Search Results (214)

Insects periodically undergo molting to replace their old epidermis for growth and morphological adaptation. Muscleblind-like (MBNL) is a multifunctional protein involved in miRNA processing. To explore the role of miRNA processing in insect molting, we characterized BmMBNL in Bombyx mori. BmMBNL exhibited spatiotemporal expression across tissues and developmental stages, with the highest levels in the epidermis and upregulation during molting. CRISPR/Cas9-mediated knockout of BmMBNL (BmMBNL-KO) caused molting defects at the 3rd and 4th instar larvae, resulting in reduced size and eventual lethality. Moreover, BmMBNL-KO individuals showed a thinner chitin layer between the new and old epidermises. RT-PCR and transcriptome analyses revealed upregulation of miR-1, miR-71, miR-263, miR-8-5p, and miR-2a-3p, which suppressed chitinase expression, ultimately leading to molting failure. This study provides novel insights into the potential correlation between BmMBNL, miRNA abundance and insect molting in Bombyx mori. Full article

Adrenocortical carcinoma (ACC) is a rare malignancy of the adrenal gland for which no curative treatment options exist in advanced stages. Analyzing the ACC cohort of The Cancer Genome Atlas, we identified that expression of the mRNA-stabilizing protein Embryonic-Lethal-Abnormal-Vision-Like RNA-Binding Protein 1 (ELAVL1) was negatively associated with patient survival. To investigate the functional role in ACC, we generated a CRISPR/Cas9-mediated ELAVL1 knockout (KO) in the ACC cell lines NCI-H295R and HAC15 and performed Next-Generation RNA Sequencing (NGS) to characterize transcriptomic changes. In NCI-H295R, NGS analysis revealed 3468 upregulated genes and 3458 downregulated genes in ELAVL1-deficient cells compared with controls. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified significant enrichment of aldosterone biosynthesis-related genes and enriched downregulation of genes associated in with “pathways in cancer.” Functionally, ELAVL1-KO cells exhibited impaired colony-forming ability, indicating reduced proliferative or clonogenic potential. Steroid profiling of cell culture supernatants further demonstrated increased aldosterone synthesis and decreased cortisol and androgen production in the KO cells, consistent with the observed transcriptional changes. Given that hypercortisolism is an established negative prognostic factor in ACC, these data suggest that ELAVL1 may represent a potential therapeutic target worth further investigation for modulating steroidogenesis in ACC patients. Full article

Pre-harvest sprouting (PHS), the premature germination of grains on the mother plant, causes substantial yield loss and grain-quality deterioration in rice under humid conditions. Although seed dormancy and germination are largely controlled by hormonal balance, the transcriptional mechanisms linking hormone signaling with metabolic adaptation during PHS remain unclear. In this study, we investigated the roles of two ethylene-responsive factor transcription factors, OsERF1 and OsERF94, in rice PHS regulation using CRISPR/Cas9-mediated knockout lines, together with physiological, gene-expression, and metabolite analyses. The oserf1-KO mutant showed reduced seed dormancy and increased germination under PHS-inducing conditions, accompanied by altered expression of abscisic acid- and gibberellin-related genes. In contrast, the oserf94-KO mutant exhibited enhanced dormancy and reduced germination, with decreased expression of hypoxia-responsive fermentation genes and impaired carbohydrate mobilization, as indicated by reduced soluble sugar and ethanol accumulation and increased starch content. These results suggest that OsERF1 contributes primarily to hormone-mediated dormancy maintenance, whereas OsERF94 supports metabolic activation required for germination under high-moisture conditions. Collectively, this study proposes a dual regulatory framework in which hormonal control and hypoxia-associated carbon metabolism coordinately determine rice PHS susceptibility. Full article

The Kelch-repeat superfamily genes played important roles in regulating plant growth and development; however, their functions in foxtail millet (Setaria italica) have not yet been characterized. In this study, SiNL4, a homolog of ZmNL4 controlling leaf width in maize, was knocked out using the CRISPR/Cas9 technology, and two homozygous knockout lines (ko1 and ko2) were obtained. Phenotypic analysis showed that compared with the wild-type Ci846, ko1 and ko2 exhibited reduced leaf width and decreased yield related traits (e.g., panicle weight, grain width, and 1000-grain weight). Cytological analysis showed that changes in leaf width of ko1 and ko2 resulted from a decrease in leaf epidermal cell width and the number of small vascular bundles (SVBs) close to the leaf edge, suggesting that SiNL4 might regulate leaf width by influencing cell expansion and the development of SVB. Spatiotemporal expression analysis indicated that the relative expression level of SiNL4 was high in the stem, leaf, and young panicle. Subcellular localization showed that SiNL4 was mainly localized in the mitochondria and plasma membrane. In addition, the T-DNA insertion mutant (Atnl4) of AT5G18590, the ortholog of SiNL4 in Arabidopsis thaliana, exhibited similar phenotypes with reduced rosette leaf width, seed width, and 1000-seed weight. Moreover, complementary expression of SiNL4 in Atnl4 not only restored the phenotypes, but also significantly increased the 1000-seed weight, indicating that the function of these two genes might be conserved. Meanwhile, we found that SiNL4 knockout caused a decrease in chlorophyll content and net photosynthetic rate (Pn), showing that SiNL4 might be involved in regulating photosynthesis. In summary, this study revealed the function of SiNL4 in regulating leaf width in foxtail millet, providing a potential gene for the genetic improvement of foxtail millet. Full article

Rapeseed (Brassica napus L.) growth and productivity are severely constrained by drought stress worldwide. Stomata are central regulators of plant transpiration and gas exchange, and therefore, represent key targets for enhancing water-use efficiency and drought tolerance. The transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4), a key regulator of the abscisic acid (ABA) signaling pathway, plays crucial roles in plant abiotic stress responses and stomatal regulation. Nevertheless, the biological functions of BnaABI4 in B. napus remain largely unclear. In this study, four BnaABI4 paralogs were identified in the elite rapeseed cultivar ZS11 through genome-wide identification and comprehensive bioinformatic analyses. Each BnaABI4 protein harbors only one conserved AP2 domain, and their promoters contain multiple stress/hormone-responsive cis-regulatory elements (CREs). We subsequently generated BnaABI4-4 overexpression (OE) lines as well as BnaABI4 CRISPR/Cas9-mediated knockout (KO) transgenic lines. Phenotypic assays demonstrated that OE line had reduced transpiration rate (Tr), stomatal conductance (Gs) and stomatal density, along with enhanced drought tolerance, whereas KO lines showed the opposite phenotype. Transcriptome profiling identified numerous differentially expressed genes (DEGs) enriched in biological pathways associated with stomatal regulation, ABA signal transduction, and drought acclimation. Further Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses confirmed significant enrichment of DEGs in processes including stomatal development, stomatal movement, reactive oxygen species (ROS) homeostasis, and drought tolerance. Collectively, our findings demonstrate that BnaABI4 negatively regulates stomatal density while positively contributing to drought tolerance in B. napus. This study lays a mechanistic foundation for genetic improvement and molecular breeding of drought-tolerant rapeseed cultivars. Full article

Wheat (Triticum aestivum L.) is a crucial global food crop that plays a central role in agricultural production and food security. The spike number per unit area (SN) is one of the three component factors of grain yield. In this study, we combined the UG-Map with 27 environments of a recombinant inbred line (RIL) population, and mapped a quantitative trait locus (QTL) for SN, QSn-7A-9048, in which the meta-QTL interval contains only one candidate gene, TraesCS7A02G-364700 (TaKMT-7A). Using the CRISPR/Cas9 system, we generated two homozygous mutant lines, aa-1 and aa-2 of TaKMT-7A, which resulted in frameshift mutations, leading to the premature termination of the translation process. The SN values for the wild type (WT), aa-1, and aa-2 were 4.48, 3.43, and 3.48, respectively. Compared with the WT, the SN of the two mutant lines significantly decreased, and no significant differences for grain number per spike (GNS) and thousand-grain weight (TGW) were detected. We also obtained two overexpression (OE) lines of TaKMT-7A, OE-1 and OE-2. The SN values for the negative control (NC), OE-1, and OE-2 were 2.31, 3.33, and 3.00, respectively. Compared with NC, the SN values in the OE lines significantly increased. The phenotypes of the knockout (KO) lines and OE lines demonstrate that TaKMT-7A acts as a positive regulator of SN in wheat. We performed RNA-Seq analysis using young tiller buds from the WT and aa-1 mutant lines at the tillering stage, and a total of 2315 differentially expressed genes (DEGs) were identified. We screened 22 wheat genes, of which 18 orthologous genes have previously been cloned and are associated with branching in rice and Arabidopsis. These genes included nitrogen transporter, amino metabolism, auxin transporter, auxin homeostasis, auxin response, auxin biosynthesis, strigolactone biosynthesis, and repress gibberellin responses. These genes may represent potential downstream targets of TaKMT-7A. Full article

Background/objectives: Epithelial ovarian cancer (EOC) is the deadliest gynaecologic malignancy, largely due to late-stage diagnosis and ineffective therapy. EOC commonly spreads through the peritoneal cavity as multicellular spheroids, which are metastatic structures that enhance survival under detachment stress, promote dissemination, and contribute to therapeutic resistance. We previously showed that ULK1, a serine/threonine kinase classically linked to macroautophagy initiation, supports EOC progression, suggesting non-canonical roles in spheroid biology and pathogenesis. Methods: CRISPR/Cas9 ULK1 knockout (ULK1KO) models were generated in OVCAR8, HEYA8, and ES2 cells. Mitochondrial degradation phenotypes were assessed in spheroids by immunoblotting and fluorescence microscopy. Label-free proteomics with bioinformatic pathway analysis identified ULK1-associated programs in EOC spheroids. Bioenergetic consequences were quantified using Seahorse ATP-Rate assays. Therapeutic interactions were evaluated using multi-dose combination matrices testing the ULK1 inhibitor DCC-3116 with metformin. Results: ULK1 modulated mitochondrial degradation in a cell-line-specific manner, either promoting or protecting against mitochondrial loss through mechanisms that were uncoupled from canonical autophagy machinery. Proteomic and bioinformatic analyses revealed significant alterations in mitochondria-related processes, aligning with emerging ULK1 functions in mitochondrial homeostasis. ULK1 loss broadly reduced OXPHOS complex proteins in EOC spheroids and consistently decreased hexokinase 2 (HK2), indicating coordinated metabolic remodeling. Seahorse profiling mirrored these shifts: OVCAR8 ULK1KO spheroids showed reduced OCR and ATP production, whereas HEYA8 and ES2 ULK1KO spheroids exhibited increased mitochondrial ATP production. Combination matrices showed potential synergy between DCC-3116 and metformin. Conclusions: These data show that ULK1 differentially regulates mitochondrial degradation across EOC spheroid models through potential mechanisms alternative to canonical autophagy machinery, while reshaping spheroid metabolism and revealing potential therapeutic vulnerabilities in advanced EOC. Full article

Glycosylation is essential for hematopoietic cell homeostasis and malignant transformation. Dysregulated expression of glycosylation genes in leukemia cells accelerates disease progression and fosters drug resistance. Therefore, targeting these genes offers a promising avenue for anti-leukemic therapy. In this study, we explore the roles of N-glycans in acute promyelocytic leukemia (APL) differentiation using the ATRA-induced wild-type NB4 (WT/ATRA) or HL-60 cell model. We found that expression of N-acetylglucosaminyltransferase IVa (GnT-IVa, encoded by the MGAT4A gene) and its product (β1,4-GlcNAc-branched N-glycan) increased significantly during differentiation, as evaluated by lectin blot, real-time PCR, and flow cytometry. Interestingly, analysis of the Gene Expression Omnibus (GEO) public data showed that MGAT4A expression is significantly lower in APL patients, and higher MGAT4A expression was associated with favorable survival in AML cohorts. To address the role of GnT-IVa in differentiation, we established MGAT4A- and MGAT4B-knockout (KO) NB4 cell lines using CRISPR/Cas9. Compared to WT/ATRA cells, MGAT4A KO, but not MGAT4B KO, markedly suppressed ATRA-induced differentiation, as evidenced by reduced expression of CD11b and CD11c. We found that CD11b is a major glycoprotein carrying β1,4-GlcNAc-branched N-glycans. This modification enhanced CD11b stability, as CD11b expression declined more rapidly in MGAT4A KO cells in the presence of cycloheximide. In addition, MGAT4A KO suppressed ERK/MAPK signaling, which contributed to differentiation. Our study highlights the critical role of GnT-IVa in regulating APL differentiation, which may provide a basis for developing new differentiation therapies for APL. Full article

Black rice is rich in anthocyanins with potential antioxidant benefits, but their specific role in storage stability remains unclear due to confounding genetic backgrounds in previous studies. In this study, we used CRISPR/Cas9-mediated gene editing to generate OsKala4 knockout lines in the black rice cultivar Heizhen (HZ), creating an isogenic system to test whether endogenous anthocyanins contribute to storage-related quality stability. Knockout lines showed blocked anthocyanin biosynthesis (0.5–0.6 vs. 155.6 mg/100 g, p < 0.001) and altered grain composition. Under accelerated aging (45 °C, 90% RH, 2 weeks), HZ maintained higher antioxidant capacity (p < 0.05) and exhibited less pronounced starch aging than the representative knockout line KO2. Apparent amylose content increased less in HZ than in KO2 (16.7% vs. 28.1%, p < 0.05). HZ also showed smaller changes in pasting, thermal, and structural properties. XRD and FTIR analyses further suggested better maintenance of starch crystallinity and molecular order in HZ under accelerated aging conditions. These results suggest that endogenous anthocyanins were associated with storage-related quality stability in black rice. However, direct mechanistic evidence and validation under natural storage conditions are still needed. Full article

Aflatoxin B1 (AFB1) is a prevalent and highly toxic mycotoxin in the food and feed chain and can directly injure the intestinal epithelium. Yet, its upstream determinants linking epithelial stress to cytotoxicity remain insufficiently defined. Here, we used porcine intestinal epithelial IPEC-J2 cells to characterize AFB1-induced cytotoxic and transcriptomic responses and to determine the role of the tight-junction scaffold, Cingulin-like 1 (CGNL1), a candidate gene identified through genome-scale CRISPR knockout library screening. The results showed that AFB1 exposure reduced cell viability in a dose-dependent manner and induced oxidative stress. RNA-seq profiling analysis revealed broad transcriptional remodeling, with activation of inflammatory pathways (including NF-κB and JAK–STAT signaling). Based on our constructed CGNL1-knockout IPEC-J2 cell line (CGNL1-KO IPEC-J2) using CRISPR/Cas9, it was found that CGNL1 deficiency markedly alleviated AFB1-induced cytotoxicity and oxidative stress. Comparative transcriptomics analysis showed that CGNL1 knockout attenuated AFB1-triggered aberrant expression of some CGNL1-dependent AFB1-responsive genes related to immune response under AFB1 challenge. Together, these findings identify CGNL1 as a potential modulator of epithelial susceptibility to AFB1 and support its involvement in the regulation of toxin-induced oxidative response. Full article

Tumor initiation and metastatic progression are driven by context-dependent genetic alterations that disrupt tumor suppressor pathways, metabolic homeostasis, and signaling networks. However, the initial drivers that transform normal cells into malignant ones and their context dependency remain elusive. To address this, we aimed to systematically identify and characterize these drivers across cancer types, species, and microenvironments. We constructed customized clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) knockout (KO) libraries targeting high-frequency mutated and downregulated genes associated with liver hepatocellular carcinoma (LIHC) and breast carcinoma (BRCA) and conducted parallel functional screens in non-cancerous mouse and human fibroblast cell lines under two-dimensional (2D), three-dimensional (3D), and in vivo conditions. Strikingly, TP53 and NF1 emerged as pan-context drivers consistently enriched across immortalization, tumorigenesis, and metastasis in both LIHC and BRCA settings, while most other identified drivers were largely species-, tissue-, and microenvironment-specific with limited cross-model overlap. Despite this heterogeneity, all drivers converge on core pathways including epigenetic regulation, metabolic reprogramming, and growth factor signaling. Unlike prior studies on established cancer cells, this work defines the genetic barriers restricting the malignant transformation of primary normal cells, offering a new framework for early cancer evolution. Full article

The manipulation of host cellular metabolism is a key strategy for flaviviruses like Japanese encephalitis virus (JEV) to establish a productive infection. This study identifies the host NADase CD38 as a central regulator of this process. Using a CRISPR/Cas9-generated CD38 knockout (KO) TM3 cell model, we found that CD38 deficiency significantly restricted the production of infectious viral particles. While loss of CD38 also partially impaired viral entry, our central finding is that CD38 primarily promotes JEV infection by suppressing a host-intrinsic metabolic defense. We show that CD38 deficiency leads to a surge in intracellular NAD+, which sustains SIRT1 activity and inactivates p53, thereby blocking the mitochondrial apoptosis required for viral propagation. The dominance of this metabolic axis was confirmed through bidirectional pharmacological interventions; while SIRT1 inhibition using EX527 restored JEV replication, SIRT1 activation using SRT1720 suppressed it in wild-type cells. Our work reveals that JEV hijacks the CD38-NAD+-SIRT1-p53 axis to overcome host metabolic defenses in reproductive cell models, establishing CD38 as a promising therapeutic target. Full article

The mitochondrial anti-viral signaling protein, MAVS, is a central regulator of innate anti-viral immunity. Recently, we demonstrated that MAVS is overexpressed in cancer, where its downregulation resulted in reduced cell proliferation and the expression and nuclear translocation of proteins associated with transcriptional regulation and inflammation. In this study, we demonstrate that CRISPR/Cas9-mediated MAVS depletion in PC-3 prostate cancer cells suppresses proliferation, disrupts immune evasion, and alters the tumor microenvironment. Proteomic profiling of the MAVS-KO cells by LC-MS/MS revealed changes in the expression of proteins associated with immunity, cell signaling, mitochondrial function, metabolism, protein synthesis and degradation, and epigenetic regulation. In contrast to MAVS-expressing cells, MAVS-KO cells implanted subcutaneously in mice formed very small tumors. This inhibited tumor growth was linked to reduced proliferation, and enhanced apoptosis, as indicated by strong TUNEL staining and elevated activated caspase-3. Importantly, the small “tumors” derived from MAVS-KO cells displayed a distinct morphology: diminished cancer stem-cell populations, an altered tumor microenvironment and inflammatory response, increased immune cell infiltration, and reduced PD-L1 expression. Together, these findings establish MAVS as a key mediator of cancer-cell survival, inflammation, and immune regulation, and, thus, its upregulation in tumors makes it a potential anti-cancer target. Full article

Malaria, caused by Plasmodium parasites, remains a global health crisis, necessitating novel therapeutic strategies targeting host–parasite interactions. During liver-stage infection, parasites exploit host vesicular trafficking machinery, particularly SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins that mediate membrane fusion. Using a CRISPR/Cas9 knockout system in HeLa cells combined with advanced microscopy of Plasmodium berghei-infected HeLa cells, we identified specific endolysosomal SNAREs including Vesicle-Associated Membrane Protein 7 (VAMP7), Vesicle-Associated Membrane Protein 8 (VAMP8), Vesicle Transport Through Interaction With T-SNAREs 1B (Vti1B), and Syntaxin 7 (Stx7) to be recruited to the parasitophorous vacuole membrane (PVM) with distinct temporal profiles. This demonstrates the parasite’s precise manipulation of host endolysosomal trafficking pathways. VAMP7 and Vti1B were localized to the PVM within 30 min post-infection, suggesting potential roles during invasion, while VAMP8 and Stx7 appeared later around 24 h post infection (hpi), coinciding with increased nutrient acquisition. Single gene deletions showed minimal impact, but combinatorial knockouts (KO) revealed critical redundancy. VAMP7-VAMP8 as well as VAMP7–Vti1B double KO significantly reduced parasite infection and growth, with Vti1B playing a dominant role. Triple KO phenotypes mirrored VAMP7-Vti1B disruption, underscoring Vti1B’s dominant role. SNARE depletion also impaired the lysosome–PVM association and LAMP1 positive vesicle recruitment. Our findings indicate Plasmodium hijacks a coordinated host SNARE network to fuse lysosomes with the PVM for nutrient uptake. Targeting Vti1B-containing complexes disrupts this pathway without host cell toxicity, offering a promising host-directed antimalarial approach. Full article

Currently, most research on CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene editing in edible fungi focuses on monokaryotic strains. However, the biological mechanisms in a monokaryotic state often do not accurately reflect the actual physiological and metabolic conditions of dikaryotic strains. Therefore, this study used two mating-type-compatible monokaryotic strains, L1 and L2, isolated from Ganoderma lucidum ‘Hunong No.1’ G0119, and employed an RNP (ribonucleoprotein)-based CRISPR/Cas9 system to successfully knock out the cyp512a3 gene in strain L2, resulting in the edited strain L2-KO-cyp512a3. The strain was single-crossed with the previously edited L1 strain L1-KO-cyp512a3 in our laboratory to obtain a dikaryotic editing strain that was homozygous at the cyp512a3 locus, named G0119-KO-cyp512a3. UPLC-MS (Ultra Performance Liquid Chromatography–Mass Spectrometry) analysis showed that compared to the starting strain G0119, the dikaryotic editing strain exhibited varying degrees of reduction in the content of eight types of ganoderic acids, including ganoderic acid Me, ganoderic acid P, ganoderic acid T1, etc., with the reduction ranging from 30.5% to 80.1%. To further validate the function of cyp512a3, we overexpressed this gene in the L1 strain. The results showed that the contents of ganoderic acid Mk, ganoderic acid S, ganoderic acid T, and ganoderic acid R in the mycelium were 0.548 ± 0.020, 1.780 ± 0.028, 2.416 ± 0.148, and 0.281 ± 0.016 mg/g (dry weight), which were 1.5 times, 1.3 times, 1.3 times, and 1.3 times that of G0119, respectively. By integrating the results of gene knockout and overexpression, it can be clearly established that cyp512a3 is a key cytochrome P450 gene regulating the biosynthesis of ganoderic triterpenoids in Ganoderma lucidum. This study not only establishes, for the first time, a homologous recombination-based gene editing system in dikaryotic strains of Ganoderma lucidum, but also provides a research paradigm based on a dikaryon-editing tool for investigating key life traits of other edible fungi. Full article