Functional & Integrative Genomics最新文献

Triple-negative breast cancer (TNBC) represents a formidable subtype with a grim prognosis. This study aims to pinpoint the molecular targets of Glycosyltransferases (GTs) in TNBC, with the goal of improving prognostic accuracy and boosting the effectiveness of immune therapies. Using publicly available datasets, we combined differentially expressed and correlated genes based on AUCell scores from single-cell sequencing. These were then subjected to enrichment analysis and utilized for constructing a risk model. A total of 780 genes were identified as being closely associated with GTs. Using 101 algorithm combinations, a 17-gene signature emerged with predictive capabilities for TNBC patient prognosis. At the same time, we examined the role of these model genes in the tumor microenvironment(TME). We identified key transcription factors correlating with GTs, including CREB3L1, which showed significant association with the CERCAM gene. Subsequently, the pro-cancerous effects of GTs were validated through a series of experiments, including CCK-8 cell viability assays, scratch wound healing assays, and Transwell migration and invasion assays. This research lays the foundation for targeted drug therapies, offering new opportunities to enhance clinical outcomes in TNBC.

Heterosis is defined as the occurrence in which F1 hybrids exhibit superior traits compared to their parental, and it plays a crucial role in the process of selecting and breeding superior plant varieties. DNA methylation, as a crucial epigenetic modification, significantly contributes to the formation of heterosis. However, the underlying mechanisms are not entirely clear. Here, this review systematically elaborates the regulatory mechanisms of DNA methylation and its epigenetic basis in heterosis. Specifically, it emphasizes deciphering its synergistic role in establishing hybrid vigor through interactions with other epigenetic factors. DNA methylation is dynamically regulated by three processes: establishment, maintenance, and removal of methylation. Parental methylation patterns, as well as the level and sites of DNA methylation, can influence the formation of heterosis. Furthermore, DNA methylation primarily contributes to heterosis by regulating transposable elements (TEs) and the expression of key genes. Additionally, DNA methylation, in conjunction with small RNAs (sRNAs) and histone modifications, collectively regulates heterosis through the RNA-directed DNA methylation (RdDM) pathway and chromatin remodeling. This review lays a foundation for the in-depth study of DNA methylation in hybrid plants, which may serve as a pivotal tool to dissect the molecular mechanisms underlying heterosis. Simultaneously, this will facilitate the application of heterosis in plant breeding, and unlock its untapped potential for hybrid trait optimization in yield, stress resilience, and ecological adaptation.

Skeletal muscle development depends on the directed differentiation of myoblasts and their fusion into myotubes. Elucidating the mechanisms governing myoblast differentiation is essential for understanding muscle formation. Although suppressor of cytokine signaling 2 (SOCS2) has been implicated in this process, its precise regulatory role remains unclear. Here, the Cytosine Base Editor (CBE) system, offers a powerful approach for studying gene-specific functions, was used to investigate SOCS2 specific functions. sgRNAs targeting the murine SOCS2 gene were designed and expression plasmids were constructed. In C2C12 myoblasts, one sgRNA (sg1) mediated efficient base editing (53.0%), introducing a point mutation at amino acid 19 that generated a premature stop codon. Monoclonal cell lines with this mutation were established using limiting dilution. Western blot (WB) analysis confirmed a significant (P < 0.01) reduction in SOCS2 protein expression in the edited cells, accompanied by elevated levels of Growth Hormone Receptor (GHR). Immunofluorescence (IF) staining further validated increased GHR expression following SOCS2 knockdown. Differentiation assays indicated that SOCS2 knockout promoted C2C12 differentiation, with significantly (P < 0.01) upregulated expression of the myogenic markers MyoD1, MyoG and MYH1. Proteomic sequencing revealed enrichment of differentially expressed proteins in the PI3K/AKT and mTOR signaling pathways. Correspondingly, WB results showed that SOCS2 knockout significantly (P < 0.05) increased the expression of AKT, mTOR, and the phosphorylated forms of PI3K, AKT, and mTOR. Together, these findings demonstrate that CBE-mediated SOCS2 knockout enhances C2C12 differentiation and activates the PI3K/AKT/mTOR signaling pathway, thereby contributing new insights into the molecular regulation of skeletal muscle development.

Background Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide. Lenvatinib is a common first-line treatment for advanced HCC. However, resistance to lenvatinib is the greatest challenge limiting its clinical application. Currently, the molecular mechanisms of resistance remain poorly understood. Methods The expression of DDX1 and Ephrin-A3 in lenvatinib-resistant HCC cells was identified via RNA-seq and Western blotting. Bioinformatic analyses were applied to explore its expression and prognostic role. The biological role of DDX1 was evaluated via CCK8, EdU, flow cytometry analyses and xenograft tumor model. The regulation between DDX1 and Ephrin-A3 was determined by mass spectrometry, coimmunoprecipitation, RNA Immunoprecipitation, and RNA stability assay. Results We successfully established lenvatinib-resistant HCC cells. The results of RNA-seq showed DDX1 and Ephrin-A3 were significantly increased in lenvatinib-resistant HCC cells compared to parental cell. The DDX1 expression in HCC tissues is positively associated with worse prognosis. DDX1 knockdown increased the sensitivity of cells to lenvatinib by inhibiting proliferation and promoting apoptosis in vitro and in vivo. Conversely, overexpression of DDX1 exhibited the opposite regulation. Moreover, DDX1 bound to Ephrin-A3 and regulated its expression levels. The effects of DDX1 overexpression on cell proliferation, apoptosis, and lenvatinib resistance were significantly blocked by Ephrin-A3 knockdown. Mechanistically, DDX1 promotes lenvatinib resistance in HCC by regulating Ephrin-A3 mRNA stability and activating the Wnt/β-catenin pathway. Conclusion: The increased DDX1 expression in HCC cells promotes lenvatinib resistance via regulating Ephrin-A3 mRNA stability and activating the Wnt/β-catenin pathway, indicating that targeting DDX1 may be an important strategy for overcoming lenvatinib resistance.

Aerococcus christensenii (A. christensenii) is a symbiotic bacterium that primarily colonizes the vagina. Infections caused by A. christensenii are rare but can also pose a significant health threat. In this study, two rare cases of A. christensenii bacteremia in pregnant women complicated with chorioamnionitis were investigated; and two strains KSW23 and KWL24, which were isolated from blood samples, were analyzed for their genomic characteristics and pathogenic potential. Whole-genome sequencing revealed that the genome sizes of KSW23 and KWL24 were approximately 1.6 Mb, and predicted multiple genes associated with pathogenicity (tuf, eno, plr/gapA, galU, galE, groEL, gndA, sugC, lplA1, mgtB, clpC, clpP, and lmb), antibiotic resistance (ermB and tet(M)), and mobile genetic elements (plasmid replicon repUS43 and transposon Tn6009). Correspondingly, these strains showed multidrug resistance to Macrolides, Lincosamides, and Tetracyclines. Pangenome analysis revealed close evolutionary relationships and significant genomic conservation between these two strains and the previously isolated strains, especially with respect to genes related to pathogenicity and antibiotic resistance. Notably, a mouse bacteremia model confirmed the pathogenicity and virulence of A. christensenii strains KSW23 and KWL24, which induced bacteremia and mortality, but not as strongly as Staphylococcus aureus (S. aureus) strain ATCC25923. Additionally, A. christensenii exhibited a robust survival ability in human blood comparable to those observed in S. aureus strain ATCC25923. To our knowledge, this study is the first genomic research on A. christensenii, and confirms the species’ bloodstream invasive capacity and pathogenicity based on genomic studies and experimental validation. These findings underscore its role as a pathogen in the ascending genital tract in the obstetric population.

Zygotic gene activation plays a pivotal role in early embryonic development by determining embryonic potential. Cumulus-oocyte complexes collected through the egg-cutting method underwent 24-hour in vitro culture at 38.5 °C under 5% CO₂ and saturated humidity. Following in vitro fertilization (IVF), embryos cultured in IVCs showed developmental rates of 82.33% (2-cell), 76.09% (4-cell), 63.34% (8-cell), 45.61% (morula), and 24.71% (blastocyst). Smart-seq transcriptome sequencing of maternal-zygotic gene transformation at the 2-cell, 4-cell, and 8-cell stages revealed pronounced expression differences at the 4-cell stage, with the greatest number of differentially expressed genes occurring between the 2-cell and 4-cell groups. The substantial upregulation of numerous genes suggests extensive transcriptional activation at the 4-cell stage to facilitate critical developmental processes, whereas most downregulated genes were maternally derived. Ribosome biogenesis in eukaryotes emerged as the most upregulated pathway, contrasting with downregulation of the MAPK signaling pathway. KEGG analysis demonstrated that ribosome biosynthesis factors primarily governed gene transcription, modification, and splicing, while MAPK signaling attenuation reflected reduced pathway activity. This sequencing analysis of early Tibetan sheep embryos, building upon optimized in vitro culture conditions, yields important data for improving embryo production and supporting assisted reproductive technologies in this species.

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The plant AT-rich sequence and zinc-binding (PLATZ) family, a group of plant-specific zinc finger transcription factors, regulates growth, development, and stress responses, yet their role in biotic stress defense remains poorly understood. Here, we report a genome-wide analysis of PLATZ genes in Cucurbita pepo and characterize their function in powdery mildew resistance. Genomic screening identified 17 PLATZ loci, which clustered into four subfamilies distributed across 13 chromosomes, with conserved gene structures and motifs within each subfamily. Promoter cis-element analysis revealed enrichment of light-, hormone-, and stress-responsive regulatory motifs. qRT-PCR profiling under powdery mildew infection showed that CpPLATZ4 was specifically upregulated in the resistant line R1 and downregulated in the susceptible line S1, thereby linking its expression to disease resistance. Subcellular localization confirmed the nuclear localization of CpPLATZ4. Yeast two-hybrid and bimolecular fluorescence complementation assays demonstrated that CpPLATZ4 interacts with Dehydration Responsive Element Binding protein 2 (CpDREB2), suggesting a potential protein complex involved in defense regulation. Transient overexpression of CpPLATZ4 enhanced resistance by triggering the accumulation of reactive oxygen species (H₂O₂ and O₂⁻), activating antioxidant enzymes (SOD, CAT, POD) and reducing malondialdehyde (MDA), thereby maintaining cell integrity and suppressing fungal hyphal growth. Conversely, silencing of CpPLATZ4 showed the opposite effect, with decreased ROS accumulation, reduced antioxidant enzyme activity, increased MDA content, and enhanced fungal colonization. These findings establish PLATZ genes as key regulators of plant defense against powdery mildew, highlighting CpPLATZ4 as a potential target for molecular breeding of disease-resistant cucurbit crops.

Objective: Colorectal carcinogenesis and progression are closely associated with metabolic dysregulation. The role of MOGAT2 in colorectal cancer (CRC) advancement and its underlying metabolic mechanisms remain unclear. This study aimed to explore how MOGAT2 influences tumorigenesis by modulating lipid metabolism. Methods: MOGAT2 expression was assessed in four CRC cell lines using qRT-PCR and Western blot. Functional consequences of MOGAT2 modulation were examined following siRNA-mediated knockdown or lentivirus-mediated overexpression in HCT116/SW620 cells. Assays measured cell proliferation, colony formation, apoptosis, invasion, and epithelial-mesenchymal transition (EMT). Key lipid metabolites and metabolic enzymes were analyzed. A CRC xenograft mouse model was used for in vivo validation. RNA sequencing and rescue experiments identified ACSM1 as a key downstream mediator. Results: MOGAT2 knockdown enhanced cell proliferation, colony formation, and invasion, as well as inhibited apoptosis. While its overexpression significantly suppressed malignant phenotypes, induced apoptosis, and inhibited EMT. Mechanistically, MOGAT2 modulated lipid metabolism by reducing FFA accumulation and regulating cholesterol transport, accompanied by downregulation of lipid synthesis enzymes (GPAT2, GPAT3, and GAAT). In vivo, MOGAT2 overexpression inhibited tumor growth, improved histopathology, and restored lipid balance. Crucially, ACSM1 was identified as a critical downstream effector. Silencing ACSM1 abolished the tumor-suppressive effects of MOGAT2 overexpression, reinstating aggressive growth, suppression of apoptosis, EMT, and metabolic dysregulation. Conclusion: MOGAT2 functions as a tumor suppressor in CRC by inhibiting proliferation, promoting apoptosis, and suppressing invasion/EMT via ACSM1-mediated metabolic reprogramming, highlighting its potential as a therapeutic target.

This work explored the mechanism of EGF affecting chronic obstructive pulmonary disease (COPD) development. The most significantly differentially expressed gene (DEG) and its downstream pathway was analyzed by Microarray analysis. By constructing COPD mouse and cell models, a series of in vivo and in vitro experiments were performed to verify whether EGF regulated COPD development by the ERBB2/DNMT3A/FAM8A1 signaling. As the most significantly DEG in COPD, EGF was associated with endoplasmic reticulum stress and exhibited the highest sensitivity as a biopredictive marker for COPD. ERBB2/DNMT3A/FAM8A1 signaling was the downstream pathway of EGF. In lung tissues of COPD mice, up-regulated EGF, ERBB2 and DNMT3A, but down-regulated FAM8A1 was found. EGF silencing improved pulmonary function and airway remodeling in COPD mice. AG-825 (ERBB2 inhibitor) relieved lung tissue damage and down-regulated GRP78, CHOP and Caspase-12 in lung tissues of COPD mice, but was counteracted by Eeyarestatin I (ERAD inhibitor). In COPD cell model, FAM8A1 up-regulation enhanced viability and proliferation; relieved apoptosis; and down-regulated GRP78, CHOP and Caspase-12. Eeyarestatin I abolished these influences of FAM8A1 on COPD cell model. DNMT3A knockdown increased FAM8A1 but decreased GRP78, CHOP and Caspase-12 in COPD cell model. FAM8A1 silencing or Eeyarestatin I treatment abrogated these influences of DNMT3A silencing. Similar to AG-825, EGF silencing enhanced viability; attenuated apoptosis; down-regulated DNMT3A; and up-regulated FAM8A1 in COPD cell model. EGF/ERBB2 represses endoplasmic reticulum-associated degradation to promote COPD development by reducing FAM8A1 via increasing DNMT3A. Blocking EGF/ERBB2 may help clinical treatment of COPD.

CRISPR-based epigenetic editing enables reversible regulation of gene expression without permanent DNA modification. The integration of artificial intelligence (AI) enhances guide RNA (gRNA) design, off-target prediction, and delivery optimization. We conducted a systematic review and meta-analysis (2015–2025) in accordance with PRISMA 2020 guidelines to evaluate the impact of AI on the precision, safety, and therapeutic efficacy of epigenetic CRISPR tools. From 540 screened records, 58 studies met inclusion criteria, of which 41 provided extractable quantitative data for meta-analysis and 17 contributed to qualitative synthesis. Random-effects models, subgroup analyses, and bias assessments were applied. Pooled analyses demonstrated strong positive effects across three domains: therapeutic efficacy (SMD = 1.67), gRNA optimization (SMD = 1.44), and off-target prediction (AUC = 0.79). Publication bias was minimal, and subgroup analyses indicated the strongest impact in therapeutic applications. Deep learning models were consistently associated with higher effect sizes. Qualitative synthesis revealed trends in interpretable AI, omics integration, and delivery innovations, underscoring AI’s role in safer and more precise CRISPR editing. Overall, AI significantly improves the precision and therapeutic performance of CRISPR-based epigenetic tools, with the strongest effects observed in therapeutic efficacy, supporting their potential for personalized gene editing.