Genomics, proteomics & bioinformatics最新文献

{"title":"A Novel IgG-IgM Autoantibody Panel Enhances Detection of Early-stage Lung Adenocarcinoma from Benign Nodules.","authors":"Rongrong Luo, Xiying Li, Ruyun Gao, Mengwei Yang, Juan Cai, Liyuan Dai, Nin Lou, Guangyu Fan, Haohua Zhu, Shasha Wang, Zhishang Zhang, Le Tang, Jiarui Yao, Di Wu, Yuankai Shi, Xiaohong Han","doi":"10.1093/gpbjnl/qzae085","DOIUrl":"10.1093/gpbjnl/qzae085","url":null,"abstract":"<p><p>Autoantibodies hold promise for diagnosing lung cancer. However, their effectiveness in early-stage detection needs improvement. In this study, we investigated novel IgG and IgM autoantibodies for detecting early-stage lung adenocarcinoma (Early-LUAD) by employing a multi-step approach, including Human Proteome Microarray (HuProtTM) discovery, focused microarray verification, and ELISA validation, on 1246 individuals consisting of 634 patients with Early-LUAD (stage 0-I), 280 patients with benign lung disease (BLD), and 332 normal healthy controls (NHCs). HuProtTM selected 417 IgG/IgM candidates, and focused microarray further verified 55 significantly elevated IgG/IgM autoantibodies targeting 32 tumor-associated antigens in Early-LUAD compared to BLD/NHC/BLD+NHC. A novel panel of 10 autoantibodies (ELAVL4-IgM, GDA-IgM, GIMAP4-IgM, GIMAP4-IgG, MGMT-IgM, UCHL1-IgM, DCTPP1-IgM, KCMF1-IgM, UCHL1-IgG, and WWP2-IgM) demonstrated a sensitivity of 70.5% and a specificity of 77.0% or 80.0% for distinguishing Early-LUAD from BLD or NHC in ELISA validation. Positive predictive values for distinguishing Early-LUAD from BLD with nodules ≤ 8 mm, 9-20 mm, and > 20 mm significantly increased from 47.27%, 52.00%, and 62.90% [low-dose computed tomography (LDCT) alone] to 79.17%, 71.13%, and 87.88% (10-autoantibody panel combined with LDCT), respectively. The combined risk score (CRS), based on the 10-autoantibody panel, sex, and imaging maximum diameter, effectively stratified the risk for Early-LUAD. Individuals with 10 ≤ CRS ≤ 25 and CRS > 25 indicated a higher risk of Early-LUAD compared to the reference (CRS < 10), with adjusted odds ratios of 5.28 [95% confidence interval (CI): 3.18-8.76] and 9.05 (95% CI: 5.40-15.15), respectively. This novel panel of IgG and IgM autoantibodies offers a complementary approach to LDCT in distinguishing Early-LUAD from benign nodules.</p>","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12032526/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SoyOD: An Integrated Soybean Multi-omics Database for Mining Genes and Biological Research.","authors":"Jie Li, Qingyang Ni, Guangqi He, Jiale Huang, Haoyu Chao, Sida Li, Ming Chen, Guoyu Hu, James Whelan, Huixia Shou","doi":"10.1093/gpbjnl/qzae080","DOIUrl":"10.1093/gpbjnl/qzae080","url":null,"abstract":"<p><p>Soybean is a globally important crop for food, feed, oil, and nitrogen fixation. A variety of multi-omics studies have been carried out, generating datasets ranging from genotype to phenotype. In order to efficiently utilize these data for basic and applied research, a soybean multi-omics database with extensive data coverage and comprehensive data analysis tools was established. The Soybean Omics Database (SoyOD) integrates important new datasets with existing public datasets to form the most comprehensive collection of soybean multi-omics information. Compared to existing soybean databases, SoyOD incorporates an extensive collection of novel data derived from the deep-sequencing of 984 germplasms, 162 novel transcriptomic datasets from seeds at different developmental stages, 53 phenotypic datasets, and more than 2500 phenotypic images. In addition, SoyOD integrates existing data resources, including 59 assembled genomes, genetic variation data from 3904 soybean accessions, 225 sets of phenotypic data, and 1097 transcriptomic sequences covering 507 different tissues and treatment conditions. Moreover, SoyOD can be used to mine candidate genes for important agronomic traits, as shown in a case study on plant height. Additionally, powerful analytical and easy-to-use toolkits enable users to easily access the available multi-omics datasets, and to rapidly search genotypic and phenotypic data in a particular germplasm. The novelty, comprehensiveness, and user-friendly features of SoyOD make it a valuable resource for soybean molecular breeding and biological research. SoyOD is publicly accessible at https://bis.zju.edu.cn/soyod.</p>","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11757165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep Amplicon Sequencing Reveals Culture-dependent Clonal Selection of Mycobacterium tuberculosis in Clinical Samples.","authors":"Jiuxin Qu, Wanfei Liu, Shuyan Chen, Chi Wu, Wenjie Lai, Rui Qin, Feidi Ye, Yuanchun Li, Liang Fu, Guofang Deng, Lei Liu, Qiang Lin, Peng Cui","doi":"10.1093/gpbjnl/qzae046","DOIUrl":"10.1093/gpbjnl/qzae046","url":null,"abstract":"<p><p>The commonly-used drug susceptibility testing (DST) relies on bacterial culture and faces shortcomings such as long turnaround time and clonal/subclonal selection biases. Here, we developed a targeted deep amplicon sequencing (DAS) method directly applied to clinical specimens. In this DAS panel, we examined 941 drug-resistant mutations (DRMs) associated with 20 anti-tuberculosis drugs with only 4 pg of initial DNA input, and reduced the clinical testing time from 20 days to 2 days. A prospective study was conducted using 115 clinical specimens, predominantly positive for the Xpert®  Mycobacterium tuberculosis/rifampicin (Xpert MTB/RIF) assay, to evaluate DRM detection. DAS was performed on culture-free specimens, while culture-dependent isolates were used for phenotypic DST, DAS, and whole-genome sequencing (WGS). For in silico molecular DST, our result based on DAS panel revealed the similar accuracy to three published reports based on WGS. For 82 isolates, application of DAS using the resistance-determining mutation method showed better accuracy (93.03% vs. 92.16%), sensitivity (96.10% vs. 95.02%), and specificity (91.33% vs. 90.62%) than WGS using the Mykrobe software. Compared to culture-dependent WGS, culture-free DAS provides a full picture of sequence variation at the population level, exhibiting in detail the gain-and-loss variants caused by bacterial culture. Our study performs a systematic verification of the advantages of DAS in clinical applications and comprehensively illustrates the discrepancies in Mycobacterium tuberculosis before and after culture.</p>","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11978391/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141319301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"iMFP-LG: Identify Novel Multi-functional Peptides Using Protein Language Models and Graph-based Deep Learning.","authors":"Jiawei Luo, Kejuan Zhao, Junjie Chen, Caihua Yang, Fuchuan Qu, Yumeng Liu, Xiaopeng Jin, Ke Yan, Yang Zhang, Bin Liu","doi":"10.1093/gpbjnl/qzae084","DOIUrl":"10.1093/gpbjnl/qzae084","url":null,"abstract":"<p><p>Functional peptides are short amino acid fragments that have a wide range of beneficial functions for living organisms. The majority of previous studies have focused on mono-functional peptides, but an increasing number of multi-functional peptides have been discovered. Although there have been enormous experimental efforts to assay multi-functional peptides, only a small portion of millions of known peptides has been explored. The development of effective and accurate techniques for identifying multi-functional peptides can facilitate their discovery and mechanistic understanding. In this study, we presented iMFP-LG, a method for multi-functional peptide identification based on protein language models (pLMs) and graph attention networks (GATs). Our comparative analyses demonstrated that iMFP-LG outperformed the state-of-the-art methods in identifying both multi-functional bioactive peptides and multi-functional therapeutic peptides. The interpretability of iMFP-LG was also illustrated by visualizing attention patterns in pLMs and GATs. Regarding the outstanding performance of iMFP-LG on the identification of multi-functional peptides, we employed iMFP-LG to screen novel peptides with both anti-microbial and anti-cancer functions from millions of known peptides in the UniRef90 database. As a result, eight candidate peptides were identified, among which one candidate was validated to process both anti-bacterial and anti-cancer properties through molecular structure alignment and biological experiments. We anticipate that iMFP-LG can assist in the discovery of multi-functional peptides and contribute to the advancement of peptide drug design.</p>","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12011362/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142712263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Novel Targeted Long-read Sequencing Approach Boosts Transcriptomic Profiling.","authors":"Xiaolong Tian, Rong Fan","doi":"10.1093/gpbjnl/qzae090","DOIUrl":"10.1093/gpbjnl/qzae090","url":null,"abstract":"","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11802469/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Variation and Interaction of Distinct Subgenomes Contribute to Growth Diversity in Intergeneric Hybrid Fish.","authors":"Li Ren, Mengxue Luo, Jialin Cui, Xin Gao, Hong Zhang, Ping Wu, Zehong Wei, Yakui Tai, Mengdan Li, Kaikun Luo, Shaojun Liu","doi":"10.1093/gpbjnl/qzae055","DOIUrl":"10.1093/gpbjnl/qzae055","url":null,"abstract":"<p><p>Intergeneric hybridization greatly reshapes regulatory interactions among allelic and non-allelic genes. However, their effects on growth diversity remain poorly understood in animals. In this study, we conducted whole-genome sequencing and RNA sequencing analyses in diverse hybrid varieties resulting from the intergeneric hybridization of goldfish (Carassius auratus red var.) and common carp (Cyprinus carpio). These hybrid individuals were characterized by distinct mitochondrial genomes and copy number variations. Through a weighted gene correlation network analysis, we identified 3693 genes as candidate growth-regulating genes. Among them, the expression of 3672 genes in subgenome R (originating from goldfish) displayed negative correlations with body weight, whereas 20 genes in subgenome C (originating from common carp) exhibited positive correlations. Notably, we observed intriguing expression patterns of solute carrier family 2 member 12 (slc2a12) in subgenome C, showing opposite correlations with body weight that changed with water temperatures, suggesting differential interactions between feeding activity and weight gain in response to seasonal changes for hybrid animals. In 40.30% of alleles, we observed dominant trans-regulatory effects in the regulatory interactions between distinct alleles from subgenomes R and C. Integrating analyses of allele-specific expression and DNA methylation data revealed that DNA methylation on both subgenomes shaped the relative contribution of allelic expression to the growth rate. These findings provide novel insights into the interactions of distinct subgenomes that underlie heterosis in growth traits and contribute to a better understanding of multiple allelic traits in animals.</p>","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11810642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141750100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decoding Spatial Complexity of Diverse RNA Species in Archival Tissues.","authors":"Junjie Zhu, Fangqing Zhao","doi":"10.1093/gpbjnl/qzae089","DOIUrl":"10.1093/gpbjnl/qzae089","url":null,"abstract":"","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784585/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug.","authors":"Zhenyong Du, Xuan Wang, Yuange Duan, Shanlin Liu, Li Tian, Fan Song, Wanzhi Cai, Hu Li","doi":"10.1093/gpbjnl/qzae074","DOIUrl":"10.1093/gpbjnl/qzae074","url":null,"abstract":"<p><p>Invasive species cause massive economic and ecological damages. Climate change has resulted in an unprecedented increase in the number and impact of invasive species; however, the mechanisms underlying these invasions are unclear. The sycamore lace bug, Corythucha ciliata, is a highly invasive species originating from North America and has expanded across the Northern Hemisphere since the 1960s. In this study, we assembled the C. ciliata genome using high-coverage Pacific Biosciences (PacBio), Illumina, and high-throughput chromosome conformation capture (Hi-C) sequencing. A total of 15,278 protein-coding genes were identified, and expansions of gene families with oxidoreductase and metabolic activities were observed. In-depth resequencing of 402 samples from native and nine invaded countries across three continents revealed 2.74 million single nucleotide polymorphisms. Two major invasion routes of C. ciliata were identified from North America to Europe and Japan, with a contact zone forming in East Asia. Genomic signatures of selection associated with invasion and long-term balancing selection in native ranges were identified. These genomic signatures overlapped with each other as well as with expanded genes, suggesting improvements in the oxidative stress and thermal tolerance of C. ciliata. These findings offer valuable insights into the genomic architecture and adaptive evolution underlying the invasive capabilities of species during rapid environmental changes.</p>","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11993305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142484014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enzyme Repertoires and Genomic Insights into Lycium barbarum Pectin Polysaccharide Biosynthesis.","authors":"Haiyan Yue, Yiheng Tang, Aixuan Li, Lili Zhang, Yiwei Niu, Yiming Zhang, Hao Wang, Jianjun Luo, Yi Zhao, Shunmin He, Chang Chen, Runsheng Chen","doi":"10.1093/gpbjnl/qzae079","DOIUrl":"10.1093/gpbjnl/qzae079","url":null,"abstract":"<p><p>Lycium barbarum, a member of the Solanaceae family, is an important eudicot with applications in both food and medicine. L. barbarum pectin polysaccharides (LBPPs) are key bioactive compounds of L. barbarum, notable for being among the few polysaccharides with both biocompatibility and biomedical activity. Although studies have analyzed the functional properties of LBPPs, the mechanisms underlying their biosynthesis and transport by key enzymes remain poorly understood. In this study, we assembled a 2.18-Gb reference genome of L. barbarum, reconstructed the first complete biosynthesis pathway of LBPPs, and elucidated the sugar transport system. We also characterized the important genes responsible for backbone extension, sidechain synthesis, and modification of LBPPs. Furthermore, we characterized the long non-coding RNAs (lncRNAs) associated with polysaccharide metabolism. We identified a specific rhamnogalacturonan I (RG-I) rhamnosyltransferase, RRT3020, which enhances RG-I biosynthesis within LBPPs. These newly identified enzymes and pivotal genes endow L. barbarum with unique pectin biosynthesis capabilities, distinguishing it from other Solanaceae species. Our findings thus provide a foundation for evolutionary studies and molecular breeding to expand the diverse applications of L. barbarum.</p>","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12011363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142570796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome Assembly and Winged Fruit Gene Regulation of Chinese Wingnut: Insights from Genomic and Transcriptomic Analyses.","authors":"Fangdong Geng, Xuedong Zhang, Jiayu Ma, Hengzhao Liu, Hang Ye, Fan Hao, Miaoqing Liu, Meng Dang, Huijuan Zhou, Mengdi Li, Peng Zhao","doi":"10.1093/gpbjnl/qzae087","DOIUrl":"10.1093/gpbjnl/qzae087","url":null,"abstract":"<p><p>The genomic basis and biology of winged fruit are interesting issues in ecological and evolutionary biology. Chinese wingnut (Pterocarya stenoptera) is an important horticultural and economic tree species in China. The genomic resources of this hardwood tree could advance the genomic studies of Juglandaceae species and elucidate their evolutionary relationships. Here, we reported a high-quality reference genome of P. stenoptera (N50 = 35.15 Mb) and performed a comparative genomic analysis across Juglandaceae species. Paralogous relationships among the 16 chromosomes of P. stenoptera revealed eight main duplications representing the subgenomes. Molecular dating suggested that the most recent common ancestor of P. stenoptera and Cyclocarya paliurus diverged from Juglans species around 56.7 million years ago (MYA). The expanded and contracted gene families were associated with cutin, suberine, and wax biosynthesis, cytochrome P450, and anthocyanin biosynthesis. We identified large inversion blocks between P. stenoptera and its relatives, which were enriched with genes involved in lipid biosynthesis and metabolism, as well as starch and sucrose metabolism. Whole-genome resequencing of 28 individuals revealed clearly phylogenetic clustering into three groups corresponding to Pterocarya macroptera, Pterocarya hupehensis, and P. stenoptera. Morphological and transcriptomic analyses showed that CAD, COMT, LOX, and MADS-box play important roles during the five developmental stages of wingnuts. This study highlights the evolutionary history of the P. stenoptera genome and supports P. stenoptera as an appropriate Juglandaceae model for studying winged fruits. Our findings provide a theoretical basis for understanding the evolution, development, and diversity of winged fruits in woody plants.</p>","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12043009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}