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Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5665_Библиотеки_им_академика_М_И_Перельмана

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3.3 Safety and Monitoring Biomarkers and Readouts 71
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PD biomarkers to assess treatment response. Mass spectrometry is a powerful technology to detect the change of these molecules before and after treatment. Histology and imaging techniques to quantify substrate inclusions in tissues have been utilized as surrogate endpoints for efficacy in the clinic. For genome regula­tion platform, mRNA detection of downstream target RNA expression is an important target engagement biomarker for preclinical studies. See Chapter10 for a comprehensive review of different methods for measuring PD biomarkers.
3.3 Safety and Monitoring Biomarkers and Readouts
Like other therapeutic modalities such as biologics and small molecule drug, safety assessment of in vivo GTx products is required at both preclinical and clinical development stages. The nonclinical safety evaluation uses small and/or large ani­mal species to establish proof‐of‐concept and safety profile of the biologically active dose levels and route of administration[23]. The nonclinical safety profile, together with preclinical pharmacology data will inform clinical dose selection and safety monitoring. Clinical data collected over the last 20 years from more than 3000 patients treated with rAAV GTx indicating the therapeutic modality is gener­ally well‐tolerated and efficacious[24]. As a wealth of preclinical and clinical data becoming available in recent years, the field is experiencing emerging knowledge and gaining mechanistic understanding of toxicities related to rAAV‐based GTx.
The treatment‐emergent safety findings with AAV GTx in patents have been associated with hepatotoxicity and thrombotic microangiopathy (TMA), and brain magnetic resonance imaging (MRI) findings of uncertain significance with some treatment‐emergent serious adverse events (TESAEs) resulting in deaths of study subjects. Other toxicities have primarily been reported in animal studies following AAV vector administration, including DRG and peripheral nerve toxici­ties, primarily seen in nonhuman primates[25]. Another potential risk of AAV vectors is oncogenicity due to integration and insertional mutagenesis. For invivo genome editing therapies, engineered nuclease‐induced off‐target editing needs to be assessed.
The contributing factors to these toxicities are quite complex and may involve variables of vector design (capsid serotype and DNA construct), dose level, dose regimen, ROA, product quality, and intrinsic patient, and disease‐specific charac­teristics. For example, rAAV serotypes and promoters have broad tissue tropism and high expression which could affect safety profiles. Higher vector dose levels have been shown to increase risk of toxicity with greater incidences and more serious adverse events (SAEs)[26].
Empty AAV capsids in the drug product are considered an impurity as they do not carry the genomic payload that exerts a therapeutic effect. There has been
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much debate on the effect of empty capsids on clinical outcome. Vector titers are determined using PCR‐based methods of quantifying copy numbers of DNA genome packaged inside the capsid. Empty capsids are thus not accounted for in dose calculation yet add to increased total AAV exposure in patients. AAV8 empty capsids are fully capable of triggering strong B and T cell immune responses in humans which pose a safety concern[27]. It has been shown that AAV8 empty capsids inhibited liver transduction in mice[28]. Conversely, it was proposed that empty capsids may act as decoys for preexisting antibody to AAV to ameliorate transduction inhibition [29]. Overall, low empty capsid content is desirable to increase the safety margin by maximizing the DNA delivered per mass of capsid protein. Finally, a patient’s preexisting immune status to wild‐type AAV, genetic background and disease severity are additional host‐related factors that may acer­bate drug toxicity. For instance, certain lysosomal or metabolic diseases have increased autoimmunity risk[30, 31].
3.3.1  Assessment ofgenotoxicity
Evaluating a therapeutics’ effect on the integrity of the genetic material is an important part of safety assessment. With regards to GTx, the main components assessed to understand genotoxicity risk include: (i) AAV vector‐mediated inser­tional mutagenesis risk; (ii) risk of germline transmission of AAV vector, and (iii) for gene therapies that utilize engineered nuclease to edit the genome, an assessment of off‐target genome editing is necessary. Genome alteration events need to be accurately detected and risks adequately assessed in preclinical and/or clinical development phases of GTx.
3.3.1.1 AAV Integration/Insertional Mutagenesis Risk
AAV genomes mostly persist in host cell nucleus as episomal circular forms[32]. Wild‐type AAVs can integrate, in low frequency, into host genomic DNA, which is mediated by the Rep protein[33]. Recombinant AAVs that lack the Rep/Cap genes are even less efficient in integration. The integration sites of rAAV are largely random though may favor open chromatin regions near actively transcribed genes[34]. Vector design (serotype and promoter) and product quality (impurity) may affect the integration outcomes but factors that influence the risk of onco­genicity remain to be further investigated.
To date, oncogenesis of hepatocellular carcinoma (HCC) associated with rAAV insertional mutagenesis has only been reported in mice[35, 36]. HCC occurs as a background tumor in most laboratory mouse strains and mice have enhanced sen­sitivity to HCC relative to humans, which argues the translatability to human. In hemophilia A dogs treated with rAAV‐FVIII and monitored for up to 10 years, 2 out of 9 dogs showed evidence of clonal expansion of hepatocytes with
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integrated rAAV 4 years post vector administration [19]. Though integrations were near oncogenes or growth control genes, no histological evidence of HCC or other lesions was observed. No clinical oncogenesis has been attributed to AAV integration in patients. Long‐term follow‐up monitoring and detection of rAAV integration should be risk‐based. More detailed information on studies, method­ologies, data analysis, and oncogenesis risk assessment associated with rAAV integration can be found in Chapter13.
3.3.1.2 AAV Germline Transmission Risk
Nonclinical safety assessment of AAV germline transmission risk is generally sup­ported by studies in the literature, a Sponsor’s AAV biodistribution studies in ani­mals evaluating gonad tissue for vector copy number, and on a case‐by‐case basis if additional developmental and reproductive toxicology studies are needed.
3.3.1.3 Off-Target Gene Editing
The field of using engineered nucleases to correct genetic disease is rapidly evolv­ing and expanding. These genome editing components such as ZFN, TALEN, and CRISPR can be designed to efficiently create double‐stranded breaks at the target DNA sites to accomplish the intended genome modification by triggering cell’s intrinsic DNA repair mechanisms. Due to imperfect specificity of the designer nucleases, off‐target cleavage sites have been detected at unintended genomic sites though in lower frequency. These off‐target effects cause short insertions and deletions (indels) and/or large genomic rearrangements, which may lead to onco­genesis. Therefore, clinical applications of genome editing tools require thorough understanding of off‐target activities and risks in both preclinical and clinical studies.
Much progress has been made in defining a workflow that incorporates multi­ple approaches to detect and quantify off‐target sites. Various in silico tools based on computer algorithms have been developed and used to predict and/or rank off‐target sites by scanning the reference human genome. It is important to note that genetic heterogeneity of individual genome variation also needs to be ana­lyzed. In vitro cell‐based and biochemical methodologies such as GUIDE‐seq, oligonucleotide capture, CIRCLE‐seq and SITE‐seq are available to perform unbi­ased, genome‐wide off‐target cleavage site identification. The computational and experimental approaches can be combined to nominate potential off‐target edit­ing sites[37]. After careful ranking of these sites based on frequency, location, oncogenic risk, etc., top sites are further validated in cell type of interest and/or invivo samples using more targeted techniques such as amplicon sequencing. In addition, large genomic alterations of chromosomal deletions, inversions and translocations also need to be evaluated. The standardized and conventional karyotyping methodologies can provide valuable analysis on chromosomal
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abnormalities at the DNA structure level. In recent years, next‐generation sequencing techniques have been developed to identify large gene modifications with greater resolution, sensitivity, and specificity [38]. Comprehensive review can be found in Chapter14.
3.3.2  Biomarkers forImmune-Mediated Toxicity
Host immune response against rAAV GTx represents a major hurdle for human applications. Natural infections of wild‐type AAVs are generally benign and have not been reported to cause any disease or illness[39], therefore, are classified as nonpathogenic. GTx, however, is distinct in introducing non‐replicative recombi­nant virus in a single high‐titer bolus dose via an unnatural ROA. Compared with biologics such as monoclonal antibody therapy, rAAVs illicit more complex immune responses due to the multi‐component nature of the therapeutic modal­ity. rAAV GTx introduces multiple foreign antigens to humans (aside from impuri­ties carried over from the production and purification process): the protein capsid, the DNA genome, and the transgene‐expressed product (protein or RNA). These components are capable of inducing strong innate and adaptive (acquired) immune responses that can affect safety and efficacy. rAAV treatment induces a high level of anti‐AAV neutralizing antibodies in animals and humans, which presents a sig­nificant limitation for vector re‐administration. For this reason, it is more critical to establish a minimum effective dose to benefit patients than other therapeutic modalities. Before rAAV treatment, a significant proportion of human populations have been naturally infected with wild‐type AAVs and acquired adaptive immu­nity, including humoral B cell‐dependent antibody response and T‐cell‐mediated cellular response. The preexisting anti‐AAV neutralizing antibody (NAb) response is more prevalent (as high as 74% prevalence for AAV2[40]) than capsid‐specific CD8+ T‐cell response and the two do not necessarily correlate. Both humoral and cellular immunities to wild‐type AAVs cross‐react with rAAV capsids, conse­quently, this may prevent efficient cell transduction and/or lead to elimination of transduced cells [41], and possibly liver toxicity and TMA. Additionally, TLR‐MyD88 sensing of high CpG content in vector DNA genome induces type 1interferon secretion and subsequent cellular response to capsids, which may lead to hepatotoxicity and loss of transgene expression. Cellular and humoral responses to transgene expressed product could further complicate the outcome or effi­ciency of GTx.
3.3.2.1 Hepatotoxicity
Dose‐dependent liver toxicity following systemic administration of rAAV has been the most common adverse event in clinical trials[42]. This was first reported in a patient receiving AAV2‐ssFIX at 2E12 vector genome per kilogram (vg/kg)
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dose in hemophilia B trial[41]. The clinical presentation was transient serum transaminase (e.g. alanine aminotransferase [ALT] and aspartate aminotrans­ferase [AST]) elevations between 4 and 6 weeks post vector infusion. The peak increase in liver enzymes coincided with decline and eventual loss of factor IX activity. This effect was associated with the appearance of AAV2 capsid‐specific CD8+ T‐cell response[43]. This cytotoxic cellular response can be detected by ELISpot where incubation of PBMCs with capsid peptides stimulates IFN‐γ secretion. The underline mechanism could be that rAAV antigen peptides activate resting memory T cells originated from previous natural infection with wild‐type AAV. There is also recent evidence that this capsid‐specific CD8+ T‐cell response reflects primary immune responses following vector administration [44]. The cytotoxic T‐cell response may destroy transduced hepatocytes and result in loss of transgene expression, thereby limiting long‐term benefits of the therapy. This type of adverse event can be managed by prophylactic or reactive intervention of glu­cocorticoid (prednisolone) or other immune‐modulating agents such as mycophe­nolate mofetil or tacrolimus. Hepatotoxicity is a known safety risk associated with Zolgensma in the treatment of children with spinal muscular atrophy based on data collected during clinical trials and in post‐marketing setting[45]. Elevated aminotransferases as well as acute liver failure warning have been added to Zolgensma label. No loss of SMN transgene expression has been reported possibly owing to the target cells of spinal motor neurons are protected from the immune response.
However, some clinical trial (NCT01687608) subjects who have received a scAAV8 vector expressing the hyperactive hFIX‐R338L variant lost transgene expression even with immune‐modulating agents[18]. The hepatotoxicity, capsid immunity, and loss of transgene expression was possibly attributed to elevated CpG content in the transgene (mostly introduced during codon optimization) stimulated TLR innate immune response which in turn potentiated adaptive response against the capsids. It has also been reported that some transaminase elevations in hemophilia trials had no evidence of capsid‐specific cellular immune response and no loss of transgene expression[46]. Lastly, death due to cholestatic liver failure was reported in pediatric patients with X‐linked myotubular myopa­thy at AAV doses greater than 1E14
Though rAAV‐induced hepatotoxicity presents a complex clinical picture, ALT and AST have been commonly used as a biomarker for reactive steroid treatment intervention. These liver enzymes are not specific to liver injury because skeletal and cardiac muscle injury often trigger ALT and AST elevation, making them unsuitable for detecting the onset of rAAV‐induced liver injury in patients with underlying muscle impairment such as Duchenne muscular dystrophy (DMD). In addition, when the liver enzyme increase is detected, the irreversible elimination of transduced liver cells might have already happened. Sensitive and specific
vg/kg[47].
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biomarkers that can predict or detect early‐onset liver injury are desirable. Serum glutamate dehydrogenase (GLDH) has been established as one of the promising biomarkers out of novel biomarker identification effort for drug‐induced liver injury. It would be worth testing whether GLDH is an early and specific biomarker to detect rAAV hepatotoxicity.
3.3.2.2 Thrombotic Microangiopathy
SAEs of hemolytic anemia, thrombocytopenia, and acute renal injury that are consistent with TMA have been observed for several clinical trials involving high doses of systemically delivered rAAVs. Two independent DMD trials (NCT03368742 and NCT03362502) of rAAV9 expressing a micro‐dystrophin with a muscle‐ specific promoter reported several cases of TMA within two weeks of vector administration at doses greater than 5E13
vg/kg level. Evidence of complement activation has been presented by the sponsors and SAEs were resolved with a C5 complement inhibitor, Ecrulizumab, and other treatments, including glucocorti­coids. Zolgensma also revealed a potential role for complement in rAAV host immune responses that induce TMA[48]. Novartis Safety Data as of 31July 2021 reported 9 cases of TMA among over 1400 patients with one death due to sepsis after TMA recovery. The risk of TMA has been updated in Zolgensma product information. Additional trials that have reported TMA include a liver‐targeted rAAV capsid LK03 to treat Severe Methylmalonic Acidemia at 5E13 (NCT04581785) and a novel capsid 4D‐C102 to treat Fabry disease at 1E13 via IV infusion (NCT04519749).
Complement is a surveillance system of innate immunity that protects the host from pathogens. Classical, alternative, and lectin pathways are three distinct but overlapping proteolytic activation cascades that lead to complement activation. All three pathways converge on C3 convertase, which leads to the formation of membrane attack complex to cause cell lysis. The rapid antibody response against the capsid detected in patients at time of TMA and high complement activation suggest that anti‐AAV and rAAV antigen‐antibody complex activated classical pathway through C1q binding to Fc portion of the antibody complex. Alternative pathway may also be involved as preclinical studies showed that AAV capsids physically interacted with many components of complement pathway and alter­native pathway activation has been linked to thrombocytopenia in NHP[49].
There have been no known preventative measures for TMA. Early detection is primarily based on clinical symptoms and frequent laboratory evaluations that monitor platelet count, renal function, and hemolytic anemia during the first two weeks. Alteration of serum complement components that are indicative of com­plement activation are useful biomarkers to confirm the involvement of comple­ment in TMA. These include consumption of complement factors (C3, C4, Factor B, Factor H, and Factor I) and increase of split products (Bb, C5b‐9) in serum. Complement activation may prime myeloid cells for cytokines secretion and
vg/kg vg/kg
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further amplification of downstream immunity. It would be helpful to test if pro­inflammatory cytokine increase is detectable at time of TMA. Additional adaptive immunity monitoring may aid in the investigation of mechanisms behind AAV‐ induced TMA toxicity.
3.3.2.3 Muscle Toxicity
Serious adverse events involving muscle have been reported by four investigational rAAV gene therapies for the treatment of DMD (NCT05096221, NCT03368742, NCT04281485, and 2020‐002093‐27). These therapies use different AAV serotypes (AAVrh7.4, AAV9, AAV8) to deliver various versions of a micro‐dystrophin transgene driven by different muscle‐specific promoters (MHCK7, CK8, MSP, and Spc5.12) through IV administration. Five participants across studies experienced muscle‐related toxicity between 3 and 7weeks in dose range of 1E13‐2E14 vg/kg. SAEs commonly exhibited extremity and bulbar muscle weakness. Three individ­ual patients experienced severe respiratory muscle compromise and increased car­diac troponin‐I levels. SAEs were resolved following immunosuppressive and other supportive treatments.
All patients affected by the SAEs share strikingly similar genotypes with genomic deletions in the N‐terminal part of the dystrophin gene. The deleted sequences are present in the transgene, rendering the patients being cross‐ reactive immunological material (CRIM)‐negative[50]. T‐cell‐mediated immune response to transgene protein epitopes corresponding to the N‐terminal deleted region was detected by positive ELISpot test in all participants with these skeletal muscle and cardiac SAEs. Anti‐dystrophin antibodies from 1 patient also mapped to N‐terminal deleted epitope[51]. Sponsors are starting to exclude patients with these at‐risk genotypes from clinical trials. This is the first report that associated anti‐transgene immune response to adverse events in humans, highlighting the importance of measuring both humoral and cellular response to transgene in DMD patients receiving rAAV GTx.
3.3.2.4  Immunogenicity Assessment forrAAV Gene Therapy
Immunogenicity to AAV‐based gene therapies is an important assessment to eval­uate efficacy and safety of the drug. Observed adverse events during clinical development have been implicated with host immune responses against AAV gene therapies, resulting in comprehensive evaluation of immunogenicity during nonclinical and clinical development. Consequently, health authorities do see immunogenicity testing as a focus area in the nonclinical and clinical setting. A comprehensive summary of regulatory considerations for rAAV GTx is summa­rized in Yang etal.[52].
Immunogenicity of AAV gene therapies is complex due to the nature of the ther­apy bearing three components: the capsid, the DNA content as well as the invivo generated active drug, paired with risk factors associated with manufacturing,
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treatment‐related risks like dose and ROA[52] and the high prevalence of preexist­ing immunity in humans [40]. Besides the immunogenicity risks listed above, patient‐related risk factors, including age and disease status, need to be considered to complete the picture of all potential immunogenicity risks and are captured in a single repository document, the immunogenicity risk assessment.
For more detailed information on AAVs immune responses in patients, mitiga­tion strategies and bioanalytical assessments please refer to Chapter5. Immune response to transgene‐expressed proteins, including genome editing reagents and methods of detection can be found in Chapter12.
3.3.3  Safety Biomarkers forNonimmune Organ-Specific Toxicity
3.3.3.1 Dorsal Root Ganglia Toxicity
Dorsal root ganglia are bilateral structures that emerge from the dorsal root of the spinal nerves. DRGs are located in the peripheral nervous system outside of the blood‐brain barrier and yet surrounded by a thin layer of CSF and have direct communication with the CSF compartment. DRG neurons relay somatosensory information, including those for pain and temperature from the peripheral nerves to the central nervous system of spinal cord and brain. In addition to primary sensory neuron cell bodies, DRGs also contain satellite glial cells that form a layer around neuronal cell bodies, small blood vessels constituted of endothelial cells and smooth muscle cells, and immune cells of macrophages and lymphocytes. Capillaries in DRG allow blood molecules to enter the DRG and interact with neuronal and nonneuronal cells.
Both systemic IV administration and CSF delivery can result in efficient trans­duction of DRGs. DRG pathology findings of mononuclear cell infiltration and inflammation, neuronal degeneration, and/or satellite glial cell proliferation have been reported for 33NHP studies involving different capsid serotype, promoters, and transgenes[8]. The DRG pathology peaked at approximately 1 month and extended to 5months followed by decrease in severity after 6months post dose. While viral purification methods and sex had no influence, ROA and dose levels are significant contributors to the incidence and severity of the toxicity. CSF local delivery (via intra‐cisterna magna or intrathecal injects) and greater than 1E13 vg/ animal had greater impact than IV administration and lower dose. Similar DRG toxicity findings have been observed in piglet, mouse, and rat studies following rAAV administration[49].
Several lines of evidence suggest that underlying mechanism of the toxicity is cellular stress due to transgene mRNA and/or protein overexpression[14]. Initial experiment of co‐administration of immunosuppressives did not mitigate DRG toxicity. Whether the immune response to rAAV vector or transgene product may
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also play a role remains to be investigated. The clinical relevance of DRG safety findings in preclinical animal studies is currently unclear.
Circulating neurofilament light chain (NFL) in serum/plasma has been identified as a noninvasive safety biomarker for AAV‐induced DRG toxicity in NHP[53]. NFL is a versatile fluid biomarker across diverse neurological diseases. Neurofilaments are abundant scaffolding proteins to support neuronal cell structure. Neurofilament light chain is one of the subunits and primarily expressed in axon of a neuron. Damage to neurons due to injury, disease, or other toxicity release NFL into both CSF and blood compartments. The Quanterix Simoa NFL assay has received Breakthrough Device designation by the FDA as a prognostic aid in relapsing‐remitting multiple sclerosis. Additional clinical validation of NFL as a prognostic biomarker has been reported for Huntington’s[54], Alzheimer’s[55], and spinocerebellar ataxia[56, 57]. NFL is a dif­ferential diagnostic biomarker in Parkinson’s disease that can discriminate between Parkinson and atypical parkinsonian disorders[58]. In addition, NFL is also being used as a surrogate endpoint for efficacy in amyotrophic lateral sclerosis program[59].
3.3.3.2 Other Target Organ Toxicity Biomarkers
Toxicity biomarkers are biomarkers that are capable of detecting liver, kidney, bone marrow, and other target organ injuries. The essential characteristics of these type of biomarker(s) are excellent specificity to tissue damage of the indicated target organ, high sensitivity to low dose toxicity, and early detection or prediction that allows timely intervention and treatment decisions. Additional ideal features include easy accessibility, noninvasive sample acquisition, and reasonably low cost. Consortium efforts involving industry and health authorities for biomarker qualification of organ toxicity have taken a translational approach. Nonclinical safety biomarkers are identified by correlating with histopathology toxicity find­ings in animal species commonly used in safety assessment. For example, cardiac troponins T (cTnT) and I (cTnI) are safety biomarkers to indicate cardiotoxicity in animals and may be used to help estimate nontoxic human dose. The utility of these biomarkers in clinical studies is validated by comparison to the current standard biomarker performance and/or functional readouts. Nephrotoxicity and cardiotoxicity biomarkers have been fully qualified for use in the clinic to monitor drug‐induced injury to kidney and heart, respectively[60]. GTx drug developers can incorporate these biomarker endpoints based on context of use into rAAV clin­ical trials to address patient safety and for decision‐making. New safety biomarkers for liver, skeletal muscle, and vascular injury are in the process of being qualified with the regulatory agencies as drug development tools to support clinical tri­als[60]. These biomarkers, though not yet qualified as drug development tools, can be used as exploratory endpoints in GTx trials for information gathering, or for decision‐making after discussion and gaining the agency’s acceptance.
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3.4   Predictive and Diagnostic Biomarkers forStudy 
Enrollment and Patient Stratification
A predictive biomarker is used to identify individuals who are more likely than similar individuals without the biomarker to experience a favorable or unfavora­ble effect from exposure to a medicinal product. The utility of predictive biomark­ers is not limited to clinical trial settings, where they can be used to either select patients for participation or to stratify patients into biomarker positive and nega­tive groups, as they can also assist in informing patient care decision. Predictive biomarkers are for example protein levels and DNA mutations. They are often chosen initially based on the mechanism of action of the drug and understanding pathophysiology. Usually, predictive biomarkers are evaluated in clinical trials comparing the outcome of individuals with and without the biomarker. There are cases where there is sufficient evidence to use a certain biomarker only in popula­tions enriched for the putative predictive biomarker.
Prognostic biomarkers on the other hand are used to identify the likelihood of a clinical event, disease recurrence, or progression in patients who have the disease or medical condition of interest. They are often used as eligibility criteria in clini­cal trials to identify patients who are more likely to have clinical events or disease progression. Thus, they are widely used as enrichment factors in drug develop­ment. Distinguishing predictive and diagnostic biomarkers can be difficult with some being both, predictive and diagnostic.
In general, all the concepts listed above apply to the clinical development of gene therapies and are very much driven by the program specifics. Especially the patient selection based on the predictive biomarkers of protein expression and/or gene mutation is of importance, given that to date AAV gene therapies are given as a single treatment with a “point of no return” once administered to a patient, reflected in the clinical development starting with an effective and safe dose to be administered into the patients predicted from an extensive preclinical program.
3.4.1 Preexisting Anti-Capsid Antibody
The prevalence of preexisting anti‐AAV capsid antibodies in humans is generally high and can reach up to 80% of the individuals, depending on a variety of factors such as age, geographic location/ethnicity, and serotype[40]. To date, in most of the clinical trials testing an AAV‐based gene therapeutic product, patients bearing preexisting antibodies above a certain threshold (titer) are excluded, to ensure an efficacious therapy and/or to avoid any possible adverse events. Such findings due to preexisting anti‐capsid antibodies, namely efficacy loss and/or adverse events have been reported in nonclinical and clinical trials[9, 41]. As our current under­standing of the effect of preexisting anti‐capsid antibodies is still limited, the