Functional & Integrative Genomics最新文献

Central airway stenosis, arising from both benign and malignant etiologies, remains challenging to treat effectively. Elucidating the underlying molecular mechanisms is therefore essential. We integrated single-cell RNA sequencing with bulk transcriptomic data to identify key mechanisms in airway stenosis. Findings were subsequently validated using molecular biology assays. Fibroblasts were identified as key contributors to fibrotic remodeling in stenotic airways. Four genes—FAM118A, RCN3, PCSK7, and REEP3—were found to promote airway stenosis. Elevated immune activity was observed in stenotic tissues and showed a positive correlation with the expression of these genes. Mechanistically, these genes facilitate stenosis by activating KRAS→PI3K-AKT pathway, leading to upregulation of fibroblast activation markers. The expression of these genes is transcriptionally regulated by TBX20. Specifically, the ILF3-AS1/miR-212-5p axis regulates FAM118A, PCSK7, and REEP3, but not RCN3. This study aims to provide insights into the pathological mechanisms underlying airway stenosis, with all findings experimentally validated through integrated molecular and cellular approaches.

Peroxidases (PRXs) are involved in diverse physiological processes, including cell elongation and lignification. However, studies on PRX genes and their tissue specificity in Medicago truncatula remain limited. In this study, 117 MtPRX genes were identified through bioinformatic analysis and classified into five distinct groups. Segmental duplications were identified as the major driving force for MtPRX expansion. Evolutionary analysis revealed closer phylogenetic relationships between MtPRX and GmPRX in soybean. Expression of MtPRXs were detected in roots, stems, leaves, flowers, seeds, and leaf buds, with members exhibiting distinct tissue-specific expression patterns. Tnt1 insertion mutants of the tissue-specific gene MtPRX76, designated mtprx76-1 and mtprx76-2, showed significantly reduced gene expression levels and decreased lignin content. Transcriptome analysis identified 3015 and 3564 differentially expressed genes (DEGs) in mtprx76-1 and mtprx76-2, respectively. GO and KEGG enrichment analyses revealed that the phenylpropanoid biosynthesis pathway was the most significantly enriched. Furthermore, transcriptional levels of 14 key regulatory genes involved in lignin biosynthesis were significantly downregulated in both mutant lines. These results demonstrate that MtPRX76 functions as a positive regulator influencing lignin biosynthesis. This study systematically characterizes the member features, sequence structures, evolutionary relationships, and tissue-specific expression patterns of the MtPRX gene family, and tissue specific expression patterns, while functionally validating MtPRX76. These findings establish a theoretical basis for understanding Class III PRX gene functions and breeding low lignin germplasm in alfalfa.

WRKYs represent a large family of plant transcription factors characterized by a highly conserved WRKY domain. WRKY transcription factors are important for plant growth, development, and responses to environmental stresses. However, this family has not been previously identified in Sesuvium portulacastrum, a typical halophyte that grows in saline soils and coastal marshlands and contributes to the stability of coastal ecosystems. Here, we identified 68 SpWRKYs from S. portulacastrum and classified them into six subclades. These genes were unevenly distributed across twenty-two chromosomes and exhibited both intra- and interspecific expansion based on segmental duplication events, orthologous gene pairs, and duplication relationships. All SpWRKY proteins contained at least one conserved WRKY domain, and their promoters contain 33 cis-elements involving abiotic stress signaling, developmental regulation, phytohormone responses, light responsiveness, and tissue-specific expression. Transcriptome analysis under cadmium, copper, and salt stress showed that many SpWRKYs were stress-responsive. Among them, SpWRKY40 and SpWRKY51 showed 3.8-fold and 4.2-fold induction in roots under cadmium treatment, which was further confirmed by quantitative real-time PCR. Subcellular localization and transient expression in tobacco, together with yeast one-hybrid experiments, demonstrated that SpWRKY40 and SpWRKY51 function as transcription activators. They bind specifically to the GTCAA and TTGACC cis-elements. Our study provides a detailed overview of the SpWRKY family and functional insights into SpWRKY40 and SpWRKY51 as transcription activators. The findings offer valuable candidate genes for future applications in improving cadmium stress tolerance in S. portulacastrum and related crop species.

Ovarian cancer (OC) remains a major threat to women’s health, with chemoresistance driven by the immunosuppressive tumor microenvironment. Formin-2 (FMN2), a cytoskeletal regulator, was investigated for its role in OC chemoresistance and macrophage polarization. Bioinformatics analysis identified high FMN2 expression in chemotherapy-resistant OC cell lines, validated experimentally. Stable FMN2 knockdown cell lines were generated via lentiviral transfection. Functional assays revealed that FMN2 overexpression conferred chemoresistance in vitro and in vivo and promoted M2 macrophage polarization via the CCL2/JAK2/STAT3 pathway. Co-culture with M2 macrophages enhanced cisplatin (DDP) resistance in OC cells, mediated by CXCL1 secretion, which activated the epithelial-mesenchymal transition (EMT) pathway. Clinically, FMN2 levels correlated with CCL2 and CD206 (M2 marker) in platinum-resistant patients, and high FMN2, CCL2, or CD206 expression predicted poorer overall and disease-free survival. This study identifies FMN2 as a key mediator of chemoresistance and immune evasion in OC, proposing FMN2-CCL2-CD206 signaling and macrophage-derived CXCL1 as therapeutic targets and prognostic markers for chemotherapy response.

The progression of age-related pathologies is strongly linked to biological aging. Identifying natural anti-aging agents to mitigate disease onset and development holds substantial therapeutic value. The natural compound Gastrodin (Gas) demonstrates promising effects in retarding aging. This study aims to explore the effects of Gas on the lifespan and antioxidant capacity of Caenorhabditis elegans (C. elegans). Additionally, it seeks to elucidate the possible mechanisms. Initially, Gas was assessed for its influence on C. elegans lifespan, mobility, lipofuscin accumulation, and oxidative stress responses. Subsequent analyses focused on Gas’s modulation of the insulin/IGF-1 pathway, mitochondrial activity, autophagic processes, and gene expression to uncover its lifespan-extending mechanisms. Gas induced a dose-dependent lifespan extension in C. elegans, peaking at 400 µM with a 17.3% increase in longevity. Gas enhanced C. elegans mobility while suppressing age-related lipofuscin deposition.Additionally, Gas lowered ROS levels and elevated antioxidant enzyme activity in C. elegans.Mechanistic studies revealed that Gas’s anti-aging effects rely on transcription factors (DAF-16, SKN-1, HSF-1) and bolster stress resistance via HSPs activation and autophagy induction. This study reveals the potential of Gas in extending the lifespan of C. elegans, emphasizes its mechanism of action by regulating antioxidant capacity, heat stress response, and autophagy pathway, and provides experimental evidence that supports the development of Gas as a candidate compound for lifespan extension.

Anthracnose, caused by the hemibiotrophic fungal pathogen Colletotrichum sublineola, is a significant constraint to sorghum production worldwide. Developing resistant cultivars is the most sustainable control strategy, but it requires constant additional sources of resistance genes. Here, we applied machine learning (ML) approaches, specifically Bootstrap Forest and Boosted Tree models, to identify single-nucleotide polymorphisms (SNPs) associated with anthracnose resistance in a panel of Senegalese sorghum accessions using publicly available phenotypic data from seedling and 8-leaf stages. The ML models identified five novel high-importance loci distinct from those found by linear model-based Genome-wide association studies (GWAS), while also reinforcing three candidates detected by both methods. The top candidates found through ML algorithms were leucine-rich repeat (LRR), F-box, aspartic peptidase, and jasmonate O-methyltransferase. Several genes were highlighted by both ML and GWAS, strengthening the evidence for their involvement. This study demonstrates the potential of ML to complement traditional GWAS in identifying candidate genes for complex traits, providing a valuable resource for future functional studies and marker-assisted selection efforts to enhance anthracnose resistance in sorghum. Given the constraints of the available population size, these results are best interpreted as an explanatory framework that highlights potential targets for further investigation and guides future functional validation, rather than as a definitive predictive tool.

Chimeric antigen receptor (CAR)-engineered natural killer (NK) cells are emerging as an exciting avenue in cancer immunotherapy due to their potent cytotoxicity to malignant cells and lower risk of graft-versus-host disease (GvHD) than conventional T cell therapies. The new technology of CRISPR/Cas9 genome editing has significantly expedited the engineering of CAR-NK cells by enabling easy, multiplex, and precise changes to enhance their efficacy, persistence, and specificity to tumors. This review focuses on the incorporation of CRISPR technology into CAR-NK cell development. It examines uses of knockout of inhibitory checkpoint genes (CISH, PD-1, and TGFBR2), as well as knock-in of CAR into safe genomic locations and multiplex editing of CAR-NK cells to improve cytotoxicity against cancer while resisting suppression from the tumor microenvironment (TME). We further explore immuno-cytokine armoring strategies by knock-in of IL-15 or IL-12, to ensure prolonged proliferation and survival of NK cells, and investigate CRISPR-mediated knockouts of immune inhibitors like NKG2A and TIGIT, to evade immune strategies used by the tumor to evade immune destruction. Furthermore, CRISPR-mediated upregulation of the homing receptor enhances NK cell tumor infiltration, addressing a major obstacle in treating solid tumors. It is significant to mention the progress in generating off-the-shelf products, which is a key step supporting the pursuit of allogeneic therapies. While substantial progress has been made, challenges remain related to optimizing CRISPR delivery, off-target effects, and enhancing in vivo persistence. Future directions of CAR-NK studies will likely capitalize on next-generation genome editing tools and synthetic biology for the development of tunable and logic-gated CAR-NK cells. Overall, this review illustrates the revolutionary capacity of combining CRISPR technology with CAR-NK immunotherapy to develop next-generation programmable and efficacious treatments for hematologic and solid malignancies.

This study presents a novel approach that integrates recombinase polymerase amplification (RPA) with PfAgo protein technology for the rapid and precise detection of the MTHFR A1298C polymorphism. Although traditional genotyping methods are effective, they are often limited by complexity, high cost, and the need for specialized equipment. The RPA-PfAgo technique harnesses the swift isothermal amplification of RPA and the high specificity and sensitivity of PfAgo-mediated DNA cleavage, completing the entire process from sample collection to detection within 90 min. The utility of this method has been substantiated through a battery of optimization experiments, parameter analysis, and assessments of sensitivity, specificity, and repeatability, along with clinical validation using oral mucosal samples. These findings indicate that this new technology not only substantially reduces detection time and cost but also offers an effective tool for personalized medicine and disease prevention with high accuracy and reliability.

Oenothera species are increasingly valued for their medicinal and ornamental qualities and serve as important models in classical cytoplasmic genetics research. The genus Oenothera L., one of the largest in the Onagraceae family, includes 18 subsections and two deep phylogenetic lineages, Clade A and Clade B. Analyzing high-quality chloroplast genomes can provide crucial insights into species classification and genus-level evolution. In this study, we report the complete chloroplast genome of Oenothera drummondii Hook., the first species from subsection Raimannia, with a total length of 167,177 bp and a GC content of 39.3%. This genome contains 129 genes and displays a typical quadripartite structure. Combining this genome with data from 16 publicly available chloroplast genomes, we conducted a comprehensive comparative and evolutionary analysis. Our results indicate that Clade B species diverged independently from Clade A species. Within Clade A, species from subsection Muniza form a distinct branch, while O. drummondii clusters closely with species from subsection Oenothera. Phylogenetic analysis correlates well with chloroplast genome structural differences, such as the loss of the infA gene in Clade B species, the expansion of the IR regions in Muniza, and a shared large inversion in the LSC region among Raimannia and Oenothera species. We also identified repeat sequences, six highly variable genes, and positively selected genes among the 17 chloroplast genomes analyzed. These findings offer valuable insights into the evolutionary processes of Oenothera species and provide a foundation for the development of future molecular markers based on the identified genes and structural variations.

Graphical Abstract

The breakthrough progress in gene editing technology has established a brand-new paradigm for gene function analysis and crop genetic improvement, and has already become the core driving force in modern agricultural biotechnology. However, traditional methods for screening edited individual plants without T-DNA insertion in their offspring are time-consuming and labor-intensive. To accelerate the identification of T-DNA-free edited plants, researchers have continuously explored various strategies to improve screening efficiency, achieving some success. Despite this progress, these strategies also exhibit varying degrees of limitations. Recently, research teams led by Cheng and Sun (2025) and Zhu et al. (2025) constructed gamete elimination systems, successfully achieving a 100% non-transgenic status in the mutant plants. This innovative approach has transformed traditional molecular testing from a "laboratory-dependent" model to "field-based real-time decision-making" providing an efficient and cost-effective solution for precision breeding.