformatics tools and the related data sciences has been growing rapidly because of their potential to identify novel microbes (e.g., by uncoupling and decoding the phylogenetic relationships among the metagenomically mined microorganisms). In accordance with those developments, this review outlines historical evolution and recent trends in the advancement of NGS technologies for deciphering the genomic potential of the living world. The discussion extends to the recent advances in the field of bioinformatic tools used for the quality control (QC), assembly, binning, taxonomic classification, functional annotation, and comparative analyses of amplicon sequences, and shotgun metagenomic sequences in terms of their merits and demerits. Specifically, the acquisition of input data in various bioinformatics tools is discussed within a modular, decision-based pipeline framework based upon their applications in the analysis for whole metagenome (PRINSEQ, Decontam, Meta-QC, DAMIAN, CLARK, Kraken, MetaPhlAn4, Metagenome analyzer (MEGAN), MetaPop, and STRONG) or amplicon sequenced data (DADA2, MOTHUR, and QIIME) has been discussed. Issues related to workflow integration, reproducibility, and interoperability are also highlighted. Future challenges are also deliberated with respect to expanding the applicability of bioinformatics tools, especially to identifying metagenomically isolated microorganisms.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"43 ","pages":"Article 102437"},"PeriodicalIF":0.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146192622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic architecture of the emerging plant pathogen Agrobacterium burrii: Complex plasmidome and prophage-driven evolution","authors":"Mohammadreza Rahimian ,&nbsp;Mohammad Aghazadeh-Soltan-Ahmadi","doi":"10.1016/j.genrep.2026.102446","DOIUrl":"10.1016/j.genrep.2026.102446","url":null,"abstract":"<div><div><em>Agrobacterium burrii</em> is an emerging plant pathogen responsible for crown gall disease. This study presents a comprehensive in silico genomic analysis of the type strain Rmᵀ, isolated from a rose gall in Iran. Bioinformatic characterization reveals a complex plasmidome comprising six large plasmids, all predicted to be conjugative, which suggests a high potential for horizontal gene transfer. Phylogenetic analysis indicates this plasmidome is polyphyletic, and one plasmid (pTiAgbu13) shows near-identity to plasmids from <em>Agrobacterium tumefaciens</em>, consistent with a recent interspecies transfer event. Notably, five plasmids were found to harbor genes conferring predicted resistance to a wide range of antibiotics, including last-resort drug classes such as vancomycin and carbapenems, highlighting <em>A. burrii</em> as a strain of interest for environmental antimicrobial resistance surveillance. The chromosome harbors a complete, high-quality temperate prophage, Ph_Agbu_1, encoding candidate anti-CRISPR and anti-defense systems. Predictive screening also identified numerous prophage-encoded hypothetical proteins as putative virulence factors. Furthermore, the genome contains biosynthetic gene clusters (BGCs) for secondary metabolites, including three for homoserine lactones, pointing to a potential complex quorum-sensing network. Collectively, these genomic features portray <em>A. burrii</em> Rmᵀ as a dynamic entity whose pathogenic potential appears driven by the interplay of its chromosome, a mosaic plasmidome, and an integrated prophage. The findings underscore the need for further functional and ecological studies to assess the implications for agriculture and public health within a One Health framework.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"43 ","pages":"Article 102446"},"PeriodicalIF":0.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146192623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diagnostic and prognostic evaluation of miRNA-93 and miRNA-223 in women with polycystic ovary syndrome","authors":"Iram Ashaq Kawa ,&nbsp;Qudsia Fatima ,&nbsp;Akbar Masood ,&nbsp;Shahnaz Ahmad Mir ,&nbsp;Irfan Mir ,&nbsp;Saika Manzoor ,&nbsp;Fouzia Rashid","doi":"10.1016/j.genrep.2026.102448","DOIUrl":"10.1016/j.genrep.2026.102448","url":null,"abstract":"<div><h3>Purpose</h3><div>Polycystic Ovary Syndrome (PCOS) is the most common endocrine disorder, which is often complicated by diagnostic challenges and inadequate treatment plans. In this study, we aimed to evaluate the differential expression of miRNA-93 and miRNA-223 in the peripheral blood of drug-naive PCOS cases, drug-treated PCOS cases, and healthy controls to assess their potential as biomarkers in monitoring the effectiveness of treatment.</div></div><div><h3>Method</h3><div>The expression of miRNA-93 and 223 from peripheral blood mononuclear cells (PBMCs) of study subjects was studied using quantitative real-time PCR. The clinical, anthropometric, hormonal, and metabolic parameters of all subjects studied for expression were investigated and compared. Further, the correlation of miRNAs with the clinical, hormonal, and metabolic profiles were assessed.</div></div><div><h3>Results</h3><div>The expression of miRNA-93 and 223 was significantly higher in PCOS women compared to healthy controls (<em>p</em> = 0.004; <em>p</em> = 0.0057). The miRNA-93 and 223 expressions in OCP-treated PCOS women were comparable with the drug-naive PCOS women (<em>p</em> = 0.662; <em>p</em> = 0.151). A significant decrease in the expression of miRNA-93 and 223 (<em>p</em> = 0.001; <em>p</em> = 0.013) in metformin-treated PCOS women compared to drug-naïve PCOS women was observed in our study. The area under the receiver operator characteristic curve for miRNA-93and 223 in drug-naïve PCOS women was 0.79 and 0.69. For mIRNA-93/ miRNA-223, the corresponding AUC in the OCP-treated PCOS women was 0.51 and 0.59. Further, for miRNA-93and 223, the corresponding AUC in the metformin-treated PCOS women was 0.77 and 0.70.</div></div><div><h3>Conclusion</h3><div>miRNA-93 levels in PBMCs have a promising ability to differentiate PCOS patients from healthy controls more precisely and sensitively than miR-223 in the Kashmiri population. Further, we suggest that miRNA-93 has the potential to be used as a biomarker to monitor the response to metformin therapy in PCOS women.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"43 ","pages":"Article 102448"},"PeriodicalIF":0.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146192624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity and population structure within Kankrej Cattle: Insights from genome-wide SNP analysis","authors":"Dhara Gor ,&nbsp;Jay Prakash Gupta ,&nbsp;Swapnil Gajjar ,&nbsp;Mayank Darji ,&nbsp;Jagdish Chaudhari ,&nbsp;Arth Chaudhari ,&nbsp;Sushil Mohapatra ,&nbsp;Pravin Purohit ,&nbsp;Shrikant Patil ,&nbsp;Harshad Panchasara","doi":"10.1016/j.genrep.2026.102438","DOIUrl":"10.1016/j.genrep.2026.102438","url":null,"abstract":"<div><div>Understanding within-breed genetic diversity is essential for informed conservation and breeding strategies in indigenous cattle. In this study, genome-wide SNP genotyping data were used to characterize genetic diversity and population structure within the Kankrej cattle population. After stringent quality control, autosomal SNPs were analyzed using supervised and unsupervised admixture, Principal Component Analysis (PCA), Discriminant Analysis of Principal Components (DAPC), and Neighbor-Joining (NJ) tree reconstruction. A reference panel comprising animals from six cattle breeds was used to infer ancestry proportions, and Kankrej cattle were classified into subgroups based on dominant (&gt;10%) ancestry components. The Kankrej population exhibited high levels of genetic variability, reflected by a high proportion of polymorphic markers (Pn &gt; 93%) and a mean minor allele frequency of 0.29. Observed and expected heterozygosity values were comparable across subgroups, with consistently negative inbreeding coefficients, indicating the absence of pronounced recent inbreeding. Runs of homozygosity (ROH) analysis further supported moderate levels of autozygosity across the population. Analysis of molecular variance (AMOVA) revealed that the majority of genetic variation (&gt;99%) was partitioned within individuals, with low but detectable differentiation among ancestry-defined subgroups (FST &lt; 0.02). Multivariate and phylogenetic analyses revealed subtle population substructure, with individuals showing HF_domi (Group of Kankrej animals having more than 10% of inheritance of HF cow) ancestry displaying greater separation, whereas Kankrej and Sahiwal_domi (Group of Kankrej animals having more than 10% of inheritance of Sahiwal cow) groups showed closer genetic proximity. Overall, the results indicate substantial shared genetic background and retained diversity within Kankrej cattle, providing a robust genomic baseline for future conservation planning and breeding program design.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"43 ","pages":"Article 102438"},"PeriodicalIF":0.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146192621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative genomic and pharmacogenomic analysis reveals novel variants and statin response patterns in Indian familial hypercholesterolemia patients","authors":"Kasinathan Kumaran ,&nbsp;Janardanan Subramonia Kumar ,&nbsp;Aarti Rajesh Agrawal ,&nbsp;Fiona D'Souza ,&nbsp;K.N. ArulJothi","doi":"10.1016/j.genrep.2026.102444","DOIUrl":"10.1016/j.genrep.2026.102444","url":null,"abstract":"<div><div>Familial Hypercholesterolemia (FH) is an autosomal dominant disorder with high LDL-C values and a high risk of premature cardiovascular disease. Due to limited research and diagnostics, FH genetic epidemiology in India is little studied. This study addresses this gap by integrating statin response pharmacogenomics with whole-exome sequencing and lipid profiling. A total of 100 patients were recruited and categorised using the Dutch Lipid Clinic Network (DLCN) criteria, of which 21 individuals with high DLCN scores underwent whole exome sequencing. Variant analysis revealed 12 <em>APOB</em> variants, including the deleterious c.1853C&gt;T (rs679899) detected in 8 patients and the benign c.6937A&gt;G (rs584542) identified in 9 patients. All these variants were analysed using ACMG-AMP guidelines, and among the 26 variants, 22 newly reported in the Indian FH population, with 3 of them, <em>APOB</em> (p.Ser3040Ter), LDLR (g.11,089,068–11,089,659), and <em>PCSK9</em> (p.Leu23dup), being globally novel. To assess therapeutic implications, pharmacogenomic screening was also performed, which identified clinically significant variations in statin metabolism genes, including <em>HMGCR</em> (c.666T&gt;C, <em>n</em> = 6), <em>SLCO1B1</em> (c.388A&gt;G, n = 6), and <em>CYP2C9</em> (c.1420G&gt;A, <em>n</em> = 5). Both <em>ABCB1</em> (c.1554 + 24 T &gt; C) and <em>ABCG2</em> (p.Gly141Lys) were associated with reduced statin response, underscoring the importance of integrating pharmacogenetic insights into treatment strategies. Our findings highlight that <em>APOB</em> variations were more frequent than <em>LDLR</em> mutations, underscoring the unique and population-specific genetic landscape of FH in India. Furthermore, the pharmacogenomic insights into statin metabolism and response reinforce the potential of tailoring therapy to the Indian population, demonstrating the critical role of precision medicine in optimising FH and cardiovascular disease management.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"43 ","pages":"Article 102444"},"PeriodicalIF":0.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146192620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CAPZB gene polymorphism and its implications for hypothyroidism: Evidence from a case-control study","authors":"Nikki Rani ,&nbsp;Salim Khan ,&nbsp;Anita Yadav ,&nbsp;Ranjan Gupta","doi":"10.1016/j.genrep.2025.102422","DOIUrl":"10.1016/j.genrep.2025.102422","url":null,"abstract":"<div><h3>Background</h3><div>Hypothyroidism<strong>,</strong> a prevalent endocrine disorder distinguished by inadequate thyroid hormone production, arises from a complex interplay of environmental and genetic factors. Emerging evidence implicates cytoskeletal regulation in thyroid function, with the capping actin protein of muscle <em>Z</em>-line subunit beta (<em>CAPZB)</em> gene, encoding the subunit of the F-actin capping protein, identified as a candidate gene. This study investigates the relationship between <em>CAPZB</em> gene polymorphism and susceptibility to hypothyroidism.</div></div><div><h3>Methods</h3><div>A case-control study was conducted involving 200 hypothyroid patients and 200 healthy controls. Genomic DNA was extracted and genotyped for rs12091047 using Polymerase chain reaction – Restriction fragment length polymorphism (PCR-RFLP) technique. Genotype and allele frequencies were compared between groups using Chi-square analysis.</div></div><div><h3>Results</h3><div>In the control group, the genotype frequency was CC (56 %), CT (43.5 %), and TT (0.5 %), while in hypothyroid patients, it was CC (41 %), CT (52 %), and TT (7 %). In the dominant model, CT and TT genotypes were significantly associated with hypothyroidism (OR- 1.831, <em>p</em>-value 0.0028). The recessive model showed an unstable estimate due to very low TT frequency in controls (<em>n</em> = 1).</div></div><div><h3>Conclusion</h3><div>The rs12091047 polymorphism in the <em>CAPZB</em> gene showed a statistical association with an increased risk of hypothyroidism in the studied population, implying that variations in cytoskeletal genes might play a role in thyroid disorders.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102422"},"PeriodicalIF":0.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145921017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The characterization and effect of Nanog on OSKM factors in large yellow croaker (Larimichthys crocea)","authors":"Ning Xi ,&nbsp;Shengkai Shi ,&nbsp;Zhaowei Zhong ,&nbsp;Dingyuan Luo ,&nbsp;Yizhen Lu ,&nbsp;Ran Li ,&nbsp;Jieyu Liao ,&nbsp;Yonghua Jiang","doi":"10.1016/j.genrep.2026.102434","DOIUrl":"10.1016/j.genrep.2026.102434","url":null,"abstract":"<div><div>The pluripotency factor Nanog plays a central role in somatic cell reprogramming and stem cell maintenance. In this study, we identified and characterized the <em>Nanog</em> gene in large yellow croaker (<em>Larimichthys crocea</em>), an economically important marine fish. The full length <em>Nanog</em> cDNA of large yellow croaker was cloned, and sequence analysis revealed a conserved homeodomain. Expression profiling showed that <em>Nanog</em> transcripts were abundant during early embryogenesis, but declined sharply after gastrulation, indicating a maternal expression pattern. In adult tissues, <em>Nanog</em> expression was predominantly detected in the gonads, with significantly higher levels in the ovary than that in the testis. Functional assays in a large yellow croaker muscle cell line (LYCMs) demonstrated that RNAi-mediated knockdown of <em>Nanog</em> impaired cell growth and morphology, whereas its overexpression enhanced proliferation and altered cell morphology towards a denser, more rounded phenotype. Furthermore, overexpression of <em>Nanog</em> promoted its own expression as well as the endogenous OSKM (<em>Oct4</em>, <em>Sox2</em>, <em>Klf4</em>, <em>c-Myc</em>) network. Conversely, individual overexpression of each OSKM factor also upregulated Nanog to varying degrees, suggesting a reciprocal regulatory loop. Based on these findings, we propose a preliminary regulatory network linking Nanog and the OSKM factors in modulating cell proliferation. This study provides the first functional insights into Nanog in <em>L. crocea</em> and establishes a foundation for future research on pluripotency regulation and induced pluripotent stem cell (iPSC) induction in fish.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102434"},"PeriodicalIF":0.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146073923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating the expression of virulence genes pilA and csuD of Acinetobacter baumannii in patients' samples in Tehran, Iran","authors":"Hadis Nazeri ,&nbsp;Amin Talebi Bezmin Abadi ,&nbsp;Abbas Ali Imani Fooladi ,&nbsp;Farid Rahimi","doi":"10.1016/j.genrep.2025.102392","DOIUrl":"10.1016/j.genrep.2025.102392","url":null,"abstract":"<div><div><em>Acinetobacter baumannii</em> is a leading cause of hospital-acquired infections and characterized by multidrug resistance and different virulence mechanisms. We aimed to characterize the antibiotic susceptibility profiles <em>of A. baumannii</em> in clinical isolates collected between 2022 and 2024. We confirmed <em>A. baumannii</em> by polymerase chain reaction (PCR) targeting <em>16S rRNA</em> in fifty samples which included tracheal aspirates, urine, blood, wound, sputum, bronchoalveolar lavage, and ascitic fluid. We tested antibiotic susceptibility according to the 2022 guidelines of the Clinical and Laboratory Standards Institute and screened for resistance genes <em>bla</em>_{<em>OXA-23-like</em>}<em>, bla</em>_{<em>OXA-24-like</em>}<em>, and bla</em>_{<em>OXA-58-like</em>} by PCR. We used reverse transcription quantitative PCR of 20 representative samples in duplicates to profile <em>pilA</em> and <em>csuD</em> expression, normalized to <em>16S rRNA</em>. <em>csuD</em> expression was higher in the target group than in controls, while <em>pilA</em> was only slightly increased; however, neither difference was statistically significant (<em>P</em> = 0.123 and <em>P</em> = 0.554, respectively), showing no meaningful differences among groups. Our findings highlight the importance of pili and chaperone–usher genes (<em>PilA and CsuD</em>) as they function in biofilm formation and adherence. Continually surveying for resistance and virulence factors is essential for guiding treatment strategies against carbapenem-resistant <em>A. baumannii</em>.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102392"},"PeriodicalIF":0.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Harnessing extracellular vesicle-associated proteins for osteoporosis: Mechanisms, therapeutic strategies, and clinical potential","authors":"Suleiman Kolawole Yusuf ,&nbsp;Abdulmajeed Isiaku ,&nbsp;Adamu Abdul Abubakar ,&nbsp;Nwachukwu Raymond Chinedu ,&nbsp;Abdulfatai Aremu ,&nbsp;Okediran Babatunde Samuel ,&nbsp;Alhaji Zubair Jaji","doi":"10.1016/j.genrep.2025.102414","DOIUrl":"10.1016/j.genrep.2025.102414","url":null,"abstract":"<div><div>Osteoporosis remains a major global health challenge characterized by bone fragility and limited regenerative capacity. Extracellular vesicles (EVs) have recently emerged as potent mediators of intercellular communication, capable of modulating bone remodeling through their protein cargo. Unlike prior reviews that emphasize RNA or general regenerative mechanisms, this article provides a protein-centric synthesis of how EV-associated proteins orchestrate osteoblast and osteoclast regulation via canonical pathways, including TGF-beta/Smad, MAPK, Wnt/beta-catenin, and PI3K/Akt. By integrating evidence from 60 in vitro, in vivo, and early clinical studies, we identify consistent trends that demonstrate mesenchymal stem cell-derived EVs promote osteoblast differentiation and mineralization while suppressing osteoclastogenesis, with delivery via hydrogels and scaffolds enhancing local retention and efficacy. Beyond summarizing preclinical data, this review highlights mechanistic convergence among EV protein cargo, comparative efficacy of delivery strategies, and a roadmap for translation addressing standardization, scalability, and regulatory challenges. Collectively, these insights position EV-associated proteins as versatile therapeutic effectors capable of bridging the gap between cellular therapy and precision drug delivery for osteoporosis.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102414"},"PeriodicalIF":0.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145836491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenolic and elemental composition of Artemisia absinthium and its protective role against ethanol-induced ER stress and TNF-α mediated inflammation in hepatic cells","authors":"Nebiye Pelin TURKER","doi":"10.1016/j.genrep.2025.102418","DOIUrl":"10.1016/j.genrep.2025.102418","url":null,"abstract":"<div><div>The aim of this study was to determine the elemental and phenolic composition of <em>Artemisia absinthium</em> and evaluate its hepatoprotective effects against ethanol-induced cytotoxicity in AML12 hepatocytes. Elemental analysis by ICP-MS revealed high levels of potassium, calcium, and phosphorus, along with essential trace elements such as Fe, Zn, and Cu. LC-MS/MS identified chlorogenic and protocatechuic acids as dominant phenolics. In MTT assays, ethanol significantly reduced cell viability (IC₅₀ = 15.63 %), whereas co-treatment with <em>A. absinthium</em> extract improved viability to 84.29 %. Gene expression analysis showed that ethanol induced ER stress and the pro-inflammatory cytokine TNF-α, which were downregulated by the extract, indicating a targeted anti-inflammatory effect. Post-treatment with <em>A. absinthium</em> also enhanced antioxidant gene expression (CAT, SOD, GSH). Flow cytometry confirmed reduced ROS levels in extract-treated cells. These findings suggest that <em>A. absinthium</em> exerts hepatoprotective effects by modulating oxidative stress, ER stress, and inflammatory signaling, highlighting the necessity for further investigation into the upstream molecular mechanisms of ROS generation.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102418"},"PeriodicalIF":0.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145836492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}