Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Molecular insights into charantin and β-carotene biosynthesis in bitter gourd (Momordica charantia L.): Gene expression dynamics and metabolite profiling","authors":"Banoth Tharun ,&nbsp;Gograj Singh Jat ,&nbsp;Manisha Mangal ,&nbsp;Vishal Sunartiya ,&nbsp;Sachin Kumar ,&nbsp;Rakesh Bhardwaj ,&nbsp;Naveen Singh ,&nbsp;Jeetendra Kumar Ranjan ,&nbsp;Avinash Tomer ,&nbsp;Deepak Singh ,&nbsp;Tusar Kanti Behera","doi":"10.1016/j.jgeb.2025.100626","DOIUrl":"10.1016/j.jgeb.2025.100626","url":null,"abstract":"<div><div>Bitter gourd is recognized for its anticancer and antidiabetic properties, largely attributed to charantin, and is also a rich source of carotenoids, including β-carotene. In this study, considerable variation was observed in both the accumulation and gene expression patterns associated with charantin and β-carotene biosynthesis across diverse genotypes. PVGy-201 exhibited the strongest gene expression profile, with the highest transcript levels for five key genes, including <em>McIDI</em> (∼16,493-fold), <em>McPMK</em> (∼694-fold), and <em>McSE</em> (∼466-fold), which corresponded with the maximum charantin content (38.53 µg/g FW). Similarly, DBGS-2 showed elevated expression of <em>McHMGR1</em> (∼271-fold) and <em>McMK</em> (∼13-fold), supporting its high charantin accumulation (35.27 µg/g FW). The wild species <em>Momordica balsamina</em> demonstrated strong expression of <em>McHMGR2</em> and <em>McSE</em>, consistent with charantin content of 29.36 µg/g FW. For β-carotene, DBGS-21-06 recorded peak expression of <em>McPSY</em> (∼17.2-fold), <em>McZDS</em> (∼4.9-fold), and <em>McCHXB</em> (∼2.8-fold), aligning with high carotenoid levels at both edible (18.46 µg/g FW) and ripening (52.31 µg/g FW) stages. Pusa Rasdar showed elevated expression of <em>McZEP</em> (∼6.9-fold) and <em>McPDS</em> (∼10.8-fold), correlating with maximum carotenoid content (19.49 µg/g FW at edible stage and 55.66 µg/g FW at ripening). DBGS-100-0 expressed <em>McLCYE1</em> (∼2.9-fold) and <em>McLCYE2</em> (∼3.1-fold), with high carotenoids (15.91 µg/g FW) at the edible stage. Collectively, PVGy-201 and DBGS-2 were identified as promising candidates for charantin enrichment, while DBGS-21-06 and Pusa Rasdar emerged as superior for β-carotene accumulation. These genotype-specific insights provide a molecular framework to support marker-assisted selection, transcriptome-based screening, and metabolic engineering for the development of nutritionally enhanced bitter gourd cultivars with stable metabolite profiles.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100626"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145693136","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 analysis of transcriptomics and drug-target networks identifies SMN1 as a novel biomarker and therapeutic target for amyotrophic lateral sclerosis","authors":"Deboral Eshak,&nbsp;Mohanapriya Arumugam","doi":"10.1016/j.jgeb.2025.100615","DOIUrl":"10.1016/j.jgeb.2025.100615","url":null,"abstract":"<div><div>Amyotrophic lateral sclerosis (ALS) is a prevalent and debilitating neurodegenerative disorder characterized by the selective degeneration of motor neurons. This study aims to unravel the molecular mechanisms underlying ALS through an integrated analysis of drug-target networks and gene expression data. Gene expression datasets related to ALS, including GSE115130 and GSE76220, were retrieved from the GEO database and systematically analyzed. Differential gene expression (DEG) analysis identified key upregulated and downregulated genes, while weighted gene co-expression network analysis (WGCNA) uncovered gene modules associated with ALS pathology. DEG analysis revealed genetic insights into ALS by pinpointing genes potentially involved in disease development and progression. WGCNA provided a systems-level understanding of ALS mechanisms, identifying highly correlated gene clusters and their relationship with clinical ALS characteristics. In the GSE115130 dataset, 6,105 genes were upregulated and 6,069 were downregulated. Conversely, the GSE76220 dataset showed 4,850 upregulated genes and 7,691 downregulated genes. Using the STRING database, a protein–protein interaction (PPI) network was constructed to investigate the functional relationships among ALS-associated genes. The findings highlighted the significant role of the survival motor neuron 1 (SMN1) gene in ALS, particularly in sporadic cases. Additionally, drug-target network mapping identified potential therapeutic targets and candidate drugs, offering valuable insights into the molecular mechanisms of ALS and possible interventions. This integrative approach underscored SMN1 as a novel diagnostic biomarker and potential therapeutic target for ALS, emphasizing its critical role in disease pathogenesis. These findings pave the way for further mechanistic studies and clinical validation, aiming to enhance therapeutic strategies for ALS.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100615"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145693135","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":"Design biology and mind–body health","authors":"Katsuyoshi Kumagai ,&nbsp;Ayumi Chiba ,&nbsp;Hiroaki Yajima","doi":"10.1016/j.jgeb.2025.100621","DOIUrl":"10.1016/j.jgeb.2025.100621","url":null,"abstract":"<div><div>Recent advances in design biology, including artificial cells, DNA nanostructures, artificial intelligence (AI)-driven molecular design, biofoundries, and next-generation genome editing, are transforming the health sciences of mind and body (HS-MB). Moving beyond traditional observational paradigms, these technologies enable predictive and design-oriented strategies for regulating stress, emotional health, achieving immune homeostasis, and managing lifestyle-related disorders. Psychological and social factors profoundly influence core physiological systems, including neuroendocrine (hypothalamic–pituitary–adrenal [HPA]) axis and cortisol rhythm, autonomic (vagal tone and heart rate variability), immune (cytokine balance and inflammatory control), metabolic (glucose–insulin regulation), and sleep–circadian systems. Artificial cells serve as controllable models for neurotransmitter signaling, immune interactions, and gut–brain communication, while DNA origami provides programmable nanocarriers that complement lipid nanoparticles (LNPs). Genome-editing innovations—such as prime, base, and epigenome editing—facilitate precise and reversible modulation of psychiatric risk genes, particularly when combined with induced pluripotent stem cell (iPSC) and brain-organoid models. Biofoundries integrate AI into Design–Build–Test–Learn (DBTL) cycles, automating molecular discovery and optimization. Ethical and regulatory considerations, including AI transparency, biocontainment, and dual-use governance, must be incorporated from the outset. Collectively, design biology, when strategically aligned with HS-MB, establishes a foundational framework for twenty-first-century medicine that bridges molecular engineering and holistic well-being.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100621"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145623554","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":"Identification of novel Menin-MLL interaction inhibitors targeting leukemia using in-silico virtual screening and structure-based drug design approaches","authors":"Amany I. Almars ,&nbsp;Shahad W. Kattan","doi":"10.1016/j.jgeb.2025.100612","DOIUrl":"10.1016/j.jgeb.2025.100612","url":null,"abstract":"<div><div>Leukemogenesis fundamentally depends on the interaction between Menin and MLL1 fusion proteins, especially in the context of aggressive mixed-lineage leukemia (MLL)-rearranged subtypes. This interaction can be disrupted to facilitate a focused therapeutic strategy. This study aimed to employ a comprehensive in silico drug repurposing strategy to identify new inhibitors of the Menin-MLL1 interaction. A comprehensive library of FDA-approved pharmaceuticals was subjected to a rigorous screening process utilizing virtual methodologies, clustering techniques, and a machine learning-based model (PSICHIC) to forecast binding affinity, subsequently complemented by molecular docking and an assessment of drug-likeness. Compounds that surpassed the antagonist value of the control (0.97076 kcal/mol) were selected for subsequent molecular docking investigations. The leading candidate, compound <strong>52920501</strong>, exhibited a remarkable binding energy of − 8.89 kcal/mol in contrast to the control (DS-1594b), alongside advantageous pharmacokinetic characteristics and electronic stability, as validated by Density Functional Theory (DFT). Consistent docking interactions with critical residues (Asn282, Asp285, Asn244) facilitated by <strong>52920501</strong>. Molecular dynamics simulations (300 ns) demonstrated that <strong>52,920,501</strong> sustained a stable interaction with Menin, promoted protein compaction, and reduced structural fluctuations. The MM/GBSA analysis conducted over the final 50 ns of the MD simulation revealed that compound <strong>52,920,501</strong> established a stable protein–ligand complex, exhibiting a final ΔTOTAL energy of − 12.83 kcal/mol. This value is comparable to the control, which recorded − 13.41 kcal/mol, yet demonstrates stronger individual interaction components. The inclusion of entropic contributions indicated a binding free energy (ΔG Binding) of − 4.75 kcal/mol for <strong>52920501</strong>, in contrast to + 7.05 kcal/mol for the control, highlighting its enhanced binding thermodynamics. The steered molecular dynamics (SMD) simulations provided additional validation of <strong>52920501</strong>′s robust binding affinity, exhibiting a greater resistance (600 kJ/mol/nm) to external pulling forces in comparison to the control. In summary, compound <strong>52,920,501</strong> presents itself as a promising therapeutic candidate, bolstered by persuasive computational data that underscores its potential as a Menin-MLL1 inhibitor. It warrants further exploration through subsequent in vitro and in vivo studies.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100612"},"PeriodicalIF":2.8,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145578752","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 potential anti-cancer mechanism for thyroid cancer: Role of Herba Epimedii via network pharmacology approach","authors":"Xuehan Wang ,&nbsp;Lin Guo ,&nbsp;Yiren Feng,&nbsp;Gang Jin","doi":"10.1016/j.jgeb.2025.100601","DOIUrl":"10.1016/j.jgeb.2025.100601","url":null,"abstract":"<div><h3>Objective</h3><div>To investigate the effective ingredients, crucial molecular targets, and the underlying molecular mechanisms associated with Herba Epimedii (HE) that exhibits anti-cancer effects for treating thyroid cancer (TC) using the network pharmacology approach.</div></div><div><h3>Methods</h3><div>The Traditional Chinese Medicine Systems Pharmacology (TCMSP) public database was analysed to identify the major bioactive ingredients and target proteins associated with HE. The Human Gene (Gene Cards) database, National Center for Biotechnology Information (NCBI) gene database, and Online Mendelian Inheritance in Man (OMIM) databases were analyzed to search for the disease targets of TC. Based on the overlapped results between HE putative targets and TC targets, the “compound-disease-target” network and a protein–protein interaction (PPI) network were constructed using Cytoscape 3.8.0. The R package was used to perform the Gene Ontology (GO) and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses. Finally, the “compound-disease-pathway-target” network was drawn by integrating all the information.</div></div><div><h3>Results</h3><div>The results indicated that there were 23 effective bioactive ingredients associated with HE, covering 203 targets, 145 of which were related to TC. Through PPI network topological analysis, 53 targets (including AKT1, JUN, MAPK1, RELA, and IL6) were identified as the major targets of HE. Results recorded from GO functional analyses revealed that significant biological processes were enriched. Results from KEGG analyses revealed that the pathways, such as the TNF, IL-17, and PI3K-Akt signaling pathways, played vital roles in the HE intervention for TC.</div></div><div><h3>Conclusion</h3><div>We revealed the potential mechanisms through which HE exerts anti-cancer effects in the case of TC. A holistic perspective on multiple ingredients, targets, and pathways has been presented, and the results can potentially help in developing new treatment methods for TC.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100601"},"PeriodicalIF":2.8,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145528328","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":"Evaluation of ARHGAP26 expression, prognostic significance, and immune infiltration in clear cell renal cell carcinoma","authors":"Aichun Long ,&nbsp;Cheng Huang ,&nbsp;Tianyun Li ,&nbsp;Yuwei Shi ,&nbsp;Cuiwei Zhang","doi":"10.1016/j.jgeb.2025.100593","DOIUrl":"10.1016/j.jgeb.2025.100593","url":null,"abstract":"<div><div>Renal clear cell carcinoma (KIRC), the most common subtype of renal cell carcinoma, is characterized by high metastatic potential and heterogeneity.The expression pattern of the <em>ARHGAP26</em> gene in KIRC, its link to patient prognosis, and its role in the TME immunoregulatory network are not well understood, with significant research gaps. We will analyze <em>ARHGAP26</em> expression using TCGA and GSCALite databases and assess its association with the tumor microenvironment using the ESTIMATE algorithm. Additionally, we will use the GEO database to examine <em>ARHGAP26</em> expression across different cell subsets in KIRC and evaluate its correlation with immune cell infiltration using TIMER 2.0. Immunohistochemistry (IHC) will be used to confirm differences in <em>ARHGAP26</em> expression between renal clear cell carcinoma (KIRC) and adjacent normal tissues. <em>ARHGAP26</em> expression is higher in KIRC, with a significant difference from normal tissues (<em>p</em> &lt; 0.001). In KIRC patients, high <em>ARHGAP26</em> expression is linked to longer overall, progression-free, and disease-specific survival, suggesting a tumor suppressor role, though it does not affect the disease-free interval. High <em>ARHGAP26</em> expression may remodel the tumor stroma and alter the tumor microenvironment by changing the tumor-to-non-tumor cell ratio.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100593"},"PeriodicalIF":2.8,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145528327","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":"Evaluation of salinity tolerance of Egyptian barley genotypes and their dehydrin 6-based single nucleotide polymorphisms (SNPs) diversity","authors":"Reda M. Gaafar ,&nbsp;Ismael A. Khatab ,&nbsp;Samah A. Mariey","doi":"10.1016/j.jgeb.2025.100614","DOIUrl":"10.1016/j.jgeb.2025.100614","url":null,"abstract":"<div><div>In many countries, freshwater sources for agricultural irrigation are scarce, making it challenging to meet the food production needs of the growing human population. Utilizing seawater for agriculture could be a potential solution for limited water resources. A lysimeter experiments evaluated fifteen barley genotypes irrigated with different levels of diluted seawater (S1 = 4.0, S2 = 8.0, and S3 = 12.0 dSm⁻¹). Morpho-physiological traits and exploring single nucleotide polymorphism (SNP) diversity among the most tolerant and sensitive genotypes during the winter seasons (2019/2020 and 2020/2021) were examined. Irrigation with diluted seawater at ECw 12.0 dSm⁻¹ significantly decreased leaf area index (by 35.54 %), total chlorophyll content (by 18.97 %), chlorophyll fluorescence (by 46.36 %), plant height (by 29.17 %), number of tillers per square meter (by 43.73 %), number of grains per spike (by 30.56 %), thousand-kernel weight (by 36.07 %), and grain yield (by 34.27 %). In contrast, early flowering was increased by 21.67 %. The Dehydrin 6 gene (<em>Dhn6</em>) partial sequences, 770 bp long, were blasted and used to detect SNPs associated with salinity among genotypes. Several SNPs were identified, with 26 variable sites when aligning the partial <em>Dhn6</em> sequences. Eleven SNPs were identified between the salt-tolerant Giza 137 and salt-sensitive Giza 132 genotypes, all located in exonic regions. These results indicate a potential role in salt tolerance for cultivar Giza 137, and the SNP markers effectively differentiated barley genotypes, which could be useful in salinity breeding programs aimed at developing salinity-tolerant barley and addressing climate change.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100614"},"PeriodicalIF":2.8,"publicationDate":"2025-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145528326","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":"Therapeutic potential of Xylocarpus granatum bark extracts: antioxidant, anti-inflammatory, cytotoxic and molecular insights","authors":"Nur-Nahar,&nbsp;Md. Ekramul Islam,&nbsp;Mst. Jannatul Mewa,&nbsp;Mst. Shahnaj Parvin","doi":"10.1016/j.jgeb.2025.100611","DOIUrl":"10.1016/j.jgeb.2025.100611","url":null,"abstract":"<div><div>Free radicals contribute to various diseases, while antioxidants, like phenolic compounds and flavonoids, counteract their effects. This study examines the antioxidant, anti-inflammatory, and cytotoxic properties of <em>Xylocarpus granatum</em> bark extracts, emphasizing ethyl acetate fraction (EAF) and the isolated compound from EAF.</div><div>The antioxidant constituents like total phenolic and flavonoid contents were quantified and antioxidant activity was evaluated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assays. The cytotoxic potential of the extracts and the isolated compound was evaluated against brine shrimp and the MCF-7 breast cancer cell line using the MTT assay. Anti-inflammatory effects were evaluated using heat-induced hemolysis and RBC membrane stabilization assays to assess membrane-stabilizing and anti-inflammatory activity. Molecular docking studies were performed using PyRx and discovery studio.</div><div>EAF demonstrated the highest total phenolic content (124.56 ± 1.35 mg GAE/g) and total flavonoid content (24.69 ± 0.48 mg QE/g), with superior performance in DPPH assays with IC₅₀ values of 3.84 µg/ml and that of pure compound, (+) catechin was 3.89 µg/ml. Anti-inflammatory effects revealed strong activity, with EAF and pure compound showing inhibition rates comparable to standard drugs like diclofenac-Na. Cytotoxicity, assessed through brine shrimp lethality and MCF-7 breast cancer cell line assays, highlighted EAF’s potent activity (LC₅₀: 24.15 µg/ml) antiproliferative efficacy in a dose-dependent manner. Molecular docking studies confirmed (+) catechin’s dual role as a COX-2/Caspase 9 inhibitor, elucidating its potential mechanisms of action.</div><div>These findings underscore the therapeutic potential of <em>Xylocarpus granatum</em> extracts, particularly EAF and the isolated compound, in managing oxidative stress, inflammation, and cancer progression.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100611"},"PeriodicalIF":2.8,"publicationDate":"2025-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145473964","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":"Comparative evaluation of E. coli expression systems for soluble hScFv-IL-17A with an unpaired CDR-L3 cysteine","authors":"Weeraya Thongkum ,&nbsp;Kanokporn Sornsuwan ,&nbsp;Thanathat Pamonsupornwichit ,&nbsp;Anuwat Weechan ,&nbsp;Natsima Viriyaadhammaa ,&nbsp;Kanchanok Kodchakorn ,&nbsp;Chatchai Tawapiwatana","doi":"10.1016/j.jgeb.2025.100613","DOIUrl":"10.1016/j.jgeb.2025.100613","url":null,"abstract":"<div><div>This study systematically evaluated <em>Escherichia coli</em> (<em>E. coli</em>) expression systems for the production of a humanized single-chain variable fragment targeting interleukin-17A (hScFv-IL-17A). A wild-type hScFv (hScFv-IL-17A-WT), derived from Secukinumab, was compared with a C97S mutant (hScFv-IL-17A-C97S) in which the unpaired cysteine residue in the light-chain complementarity-determining region 3 (CDR3) was substituted with serine. The primary objectives were to identify an optimal expression system for soluble protein production and to assess the functional consequences of the C97S mutation. Protein solubility, yield, and antigen-binding properties were evaluated across expression on three <em>E. coli</em> strains: Origami B (DE3), SHuffle, and BL21 (DE3) incorporating the DisCoTune system. Analyses were performed using SDS-PAGE, Western blotting, enzyme-linked immunosorbent assay (ELISA), and biolayer interferometry (BLI). Among the systems tested, BL21 (DE3) with DisCoTune yielded the highest levels of soluble expression for both variants. Although the C97S mutation enhanced soluble protein yield in this system, it significantly impaired functional activity. The hScFv-IL-17A-WT exhibited a strong binding affinity (K_D = 3.64 × 10⁻⁸ M), whereas the hScFv-IL-17A-C97S demonstrated an approximately 10-fold reduction in affinity. Competitive ELISA further confirmed that both variants recognized the same epitope as a neutralizing monoclonal antibody. Structural modeling predicted that the C97S substitution imposed a moderate stability penalty without inducing major conformational alterations, consistent with the observed reduction in binding affinity. Collectively, these findings indicate that while the C97S mutation improves soluble expression, it compromises biological activity. The hScFv-IL-17A-WT produced in BL21 (DE3) using the DisCoTune system represents the most promising candidate for subsequent therapeutic development.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100613"},"PeriodicalIF":2.8,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145473965","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 multi-omics analysis identifies genetically supported druggable targets for inflammatory bowel disease","authors":"Si-Chun Gu ,&nbsp;Si-lu Zeng ,&nbsp;Wei Zhang ,&nbsp;Chang-Yi Shen ,&nbsp;Can-Xing Yuan ,&nbsp;Yu Song ,&nbsp;Qing Ye","doi":"10.1016/j.jgeb.2025.100608","DOIUrl":"10.1016/j.jgeb.2025.100608","url":null,"abstract":"<div><h3>Background</h3><div>Inflammatory bowel disease (IBD), encompassing Crohn’s disease (CD) and ulcerative colitis (UC), represents a set of chronic, immune-mediated gastrointestinal disorders with increasing global prevalence. Current therapeutic options are limited, highlighting the need for novel drug targets.</div></div><div><h3>Objective</h3><div>To systematically identify druggable genes with potential causal roles in IBD through integrative multi-omics analyses, leveraging genetic, transcriptomic, and epigenomic datasets.</div></div><div><h3>Method</h3><div>We implemented summary-data-based Mendelian randomization (SMR) to assess the causal relevance of druggable genes in IBD, using large-scale genome-wide association study (GWAS) data from the International Inflammatory Bowel Disease Genetics Consortium (IIBDGC). Replication analyses were performed in the FinnGen cohort. Genetic instruments for druggable genes were derived from the methylation and gene expression levels. To strengthen the causal inference, Bayesian colocalization was applied to distinguish true causal loci from linkage between candidate druggable genes and IBD. Phenome-wide association studies (PheWAS), in silico drug repurposing predictions, and molecular docking simulations were conducted to implicate the possibility of targeted therapeutic drugs for future clinical applications.</div></div><div><h3>Results</h3><div>The study identified Thrombospondin-3 (THBS3), Retinoic Acid Receptor-Related Orphan Receptor C (RORC), and Tumor Necrosis Factor Receptor Superfamily Member 25 (TNFRSF25) as potential drug targets for IBD and its subtypes. These genes showed consistent associations with IBD across different biological levels and replication datasets. Molecular docking analyses predicted candidate drugs, including AM580, Dasatinib, 25-Hydroxycholesterol, Medroxyprogesterone acetate, 3,3′-Diindolylmethane, and Hesperidin, which exhibited strong binding affinities to the target proteins.</div></div><div><h3>Conclusion</h3><div>Our multi-layered omics framework provided genetically anchored evidence for the role of THBS3, RORC, and TNFRSF25 as druggable targets in IBD. The identified candidate drugs offered new avenues for therapeutic intervention. Further clinical validation is warranted to harness these targets for the development of effective IBD treatments.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100608"},"PeriodicalIF":2.8,"publicationDate":"2025-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145473967","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}