Artificial Intelligence-Assisted CRISPR Gene Editing: Current Advances, Clinical Challenges, and Future Directions in Precision Medicine.

Exploiting SNPs for biallelic CRISPR mutations in the outcrossing woody perennial Populus reveals 4-coumarate:CoA ligase specificity and redundancy.

With the technological revolution, precision medicine has become a possible entity in the present times. Genome editing, a genetic engineering tool, has added a new dimension to diagnostics and therapeutics in healthcare. Amongst the genome editing tools, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) stands out for its efficiency, versatility, and precision. CRISPR refers to a genetic scissor that can precisely edit specific parts of DNA accurately and comprises three steps: identification, editing, and repair. CRISPR has seen various applications in medicine from treating genetic and infectious diseases to cancer therapy. In dentistry, CRISPR technology is in its initial stages and has shown potential in periodontitis, dental caries, head and neck cancer, orthodontics, craniofacial defects, and viral infections. CRISPR by host response modulation offers personalized periodontal care, inhibits biofilm formation to prevent dental caries, personalized cancer treatment by targeting responsible genes, provides genetic information on the aetiology of craniofacial malformations, and helps in understanding viral infections and targeted therapies. This customized precision approach opens new avenues to improved treatment outcomes. CRISPR technology is not devoid of challenges, it has ethical challenges, immunogenicity, and off-target effects, yet, it holds promise as a future diagnostic and therapeutic approach if implemented with care.

In It Together

Introduction Exploring the function of every gene is a challenging task. There is a paradigm shift of RNA interference with the introduction of clustered regularly interspaced short palindromic repeat (CRISPR)-based genome-wide screening. CRISPR-based screening can detect the loss-of-function and gain-of-function targets. Many DNA-binding proteins are engineered as effective tools for modulating gene expression and for investigating therapeutic targets for a spectrum of diseases. Among them, CRISPR-Cas9 has received extensive attention with its potential for screening cancer treatment targets. Areas covered This article reviews CRISPR toolkit and its applications in screening cancer therapeutic targets, especially genome-wide screens using different CRISPR-Cas9 systems. We compare and summarize the characteristics of CRISPR systems, which would be helpful for understanding and optimizing current CRISPR toolkits, as well as reflecting on the potential future development and clinical applications of CRISPR screens. Expert opinion The application of CRISPR-based therapeutic target screening is broadly used in cancer drug development. Its application in cancer immunotherapy and precision oncology is blooming. Nevertheless, more effective methods of Cas protein delivery and the development of more accurate and efficient genome-editing tools are needed.

Genome editing technology and applications with the type I CRISPR system

Chapter 19 - Patenting dynamics in CRISPR gene editing technologies

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and other gene-editing technologies have revolutionized genetic research by enabling precise, targeted modifications of DNA sequences. This paper provides a comprehensive exploration of CRISPR technology, detailing its development, mechanism of action, and versatility in diverse applications. From advancements in medicine, including therapeutic interventions for genetic disorders, to innovations in agriculture aimed at enhancing crop resilience and yield, CRISPR's transformative potential is vast. However, the rapid evolution of gene editing presents significant ethical and societal challenges, particularly concerning human germline editing, ecological impacts, and issues of accessibility and equity. This paper examines these ethical considerations, emphasizing the need for robust regulatory frameworks and responsible scientific practices. It also projects the future trajectory of gene editing technologies, speculating on emerging trends, possible breakthroughs, and the global implications of CRISPR in fields such as personalized medicine, synthetic biology, and biotechnology. By critically analyzing current applications and addressing ethical concerns, this study aims to provide a balanced perspective on CRISPR's potential to reshape genetic research while advocating for ethical governance and public engagement in its ongoing development. CRISPR’s ability to target specific genes with high accuracy has made it an invaluable tool not only in research laboratories but also in clinical settings, where it shows promise in treating previously incurable diseases. Recent advancements have extended CRISPR’s applications beyond simple gene knockout, allowing for base editing, prime editing, and epigenetic modifications that expand the possibilities for genetic correction and enhancement. As scientists explore using CRISPR in complex organisms, the precision and control required for safe and effective treatments become a key focus, particularly in addressing off-target effects that could lead to unintended genetic consequences.

Massively parallel CRISPR off-target detection enables rapid off-target prediction model building

ABSTRACTGenome editing technologies, particularly clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9, have transformed biomedical research by enabling precise genetic modifications. Due to its efficiency, cost-effectiveness and versatility, CRISPR has been widely applied across various stages of research, from fundamental biological investigations in preclinical models to potential therapeutic interventions. In nephrology, CRISPR represents a groundbreaking tool for elucidating the molecular mechanisms underlying kidney diseases and developing innovative therapeutic approaches. This review synthesizes the latest advancements in CRISPR-based gene editing within nephrology, highlighting its applications in genetic kidney disorders, polygenic nephropathies and functional genomic studies. Preclinical studies utilizing CRISPR-engineered kidney organoids and animal models have provided crucial insights into disease pathophysiology, offering platforms for drug discovery and precision medicine. Additionally, CRISPR-based functional screens have identified novel disease-associated pathways, particularly in diabetic nephropathy and glomerular disorders. Beyond experimental research, the therapeutic potential of CRISPR in nephrology is emerging, with recent advances in base editing and prime editing demonstrating the feasibility of correcting pathogenic mutations in conditions such as Alport syndrome and autosomal dominant polycystic kidney disease. Moreover, CRISPR plays a pivotal role in xenotransplantation, with gene-edited porcine kidneys addressing key immunological and virological barriers. Despite its promise, clinical translation faces challenges, including delivery efficiency, off-target effects and ethical considerations. This review provides an overview of the current state and future directions of CRISPR-based gene editing in nephrology, underscoring its transformative potential in advancing kidney disease research and therapeutics.

Monogenic diabetes represents approximately 1-5% of all diabetes cases globally, with mutations in over 40 genes causing various forms of maturity onset diabetes of the young (MODY) and neonatal diabetes mellitus. The emergence of clustered regularly interspaced short palindromic repeats (CRISPR) technology has revolutionized therapeutic approaches for genetic disorders, offering unprecedented precision in correcting disease-causing mutations. This review examined the current state of CRISPR based gene editing applications for monogenic diabetes, analyzing therapeutic strategies, molecular mechanisms, and clinical translation challenges. A comprehensive literature search was conducted using PubMed and Web of Science databases from 2012-2025, focusing on peer reviewed articles describing CRISPR applications in monogenic diabetes models and clinical studies. Recent advances demonstrated successful correction of pathogenic variants in HNF1A, HNF4A, INS, and KCNJ11 genes using base editing and prime editing technologies, with correction efficiencies ranging from 15-85% in cellular models. Clinical applications showed promise for treating MODY subtypes, with patient derived induced pluripotent stem cells (iPSCs) serving as valuable platforms for personalized therapy development. Current limitations include delivery challenges, off target effects, and regulatory considerations for germline editing. CRISPR based approaches represent a paradigm shift toward precision medicine for monogenic diabetes, with base editing and prime editing emerging as safer alternatives to traditional nuclease-based systems for therapeutic applications. Keywords: CRISPR gene editing, Monogenic diabetes, Precision medicine, Base editing, Prime editing

Systematic evaluation of genome-wide Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) off-target profiles is a fundamental step for the successful application of the CRISPR system to clinical therapies. Many experimental techniques and in silico tools have been proposed for detecting and predicting genome-wide CRISPR off-target profiles. These techniques and tools, however, have not been systematically benchmarked. A comprehensive benchmark study and an integrated strategy that takes advantage of the currently available tools to improve predictions of genome-wide CRISPR off-target profiles are needed. We focused on the specificity of the traditional CRISPR SpCas9 system for gene knockout. First, we benchmarked 10 available genome-wide off-target cleavage site (OTS) detection techniques with the published OTS detection datasets. Second, taking the datasets generated from OTS detection techniques as the benchmark datasets, we benchmarked 17 available in silico genome-wide OTS prediction tools to evaluate their genome-wide CRISPR off-target prediction performances. Finally, we present the first one-stop integrated Genome-Wide Off-target cleavage Search platform (iGWOS) that was specifically designed for the optimal genome-wide OTS prediction by integrating the available OTS prediction algorithms with an AdaBoost ensemble framework.

Patents and technology transfer in CRISPR technology.

Repairing the central nervous system (CNS) remains one of the most difficult obstacles to overcome in translational neurosciences. This is due to intrinsic growth inhibitors, extracellular matrix issues, the glial scar–form barrier, chronic neuroinflammation, and epigenetic silencing. The purpose of this review is to bring together findings from recent developments in genome editing and computational approaches, which center around the possible convergence of clustered regularly interspaced short palindromic repeats (CRISPR) platforms and artificial intelligence (AI), towards precision neuroregeneration. We wished to outline possible ways in which CRISPR-based systems, including but not limited to Cas9 and Cas12 nucleases, RNA-targeting Cas13, base and prime editors, and transcriptional regulators such as CRISPRa/i, can be applied to potentially reactivate axon-growth programs, alter inhibitory extracellular signaling, reprogram or lineage transform glia to functional neurons, and block oncogenic pathways in glioblastoma. In addition, we wanted to highlight how AI approaches, such as single-cell multi-omics, radiogenomic prediction, development of digital twins, and design of adaptive clinical trials, will increasingly be positioned to act as system-level architects that allow translation of complex datasets into predictive and actionable therapeutic approaches. We examine convergence consumers in spinal cord injury and adaptive neuro-oncology and discuss expanse consumers in ischemic stroke, Alzheimer’s disease, Parkinson’s disease, and rare neurogenetic syndromes. Finally, we discuss the ethical and regulatory landscape around beyond off-target editing and genomic stability of CRISPR, algorithmic bias, explainability, and equitable access to advanced neurotherapies. Our intent was not to provide a comprehensive inventory of possibilities but rather to provide a conceptual tool where CRISPR acts as a molecular manipulator and AI as a computational integrator, converging to create pathways towards precision neuroregeneration, personalized medicine, and adaptive neurotherapeutics that are ethically sound.

CRISPR: The frontier technology of next-generation RNA detection

The clustered regularly interspaced short palindromic repeats (CRISPR) system offers cost-effectiveness, high efficiency, precision, and ease of use compared to traditional gene editing techniques. In this study, we employed findings from prestigious investigations to develop an optimized approach for generating knockout cancer cell lines using a transient transfection method. This protocol introduces a distinctive approach that follows rigorous guidelines for designing gRNA to reduce off-target effects, a major challenge in CRISPR applications. Our step-by-step instructions allow researchers, particularly those with limited laboratory equipment and funding, as well as those undertaking CRISPR projects for the first time, to generate knockout cell lines using CRISPR technology in just ten weeks. This protocol covers all needs for enhancing various yields, such as transfection efficiency, and includes leveraging robust bioinformatics tools, conducting essential assays, isolating monoclonal cells via limiting dilution, validating knockout cells, and providing comprehensive troubleshooting recommendations. Using this method, we successfully created several new generations of colorectal cancer cell lines with monoallelic and biallelic knockouts of the epithelial cell adhesion molecule (EpCAM) gene. Our method, optimized for a wide spectrum of cancer cell lines, makes CRISPR more accessible for applications in personalized and precision medicine. It expands opportunities for novel investigations into cancer mechanisms and paves the way for potential therapeutic interventions.