Source 1review2023Research
Toolkit/base editing
base editing
Also known as: BE
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Here, the latest research progresses in AAV-mediated gene editing and silencing strategies to modify that the genetic ocular diseases are systematically outlined, especially by base editing and prime editing.
Usefulness & Problems
Why this is useful
Base editing is named as one of the gene-editing strategies compared in the review for HbF modulation.; gene-editing strategies for HbF modulation; Base editing is described as a next-generation DSB-free editing approach for precision engineering beyond conventional CRISPR nuclease cutting.; DSB-free genome editing in CAR-NK engineering; Base editing is named as an advance that can be integrated into the translational roadmap for neurological nonsense mutation disorders.; precision-based correction strategies for nonsense mutation disorders; Base editing is named as an emerging innovation that expands the functional genome-editing landscape. The abstract does not provide additional mechanistic detail in Capsicum.; expanding the functional genome-editing landscape; Base editing is described as a gene editing approach for optimizing CAR-T cells.; optimizing CAR-T cells; enhancing efficacy; managing toxicity; improving accessibility; Base editing is described as an emerging genetic engineering technology explored in the review. It is linked in the abstract to the creation of smart tissues with dynamic environmental responses.; emerging genetic engineering in tissue engineering; creating smart tissues; Base editing is presented as a gene-editing modality for HSC engineering that can make edits without relying on HDR.; HDR-independent editing in HSC engineering; Base editing is presented as a next-generation genome-editing innovation for precise and reversible modulation of psychiatric risk genes.; precise modulation of psychiatric risk genes; reversible modulation of psychiatric risk genes; Base editing is presented as an advanced CRISPR modality that improves precision and reduces genomic damage. The abstract highlights this as especially advantageous in post-mitotic neurons.; improving editing precision; reducing genomic damage; Base editing is presented as a precision genome editing approach that directly corrects pathogenic variants by enabling targeted single-nucleotide conversions. The abstract frames it as an alternative to conventional CRISPR-Cas editing for IRDs.; direct correction of pathogenic variants in inherited retinal diseases; targeted single-nucleotide conversion in post-mitotic retinal cells; Base editing is presented as a gene-editing strategy being applied through AAV-mediated ocular gene therapy. The review highlights it as part of recent progress for modifying genetic ocular diseases.; AAV-mediated gene editing for genetic ocular diseases
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Base editing is named as one of the gene-editing strategies compared in the review for HbF modulation.
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gene-editing strategies for HbF modulation
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Base editing is described as a next-generation DSB-free editing approach for precision engineering beyond conventional CRISPR nuclease cutting.
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DSB-free genome editing in CAR-NK engineering
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Base editing is named as an advance that can be integrated into the translational roadmap for neurological nonsense mutation disorders.
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precision-based correction strategies for nonsense mutation disorders
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Base editing is named as an emerging innovation that expands the functional genome-editing landscape. The abstract does not provide additional mechanistic detail in Capsicum.
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expanding the functional genome-editing landscape
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Base editing is described as a gene editing approach for optimizing CAR-T cells.
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optimizing CAR-T cells
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enhancing efficacy
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managing toxicity
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improving accessibility
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Base editing is described as an emerging genetic engineering technology explored in the review. It is linked in the abstract to the creation of smart tissues with dynamic environmental responses.
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emerging genetic engineering in tissue engineering
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creating smart tissues
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Base editing is presented as a gene-editing modality for HSC engineering that can make edits without relying on HDR.
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HDR-independent editing in HSC engineering
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Base editing is presented as a next-generation genome-editing innovation for precise and reversible modulation of psychiatric risk genes.
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precise modulation of psychiatric risk genes
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reversible modulation of psychiatric risk genes
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Base editing is presented as an advanced CRISPR modality that improves precision and reduces genomic damage. The abstract highlights this as especially advantageous in post-mitotic neurons.
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improving editing precision
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reducing genomic damage
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Base editing is presented as a precision genome editing approach that directly corrects pathogenic variants by enabling targeted single-nucleotide conversions. The abstract frames it as an alternative to conventional CRISPR-Cas editing for IRDs.
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direct correction of pathogenic variants in inherited retinal diseases
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targeted single-nucleotide conversion in post-mitotic retinal cells
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Base editing is presented as a gene-editing strategy being applied through AAV-mediated ocular gene therapy. The review highlights it as part of recent progress for modifying genetic ocular diseases.
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AAV-mediated gene editing for genetic ocular diseases
Problem solved
It is presented as an approach used to modulate HbF expression in the context of sickle cell disease.; provides an alternative gene-editing strategy for HbF modulation; It addresses DSB-associated genotoxic stress that accompanies nuclease-based CRISPR-Cas9 editing.; reducing or eliminating DSB-associated genotoxic stress from nuclease cutting; It contributes to precision-based molecular correction strategies.; molecular correction of nonsense mutation disorders; The abstract associates base editing with improving CAR-T efficacy, toxicity management, and accessibility.; addresses limitations in CAR-T optimization; The review frames it as part of the toolkit for making tissue constructs more responsive and functionally tailored.; supports development of genetically engineered tissues with dynamic environmental responsiveness; It helps address the limitation of HDR dependence in HSC editing workflows.; avoids the need for HDR during editing; It addresses the need for precise and reversible modulation of psychiatric risk genes in design-biology workflows.; enabling precise and reversible genome-level modulation in psychiatric risk gene contexts; It is positioned as helping make CRISPR therapeutics safer and more precise in neurodegenerative disease settings.; addresses precision limitations of CRISPR therapeutics; reduces genomic damage in post-mitotic neurons; It addresses limitations of gene augmentation and conventional CRISPR approaches by enabling direct variant correction without relying on double-strand DNA cleavage or repair. This is highlighted as especially relevant for post-mitotic retinal cells.; offers an alternative to gene augmentation when AAV packaging capacity is restrictive; avoids double-strand DNA cleavage or repair processes associated with conventional CRISPR-Cas editing; It is framed as a way to modify genetic causes of ocular disease. The review positions it within therapeutic gene-editing strategies rather than simple gene addition.; modifying disease-causing genetic lesions in ocular disease contexts
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It is presented as an approach used to modulate HbF expression in the context of sickle cell disease.
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provides an alternative gene-editing strategy for HbF modulation
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It addresses DSB-associated genotoxic stress that accompanies nuclease-based CRISPR-Cas9 editing.
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reducing or eliminating DSB-associated genotoxic stress from nuclease cutting
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It contributes to precision-based molecular correction strategies.
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molecular correction of nonsense mutation disorders
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The abstract associates base editing with improving CAR-T efficacy, toxicity management, and accessibility.
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addresses limitations in CAR-T optimization
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The review frames it as part of the toolkit for making tissue constructs more responsive and functionally tailored.
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supports development of genetically engineered tissues with dynamic environmental responsiveness
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It helps address the limitation of HDR dependence in HSC editing workflows.
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avoids the need for HDR during editing
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It addresses the need for precise and reversible modulation of psychiatric risk genes in design-biology workflows.
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enabling precise and reversible genome-level modulation in psychiatric risk gene contexts
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It is positioned as helping make CRISPR therapeutics safer and more precise in neurodegenerative disease settings.
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addresses precision limitations of CRISPR therapeutics
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reduces genomic damage in post-mitotic neurons
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It addresses limitations of gene augmentation and conventional CRISPR approaches by enabling direct variant correction without relying on double-strand DNA cleavage or repair. This is highlighted as especially relevant for post-mitotic retinal cells.
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offers an alternative to gene augmentation when AAV packaging capacity is restrictive
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avoids double-strand DNA cleavage or repair processes associated with conventional CRISPR-Cas editing
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It is framed as a way to modify genetic causes of ocular disease. The review positions it within therapeutic gene-editing strategies rather than simple gene addition.
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modifying disease-causing genetic lesions in ocular disease contexts
Problem links
addresses limitations in CAR-T optimization
LiteratureThe abstract associates base editing with improving CAR-T efficacy, toxicity management, and accessibility.
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The abstract associates base editing with improving CAR-T efficacy, toxicity management, and accessibility.
addresses precision limitations of CRISPR therapeutics
LiteratureIt is positioned as helping make CRISPR therapeutics safer and more precise in neurodegenerative disease settings.
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It is positioned as helping make CRISPR therapeutics safer and more precise in neurodegenerative disease settings.
avoids double-strand DNA cleavage or repair processes associated with conventional CRISPR-Cas editing
LiteratureIt addresses limitations of gene augmentation and conventional CRISPR approaches by enabling direct variant correction without relying on double-strand DNA cleavage or repair. This is highlighted as especially relevant for post-mitotic retinal cells.
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It addresses limitations of gene augmentation and conventional CRISPR approaches by enabling direct variant correction without relying on double-strand DNA cleavage or repair. This is highlighted as especially relevant for post-mitotic retinal cells.
avoids the need for HDR during editing
LiteratureIt helps address the limitation of HDR dependence in HSC editing workflows.
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It helps address the limitation of HDR dependence in HSC editing workflows.
enabling precise and reversible genome-level modulation in psychiatric risk gene contexts
LiteratureIt addresses the need for precise and reversible modulation of psychiatric risk genes in design-biology workflows.
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It addresses the need for precise and reversible modulation of psychiatric risk genes in design-biology workflows.
modifying disease-causing genetic lesions in ocular disease contexts
LiteratureIt is framed as a way to modify genetic causes of ocular disease. The review positions it within therapeutic gene-editing strategies rather than simple gene addition.
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It is framed as a way to modify genetic causes of ocular disease. The review positions it within therapeutic gene-editing strategies rather than simple gene addition.
molecular correction of nonsense mutation disorders
LiteratureIt contributes to precision-based molecular correction strategies.
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It contributes to precision-based molecular correction strategies.
offers an alternative to gene augmentation when AAV packaging capacity is restrictive
LiteratureIt addresses limitations of gene augmentation and conventional CRISPR approaches by enabling direct variant correction without relying on double-strand DNA cleavage or repair. This is highlighted as especially relevant for post-mitotic retinal cells.
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It addresses limitations of gene augmentation and conventional CRISPR approaches by enabling direct variant correction without relying on double-strand DNA cleavage or repair. This is highlighted as especially relevant for post-mitotic retinal cells.
provides an alternative gene-editing strategy for HbF modulation
LiteratureIt is presented as an approach used to modulate HbF expression in the context of sickle cell disease.
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It is presented as an approach used to modulate HbF expression in the context of sickle cell disease.
reduces genomic damage in post-mitotic neurons
LiteratureIt is positioned as helping make CRISPR therapeutics safer and more precise in neurodegenerative disease settings.
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It is positioned as helping make CRISPR therapeutics safer and more precise in neurodegenerative disease settings.
reducing or eliminating DSB-associated genotoxic stress from nuclease cutting
LiteratureIt addresses DSB-associated genotoxic stress that accompanies nuclease-based CRISPR-Cas9 editing.
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It addresses DSB-associated genotoxic stress that accompanies nuclease-based CRISPR-Cas9 editing.
supports development of genetically engineered tissues with dynamic environmental responsiveness
LiteratureThe review frames it as part of the toolkit for making tissue constructs more responsive and functionally tailored.
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The review frames it as part of the toolkit for making tissue constructs more responsive and functionally tailored.
Published Workflows
Objective: Systematically address translational barriers for readthrough therapy in neurological nonsense mutation disorders.
Why it works: The roadmap is proposed to bridge the translational gap by decomposing the problem into detection, delivery, decoding, and durability, then integrating advances across these areas.
override premature termination codonsrestore full-length protein expressioncontext-aware molecular correctionpatient identification and biomarker profilingengineered vectors for CNS targetingmachine learningnanocarriersbase editingadaptive trial designs
Stages
- 1.Detection(decision_gate)
This stage exists to identify appropriate patients and profile biomarkers before downstream therapeutic decisions.
Selection: precision patient identification and biomarker profiling
- 2.Delivery(decision_gate)
This stage exists to address the delivery barrier by using engineered vectors for CNS targeting.
Selection: engineered vectors for CNS targeting
- 3.Decoding(functional_characterization)
This stage exists to perform the molecular correction step in a context-aware manner.
Selection: context-aware molecular correction
- 4.Durability(confirmatory_validation)
This stage exists to evaluate whether therapeutic benefit is safe and effective over the long term.
Selection: long-term safety and efficacy
Objective: Accelerate the development of climate-resilient Capsicum cultivars with optimized metabolic traits.
Why it works: The abstract argues that combining molecular insight from transcriptional, metabolic, and epigenetic analysis with precision phenotyping and genome editing should enable targeted reprogramming of regulatory loci that control adaptive responses and metabolic outputs.
transcription factor modulationosmotic adjustmentreactive oxygen species detoxificationhormonal crosstalksecondary metabolite biosynthesismulti-omics-guided gene discoveryprecision phenotypingCRISPR/Cas-mediated genome editingnext-generation genome editing
Stages
- 1.multi-omics-guided gene discovery(in_silico_filter)
The abstract positions multi-omics-guided gene discovery as the upstream step that identifies targets for subsequent genome editing.
Selection: Identification of key regulatory loci and stress-resilience frameworks from integrated transcriptional, metabolic, and epigenetic information.
- 2.precision phenotyping(functional_characterization)
The abstract includes precision phenotyping as a core component of the proposed framework linking molecular targets to cultivar-level performance.
Selection: Phenotypic assessment within the proposed framework for climate resilience and optimized metabolic traits.
- 3.next-generation genome editing(confirmatory_validation)
The abstract presents genome editing as the intervention step that operationalizes targets identified through transcription factor analysis and multi-omics-guided discovery.
Selection: Precise reprogramming of key regulatory loci to enhance adaptive responses.
Objective: Automate molecular discovery and optimization in biofoundries by integrating AI into Design-Build-Test-Learn cycles.
Why it works: The abstract states that biofoundries integrate AI into DBTL cycles, automating molecular discovery and optimization.
AI integrationbiofoundry automationDesign-Build-Test-Learn workflow
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete method used to build, optimize, or evolve an engineered system.
Mechanisms
direct pathogenic variant correctiongenome editing without double-strand dna cleavagehdr-independent editingPhotocleavagetargeted single-nucleotide conversionTranslation ControlTechniques
No technique tags yet.
Target processes
editingmanufacturingrecombinationtranslationInput: Light
Implementation Constraints
cofactor dependency: requires exogenous cofactorencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: payload burdenimplementation constraint: spectral hardware requirementoperating role: builderswitch architecture: cleavage
The abstract supports that its use must be paired with delivery and long-term safety and efficacy planning.; must be integrated with delivery and durability considerations; requires integration into tissue engineering and cell engineering workflows; The abstract supports that delivery is a major requirement and challenge, but does not specify editor class, guide format, or delivery vehicle.; delivery remains a key optimization problem; The abstract specifically situates these genome-editing approaches alongside iPSC and brain-organoid models.; particularly discussed in combination with iPSC and brain-organoid models; The abstract indicates that successful use depends on delivery platforms for genome editors, including viral and emerging non-viral systems, and on optimization for outer-retina delivery. Manufacturing capacity and delivery engineering are described as practical prerequisites.; requires effective delivery of genome editors to the outer retina; translation depends on managing off-target risk and manufacturing barriers; The abstract supports that this approach is discussed in conjunction with AAV delivery. It does not specify editor architecture, guide design, or packaging details.; discussed specifically in an AAV-mediated context
The abstract does not provide evidence that base editing alone resolves CNS delivery or patient-stratification challenges.; the abstract still identifies inefficient CNS delivery, variable efficacy, and durability concerns as translational barriers; The abstract does not provide direct evidence for specific implementation outcomes or comparative advantages. Broader challenges such as stability and scalability still apply.; the abstract does not specify base-editing-specific limitations; field-wide challenges include long-term genetic stability and scalability; It does not remove delivery-related barriers, which the review states still need to be addressed.; delivery challenges need to be addressed; The abstract states that base editing still faces limited photoreceptor editing efficiency, off-target risk, interspecies variability, and manufacturing barriers. Delivery to the outer retina also remains suboptimal.; limited editing efficiency in photoreceptors; potential risks of off-target effects; delivery to the outer retina remains suboptimal; barriers in large-scale vector manufacturing; interspecies variability in therapeutic response; The abstract does not establish which ocular indications, mutation classes, or delivery constraints base editing cannot address. It also does not provide comparative efficacy or safety limits.; specific performance, scope, and constraints are not detailed in the abstract
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Source 2primary paper2025MED
Source 3primary paper2025MED
Source 4primary paper2026MED
Source 5review2025MED
Source 6review2025MED
Source 7primary paper2025MED
Ranked Claims
The review compares prime editing with CRISPR-Cas9 and Base editing as gene-editing strategies for HbF modulation.
This review also provides a comparative overview of prime editing and other gene-editing strategies for HbF modulation, such as CRISPR-Cas9 and Base editing.
Prime editing has emerged as an experimental approach capable of introducing multiple HPFH-like mutations within b3-globin promoters.
Regarding advances in b3-globin editing, "prime editing", although still in the experimental phase, has recently emerged as an innovative approach capable of introducing multiple HPFH-like mutations within b3-globin promoters...
CRISPR/Cas systems, base editing, and prime editing offer novel approaches to optimize CAR-T cells.
Base editing and prime editing provide alternatives for directly correcting pathogenic variants in inherited retinal diseases.
Recent breakthroughs in precision genome editing, particularly base editing (BE) and prime editing (PE), have provided alternatives capable of directly correcting pathogenic variants.
The review identifies long-term genetic stability, scalability, and off-target effects as challenges for genetically engineered tissues.
We address the field's challenges, including long-term genetic stability, scalability, and off-target effects, while also considering the ethical implications and evolving regulatory landscape of genetically engineered tissues.
Base editing and prime editing circumvent double-strand DNA cleavage or repair processes typically induced by conventional CRISPR-Cas editing systems, offering advantages in post-mitotic retinal cells.
both circumventing the double-strand DNA cleavage or repair processes typically induced by conventional CRISPR-Cas editing systems, thereby offering advantages in post-mitotic retinal cells
Electroporation and other non-viral delivery methods may offer safer gene editing for HSCs but require further optimization.
Lentiviral vectors were the most common delivery method in the reviewed studies, but insertional mutagenesis remains a concern.
CRISPR-based diagnostics such as SHERLOCK and DETECTR, together with AI-assisted sgRNA design and machine-learning off-target prediction, enhance the safety, stratification, and monitoring of CRISPR therapeutics.
Base editing avoids the need for HDR but still faces delivery challenges in HSC applications.
CRISPR/Cas9 provides precise editing in HSCs but is limited by low HDR efficiency in quiescent HSCs.
The review describes base editing and synthetic genetic circuits as emerging technologies explored for creating smart tissues capable of dynamic environmental responses.
Emerging technologies in genetic engineering, including base editing and synthetic genetic circuits, have been explored for their potential to create "smart" tissues capable of dynamic environmental responses.
CAR-engineered HSCs showed durable tumor clearance and multilineage immune reconstitution in the reviewed preclinical evidence.
Leveraging gene editing has the potential to transform CAR-T therapy into a more potent, safer, and broadly applicable modality for cancer and beyond.
The review states that integrating genetic engineering with 3D-bioprinting, microfluidics, and smart biomaterials expands the horizons of complex tissue fabrication.
We further investigate the integration of these genetic approaches with emerging technologies such as 3D-bioprinting, microfluidics, and smart biomaterials, which collectively expand the horizons of complex tissue fabrication.
Clinical translation of base editing and prime editing for inherited retinal diseases is limited by low photoreceptor editing efficiency, interspecies variability, off-target risk, and large-scale vector manufacturing barriers.
critical challenges remain before clinical application can be realized, including limited editing efficiency in photoreceptors, interspecies variability in therapeutic response, potential risks of off-target effects, and barriers in large-scale vector manufacturing
Base editing enables targeted single-nucleotide conversions.
BE enables targeted single-nucleotide conversions
Prime editing allows precise insertions and deletions.
PE further allows for precise insertions and deletions
Base editing, prime editing, CRISPRi/a, and RNA-targeting Cas systems improve precision and reduce genomic damage, which is particularly advantageous in post-mitotic neurons.
Preclinical investigations in murine and non-human primate models have demonstrated feasibility, molecular accuracy, and preliminary safety profiles of base editing and prime editing platforms for targeting IRD-associated mutations.
Preclinical investigations across murine and non-human primate models have demonstrated the feasibility, molecular accuracy, and preliminary safety profiles of these platforms in targeting IRD-associated mutations.
The review examines CRISPR-Cas9, TALENs, and synthetic biology as genetic engineering approaches for modifying cellular behaviors and functions in tissue engineering.
We critically examine the application of advanced genetic engineering techniques, including CRISPR-Cas9, TALENs, and synthetic biology, in modifying cellular behaviors and functions for tissue engineering.
Suicide gene strategies were effective in mitigating safety risks in the reviewed HSC engineering context.
The review covers characteristics of different AAV delivery routes in ocular clinical applications.
The review discusses progress of AAV in ocular optogenetic therapy.
The review outlines recent progress in AAV-mediated gene editing and silencing strategies for genetic ocular diseases, especially base editing and prime editing.
AAV is presented as one of the most promising viral gene delivery tools for ocular gene therapy because it can infect various tissue types and is considered relatively safe.
An increasing number of clinical trials of AAV-mediated gene therapy are underway for ocular diseases.
The eye is described as a favorable organ for AAV gene therapy because its limited volume is suitable for small doses that can achieve stable transduction.
The review identifies difficulties in the clinical transformation of AAV-mediated ocular gene therapy.
Approval Evidence
11 sources22 linked approval claimsfirst-pass slug base-editing
By integrating advances in machine learning, nanocarriers, base editing, and adaptive trial designs
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next-generation, DSB-free base and prime editors reduce or eliminate the DSB-associated genotoxic stress observed with nuclease cutting
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This review also provides a comparative overview of prime editing and other gene-editing strategies for HbF modulation, such as CRISPR-Cas9 and Base editing.
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Recent breakthroughs in precision genome editing, particularly base editing (BE) and prime editing (PE), have provided alternatives capable of directly correcting pathogenic variants. BE enables targeted single-nucleotide conversions.
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Advanced modalities, including base and prime editing, CRISPRi/a, and RNA-targeting Cas systems, improve precision and reduce genomic damage
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Genome-editing innovations-such as prime, base, and epigenome editing-facilitate precise and reversible modulation of psychiatric risk genes.
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Base editing technologies, while not requiring HDR, present their own delivery challenges that need to be addressed.
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Emerging technologies in genetic engineering, including base editing and synthetic genetic circuits, have been explored for their potential to create "smart" tissues capable of dynamic environmental responses.
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Emerging gene editing technologies, such as CRISPR/Cas systems, base editing, and prime editing, offer novel approaches to optimize CAR-T cells
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Emerging innovations, including base editing, prime editing, and novel nucleases like Cas12a and Cas13d, are expanding the functional genome-editing landscape.
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Here, the latest research progresses in AAV-mediated gene editing and silencing strategies to modify that the genetic ocular diseases are systematically outlined, especially by base editing and prime editing.
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comparison scopesupports
The review compares prime editing with CRISPR-Cas9 and Base editing as gene-editing strategies for HbF modulation.
This review also provides a comparative overview of prime editing and other gene-editing strategies for HbF modulation, such as CRISPR-Cas9 and Base editing.
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design objectivesupports
Next-generation precision engineering tools are proposed to enhance three efficacy pillars in CAR-NK cells: persistence, trafficking, and tumor eradication.
These advanced technologies enable the precise enhancement of three fundamental pillars of efficacy: Persistence through endogenous cytokine armoring and metabolic engineering; Trafficking via chemokine receptor matching and stromal barrier degradation; and Tumor Eradication using logic-gated targeting, immunomodulatory payloads, and bispecific engagers.
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mechanistic advantagesupports
DSB-free base and prime editors reduce or eliminate DSB-associated genotoxic stress compared with nuclease cutting.
next-generation, DSB-free base and prime editors reduce or eliminate the DSB-associated genotoxic stress observed with nuclease cutting
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strategysupports
Integrating machine learning, nanocarriers, base editing, and adaptive trial designs provides a structured strategy to bridge the translational gap.
By integrating advances in machine learning, nanocarriers, base editing, and adaptive trial designs, this roadmap provides a structured strategy to bridge the translational gap.
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translation barriersupports
Clinical translation of readthrough therapies remains hampered by inefficient CNS delivery, variable efficacy, and the absence of personalized stratification.
Yet clinical translation remains hampered by inefficient CNS delivery, variable efficacy, and the absence of personalized stratification.
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workflow strategysupports
Base editing, epigenetic reprogramming, targeted transposon systems, and synthetic biology circuits can be synergistically integrated to overcome critical clinical challenges in CAR-NK engineering.
We detail how base editing, epigenetic reprogramming, targeted transposon systems, and synthetic biology circuits can be synergistically integrated to overcome critical clinical challenges.
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application claimsupports
CRISPR/Cas systems, base editing, and prime editing offer novel approaches to optimize CAR-T cells.
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application scopesupports
Design biology advances including artificial cells, DNA nanostructures, AI-driven molecular design, biofoundries, and next-generation genome editing are transforming mind-body health sciences.
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capabilitysupports
Base editing and prime editing provide alternatives for directly correcting pathogenic variants in inherited retinal diseases.
Recent breakthroughs in precision genome editing, particularly base editing (BE) and prime editing (PE), have provided alternatives capable of directly correcting pathogenic variants.
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capabilitysupports
Prime editing, base editing, and epigenome editing facilitate precise and reversible modulation of psychiatric risk genes.
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challenge summarysupports
The review identifies long-term genetic stability, scalability, and off-target effects as challenges for genetically engineered tissues.
We address the field's challenges, including long-term genetic stability, scalability, and off-target effects, while also considering the ethical implications and evolving regulatory landscape of genetically engineered tissues.
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comparative advantagesupports
Base editing and prime editing circumvent double-strand DNA cleavage or repair processes typically induced by conventional CRISPR-Cas editing systems, offering advantages in post-mitotic retinal cells.
both circumventing the double-strand DNA cleavage or repair processes typically induced by conventional CRISPR-Cas editing systems, thereby offering advantages in post-mitotic retinal cells
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contextual combinationsupports
The utility of next-generation genome editing for psychiatric risk gene modulation is particularly highlighted when combined with iPSC and brain-organoid models.
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editing tradeoffmixed
Base editing avoids the need for HDR but still faces delivery challenges in HSC applications.
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emerging capabilitysupports
The review describes base editing and synthetic genetic circuits as emerging technologies explored for creating smart tissues capable of dynamic environmental responses.
Emerging technologies in genetic engineering, including base editing and synthetic genetic circuits, have been explored for their potential to create "smart" tissues capable of dynamic environmental responses.
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future potentialsupports
Leveraging gene editing has the potential to transform CAR-T therapy into a more potent, safer, and broadly applicable modality for cancer and beyond.
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limitationsupports
Clinical translation of base editing and prime editing for inherited retinal diseases is limited by low photoreceptor editing efficiency, interspecies variability, off-target risk, and large-scale vector manufacturing barriers.
critical challenges remain before clinical application can be realized, including limited editing efficiency in photoreceptors, interspecies variability in therapeutic response, potential risks of off-target effects, and barriers in large-scale vector manufacturing
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mechanismsupports
Base editing enables targeted single-nucleotide conversions.
BE enables targeted single-nucleotide conversions
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performance advantagesupports
Base editing, prime editing, CRISPRi/a, and RNA-targeting Cas systems improve precision and reduce genomic damage, which is particularly advantageous in post-mitotic neurons.
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preclinical evidencesupports
Preclinical investigations in murine and non-human primate models have demonstrated feasibility, molecular accuracy, and preliminary safety profiles of base editing and prime editing platforms for targeting IRD-associated mutations.
Preclinical investigations across murine and non-human primate models have demonstrated the feasibility, molecular accuracy, and preliminary safety profiles of these platforms in targeting IRD-associated mutations.
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Comparisons
Source-stated alternatives
The abstract explicitly mentions prime editing and CRISPR-Cas9 as alternative gene-editing strategies in the same comparison.; The abstract contrasts base editing with DSB-based CRISPR-Cas9 and also mentions prime editing, targeted transposon systems, and synthetic or epigenetic circuits as other next-generation approaches.; The source also mentions suppressor tRNAs, RNA editing, and CRISPR-based platforms.; The abstract groups base editing with prime editing and novel nucleases such as Cas12a and Cas13d.; The abstract contrasts base editing with CRISPR/Cas systems and prime editing as related gene editing modalities.; The abstract places base editing alongside synthetic genetic circuits and within a broader landscape that includes CRISPR-Cas9 and TALENs.; The review contrasts base editing with CRISPR/Cas9 approaches that rely on HDR for some edits.; The abstract contrasts base editing with gene augmentation strategies and with conventional CRISPR-Cas editing systems that induce double-strand DNA cleavage or repair. It also discusses prime editing as a related precision editing alternative.; Prime editing and gene silencing are named as adjacent AAV-mediated strategies in the same review.
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The abstract explicitly mentions prime editing and CRISPR-Cas9 as alternative gene-editing strategies in the same comparison.
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The abstract contrasts base editing with DSB-based CRISPR-Cas9 and also mentions prime editing, targeted transposon systems, and synthetic or epigenetic circuits as other next-generation approaches.
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The source also mentions suppressor tRNAs, RNA editing, and CRISPR-based platforms.
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The abstract groups base editing with prime editing and novel nucleases such as Cas12a and Cas13d.
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The abstract contrasts base editing with CRISPR/Cas systems and prime editing as related gene editing modalities.
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The abstract places base editing alongside synthetic genetic circuits and within a broader landscape that includes CRISPR-Cas9 and TALENs.
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The review contrasts base editing with CRISPR/Cas9 approaches that rely on HDR for some edits.
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The abstract contrasts base editing with gene augmentation strategies and with conventional CRISPR-Cas editing systems that induce double-strand DNA cleavage or repair. It also discusses prime editing as a related precision editing alternative.
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Prime editing and gene silencing are named as adjacent AAV-mediated strategies in the same review.
Source-backed strengths
DSB-free; reduces or eliminates DSB-associated genotoxic stress; highlighted as an advance integrated into the roadmap; presented as an emerging innovation in genome editing; Presented as an emerging gene editing technology for CAR-T optimization; presented as an emerging technology with potential for smart tissue design; does not require HDR; precise; reversible; improves precision; reduces genomic damage; particularly advantageous in post-mitotic neurons; enables targeted single-nucleotide conversions; may be advantageous in post-mitotic retinal cells because it circumvents double-strand DNA cleavage or repair; highlighted as a notable recent research direction in the review
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DSB-free
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reduces or eliminates DSB-associated genotoxic stress
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highlighted as an advance integrated into the roadmap
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presented as an emerging innovation in genome editing
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Presented as an emerging gene editing technology for CAR-T optimization
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presented as an emerging technology with potential for smart tissue design
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does not require HDR
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precise
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reversible
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improves precision
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reduces genomic damage
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particularly advantageous in post-mitotic neurons
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enables targeted single-nucleotide conversions
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may be advantageous in post-mitotic retinal cells because it circumvents double-strand DNA cleavage or repair
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highlighted as a notable recent research direction in the review
Compared with CRISPR/Cas9
The abstract explicitly mentions prime editing and CRISPR-Cas9 as alternative gene-editing strategies in the same comparison.; The abstract contrasts base editing with DSB-based CRISPR-Cas9 and also mentions prime editing, targeted transposon systems, and synthetic or epigenetic circuits as other next-generation approaches.; The source also mentions suppressor tRNAs, RNA editing, and CRISPR-based platforms.; The abstract contrasts base editing with CRISPR/Cas systems and prime editing as related gene editing modalities.; The abstract places base editing alongside synthetic genetic circuits and within a broader landscape that includes CRISPR-Cas9 and TALENs.; The review contrasts base editing with CRISPR/Cas9 approaches that rely on HDR for some edits.; The abstract contrasts base editing with gene augmentation strategies and with conventional CRISPR-Cas editing systems that induce double-strand DNA cleavage or repair. It also discusses prime editing as a related precision editing alternative.
Shared frame: source-stated alternative in extracted literature
Strengths here: DSB-free; reduces or eliminates DSB-associated genotoxic stress; highlighted as an advance integrated into the roadmap.
Relative tradeoffs: the abstract still identifies inefficient CNS delivery, variable efficacy, and durability concerns as translational barriers; the abstract does not specify base-editing-specific limitations; field-wide challenges include long-term genetic stability and scalability.
Source:
The abstract explicitly mentions prime editing and CRISPR-Cas9 as alternative gene-editing strategies in the same comparison.
Source:
The abstract contrasts base editing with DSB-based CRISPR-Cas9 and also mentions prime editing, targeted transposon systems, and synthetic or epigenetic circuits as other next-generation approaches.
Source:
The source also mentions suppressor tRNAs, RNA editing, and CRISPR-based platforms.
Source:
The abstract contrasts base editing with CRISPR/Cas systems and prime editing as related gene editing modalities.
Source:
The abstract places base editing alongside synthetic genetic circuits and within a broader landscape that includes CRISPR-Cas9 and TALENs.
Source:
The review contrasts base editing with CRISPR/Cas9 approaches that rely on HDR for some edits.
Source:
The abstract contrasts base editing with gene augmentation strategies and with conventional CRISPR-Cas editing systems that induce double-strand DNA cleavage or repair. It also discusses prime editing as a related precision editing alternative.
Compared with CRISPR/Cas9 system
The abstract explicitly mentions prime editing and CRISPR-Cas9 as alternative gene-editing strategies in the same comparison.; The abstract contrasts base editing with DSB-based CRISPR-Cas9 and also mentions prime editing, targeted transposon systems, and synthetic or epigenetic circuits as other next-generation approaches.; The source also mentions suppressor tRNAs, RNA editing, and CRISPR-based platforms.; The abstract contrasts base editing with CRISPR/Cas systems and prime editing as related gene editing modalities.; The abstract places base editing alongside synthetic genetic circuits and within a broader landscape that includes CRISPR-Cas9 and TALENs.; The review contrasts base editing with CRISPR/Cas9 approaches that rely on HDR for some edits.; The abstract contrasts base editing with gene augmentation strategies and with conventional CRISPR-Cas editing systems that induce double-strand DNA cleavage or repair. It also discusses prime editing as a related precision editing alternative.
Shared frame: source-stated alternative in extracted literature
Strengths here: DSB-free; reduces or eliminates DSB-associated genotoxic stress; highlighted as an advance integrated into the roadmap.
Relative tradeoffs: the abstract still identifies inefficient CNS delivery, variable efficacy, and durability concerns as translational barriers; the abstract does not specify base-editing-specific limitations; field-wide challenges include long-term genetic stability and scalability.
Source:
The abstract explicitly mentions prime editing and CRISPR-Cas9 as alternative gene-editing strategies in the same comparison.
Source:
The abstract contrasts base editing with DSB-based CRISPR-Cas9 and also mentions prime editing, targeted transposon systems, and synthetic or epigenetic circuits as other next-generation approaches.
Source:
The source also mentions suppressor tRNAs, RNA editing, and CRISPR-based platforms.
Source:
The abstract contrasts base editing with CRISPR/Cas systems and prime editing as related gene editing modalities.
Source:
The abstract places base editing alongside synthetic genetic circuits and within a broader landscape that includes CRISPR-Cas9 and TALENs.
Source:
The review contrasts base editing with CRISPR/Cas9 approaches that rely on HDR for some edits.
Source:
The abstract contrasts base editing with gene augmentation strategies and with conventional CRISPR-Cas editing systems that induce double-strand DNA cleavage or repair. It also discusses prime editing as a related precision editing alternative.
Compared with genetic circuits
The abstract places base editing alongside synthetic genetic circuits and within a broader landscape that includes CRISPR-Cas9 and TALENs.
Shared frame: source-stated alternative in extracted literature
Strengths here: DSB-free; reduces or eliminates DSB-associated genotoxic stress; highlighted as an advance integrated into the roadmap.
Relative tradeoffs: the abstract still identifies inefficient CNS delivery, variable efficacy, and durability concerns as translational barriers; the abstract does not specify base-editing-specific limitations; field-wide challenges include long-term genetic stability and scalability.
Source:
The abstract places base editing alongside synthetic genetic circuits and within a broader landscape that includes CRISPR-Cas9 and TALENs.
Compared with prime-editing
The abstract explicitly mentions prime editing and CRISPR-Cas9 as alternative gene-editing strategies in the same comparison.; The abstract contrasts base editing with DSB-based CRISPR-Cas9 and also mentions prime editing, targeted transposon systems, and synthetic or epigenetic circuits as other next-generation approaches.; The abstract groups base editing with prime editing and novel nucleases such as Cas12a and Cas13d.; The abstract contrasts base editing with CRISPR/Cas systems and prime editing as related gene editing modalities.; The abstract contrasts base editing with gene augmentation strategies and with conventional CRISPR-Cas editing systems that induce double-strand DNA cleavage or repair. It also discusses prime editing as a related precision editing alternative.; Prime editing and gene silencing are named as adjacent AAV-mediated strategies in the same review.
Shared frame: source-stated alternative in extracted literature
Strengths here: DSB-free; reduces or eliminates DSB-associated genotoxic stress; highlighted as an advance integrated into the roadmap.
Relative tradeoffs: the abstract still identifies inefficient CNS delivery, variable efficacy, and durability concerns as translational barriers; the abstract does not specify base-editing-specific limitations; field-wide challenges include long-term genetic stability and scalability.
Source:
The abstract explicitly mentions prime editing and CRISPR-Cas9 as alternative gene-editing strategies in the same comparison.
Source:
The abstract contrasts base editing with DSB-based CRISPR-Cas9 and also mentions prime editing, targeted transposon systems, and synthetic or epigenetic circuits as other next-generation approaches.
Source:
The abstract groups base editing with prime editing and novel nucleases such as Cas12a and Cas13d.
Source:
The abstract contrasts base editing with CRISPR/Cas systems and prime editing as related gene editing modalities.
Source:
The abstract contrasts base editing with gene augmentation strategies and with conventional CRISPR-Cas editing systems that induce double-strand DNA cleavage or repair. It also discusses prime editing as a related precision editing alternative.
Source:
Prime editing and gene silencing are named as adjacent AAV-mediated strategies in the same review.
Compared with stimuli-sensitive genetic circuits
The abstract places base editing alongside synthetic genetic circuits and within a broader landscape that includes CRISPR-Cas9 and TALENs.
Shared frame: source-stated alternative in extracted literature
Strengths here: DSB-free; reduces or eliminates DSB-associated genotoxic stress; highlighted as an advance integrated into the roadmap.
Relative tradeoffs: the abstract still identifies inefficient CNS delivery, variable efficacy, and durability concerns as translational barriers; the abstract does not specify base-editing-specific limitations; field-wide challenges include long-term genetic stability and scalability.
Source:
The abstract places base editing alongside synthetic genetic circuits and within a broader landscape that includes CRISPR-Cas9 and TALENs.
Compared with transcription activator-like effector nucleases
The abstract places base editing alongside synthetic genetic circuits and within a broader landscape that includes CRISPR-Cas9 and TALENs.
Shared frame: source-stated alternative in extracted literature
Strengths here: DSB-free; reduces or eliminates DSB-associated genotoxic stress; highlighted as an advance integrated into the roadmap.
Relative tradeoffs: the abstract still identifies inefficient CNS delivery, variable efficacy, and durability concerns as translational barriers; the abstract does not specify base-editing-specific limitations; field-wide challenges include long-term genetic stability and scalability.
Source:
The abstract places base editing alongside synthetic genetic circuits and within a broader landscape that includes CRISPR-Cas9 and TALENs.
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