Human Genome Editing: FDA Draft Guidance Summary

Consideration for Developing Gene Editing Product 

1. Genome Editing Methods:

• Genome editing can be achieved through nuclease-dependent or nuclease-independent methods.
• Nuclease-dependent methods involve introducing site-specific breaks in DNA using technologies like zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), modified-homing endonucleases, and CRISPR-associated (Cas) nucleases. These breaks can lead to modification of the DNA sequence at the cleavage site.
• Nuclease-independent methods can change DNA sequences without cleaving the DNA and include techniques like base editing and synthetic triplex-forming peptide nucleic acids.
• The choice of GE technology should consider factors such as the mechanism of action, the ability to target specific DNA sequences, and the potential to optimize components for efficiency, specificity, or stability.

2. Type and Degree of Genomic Modification:

• Different GE approaches rely on DNA repair pathways such as homology directed repair (HDR) and non-homologous end-joining (NHEJ) to perform genomic modifications.
• HDR uses a homologous DNA sequence as a repair template, while NHEJ rejoins cleaved DNA ends without a template.
• Consideration should be given to the type and degree of genomic modification required for the desired therapeutic effect, as this can vary based on the medical condition and patient population.
• It's important to note that these processes can result in unintended DNA insertions or deletions (indels) with potential unforeseen consequences.

3. Genome Editing Component Delivery Method:

• The choice of the optimal delivery method for GE components should consider factors such as the capacity of the delivery vector, targeted delivery efficiency, and component persistence and stability.
• Prolonged persistence of certain GE components (e.g., nucleases) can increase the risk of unintended genomic modifications, including off-target editing and chromosomal rearrangements.
• The method for delivering GE components may depend on whether the product involves ex vivo or in vivo genomic modification.
• Ex vivo modifications are performed outside the body, with modified cells subsequently administered to the patient.
• In vivo modifications are introduced directly into the patient's body.
• Different cell types may require specific delivery methods, such as electroporation, viral vectors, nanoparticles, or ribonucleoprotein complexes (RNPs) for CRISPR/Cas9.
• The chosen delivery method should align with the intended use and target indication, and considerations include the ability to control expression of the delivered components and potential for toxicity or pre-existing immunity.

Chemistry, Manufacturing, and Controls (CMC) Recommendations:

• This section refers to general CMC considerations for manufacturing, testing, and release of human GE products, which are similar to conventional drug products.
• Additional CMC recommendations specific to human GE products are provided for the design, manufacture, and testing of GE components and the drug product (DP).

Genome Editing Component Design:

• Sponsors are encouraged to use design platforms that are most suitable for their genomic target and the intended type of genomic modification.
• The Investigational New Drug (IND) application should include a description of the design and screening processes for GE components, along with the sequences of these components.
• Optimization of GE components is recommended to reduce the potential for off-target genome modification. Optimization can target the editor or the targeting elements, depending on the GE technology used.
• The IND should provide a detailed strategy for optimization, including steps to inhibit degradation of GE components.

Genome Editing Component Manufacture and Testing:

• GE components can be administered in vivo using nanoparticles, plasmids, or viral vectors or used for ex vivo cell modification.
• The IND should describe how each GE component is manufactured, purified, and tested. This includes providing flow diagrams, narratives, lists of reagents, and certificates of analysis.
• Detailed information about the quality control and quality assurance programs, product tracking and segregation procedures, and shipping procedures should be included for each GE component manufacturing site.
• Manufacturing of GE components must adhere to Current Good Manufacturing Practices (CGMP) standards, especially for later-phase studies and licensure.
• Testing for GE components should cover aspects like sterility, identity, purity, functionality, and process residuals. Analytical procedures, including sensitivity and specificity, should be outlined.
• Stability studies should be conducted on all GE components to assess attributes such as purity and functionality that may be affected during storage.

Drug Product Manufacture and Testing:

• The IND should provide a detailed description of the DP manufacturing process, in-process controls, and reagents used.
• If the DP is intended to be sterile but cannot be terminally sterilized, measures taken to ensure aseptic processing should be described.
• Testing of the DP should ensure that it meets acceptable limits for identity, potency/strength, quality, and purity. This testing should address any safety concerns introduced during manufacturing or identified in preclinical studies.
• For in vivo-administered GE DPs, testing should include the determination of GE efficiency and specificity. Sterility testing is also recommended.
• Detailed descriptions of analytical procedures, including accuracy, precision, sensitivity, and specificity, should be provided.
• DP specifications should be based on starting materials, manufacturing processes, desired final product attributes, and preclinical studies.

Specific recommendations are provided for two types of human GE DPs:

• In vivo-administered DPs: These may involve plasmids, vectors, or nanoparticles. The DP description should include manufacturing and testing details for the relevant components, along with efficiency assessments.
• Ex vivo-modified DPs: Manufacturing processes should include controls and testing for critical steps affecting efficiency and specificity of editing. Testing should encompass on-target editing efficiency, off-target editing frequency, chromosomal rearrangements, residual GE components, and total number of genome-edited cells.
• Potency assays should be developed to measure the properties and functional outcomes of the GE in the DP. Surrogate potency tests may be acceptable if they correlate with functional outcomes.
• Additional testing and criteria may be necessary for allogeneic human cell products used to treat multiple patients

Recommentations for Preclinical Studies

General Objectives of Preclinical Studies:

• The overall objectives of preclinical studies for investigational GE products are similar to those for gene therapy products, as described in FDA's "Preclinical Assessment of Investigational Cellular and Gene Therapy Products" guidance.
• These objectives include identifying a biologically active dose range, determining an initial clinical dose level, evaluating safety of the proposed route of administration (ROA), supporting the target patient population, and identifying potential toxicities and monitoring parameters.
• These objectives are essential for establishing the scientific rationale and feasibility of clinical trials with GE products.

Specific Recommendations for Preclinical Studies:

• Preclinical in vitro and in vivo proof-of-concept (POC) studies are recommended to establish feasibility and support the scientific rationale for clinical trials.
• In vitro models should be considered to evaluate the activity of the GE product in the target cell type(s) for genomic modification.
• Animal species and models selected for in vivo studies should demonstrate a biological response to the investigational GE product or a species-specific surrogate product.
• Preclinical safety studies should be designed to identify potential risks associated with GE product administration, including delivery modality, expression of GE components, genomic modification, and gene product expression.
• Safety assessment should include the identification and characterization of off-target activity, chromosomal rearrangements, and their biological consequences, when feasible.
• In vivo preclinical safety studies should align with planned clinical trials in terms of dose range, ROA, delivery device, dosing schedule, and evaluation endpoints.
• Biodistribution studies are recommended to characterize the distribution, persistence, and clearance of the GE product and expressed GE components in vivo.

Characterization of Activity and Safety:

• The investigational GE product should be evaluated in definitive POC and safety studies, using the clinical cell source for ex vivo-modified products.
• In some cases, a surrogate GE product may be used in preclinical studies, provided scientific justification and biological relevance are established.
• Each GE product lot used in preclinical studies should be characterized according to appropriate specifications.

Assessment of Activity:

• Preclinical POC studies should assess specificity and efficiency of editing, functionality of the corrected or expressed gene product, editing efficiency required for the desired therapeutic effect, durability of genomic modification, and effects of genetic variation on editing activity.

Assessment of Safety:

• Preclinical studies should identify and characterize risks of GE at on- and off-target loci.
• Identification of off-target editing activity should include type, frequency, and location of all off-target editing events.
• Multiple methods, including genome-wide analysis, should be used for identifying potential off-target sites, preferably using target human cell types from multiple donors.
• Bona fide off-target sites should be verified using methods with adequate sensitivity.
• Appropriate controls should be included to ensure assay quality and interpretability.
• Assessment should include genomic integrity, chromosomal rearrangements, insertions or deletions, integration of exogenous DNA, potential oncogenicity, insertional mutagenesis, immunogenicity, kinetic profile of GE component expression and editing activity, viability, selective survival advantage of edited cells, preservation of cell functionality, and evaluation of potential germline modification.

Recommentation for Clinical Studies

Clinical Trial Design:

• Clinical development programs for human GE products should address both the risks associated with the product itself and the additional risks associated with GE, including potential unintended consequences of on- and off-target editing.
• Clinical trial design should include appropriate patient selection, efficient and safe product administration, safety monitoring, and choice of endpoints.
• Long-term follow-up is recommended for subjects receiving human GE products to evaluate clinical safety.

Study Population:

• Selecting the appropriate study population is crucial. Consideration should be based on the product's mechanism of action (MOA), disease context, potential benefits, risks, availability of alternative treatments, and disease severity.
• Generally, first-in-human trials involving human GE products should enroll subjects for whom no other treatment options are available or acceptable.
• Subjects with severe or advanced disease may be more willing to accept the risks of the investigational product.

Dose and Dose Schedules:

• Safe and effective product delivery methods should be used to minimize potential adverse events related to product administration.
• Delivery and dose schedules should be supported by preclinical data and, where available, guided by previous clinical experience from similar products.

Treatment Plan:

• To mitigate risks associated with the GE product, subject enrollment should be staggered, with a specified interval between product administrations to monitor for acute and subacute adverse events (AEs).
• Cohort size should be chosen based on the patient population, acceptable risk, tolerability, feasibility, and pharmacologic activity.

Monitoring and Follow-Up:

• A comprehensive safety monitoring strategy with a well-defined toxicity grading system and a toxicity management plan is crucial for clinical trials.
• Monitoring should include off-target editing, unintended consequences of editing, aberrant cellular proliferation, immunogenicity, and tumorigenicity.
• Applicable reporting requirements for adverse experiences must be followed.
• Long-term follow-up (LTFU) should be conducted for at least 15 years after product administration due to the potential long-term effects of editing.

Study Endpoints:

• Study endpoints should be based on the proposed indication and reflect a clinically meaningful effect of the GE product.
• Efficacy studies should select primary endpoints that demonstrate clinical benefit.

Special Considerations for Research Involving Children:

• Clinical studies should enroll individuals who can understand and consent to study procedures and risks.
• For studies involving children with greater than minimal risk, the prospect of direct clinical benefit to children should be evidence-based.
• Preliminary data on safety and feasibility should be obtained from adult subjects before enrolling pediatric subjects, and an effort should be made to enroll adolescents before younger children and infants when appropriate.

Reference

https://www.fda.gov/regulatory-information/search-fda-guidance-documents/human-gene-therapy-products-incorporating-human-genome-editing