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Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5943_Библиотеки_им_академика_М_И_Перельмана

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the same delivery system/procedure as planned for the clinical study should be feasible, which may not always be the case in small animals like mice. The selected species should reflect the patient population regarding disease‐specific physiolog­ical conditions (e.g. blood‐ocular barrier could be impaired in patients), sex, and age and is biologically responsive to the expressed therapeutic transgene[1]. It also needs to be considered that, preexisting immunity as well as immune responses mounted to the administered GT product and its expression products may affect the BD profile of the vector and the transgene expression product(s) and may be associated with adverse events (e.g. liver enzyme increase) [15]. Nonhuman primates may be the best choice to assess immune‐related effects on BD or to evaluate new regulatory elements, whereas disease models in most cases will be only available in mice. In vitro studies comparing transduction efficiency and transgene expression in human and animal target and nontarget cells can support species selection. This is of special importance when new AAV capsids and regulatory elements like promoters are used as components of the GT. In such cases, small stand‐alone BD studies using qualitative or semiquantitative readouts like bioluminescence imaging may be used to confirm the invitro data before pivotal nonclinical studies with larger numbers of animals are performed[1, 13]. Nonclinical or clinical studies performed with the same AAV capsid and/or pro­moter in combination with another transgene as well as literature data may also help to select a biologically relevant species.
An appropriate number of animals should be evaluated at each BD sampling time point. ICH S12 guideline (note 2) recommends the use of a minimum of 5 rodents or 3non‐rodents per sex/group/time point[1, 15]. The total number of animals can be achieved combining the BD data of several studies in case they were conducted using the same material, dose, and route of administration (ROA)[1].
Evaluation of preexisting immunity prior to inclusion in nonclinical studies should be considered to support data interpretation, especially in nonhuman pri­mates and other non‐rodent species [1]. Animals with preexisting immunity should be randomized to the study groups in nonclinical studies. It needs to be considered that exclusion of animals from nonclinical studies based on preexist­ing immunity might impact patient inclusion in clinical trials. Collection of sam­ples for analysis of treatment‐induced immune responses may also be considered to support data interpretation, if necessary[1].
The test article, administered in BD studies as well as the delivery device should be representative of the intended clinical device and clinical material considering important product characteristics, the manufacturing process, and final clinical formulation as changes in the manufacturing process or in the delivery procedure can affect product quality and thus the BD profile of a GT product[12, 1, 8]. For example, product impurities like empty capsids or non‐functionally filled capsids
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can interfere with the uptake of the functional GT product and reduce exposure of target and nontarget tissues to the GT vector and its expression products. Other contaminations like host cell or helper virus‐derived proteins, miss‐folded pro­teins, aggregates, CpG‐rich DNA impurities might induce additional immune reactions to the administered GT product[16].
The administered dose as well as the ROA can affect the BD profile of a GT product, including the cell types that are transduced and the immune response induced against the GT vector and its transgene expression product(s). For exam­ple, a local intrathecal administration of an AAV9 vector having a tissue tropism for CNS, lung, liver, heart, and muscle will result in a different BD profile (e.g. increased number of vector genomes in CNS) when compared to intravenous administration (e.g. majority of the vector DNA in peripheral tissues)[17–19] and even differences in the administered dose could result in different BD patterns. Therefore, BD in nonclinical studies should be assessed for the expected maxi­mum dose level in toxicity studies, which should equate to or exceed the highest anticipated clinical dose level[1].
A vehicle control group, usually the formulation buffer, should also be included in the nonclinical studies. As the capsid is a component of the AAV GT, which can induce an immune response potentially associated with adverse observations, an empty capsid vehicle control is not warranted.
The sample collection time points should sufficiently characterize the BD pro­file of the GT product[1]. The collected samples should cover the maximum expo­sure of the GT product to target and nontarget tissues/biofluids and should sufficiently describe the steady‐state period to estimate persistence. For example, in a study with a duration of 4weeks, samples might be collected at least one and two weeks after administration of the GT product and at the end of the study. In a 13weeks study, the second sample might be taken between week four and eight instead of week two. Early invivo BD studies conducted with the same AAV vector using a reporter gene like luciferase instead of the transgene of interest in combi­nation with bioluminescence imaging can support the selection of appropriate BD sampling time points after GT product administration[1]. To minimize potential cross‐contamination, BD sampling should follow a prespecified process, e.g. start­ing with animals of the vehicle control group followed by the nontarget tissues of dosed animals expected to have the lowest exposure before collecting the tissues targeted by the vector according to its tissue tropism. It is important to document the order of sample collection[1] as this may support data interpretation in case unexpected BD patterns are observed.
The following core panel of tissues/biofluids should be collected: blood, injec­tion site(s), kidney, liver, heart, lung, spleen, brain, spinal cord (cervical, thoracic, and lumbar), gonads, and adrenal gland[1]. Based on additional considerations,
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including GT product properties like vector type/tropism, expression product, ROA as well as disease pathophysiology, existing nonclinical data, and the intended clinical population the core panel may be expanded or even reduced. For example, additional tissues/biofluids may include vitreous fluid, eyes, optic nerve, bone marrow, dorsal root ganglia, cerebrospinal fluid, peripheral nerves, or drain­ing lymph nodes[1]. In cases where systemic exposure is not expected (e.g. sub­retinal administration) collection of a reduced panel of tissues/biofluids might be sufficient. Usually, the vector DNA is measured and, depending on the GT prod­uct, the transgene expression product(s) (RNA, protein) are analyzed in BD sam­ples containing the vector DNA[4, 15].
Animals and humans usually mount an immune response against the viral vec­tor of the GT product and the probability that the human protein expressed from the transgene also induces an immune response is quite high in nonhuman spe­cies. Therefore, sampling of plasma/serum samples for immunogenicity analysis correlating with the BD sampling time points is recommended. In case of unex­pected efficacy and/or safety findings, the immunogenicity data can support data interpretation[1, 5].
Shedding of a GT product depends on the vector’s tissue tropism, the adminis­tered dose, and the ROA. Immune responses mounted against a GT product may increase the clearance of the vector resulting in reduced duration of vector shed­ding. Factors affecting the immune reaction to a GT product are the patient immune status, product design (e.g. CpG content, AAV capsid) as well as product impurities[9]. Recombinants of the replication‐incompetent AAV vector and the replication‐competent helper virus generated during manufacturing may result in a replication‐competent GT product with a prolonged shedding period. Such product‐related impurities should be avoided or eliminated.
Nonclinical shedding evaluation should be performed in an animal species or model that is biologically relevant for the tested GT product[9, 10]. This means that the shedding pattern of the vector DNA should mimic the shedding expected in humans. If the selected animals cannot mount an immune response to the GT product, the observed shedding pattern reflects the maximum duration of vector shedding. The highest dose and same ROA and regimen as planned in the clinical studies should be used and the administered test article as well as the delivery device should be representative of the intended clinical material and device[9, 10]. Nevertheless, the nonclinical shedding profile might not directly correlate with human shedding, reflecting different cellular and tissue sequestration, and will therefore not replace shedding evaluation in clinical studies.
The sampling frequency usually follows practical considerations and depends on each type of secreta and excreta[9, 10]. Sampling should start directly after dosing and may be more frequent in the first weeks (e.g. sampling on day 1, 3, 7,
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10, 14 and then weekly, later monthly depending on study duration and shed material in the samples). Duration of the shedding assessment depends on factors like the natural course of infection of the parental virus, persistence of the vector in target and nontarget tissues, and potential immune responses to the GT prod­uct as well as of the duration of the nonclinical pharmacology or toxicology study. The shedding observation period can be shortened for a particular sample type if multiple consecutive negative samples (e.g. >3 consecutive values below LOD) are observed[9, 10].
Sample types to be analyzed for shedding are selected based on the characteris­tics of the vector, the ROA, and the animal species used in the study and may include urine, feces, saliva, and semen, but also buccal swabs, nasal swabs, bron­chial lavage, tears, and nasopharyngeal fluids as appropriate [20]. Some of the sample types might not be accessible in every species.
For replication‐incompetent viral vectors like AAV vectors, vector shedding is sufficiently assessed detecting the vector DNA (incl. the transgene sequence). An additional infectivity assay, as requested for replication‐competent viruses to detect the intact virus, is not required[9, 10].
BD and shedding assessment can be integrated in Good Laboratory Practice (GLP) compliant toxicology studies and/or in pharmacology studies that might not be conducted under GLP. Even when BD/shedding assessment is integrated in a GLP toxicology study, BD/shedding samples can be analyzed without GLP com­pliance. However, good quality, integrity, and reliability of the generated data must be ensured[1, 5].
Currently, the vector genome DNA and/or the transgene mRNA of a GT prod­uct is measured in tissues/biofluids and secreta/excreta using nucleic acid ampli­fication methods like quantitative PCR (qPCR) and digital droplet PCR (ddPCR)[15]. It is important to assess and document method performance param­eters like sensitivity (LOQ, LOD), specificity, accuracy, reproducibility, and spike recovery during method development. Matrix interferences, expected in secreta/ excreta (e.g. proteases, nucleases, ions, salts, bacterial DNA) need to be considered and addressed during method development and characterization[12, 4, 8–10]. The BD/shedding data usually are given relative to the genomic DNA as vector copy number/μg genomic DNA or in case of some biofluids like CSF or excreta like urine as vector copy number/volume (μL or mL)[1, 4, 8]. In situ hybridization (ISH) may be used to assess the morphology‐based distribution of the DNA/ mRNA to the different cell types within an organ/tissue.
The expressed transgene protein can be quantitatively or qualitatively detected using enzyme‐linked immunosorbent assay (ELISA), LC/MS, flow cytometry, Western blot, or various invivo and exvivo imaging techniques. Immunohistochemistry (IHC) may be used for morphology‐based BD analysis[12].
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Immune responses can be analyzed using ligand binding assays to determine total antibodies or cell‐based assays for determination of transduction inhibiting or neutralizing antibodies[21–24].
The preparation of a separate BD report is of advantage especially in cases where the BD data of two or more studies are combined to generate the full data set. Such a BD report can then be attached to the submission‐relevant pharmacol­ogy and/or toxicology study report(s). The shedding data as well as considerations on risk of transmission to third parties should be provided with the environmental risk assessment[4].
4.1.2.2  Examples
In a GT development program, a liver targeting AAV2/8 vector was designed to express the human arylsulfatase B (ARSB) under the control of the liver‐specific thyroxine‐binding globulin (TBG) promoter to replace the missing enzyme in patients with Mucopolysaccharidosis Type VI[25]. In this program, a very com­prehensive BD (vector DNA, mRNA, protein) and vector shedding evaluation was performed.
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After intravenous administration of 2 × 10
vg copies/kg AAV2/8.TBG.hARSB (corresponding to the expected highest clinical dose) to mice, BD was assessed on day 15 and 180in the following tissues: adrenal gland, aorta, bone marrow, cervi­cal spinal cord, duodenum, brain, forestomach, gallbladder, glandular stomach, thyroid with parathyroid, heart, inguinal lymph node, kidney, liver, left ovary, left testis, left tail epididymis, lung, mammary gland, esophagus, pancreas, pituitary gland, rectum, salivary gland, skin, spleen, sternum, seminal vesicles, and uterus. Additionally, blood, urine, and stool were collected for shedding analysis. Blood samples were collected before and on day 2, 9, 15, 23, 37, and 60 (optional) after administration of the test article, whereas urine and stool were collected before and on day 2, 4, 11, 14, 22, 37 (optional), and 60 (optional) after administration.
Vector DNA was analyzed using a quantitative PCR method with a LOQ of 50
copies/μg gDNA and a LOD of 15
vg copies/μg gDNA for tissues and stool. For
vg
plasma and urine, LOQ and LOD were 30 vg copies/well and 9 vg copies/well, respectively. hASRB RNA expression was analyzed by a quantitative qRT‐PCR method with an LOQ of 625 RNA copies/μg total RNA and an LOD of 188 RNA copies/μg total RNA. The enzymatic activity of the transgene protein was meas­ured using a fluorescence‐labeled substrate directly in homogenized tissue.
The observed vector DNA BD pattern showed the typical liver tropism as
6
expected for AAV8with vector DNA levels of around 10
5
day 15 and between 10
and 106vg copies/μg gDNA on day 180 after test article
vg copies/μg gDNA on
administration. Vector DNA levels detected in the gallbladder and adrenal gland were about 1–2 log scales lower compared to the liver. In all other tissues, the
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vector DNA level were below 104vg copies/μg gDNA on day 15 and 180 after dos­ing. In line with other AAV BD studies in different species, low vector DNA levels above the LOD of the PCR method were observed in the gonads of the mice on day 15 and 180. The liver vector DNA level was quite stable until day 180 after dosing, whereas a general decline from day 15 to day 180was observed in most of the other tissues. In line with other nonclinical studies, a statistically higher vector DNA level was observed in male liver when compared to females on day 15 and 180 after test article administration.
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The highest hARSB mRNA expression with >10
RNA copies/μg total RNA was observed in liver and gallbladder with a slight decrease of expression from day 15 to day 180 after dosing. Interestingly, a quite high ARSB expression was also observed in adrenal gland, stomach, spinal cord, and intestine on day 15 although the liver (hepatocyte) specific TBG promoter was used mainly due to expression of TBG in these tissues. Transgene expression in these tissues mainly disappeared until day 180in alignment with the decline of the vector DNA.
The enzymatic activity of the transgene protein was measured in liver, kidney, and spleen tissue. The highest activity was observed in the liver. hARSB activity was 8‐ and 40‐fold lower in the spleen and kidney, respectively.
Vector shedding was observed until day 11 and day 14 after dosing in urine and stool, respectively. Plasma was cleared on day 23.
As vector DNA was detected in the mice gonads, a further evaluation was per­formed to investigate the risk of germline transmission after administration of the same test article dose to rabbits. In this study, sperm was collected to determine vector shedding in rabbit semen taking the duration of spermatogenesis (42–48days in rabbits) into account. Samples for shedding analysis were taken on day 4, 8, 16, 31, 61, 91, 121, and 150 after dosing. In this study, vector DNA shedding in sperm disappeared after day 8 demonstrating that it is transient in rabbits. In other stud­ies, AAV8 vector shedding in semen was observed up to 13weeks after dosing in rabbits[26]. Shedding was shown to be dose‐dependent and may depend on sev­eral factors like frequency of semen collection.
In another study in NHPs, an scAAV2/8 vector expressing human FIX under a liver‐specific promoter, the vector DNA has cleared from plasma, urine, saliva,
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vg copies/kg[27].
and stool by day 10 after administration of 2
× 10
4.1.3 Clinical Biodistribution and Shedding Studies
forAAV Vectors
Clinical BD data can help understanding the exposure‐efficacy relationship in humans and verify the predictions made based on nonclinical study data.
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Shedding data are required in clinical trials to evaluate the potential risk associated with transmission of a GT product to third parties (e.g. study nurses, physicians, and patient’s family members) and the potential risk to the environment[4, 9, 10].
4.1.3.1  General Considerations inViral Shedding Studies inthe 
Clinical Setting
The same factors as already discussed in the nonclinical section will affect vector shedding in the clinical studies. The design of clinical shedding studies therefore depends on the available information about the biological properties of the paren­tal virus or vector (including tissue tropism, replication‐competency), the admin­istered dose and ROA, and the patient population. The immune status of the patient population and possible immunosuppressive treatments need considera­tion as this might impact vector shedding.
Shedding usually is assessed in initial clinical studies like first‐in‐human stud­ies and can be omitted in later clinical trials provided that sufficient shedding data were collected in good quality in the early clinical studies and a consistent shed­ding pattern was observed in the patients[10]. If the dose, treatment regimen or anything else potentially affecting shedding is modified in later clinical studies additional shedding analysis may be required. Therefore, FDA suggests perform­ing shedding analysis for non‐replication competent vectors like AAVs in phase II instead of phase I studies[9].
Nonclinical data, data from relevant clinical studies (e.g. GT product with same AAV capsid, ROA, dose), and the characteristics of the virus/vector can inform the sampling duration and frequency and can guide the decision on which samples to collect in clinical studies. Sampling will probably be more frequent in the first days or weeks after administration and may be less frequent at later time points (months or years). A potential sampling scheme for a systemically administered AAV GT product could be as follows: weekly up to 16weeks, then monthly up to one year and then every 3months[28]. Sample collection and analysis usually is stopped for a particular sample type when multiple consecutive samples are tested negative (>3 samples below the LOD of the method)[9].
The same technologies and method parameters as described for sample analysis in the nonclinical section do apply to the clinical setting.
When shedding is observed the potential risk for the environment and third parties (e.g. study personnel, family members) associated with transmission of the vector must be evaluated and provided with the environmental risk assess­ment. The risk assessment may consider the properties of the GT product, e.g. natural route of infection, amount of shed material, duration of shedding, patho­genicity of the virus, replication competence, latency, and characteristics of the
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transgene[4]. Although AAV‐based GT products may be associated with a lower risk for third parties as the virus is replication‐deficient and non‐pathogenic, pre­cautions (e.g. contraceptive measures in case the GT product is shed through the seminal fluid) may be warranted[4, 28].
4.1.3.2  Biodistribution Characterization inHuman: Necessity 
and Concerns
In nonclinical studies, efficacy and safety findings can be correlated to the expo­sure with the vector DNA and/or the transgene product(s). In clinical studies, such a correlation is often not possible as the target tissues/organs as well as most nontarget tissues/organs can only be accessed via biopsies. In most cases, such biopsies are not recommended from ethical perspectives. Therefore, the BD data evaluation in clinical studies often is limited to analysis of blood samples (serum/ plasma, cellular fraction).
4.1.3.3  Examples
Viral shedding has been studied in the majority of AAV clinical trials so far[28–31], as requested by the respective guidelines[4, 5, 9, 10].
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After infusion of 6 × 10
vg copies/kg AAV2/8.TBG.hARSB, AAV vector shed­ding was detected in median for 13.8 weeks (13.1–23.8) in serum, 4.5 weeks (3.0–6.8) in saliva, 1.3 weeks (0.6–23.0) in urine, and 13.0weeks (11.2–13.3) in stool above the LOD[31].
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After infusion of 2 × 10
vg copies/kg, corresponding to the dose administered to mice, described in Section 4.1.2.2, AAV vector shedding above the LOD was detected for up to 15weeks in serum compared to 23days in mouse plasma, and for up to 6 or 7weeks in urine or stool compared to 11 and 14days in the corre­sponding mouse matrix[25, 31]. Overall, the shedding time windows observed in humans were not the same as in mice.
Vector DNA was analyzed using a quantitative PCR method with a LOQ of 50 vg copies/μg gDNA and a LOD of 15 vg copies/μg gDNA for tissues and stool. For serum, saliva, and urine, LOQ and LOD were 30 vg copies/well and 9 vg copies/ well, respectively[25, 31].
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After intravenous administration of 2 × 10
vg/kg AAV2‐FIX in a hemophilia B trial, rAAV2‐FIX vector was detectable in urine up to 4weeks and in semen up to 16weeks[29]. In another trial, the vector has cleared from urine, semen, stool,
12
and saliva 6weeks after intravenous administration of 2 × 10
vg/kg scAAV2/8‐ LP1‐hFIXco[30]. Depending on the AAV serotype, the ROA and the administered dose, the shedding pattern as well as the time to clearance may vary.
Analysis of BD usually is limited to analysis of the vector DNA in plasma/serum
and blood cells[28, 30]. In clinical trials in patients with Duchenne muscular
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dystrophy, biopsies of the muscle were taken to analyze at least the distribution of the transgene protein to the target tissue, but no information on vector copy num­bers in muscle tissue was shared[32].
4.1.4  Gaps and Challenges onBiodistribution and 
Shedding Characterization
Analysis of BD is not possible in most clinical studies for ethical reasons and suc­cessful exposure to the target tissue/organ in humans can only be confirmed indi­rectly via expression of the transgene expression product(s) and/or efficacy readouts from the patients.
Especially when modified components like a redesigned tissue‐specific promoter and/or an engineered capsid are used in a GT product, successful transgene expres­sion observed in nonclinical species may not always translate into humans due to potential species differences in capsid tropism and/or regulation of transcription. Therefore, viral transduction efficiency and transgene expression usually is com­pared invitro using cell lines from nonclinical species and human cell lines before nonclinical and clinical studies are performed. However, cell lines are not always predictive for the cells embedded in its tissue/organ invivo. In cases where non­clinical transgene expression does not translate into clinic, complexity of the GT product will make root cause analysis difficult especially when more than one engineered component is used in that GT product. For example, when an engi­neered AAV capsid is used in combination with a redesigned tissue‐specific pro­moter, both elements of the GT product contribute to the BD and transgene expression profile and each of them could be responsible for a lack of treatment response in humans. When BD of the vector DNA as well as the expression of the transgene cannot be assessed in such a case, it is challenging to identify the exact reason for the missing treatment efficacy.
Shedding samples may be collected over a timeframe of more than one year, especially when higher doses of a GT product were administered. As the patients may not always be at the clinical site when samples must be taken, appropriate sample storage and transport to the clinical site must be ensured to generate reli­able shedding data. Such aspects need to be considered early during bioanalytical method development and should be reflected in the analyte stability assessment in the respective matrices. Matrices like stool heavily vary between patients and within an individual patient depending on dietary habits and medication intake. For example, the water content in the stool might be higher after a vegetable meal compared to a meat meal and the foreign DNA content might be heavily reduced after a treatment with antibiotics. Therefore, some authorities may ask to provide the shedding data for stool based on both, copies/μg DNA and copies/mg stool or
 
denote molecular species and processes relevant to pharmacodynamics and efficacy
Transgene
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copies/ml stool. Shedding results in urine also vary depending on the drinking habits of a patient and on the sampling time point, e.g. early in the morning vs. afternoon. Medication intake may also affect urine secretion and thus the shed­ding result. Therefore, varying results in such matrices within or between patients should not be overinterpreted.
4.2 Pharmacokinetic/Pharmacodynamic (PK/PD)
Modeling and Clinical Dose Selection ofGene Therapy
4.2.1  Overview onPK/PD and Dose Selection Strategies  forGene Therapy
The foundation of PK/PD for recombinant AAV is its biological pathway after invivo administration. AAV BD, transfection, and transgene expression processes that are relevant to downstream pathways of pharmacodynamics and potential adverse events are depicted in Figure4.1. Clinical dose selection for recombinant AAV should be based on both safety and pharmacology/efficacy, and consider all applicable processes in Figure4.1, especially those that are particularly relevant for safety and efficacy.
AAV in
non-target
tissues
Biodistribution
bodily
uids
Target tissue
uptake
Secretion
(if applicable)
Clearance
Delivery
AAV
dose
Clearance
denote where potential safety signals or adverse events may occur
AAV in
Circulating
transgene
protein
Figure4.1  Biodistribution and transgene expression pathways of a recombinant AAV
relevant to Its safety and pharmacodynamics/efficacy.
antigens
AAV in
cytoplasm
Intracellular
transgene
protein
Capsid
Entry to nucleus;
Uncoating;
2nd strand synthesis
or annealing
Short- and long-term loss
Translation
Episomal
vector
genomes
Transcription
Degradation
mRNA