Search Results (209)

Background: Tumor invasion is the central barrier to effective immunotherapy in lung adenocarcinoma (LUAD) and glioblastoma. Cell adhesion signaling critically shapes tumor–microenvironment interactions, yet the upstream regulators coordinating these invasive programs at single-cell resolution remain incompletely understood. Methyltransferase Like protein 7B (METTL7B) has recently emerged as a candidate oncogenic regulator, but its lineage-specific functions and the potential downstream effectors are unclear. Methods: We integrated publicly available single-cell RNA sequencing datasets from LUAD and glioblastoma with The Cancer Genome Atlas (TCGA) transcriptomic analyses to resolve METTL7B-associated malignant cell states and microenvironmental interactions. Functional enrichment analyses identified invasion- and focal adhesion pathways linked to METTL7B expression. Gain- and loss-of-function experiments were conducted in LUAD and glioblastoma cell lines to validate downstream cell adhesion effectors. Spatial expression patterns were examined using immunofluorescence, and transwell assays were used to assess migratory and invasive phenotypes. Results: Single-cell analyses revealed that METTL7B was selectively enriched in malignant epithelial cells in LUAD and glioblastoma and defined a transcriptional program characterized by cell adhesion signaling. Integrin Alpha 3 (ITGA3) emerged as a conserved downstream effector of METTL7B, with progressive upregulation from minimally invasive to invasive LUAD and glioblastoma. Functional perturbation confirmed that METTL7B enhances tumor cell migration and invasion through integrin-associated pathways. Conclusions: METTL7B acts as a potential lineage-enriched regulator of invasive tumor states by activating cell adhesion signaling in LUAD and glioblastoma. These findings position METTL7B as a putative prognostic factor for strategies aimed at limiting invasion in lung cancer and glioblastoma. Full article

Regulated cardiomyocyte death is a central contributor to myocardial infarction (MI)-associated injury. Mixed lineage kinase domain-like protein (MLKL), a key effector of necroptosis, has been implicated in cardiovascular disease; however, its role in MI remains incompletely defined. MLKL expression was evaluated in hypoxia-treated cardiomyocytes, infarcted murine hearts, and human cardiac tissue. MLKL function was investigated using siRNA-mediated knockdown in neonatal mouse cardiomyocytes and genetic deletion in mice subjected to left anterior descending (LAD) coronary artery ligation. Apoptosis- and pyroptosis-related signaling were assessed by immunoblotting and immunostaining. RIP3 expression and regulation were examined at both protein and mRNA levels, and the RIP3 inhibitor GSK’872 was used to assess pathway dependence. MLKL expression was increased in hypoxic cardiomyocytes, infarcted mouse hearts, and human failing cardiac tissue. Unexpectedly, MLKL deficiency was associated with aggravated myocardial injury, impaired cardiac function, and increased fibrosis following MI. Mechanistically, MLKL deficiency was associated with increased RIP3 protein abundance without a corresponding increase in RIP3 mRNA, consistent with post-transcriptional regulation. Further analyses indicated that MLKL deficiency reduced RIP3 ubiquitination and impaired proteasome-mediated degradation, resulting in RIP3 stabilization. Elevated RIP3 levels were accompanied by increased expression of apoptosis- and pyroptosis-related proteins, particularly at early time points after MI. Pharmacological inhibition of RIP3 with GSK’872 was associated with reduced apoptosis- and pyroptosis-related signaling and improved cardiac function. MLKL deficiency is associated with stabilization of RIP3 and enhanced activation of apoptosis- and pyroptosis-related signaling following MI, contributing to aggravated myocardial injury. These findings support a regulatory role for the MLKL–RIP3 axis in cardiomyocyte death and suggest that targeting RIP3 may represent a potential therapeutic strategy in myocardial infarction. Full article

Background: A major technical challenge in single-cell transcriptomics is the absence of an integrative analytic pipeline that can simultaneously leverage gene regulatory network (GRN) architecture, AI-assisted gene panel discovery, and functional relevance analyses to generate coherent biological insights. Existing approaches often treat these components independently, focusing on clusters, marker genes, or predictive features without integrating them into a mechanistically grounded framework. Consequently, comprehensive screening that links regulatory association, gene signature screening, and functional interpretation within single-cell datasets remains limited, underscoring the need for an integrated strategy. Methods: We developed an integrative bioinformatics pipeline based on Gene regulatory network–AI–Functional Analysis (GAFA), combining latent-space integration, unsupervised clustering, diffusion pseudotime analysis, lineage-resolved generalized additive modeling, GRN inference, and machine learning-based gene panel discovery. This framework enables systematic mapping of cell-state structure, reconstruction of differentiation and effector trajectories, and identification of transcriptional and regulatory features strongly associated with clinical outcomes. As a case study, we applied the pipeline to NK cell transcriptomes from six CML patients (two early relapse, two late relapse, two durable treatment-free remission—TFR; 15 samples) collected at TKI discontinuation and 6–12 months after therapy cessation. Results: We reanalyzed publicly available scRNA-seq data from a previously published CML cohort to evaluate NK-cell transcriptional programs associated with treatment-free remission and relapse. We resolved six transcriptionally distinct NK cell states spanning CD56^bright-like cytokine-responsive, early activated, terminally mature, cytotoxic, lymphoid trafficking, and HLA-DR⁺ immunoregulatory populations, each exhibiting outcome-specific compositional differences. Pseudotime analysis revealed two major NK cell lineages—a maturation trajectory and a cytotoxic effector trajectory. TFR samples displayed balanced occupancy of both lineages, whereas early relapse samples showed marked depletion of the maturation branch and preferential accumulation in cytotoxic end states. AI-guided feature selection and random forest modeling identified an 18-gene panel that distinguished NK cells from TFR and relapse samples in an exploratory manner. Among them, CST7, FCER1G, GNLY, GZMA, and HLA-C were conventional NK-associated genes, whereas ACTB, CYBA, IFITM2, IFITM3, LYZ, MALAT1, MT2A, MYOM2, NFKBIA, PIM1, S100A8, S100B, and TSC22D3 were novel. The GRN inference further uncovered outcome-specific regulatory modules, with RUNX3, EOMES, ELK4, and REL regulons enriched in TFR, whereas FOSL2 and MAF regulons were enriched in relapse, and their downstream targets linked to IFN-γ signaling, metabolic reprogramming, and immunoregulatory feedback circuits. Conclusions: This AI-enabled single-cell analysis demonstrates how NK cell state composition, differentiation trajectories, and regulatory network rewiring collectively shape TFR versus relapse following TKI discontinuation in CML. The integrative pipeline provides a modular framework that could be extended to additional datasets for data-driven biomarker discovery and mechanistic stratification, and highlights candidate transcriptional regulators and NK cell programs that may be leveraged to improve remission durability, pending validation in larger patient cohorts. Full article

Background: Psoriasis frequently relapses after treatment withdrawal, consistent with persistent epigenetic programs in lesional immune cells. Lysine acetylation is a reversible regulatory layer linking chromatin accessibility, transcription factor activity, and immune-cell effector programs; yet, its cell-type-resolved landscape and clinical stratification value in psoriasis remain incompletely defined. Methods: We integrated four bulk transcriptome cohorts of psoriatic and healthy skin (746 psoriasis, 515 controls) with two public skin scRNA-seq datasets. A diagnostic acetylation-regulator signature was derived from 33 curated acetylation regulators, and acetylation endotypes were defined by unsupervised clustering. The cell-type-specific expression was mapped at the single-cell resolution. Key regulators were validated by quantitative real-time polymerase chain reaction (qRT-PCR) in an imiquimod-induced psoriasis-like mouse model, and further verified in an independent dataset (GSE136757). Motif enrichment and drug–target mining were used to prioritize transcriptional regulators and candidate epigenetic therapeutics. Results: Sixteen acetylation regulators were differentially expressed in bulk skin, with histone deacetylase (HDAC1) showing the strongest upregulation and lysine acetyltransferase (KAT2A) the strongest downregulation. A 13-gene acetylation signature discriminated psoriasis from controls (area under the curve, AUC 0.886) and separated lesional samples into two acetylation endotypes with divergent pathway states (hypoxia–glycolysis versus oxidative-stress-dominated programs). Single-cell mapping demonstrated immune-restricted acetylation modules, including CREB binding protein (CREBBP)-enriched neutrophils, histone deacetylase 1 (HDAC1)-high cluster of differentiation (CD)8⁺ T cells, and lysine acetyltransferase 6A (KAT6A)/lymphoid enhancer binding factor (LEF1)-enriched CD4⁺ and regulatory T cell (Treg) subsets, coincident with interleukin (IL)-17-related inflammatory programs. In mice, qRT-PCR confirmed the coordinated dysregulation of hub genes and highlighted Hnf1a and Kat6a as reproducible candidates. External validation using the GSE136757 dataset further supports their robust diagnostic performance. Motif analysis nominated interferon regulatory factor (IRF4), YY transcription factor (YY2), and zinc finger protein (ZNF404) as putative transcriptional mediators downstream of acetylation programs, and drug–target mining prioritized epigenetic compounds with subtype-relevant potential, including histone deacetylase (HDAC) inhibitors (e.g., entinostat) and the p300/CREB binding protein (CBP) inhibitor A485. Conclusions: This integrative atlas links acetylation regulators to specific immune compartments, defines acetylation endotypes associated with distinct inflammatory programs, and provides a rationale for stratified epigenetic target selection in psoriasis. Full article

The discovery of bidirectional microRNA transfer between two organisms during plant–microbe interactions and the ability of some fungal pathogens to absorb double-stranded RNA (dsRNA) or short interfering RNA (siRNA) from the environment provided an impetus for exploiting this mechanism in plant defense against pathogens. In this study, we investigated the role of conserved wheat microRNAs (miRNAs), miRNA408 and miRNA159, in inducing plant defense responses and suppressing the virulence of the phytopathogenic ascomycete fungus Parastagonospora nodorum, mediated by necrotrophic effectors (NEs) encoded by SnTox genes regulated by fungal transcription factors (TFs). The foliar spraying with in vitro synthesized siRNA408 and siRNA159 duplexes before inoculation with SnTox3-producing P. nodorum isolate increased wheat plant resistance to the SnB isolate and suppressed the pathogen growth and development. Most likely, silencing of the miRNA408 target genes TaCAT-2A, TaCAT-2B, and TaCLP1, and the miRNA159 target gene TaMYB65, led to the induction of a defense response of wheat plants against P. nodorum. This defense response was characterized by a decrease in the catalase activity, accumulation of hydrogen peroxide, activation of the expression of salicylic acid signaling pathway genes (TaWRKY13, TaPR1), and suppression of the expression of ethylene signaling pathway genes (TaEIN3, TaPR3). We demonstrated for the first time the ability of siRNA159 and siRNA408 to penetrate the mycelium of the pathogen P. nodorum and be involved in the cross-kingdom regulation of fungal genes to suppress the expression of some genes of NE (SnToxA, SnTox3) and fungal TFs (SnStuA). We predicted potential targets for wheat miRNA408 and miRNA159 in the P. nodorum transcriptome, making spray-induced gene silencing (SIGS) promising for use against this pathogen. These results provide valuable insights for studying the cross-kingdom transfer of plant miRNAs. Full article

Innate-like T cells (ILTCs) link innate immune responses with adaptive immune functions. This group includes invariant natural killer T (iNKT) cells, mucosa-associated invariant T (MAIT) cells, and γδ T cells. ILTCs detect transformed or stressed cells via non-classical antigen presentation pathways. For example, iNKT cells recognize CD1d-presented glycolipids, MAIT cells respond to MR1-presented metabolites from riboflavin pathways, and γδ T cells sense phosphoantigens through butyrophilin-dependent mechanisms and stress ligands. These features support early tumor control and shape downstream immunity by promoting dendritic cell activation, NK cell function, and priming of tumor-reactive CD8⁺ T cells. In established tumors, ILTC activity is frequently suppressed. Reduced antigen presentation, inhibitory cytokines, hypoxia, and metabolic constraints, including lactate accumulation and kynurenine production, limit effector responses and promote hyporesponsive states. Transcriptional regulators such as TOX, NR4A family members, and BATF are associated with these programs. This review discusses ILTC roles in tumor surveillance, immune escape, and therapeutic strategies to restore their function. Full article

The survival and activation of both effector and regulatory CD4⁺T cells are promoted by cytokines in a complex series of interactions. Alloantigen-specific Regulatory T cells (Treg) constitutively express IL-2 receptor (CD25) and Foxp3. This discovery arose as the cells that transfer the alloantigen-specific transplant tolerance die in culture with specific alloantigens, unless the cultures are supplemented with cytokines from activated lymphocytes. One such cytokine was IL-2, but other cytokines are essential. We describe how the activation of Treg by antigens depends on cytokines produced by antigen-activated effector T cells. These cytokines also drive in parallel the activation of Treg. The Treg are induced to express similar transcription factors and chemokine receptors and have a similar cytokine responsiveness to the activated T effector cells. The activation of Treg by antigens is a two-step process: the first requires cytokines produced by effector T cells early in their activation, and the second step is driven by cytokines produced later by effector T cells during activation. Cytokines from Type 1 responses promote the induction of Th1-like Treg. Likewise, cytokines produced in Type 2, Type 3, and Tfh responses induce different pathways of Treg activation. Understanding the pathways for the activation and expansion of potent antigen-specific Treg will help produce Treg to control allograft rejection or autoimmunity. Currently, the complexity of the numerous potential pathways of activation of Treg remains incompletely understood. The dogma that IL-2 is the only driver of Treg activation may have hindered the development of highly potent antigen-specific Treg for therapy. Full article

The genus Xanthomonas comprises devastating plant pathogens responsible for significant yield losses in globally critical crops such as rice (Oryza sativa L.), citrus (Citrus L. spp.), cassava (Manihot esculenta Crantz), and tomato (Solanum lycopersicum L.). This review synthesizes current knowledge on the molecular mechanisms driving Xanthomonas pathogenicity, including the type III secretion system (T3SS) that translocates effector proteins, transcription activator-like effectors (TALEs) that reprogram host transcription, and extracellular polysaccharides (EPS) that promote biofilm formation and immune evasion, which collectively enable host colonization, immune suppression, and disease progression. Rapid adaptation through genomic plasticity and horizontal gene transfer (HGT) exacerbates challenges in disease management by facilitating evasion of host defenses and environmental stressors. Economically, Xanthomonas spp. inflict billions in annual losses through crop damage, trade restrictions, and eradication efforts, disproportionately affecting resource-limited regions. Emerging antibiotic resistance and climate-driven shifts in pathogen distribution further threaten food security. Sustainable strategies, such as CRISPR-based genome editing to disrupt susceptibility genes, biocontrol agents (e.g., Bacillus and Pseudomonas spp.), and nanotechnology-driven antimicrobials offer promising alternatives to conventional copper-based and chemical controls. This review underscores the urgent need for integrated, climate-resilient management approaches to mitigate the ecological and socioeconomic impacts of Xanthomonas diseases, bridging genomic insights with innovative control measures, to address escalating threats posed by these pathogens in a changing global climate. Full article

Genome editing (GE) has transformed medicine by allowing precise changes to DNA, offering potential treatments for a range of inherited and acquired disorders. Several technologies support these advances, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)-based systems, of which the latter has emerged as the most accessible, versatile, and popular. While GE holds great promise, its clinical use requires careful attention to safety, ethics and regulatory standards. Inadvertent on- and off-target DNA alterations and unintended modification of non-target cells pose major technical challenges, while bioethical considerations and the need for harmonized safety standards create regulatory challenges. The Food and Drug Administration (FDA) and European Medicines Agency (EMA), as regulatory agencies for key advanced therapy markets, provide detailed guidance on these aspects, emphasizing rigorous preclinical testing, patient monitoring, ethical consent, and compliance with legal frameworks. This concise review summarizes what is currently published in the scientific literature and recommended by regulatory agencies, providing an overview of the responsible clinical application of GE, with emphasis on patient safety, adherence to regulatory guidance, and ethical practice. Full article

Plant immunity research is being reshaped by integrative multi-omics approaches that connect transcriptomic, proteomic, and interactomic data to build systems-level views of plant–pathogen interactions. This review outlines the scope and methodological landscape of these approaches, with particular emphasis on how transcriptomic and proteomic insights converge through network-based analyses to elucidate defense regulation. Transcriptomics captures infection-induced transcriptional reprogramming, while proteomics reveals protein abundance changes, post-translational modifications, and signaling dynamics essential for immune activation. Network-driven computational frameworks including iOmicsPASS, WGCNA, and DIABLO enable the identification of regulatory modules, hub genes, and concordant or discordant molecular patterns that structure plant defense responses. Interactomic techniques such as yeast two-hybrid screening and affinity purification–mass spectrometry further map host–pathogen protein–protein interactions, highlighting key immune nodes such as receptor-like kinases, R proteins, and effector-targeted complexes. Recent advances in machine learning and gene regulatory network modeling enhance the predictive interpretation of transcription–translation relationships, especially under combined or fluctuating stress conditions. By synthesizing these developments, this review clarifies how integrative multi-omics and network-based frameworks deepen understanding of the architecture and coordination of plant immune networks and support the identification of molecular targets for engineering durable pathogen resistance. Full article

The X-ray structural analysis of the N-terminal domain cavity from eleven transcription regulators (TFs) of the Fumarate Nitrate Reduction regulator/cAMP Regulator Protein family shows several significant trends. The conservancy of effector-binding phosphate binding cassette features in three TFs suggests a closer connection among them than the one obtained through the comparison of overall amino acid sequences. Conversely, there are also three clearly different allosteric activation mechanisms, which most likely evolved independently. Interestingly, several TFs of this family adopt the DNA-binding conformation without binding any ligand; instead, the buried region corresponding to the “allosteric” cavity is partially filled with salt bridges (which is also the case for two allosteric apo TFs). One plausible conclusion from these observations is that the non-allosteric TFs evolved from an allosteric counterpart and used salt bridges to fill and stabilize the formally polar ligand-binding cavity. O₂-sensing TFs share some residues in the relevant N-terminal domain cavity and might have had an already non-allosteric common ancestor. Full article

Cyanobacteria harbor sophisticated molecular defense systems that have evolved over billions of years to protect against viral invasion and foreign genetic elements. These ancient photosynthetic organisms possess a diverse array of restriction-modification (R-M) systems and CRISPR-Cas arrays that present challenges for genetic engineering, but also offer unique opportunities for cancer-targeted biotechnological applications. These systems exist in prokaryotes mainly as defense mechanisms but they are currently used in molecular applications as gene editing tools. Moreover, latest developments in nucleases such as zinc finger nucleases (ZFNs), TALENs (transcription-activator-like effector nucleases) are discussed. A comprehensive genomic analysis of 126 cyanobacterial species found 89% encode multiple R-M systems, averaging 3.2 systems per genome, creating formidable barriers to transformation but also providing molecular machinery that could be harnessed for precise recognition and targeting of cancer cells. This review critically examines the dual nature of these defense systems, their ecological functions, and the emerging strategies to translate their molecular precision into advanced anticancer therapeutics. Hence, the review main objectives are to explore the recent understanding of these mechanisms and to exploit the knowledge gained in opening new avenues for cancer-focused targeted interventions, while acknowledging the significant challenges to translate these systems from laboratory curiosities to practical applications. Full article

Pathogenic bacteria utilize a type III secretion system (T3SS) to inject type III effectors (T3Es) into plant cells, suppressing plant immunity and facilitating colonization. Paracidovorax citrulli, the causal agent of bacterial fruit blotch (BFB) of Cucurbitaceae crops, harbors a functional T3SS like many other plant pathogens. The expression of its T3SS and T3Es is regulated by the two-component system response regulators HrpG and HrpX. Here, we demonstrate that the aspartic acid (Asp) residues at positions 52 and 60 in P. citrulli HrpG are essential for its complete function. Plasmid-mediated complementation of the ΔhrpG mutant with hrpG carrying Asp52→alanine (Ala) or Asp60→Ala mutations failed to restore the ability of P. citrulli to induce a hypersensitive response (HR) in tobacco, whereas the Asp46→Ala mutation fully rescued this phenotype. Furthermore, genomic hrpG point mutations generating strains Aac5 (D52A) and Aac5 (D60A) abolish the activation of hrpX transcription, resulting in decreased HrpX accumulation. Collectively, Asp 52 and Asp 60 in P. citrulli HrpG are essential for transcriptional activation activity of hrpX and HR induction, serving as a potential phosphorylation site (Asp 52) for upstream histidine kinases and a Mg²⁺ coordination site (Asp 60). Given that conserved Asp residues often function as phosphorylation sites in two-component system response regulators, this study provides a foundation for identifying upstream histidine kinases that modulate HrpG activity in P. citrulli. Full article

Metastasis is still the leading cause of cancer-related death. It happens when disseminated tumor cells (DTCs) successfully navigate a series of steps and adapt to the unique conditions of distant organs. In this review, key molecular and immune mechanisms that shape metastatic spread, long-term survival, and eventual outgrowth are examined, with a focus on how tumor-intrinsic programs interact with extracellular matrix (ECM) remodeling, angiogenesis, and immune regulation. Gene networks that sustain tumor-cell plasticity and invasion are described, including EMT-linked transcription factors such as SNAIL and TWIST, as well as broader transcriptional regulators like SP1. Also, how epigenetic mechanisms, such as EZH2 activity, DNA methylation, chromatin remodeling, and noncoding RNAs, lock in pro-metastatic states and support adaptation under therapeutic pressure. Finally, proteases and matrix-modifying enzymes that physically and biochemically reshape tissues, including MMPs, uPA, cathepsins, LOX/LOXL2, and heparinase, are discussed for their roles in releasing stored growth signals and building permissive niches that enable seeding and colonization. In parallel, immune-evasion strategies that protect circulating and newly seeded tumor cells are discussed, including platelet-mediated shielding, suppressive myeloid populations, checkpoint signaling, and stromal barriers that exclude effector lymphocytes. A major focus is metastatic dormancy, cellular, angiogenic, and immune-mediated, framed as a reversible survival state regulated by stress signaling, adhesion cues, metabolic rewiring, and niche constraints, and as a key determinant of late relapse. Tumor-specific metastatic programs across mesenchymal malignancies (osteosarcoma, chondrosarcoma, and liposarcoma) and selected high-burden cancers (melanoma, hepatocellular carcinoma, glioblastoma, and breast cancer) are highlighted, emphasizing shared principles and divergent organotropisms. Emerging therapeutic strategies that target both the “seed” and the “soil” are also discussed, including immunotherapy combinations, stromal/ECM normalization, chemokine-axis inhibition, epigenetic reprogramming, and liquid-biopsy-enabled minimal residual disease monitoring, to prevent reactivation and improve durable control of metastatic disease. Full article

The phenomenon of transgene silencing was first observed shortly after the generation of the initial transgenic plants. The vast body of experimental data accumulated since then constitutes an invaluable resource for dissecting the mechanisms of epigenetic gene regulation. Silencing operates at either the transcriptional (TGS) or post-transcriptional (PTGS) level and is predominantly mediated by small interfering RNAs (siRNAs). Although these two epigenetic pathways involve distinct sets of proteins and enzymes, they share fundamental mechanistic features: the generation of double-stranded RNA (dsRNA), its processing into siRNAs by DICER-LIKE (DCL) enzymes, and the assembly of an Argonaute-centered effector ribonucleoprotein complex (RISC). Guided by sequence-specific siRNAs, this complex identifies complementary target sequences with high precision. A comprehensive understanding of these regulatory pathways enables the targeted induction or suppression of specific plant genes. This review traces the history of experimental findings regarding the loss of recombinant gene activity in transformants and their progeny, which collectively established the foundation for elucidating the molecular mechanisms of transgene silencing. Full article