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4.1 Biodistribution and Viral Shedding 91
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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 invitro 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 3non‐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 4weeks, 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
13weeks study, the second sample might be taken between week four and eight
instead of week two. Early invivo 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 invivo and exvivo 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.
12
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 180in 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 AAV8with vector DNA levels of around 10
5
day 15 and between 10
and 106vg 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 104vg 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 180was 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.
6
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
180in 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 (42–48days
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 13weeks 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,
12
vg copies/kg[27].
and stool by day 10 after administration of 2
× 10
4.1.3 Clinical Biodistribution and Shedding Studies
forAAV 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 inViral Shedding Studies inthe
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 16weeks, then monthly up to
one year and then every 3months[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 inHuman: 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].
12
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 13.0weeks (11.2–13.3) in
stool above the LOD[31].
12
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 15weeks in serum compared to 23days in mouse plasma, and
for up to 6 or 7weeks in urine or stool compared to 11 and 14days 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].
12
After intravenous administration of 2 × 10
vg/kg AAV2‐FIX in a hemophilia B
trial, rAAV2‐FIX vector was detectable in urine up to 4weeks and in semen up to
16weeks[29]. In another trial, the vector has cleared from urine, semen, stool,
12
and saliva 6weeks 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 onBiodistribution 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 invitro 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 invivo. 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 ofGene Therapy
4.2.1 Overview onPK/PD and Dose Selection Strategies
forGene Therapy
The foundation of PK/PD for recombinant AAV is its biological pathway after
invivo administration. AAV BD, transfection, and transgene expression processes
that are relevant to downstream pathways of pharmacodynamics and potential
adverse events are depicted in Figure4.1. Clinical dose selection for recombinant
AAV should be based on both safety and pharmacology/efficacy, and consider all
applicable processes in Figure4.1, 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
Figure4.1 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
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