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References 427
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6 Food and Drug Administration (FDA) (2022). Premarket Notification 510(k).
https://www.fda.gov/medical­preparing- correct- submission/premarket- notification- 510k (accessed 17 October 2023).
7 Food and Drug Administration (FDA) (2016). Premarket approval (PMA). https://
www.fda.gov/medical­correct- submission/premarket- approval- pma (accessed 17 October 2023).
8 Food and Drug Administration (FDA) (2003). Guidance for industry and FDA
staff premarket approval application modular review. November 2003.
9 Food and Drug Administration (FDA) (2019). Acceptance and filing reviews for
premarket approval applications (PMAs) guidance for industry and food and drug administration staff. December 2019.
10 Food and Drug Administration (FDA) (2022). Humanitarian device exemption.
October 3, 2022. https://www.fda.gov/medical- devices/premarket- submissions­selecting- and- preparing- correct- submission/humanitarian- device- exemption (accessed 17 October 2023).
11 Food and Drug Administration (FDA) (2019). Humanitarian device exemption
(HDE) program guidance for industry and food and drug administration staff. September 6, 2019.
12 Food and Drug Administration (FDA) (2023). Requests for feedback and
meetings for medical device submissions: the Q‐submission program. June 2023.
13 Regulation (EU) 2017/746 of the European Parliament and of the Council of
5 April 2017 on invitro diagnostic medical devices and repealing Directive 98/79/ EC and Commission Decision 2010/227/EU2017/746.
14 European Union Commission (2021). Regulation (EU) 2017/746 of the European
Parliament and of the Council of 5 April 2017 on invitro diagnostic medical devices and repealing Directive 98/79/EC and Commission Decision 2010/227/EU. October 2021.
15 Medicines & Healthcare products Regulatory Agency (2023). Standard
implementation of the future regulations. https://www.gov.uk/government/ publications/implementation­extension- of- standstill- period/implementation- of- the- future- regulations (accessed 27July 2023).
16 Government of Canada (2016). Guidance document: guidance for the risk‐based
classification system for invitro diagnostic devices (IVDDs). https://www.canada .ca/en/health- canada/services/drugs- health- products/medical- devices/ application- information/guidance- documents/guidance- document- guidance­risk- based- classification- system- vitro.html (accessed 17 October 2023).
17 Pharmaceutical and Food Safety Bureau (2013). Ministry of Health, Labour and
Welfare. Notification on approval application for invitro companion diagnostics and corresponding therapeutic products. July 2013.
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18 National Medical Products Administration (NMPA) (2023). http://english.nmpa
.gov.cn/ (accessed 17 October 2023).
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diseases guidance for industry. January 2020.
20 Food and Drug Administration (FDA) (2020). Human gene therapy for
hemophilia guidance for industry. January 2020.
21 Food and Drug Administration (FDA) (2015). Considerations for the design of
early‐phase clinical trials of cellular and gene therapy products guidance for industry. June 2015.
22 Food and Drug Administration (FDA) (2023). List of cleared or approved
companion diagnostic devices (invitro and imaging tools). May 23, 2023. https:// www.fda.gov/medical­companion- diagnostic- devices- in- vitro- and- imaging- tools (accessed 6 October 2023).
devices/in- vitro- diagnostics/list- cleared- or- approved-
Section V
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Regulatory Perspectives onGene Therapy
429
18
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Current Regulatory Landscape forGene Therapy Product Development and theRole ofBiomarkers
Laura I. Salazar-Fontana PhD1 and Mike Havert PhD
1
LAIZ Regulatory Science Consulting, Lausanne, Switzerland
2
Gene Therapy Partners, LLC, Arlington, Virginia, USA
2
18.1 Introduction
Scientists have long ago linked genes to biological traits and features. Hershey and Chase demonstrated in 1952 that DNA was the basis for inheritance and the early experiments that followed provided the basic understanding of how DNA is passed from parent to progeny and used as a set of instructions for a cell[1]. Visionary scientists hypothesized that genetic modification through the introduc­tion of exogenous DNA could be the basis for disease treatments[2]. By providing new genetic coding sequences, one could reprogram cells to perform a new func­tion or restore a missing function. Instead of providing a protein, a chemical drug, or a metabolite, these scientists were dreaming of ways to alter genes. It was in July of 2012 that the European Medicines Agency (EMA) granted approval for the first gene therapy product, Glybera®, an adeno‐associated viral vector engineered to deliver a corrected form of the enzyme lipoprotein lipase to the muscle tissue of patients suffering from a severe deficiency in this enzyme. Five years later, three approvals by the U.S. Food and Drug Administration (FDA) marked a breakout in which two exvivo gene‐modified products (Kymriah®, Yescarta®) and one direct in vivo gene transfer product (Luxturna®) were approved. Collectively termed gene therapy (GT), these products established a new pharmaceutical classifica­tion and the formal recognition of genetic modification of human cells as a new treatment paradigm.
431
Drug Development for Gene Therapy: Translational Biomarkers, Bioanalysis, and Companion Diagnostics, First Edition. Edited by Yanmei Lu and Boris Gorovits.
© 2024 John Wiley & Sons, Inc. Published 2024 by John Wiley & Sons, Inc.
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Yet, making changes to the genome of living human cells does not come without risk. The path to these GT approvals was long and winding. The development of gene delivery vectors, such as replication‐defective retrovirus and adenovirus, coupled with encouraging results in preclinical disease models, led to early initia­tion of several National Institutes of Health (NIH) funded clinical trials in the 1990s. Unfortunately, these early trials exposed serious treatment‐related toxici­ties, such as inflammatory responses to in vivo administered viral vectors and malignancies caused by retroviral‐mediated insertional activation of proto‐ oncogenes[3, 4]. These setbacks fueled more basic research in virology, immunol­ogy, cell biology, and model development, which ultimately led to successful clinical translation using engineered lentiviral (LVV) and adeno‐associated viral (AAV) vectors. In the time since 2012, we have had 19 gene therapy approvals worldwide, including genetically modified cell therapy products, and 28 GT are currently under regulatory evaluation[5]. These approved products have had to meet a high standard for demonstrating that clinical benefit clearly outweighted the potential risks associated with genetic modification and the potential long‐ term consequences of this new pharmaceutical modality.
This chapter provides an overview of the biomarkers that have been used from the start of gene therapy trials in support of regulatory filings and how they have evolved over time. The future for GT remains promising as we are better able to design and select safer and more effective product candidates based on the knowl­edge gained from multiple biomarkers. The value of evaluating new, particularly those related to immune toxicities, is further discussed.
18.2 What is Gene Therapy?
Gene therapy products (GTP) are a diverse group of biotherapeutics that are gen­erally developed to treat conditions for which there are limited or no effective treatments[6].
The FDA has regulated what it calls human gene therapy as biologic products since 1993[7]. FDA guidance describes gene therapy as products seeking to mod­ify or manipulate the expression of a gene or to alter the biological properties of living cells for therapeutic use[8, 9, 10, 11]. Through the transcription or the translation of transferred genetic material, or by specifically altering host (human) genetic sequences. Some examples of gene therapy products include nucleic acids (e.g. plasmids, invitro transcribed ribonucleic acid (RNA)), genetically modified microorganisms (e.g. viruses, bacteria, fungi), engineered site‐specific nucleases used for human genome editing (e.g. CRISPR/Cas9), and exvivo genetically modi­fied human cells. Whereas EMA defines gene therapy medicinal products (GTMP)
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as a biological medicinal product that consists of a recombinant nucleic acid that once administered to human beings can regulate, repair, replace, add, or delete a genetic sequence; thus, GTMP mediate their therapeutic, prophylactic, or diag­nostic effect through the recombinant nucleic acid sequence they contain, or through the product of genetic expression of this sequence[12]. Although there is no universal definition of GTP, the World Health Organization (WHO) has recently published a document aimed to achieve worldwide regulatory consensus on this definition [13]. For now, both developers and regulatorsdistinguish GTP from therapeutic proteins (so‐called “biotech” products) by categorizing them as “advanced” therapy products, and regulatory agencies anticipate the same level of quality, safety, and efficacy evidence to attain a positive benefit:risk assessment to support the approval and commercialization of a new GTP/GTMP[6].
18.3 Biomarkers Defined
Biomarkers are objective and quantifiable characteristics of biological pro­cesses[14]. The first definition was formally proposed by the National Institutes of Health (NIH) biomarkers working group back in 1998 and amended by the International Program on Chemical Safety, led by the WHO in coordination with the United Nations (UN), in 2001. The NIH working group defined biomarkers as a “characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention”[15]. Whereas, the WHO definition added to the NIH definition the utility that these measurements could have to predict the out­come and/or incidence of a disease by taking into consideration the effects of treatment, interventions, and environmental factors, such as pollutants, in the biological processes, and classified them into biomarkers of exposure, effect, and susceptibility[16].
But it was not until 2004with the announcement of FDA’s critical path initia­tive, that biomarkers could be accepted as part of the preliminary proof of safety and effectiveness of new therapeutic products with the goal of accelerating prod­uct development. The aim of this initiative was to enable the combination of new scientific and predictive methods to ease the transition between the laboratory concept to clinical development culminating in product commercialization[17].
Biomarkers can provide researchers and regulators with interim evidence con­cerning the safety and efficacy of a given treatment while more definitive clinical data are collected. For example, surrogate endpoints can be accepted as a prelimi­nary proof of efficacy if they have been well‐characterized for any given biological process. Yet for a biomarker to be considered a surrogate endpoint, there must be
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solid scientific evidence (e.g. epidemiological, therapeutic, and/or pathophysio­logical) demostrating that the chosen biomarker can also consistently and accu­rately predict a clinical outcome, either a benefit or a harm. In this case, the biomarker can be proposed as a surrogate support product development, but acceptance will be granted on a case‐by‐case basis, and very rarely to replace a clinical endpoint.
The use of biomarkers in the development of gene therapy products is further
discussed in the following sections.
endpoint to the regulatory agencies to
18.4 Early Gene Therapy Biomarkers
The first human GT clinical protocol approved by the NIH involved the genetic marking of exvivo expanded lymphocytes. Researchers at the National Cancer Institute (NCI) used a murine gamma retrovirus (Maloney murine leukemia retrovirus, produced using PA317/LNL6‐c8) encoding a bacterial neomycin resistance gene (NeoR) to tag tumor‐infiltrating lymphocytes (TILs) extracted from a metastatic melanoma tumor sample[18]. As the first openly deliberated gene transfer into humans, a number of practical, safety and ethical considera­tions were pondered before NIH approved and initiated this study. These con­siderations actually paved the road to future studies by and define three key biological response signals that have ever since used as relevant biomarkers for GTP.
The first of the biological responses was and still is the detection of replication‐ competent virus. Because, GTP has traditionally relied on modified viral vectors (for gene transfer and genetic modification of human cells they may revert to virulence and possibly become pathogenic when administered to humans. As such, it is important to understand whether these GTP contain self‐replicating viruses that might harm patients or others exposed to treatments, such as car­egivers or family contacts, specially if the chosen viral vector is an engineered retrovirus. The presence of replication‐competent virus may be difficult to detect in the final drug product as is the persistence of vector sequences with the potential for mobilization and/or activation through recombination due to envi­ronmental triggers. Therefore, replication‐competent virus testing has been used as a quality attribute and as required patient safety biomarker for all retroviral/lentiviral vector GT investigational studies. Currently, screening for replication‐competent retrovirus (RCR) or replication‐competent lentivirus (RCL) infection in study subjects is performed by either serologic detection of retroviral specific antibodies or analysis of patient peripheral blood mononuclear cells (PBMC) by PCR for retroviral specific DNA sequences. Positive screen tests are followed by a direct coculture assay to obtain and characterize the infectious
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viral isolate[19]. Recommendations for sample collection include a pretreatment time, followed by collection after three (3), six (6), and twelve (12) months post administration, and yearly for up to fifteen (15) years (FDA) or until data indicate that there is no longer risk to be followed with a minimum of 5 years for viral vectors with no risk for integration, latency or reactivation potential (EMA)[20]. All commercial products approved so far have assessed long‐term impacts on secondary malignancies and the potential for RCR/RCL generation in 15/20‐year patient registry studies that consisted of 500 and 2500 patients[21]. The Center for International Blood and Marrow Transplant Research (CBMTR) has man­aged registry studies in for the United States and Japan and similarly the European Bone Marrow Transplant (EBMT) has outlined plans for registry stud­ies in the European Union (EU)[22]. To date, substantial amount of data on the safety of retroviral vectors in clinical applications has been collected. To date, no RCR/RCL or delayed adverse event related to replication‐competent virus has been reported in subjects who have received retroviral vector‐based treat­ments[23]. Current guidance by FDA suggests that sponsors may discontinue RCL/RCR testing at some point after some initial data has been collected with some limited exemptions.
A second biomarker used in this first NIH‐approved study was aimed to track the exogenous nucleic acid contained in the genetically modified lymphocytes. Both Southern blot and PCR for the bacterial NeoR transgene were used as over­lapping semi‐quantitative assays to distinguish exogenous nucleic acid (the bacte­rial neomycin resistance gene) inserted into marked lymphocytes from sequences present in the human genome. The investigators found that the genetically modi­fied TILs were able to survive at the tumor site and in circulation for months, although the results were somehow limited in their ability to compare and quan­titatively assess TIL numbers.
Nowadays, improvements to the early PCR assays allow more quantitative assessments. Real‐time PCR, or quantitative PCR (qPCR), is now a well‐ established technology that measures the accumulation of DNA products ampli­fied during a PCR reaction. Also, digital PCR (dPCR) offers further improvements in the sensitivity and precision of this approach. These quantitative PCR method­ologies have become the regulatory standard for today’s biodistribution and shedding studies.
Evaluating the biodistribution of a gene therapy vector is also an important first step in the design and understanding of a GT to support its potential therapeutic effect and safety risk. Biodistribution studies are performed to determine the dis­semination and the GT persistence in both target and non‐target tissues upon direct invivo administration. Two FDA guidance documents outline the need for biodistribution studies and there is a current effort underway to draft an ICH document to harmonize approaches [8, 24, 25]. FDA guidance suggests that a
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biodistribution study be done in combination with an animal toxicology study because the location and persistence of the GT vector can help with the interpre­tation of toxicology assessments. In addition, the extent of long‐term follow‐up (LTFU) in patients may be guided by product biodistribution studies in animals. It also recommends developers to sample a panel of tissues, at a minimum (blood, injection site(s), gonads, brain, liver, kidneys, lung, heart, and spleen) and assess vector copy number with a sensitivity of not less than 50 copies per microgram of cellular DNA (or about 10e5 cells). General recommendation is that five (5) animals/sex/timepoint and for collections to include tissues prior to peak, steady‐ state (i.e. plateau), and declining (if feasible)[8, 25]. Similar considerations for the concurrent evaluation of biodistribution and toxicity in pre‐clinical studies are contemplated by EMA with a clear recommendation to adequately justify the choice of endpoints and biomarkers predictive of toxicity in animals[26].
Many GT developers now go beyond a minimal biodistribution assessment and screen different product candidate to select those with optimal cell/tissue target­ing in an animal model. In these situations, developers will likely assess not only vector uptake but also gene expression using a variety of tissue imaging, immuno­histochemistry, and in situ hybridization techniques to ensure that not only is the vector delivered to the correct tissue but also that a target efficacy threshold for transgene (TG) expression can be reached.
Non‐clinical biodistribution studies may also inform the design of clinical shed­ding studies. Clinical shedding studies may be used to understand potential envi­ronmental release of a gene‐modified product and potential transmission to others within the environment. Many times, the most practical means to deter­mine whether a GT is shed is by PCR.
As the application of detection methods, such as quantitative PCR, has evolved since the first GT trials to include biodistribution and shedding, so has the ability to detect the location of a TG and its integration sites within a host genome. Southern blot analysis and restriction fragment length polymorphism have been used in early gene mapping studies. Early retroviral insertion site analysis began with the isolation of genomic DNA, digestion by sequence‐specific restriction endonucleases, and linear PCR amplification using a retroviral‐specific primer (LAM‐PCR). The measurement of the clonality of insertion sites is a current FDA recommendation to assess oligoclonality and blood dysplasia, which could be a potential early indication for cancer.
A third important biomarker was the detection of a biological activity of the genetically‐marked cells. Although in the TIL study, demonstrating that the modified T cells had anti‐tumor activity or retained Neo resistance could not be assessed, it was hypothesized that Neo resistance could be used as a selection marker for more potent tumor‐directed lymphocytes in the future. Demonstration of invivo functional activity for the genetically modified cells would have to wait
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for the second NIH‐approved human gene transfer study. Shortly after the 1988 TIL approval, a second protocol was approved by the NIH that involved the gene correction of peripheral blood cells for the treatment of severe combined immune deficiency (SCID) caused by the adenosine deaminase (ADA) deficiency. As before with the gene marked TIL, this approach used retroviral‐mediated gene transfer and careful consideration was given to the risks associated with a geneti­cally modified virus and the generation of RCR. As with the TIL study, biomarkers for RCR indicated no RCR was generated in study subjects and the biodistribution and persistence of genetically modified cells was assessed for up to 10 humans. Interestingly, a biomarker of functional activity of the gene‐modified cells was assessed by measuring ADA activity present in peripheral blood sam­ples[27]. This second study reported results for all three biomarkers and it has set the standard for many years to come. It was not until the mid‐2010s that this set of biomarkers was substantially reevaluated and expanded with the introduction of high‐dose systemic AAV gene therapy and the expansion of LVV gene‐modified cell products.
years in
18.5 Current Expectations forGeneTherapy Biomarkers
Gene therapy has evolved significantly since the early 1990’s, and in vivo gene delivery has moved from a concept to reality. Initial experiments with invivo gene therapy suggested that the immunotoxicity of the delivery system was a significant concern and limited the effectiveness of the gene therapy[28]. Currently, AAV vec­tors are widely used for invivo GT because they are non‐pathogenic in humans, are replication‐defective, mostly non‐integrative (episomal localization), and can transduce a large variety of tissues depending on the selected serotype [29, 30]. Five AAV‐mediated gene therapies are available to patients as of 2023, these include Luxturna®, Zolgensma®, Roctavaria®, Hemgenix® and Elevidys®. Even with this promising set of approvals, treatment‐emergent serious adverse events (TESAEs) have fuel interest in understanding and developing immune toxicity related biomarkers (discussed below under “Immune‐toxicity biomarkers”).
The field has continued to make progress with ex vivo gene‐modified cells as well. It was apparent from early clinical trials that genetically modified cells could be detected for long periods of time (up to 10 years), and in fact tracking the expan­sion and persistence of gene‐marked anti‐CD19‐CAR T cells has correlated with treatment responses and appears to be the best predictor of CAR T efficacy[31]. However, gene‐modified cell products also had the potential to trigger delayed adverse events, including cancer and autoimmunity. The field has moved to “safer” approaches that cause less genotoxicity. Even still, for all gene therapy