Current Genomics最新文献

{"title":"Whole Genome Sequences of Cryptotympana Atrata Fabricius, 1775 (Hemiptera: Cicadidae) in the Korean Peninsula: Insights into Population Structure with Novel Pathogenic Or Symbiotic Candidates","authors":"Jeong Sun Park, Jina Kim, Yeha Kim, Ki Hwan Kim, Woori Kwak, Iksoo Kim","doi":"10.2174/0113892029314148240820082402","DOIUrl":"https://doi.org/10.2174/0113892029314148240820082402","url":null,"abstract":"Background: The blackish cicada (Cryptotympana atrata) exhibits unique characteristics and is one of the model cicadas found in the Korean Peninsula. It is a species of southern origin, prefers high temperatures, and is listed as a climate-sensitive indicator species in South Korea. Therefore, this species can be utilized to study the impact of climate change on the genetic diversity and structure of populations. However, research on the genome of C. atrata is limited. Methods: We sequenced the genome of an individual collected from South Korea and constructed a draft genome. Additionally, we collected ten specimens from each of the five regions in South Korea and identified single nucleotide variants (SNVs) for population genetic analysis. The sequencing library was constructed using the MGIEasy DNA Library Prep Kit and sequenced using the MGISEQ-2000 platform with 150-bp paired-end reads. Results: The draft genome of C. atrata was approximately 5.0 Gb or 5.2 Gb, making it one of the largest genomes among insects. Population genetic analysis, which was conducted on four populations in South Korea, including both previously distributed and newly expanded regions, showed that Jeju Island, a remote southern island with the highest average temperature, formed an independent genetic group. However, there were no notable genetic differences among the inland populations selected based on varying average temperatures, indicating that the current population genetic composition on the Korean Peninsula is more reflective of biogeographic history rather than climate- induced genetic structures. Additionally, we unexpectedly observed that most individuals of C. atrata collected in a specific locality were infected with microbes not commonly found in insects, necessitating further research on the pathogens within C. atrata. Conclusion: This study introduces the draft genome of C. atrata, a climate-sensitive indicator species in South Korea. Population analysis results indicate that the current genetic structure of C. atrata is driven by biogeographic history rather than just climate. The prevalence of widespread pathogen infections raises concerns about their impact on C. atrata. Considering the scarcity of publicly available genomic resources related to the family Cicadidae, this draft genome and population data of C. atrata are expected to serve as a valuable resource for various studies utilizing cicada genomes.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"87 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181519","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":"ResUbiNet: A Novel Deep Learning Architecture for Ubiquitination Site Prediction","authors":"Zixin Duan, Yafeng Liang, Xin Xiu, Wenjie Ma, Hu Mei","doi":"10.2174/0113892029331751240820111158","DOIUrl":"https://doi.org/10.2174/0113892029331751240820111158","url":null,"abstract":"Introduction: Ubiquitination, a unique post-translational modification, plays a cardinal role in diverse cellular functions such as protein degradation, signal transduction, DNA repair, and regulation of cell cycle. Method: Thus, accurate prediction of potential ubiquitination sites is an urgent requirement for exploring the ubiquitination mechanism as well as the disease pathogenesis associated with ubiquitination processes. Results: This study introduces a novel deep learning architecture, ResUbiNet, which utilized a protein language model (ProtTrans), amino acid properties, and BLOSUM62 matrix for sequence embedding and multiple state-of-the-art architectural components, i.e., transformer, multi-kernel convolution, residual connection, and squeeze-and-excitation for feature extractions. Conclusion: The results of cross-validation and external tests showed that the ResUbiNet model achieved better prediction performances in comparison with the available hCKSAAP_UbSite, RUBI, MDCapsUbi, and MusiteDeep models.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"7 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181518","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":"Genomic Face-Off: An In Silico Comparison of the Probiotic Potential of Lactobacillus spp. and Akkermansia muciniphila","authors":"Nayeema Bulbul, Jinath Sultana, Ashrafus Safa, Md. Asaduzzaman Shishir, Bakhtiar Ul Islam, Md. Fakruddin, Md. Abu Bakar karim","doi":"10.2174/0113892029317403240815044408","DOIUrl":"https://doi.org/10.2174/0113892029317403240815044408","url":null,"abstract":"Introduction: The gut microbiota plays a crucial role in maintaining human health, and probiotics have gained significant attention for their potential benefits. Among the diverse array of gut bacteria, Akkermansia muciniphila, and Lactobacillus spp. have emerged as promising candidates for their putative probiotic properties. Method: In this study, we conducted a comprehensive comparative in silico analysis of the genomes of A. muciniphila and Lactobacillus to decipher their probiotic potential. Utilizing a range of bioinformatics tools, we evaluated various genomic attributes, including functional gene content, metabolic pathways, antimicrobial peptide production, adhesion factors, and stress response elements. These findings revealed distinctive genomic signatures between the two genera. A. muciniphila genomes exhibited a high prevalence of mucin-degrading enzymes, suggesting a specialized adaptation for mucin utilization in the gut environment. Results: Additionally, the presence of specific pathways for short-chain fatty acid production highlighted its potential impact on host health. Lactobacillus genomes, on the other hand, demonstrated a diverse repertoire of functional genes associated with probiotic attributes, including the production of antimicrobial peptides and adhesion factors, indicating potential for host-microbe interactions and immune modulation. Furthermore, this analysis unveiled the genetic basis of stress tolerance in both genera, revealing conserved mechanisms for surviving the dynamic conditions of the gut ecosystem. Conclusion: This study also shed light on the distribution of antibiotic-resistance genes, allowing us to assess safety concerns associated with their potential use as probiotics. Overall, this comparative in silico exploration provides valuable insights into the genomic foundation of A. muciniphila and Lactobacillus probiotic potential. These findings contribute to the understanding of their respective roles within the gut microbiota and offer a foundation for further experimental investigations. As probiotic applications continue to expand, this study advances our knowledge of the genetic underpinnings that govern their functionality and highlights promising avenues for future therapeutic interventions and personalized health strategies.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"10 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181520","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":"An Assessment of the Degradation Potential and Genomic Insights Towards Hydroxylated Biphenyls by Rhodococcus opacus Strain KT112-7","authors":"Darya Egorova, Bjorn Olsson, Tatyana Kir'yanova, Elena Plotnikova","doi":"10.2174/0113892029319746240812051356","DOIUrl":"https://doi.org/10.2174/0113892029319746240812051356","url":null,"abstract":"Background: Hydroxylated biphenyls are currently recognized as secondary pollutants that are hazardous to animals and humans. Bacterial degradation is the most effective method for the degradation of hydroxylated biphenyls. Several strains capable of degrading polychlorinated biphenyls have been described, which also degrade hydroxylated biphenyls. Objectives: 1) To study the biodegradative properties of the Rhodococcus opacus strain KT112-7 towards mono-hydroxylated biphenyls. 2) To analyze the genome of the Rhodococcus opacus strain KT112-7. 3) To identify the genetic basis for the unique biodegradative potential of the Rhodococcus opacus strain KT112-7. Methods: A genome analysis of the strain KT112-7 was conducted based on whole-genome sequencing using various programs and databases (Velvet, CONTIGuator, RAST, KEGG) for annotation and identification of protein-coding sequences. The strain KT112-7 was cultivated in a K1 mineral medium supplemented with mono-hydroxy biphenyls or mono-hydroxybenzoic acids as the carbon source. For the growth test mono-hydroxybiphenyls or mono-hydroxybenzoic acids were dosed at concentrations of 0.5 g/L and 1.0 g/L correspondently, and the bacterial growth was monitored by the optical density. For the biodegradative activity test, mono-hydroxybiphenyls were dosed at a concentration of 0.1 g/L in vials, inoculated with late exponential phase bacteria previously acclimated on biphenyl. Compound analysis was performed using GC-MS, HPLC, and spectrophotometry. Results: It was found that the genome of strain KT112-7 consists of a chromosome and 2 plasmids. Biphenyl degradation genes (bph genes) were identified on plasmid PRHWK1 and the chromosome, as well as hydroxybenzoic acid degradation genes on the chromosome. The strain KT112-7 was shown to degrade mono-hydroxylated biphenyls to basal metabolic compounds of the cell, with the highest destructive activity observed towards 3- and 4-hydroxylated biphenyls (98%). Conclusion: The Rhodococcus opacus strain KT112-7 is characterized by genetic systems that contribute to its high biodegradative potential towards mono-hydroxylated biphenyls and their metabolites. Thus, the strain KT112-7 is promising for use in hydroxybiphenyl degradation technologies.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"19 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181536","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":"High-Throughput Sequencing Revealing BCR and TCR Repertoires as Potential Prognostic Biomarkers for Pediatric Patients with B-ALL","authors":"Fu Li, Xiaomei Yang, Xiuxiu Wang, Jiajia Mi, Xiao Mou, Li Song, Libo Zheng","doi":"10.2174/0113892029319425240813074610","DOIUrl":"https://doi.org/10.2174/0113892029319425240813074610","url":null,"abstract":"Background: B-ALL is a hematologic malignancy that recurs in approximately 10-20% of children and has a poor prognosis. New prognostic biomarkers are needed to improve individualized therapy and achieve better clinical outcomes. Methods: In this study, high-throughput sequencing technology was used to detect the BCR and TCR repertoires in children with B-ALL. Results: We observed a gradual increase in the diversity of the BCR and TCR repertoires during the developmental stages (Pro-, Common-, Pre-B-ALL) of precursor B-ALL cells. Conversely, as minimal residual disease (MRD) levels on day 19 of induction therapy increased, the BCR/TCR repertoire diversity decreased. Furthermore, the BCR/TCR repertoire diversity was significantly greater in B-ALL patients at low risk and those harboring the ETV6/RUNX1 fusion than in patients with medium-risk disease and those harboring the ZNF384 fusion. Notably, the abundance of BCR/TCR clones varied significantly among patients with B-ALL and different clinical characteristics. Specifically, patients with Pre-B-ALL, low-risk disease, D19MRD levels <1%, and harboring the ETV6/RUNX1 fusion exhibited a predominance of BCR/TCR small clones. In our study, we noted an imbalanced occurrence of V and J gene utilization among patients with BALL; however, there seemed to be no discernible correlation with the clinical attributes. Conclusion: BCR/TCR repertoires are expected to be potential prognostic biomarkers for patients with B-ALL.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"2 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181537","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":"The Regulatory Landscape of Biobanks In Europe: From Accreditation to Intellectual Property","authors":"Antonella Corradi, Giuseppina Bonizzi, Elham Sajjadi, Francesca Pavan, Marzia Fumagalli, Luigi Orlando Molendini, Massimo Monturano, Cristina Cassi, Camilla Rosella Musico, Luca Leoni, Chiara Frascarelli, Oriana Pala, Elena Guerini-Rocco, Adriana Albini, Roberto Orecchia, Nicola Fusco","doi":"10.2174/0113892029313697240729091922","DOIUrl":"https://doi.org/10.2174/0113892029313697240729091922","url":null,"abstract":": Biobanks are necessary resources for the storage and management of human biological materials, such as biofluids, tissues, cells, or nucleotides. They play a significant role in the development of new treatments and the advancement of basic and translational research, especially in the field of biomarkers discovery and validation. The regulatory landscape for biobanks, which is necessary to safeguard both privacy and scientific discoveries, exhibits significant heterogeneity across different countries and regions. This article outlines the standards that modern biobanks should fulfill in the European Union (EU), including general, structural, resource, process, and quality requirements. Special attention is given to the importance of transparency and donor consent following the General Data Protection Regulation (GDPR) and the ISO 20387:2018, the international standard specifies general requirements for biobanks. A dedicated section covers the preparation of donor information materials, emphasizing consent for research involvement and personal data processing. The delicate balance between donors' privacy rights and scientific research promotion is also discussed, with a focus on the patenting and economic use of biological material- derived inventions and data. Considering these factors, it would be warranted to refine legal frameworks and foster interdisciplinary collaboration to ethically and responsibly expand biobanking.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"159 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141871280","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":"Integrative Bioinformatics Analysis for Targeting Hub Genes in Hepatocellular Carcinoma Treatment","authors":"Indu Priya Gudivada, Krishna Chaitanya Amajala","doi":"10.2174/0113892029308243240709073945","DOIUrl":"https://doi.org/10.2174/0113892029308243240709073945","url":null,"abstract":"Background: The damage in the liver and hepatocytes is where the primary liver cancer begins, and this is referred to as Hepatocellular Carcinoma (HCC). One of the best methods for detecting changes in gene expression of hepatocellular carcinoma is through bioinformatics approaches. Objective: This study aimed to identify potential drug target(s) hubs mediating HCC progression using computational approaches through gene expression and protein-protein interaction datasets. Methodology: Four datasets related to HCC were acquired from the GEO database, and Differentially Expressed Genes (DEGs) were identified. Using Evenn, the common genes were chosen. Using the Fun Rich tool, functional associations among the genes were identified. Further, protein-protein interaction networks were predicted using STRING, and hub genes were identified using Cytoscape. The selected hub genes were subjected to GEPIA and Shiny GO analysis for survival analysis and functional enrichment studies for the identified hub genes. The up-regulating genes were further studied for immunohistopathological studies using HPA to identify gene/protein expression in normal vs HCC conditions. Drug Bank and Drug Gene Interaction Database were employed to find the reported drug status and targets. Finally, STITCH was performed to identify the functional association between the drugs and the identified hub genes. Results: The GEO2R analysis for the considered datasets identified 735 upregulating and 284 downregulating DEGs. Functional gene associations were identified through the Fun Rich tool. Further, PPIN network analysis was performed using STRING. A comparative study was carried out between the experimental evidence and the other seven data evidence in STRING, revealing that most proteins in the network were involved in protein-protein interactions. Further, through Cytoscape plugins, the ranking of the genes was analyzed, and densely connected regions were identified, resulting in the selection of the top 20 hub genes involved in HCC pathogenesis. The identified hub genes were: KIF2C, CDK1, TPX2, CEP55, MELK, TTK, BUB1, NCAPG, ASPM, KIF11, CCNA2, HMMR, BUB1B, TOP2A, CENPF, KIF20A, NUSAP1, DLGAP5, PBK, and CCNB2. Further, GEPIA and Shiny GO analyses provided insights into survival ratios and functional enrichment studied for the hub genes. The HPA database studies further found that upregulating genes were involved in changes in protein expression in Normal vs HCC tissues. These findings indicated that hub genes were certainly involved in the progression of HCC. STITCH database studies uncovered that existing drug molecules, including sorafenib, regorafenib, cabozantinib, and lenvatinib, could be used as leads to identify novel drugs, and identified hub genes could also be considered as potential and promising drug targets as they are involved in the gene-chemical interaction networks. Conclusion: The present study involved various integrated bioinformatics approaches, analyzing gen","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"26 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141754006","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":"Melocular Evolution on Cold Temperature Adaptation of Chinese Rhesus Macaques","authors":"Xuan Wang, Ming-Hong Feng, Shao-Bo Wang, Hong Shi","doi":"10.2174/0113892029301969240708094053","DOIUrl":"https://doi.org/10.2174/0113892029301969240708094053","url":null,"abstract":"Introduction: Currently, macaques are used as animal models for human disease in biomedical research. There are two macaques species widely used as animal models, i.e., cynomolgus macaques and rhesus macaques. Method: These two primates distribute widely, and their natural habitats are different. Cynomolgus macaques distribute in tropical climates, while rhesus macaques mostly distribute in relatively cold environments, and cynomolgus macaques have a common frostbite problem during winter when they are transferred to cold environments. In order to explore the molecular mechanisms underlying the temperature adaptation in macaques, genetic analysis and natural selection tests were performed. Based on the analysis of heat shock protein genes, DNAJC22, DNAJC28, and HSF5 showed positive selection signals. To these 3 genes, the significantly differential expression had been confirmed between cynomolgus macaques and Chinese rhesus macaques. Molecular evolution analysis showed that mutations of DNAJC22, DNAJC28, and HSF5 in Chinese rhesus macaques could enable them to gain the ability to rapidly regulate body temperature. The heat shock proteins provided an important function for Chinese rhesus macaques, allowing them to adapt to a wide range of temperatures and spread widely. Results: The selection time that was estimated suggested that the cold adaptation of Chinese rhesus macaques coincided with the time that the modern human populations migrated northward from tropic regions to relatively cold regions, and the selection genes were similar. Conclusion: This study elucidated the evolutionary history of cynomolgus macaques and rhesus macaques from molecular adaptation. Furthermore, it provided an evolutionary perspective to reveal the different distribution and adaptation of macaques. Cynomolgus macaques is an ideal biomedical animal model to mimic human natural frostbite.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"57 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141609437","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":"Pan-Genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges","authors":"Akansha Sarwad, Spoorti Hosgoudar, Prachi Parvatikar","doi":"10.2174/0113892029311541240627111506","DOIUrl":"https://doi.org/10.2174/0113892029311541240627111506","url":null,"abstract":": A pan-genome is a compilation of the common and unique genomes found in a given species. It incorporates the genetic information from all of the genomes sampled, producing a big and diverse set of genetic material. Pan-genomic analysis has various advantages over typical genomics research. It creates a vast and varied spectrum of genetic material by combining the genetic data from all the sampled genomes. Comparing pan-genomics analysis to conventional genomic research, there are a number of benefits. Although the most recent era of pan-genomic studies has used cutting-edge sequencing technology to shed fresh light on biological variety and improvement, the potential uses of pan-genomics in improvement have not yet been fully realized. Pangenome research in various organisms has demonstrated that missing genetic components and the detection of significant Structural Variants (SVs) can be investigated using pan-genomic methods. Many individual-specific sequences have been linked to biological adaptability, phenotypic, and key economic attributes. This study aims to focus on how pangenome analysis uncovers genetic differences in various organisms, including human, and their effects on phenotypes, as well as how this might help us comprehend the diversity of species. The review also concentrated on potential problems and the prospects for future pangenome research.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"29 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141548802","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-Knockdown Methods for Silencing Nuclear-Localized Insulin Receptors in Lung Adenocarcinoma Cells: A Bioinformatics Approach","authors":"Qiu Ren, Hui Ma, Lingling Wang, Jiayu Qin, Miao Tian, Wei Zhang","doi":"10.2174/0113892029298721240627095839","DOIUrl":"https://doi.org/10.2174/0113892029298721240627095839","url":null,"abstract":"Background: Lung adenocarcinoma, the predominant subtype of lung cancer, presents a significant challenge to public health due to its notably low five-year survival rate. Recent epidemiological data highlights a concerning trend: patients with pulmonary adenocarcinoma and comorbid diabetes exhibit substantially elevated mortality rates compared to those without diabetes, suggesting a potential link between hyperinsulinemia in diabetic individuals and accelerated progression of pulmonary adenocarcinoma. Insulin Receptor (IR) is a tyrosine-protein kinase on the cell surface, and its over-expression is considered the pathological hallmark of hyperinsulinemia in various cancer cell types. Research indicates that IR can translocate to the nucleus of lung adenocarcinoma cells to promote their proliferation, but its precise molecular targets remain unclear. This study aims to silence IRs in lung adenocarcinoma cells and identify key genes within the ERK pathway that may serve as potential molecular targets for intervention. Methods: Gene expression data from lung adenocarcinoma and para cancer tissues were retrieved from the Gene Expression Omnibus (GEO) database and assessed through \"pheatmap\", GO annotation, KEGG analysis, R calculations, Cytoscape mapping, and Hub gene screening. Significant genes were visualized using the ggplot2 tool to compare expression patterns between the two groups. Additionally, survival analysis was performed using the R \"survminer\" and \"survival\" packages, along with the R \"pathview\" package for pathway visualization. Marker genes were identified and linked to relevant signaling pathways. Validation was conducted utilizing real-time quantitative polymerase chain reaction and immunoblotting assays in an A549 lung cancer cell model to determine the roles of these marker genes in associated signaling cascades. Results: The study examined 58 lung adenocarcinoma samples and paired para-neoplastic tissues. Analysis of the GSE32863 dataset from GEO revealed 1040 differentially expressed genes, with 421 up-regulated and 619 down-regulated. Visualization of these differences identified 172 significant alterations, comprising 141 up-regulated and 31 down-regulated genes. Functional enrichment analysis using Gene Ontology (GO) revealed 56 molecular functions, 77 cellular components, and 816 biological processes. KEGG analysis identified 17 strongly enriched functions, including cytokine interactions and tumor necrosis factor signaling. Moreover, the ERK signaling pathway was associated with four Hub genes (FGFR4, ANGPT1, TEK, and IL1B) in cellular biological processes. Further validation demonstrated a positive correlation between IL-1B expression in the ERK signaling pathway and lung cancer through real-time fluorescence quantitative enzyme- linked reaction with immunoblotting assays. Conclusion: In IR-silenced lung adenocarcinoma, the expression of the IL-1B gene exhibited a positive correlation with the ERK signaling pathway.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"21 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141548803","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}