Functional & Integrative Genomics最新文献

Esophageal carcinoma (ESCA) is a highly aggressive malignancy with a poor prognosis. The apelin gene (APLN) encodes a secreted peptide involved in various physiological processes, but its role in ESCA progression and chemoresistance remains unclear. We integrated transcriptomic data from the TCGA and GEO databases with CRISPR screening to identify key oncogenes in ESCA. ALPN was identified as a key gene. Functional assays both in vitro and in vivo were conducted to explore the biological role of APLN. Mechanistic studies explored the involvement of APLN in the regulation of autophagy and chemoresistance. Furthermore, we developed an exosome-based siRNA delivery system targeting APLN and constructed a prognostic nomogram incorporating APLN expression. APLN was significantly overexpressed in ESCA tissues and correlated with poor patient prognosis. DNA hypomethylation contributed to APLN upregulation. Functional experiments demonstrated that APLN knockdown suppressed tumor cell proliferation, induced apoptosis, and increased sensitivity to cisplatin. Mechanistically, APLN promoted autophagic flux, which mediated chemoresistance in ESCA cells. Exosome-mediated delivery of APLN siRNA effectively inhibited tumor growth in vivo without causing systemic toxicity. Additionally, a nomogram combining APLN expression with clinical stage accurately predicts patient survival, providing a practical tool for individualized prognosis. Our study identified APLN as a novel driver of ESCA progression and chemoresistance through the regulation of autophagy. Targeting APLN via exosome-based siRNA delivery is a promising therapeutic strategy. Moreover, the APLN-based prognostic nomogram has potential for guiding personalized treatment decisions in ESCA patients.

Hepatocellular carcinoma (HCC) is a highly prevalent and lethal malignancy with complex pathogenesis and limited treatment options. Exosomes play crucial roles in HCC development and progression. This study aimed to comprehensively investigate the differential expression and functional roles of lipocalin-2 (LCN2) in HCC exosomes. Bioinformatics analysis of the GSE199509 dataset identified 4518 differential expression genes (DEGs) between HCC patient-derived exosomes and normal controls, with LCN2 being highly expressed in HCC exosomes. In vitro experiments showed that LCN2 was significantly enriched in exosomes from HCC cell lines (SMMC-7721 and HepG2). HCC-derived exosomes induced M2 macrophage polarization, which promoted HCC cell migration, invasion, and proliferation. Knockdown of LCN2 attenuated HCC exosome-induced M2 macrophage polarization and reduced the pro-tumor effects on HCC cells. Mechanistically, LCN2 inhibited Nedd4-1-mediated ubiquitination and degradation of SR-BI in a Nedd4-1-dependent manner. SR-BI overexpression reversed the effects of LCN2 knockdown on macrophage polarization and HCC cell proliferation. In vivo mouse models demonstrated that LCN2 knockdown inhibited tumor growth in wild-type mice but not in SR-BI knockout mice. These findings suggest that LCN2 plays a pivotal role in HCC progression through modulating macrophage polarization and interacting with SR-BI. Targeting the LCN2-SR-BI axis may represent a novel therapeutic strategy for HCC. Additionally, exosomal LCN2 could be a potential biomarker for HCC diagnosis and prognosis. However, further pre-clinical and clinical studies are needed to validate these findings.

Type II ketosis in dairy cows is a common metabolic disorder characterized by hepatic lipid metabolism dysregulation. To investigate hepatic tissue heterogeneity and underlying molecular mechanisms in type II ketosis, this study utilized an integrated multi-omics and functional validation strategy. Serum (n = 20), plasma (n = 6), and liver tissue (n = 1 to 3) samples were obtained from Holstein cows in the early postpartum period (3 to 15 days), comparing ketotic and healthy groups. The experimental design combined plasma metabolomics (3 d postpartum, n = 6), cellular metabolomics (n = 6), single-nucleus RNA sequencing (snRNA-seq; 3 d postpartum, n = 1), bulk RNA-seq of hepatocytes (n = 6), and functional assays performed in primary bovine hepatocytes isolated from healthy donor livers (n = 3). This comprehensive framework enabled a systematic exploration of metabolic dysregulation, cellular diversity, and key disease-associated regulatory pathways. The study identified 15 potential biomarkers and extensive dysregulation of metabolic pathways. Liver tissues comprised 14 distinct cell types, with spatially heterogeneous hepatocyte subpopulations localized in periportal, midlobular, and central venous zones. Central venous hepatocytes were pivotal in lipid metabolism, whose reduction amplified interactions between hepatic stellate and endothelial cells, activating lipid-related pathways and driving disease progression. Critically, the ketone body-butyrate-HADHA axis was identified as a central pathogenic pathway. Silencing HADHA alleviated lipid metabolic dysfunction in hepatocytes induced by exogenous NEFA. Notably, HADHA exhibited dual regulatory roles in hepatic lipid metabolism under distinct pathological contexts. This study bridges hepatic cellular dynamics with systemic metabolic dysregulation, laying a theoretical foundation for mitigating lipid metabolism disorders in dairy cattle and informing translational applications in veterinary medicine.

Endometriosis (EMs) affects the physical and mental health of a wide range of women of childbearing age. Exploring specific diagnostic targets and screening potential therapeutic drugs will help early diagnosis and improve prognosis. The diagnostic and therapeutic potential of ETS homologous factor (EHF) and Gamma linolenic acid (GLA) remains to be explored. Based on RNA sequencing of GEO datasets and local clinical samples, LASSO and SVM-RFE machine learning algorithms were used to screen out the key gene (EHF). Explore the expression level of EHF and its effects on the malignant biological behavior and regulatory mechanism of endometriosis cells (12z). Based on the positive and negative correlation genes of EHF, cMap analysis and molecular docking were performed to screen out the potential therapeutic drug (GLA). Explore the therapeutic effects of GLA on endometriosis in vivo and in vitro. EHF was abnormally low in endometriosis tissues and cells. Overexpression of EHF could inhibit malignant phenotypes such as cell proliferation, migration, invasion, and angiogenesis, and inhibit the PI3K/AKT/mTOR axis, leading to cell cycle arrest and inhibiting epithelial-mesenchymal transition (EMT). GLA could play a potential therapeutic role in vivo and in vitro with low normal cell toxicity. EHF is a potential protective gene for endometriosis, and its overexpression could inhibit the malignant biological phenotype, cell cycle and EMT by inhibiting the PI3K/AKT/mTOR axis. GLA screened based on EHF could be used as a potential therapeutic drug to play a therapeutic role in vitro and in vivo. This study screened and validated specific diagnostic targets (EHF) and potential therapeutic drugs (GLA) for endometriosis based on clinical tissue sample tissue, cells, RNA sequencing, in vivo and in vitro experiments to assist in the early diagnosis and prognosis improvement of EMs.

Wheat production is increasingly threatened by biotic and abiotic stresses, with stripe rust, caused by Puccinia striiformis f. sp. tritici being among the most devastating diseases. To dissect stripe rust resistance mechanisms, 329 diverse wheat genotypes were evaluated across six distinct environments in India (three locations over two years). The panel exhibited wide variation for stripe rust resistance and was genotyped using a 35K SNP-array. Genome-wide association study (GWAS) revealed 49 significant marker–trait associations (MTAs), explaining 1.58% to 29.7% of phenotypic variation, with notable quantitative-trait locus (QTL) hotspots on chromosomes 2A, 3B and 4B. Several MTAs co-localized with known resistance loci, while AX-92621629 appeared novel, suggesting new genomic region contributing to adult plant resistance. Candidate genes near significant single-nucleotide polymorphisms (SNPs) were enriched for defense-related functions, including nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins, receptor-like kinases and transcription factors involved in defense signaling. To further investigate resistance mechanisms, metabolomic profiling, phytohormone and flavonoid dynamics were conducted on two contrasting wheat genotypes (resistant SKUA_415; susceptible SKUA_246) using untargeted Gas Chromatography–Mass Spectrometry (GC‒MS) and Liquid Chromatography–Mass Spectrometry (LC‒MS) approaches. Key defense-related metabolites, including myo-inositol, ketoglutaric acid, rutin and schaftoside and kaempferol derivatives were identified. These metabolites were downregulated in SKUA_246 following infection, while SKUA_415 showed up-regulation of defense phytohormones, anthocyanins and flavonoids. The two contrasting genotypes also exhibited clear allelic differentiation at key resistance-linked SNP loci, consistent with their divergent metabolomic responses. This study highlights identification of promising genes/QTLs/MTAs and metabolic markers for breeding next-generation stripe rust resistant wheat cultivars.

Totipotency, the capacity of a single cell to regenerate a complete organism, is the central to plant developmental plasticity and underpins plant regeneration via somatic embryogenesis and/or organogenesis, a cornerstone of plant biotechnology, including transgenics and genome editing. A recent study, by using time-resolved single-cell and spatial transcriptomic analysis, Tang et al. 2025 shows that LEAFY COTYLEDON2 (LEC2) can reprogram a defined epidermal lineage, SPEECHLESS (SPCH)-expressing meristemoid mother cells (MMCs), into somatic embryo founder cells (SEFCs) by cooperating with SPCH to activate local auxin biosynthesis (TAA1/YUC4), producing a GMC-auxin transitional state that enables transcriptional and chromatin reconfiguration toward totipotency. This lineage-specific, auxin-driven route both refines conceptual models of plant reprogramming and offers practical levers to improve plant regeneration and transformation in crops.

Cereals are crucial sources of food for human and animal populations worldwide. Their grain and fodder primarily serve as sources of energy and nutrition. Cereal production is hampered because of the prevalent abiotic stress worldwide. Abiotic stresses such as drought, salinity, extreme temperatures, and heavy metal toxicity significantly reduce global cereal crop production. Previously, traditional breeding and transgenic technology have been promising and potent approaches used to mitigate unfavourable abiotic stresses, enhancing crop production to some extent. The recent advent of more potent genome-editing technologies, particularly Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), has revolutionized the pace of crop improvement programs. Genome-editing technology using engineered nucleases offers significant opportunities for crop improvement. Genome editing tools include Meganucleases, Zinc Finger Nucleases (ZFN), Transcription activator-like effector nucleases (TALENs), and CRISPR/CRISPR-associated protein (Cas). Among all genome-editing tools, CRISPR/Cas9 has been widely used to improve crop cultivars due to its specificity, simplicity, robustness, and flexibility. Recent progress in genome-editing technology have improved various plant traits in cereals. Among these traits, cereal genotypes have shown substantial advances in the last decade, particularly in enhanced tolerance to abiotic stress, enabled by genome-editing tools. This review summarizes the recently developed cereal cultivars for abiotic stress tolerance that employ different genome-editing technologies, including the most recent additions, prime editing and base editing. These improved cereal cultivars perform better and maintain higher yields under adverse abiotic stresses.

Intrahepatic cholangiocarcinoma (iCCA) is a highly malignant liver cancer with limited treatment options. Recent evidence implicates lactate metabolism as playing a crucial role in tumor progression, but its precise contribution in iCCA remains unclear. In this study, lactate metabolism-related genes (LMRGs) in iCCA were identified through analyses of bulk and single-cell RNA sequencing data, diagnostic models were developed using machine learning algorithms, and the functional significance of candidate genes was validated through a combination of in vitro and in vivo experiments. 38 differentially expressed LMRGs were identified, and two genes, HMGCL and PCK1, were selected as robust diagnostic biomarkers. A nomogram incorporating both markers achieved excellent diagnostic performance (AUC = 0.999). Single-cell analyses revealed cell-type-specific expression and extensive intercellular communication involving these genes. Functional studies demonstrated that PCK1 acts as a tumor suppressor, concurrently reducing lactate accumulation, downregulating protein lactylation, and inhibiting the PI3K-AKT signaling pathway. Overexpressing PCK1 significantly impaired iCCA cell proliferation, migration, and invasion. These results indicate PCK1 is a key lactate metabolism-related tumor suppressor in iCCA. PCK1 exerts its anti-tumor effects by coordinately suppressing lactate accumulation and inhibiting the PI3K-AKT signaling pathway, positioning it as a promising diagnostic biomarker and therapeutic target for iCCA.

Zinc (Zn) and Iron (Fe) are essential trace elements for human health, yet deficiencies in both are widespread worldwide. As a major staple crop, wheat is an important dietary source of Zn and Fe. However, the concentrations of Zn and Fe in common wheat grains are generally low, making it necessary to enhance the nutritional value of wheat. This study first elaborated that both elements are absorbed by wheat via “Strategy II”, which relies on phytosiderophores (such as mugineic acids) and related transporter proteins (e.g., YSL and ZIP families). Nicotianamine (NA) plays a key chelating role in the long-distance transport of Zn and Fe. Therefore, we further analyzed the NAS gene family in wheat, which showed high genetic diversity, unique gene structures, distinct evolutionary features, and was subject to purifying selection. Expression profiling revealed that NAS genes were tissue-specific and responsive to various stress conditions. The overexpression of TaNAS4-A in rice, as well as the silencing of TaNAS4-A in wheat using BSMV-VIGS, confirmed the role of TaNAS4-A in enhancing NAS enzyme catalytic efficiency, promoting phytosiderophore secretion, and increasing the accumulation of Zn and Fe in grains. Additionally, this study suggested that NAS genes may confer other functions, such as stress resistance, which deserve further investigation. This research provides a theoretical basis for Zn and Fe biofortification in wheat.