FDA Guidance on Shedding and Environmental Impact in Clinical Trials Involving Gene Therapy Products

Abstract

Introduction:

The US regulatory environment is evolving to accommodate a boom in gene therapy research. The 2019 version of the National Institutes of Health (NIH) Guidelines on Research Involving Recombinant or Synthetic Nucleic Acid Molecules (NIH Guidelines) lacks an appendix providing specific guidance for Institutional Biosafety Committee (IBC) review of clinical trials.

Discussion:

As the field matures, the burden of Federal oversight for clinical trials of investigational products containing recombinant or synthetic nucleic acid molecules is shifting toward the Food and Drug Administration (FDA). This report summarizes recent FDA guidance documents on shedding and considerations for environmental impact assessments highlighting key points pertinent to IBC review.

Conclusion:

This report helps biosafety professionals understand the evolving regulatory framework for gene therapy products. Knowledge of the guidance documents discussed in this report will assist biosafety professionals in addressing issues pertaining to shedding and environmental impact during IBC review of clinical trials.

Introduction

We previously described how the US regulatory environment is evolving to accommodate a boom in gene therapy research.¹ In the two previous revisions to the National Institutes of Health (NIH) guidelines, the NIH Office of Science Policy (OSP) sequentially shifted regulatory oversight of human gene therapy research from the NIH Recombinant DNA Advisory Committee (RAC) to the Food and Drug Administration (FDA).² The April 2016 version of NIH Guidelines, which were issued in part to evolve the process for review by the NIH RAC, instructed the local oversight bodies (the Institutional Review Board [IRB] and the Institutional Biosafety Committee [IBC]) at the initial site for each study to determine the necessity for RAC review. Subsequently, the 2019 version of NIH Guidelines lacked an appendix providing specific guidance on IBC review of clinical trials and also eliminated the process for requesting RAC review. Many of the items contained in prior versions of NIH Guidelines are now in a separate guidance document known as Points to Consider.³

As the field matures, the burden of Federal oversight for clinical trials using investigational products containing recombinant or synthetic nucleic acid molecules is shifting away from the NIH toward the FDA.

FDA Guidance Documents with Bearing on IBC Review

As needed, the FDA releases guidance documents to aid in the development and testing of drugs as well as submission of applications and supporting documents to the FDA. The FDA Center for Biologics Evaluation and Research (CBER) regulates investigational products containing recombinant or synthetic nucleic acid molecules as biologics and has posted various guidance documents with bearing on IBC review (Table 1).⁴ The FDA defines gene therapy products as “products that mediate their effects by transcription and/or translation of transferred genetic material and/or by integrating into the host genome and that are administered as nucleic acids, viruses, or genetically engineered microorganisms. The products may be used to modify cells in vivo or transferred to cells ex vivo before administration to the recipient.”⁵

Table 1.

Food and Drug Administration guidance documents with bearing on Institutional Biosafety Committee review

Date	Title
3/2022	Consideration for the Development of Chimeric Antigen Receptor T Cell Products: Draft Guidance for Industry
3/2022	Human Gene Therapy Products Incorporating Human Genome Editing: Draft Guidance for Industry
1/2021	Human Gene Therapy for Neurodegenerative Diseases: Draft Guidance for Industry
1/2020	Chemistry, Manufacturing and Control (CMC) Information for Human Gene Therapy Investigational New Drug Applications (INDs): Guidance for Industry
1/2020	Long-Term Follow-Up After Administration of Human Gene Therapy Products: Guidance for Industry
1/2020	Testing of Retroviral Vector-Based Human Gene Therapy Products for Replication Competent Retrovirus During Manufacture and Patient Follow-Up: Guidance for Industry
1/2020	Human Gene Therapy for Hemophilia: Guidance for Industry
1/2020	Human Gene Therapy for Rare Diseases: Guidance for Industry
1/2020	Human Gene Therapy for Retinal Disorders: Guidance for Industry
9/2016	Recommendations for Microbial Vectors Used for Gene Therapy: Guidance for Industry
8/2015	Design and Analysis of Shedding Studies for Virus or Bacteria-Based Gene Therapy and Oncolytic Products: Guidance for Industry
6/2015	Considerations for the Design of Early-Phase Clinical Trials of Cellular and Gene Therapy Products: Guidance for Industry
3/2015	Determining the Need for and Content of Environmental Assessments for Gene Therapies, Vectored Vaccines and Related Recombinant Viral or Microbial Products: Guidance for Industry

Guidance documents represent the current thinking of the FDA on the topics covered. They are not regulatory requirements, and alternative approaches can be utilized if they satisfy the requirements of the applicable statues and regulations. Research sponsors are encouraged to contact the FDA to discuss alternatives to the FDA's recommendations if they better suit the needs of their study and are justifiable.

Although the FDA guidance documents do not directly affect IBC review like the NIH Guidelines, they set the standard for writing the clinical research protocols that are reviewed by IBCs. Although the FDA guidance documents are typically meant for manufacturers (either pharmaceutical companies serving as research sponsors or investigators at institutions) rather than biosafety professionals and IBCs, some of the content can be useful in the IBC review process. Each of the following sections pertain to a specific FDA guidance document regarding shedding and environmental impact assessments. Key timepoints pertinent to the IBC risk assessment are summarized in Table 2.

Table 2.

Key timepoints pertinent to generation of shedding data and environmental risk assessment in the regulatory pathway for virus or bacteria based gene therapy products

Considerations for Shedding

The FDA's view on shedding studies for gene therapy investigational products comprising viruses or bacteria is outlined in the guidance, Design and Analysis of Shedding Studies for Virus or Bacteria-Based Gene Therapy and Oncolytic Products.⁶ The guidance does not cover plasmids, peptides, or genetically modified mammalian cells, as the FDA does not consider those types of agents in this context as infectious or transmissible. The FDA acknowledges that shedding raises the possibility of transmission from treated to untreated individuals, such as close contacts and healthcare professionals.

The FDA recommends collection of shedding data from preclinical animal models, if the oncolytic or virus-based gene therapy product meets any of the following criteria:

• Humans have not been previously exposed to the product, as in the case of a nonhuman bacterial or viral strain.

• The product has been previously administered to humans but has been modified to achieve a different in vivo tropism than the parent strain.

• The product has been previously administered to humans; however, a change in the route of administration is proposed.

• Humans have not been previously exposed to the product, and the route of administration differs from the natural route of exposure/infection.

Considerations for selection of animal models for shedding studies include the permissiveness or susceptibility of the animal to infection to the agent under investigation and any pre-existing immunity that may affect infectivity or clearance.

When designing shedding studies, investigators are encouraged to consider the following criteria:

• Replication-competent agents may multiply or replicate in the host, which may increase the extent and duration of shedding.

• Immunogenicity: Highly immunogenic agents may be cleared more rapidly from circulation than poorly immunogenic agents. Furthermore, shedding periods may decrease with subsequent inoculations or booster doses due to the host's immunological memory.

• Agents capable of persistence or latency may exhibit shedding periods that are intermittent and unpredictable.

• Agents with altered tropism compared with the parental strain may exhibit altered shedding profiles as they are targeted to different tissues or organs.

• Stability of attenuation: Agents with higher potential for recombination, reversion, or loss of attenuation may exhibit altered shedding profiles.

• The route of administration should be considered when determining the anatomical sites to be sampled and the samples to be collected for shedding (e.g., swabs at the site of injection vs. urine, feces, or saliva).

Replication competency factors heavily into the FDA's considerations for the clinical phase in which shedding data should be collected. The FDA recommends collection of shedding data from use of replication-competent agents starting at phase I clinical trials. Sponsors may be required to continue to collect shedding data through clinical trial phases II and III, especially if the dose and regimen are altered or expanded upon from phase I.

The FDA recommends collection of shedding data from use of replication-deficient agents at clinical phase II as the dose and regimen have been selected after phase I trials. Compared with replication-competent agents, shedding of replication-deficient agents is expected to be of shorter duration and associated with lower potential for transmission.

Sampling should begin immediately after product administration irrespective of replication competency. Although shedding is likely greatest shortly after inoculation, a second peak may take place with replication-competent agents. Analysis of sampling should continue until three consecutive data points are obtained at or below the limit of detection (LOD). If shedding does not reach the LOD, sampling should continue until results demonstrate a plateau over three consecutive data points. The factors to consider for clinical shedding studies are comparable with those listed above for preclinical animal models.

At least one of the assays used to measure shedding should be quantitative, such as quantitative polymerase chain reaction (PCR). Assays for viral infectivity may include readouts such as tissue culture infectious dose 50, plaque forming units, or focus-forming units. Detection of dividing bacteria may be reported as colony forming units. Assays limited to use of quantitative PCR are adequate for detection of replication-deficient vectors.

As transmission to untreated individuals is a low probability event, monitoring such individuals is not typically recommended. However, if there is potential for transmission to untreated individuals, investigators may be required to assess the possibility.

Considerations for Environmental Impact

The National Environmental Policy Act of 1969 (NEPA) requires all Federal agencies to assess the environmental impacts of their actions and to ensure that the interested and affected public is informed of the environmental analyses. FDA's NEPA policies and procedures can be found under 21 CFR Part 25. These regulations specify that all applications requesting agency action (e.g., investigational new drugs [INDs] and marketing approvals) must be accompanied by either an environmental assessment (EA) or a claim of categorical exclusion. The FDA evaluates the information contained in an EA to determine whether the preparation of an environmental impact statement (EIS) is necessary. If the proposed action will not significantly affect the quality of the environment, then the FDA will provide a letter finding of no significant impact (FONSI). The FDA issued guidance on, “Determining the need for and content of environmental assessments for gene therapies, vectored vaccines and related recombinant viral or microbial products.”⁷

All applications for either an IND or final marketing approval (also known as a biologicals license application, BLA) must be accompanied with either an EA or a claim of categorical exclusion. Submissions that typically receive categorical exclusions include:

• BLA applications if the FDA's actions do not increase the use of the active moiety; or

• BLA applications for substances that occur naturally in the environment if FDA actions do not significantly alter the concentration or distribution of the substance, its metabolites, or degradation products in the environment; or

• IND applications.

The final exclusion criteria are of importance to IBCs, as research use of most drugs requires an IND. As such, research use of most drugs is excluded from an EA unless the FDA feels an extraordinary circumstance may occur where issuing the IND may significantly affect the quality of the environment.

The FDA believes that, in most cases, agency action on an IND for a clinical study using a gene therapy viral vector will not significantly affect the quality of the environment because, in brief, these clinical trials are closely monitored and are limited to a designated study group.

“In the event FDA action on an IND would increase the use of a drug, the agency's experience has demonstrated that significant environmental effects would not occur because the investigational use is limited and controlled”⁸ (62 FR 40570 at 40578). In addition, the preamble to the Final Rule went on to state, “In the event FDA has reason to believe its action on an IND may significantly affect the environment, FDA will invoke the provision relating to ‘extraordinary circumstances' and require an EA.” (Id. at 40579)

The threshold for “significantly” affecting the quality of the environment is defined under 40 CFR 1508.27 as:

• The degree to which the effects of the gene therapy viral vector on the quality of the environment are likely to be highly controversial (40 CFR 1508.27(b)(4)).

• The degree to which the possible effects of the gene therapy viral vector on the human environment are highly uncertain or involve unique or unknown risks (40 CFR 1508.27(b)(5)).

• The degree to which the gene therapy viral vector may adversely affect an endangered or threatened species or its habitat that has been determined to be critical under the Endangered Species Act of 1973 (40 CFR 1508.27(b)(9)).

• Whether the effects of the gene therapy viral vector on the environment threaten a violation of Federal, State, or local law or requirements imposed for the protection of the environment (40 CFR 1508.27(b)(10)).

The threshold for requiring an EA is much lower once the clinical trials have generated enough data for the research sponsor to request marketing approval in the form of a BLA. In contrast to clinical trials, BLA submissions for gene therapy viral vectors that do not “occur naturally in the environment” require an EA. Gene therapy viral vectors that express a functional protein coding sequence that originates from a genus that is different from the viral vector's parental strain would require EAs at the time of BLA submission. Any of the following would not require an EA as they are deemed to “occur naturally in the environment”:

• Gene therapy viral vectors expressing a protein originating from the genus of the parental strain, or

• gene therapy viral vectors that differ from the wild type by a point mutation or deletion, or

• gene therapy viral vectors that have been killed or inactivated using a validated manufacturing step or with lot release criteria, or

• genetically modified human cells.

Contents of an EA

The structure of EAs is outlined in FDA Guidance for Industry: EA of Human Drug and Biologics Applications.⁹ The must include four sections:

• Identification of substance subject to proposed action,

• identifying and assessing potential environmental effects,

• mitigation measures, and

• alternatives to the proposed action.

The identification of substance subject to proposed action includes a description of the gene therapy viral vector as well as potential metabolites, degradants, or byproducts released into the environment. If the agent becomes degraded after administration only, the excreted degradation products need to be described. For example, viral vectors that degrade in vivo might only shed vector DNA. The EA would include PCR results showing the presence of vector DNA in excreta and the lack of intact viral particles. The EA should also disclose potential contaminants or variants of the gene therapy viral vector, such as revertants to wild type or replication-competent virus. For example, when utilizing replication-deficient adenovirus, the FDA recommends less than one replication-competent adenovirus virion per dose of 3 × 10¹⁰ viral particles.¹⁰

The FDA requires a risk assessment involving known and reasonably foreseeable consequences of environmental release in the section titled, Identifying and Assessing Potential Environmental Effects. Submitters are asked to assess the virulence of the excreted products to animals, plants, and microorganisms. The risk assessment includes the likely environmental distribution of the product, environmental stability, ability to grow or replicate, susceptibility to drugs (e.g., antibiotics, antivirals, or biocides), genetic stability, and durability in the environment. Submitters are asked to determine the magnitude of environmental impact ranging from negligible and self-limiting to severe, having serious effects or leading to long-term permanent harmful consequences.

The author of the EA is asked to provide mitigation measures intended to avoid or mitigate environmental risk stemming from excretion of the drug product or its metabolites that typically include:

• requirements for hygienic measures and waste treatment,

• handling gene therapy viral vectors under appropriate biocontainment,

• mMinimizing patient contact with susceptible populations or species, and

• control measures to minimize aerosol formation.

If potential adverse environmental impacts are identified, the EA must include alternatives that offer lower environmental risks.

If the FDA determines that issuing the marketing approval will not significantly affect the quality of the environment, then the FDA will provide a letter FONSI. If the FDA determines that issuing a marketing approval for the drug poses an environmental risk, the agency will issue an EIS that must provide a full and fair discussion of the environmental impacts to inform decision makers and the public of reasonable alternatives and actions that can be taken to minimize environmental impacts (40 CFR 1502.1).

Discussion

Gene therapy is an area of booming growth within the pharmaceutical industry. As such, many pharmaceutical industry professionals experienced in the nuances of small molecule drugs are new to the unique requirements of gene therapy and IBC review. In contrast, the explosive growth in gene therapy research means many biosafety professionals and IBCs familiar with research use of recombinant and synthetic nucleic acid molecules in the laboratory and animal setting are starting to encounter the unique challenges posed by clinical trials. These gaps and professional differences can introduce inefficiencies in the IBC review process.

Unlike principal investigators in the academic setting, pharmaceutical companies are more focused on meeting the FDA's regulatory requirements and are just now becoming familiar with the nature of IBC review. Drug manufacturers must obtain an IND to use their investigational product in clinical trials taking place across state lines and for the data from those trials to be admissible to the FDA for marketing approval. Preclinical testing of investigational products and the design of clinical trials are done to comply with FDA guidance and requirements to obtain the IND.

Occasionally study documents do not provide sufficient information for the IBC to perform its risk assessment when reviewing clinical trials. If the clinical protocol and investigator's brochure do not adequately describe the risk of shedding, the IBC can request shedding data from prior trials and/or preclinical animal models. Preclinical animal models are the only source of shedding data available for phase I trials that are a first in human experience.

If the study personnel submitting for IBC review are unaware of preclinical shedding data, the FDA guidance document (Design and Analysis of Shedding Studies for Virus or Bacteria-Based Gene Therapy and Oncolytic Products) can be provided outlining the nature of the data requested.

Sometimes shedding data are not available for early phase trials of investigational products. The FDA allows manufacturers to claim a categorical exclusion from an EA for IND applications. If the FDA reviewer feels granting the IND would not pose an extraordinary circumstance presenting a significant risk to the environment, then the IND may be granted without an EA. Granting of categorical exclusions is the norm for IND submissions. IBCs can request a copy of the exclusion letter to assuage concerns about legal liability from shedding during a clinical trial.

IBCs may be concerned with the FDA's criteria for assessing shedding during clinical trials. Although the FDA recommends that collection of shedding data from use of replication-competent agents begins at phase I, collection of shedding data from use of replication-deficient agents is not recommended until phase II after the dose and regimen have been selected at the conclusion of phase I. Although the FDA guidance recommends timepoints for collection of samples to assess shedding, it does not specify a timeframe for generating the data. However, it does require the data for consideration at the time of marketing approval. As such, in a worst-case scenario, shedding data might not be generated until the conclusion of a trial after shedding and exposures have taken place potentially involving many research subjects across a multisite study. Biosafety professionals and IBCs play an important role in protecting the researchers, community, and environment from exposure and the consequences of shedding during clinical trials.

A greater emphasis should be placed on improving the body of knowledge about viral shedding from gene therapy trials to allow for evidence-based risk assessment. To date there is no central database for reporting viral shedding. The recently published FDA guidance described in this report is the closest the field has come to establishing standardized methodology for assaying viral shedding. The most comprehensive review of shedding data from peer reviewed publications about gene therapy trials we have found looked at 100 publications and analyzed data from 1619 patients across studies utilizing the most common viral vectors (retro/lentivirus, adenovirus, adeno-associated virus, and poxviruses such as vaccinia and canary pox).¹¹ The authors found only 39% of publications included shedding data, highlighting the lack of emphasis placed on this concern. The lack of standardized methodology for assaying and reporting complicates direct comparisons across studies and between vector types. The authors found the occurrence of shedding mainly depended on type of vector, route of administration, and dose. Samples positive for viral shedding are typically derived from excreta that are either close to or anatomically downstream from the site of administration. For example, inhalation or intranasal administration is associated with shedding in saliva and nasopharyngeal samples. Skin, scab, and bandage samples tested positive after intradermal inoculation. Shedding in semen was reported in studies involving injection into the prostate and hepatic artery. Blood and urine most frequently tested positive for viral shedding across the varying routes of administration. The lack of standardized methodology for assaying, reporting, and compiling shedding data precludes a quantitative analysis of viral shedding risk. The unknowns pose a level of risk to the community, especially close contacts of the research subjects, clinical research personnel processing samples from research subjects, and the environment.

IBC review can play an important role in protecting all parties involved when gaps exist that potentially allow shedding and exposure to the research staff, community, and environment during a clinical trial. IBCs can recommend precautions be taken to mitigate the risk of shedding from a research subject leading to transmission to other individuals and the environment. Depending on the expected route of shedding, precautions can include personal protective equipment, protective clothing, abstaining from activities likely to lead to transmission, and isolating at home or domiciling at the research site during the expected shedding period. Such actions should be discussed and negotiated with the IRB, principal investigator, and manufacturer to ensure all parties agree on the best course of action and ensure compliance. NIH guidelines and the Biosafety in Microbiological and Biomedical Laboratories (BMBL) do not specifically address risk assessment and risk mitigation for clinical trials taking place in the clinical setting, when research subjects leave the clinic or the potential for at home dosing. Such guidance would be beneficial given the growth of clinical research on biopharmaceuticals containing recombinant or synthetic nucleic acid molecules.

Lastly, we discuss reproductive considerations. Inclusion criteria for gene therapy studies routinely include subjects agreeing to use barrier contraceptives or abstaining from sexual intercourse for a specified duration during the study. However, there are no specific harmonized international regulatory guidelines on birth control requirements and pregnancy prevention within clinical trials. The International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) provides some recommendations in M3(R2)1 regarding circumstances in which “highly effective” methods should be used. However, the guidance document does not suggest what methods might achieve the desired level of “high” efficacy.¹² During review of the IND, the FDA is likely to require use of barrier contraception or abstinence as inclusion criteria.

Conclusion

As the responsibility for oversight of clinical trials involving recombinant or synthetic nucleic acid molecules shifts at the Federal level from NIH Guidelines to the FDA, biosafety professionals and IBCs must adapt to the evolving regulatory environment. By becoming familiar with the guidance documents issued by the FDA, biosafety professionals can better anticipate challenges in review of clinical trials and develop institutional policies, procedures, or guidance documents to aid in IBC review of clinical trials while at the same time ensuring the protection of research subjects, close contacts, research personnel, the institution, the community, and the environment.

Authors' Disclosure Statement

The authors are employed by Advarra, a for-profit entity providing independent IBC and IRB reviews.

Funding Information

No funding was received for this article.