Search Results (649)

Genome-wide association studies (GWAS) have transformed the study of chronic kidney disease (CKD) by identifying hundreds of genetic loci associated with multiple aspects of kidney function, including albuminuria and CKD risk factors, in diverse populations. A major challenge is translating statistically significant signals into causal genes and mechanisms, as most CKD-associated variants lie in non-coding regulatory regions and often act in a cell type- and context-specific manner. In this review, we provide an overview of the current strategies for moving from GWAS signals toward the identification of causal genes for CKD. We discuss advances in four areas: statistical and functional fine-mapping, molecular quantitative trait locus (QTL) mapping, colocalization, and transcriptome-wide associations, highlighting the advantages and disadvantages of each. We further examined how emerging kidney-specific single-cell, single-nucleus, and spatial transcriptomic atlases have enabled the mapping of genetic risk to specific renal cell types and microanatomical niches. By combining these approaches with chromatin interaction data, multi-omics analytics, and clustered regularly interspaced short palindromic repeats (CRISPR)-based studies, the process of generating causal relationships and mechanistic understanding has been further refined. Importantly, this review provides a unifying framework that synthesizes cross-sectional and longitudinal GWAS with kidney-specific functional genomics to distinguish genetic determinants of CKD susceptibility from modifiers of disease progression, thereby highlighting how regulatory variation and disease trajectories inform precision nephrology. As a result, we can provide insights into the role of genetically informed gene prioritization for experimentation, therapeutic target discovery, and the development of a framework for precision nephrology. Together, these advancements highlight how human genetics, in conjunction with functional genomics and experimental biology, can link an association signal to a clinically relevant interpretation of CKD. Full article

Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide. Compared with traditional two-dimensional (2D) models, patient-derived CRC organoids more faithfully preserve the genomic, transcriptomic, and architectural features of primary tumors, making them a powerful intermediate platform bridging basic discovery and clinical translation. Over the past several years, organoid systems have rapidly expanded beyond conventional epithelial-only cultures toward increasingly complex architectures, including immune-organoid co-culture models and mini-colon systems that enable long-term, spatially resolved tracking of tumor evolution. These advanced platforms, combined with high-throughput technologies and clustered regularly interspaced short palindromic repeats (CRISPR)-based functional genomics, have substantially enhanced our ability to dissect CRC mechanisms, identify therapeutic vulnerabilities, and evaluate drug responses in a physiologically relevant context. However, current models still face critical limitations, such as the lack of systemic physiology (e.g., gut–liver or gut–brain axes), limited standardization across platforms, and the need for large-scale, prospective clinical validation. These gaps highlight an urgent need for next-generation platforms and computational frameworks. The development of high-throughput multi-omics, CRISPR-based perturbation, drug screening technologies, and artificial intelligence-driven predictive approaches will offer a promising avenue to address these challenges, accelerating mechanistic studies of CRC, enabling personalized therapy, and facilitating clinical translation. In this perspective, we propose a roadmap for CRC organoid research centered on two major technical pillars: advanced organoid platforms, including immune co-culture and mini-colon systems, and mechanistic investigations leveraging multi-omics and CRISPR-based functional genomics. We then discuss translational applications, such as high-throughput drug screening, and highlight emerging computational and translational strategies that may support future clinical validation and precision medicine. Full article

Cardiovascular disease (CVD) remains the leading cause of morbidity and mortality, despite advances in pharmacological prevention and treatment. The burden of CVD necessitates implementing the treatment of risk factors including dyslipidemia. Pharmaceutical advancements and in depth understanding of pathophysiology have enabled innovative therapies targeting pathways underlying lipoprotein metabolism disorders. Angiopoietin protein-like 3 (ANGPTL3) plays a crucial role in the regulation of lipoprotein metabolism, therefore being a potential therapeutic target. Inhibition of ANGPTL3 has emerged as a new therapeutic strategy to reduce LDL-cholesterol levels independent of the LDL receptor function. Therapeutic approaches for ANGPTL3 inhibition range from monoclonal antibodies to nucleic acid therapeutics including antisense oligonucleotides and small interfering RNAs. In this review, we briefly explain the structure and mechanism of action of ANGPTL3 and discuss the therapeutic approaches for targeting ANGPTL3 in the clinical setting. We also discuss Evinacumab, a monoclonal antibody, its structure, mechanism of action, safety, tolerability, pharmacokinetics, and pharmacodynamics, as well as its clinical trial-derived results. The antisense oligonucleotides modify ANGPTL3 mRNA to inhibit protein production, and small interfering RNAs induce mRNA degradation; results from clinical trials were reviewed in detail. Finally, we discuss promising gene editing approaches including clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems. Full article

Background: Diabetic nephropathy (DN) is largely driven by transforming growth factor-β1 (TGF-β1)-mediated fibrosis. Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) ribonucleoprotein (RNP) complexes offer precise gene disruption, yet effective non-viral delivery remains a challenge. This study developed cationic lipid-based hybrid nanostructured lipid carriers (NLCs) for intracellular delivery of TGFB1-targeting RNP as an early-stage platform for DN gene modulation. Methods: A single-guide RNA (sgRNA) targeting human TGFB1 was assembled with Cas9 protein (1:1 and 1:2 molar ratios). Hybrid NLCs comprising squalene, glyceryl trimyristate, and the cationic lipid 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) were formulated via optimized emulsification–sonication to achieve sub-100 nm particles. Physicochemical properties, including polydispersity index (PDI), were assessed via dynamic light scattering (DLS), while silencing efficacy in HEK293T cells was quantified using quantitative reverse transcription PCR (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA). Results: Optimized NLCs achieved hydrodynamic diameters of 65–99 nm (PDI < 0.5) with successful RNP complexation. The 1:2 Cas9:sgRNA formulation produced the strongest gene-editing response, reducing TGFB1 mRNA by 67% (p < 0.01) compared with 39% for the 1:1 ratio. This translated to a significant reduction in TGF-β1 protein (p < 0.05) within 24 h. Conclusions: DOTAP-based hybrid NLCs enable efficient delivery of CRISPR–Cas9 RNP and achieve significant suppression of TGFB1 expression at both transcriptional and protein levels. These findings establish a promising non-viral platform for upstream modulation of profibrotic signaling in DN and support further evaluation in kidney-derived cells and in vivo renal models. Full article

The genus Aspergillus comprises over 600 species of filamentous fungi. This genus significantly impacts human health, food fermentation, and industrial biotechnology. With the in-depth research and applications of Aspergillus species in many fields, the establishment of efficient gene editing technologies is crucial for functional genomics studies and cell factory development. The clustered regularly interspaced short palindromic repeats and associated protein (CRISPR-Cas9) system, as a newly developed and powerful genome editing tool, has demonstrated exceptional potential for precise genetic modifications in various Aspergillus species. The continuous advancement of CRISPR-Cas9 technology has enabled precise gene editing and modification in both pathogenic and industrial Aspergillus strains, thereby driving innovations in pathogenicity attenuation, metabolic engineering, and functional genomics. Therefore, this review provides a concise overview of the CRISPR-Cas9 system, detailing its composition, working mechanism, and key functional features such as the role of the Cas9 protein and the protospacer adjacent motifs (PAMs). Subsequently, we focus on the transformative applications of CRISPR-Cas9 in Aspergillus species, discussing its pivotal roles in elucidating pathogenic mechanisms, disrupting mycotoxin biosynthesis, and employing metabolic engineering to enhance the production of industrial enzymes, organic acids, and valuable natural products. Finally, we discuss future challenges and promising opportunities for applying CRISPR-Cas9 technology to advance the industrial biotechnology of Aspergillus species. Full article

Background/Objectives: Approved for treatment of acute leukemia, gemtuzumab ozogamicin (GO) and inotuzumab ozogamicin (InO) are antibody–drug conjugates (ADCs) that deliver a toxic calicheamicin (CLM) derivative. The resistance mechanisms to GO/InO remain incompletely understood. Methods: We performed a genome-wide clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 screen for CLM sensitivity genes, and then performed confirmatory cytotoxicity assays. Results: Several DNA damage pathway regulation genes were identified, most notably TP53. Across 13 acute leukemia cell lines, the six TP53-mutant cell lines (TP53^MUT) were indeed 10- to 1000-fold less sensitive to CLM than the seven TP53^WT cell lines. In five TP53^WT/KO syngeneic cell line pairs we generated, TP53^KO cells were significantly less sensitive to CLM than their TP53^WT counterparts. In TP53^WT but not TP53^MUT cells, the MDM2 inhibitor and p53 activator, idasanutlin, enhanced CLM cytotoxicity, demonstrating that decoupling of cells from MDM2-p53 regulation sensitizes leukemia cells to CLM. The ATM inhibitors AZD1390 and lartesertib also significantly enhanced CLM efficacy but did so independent of the TP53 status. In contrast, neither an ATR inhibitor, Chk1/Chk2 inhibitor, Chk2 inhibitor, or a PARP inhibitor significantly impacted CLM-induced cytotoxicity across the thirteen cell lines. Together, our studies identify ATM, MDM2, and TP53—which are in the same cellular response to DNA damage pathway—as key modulators of CLM-induced cytotoxicity in acute leukemia cells. Conclusions: These results support further evaluation of combination therapies with corresponding small-molecule inhibitors (currently pursued for therapy of other cancers) toward clinical testing as novel strategies to increase the efficacy of CLM-based ADCs such as GO and InO. Full article

The scarlet gene encodes an ATP-binding cassette transporter involved in eye pigmentation across various insect species. In this study, we functionally characterized the scarlet homolog (Gbst) in the cricket Gryllus bimaculatus, a hemimetabolous model organism. Clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9-mediated knockout of Gbst generated a stable yellow-eyed mutant line (Gbst^−/−) with changed pigmentation evident from embryogenesis through adulthood. Quantitative real-time PCR analysis showed that scarlet expression was extremely low in Gbst^−/−, and the transcript levels of white and brown were also reduced. Histological sections of the compound eyes showed that both WT and Gbst^−/− mutant possessed complete and well-defined ommatidial structures, indicating that the scarlet gene does not affect compound eye structure. In addition, reproduction tests showed that knockout of the Gbst gene did not affect egg production or embryonic viability. These findings demonstrate that Gbst is a key factor involved in eye pigmentation in G. bimaculatus, and has potential for application as a visual transgenic marker gene. Full article

Vascular diseases (VDs) and cardiovascular diseases (CVDs) are the leading causes of morbidity and mortality worldwide. Current diagnostic and therapeutic approaches are limited by insufficient resolution and a lack of mechanistic understanding at the cellular level. Traditional imaging and clinical assays do not fully capture the dynamic molecular and structural complexities underlying vascular pathology. Recent technological innovations, including single-cell and spatial transcriptomics, super-resolution and photoacoustic imaging, microfluidic organ-on-chip platforms, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-based gene editing, and artificial intelligence (AI), have created new opportunities for investigating the cellular and molecular basis of VDs. These techniques enable high-resolution mapping of cellular heterogeneity and functional alterations, facilitating the integration of large-scale data for biomarker discovery, disease modeling, and therapeutic development. This review focuses on evaluating the translational readiness, limitations, and potential clinical applications of these emerging technologies. Understanding the cellular and molecular mechanisms of VDs is essential for developing targeted therapies and precise diagnostics. Integrating single-cell and multiomics approaches highlights disease-driving cell types and gene programs. Optogenetics and organ-on-chip platforms allow for controlled manipulation and physiologically relevant modeling, while AI enhances data integration, risk prediction, and clinical interpretability. Future efforts should prioritize multi-center, large-scale validation studies, harmonization of assay protocols, and integration with clinical datasets and human samples. Multi-omics approaches and computational modeling hold promise for unraveling disease complexity, while advances in regulatory science and digital simulation (such as digital twins) may further accelerate personalized medicine in vascular disease research and treatment. Full article

The rapid global expansion of genetically modified (GM) crops requires fast, on-site detection methods. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated (CRISPR/Cas) systems offer a promising platform for decentralized GM organism (GMO) monitoring. This review focuses specifically on the application of this technology in agriculture and food supply chains, diverging from previous reviews centered on clinical diagnostics. We examine the mechanisms of key CRISPR effectors (e.g., Cas12a, Cas13a) and their integration into diagnostic platforms (e.g., DETECTR, SHERLOCK) for detecting transgenic elements (e.g., CaMV35S promoter). A dedicated comparison of signal readout modalities, including fluorescence, lateral flow, and electrochemical sensing, highlights their suitability for different GMO detection scenarios, from field screening to laboratory confirmation. Finally, we discuss current challenges, including multiplexing and standardization, and outline future directions, such as the engineering of novel Cas variants and integration with smartphone technology. CRISPR-based diagnostics are poised to become indispensable tools for decentralized, efficient, and reliable GMO detection. Full article

Bacteria encode a broad range of survival and defence systems, including CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas systems, restriction-modification systems, and toxin–antitoxin (TA) systems, which are involved in bacterial regulation and immunity. The traditional view holds that CRISPR-Cas systems and TA systems are two independent defense lines in prokaryotes. However, groundbreaking studies in recent years have revealed multi-level functional coupling between them. This review systematically elaborates on this mechanism, focusing on three types of TA systems that mediate the core correlation of CRISPR-Cas systems: CreTA maintains the evolutionary stability of CRISPR-Cas systems through an addiction mechanism; CreR enables self-regulation of CRISPR-Cas expression; and CrePA provides herd immunity by triggering abortive infection after the CRISPR-Cas system has been destroyed by Anti-CRISPRS protein. Additionally, we discuss the evolutionary homology between the type III toxin AbiF and the type VI CRISPR effector Cas13, offering a new perspective for understanding the origin of CRISPR-Cas systems. These findings not only reveal the functional coupling of prokaryotic defense systems but also provide a powerful theoretical framework and practical solutions for addressing stability challenges in CRISPR technology applications. Full article

Cabbage (Brassica oleracea var. capitata) is a biennial plant. Gene editing technology has not been extensively studied in this species. In this study, we report the induction of highly efficient and heritable transgenic roots in cabbage using the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) gene editing system, followed by the regeneration of whole plants from these transgenic roots. We designed and constructed a CRISPR/Cas9 gene editing vector targeting the immune regulatory gene PUB13 (PLANT U-BOX 13) and introduced it into plants through Agrobacterium-mediated transformation. By performing targeted mutations on PUB13, transgenic roots were obtained, the optimal TDZ (Thidiazuron) concentration for bud induction (0.9 mg·L⁻¹) was determined, and then an efficient transformation protocol from transgenic roots to plants was established, leading to the regeneration of gene-edited plants. In summary, we successfully generated gene-edited cabbage (Brassica oleracea var. capitata) plants through PUB13 gene mutagenesis using an innovative transgenic root regeneration approach. A new pathway for obtaining gene-edited cabbage plants was established. Full article

This article aims to point out new perspectives opened by genomics and epigenomics in skin rejuvenation strategies which target the main hallmarks of the ageing. In this respect, this article presents a concise overview on: the clinical relevance of the most important clocks and biomarkers used in skin anti-ageing strategy evaluation, the fundamentals, the main illustrating examples preclinically and clinically tested, the critical insights on knowledge gaps and future research perspectives concerning the most relevant skin anti-ageing and rejuvenation strategies based on novel epigenomic and genomic acquisitions. Thus the review dedicates distinct sections to: senolytics and senomorphics targeting senescent skin cells and their senescent-associated phenotype; strategies targeting genomic instability and telomere attrition by stimulation of the deoxyribonucleic acid (DNA) repair enzymes and proteins essential for telomeres’ recovery and stability; regenerative medicine based on mesenchymal stem cells or cell-free products in order to restore skin-resided stem cells; genetically and chemically induced skin epigenetic partial reprogramming by using transcription factors or epigenetic small molecule agents, respectively; small molecule modulators of DNA methylases, histone deacetylases, telomerases, DNA repair enzymes or of sirtuins; modulators of micro ribonucleic acid (miRNA) and long-non-coding ribonucleic acid (HOTAIR’s modulators) assisted or not by CRISPR-gene editing technology (CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats); modulators of the most relevant altered nutrient-sensing pathways in skin ageing; as well as antioxidants and nanozymes to address mitochondrial dysfunctions and oxidative stress. In addition, some approaches targeting skin inflammageing, altered skin proteostasis, (macro)autophagy and intercellular connections, or skin microbiome, are very briefly discussed. The review also offers a comparative analysis among the newer genomic/epigenomic-based skin anti-ageing strategies vs. classical skin rejuvenation treatments from various perspectives: efficacy, safety, mechanism of action, evidence level in preclinical and clinical data and regulatory status, price range, current limitations. In these regards, a concise overview on senolytic/senomorphic agents, topical nutrigenomic pathways’ modulators and DNA repair enzymes, epigenetic small molecules agents, microRNAs and HOTAIRS’s modulators, is illustrated in comparison to classical approaches such as tretinoin and peptide-based cosmeceuticals, topical serum with growth factors, intense pulsed light, laser and microneedling combinations, chemical peels, botulinum toxin injections, dermal fillers. Finally, the review emphasizes the future research directions in order to accelerate the clinical translation of the (epi)genomic-advanced knowledge towards personalization of the skin anti-ageing strategies by integration of individual genomic and epigenomic profiles to customize/tailor skin rejuvenation therapies. Full article

Head-and-neck squamous cell carcinoma (HNSCC) remains a lethal malignancy with stagnant survival despite advances in surgery, radiotherapy, and systemic therapy. Beyond cetuximab and PD-1 inhibitors, there are only a few targeted options, which benefit only a minority of patients, underscoring the need for new biomarkers and druggable dependencies. Genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) Cas9 screening now enables systematic, high-specificity investigation of gene function to reveal determinants of tumor proliferation, survival, and therapy response. Compared with RNA interference, CRISPR provides cleaner on-target knockout and more interpretable phenotypes, allowing efficient discovery of essential genes and synthetic-lethal interactions. Although the Cancer Dependency Map profiled 89 OSCC/HNSCC lines to nominate baseline dependencies, drug-perturbed states critical for understanding platinum resistance remain underexplored. Only a handful of HNSCC studies have applied genome-wide CRISPR cas9 screening: two mapped core essential genes; two mapped cisplatin resistance and radiation resistance; and others uncovered synthetic-lethal targets, including vulnerabilities to mTOR inhibition, EGFR inhibition, glutamine metabolism inhibition, and host determinants of oncolytic HSV-1 efficacy. This review synthesizes these findings, highlights methodological considerations (library design, coverage, and treatment duration), and integrates complementary functional data to prioritize targets for rational combinations. This review also provides information on the TCGA database and in vivo CRISPR screening that can accelerate precision therapeutics for patients with HNSCC. Full article

Molecular network analysis offers powerful insights for plant improvement by capturing complex regulatory interactions. However, translating omics data across species presents significant challenges. Non-model crops such as soybean and lupin often lack comprehensive genomic resources, which complicates network analysis. Model species (e.g., Arabidopsis thaliana) provide rich data but may lack legume-specific pathways. This review synthesizes these challenges and examines legume networks in soybean, lupin, and the model legume, Medicago truncatula. Strategies such as multi-omics integration and Artificial Intelligence (AI)-driven tools, combined with wet lab validation studies such as clustered regularly interspaced short palindromic repeats (CRISPR), are discussed to bridge the gap between discovery and application. Ultimately, we conclude that cross-species multi-omics integration, empowered by AI and validated by gene editing, will be pivotal for translating network discoveries into resilient legume crops. Strategic investments in under-researched non-model legumes and advanced molecular tools are essential to ensure sustainable agriculture and future crop resilience. Full article