Genes & genomics最新文献

{"title":"Hierarchical structural component model for pathway analysis of multinomial phenotypes.","authors":"Md Kamruzzaman, Taewan Goo, Taesung Park","doi":"10.1007/s13258-025-01655-6","DOIUrl":"https://doi.org/10.1007/s13258-025-01655-6","url":null,"abstract":"","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553315","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":"De novo somatic mosaicisms of INF2 and TRPV4 in patients with Charcot-Marie-Tooth disease.","authors":"Ah Jin Lee, Sumaira Kanwal, Manisha Awasthi, Byung-Ok Choi, Ki Wha Chung","doi":"10.1007/s13258-025-01643-w","DOIUrl":"10.1007/s13258-025-01643-w","url":null,"abstract":"<p><strong>Background: </strong>Somatic mosaicism is caused by a postzygotic de novo mutation. It is a very rare genetic event, and mosaic cases have been reported only very limitedly among Korean patients with peripheral neuropathies, including Charcot-Marie-Tooth disease (CMT) so far.</p><p><strong>Objective: </strong>This study was performed to identify and characterize somatic mosaicism in Korean families with CMT.</p><p><strong>Methods: </strong>Genetic causes were identified by whole exome sequencing (WES) and a subsequent filtering process of the variants. The level of mosaicism for the de novo somatic mutations was determined by counting altered sequences from approximately 100 colonies/mutation and the ratio of altered sequences per total reads at the mutation site using the WES data.</p><p><strong>Results: </strong>We observed two cases of somatic mosaicism in different families with CMT: p.Cys104Tyr in INF2 (male with CMT1) and p.Ser729Arg in TRPV4 (female with CMT2). The approximate levels of mosaicism were determined to be 24% and 30% in the blood, respectively. A man with the INF2 mutation showed very mild symptoms, while a woman with the TRPV4 mutation showed severe clinical phenotypes. The INF2 mutation is specifically considered a case of gonadal mosaicism. In addition, we confirmed that the p.Cys104Tyr in INF2 is associated with the CMT1 phenotype without focal segmental glomerulosclerosis (FSGS).</p><p><strong>Conclusion: </strong>This study may be the first or second report for the INF2 and TRPV4 mosaicism. The degrees of the phenotypic severity for the mosaic mutations probably depend on the mutation sites and the levels of mosaicism in the affected tissues. This study suggests that somatic mosaicism may contribute to inter- or intra-familial phenotypic heterogeneity.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"797-806"},"PeriodicalIF":1.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143997365","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":"Effects of Zonula occludens-1 (ZO-1) tight junction protein on tumor characteristics in human ovarian cancer cells.","authors":"Hyung Joon Yoon, Do-Ye Kim, Hyojin An, Min-Hye Kim, Seongsoo Choi, Eun-Ji Ko, Heungyeol Kim, Ji Young Lee, Wan Kyu Eo, Min Young Kim, Ki Hyung Kim, Hee-Jae Cha","doi":"10.1007/s13258-025-01649-4","DOIUrl":"10.1007/s13258-025-01649-4","url":null,"abstract":"<p><strong>Background: </strong>Ovarian cancer is among the most lethal malignancies affecting women, largely due to its asymptomatic progression in early stages, rapid advancement, and high mortality rate. Tight junction protein 1 (TJP1), also known as Zonula occludens-1 (ZO-1), plays a critical role in epithelial and endothelial cell integrity by regulating paracellular permeability. Additionally, ZO-1 is involved in cell-cell communication networks, influencing cellular proliferation, differentiation, and metastasis. While previous studies have demonstrated the significance of ZO-1 in tumorigenesis and cancer progression, its precise mechanistic role remains to be fully elucidated.</p><p><strong>Objective: </strong>This study aims to investigate the functional role of ZO-1 in human ovarian cancer cells to provide a molecular perspective on its impact on tumor progression.</p><p><strong>Methods: </strong>Human ovarian cancer cell lines SNU119 and SKOV3 were utilized. ZO-1 knockout (KO) was achieved using the Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated protein 9 (CRISPR-Cas9) system in combination with single-guide RNA (sgRNA) targeting ZO-1. Hygromycin B selection was employed to establish stable ZO-1 KO SNU119 and ZO-1 KO SKOV3 cell lines. The successful knockout of ZO-1 was confirmed at both the transcript and protein levels via real-time quantitative PCR (RT-qPCR) and Western blotting. Functional assays, including cell proliferation, migration, and invasion assays, were conducted to assess the effects of ZO-1 KO on key tumor-associated characteristics.</p><p><strong>Results: </strong>CRISPR-Cas9-mediated ZO-1 KO in SNU119 and SKOV3 ovarian cancer cell lines resulted in a significant reduction of ZO-1 expression at both the transcript and protein levels. The loss of ZO-1 led to a disruption of cell-cell junctions. Functionally, ZO-1 KO cells exhibited reduced proliferation, whereas cell migration and invasion were significantly enhanced, suggesting a shift toward a more aggressive phenotype.</p><p><strong>Conclusion: </strong>The findings indicate that ZO-1 KO in ovarian cancer cells suppresses cell proliferation while promoting migratory and invasive properties, hallmarks of tumor progression. These results underscore the complex role of ZO-1 in ovarian cancer and highlight the need for further investigation into its broader regulatory impact on oncogenic pathways.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"867-875"},"PeriodicalIF":1.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144142440","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":"Molecular cloning, expression analysis, and functional characterization of Intelectin-1 from Chinese giant salamanders (Andrias davidianus).","authors":"Haolin Mo, Kexin Liu, Xiaoran An, Yongqing Chen, Jiajia Yu, Huixia Yu, Mingxing Yao, Weijia Song, Yang Li, Lixin Wang","doi":"10.1007/s13258-025-01630-1","DOIUrl":"10.1007/s13258-025-01630-1","url":null,"abstract":"<p><strong>Background: </strong>Intelectin (ITLN) plays a pivotal role in innate immunity, inflammatory responses, and tumor progression. However, its physiological roles in caudate amphibians, such as Andrias davidianus, remain elusive.</p><p><strong>Objective: </strong>A proto-type of intelectin (AdITLN1) from A. davidianus was characterized, following which an AdITLN1 homology model was generated to analyze its expression profiles and functional characterizations.</p><p><strong>Methods: </strong>The intelectin1 gene (AdITLN1) was cloned, and its evolutionary relationship with ITLN1 from other species was explored. Additionally, a homology model was generated using Molecular Operating Environment (MOE) software, and the active binding pocket of AdITLN1 was identified. Infections with Aeromonas hydrophila were conducted to analyze changes in ITLN1 transcript levels in liver tissue. Finally, recombinant A. davidianus ITLN1 protein (rAdITLN1) was synthesized using prokaryotic expression, and its bacterial agglutination activity and impact on macrophage phagocytosis were examined.</p><p><strong>Results: </strong>Multiple sequence alignment and phylogenetic analysis indicated that AdITLN1 shared the closest evolutionary relationship with amphibians, with its structure being similar to that of human intelectin1 and Xenopus Embryonic Epidermal Lectin. Moreover, AdITLN1 mRNA was expressed in a wide range of tissues and was significantly up-regulated post-A. hydrophila infection. Meanwhile, the AdITLN1 protein was successfully expressed and purified in Escherichia coli (E. coli) BL21 (DE3). The recombinant AdITLN1 (rAdITLN1) displayed strong agglutination activity against different Gram-negative and Gram-positive bacteria. Lastly, The phagocytosis of rAdITLN1-treated E. coli by macrophages was significantly enhanced.</p><p><strong>Conclusion: </strong>The results of the present study demonstrated that AdITLN1 was a multifunctional immune protein with potent immunomodulatory activity. This study offers valuable insights into disease control in giant salamanders and the conservation of natural resources.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"843-853"},"PeriodicalIF":1.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656904","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":"Identification of genetic signatures of positive selection in apes linked to life-history trait adaptations.","authors":"Yoo-Rim Roh, Kiejung Park, Young Jun An, Hyung-Soon Yim, Jung-Hyun Lee","doi":"10.1007/s13258-025-01647-6","DOIUrl":"10.1007/s13258-025-01647-6","url":null,"abstract":"<p><strong>Background: </strong>Apes, including humans, exhibit distinctive life history traits such as increased brain mass, delayed sexual maturity, and extended longevity compared to non-ape primates. These pronounced interspecific differences likely arise from underlying genetic architecture. However, the molecular mechanisms contributing to these traits remain largely unknown.</p><p><strong>Objective: </strong>This study aims to identify genetic factors under positive selection that may have contributed to the evolution of ape-specific life history traits, particularly extended longevity.</p><p><strong>Methods: </strong>Comparative genomic analyses were performed between 7 ape species and 22 non-ape primate taxa to identify positively selected genes (PSGs). Functional enrichment analyses were conducted to determine the biological processes associated with these PSGs. Additionally, expression analyses were carried out to assess tissue-specific patterns and their potential roles in neurodevelopment and systemic homeostasis.</p><p><strong>Results: </strong>A total of 143 PSGs were idetntified, showing significant enrichment in biological processes including homeostatic regulation, protein complex assembly, and G protein-coupled receptor signaling pathways. Among these, ADCY5, PRKCB, and IL2 were of particular interest due to their established roles in longevity-associated mechanisms. Expression analyses revealed tissue-specific patterns suggesting potential involvement in brain evolution, neurodevelopment, and glucose homeostasis.</p><p><strong>Conclusion: </strong>This study provides molecular insights into the genetic mechanisms underlying longevity in apes and highlights key biological processes that may have contributed to the evolution of ape-specific life history traits. These findings enhance our understanding of how positive selection has shaped complex phenotypes, particularly extended lifespan, in the ape lineage.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"807-822"},"PeriodicalIF":1.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143980281","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":"Gene expression profile in ulcerative colitis patients: FOXO4, ALDOB, SLC26A3, SOD2 genes as potential biomarkers.","authors":"Yakup Ülger, Anıl Delik","doi":"10.1007/s13258-025-01625-y","DOIUrl":"10.1007/s13258-025-01625-y","url":null,"abstract":"<p><strong>Background: </strong>Ulcerative colitis (UC) is a complex, chronic inflammatory disease that primarily impacts the colon mucosa. One of the key pathological contributors to the development and progression of inflammatory bowel disease (IBD) is oxidative stress, which results in reactive oxygen species (ROS)-induced mucosal damage. This stress leads to dysfunction of the intestinal barrier.</p><p><strong>Objectives: </strong>The purpose of this study is to examine the expression levels of genes involved in various inflammatory pathways, including autophagy, unfolded protein response (UPR), ubiquitination, metabolic pathways, and immune responses in the colon mucosa of patients with UC.</p><p><strong>Material and methods: </strong>Patients diagnosed with UC at Çukurova University, Balcalı Hospital, Gastroenterology Department between December 2023 and January 2024 were included in this prospective study. A total of 40 participants were included in the study: 27 ulcerative colitis patients and 13 controls. To isolate high-quality RNA, colon biopsy material obtained during colonoscopy was immediately placed in stabilization solution and stored at - 80 degrees Celsius. The relative quantification of target gene mRNA was determined using a Light Cycler. Subsequently, differences in gene expression between patients and the control group were evaluated using the Mann-Whitney U and Kruskal-Wallis tests.</p><p><strong>Results: </strong>In our study, FOXO4 gene expression increased in UC patients during both active and remission phases compared to the control group. The high expression of this gene is associated with its role in inflammation and cell death processes. Additionally, the high expression of ALDOB and SLC26A genes is linked to increased inflammation and energy demand. Lastly, the elevated expression of the SOD2 gene can be considered a response to oxidative stress-related inflammatory processes in the disease.</p><p><strong>Conclusion: </strong>These findings propose that these genes could serve as potential biomarkers for genomic identification and understanding the pathogenesis of UC.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"833-842"},"PeriodicalIF":1.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735756","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 analysis revealed that short-day treatment of seedlings promotes flowering in maize (Zea mays L.).","authors":"Chunlei Li, Hongquan Mao, Xiaoxue Fan, Meihui Yu, Xiaoming Yu","doi":"10.1007/s13258-025-01640-z","DOIUrl":"10.1007/s13258-025-01640-z","url":null,"abstract":"<p><strong>Background: </strong>In this study, blockage of transition from vegetative to reproductive growth was observed in short-day maize (Zea mays L.) varieties under long-day conditions.</p><p><strong>Methods: </strong>Two short-day varieties, namely, CML116 and CML493, were cultivated under long-day conditions at various time points of short-day treatments of seedlings. Notably, short-day treatment was started at the three-leaf stage and ended at the five- (5 L), seven- (7 L) and nine-leaf (9 L) stages. Moreover, transcriptomic analysis (RNA-seq) was carried out to examine the gene expression profiles.</p><p><strong>Results: </strong>The results of gene functional analysis showed that DEGs related to light stimulation and circadian rhythm had different expression patterns among various groups. Additionally, ZmCO, ZmSOC1, ZmFT and ZmHY5 acted as the key regulators of the transition process from vegetative to reproductive growth. Furthermore, the expression of most CO transcripts reached a peak at 5 L in both CML493 and CML116 but decreased in the subsequent short-day treatment.</p><p><strong>Conclusions: </strong>It is possible that accumulation of CO and FT at the seedling stage facilitated transition from vegetative to reproductive growth. In addition, long-day conditions were not conducive to the accumulation of CO and FT as well as their downstream target, SOC1. Moreover, accumulation of the HY5 protein promoted photomorphogenesis, which played a positive role in promoting the normal development of maize plants.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"855-866"},"PeriodicalIF":1.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794731","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":"Role of heat shock proteins and analysis of gene expression in response to high temperatures in date palm (Phoenix dactylifera).","authors":"Seo-Won Yoo, Jae-Han Choi, Seok Won Jeong, Youn-Il Park, Young-Ji Byon, Man-Ho Oh","doi":"10.1007/s13258-025-01648-5","DOIUrl":"10.1007/s13258-025-01648-5","url":null,"abstract":"<p><strong>Background: </strong>Date palm (Phoenix dactylifera L.) is an important agricultural crop in the Middle East and North Africa. The productivity of agricultural crops and physiological function of plants can be greatly affected by climate change that is currently ongoing. According to a recent study, heat waves caused by global warming and climate change will continue to worsen. Therefore, it is necessary to enhance the tolerance of plants, promote growth, and study solutions to reduce yield losses.</p><p><strong>Objective: </strong>The objective of this study is to investigate the role of specific heat-shock proteins (HSPs) from date palm in conferring heat tolerance to plants by analyzing gene expression and generating transgenic Arabidopsis thaliana.</p><p><strong>Methods: </strong>qRT-PCR was used to analyze 49 genes in date palms ('Sukkary' and 'Medjool') exposed at 37 °C for 2 h for heat-shock genes (HSPs). We selected specific heat-shock genes and generated transgenic Arabidopsis plants including PdHSP17.6, PdHSP22.0, PdHSP23.6, and PdHSP26.5. Photosynthetic efficiency (Fv/Fm) was assessed under heat-stress conditions.</p><p><strong>Results: </strong>Transgenic Arabidopsis plants expressing date palm HSP genes maintained higher photosynthetic efficiency under heat stress compared to non-transgenic plants, indicating enhanced thermotolerance.</p><p><strong>Conclusion: </strong>These findings suggest that the introduced HSP genes play a critical role in enabling transgenic Arabidopsis to maintain the photosynthetic efficiency under heat stress, supporting the hypothesis that these genes contribute to thermotolerance in plants.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"823-832"},"PeriodicalIF":1.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144007917","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":"OTOP3 functions as an oncogenic regulator of ferroptosis-mediated colorectal cancer progression.","authors":"Yu Jin Lee, Yeo Jeong Han, Je Joung Oh, Seung-Young Kim, Jaehoon Cho, Ji Hoon Jung","doi":"10.1007/s13258-025-01657-4","DOIUrl":"https://doi.org/10.1007/s13258-025-01657-4","url":null,"abstract":"<p><strong>Background: </strong>OTOP3, a proton channel located at 17q25.1, drives colorectal cancer growth by enhancing c-Myc stability and inhibiting ferroptosis through GPX4 regulation. Inhibition of OTOP3 suppresses CRC proliferation via c-Myc destabilization, ROS accumulation, and lipid peroxidation, while modulating metabolic shifts linked to the Warburg effect. These findings position OTOP3 as a novel therapeutic target for CRC by disrupting oncogenic signaling and ferroptosis resistance.</p><p><strong>Objective: </strong>To investigate OTOP3's role in CRC growth/metastasis and its link to ferroptosis and metabolic reprogramming. To evaluate OTOP3 targeting as a therapeutic strategy.</p><p><strong>Methods: </strong>Colorectal cancer (CRC) cell lines were transfected with OTOP3 siRNA to suppress gene expression, followed by cell viability assays to assess proliferation changes. Western blotting quantified c-Myc and GPX4 levels, while fluorescent probes measured ROS accumulation and lipid peroxidation. Ferroptosis induction was validated using ferroptosis inhibitors, and glycolytic activity was analyzed via glycolysis-related gene expression and lactate production assays.</p><p><strong>Results: </strong>OTOP3 inhibition destabilized c-Myc, suppressed proliferation, and induced ferroptosis via GPX4 reduction, ROS accumulation, and lipid peroxidation. Altered glycolysis factors indicated enhanced Warburg effect.</p><p><strong>Conclusion: </strong>Our study provides compelling evidence that targeting OTOP3 effectively suppresses colorectal cancer proliferation by reducing c-Myc protein stability and inducing ferroptosis. These effects are closely associated with metabolic shifts characteristic of the Warburg effect, emphasizing OTOP3 as a potential therapeutic target in colorectal cancer treatment.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144527551","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":"In silico screening of epitopes as potential vaccine candidates against pathogenic Acinetobacter baumannii.","authors":"Md Minarul Islam, Kyudong Han, Ye-Ji Bang, Je Chul Lee, Woo Shik Shin, Man Hwan Oh","doi":"10.1007/s13258-025-01656-5","DOIUrl":"https://doi.org/10.1007/s13258-025-01656-5","url":null,"abstract":"<p><strong>Background: </strong>Multidrug-resistant (MDR) Acinetobacter baumannii (A. baumannii) poses a pressing threat to global healthcare settings, as most antibiotics are ineffective against this nosocomial pathogen. Vaccines, particularly peptide-based vaccines, offer a promising and effective strategy to deal with these infections.</p><p><strong>Objective: </strong>This study aimed to evaluate the potential of epitopes derived from the OmpA protein of A. baumannii as vaccine candidates for combating this pathogen.</p><p><strong>Methods: </strong>This study employed advanced bioinformatic tools to identify potential epitopes for vaccine candidates against A. baumannii infections. IEDB and SYFPEITHI were used to identify T-cell epitopes of A. baumannii OmpA protein. The epitopes were filtered based on score, clustering, human similarity, immunogenicity, cytokine response, and safety. Epitopes with high scores and both class-I and class-II sites were selected. Three epitopes were chosen for molecular docking and physicochemical evaluation as potential vaccine candidates.</p><p><strong>Results: </strong>Three epitopes (EP1, EP2, and EP3) derived from A. baumannii OmpA were found to effectively bind with specific human leukocyte antigen (HLA) alleles. These epitopes have shown promising potential to elicit both cellular and humoral immune responses. Their physicochemical and immunological properties were thoroughly evaluated, indicating strong antigenic potential, non-toxicity, lack of allergenic properties, good binding affinity, and wide population coverage. The epitopes' two- and three-dimensional structures were predicted, and they were docked with their respective HLA alleles to assess their ability to stimulate innate immune responses. The predicted epitopes and HLA-allelic complexes exhibited excellent binding affinity, optimal Root Mean Square Deviation (RMSD) values, favorable physicochemical properties, and high-quality structural characteristics.</p><p><strong>Conclusions: </strong>This study identified epitopes that hold promise as potential solutions for combating multidrug-resistant A. baumannii, pending validation through wet lab experiments and clinical trials.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144495840","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}