Functional & Integrative Genomics最新文献

Higher phytoglycogen in Su1-based sweetcorn kernels have created a niche market in Europe and Americas due to its distinct aroma, flavour and tenderness as well as plump and juicy texture over Shrunken2 (Sh2)-based sweetcorn. Unavailability of diverse Su1-based inbreds poses challenge for Su1-based hybrid development. Here, we introgressed mutant Su1 gene into four elite Sh2-based parental lines of two Sh2-based sweetcorn hybrids (PSSC-1 and PSSC-2) using molecular breeding in two backcrosses. Su1-based (SuDel36) and Sh2-based (SNP_AG1) markers were successfully used for foreground selection in backcross generations, that followed Mendelian segregation, although segregation distortion was observed in a few cases. More than 94% recurrent parent genome was recovered using SSR markers. Su1-based inbreds possessed significantly higher phytoglycogen (24.3%) over recurrent parents (5.6%). Across environments, Su1-based reconstituted hybrids also possessed higher phytoglycogen (25.8%) compared to original hybrids (5.5%). The Su1-based inbreds and hybrids possessed 14.4% and 13.9% sucrose, respectively. These inbreds and hybrids resembled their original versions for various agronomic traits. These newly developed Su1-based sweetcorn hybrids possess great potential in export markets, besides serving as a rich source of phytoglycogen in cosmetics, pharmaceuticals and nutraceuticals industries. This is the first report on development of phytoglycogen-enriched Su1-based sweetcorn hybrids using accelerated breeding. This is likely to promote broader industrial applications of phytoglycogen, thereby unveiling the underexplored potential of Su1-based sweet corn.

The wings has played a crucial role in the survival and reproduction of insects. The structure of flat insect wings is established through the adhesion of the dorsal and ventral epidermal layers, a process that is contingent upon the dynamics of the basal extracellular matrix (ECM). However, compared with basal ECM, the function of apical ECMs during the wing development remains inadequately understood. In this study, we identified a zona pellucida (ZP) family gene, piopio (pio), as important components of the aECM. This gene exhibited high expression levels in the wing discs of both Bombyx mori and Drosophila melanogaster. Disruption of the gene in these two species resulted in impaired adhesion of the wing layers, leading to the formation of blistered wings. Moreover, the loss-of-function of pio prevented the degradation of the basal ECM, a critical phase required for initial adhesion of wing. Additionally, we observed a similar phenotypic manifestation in two pest species, Tribolium castaneum and Locusta migratoria, thereby confirming the conserved function of the pio gene in the wing development of insects. Our findings not only advance understanding of ZP proteins in insect wing morphogenesis but also propose pio as a potential target for pest control.

Breast cancer (BC) remains a leading cause of cancer-related mortality among women worldwide, with treatment resistance posing a significant clinical challenge. Circular RNAs (circRNAs), a class of non-coding RNAs, have gained increasing attention as key regulators of gene expression, influencing BC pathogenesis, progression, and therapeutic response. This review explores the mechanistic insights into circRNA functions in BC, focusing on their involvement in tumor proliferation, metabolic reprogramming, epithelial-mesenchymal transition (EMT), angiogenesis, metastasis, and apoptosis. Additionally, we highlight the crosstalk between circRNAs and microRNAs, emphasizing their potential as diagnostic and prognostic biomarkers. Beyond their roles in tumor biology, circRNAs are implicated in drug resistance, modulating responses to chemotherapy, targeted therapy, and endocrine treatment. Despite their promising applications, challenges remain, including the complexity of circRNA interactions, and the development of robust preclinical models. Addressing these challenges through interdisciplinary research integrating genomics, transcriptomics, and functional studies will pave the way for circRNA-based therapeutic strategies and personalized medicine approaches in BC management.

Biomarkers identified through integrated bioinformatics approaches often exhibit limited temporal stability during sepsis progression. To address this limitation, temporal changes in the serum transcriptome of sepsis patients were analyzed at multiple time points to investigate underlying pathological mechanisms. The datasets GSE54514 and GSE212092 from the Gene Expression Omnibus (GEO) database were used for gene identification and validation. The key marker RAPGEF6 with temporal characteristics was identified by integrating time-series clustering analysis, differential expression analysis, weighted gene co-expression network analysis (WGCNA), and single-cell data analysis. Stable RAPGEF6-knockdown RAW264.7 macrophages were generated using lentiviral shRNA delivery to investigate the role of RAPGEF6 in sepsis. A total of 2,701 genes showed time-associated expression patterns during sepsis progression. Integrative analysis combining differential expression and WGCNA-derived modules identified three hub genes: RAPGEF6, CHD9, and POGULT1. RAPGEF6 showed the highest area under the receiver operating characteristic curve (AUROC) of 0.9206 (95% CI: 0.8383-1). Immune infiltration analysis indicated that RAPGEF6 had the strongest correlation with M1 macrophages (correlation coefficient = 0.42). The analysis of single-cell data targeting key genes and external experiments confirmed this finding. RAPGEF6 expression in macrophages increased during the early phase of lipopolysaccharide (LPS) stimulation and then decreased over time. Stable knockout of RAPGEF6 in macrophages using lentiviral vectors attenuated LPS-induced inflammatory responses and oxidative stress by inhibiting NF-κB-mediated necroptosis. Time-series transcriptomic analysis revealed highly dynamic gene expression trajectories in sepsis patients. RAPGEF6, identified as a key biomarker with temporal characteristics, may regulate inflammation and oxidative stress via NF-κB-mediated necroptosis.

As an important cash crop, cotton is susceptible to drought stress, which leads to reduced yields. Receptor-like protein kinases are widely distributed in plants and play important roles in plant growth, development and stress response. In this study, 94 L-type LecRLK genes were identified in upland cotton, while 88, 49 and 55 LecRLK genes were identified in 3 additional cotton species, respectively. The LecRLKs were divided into four groups by phylogenetic and evolutionary analysis among Five species (Arabidopsis thaliana and four cotton species). In upland cotton, LecRLK was evenly distributed in the two subgenomes and was mostly localized to the cell membrane. The Ka/Ks values of 90% of the GhLecRLK genes were less than 1, indicating that GhLecRLK family genes were purified and selected. Analysis of promoter cis-acting elements revealed that the GhLecRLK gene contained multiple ABA and MYB response elements, and GO enrichment analysis revealed that the GhLecRLK gene was enriched in the biological process of hydrogen peroxide metabolism. RNA-seq analysis showed that some GhLecRLK genes were higher expression at 6–12 h after induction by drought stress. These highly expressed genes were verified by qRT-PCR in drought-tolerant material (Xinluzao 45) and drought-sensitive material (Xinluzao 26). GhLecRLK90 was significantly highly expressed at 6 h after drought stress induction, and the difference in expression between the two groups was significant. Viral-induced gene silencing (VIGS) of GhLecRLK90 was performed in the drought-tolerant material (Xinluzao 45), and the silenced plants exhibited severe wilting and had significantly lower peroxidase (SOD and POD) activity than the control plants. These results suggest that GhLecRLK90 potentially regulates peroxidase activity in response to drought stress.

Peanut (Arachis hypogaea L.), a globally important oilseed crop, increasingly challenged by rising edible oil demands as well as biotic and abiotic stresses. This review synthesizes recent advances in peanut genomics, evolutionary biology, and breeding technologies to address these challenges aimed at improving yield, oil quality, and resilience. Cultivated peanut is an allotetraploid (AABB), derived from hybridization of the diploid ancestors, A. duranensis and A. ipaensis followed by polyploidization. However, competing evolutionary models highlight unresolved aspects of its domestication history. Advances in sequencing have enabled the high-quality genome assembly of cultivated peanuts, facilitating the development of markers (SSRs, SNPs), trait dissection, and cross omics integration. Genomic studies reveal asymmetric subgenome evolution, chromosomal rearrangements, and structural variations associated with key traits like oil biosynthesis and stress adaptation. Markers assisted selection (MAS) and genomic selection (GS) now accelerate breeding by enabling accurate prediction of complex traits, including yield, disease resistance, and oil quality. Genome editing via CRISPR-Cas9 has transformed trait improvement by enabling accurate modifications in fatty acid desaturases (FAD2), allergen genes, and stress regulators. Multi-omics strategies like transcriptomics, proteomics, metabolomics, lipidomics, and single-cell atlases uncover cell-type specific networks governing pod development and drought responses. Despite progress, polyploid complexity, low transformation efficiency, and genotype-environment interactions remain bottlenecks. Future efforts must leverage pangenomes, machine learning, and high throughput phenotyping to bridge these gaps. This review highlights the potential of integrated genomics and precision breeding to develop high oleic, climate resilient peanut varieties, critical for global food and nutritional security.

Neutrophils are the most abundant granulocyte population and have important functions such as defense against pathogens. However, they show significant Heterogeneity and play more complex roles in tumors. The theory of two-tiered differentiation of neutrophils is insufficient to summarize their phenotypic and functional Heterogeneity. Therefore, specific regulatory mechanisms remain to be explored and neutrophil-based therapeutic regimens remain challenging. Here, we generated a single-cell atlas of neutrophils from 462 patients with 21 cancer types, revealing their heterogeneity, with CXCR2 + VNN2 + Neu as the main functional subpopulation exerting immunosuppressive effects. Spatial transcriptomic analysis across pan-cancer tissues revealed an association between fibroblast activity and the phenotypic transition of CXCR2 + VNN2 + Neu, potentially enabling their acquisition of immunosuppressive functions via ligand-receptor interactions, cytokine signaling, and extracellular vesicle communication. These findings imply that tumor microenvironment components may contribute to the heterogeneous prognostic associations observed between neutrophils and clinical outcomes in pan-cancer patients. Subsequently, we constructed a gene regulatory network to demonstrate the specific regulatory mechanisms of CXCR2 + VNN2 + Neu and identified BACH1 and ATF2 as potential therapeutic targets. Combination therapy may enhance the efficacy of neutrophil-based therapeutic regimens. Analysis of pan-cancer immunotherapy cohorts revealed a significant correlation between CXCR2 + VNN2 + Neu phenotypic transition and immunotherapy resistance in patients. We finally constructed a deep learning model named Deepsurv to accurately stratify pan-cancer patients based on the CXCR2 + VNN2 + Neu Phenotypic Transition Gene Regulatory Network (CVN-GRN) and predict the prognosis of the patients, which achieved the desired results.

Taste value of rice grain is one of the key determinants of its quality, regulated through a complex molecular module. It was revealed that amylose is the key determinant of rice grain quality and precise manipulation of amylose could able to enhance rice grain dietary quality. Together with amylose, grain protein content (GPC) also plays a crucial role to maintaining grain quality and higher accumulation glutelin can deteriorate grain quality. Recently, Cao et al. (2025) demonstrated that the OsGATA7-SMOS1-OsGluA2 module enhances grain taste value by reducing GPC in the elite haplotype OsGATA7^Hap1 and SMOS1^Hap1, providing a holistic approach to improve rice grain quality.

Type 2 diabetes mellitus (T2DM) is a severe metabolic disorder in which pancreatic injury plays a pivotal role in disease progression. Tanshinone IIA (TanIIA), a bioactive compound extracted from Salvia miltiorrhiza, has shown therapeutic potential in diabetes management. However, its protective effects on pancreatic injury and underlying pharmacological mechanisms remain unclear. In this study, TanIIA significantly reduced fasting blood glucose, improved insulin resistance, and alleviated islet structural damage and β-cell apoptosis. Potential TanIIA targets were initially predicted through integrated network pharmacology, weighted gene co-expression network analysis (WGCNA), and differential gene expression analysis. Based on these integrated data, five machine learning algorithms were applied to identify candidate targets. PTGS2, NR4A2, MGLL, GABRA2, and IL-6 were determined to be core targets and were validated by qRT-PCR, with functional enrichment indicating that the JAK-STAT pathway is a key regulatory axis. Molecular docking revealed strong binding affinities between TanIIA and these core targets, with calculated binding energies of -8.7 (PTGS2), -7.6 (NR4A2), -9.8 (MGLL), -8.3 (GABRA2), and − 7.5 (IL-6) kcal/mol. Furthermore, molecular dynamics simulations confirmed the stable interaction between TanIIA and IL-6. In vivo experiments further demonstrated that TanIIA modulated the IL-6/JAK2/STAT3 pathway In vivo experiments further demonstrated that TanIIA modulated the IL-6/JAK2/STAT3 pathway, suppressed proinflammatory cytokines, promoted anti-inflammatory IL-10 expression, and regulated macrophage polarization, thereby improving the inflammatory microenvironment in islets. Additionally, TanIIA activated the PI3K-AKT pathway, alleviated glucolipotoxicity-induced endoplasmic reticulum (ER) stress, and downregulated ER stress-related proteins including p-IRE1α, GRP78, XBP1s, and CHOP, ultimately inhibiting β-cell apoptosis. Collectively, these findings suggest that TanIIA ameliorates pancreatic damage in T2DM mice by targeting inflammation and ER stress through IL-6/JAK2/STAT3 signaling, providing new mechanistic insights into its antidiabetic potential.