Functional & Integrative Genomics最新文献

{"title":"Genome-wide identification and functional analysis of TCX gene family and the critical role of GhTCX17 in response to drought and salt stress in cotton.","authors":"Yangyang Wei, Jingjing Zhai, Shuaikang Geng, Shaoliang Zhang, Yongqing Zhao, Bingkai Cui, Huiyun Shan, Yanhua Li, Cong Wang, Pengtao Li, Yuling Liu, Quanwei Lu, Baohong Zhang, Renhai Peng","doi":"10.1007/s10142-025-01632-y","DOIUrl":"https://doi.org/10.1007/s10142-025-01632-y","url":null,"abstract":"<p><p>Cotton is an important natural fiber crop. The Tesmin/TSO1-like CXC (TCX) gene family plays an important role in plant resistance to environmental stress, and its mechanism is still not clear in cotton. In this study, we systematically identified the potential functions of TCX family genes in cotton were investigated based on genome identification, phylogenetic and genomic analyses, chromosome mapping and cis-regulatory element prediction. A total of 79 TCX genes were identified in the genome-wide analysis of four cotton species. Chromosomal localization and synteny analysis revealed that the TCX gene family was relatively conservative and fragment replication was the main amplification mode of TCX gene family during cotton evolution. Cis-element analysis showed that there were a plenty of elements related to light response, hormone response and abiotic stress response in the TCX gene promoter. Gene expression analysis based on RNA-seq and qRT-PCR showed that TCX genes were responsive to abiotic stress. The key gene GhTCX17 was cloned for functional verification. GhTCX17 protein was localized in the nucleus. Under drought and salt stress, silencing GhTCX17 gene plants showed leaf wilting aggravation, decreased total antioxidant capacity, increased malondialdehyde content compared with control plants, implied the reducing drought and salt tolerance of silencing GhTCX17 gene in cotton. This study revealed the evolution and function diversity of the TCX gene family and laid an important foundation for further study to dissect TCX gene family functioning mechanisms on cotton stress resistance.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"129"},"PeriodicalIF":3.9,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144300907","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":"QBEmax redefines the precise base editing in crop plants.","authors":"Muhammad Waseem Sajjad, Fatima Muzamil, Rubab Zahra Naqvi, Imran Amin","doi":"10.1007/s10142-025-01638-6","DOIUrl":"https://doi.org/10.1007/s10142-025-01638-6","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"127"},"PeriodicalIF":3.9,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281884","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-omics insights into abiotic stress responses: bridging functional genomics and precision crop breeding.","authors":"Tayachew Admas, Shu Jiao, Rui Pan, Wenying Zhang","doi":"10.1007/s10142-025-01633-x","DOIUrl":"https://doi.org/10.1007/s10142-025-01633-x","url":null,"abstract":"<p><p>Crop production has been regarded as the major goal of agricultural activities, but the rapidly growing population and climate change have become more complex in the agricultural systems. Abiotic stress greatly affects crop productivity globally; developing more resilient crop varieties has become imperative. However, we can understand how plants tolerate abiotic stress better by using new methods that combine different scientific approaches like pan-genomics, pan-transcriptomics, pan-proteomics, pan-metabolomics, and pan-phenomics. Investigations using a pan-omics approach are necessary to consider the variation resulting from complex interactions among genes, proteins, metabolites, and regulatory networks within a species. A comparative study of core, dispensable, and unique components across different accessions assists in identifying novel genes, proteins, and metabolites responsible for stress tolerance. Moreover, databases and online repositories now enable the storage, analysis, and retrieval of data generated by high-throughput technologies. The combination provides guidelines for researchers to harness the potential of pan-omics in promoting sustainable agricultural practices. Therefore, the review focuses on recent trends in pan-omics for studying abiotic stress responses and their applications in crop improvement. It also highlights the application of artificial intelligence (AI) in data integration and monitoring crop environments.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"128"},"PeriodicalIF":3.9,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281883","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":"Doubling the grain: Harnessing the power of DG1 promoter inversion in sorghum.","authors":"Tilak Chandra","doi":"10.1007/s10142-025-01637-7","DOIUrl":"https://doi.org/10.1007/s10142-025-01637-7","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"126"},"PeriodicalIF":3.9,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144273898","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":"Genome-resolved metagenomics from short-read sequencing data in the era of artificial intelligence.","authors":"Hajra Qayyum, Zaara Ishaq, Amjad Ali, Masood Ur Rehman Kayani, Lisu Huang","doi":"10.1007/s10142-025-01625-x","DOIUrl":"https://doi.org/10.1007/s10142-025-01625-x","url":null,"abstract":"<p><p>Genome-resolved metagenomics is a computational method that enables researchers to reconstruct microbial genomes from a given sample directly. This process involves three major steps, i.e. (i) preprocessing of the reads (ii) metagenome assembly, and (iii) genome binning, with (iv) taxonomic classification, and (v) functional annotation as additional steps. Despite the availability of multiple bioinformatics approaches, metagenomic data analysis encounters various challenges due to high dimensionality, data sparseness, and complexity. Meanwhile, integrating artificial intelligence (AI) at different stages of data analysis has transformed genome-resolved metagenomics. Though the application of machine learning and deep learning in metagenomic annotation started earlier, the emergence of better sequencing technologies, improved throughput, and reduced processing time have rendered the initial models less efficient. Consequently, the number of AI-based metagenomics tools is continuously increasing. The recent AI-based tools demonstrate superior performance in handling complex and multi-dimensional metagenomics data, offering improved accuracy, scalability, and efficiency compared to traditional models. In this paper, we reviewed recent AI-based tools specifically developed for short-read metagenomic data, and their underlying models for genome-resolved metagenomics. It also discusses the performance of these tools and overviews their usability in metagenomics research. We believe this study will provide researchers with insights into the strengths and limitations of current AI-based approaches, serving as a valuable resource for selecting appropriate tools and guiding future advancements in genome-resolved metagenomics.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"124"},"PeriodicalIF":3.9,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257058","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":"CRISPR/Cas9-mediated editing of jasmonic acid pathways to enhance biotic & abiotic stress tolerance: An overview & prospects.","authors":"Jaspreet Kaur, Ananthu Viswanathan P, Vinay Kumar Bari","doi":"10.1007/s10142-025-01623-z","DOIUrl":"https://doi.org/10.1007/s10142-025-01623-z","url":null,"abstract":"<p><p>Food security is becoming increasingly important as the world's population grows, and the likelihood that climate change could impair agricultural supply complicates matters further. However, plants actively suppress growth as an adaptation strategy to enhance survival under stress conditions. Phytohormone jasmonates (JAs) regulate various physiological processes, including plant growth, development, and senescence. Plant biotic and abiotic stress responses cause dynamic shifts in the metabolism and signaling of JAs, suggesting that JAs response impacts plant development and resistance to various stresses. The JAs-associated responses depend on core components of JAs -signaling, including the transcriptional repressors protein JAZ and the transcription factor MYC2. While traditional breeding has greatly benefited the world, this approach has several disadvantages, such as the emergence of undesirable traits and species barriers. Genome editing technology has revolutionized plant biology research and has significant ramifications for agriculture and global food security, particularly in light of climate change and population growth. CRISPR/Cas9 and its derivative tools have been used for genome editing in numerous crops to improve or alter desired plant phenotypes. This review summarizes JA's role in plant stress and defense and how CRISPR/Cas9-editing technology modifies plant JA's responses, especially against biotic and abiotic stress.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"125"},"PeriodicalIF":3.9,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257057","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":"Unveiling the Therapeutic Potential of Targeting RRM2 in Hepatocellular Carcinoma: An Integrated In Silico and In Vitro Study.","authors":"Lobna Ibrahim, Rania Hassan Mohamed, Mahmoud M Tolba, Sara M Radwan, Nadia M Hamdy, Mahmoud Elhefnawi","doi":"10.1007/s10142-025-01630-0","DOIUrl":"10.1007/s10142-025-01630-0","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"123"},"PeriodicalIF":3.9,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12152083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257059","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":"Integrated muti-omics data and machine learning reveal CD151 as a key biomarker inducing chemoresistance in metabolic syndrome-related early-onset left-sided colorectal cancer.","authors":"Yingdong Hou, Hubin Xia, Chenshan Xu, Yuhua Yu, Chenghao Ji, Wenli Ruan, Wencheng Kong, Yifeng Zhou, Xiaofeng Zhang","doi":"10.1007/s10142-025-01634-w","DOIUrl":"10.1007/s10142-025-01634-w","url":null,"abstract":"<p><p>Emerging evidence has suggested a potential pathological association between early-onset left-sided colorectal cancer (EOLCC) and metabolic syndrome (MetS). However, the underlying genetic and molecular mechanisms remain insufficiently elucidated. This study aimed to identify and characterize key biomarkers associated with the progression and treatment response of MetS-related EOLCC. An in-hospital cohort was utilized to assess the clinical implications of primary tumor location in early-onset colorectal cancer (EOCRC). Differentially expressed genes (DEGs) and weighted gene coexpression network analysis (WGCNA) were employed to identify genes potentially associated with MetS-related EOLCC. Functional enrichment analyses were conducted to explore the underlying mechanisms. Candidate biomarkers were screened using random forest (RF) and support vector machine-recursive feature elimination (SVM-RFE) algorithms. Survival relevance, expression profiles, and diagnostic performance were analyzed to identify key biomarkers. Treatment responses were evaluated, and potential therapeutic compounds were identified through molecular docking. Single-cell RNA sequencing (scRNA-seq) data and in vitro experiments were used to validate gene expression and functional characteristics. The in-hospital cohort revealed a higher proportion of EOLCC among EOCRC patients. Using the edgeR package and WGCNA, we identified coexpressed genes common to both EOLCC and MetS, significantly enriched in pathways associated with stromal remodeling and metabolic regulation. Machine learning algorithms highlighted three candidate biomarkers. Among them, only CD151 was associated with prognosis and advanced disease stage. CD151 was strongly correlated with stromal remodeling and chemoresistance. Additionally, potential therapeutic compounds targeting MetS-related EOLCC were identified via molecular docking. scRNA-seq analysis confirmed the expression and functional patterns of CD151, particularly in tumor cells. The bioinformatics results were further validated through quantitative real-time PCR (qRT-PCR), western blotting, and immunohistochemical (IHC) staining. This study identified CD151 as a key biomarker in MetS-related EOLCC, offering valuable insights into prognosis, tumor biology, and personalized treatment strategies. CD151 may serve as a reference for future research and clinical applications targeting this disease subtype.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"122"},"PeriodicalIF":3.9,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12146227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144245577","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":"PIN1 serves as a prognostic and therapeutic biomarker in lung adenocarcinoma.","authors":"Juncheng Yu, Xiao Lu, Dong Zhou, Jiao Zhang, Xufeng Deng, Xiaobing Liu, Kai Wang, Shuangqing Liao, Hong Zheng, Jigang Dai","doi":"10.1007/s10142-025-01629-7","DOIUrl":"https://doi.org/10.1007/s10142-025-01629-7","url":null,"abstract":"<p><p>Lung adenocarcinoma (LUAD) remains a leading cause of cancer-related mortality worldwide, with limited response rates and resistance to targeted therapies and immunotherapies. Pin1, a phosphorylation-specific peptidyl-prolyl isomerase, has been implicated in multiple oncogenic pathways; however, its role in LUAD is not fully understood. We conducted an integrative analysis using public datasets (TCGA, GEO, HPA), LUAD tissue microarrays, malignant pulmonary nodule specimens, and cell line models to investigate the expression and function of PIN1 in LUAD. Functional assays, immunohistochemistry, and in vivo xenograft models were employed to validate the biological effects of PIN1 in LUAD progression and treatment response. PIN1 expression was significantly downregulated in LUAD tissues compared to adjacent normal lung tissues. High PIN1 expression was associated with improved overall survival, increased immune cell infiltration, and enhanced response to immunotherapy. Overexpression of PIN1 inhibited proliferation and migration while promoting apoptosis of LUAD cells in vitro and in vivo. Mechanistically, high PIN1 expression activated downstream pAKT and pMAPK signaling, potentially contributing to EGFR-TKI resistance despite unchanged pEGFR levels. Moreover, functional enrichment analysis and immune profiling revealed that PIN1 is positively associated with antitumor immune responses in LUAD, contrasting its immunosuppressive role in other cancers. PIN1 exhibits tumor-suppressive activity in LUAD and may serve as a promising biomarker for prognosis and therapeutic response. These findings underscore the context-dependent role of PIN1 and support further exploration of its mechanistic involvement in LUAD immunobiology and targeted therapy resistance.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"121"},"PeriodicalIF":3.9,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144232901","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":"BIRC5 as a master regulator in HCC: unraveling its role in tumor survival and therapeutic potential.","authors":"Aya M Ayoub, Elham Abdel-Badiea Mahmoud, Rania Hassan Mohamed, Mahmoud M Tolba, Nahla S Hassan, Mohamed Ghazy, Mahmoud ElHefnawi","doi":"10.1007/s10142-025-01615-z","DOIUrl":"10.1007/s10142-025-01615-z","url":null,"abstract":"<p><p>Hepatocellular carcinoma (HCC) is one of the most prevalent and lethal malignancies worldwide, with limited effective therapeutic options. Identifying novel targets is crucial for improving treatment strategies. In this study, we integrated bioinformatics and experimental approaches to uncover key regulatory genes in HCC. BIRC5 (survivin) emerged as a central hub gene, playing a pivotal role in apoptosis inhibition and cell cycle regulation. Using CRISPR-Cas9-mediated knockout in HepG2 cells, we demonstrated that BIRC5 depletion significantly suppressed cell proliferation and migration while inducing apoptosis. Furthermore, BIRC5 knockout led to cell cycle arrest, cytokinesis defects, and autophagy activation, highlighting its essential role in tumor maintenance. Functional assays, including colony formation, wound healing, flow cytometry, gene expression profiling, and transmission electron microscopy, validated these findings. Notably, the downregulation of key oncogenic pathways, including PI3K and AURKA, underscores the critical function of BIRC5 in sustaining HCC cell survival and proliferation. These results position BIRC5 as a promising therapeutic target, with the potential to disrupt tumor growth and metastasis. Targeting BIRC5 could offer a novel strategy for improving HCC treatment outcomes, paving the way for more effective therapeutic interventions against this aggressive cancer.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"120"},"PeriodicalIF":3.9,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12141170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144223965","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}