Current Genomics最新文献

{"title":"Bioinformatics Analysis of Lactylation-related Biomarkers and Potential Pathogenesis Mechanisms in Age-related Macular Degeneration.","authors":"Chenwei Gui, Yan Gao, Rong Zhang, Guohong Zhou","doi":"10.2174/0113892029291661241114055924","DOIUrl":"10.2174/0113892029291661241114055924","url":null,"abstract":"<p><strong>Background: </strong>Lactylation is increasingly recognized to play a crucial role in human health and diseases. However, its involvement in age-related macular degeneration (AMD) remains largely unclear.</p><p><strong>Objectives: </strong>The aim of this study was to identify and characterize the pivotal lactylation-related genes and explore their underlying mechanism in AMD.</p><p><strong>Methods: </strong>Gene expression profiles of AMD patients and control individuals were obtained and integrated from the GSE29801 and GSE50195 datasets. Differentially expressed genes (DEGs) were screened and intersected with lactylation-related genes for lactylation-related DEGs. Machine learning algorithms were used to identify hub genes associated with AMD. Subsequently, the selected hub genes were subject to correlation analysis, and reverse transcription quantitative real-time PCR (RT-qPCR) was used to detect the expression of hub genes in AMD patients and healthy control individuals.</p><p><strong>Results: </strong>A total of 68 lactylation-related DEGs in AMD were identified, and seven genes, including <i>HMGN2</i>, <i>TOP2B</i>, <i>HNRNPH1</i>, <i>SF3A1</i>, <i>SRRM2</i>, <i>HIST1H1C</i>, and <i>HIST1H2BD</i> were selected as key genes. RT-qPCR analysis validated that all 7 key genes were down-regulated in AMD patients.</p><p><strong>Conclusion: </strong>We identified seven lactylation-related key genes potentially associated with the progression of AMD, which might deepen our understanding of the underlying mechanisms involved in AMD and provide clues for the targeted therapy.</p>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"26 3","pages":"191-209"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12105335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144157265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity.","authors":"Ujwal Dahal, Anu Bansal","doi":"10.2174/0113892029325491240919151045","DOIUrl":"10.2174/0113892029325491240919151045","url":null,"abstract":"<p><p>Analyzing prokaryotic codon usage trends has become a crucial topic of study with significant ramifications for comprehending microbial genetics, classification, evolution, and the control of gene expression. This review study explores the numerous facets of prokaryotic codon usage patterns, looking at different parameters like habitat and lifestyle across broad groups of prokaryotes by emphasizing the role of codon reprogramming in adaptive strategies and its integration into systems biology. We also explored the numerous variables driving codon usage bias, including natural selection, mutation, horizontal gene transfer, codon-anticodon interaction, and genomic composition in prokaryotes through a thorough study of current literature. Furthermore, a special session on codon usage on pathogenic prokaryotes and the role of codon usage in the phylogeny of prokaryotes has been discussed. We also looked at the various software and indices that have been recently applied to prokaryotic genomes. The promising directions that lay ahead to map the future of codon usage research on prokaryotes have been emphasized. Codon usage variations across prokaryotic communities could be better understood by combining environmental, metagenomic, and system biology approaches.</p>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"26 2","pages":"81-94"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12105230/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144157254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CDT1 is a Potential Therapeutic Target for the Progression of NAFLD to HCC and the Exacerbation of Cancer.","authors":"Xingyu He, Jun Ma, Xue Yan, Xiangyu Yang, Ping Wang, Lijie Zhang, Na Li, Zheng Shi","doi":"10.2174/0113892029313473240919105819","DOIUrl":"10.2174/0113892029313473240919105819","url":null,"abstract":"<p><strong>Aims: </strong>This study aimed to identify potential therapeutic targets in the progression from non-alcoholic fatty liver disease (NAFLD) to hepatocellular carcinoma (HCC), with a focus on genes that could influence disease development and progression.</p><p><strong>Background: </strong>Hepatocellular carcinoma, significantly driven by non-alcoholic fatty liver disease, represents a major global health challenge due to late-stage diagnosis and limited treatment options. This study utilized bioinformatics to analyze data from GEO and TCGA, aiming to uncover molecular biomarkers that bridge NAFLD to HCC. Through identifying critical genes and pathways, our research seeks to advance early detection and develop targeted therapies, potentially improving prognosis and personalizing treatment for NAFLD-HCC patients.</p><p><strong>Objectives: </strong>Identify key genes that differ between NAFLD and HCC; Analyze these genes to understand their roles in disease progression; Validate the functions of these genes in NAFLD to HCC transition.</p><p><strong>Methods: </strong>Initially, we identified a set of genes differentially expressed in both NAFLD and HCC using second-generation sequencing data from the GEO and TCGA databases. We then employed a Cox proportional hazards model and a Lasso regression model, applying machine learning techniques to the large sample data from TCGA. This approach was used to screen for key disease-related genes, and an external dataset was utilized for model validation. Additionally, pseudo-temporal sequencing analysis of single-cell sequencing data was performed to further examine the variations in these genes in NAFLD and HCC.</p><p><strong>Results: </strong>The machine learning analysis identified IGSF3, CENPW, CDT1, and CDC6 as key genes. Furthermore, constructing a machine learning model for CDT1 revealed it to be the most critical gene, with model validation yielding an ROC value greater than 0.80. The single-cell sequencing data analysis confirmed significant variations in the four predicted key genes between the NAFLD and HCC groups.</p><p><strong>Conclusion: </strong>Our study underscores the pivotal role of CDT1 in the progression from NAFLD to HCC. This finding opens new avenues for early diagnosis and targeted therapy of HCC, highlighting CDT1 as a potential therapeutic target.</p>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"26 3","pages":"225-243"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144157266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influenza Virus Genomic Mutations, Host Barrier and Cross-species Transmission.","authors":"Wenyan Xiong, Zongde Zhang","doi":"10.2174/0113892029316603240926051325","DOIUrl":"10.2174/0113892029316603240926051325","url":null,"abstract":"<p><p>Influenza is a global epidemic infectious disease that causes a significant number of illnesses and deaths annually. Influenza exhibits high variability and infectivity, constantly jumping from birds to mammals. Genomic mutations of the influenza virus are a central mechanism leading to viral variation and antigenic evolution. Amino acid substitutions and avoidance of microRNA recognition elements are crucial in facilitating the virus to cross species barriers. This review summarizes the types of genomic mutations in the influenza virus, their roles and mechanisms in crossing species barriers, and analyzes the impact of these mutations on human health.</p>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"26 3","pages":"161-174"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12105246/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144157267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>JAG2</i>: A Potential Biomarker for Microtia Identified by Integrated RNA Transcriptome Analysis.","authors":"Xu Wu, Yaoyao Fu, Jing Ma, Chenlong Li, Tianyu Zhang, Aijuan He","doi":"10.2174/0113892029311725240911065539","DOIUrl":"10.2174/0113892029311725240911065539","url":null,"abstract":"<p><strong>Introduction: </strong>Microtia, a prevalent congenital maxillofacial deformity, significantly impacts the physical and psychological health of children. Its etiology, especially in non-syndromic cases, remains a complex and partially understood domain, complicating etiological treatment. Recent studies pointed to a genetic predisposition in non-syndromic microtia, yet research on susceptible or pathogenic genes is limited.</p><p><strong>Objectives: </strong>This study focused on identifying key biomarker genes in microtia cartilage to elucidate pathogenesis and assist in prenatal diagnosis.</p><p><strong>Methods: </strong>We first collated two bulk transcriptome datasets from the GEO database, followed by functional enrichment analysis and Weighted Gene Co-expression Network Analysis (WGCNA) to pinpoint differentially expressed genes (DEGs) and gene modules. The subsequent intersection of DEGs with WGCNA modules, aided by support vector machine-recursive feature elimination (SVM-RFE) and protein-protein interaction (PPI) networks, predicted potential susceptibility genes for microtia. Finally, we integrated bulk RNA sequencing with single-cell data <i>via</i> the \"scissor\" R package and further validated it with Real-time PCR and immunofluorescence.</p><p><strong>Results: </strong>We identified <i>JAG2</i> as a prominent biomarker for microtia, evidenced by its significant upregulation in microtia cartilage.</p><p><strong>Conclusion: </strong>Our findings implicate <i>JAG2</i> in microtia development and suggest its role in chondrocyte maturation and differentiation through Notch signaling pathway activation, shedding light on the potential pathogenesis of microtia.</p>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"26 3","pages":"210-224"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12105267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144157264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic Landscape of Colorectal Mucinous Adenocarcinoma has Similarity with Intestinal Goblet Cell Differentiation","authors":"Jianbo Liu, Siyuan Qiu, Xiaorui Fu, Bin Zhou, Ruijuan Zu, Zhaoying Lv, Yuan Li, Lie Yang, Zongguang Zhou","doi":"10.2174/0113892029312303240821080358","DOIUrl":"https://doi.org/10.2174/0113892029312303240821080358","url":null,"abstract":"Introduction: Colorectal mucinous adenocarcinoma (MC) differs from adenocarcinoma (AD) in clinical features and molecular characteristics. The current treatment of colorectal MC is not precise enough, and the molecular characteristics remain unclear. The study aims to explore the difference between colorectal MC and AD on the transcriptome level for the possibility of treating colorectal MC precisely. Methods: The data of colorectal cancer (CRC) patients from The Cancer Genome Atlas (TCGA) database was assessed, and then differential analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify the differential hub RNAs between colorectal MC and AD. Differential hub lncRNAs and hub RNA of significant modules were validated by quantitative real-time PCR (qRT-PCR) among different colon cancer cell lines. Results: In total, 1680 differential expressed RNAs (DERs) were found by comparing colorectal MC (52, 13.3%) with AD (340, 86.7%). Through the WGCNA, a mucin-associated RNA module was identified, while some others might be associated with unique immune progress. Finally, 6 differential hub RNAs in the mucin-associated RNA module (CTD-2589M5.4, RP11-234B24.2, RP11-25K19.1 and COLCA1) were validated by qRT-PCR and showed higher expression levels in mucin-producing colorectal cell lines (Ls174T and HT-29). Conclusion: This study suggests that clinical treatments for colorectal MC should be differentiated from AD. Further exploration of enterocyte (goblet cell) differentiation with tumor genesis and the distinct immune progression of MC may help to identify key therapeutic targets for colorectal MC. Further research on the application of immunotherapy to colorectal MC is needed.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"146 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181516","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 Insight into Immunological Therapeutic Approach against Cancer: Potential Anti-Cancer Vaccines","authors":"Arjun Singh Kohli, Somali Sanyal, Radhey Shyam Kaushal, Manish Dwivedi","doi":"10.2174/0113892029319505240821063238","DOIUrl":"https://doi.org/10.2174/0113892029319505240821063238","url":null,"abstract":"The development of a cancer vaccine comes with its complications and designing and developing a vaccine against foreign invaders such as bacterial and viral particles is not as complex and multi-faceted as the preparation of immunotherapy for host-infected cells which resemble our own body cells. The entire research and development framework of designing a vaccine for cancerous cells lies entirely on the remarkable aspect of notifying specific interactions and acclimatising the immune system. This review aims to compile the several fronts research-based methodology applies to in terms of developing a therapeutic, preventive or personalised vaccine for cancer . The approach lays focus on the identification and selection of targets for vaccine development which have come to light as immune biomarkers. Furthemore, significant aspects of personalised and precision vaccines and the fine line that runs between these approaches have also been discussed.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"173 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181517","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":"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}