gene editing

Mechanistic insight into microbial mediated heavy metal uptake and tolerance

Heavy metal (HM) contamination has become a critical threat to the agro-environment, impairing soil fertility, reducing crop productivity, and disrupting ecological balance. It often displays stunted growth, chlorosis, root rot, and ultimately death of plants in severe cases. Due to increased anthropogenic activities, HM accumulation in agricultural soils is rising to an extent and thus adversely affecting the crop productivity, soil health, environmental quality and human health therefore; sustainable strategies for remediation are urgently needed. Microbial bioremediation offers a promising solution by employing the natural ability of microorganisms such as phosphate solubilizers, nitrogen fixers as well as potassium solubilizers to detoxify, immobilize, or transform HM into less toxic forms. This review highlights that microbe-based bioremediation is an effective and sustainable approach for removing HM contaminants in agricultural soil. It highlights specific mechanisms employed by microbes including: biosorption, transportation, sequestering, and detoxification that causes immobilization of HMs and reduces their toxic effect. Furthermore, this review also discusses how integrating advance biotechnological tools with microbial remediation strategies, have the potential to enhance sustainability of agricultural systems. Despite the key advantages, optimizing microbial efficiency for bioremediation still remains a major challenge. Future research focuses on integration of advanced biotechnological interventions, including gene editing, CRISPR-Cas, and improved microbial formulations, to enhance the efficiency and resilience of remediation strategies.

MAP3K14 (NIK) synonymous variants drive altered splicing to activate NF-κB in mature B-cell malignancies

Genetic alterations activating NF‑κB have been described in mature B‑cell malignancies. These alterations include loss of the negative regulator TRAF3, allowing NIK (NF‑κB-inducing kinase) to drive non-canonical NF‑κB (ncNF‑κB) signaling. In this study, we characterized two recurrent synonymous variants of MAP3K14, the gene encoding NIK, across mature B‑cell malignancies including chronic lymphocytic leukemia, lymphoplasmacytic lymphoma/Waldenström's macroglobulinemia, multiple myeloma and mantle cell lymphoma. These variants were shown to introduce splice donor sites that result in removal of the critical TRAF3 binding motif. Cell line models prime edited to contain the synonymous variants demonstrated NF‑κB activation and transcriptional reprogramming with enhanced cell proliferation and survival, as well as increased secretion of several cytokines/chemokines including IP10/CXCL10. We also characterized distinctive cell surface proteomic changes with NF‑κB activation, identifying candidate markers (e.g.,CD132/IL‑2Rγ) for assessing NF‑κB activation at a single cell level using flow cytometry. This study expands the spectrum of genetic lesions that result in activation of NF‑κB in mature B‑cell malignancies and highlights our incomplete understanding of NF‑κB drivers in mature B‑cell malignancies.

Molecular Mechanisms and Regulation of Anthocyanin Biosynthesis in Rosaceae Fruits: A Review

ABSTRACT Anthocyanin accumulation in Rosaceae fruits is governed by a multi‐layered regulatory network integrating transcriptional control, epigenetic modulation, environmental signaling, and metabolic flux allocation. This review presents a critical synthesis of recent advances in this field, moving beyond descriptive gene lists to examine the mechanistic underpinnings of pigment regulation. We first outline the core biosynthetic pathway and post‐synthetic modifications that ensure pigment stability. The central focus is on the MYB–bHLH–WD40 transcriptional complex and its integration with epigenetic mechanisms (DNA methylation, histone modifications, non‐coding RNAs) and post‐transcriptional regulation. We further examine how environmental cues—light, temperature, and hormones—are transduced through these molecular networks, and analyze metabolic flux control at pathway branch points. A cross‐species comparative perspective across major Rosaceae crops ( Malus , Pyrus , Fragaria , Prunus ) reveals conserved regulatory nodes and genus‐specific innovations. Finally, we discuss how this integrated knowledge, combined with multi‐omics and gene editing tools, is driving targeted strategies in molecular breeding and postharvest quality management. This framework provides a foundation for rational manipulation of fruit coloration and nutritional quality.

TPST Gene Knock‐Out Eliminates Tyrosine Sulfation on a Recombinant Antibody Produced in CHO Cells

ABSTRACT Tyrosine sulfation is a post‐translational modification that has been reported to occur infrequently on recombinant monoclonal antibodies (mAbs). We recently demonstrated that tyrosine sulfation occurred on a bispecific antibody (bsAb) produced in Chinese hamster ovary (CHO) cells, using a multi‐enzymatic approach in combination with intact mass and peptide‐based mass spectrometry analysis supplemented with the use of synthetic peptides. Tyrosine sulfation needs to be controlled during the manufacturing process due to potential undesired effects, such as impact on potency and immunogenicity. Here, we report that tyrosine sulfation was not significantly inhibited by the addition of chemical inhibitors, such as sodium chlorate. Individual knockout and double knockout (DKO) of two key genes in the tyrosine sulfation pathway were carried out sequentially. Tyrosyl protein sulfotransferase 1/2 (TPST1/2) DKO by CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR‐associated protein‐9 nuclease)‐mediated gene editing eliminated tyrosine sulfation while maintaining cell growth, antibody production, and overall product quality.

59 GPNMB:CD44 Signaling Drives Tumor Progression in Translocation Renal Cell Carcinoma

Abstract Background MiT/TFE-rearranged, translocation renal cell carcinoma (tRCC) is characterized by gene fusions involving TFE3 or TFEB, and is a rare, aggressive non-ccRCC, often occurring in children and with few biomarkers or targeted therapy options. TFE3 is the most commonly translocated gene with ASPSCR1, PRCC and SFPQ as fusion partners. GPNMB (Glycoprotein non-metastatic melanoma protein B) is a canonical transcriptional target of MiT/TFE proteins expressed at low levels in normal tissues but upregulated in numerous MiT/TFE-driven tumors (e.g. tRCC), where it is associated with poor prognosis. GPNMB can also be cleaved at its ECD by metalloproteinases and secreted from the surface of cancer cells. Soluble GPNMB can thus be detected in the serum of cancer patients and function as a surrogate biomarker. CD44, the primary receptor for GPNMB, is a tumor-associated antigen linked to cancer invasion, metastases and stemness, and is associated with poor prognosis in many cancers. The aim of the current study was to characterize the biology of GPNMB and CD44 in pre-clinical models of tRCC Methods We used the following human cell line models: As in vitro pre-clinical companion models we analyzed cells with stable doxycycline-inducible expression of WT-TFE3, PRCC-TFE3, SFPQ-TFE3 and NONO-TFE3 fusions using a) the Flp-In T-RExTM system in HEK293 cells, b) rtTA3 (Tet-on) system in HK2 proximal tubular epithelial cells and c) patient derived UOK cells with TFE3-fusion transgenes, comparing them to UOK cells from ccRCC patients. We also generated a novel transgenic knock-in mouse expressing the SFPQ-TFE3 fusion. We crossed SFPQ-TFE3LSL knock-in mice to 1) KSP-Cadherin 16 Cre mice that express Cre recombinase in the distal tubular epithelial cells and collecting ducts of the kidney. 2) Tamoxifen-inducible, Pax8- ERTCre mice diffusely expressing Cre recombinase following kidney development. We also examined tumorigenesis in the previously described PRCC-TFE3LSL; Ksp-Cre mice (W. Marston Linehan, NIH), and in an ASPSCR1-TFE3 PDX mouse model and a LN metastatic lesion from a patient with the ASPSCR1-TFE3 fusion (Dr. John Copland, Mayo Clinic). We are also currently examining blood serum, EDTA plasma and urine samples from non-metastatic and metastatic ccRCC and tRCC cases, obtained courtesy of the Kidney Cancer Program at Johns Hopkins. Results To further characterize GPNMB functionality and value as a cell-surface therapeutic target in tRCC, we engineered cell lines with genomic deletion of GPNMB via CRSIPR-Cas9 editing. Deletion of GPNMB in PRCC-TFE3 cell lines [UOK120/UOK124] significantly decreased clonogenic growth in 2D, spheroid size and viability and tumor xenograft growth in NSG mice and was associated with a decrease in phosphorylation of mTORC1 substrates [p-P70S6K, p-4EBP1]. We then examined expression of CD44, the primary receptor for GPNMB, and a tumor-associated antigen associated with poor prognosis in many cancers. Expression of CD44 and its ligand SPP1/OPN, was significantly increased in bulk RNA-Seq data from multiple transgenic models of SFPQ-TFE3, PRCC-TFE3 and ASPSCR1-TFE3, in human tRCC cases compared to normal kidney, and in SFPQ-TFE3/ PRCC-TFE3 transgenic kidney tumors and an ASPSCR-TFE3 PDX model, by immunoblotting and IHC, with increased membrane localization. shRNA-mediated depletion of CD44 profoundly and specifically decreased clonogenicity of multiple TFE3-fusion lines, with no effect seen in ccRCC lines. Conclusions In conclusion, GPNMB regulates the growth of tRCC cells, potentially via an autocrine mechanism involving its receptor CD44, and targeting GPNMB-CD44 signaling may be of therapeutic benefit in tRCC. DOD CDMRP Funding yes

A-to-I editing modifies the target and role of miR-376a-3p in papillary thyroid cancer

Molecular Scissors With a Search Bar: A Contemporary Synthesis Review of CRISPR and the Editing of the Genome

This article presents a narrative review of CRISPR and the Editing of the Genome in the context of Biology. The literature on this topic has expanded substantially over recent decades, yet it remains fragmented across subfields, methods, and national research traditions. Drawing on an interpretive synthesis of representative contributions, the review reconstructs the historical development of the area, examines the conceptual foundations and definitional disputes that organize its debates, and maps the contemporary landscape of research, including the methodological shift toward data-intensive approaches and the institutional pressures that shape publication practice. Particular attention is given to the role of CRISPR and gene editing as organizing themes, and to the conditions under which findings from different research traditions can be brought into productive comparison. The review identifies three synthetic conclusions: the literature is cumulatively strong but organizationally weak; methodological pluralism is better understood as a resource than as a defect; and the growing practical salience of the topic raises the stakes of its unresolved conceptual questions. An agenda for future work is proposed, emphasizing integrative research designs, transparent synthesis practices, and the protection of definitional and infrastructural work on which cumulative progress depends. The article is intended as both a reference map for newcomers and a provocation for specialists in Biology.

Diagnosis and management of bacterial stripe in maize: Current limitations and perspectives for the control of Acidovorax avenae subsp. avenae

Maize (Zea mays L.) is one of the most important cereal crops worldwide, playing a fundamental role in food security, animal nutrition, and industrial production. Among the bacterial diseases affecting maize, bacterial stripe caused by Acidovorax avenae subsp. avenae has emerged as a significant phytosanitary concern due to its wide host range, seedborne nature, and capacity to survive in crop residues and alternative hosts. This review aimed to synthesize current knowledge regarding the biology, epidemiology, symptomatology, diagnosis, and management of A. avenae subsp. avenae, highlighting existing limitations and future perspectives for disease control. A narrative literature review was conducted using scientific publications indexed in national and international databases, with emphasis on studies published between 2020 and 2026. The pathogen causes characteristic water-soaked lesions that develop into elongated chlorotic and necrotic stripes, leading to reductions in photosynthetic capacity and crop performance. Recent advances in molecular diagnostics, including polymerase chain reaction (PCR), quantitative PCR (qPCR), sequencing technologies, and genomic approaches, have improved pathogen detection and epidemiological investigations. However, disease management remains challenging due to the limited availability of resistant cultivars and the inconsistent efficacy of chemical and biological control measures. Integrated disease management, combining cultural practices, pathogen-free seeds, biological control agents, host resistance, and disease monitoring, currently represents the most effective strategy. Emerging technologies such as remote sensing, artificial intelligence, precision agriculture, and gene-editing tools offer promising opportunities for improving disease detection, surveillance, and control. Future research should focus on pathogen diversity, host–pathogen interactions, resistance mechanisms, and climate change effects to support the development of sustainable management strategies for bacterial stripe in maize production systems.

CRISPR-Based Gene Editing in Human and Animal Health: Revolutionizing Disease Resistance and Treatment

CRISPR gene-editing technology has revolutionized modern genetics, offering precise and efficient modifications across multiple domains, including human medicine, agriculture, and veterinary science. This study explores the diverse applications of CRISPR, highlighting its role in treating genetic disorders such as sickle cell anemia and Duchenne muscular dystrophy, advancing cancer immunotherapies, and developing CRISPR-based antiviral therapies for HIV and COVID-19. In agriculture, CRISPR has facilitated the development of disease-resistant livestock, enhanced crop yields, and improved food sustainability. Additionally, CRISPR is being integrated with artificial intelligence (AI) and bioinformatics to optimize gene-editing accuracy, predict off-target effects, and accelerate drug discovery. Despite these advancements, CRISPR faces significant challenges, including ethical dilemmas surrounding germline editing, regulatory inconsistencies across countries, high costs of gene therapies, and concerns about genetic inequality. The legal and social implications of CRISPR remain complex, requiring global cooperation to establish standardized regulations and ensure equitable access to genetic therapies. Emerging innovations such as base editing, prime editing, and epigenetic modifications offer promising solutions to improve CRISPR’s precision and safety. Looking ahead, CRISPR’s long-term success will depend on responsible scientific advancements, ethical oversight, and public acceptance. With the continued refinement of gene-editing techniques and AI-driven CRISPR optimizations, this technology holds the potential to revolutionize medicine, agriculture, and environmental conservation. However, careful implementation and transparent discussions are essential to navigate the ethical, legal, and societal challenges that accompany CRISPR’s rapid development.

CRISPR/Cas9 genome editing as a precision tool for accelerating vegetable breeding and crop improvement

Meeting the increasing demand for safe, nutritious, and climate-resilient food requires innovative strategies to enhance vegetable productivity and quality while overcoming the limitations of conventional breeding. Vegetables are vital sources of essential nutrients, vitamins, minerals, and bioactive compounds; however, their genetic improvement remains constrained by long generation cycles, complex reproductive biology, and labor-intensive selection processes. Therefore, modern breeding practices are needed on an urgent basis to speed up the generation time of vegetable cultivars. The emerging genome editing techniques complement conventional breeding approaches by enabling the rapid development of improved cultivars with targeted agronomic, nutritional and stress resilience traits. Among genome editing tools, the clustered regularly interspaced short palindromic repeats (CRISPR) /CRISPR-associated protein-9 (Cas9) genome editing technique has received extensive attention in recent years due to its precise and highly efficient editing in genomes. This review provides a critical assessment of recent advances in CRISPR/Cas9-mediated vegetable improvement, with emphasis on applications in yield enhancement, nutritional quality improvement, abiotic and biotic stress tolerance, and de novo domestication. Furthermore, we highlight the emerging integration of CRISPR/Cas9 with speed breeding and artificial intelligence (AI)-guided target selection as a next-generation breeding strategy to accelerate gene discovery, improve editing precision, shorten generation cycles, and facilitate the development of transgene-free (T-DNA-free) elite vegetable cultivars. We also critically evaluate the current bottlenecks in vegetable genome editing and discuss future opportunities for integrating advanced genome editing technologies, AI-enabled approaches, and accelerated breeding pipelines to overcome these challenges and facilitate the development of sustainable, climate-resilient vegetable crops.

CRISPR-Based Therapeutic Approaches in Lung Cancer

This research paper explores the potential of CRISPR-based therapeutic approaches in the diagnosis, treatment, and management of lung cancer. It examines how CRISPR-Cas genome-editing technologies can be used to identify and modify cancer-associated genes, investigate molecular mechanisms of tumor development, and develop targeted therapeutic strategies. The study highlights the potential applications of CRISPR in precision oncology, including gene correction, cancer-cell targeting, drug resistance research, and personalized treatment. It also discusses current challenges and limitations, including off-target effects, delivery systems, tumor heterogeneity, safety concerns, and ethical considerations, while emphasizing the future potential of CRISPR technology in improving lung cancer therapy.

Regulatory divergence of duplicated VIH genes links phosphate signaling to nodule development in Medicago truncatula