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1.  Absolute Determination of Single-Stranded and Self-Complementary Adeno-Associated Viral Vector Genome Titers by Droplet Digital PCR 
Human Gene Therapy Methods  2013;25(2):115-125.
Abstract
Accurate titration of adeno-associated viral (AAV) vector genome copies is critical for ensuring correct and reproducible dosing in both preclinical and clinical settings. Quantitative PCR (qPCR) is the current method of choice for titrating AAV genomes because of the simplicity, accuracy, and robustness of the assay. However, issues with qPCR-based determination of self-complementary AAV vector genome titers, due to primer–probe exclusion through genome self-annealing or through packaging of prematurely terminated defective interfering (DI) genomes, have been reported. Alternative qPCR, gel-based, or Southern blotting titering methods have been designed to overcome these issues but may represent a backward step from standard qPCR methods in terms of simplicity, robustness, and precision. Droplet digital PCR (ddPCR) is a new PCR technique that directly quantifies DNA copies with an unparalleled degree of precision and without the need for a standard curve or for a high degree of amplification efficiency; all properties that lend themselves to the accurate quantification of both single-stranded and self-complementary AAV genomes. Here we compare a ddPCR-based AAV genome titer assay with a standard and an optimized qPCR assay for the titration of both single-stranded and self-complementary AAV genomes. We demonstrate absolute quantification of single-stranded AAV vector genomes by ddPCR with up to 4-fold increases in titer over a standard qPCR titration but with equivalent readout to an optimized qPCR assay. In the case of self-complementary vectors, ddPCR titers were on average 5-, 1.9-, and 2.3-fold higher than those determined by standard qPCR, optimized qPCR, and agarose gel assays, respectively. Droplet digital PCR-based genome titering was superior to qPCR in terms of both intra- and interassay precision and is more resistant to PCR inhibitors, a desirable feature for in-process monitoring of early-stage vector production and for vector genome biodistribution analysis in inhibitory tissues.
doi:10.1089/hgtb.2013.131
PMCID: PMC3991984  PMID: 24328707
2.  Genetic Diseases, Immunology, Viruses, and Gene Therapy 
Human Gene Therapy  2014;25(4):257-261.
doi:10.1089/hum.2014.2511
PMCID: PMC3996976  PMID: 24754432
3.  Hepatic regulatory T cells and Kupffer cells are crucial mediators of systemic T cell tolerance to antigens targeting murine liver 
Hepatology (Baltimore, Md.)  2009;50(2):612-621.
The mechanisms of tolerance in the liver that limit susceptibility to food allergy and that mediate the acceptance of liver transplants even with a complete MHC mismatch remain poorly defined. Here we report that in a model of liver-directed gene transfer cytotoxic T lymphocyte (CTL) responses to non-self antigens are controlled by hepatic regulatory T cells (Tregs) that secrete the immunosuppressive cytokine interleukin (IL)-10 in response to the antigen. In addition, Kupffer cells (KCs), normally thought to initiate immune responses, are rendered tolerogenic in this context. The depletion of KCs results in a complete abrogation of IL-10 production by hepatic Tregs, indicating an interaction between Tregs and KCs in the induction of tolerance.
Conclusion
Our study suggests that hepatic Tregs together with KCs create a local suppressive microenvironment that prevents the establishment of the CTL response. These mechanisms provide pivotal insights and may prove instrumental in the tolerization toward non-self therapeutic proteins delivered to the liver.
doi:10.1002/hep.23043
PMCID: PMC4380144  PMID: 19575456
Liver tolerance; cytotoxic T lymphocyte suppression; hepatic regulatory T cells; Kupffer cells; interleukin-10
4.  Increased Mucosal CD4+ T Cell Activation in Rhesus Macaques following Vaccination with an Adenoviral Vector 
Journal of Virology  2014;88(15):8468-8478.
ABSTRACT
The possibility that vaccination with adenovirus (AdV) vectors increased mucosal T cell activation remains a central hypothesis to explain the potential enhancement of HIV acquisition within the Step trial. Modeling this within rhesus macaques is complicated because human adenoviruses, including human adenovirus type 5 (HAdV-5), are not endogenous to macaques. Here, we tested whether vaccination with a rhesus macaque-derived adenoviral vector (simian adenovirus 7 [SAdV-7]) enhances mucosal T cell activation within rhesus macaques. Following intramuscular SAdV-7 vaccination, we observed a pronounced increase in SAdV-7-specific CD4+ T cell responses in peripheral blood and, more dramatically, in rectal mucosa tissue. Vaccination also induced a significant increase in the frequency of activated memory CD4+ T cells in SAdV-7- and HAdV-5-vaccinated animals in the rectal mucosa but not in peripheral blood. These fluctuations within the rectal mucosa were also associated with a pronounced decrease in the relative frequency of naive resting CD4+ T cells. Together, these results indicate that peripheral vaccination with an AdV vector can increase the activation of mucosal CD4+ T cells, potentially providing an experimental model to further evaluate the role of host-vector interactions in increased HIV acquisition after AdV vector vaccination.
IMPORTANCE The possibility that vaccination with a human adenovirus 5 vector increased mucosal T cell activation remains a central hypothesis to explain the potential enhancement of human immunodeficiency virus (HIV) acquisition within the Step trial. In this study, we tested whether vaccination with a rhesus macaque-derived adenoviral vector in rhesus macaques enhances mucosal CD4+ T cell activation, the main cell target of simian immunodeficiency virus (SIV)/HIV. The results showed that vaccination with an adenoviral vector indeed increases activation of mucosal CD4+ T cells and potentially increases susceptibility to SIV infection.
doi:10.1128/JVI.03850-13
PMCID: PMC4135938  PMID: 24829340
5.  The First Journal on Human Gene Therapy Celebrates its 25th Anniversary 
Human Gene Therapy  2014;25(1):1-2.
doi:10.1089/hum.2013.2528
PMCID: PMC3900113  PMID: 24444178
6.  Biodistribution of AAV8 Vectors Expressing Human Low-Density Lipoprotein Receptor in a Mouse Model of Homozygous Familial Hypercholesterolemia 
Abstract
Recombinant adeno-associated viral vectors based on serotype 8 (AAV8) transduce liver with superior tropism following intravenous (IV) administration. Previous studies conducted by our lab demonstrated that AAV8-mediated transfer of the human low-density lipoprotein receptor (LDLR) gene driven by a strong liver-specific promoter (thyroxin-binding globulin [TBG]) leads to high level and persistent gene expression in the liver. The approach proved efficacious in reducing plasma cholesterol levels and resulted in the regression of atherosclerotic lesions in a murine model of homozygous familial hypercholesterolemia (hoFH). Prior to advancing this vector, called AAV8.TBG.hLDLR, to the clinic, we set out to investigate vector biodistribution in an hoFH mouse model following IV vector administration to assess the safety profile of this investigational agent. Although AAV genomes were present in all organs at all time points tested (up to 180 days), vector genomes were sequestered mainly in the liver, which contained levels of vector 3 logs higher than that found in other organs. In both sexes, the level of AAV genomes gradually declined and appeared to stabilize 90 days post vector administration in most organs although vector genomes remained high in liver. Vector loads in the circulating blood were high and close to those in liver at the early time point (day 3) but rapidly decreased to a level close to the limit of quantification of the assay. The results of this vector biodistribution study further support a proposed clinical trial to evaluate AAV8 gene therapy for hoFH patients.
doi:10.1089/humc.2013.082
PMCID: PMC4003465  PMID: 24070336
7.  Vector Sequences Are Not Detected in Tumor Tissue from Research Subjects with Ornithine Transcarbamylase Deficiency Who Previously Received Adenovirus Gene Transfer 
Human Gene Therapy  2013;24(9):814-819.
Abstract
A 66-year-old woman heterozygous for a mutation in the ornithine transcarbamylase gene (Otc) participated in a phase I gene therapy trial for OTC deficiency. She received an adenovirus (Ad) vector expressing the functional OTC gene by intraportal perfusion. Fourteen years later she developed and subsequently died of hepatocellular carcinoma. A second subject, a 45-year-old woman, enrolled in the same trial presented with colon cancer 15 years later. We sought to investigate a possible association between the development of a tumor and prior adenoviral gene transfer in these two subjects. We developed and validated a sensitive nested polymerase chain reaction assay for recovering recombinant Ad sequences from host tissues. Using this method, we could not detect any Ad vector DNA in either tumor or normal tissue from the two patients. Our results are informative in ruling out the possibility that the adenoviral vector might have contributed to the development of cancer in those two subjects.
Zhong and colleagues use a nested PCR assay to examine whether adenoviral gene transfer led to the development of cancer in two clinical research subjects with ornithine transcarbamylase deficiency. Using this approach, they were unable to detect adenovirus vector genomes in normal or tumor tissues from the subjects more than a decade after vector infusion. These results suggest that adenoviral gene transfer was an unlikely contributor to the colon cancer or hepatocellular carcinoma observed in the two research subjects.
doi:10.1089/hum.2013.118
PMCID: PMC3768231  PMID: 24010702
8.  Enhancing the Utility of Adeno-Associated Virus Gene Transfer through Inducible Tissue-Specific Expression 
Human Gene Therapy Methods  2013;24(4):270-278.
Abstract
The ability to regulate both the timing and specificity of gene expression mediated by viral vectors will be important in maximizing its utility. We describe the development of an adeno-associated virus (AAV)-based vector with tissue-specific gene regulation, using the ARGENT dimerizer-inducible system. This two-vector system based on AAV serotype 9 consists of one vector encoding a combination of reporter genes from which expression is directed by a ubiquitous, inducible promoter and a second vector encoding transcription factor domains under the control of either a heart- or liver-specific promoter, which are activated with a small molecule. Administration of the vectors via either systemic or intrapericardial injection demonstrated that the vector system is capable of mediating gene expression that is tissue specific, regulatable, and reproducible over induction cycles. Somatic gene transfer in vivo is being considered in therapeutic applications, although its most substantial value will be in basic applications such as target validation and development of animal models.
Chen and colleagues describe the development of an AAV-based vector with tissue-specific gene regulation, using the ARGENT dimerizer-inducible system. They demonstrate that administration of these vectors via either systemic or intrapericardial injection leads to gene expression that is tissue specific, regulatable, and reproducible over induction cycles.
doi:10.1089/hgtb.2012.129
PMCID: PMC3753727  PMID: 23895325
10.  Lessons Learned from the Clinical Development and Market Authorization of Glybera 
Bryant and colleagues follow the development of Glybera (alipogene tiparvovec), the first gene therapy product approved in the European Union, from early preclinical studies through the approval process. They review key data from human and animal studies with an emphasis on issues that will be critical to other gene therapy products. The article concludes with an analysis of the complex review process that eventually led to Glybera's approval.
doi:10.1089/humc.2013.087
PMCID: PMC3992977  PMID: 23808604
11.  Hypothesis of Long-Term Outcome after Coronary Revascularization in Japanese Patients Compared to Multiethnic Groups in the US 
PLoS ONE  2015;10(5):e0128252.
Background
Ethnicity has a significant impact on coronary artery disease (CAD). This study investigated the long-term outcomes of Japanese patients undergoing revascularization compared with US patients belonging to multiple ethnic groups.
Methods and Results
We evaluated clinical outcomes, based on ethnicity, of patients included in the Coronary Revascularization Demonstrating Outcome (CREDO-Kyoto) and the Texas (US) Heart Institute Research Database (THIRDBase) registries. For the analysis, we included 8871 patients from the CREDO-Kyoto registry (median follow-up period [FU], 3.5 years; interquartile range [IQR], 2.6–4.3) and 6717 patients from the THIRDBase registry (FU, 5.2 years; IQR, 3.8–6.5) who underwent percutaneous coronary intervention or bypass surgery. Cox proportional hazard models were constructed to compare the adjusted long-term outcomes for each ethnic group. A total of 8871 Japanese, 5170 Caucasians, 648 African-Americans, 817 Hispanics, and 82 Asian-Americans were identified. When adjusted, Japanese patients had significantly better outcomes than US patients, classified by ethnicity (Caucasians: hazard ratio [HR], 1.56; 95% confidence interval [CI], 1.35–1.79; Hispanics: HR, 1.53; 95% CI, 1.22–1.93; African-Americans: HR, 2.03; 95% CI, 1.62–2.56), except for Asian-Americans (HR, 0.84; 95% CI. 0.38–1.89) who had outcomes similar to Japanese patients.
Conclusion
Our findings indicate better survival outcomes in re-vascularized Japanese CAD patients compared to major ethnic groups in the US, including Caucasian, Hispanic, and African-American CAD patients. The characteristics and outcomes of Japanese CAD patients were similar to those of Asian-Americans, despite the sample size limitations in the US dataset.
doi:10.1371/journal.pone.0128252
PMCID: PMC4449105  PMID: 26023784
12.  The structure of AAVrh32.33, a Novel Gene Delivery Vector 
Journal of structural biology  2014;186(2):308-317.
The Adeno-Associated viruses (AAVs) are being developed as gene delivery vectors for therapeutic clinical applications. However, the host antibody immune response directed against their capsid, prevalent in ~40–70% of the general population, depending on serotype, negatively impacts efficacy. AAVrh32.33, a novel vector developed from rhesus macaques isolates, has significantly lower seroprevalence in human populations compared to AAV2 and AAV8, which are both in clinical use. To better understand the capsid determinants of this differential immune response to AAVrh32.33, its structure was determined by X-ray crystallography to 3.5 Å resolution. The capsid viral protein (VP) structure conserves the eight-stranded β-barrel core and αA helix reported for other parvoviruses and the distinct capsid surface topology of the AAVs: a depression at the icosahedral two-fold axis, three protrusions surrounding the three-fold axis, and a depression surround a cylindrical channel at the five-fold axis. A comparison to AAV2, AAV4, and AAV8, to which AAVrh32.33 shares ~61%, ~81%, and ~63% identity, respectively, identified differences in previously defined AAV VP structurally variable regions (VR-1 to VR-IX) which function as receptor attachment, transduction efficiency, and/or antigenic determinants. This structure thus provides a 3D platform for capsid engineering in ongoing efforts to develop AAVrh32.33, as well as other AAV serotypes, for tissue targeted gene-therapy applications with vectors that can evade pre-existing antibody responses against the capsid. These features are required for full clinical realization of the promising AAV gene delivery system.
doi:10.1016/j.jsb.2014.03.020
PMCID: PMC4085184  PMID: 24704217
AAVrh32.33; X-ray crystallography; Parvovirus; Gene therapy; Adeno-associated virus; Virus capsid structure
13.  Adeno-Associated Virus 9-Mediated Airway Expression of Antibody Protects Old and Immunodeficient Mice against Influenza Virus 
Clinical and Vaccine Immunology : CVI  2014;21(11):1528-1533.
Influenza causes serious and sometimes fatal disease in individuals at risk due to advanced age or immunodeficiencies. Despite progress in the development of seasonal influenza vaccines, vaccine efficacy in elderly and immunocompromised individuals remains low. We recently developed a passive immunization strategy using an adeno-associated virus (AAV) vector to deliver a neutralizing anti-influenza antibody at the site of infection, the nasal airways. Here we show that young, old, and immunodeficient (severe combined immunodeficient [SCID]) mice that were treated intranasally with AAV9 vector expressing a modified version of the broadly neutralizing anti-influenza antibody FI6 were protected and exhibited no signs of disease following an intranasal challenge with the mouse-adapted H1N1 influenza strain A/Puerto Rico/8/1934(H1N1) (PR8) (Mt. Sinai strain). Nonvaccinated mice succumbed to the PR8 challenge due to severe weight loss. We propose that airway-directed AAV9 passive immunization against airborne infectious agents may be beneficial in elderly and immunocompromised patients, for whom there still exists an unmet need for effective vaccination against influenza.
doi:10.1128/CVI.00572-14
PMCID: PMC4248762  PMID: 25209558
14.  Mapping the Structural Determinants Responsible for Enhanced T Cell Activation to the Immunogenic Adeno-Associated Virus Capsid from Isolate Rhesus 32.33 
Journal of Virology  2013;87(17):9473-9485.
Avoiding activation of immunity to vector-encoded proteins is critical to the safe and effective use of adeno-associated viral (AAV) vectors for gene therapy. While commonly used serotypes, such as AAV serotypes 1, 2, 7, 8, and 9, are often associated with minimal and/or dysfunctional CD8+ T cell responses in mice, the threshold for immune activation appears to be lower in higher-order species. We have modeled this discrepancy within the mouse by identifying two capsid variants with differential immune activation profiles: AAV serotype 8 (AAV8) and a hybrid between natural rhesus isolates AAVrh32 and AAVrh33 (AAVrh32.33). Here, we aimed to characterize the structural determinants of the AAVrh32.33 capsid that augment cellular immunity to vector-encoded proteins or those of AAV8 that may induce tolerance. We hypothesized that the structural domain responsible for differential immune activation could be mapped to surface-exposed regions of the capsid, such as hypervariable regions (HVRs) I to IX of VP3. To test this, a series of hybrid AAV capsids was constructed by swapping domains between AAV8 and AAVrh32.33. By comparing their ability to generate transgene-specific T cells in vivo versus the stability of transgene expression in the muscle, we confirmed that the functional domain lies within the VP3 portion of the capsid. Our studies were able to exclude the regions of VP3 which are not sufficient for augmenting the cellular immune response, notably, HVRs I, II, and V. We have also identified HVR IV as a region of interest in conferring the efficiency and stability of muscle transduction to AAVrh32.33.
doi:10.1128/JVI.00596-13
PMCID: PMC3754105  PMID: 23720715
15.  An AAV Vector-Mediated Gene Delivery Approach Facilitates Reconstitution of Functional Human CD8+ T Cells in Mice 
PLoS ONE  2014;9(2):e88205.
In the present study, a novel adeno-associated virus (AAV) vector-mediated gene delivery approach was taken to improve the reconstitution of functional CD8+ T cells in humanized mice, thereby mimicking the human immune system (HIS). Human genes encoding HLA-A2 and selected human cytokines (A2/hucytokines) were introduced to an immune-deficient mouse model [NOD/SCID/IL2rγnull (NSG) mice] using AAV serotype 9 (AAV9) vectors, followed by transplantation of human hematopoietic stem cells. NSG mice transduced with AAV9 encoding A2/hucytokines resulted in higher levels of reconstitution of human CD45+ cells compared to NSG mice transduced with AAV9 encoding HLA-A2 alone or HLA-A2-transgenic NSG mice. Furthermore, this group of HIS mice also mounted the highest level of antigen-specific A2-restricted human CD8+ T-cell response upon vaccination with recombinant adenoviruses expressing human malaria and HIV antigens. Finally, the human CD8+ T-cell response induced in human malaria vaccine-immunized HIS mice was shown to be functional by displaying cytotoxic activity against hepatocytes that express the human malaria antigen in the context of A2 molecules. Taken together, our data show that AAV vector-mediated gene delivery is a simple and efficient method to transfer multiple human genes to immune-deficient mice, thus facilitating successful reconstitution of HIS in mice. The HIS mice generated in this study should ultimately allow us to swiftly evaluate the T-cell immunogenicity of various human vaccine candidates in a pre-clinical setting.
doi:10.1371/journal.pone.0088205
PMCID: PMC3916402  PMID: 24516613
16.  Adeno-Associated Virus Serotype 8 Gene Therapy Leads to Significant Lowering of Plasma Cholesterol Levels in Humanized Mouse Models of Homozygous and Heterozygous Familial Hypercholesterolemia 
Human Gene Therapy  2012;24(1):19-26.
Abstract
Familial hypercholesterolemia (FH) is a life-threatening genetic disease caused by mutations in the gene encoding low-density lipoprotein receptor (LDLR). As a bridge to clinical trials, we generated a “humanized” mouse model lacking LDLR and apolipoprotein B (ApoB) mRNA editing catalytic polypeptide-1 (APOBEC-1) expression and expressing a human ApoB100 transgene in order to permit more authentic simulation of in vivo interactions between the clinical transgene product, human LDLR (hLDLR), and its endogenous ligand, human ApoB100. On a chow diet, the humanized LDLR-deficient mice have substantial hypercholesterolemia and a lipoprotein phenotype more closely resembling human homozygous FH (hoFH) than in previous mouse models of FH. On injection of an adeno-associated virus serotype 8 (AAV8) vector encoding the human LDLR cDNA, significant correction of hypercholesterolemia was realized at doses as low as 1.5×1011 genome copies (GC)/kg. Given that some patients with heterozygous FH (heFH) cannot be adequately treated with current therapy, we then extended our studies to similarly “humanized” mice that were heterozygous for LDLR deficiency, and that have a lipoprotein phenotype resembling heterozygous FH. Injection of AAV8-hLDLR brought about significant reduction in total and LDL cholesterol at doses as low as 5×1011 GC/kg. Collectively, these data demonstrate the safety and efficacy of the liver-specific AAV8-hLDLR vector in the treatment of humanized mice modeling both hoFH and heFH.
Kassim and colleagues demonstrate that injection of an adeno-associated virus serotype 8 (AAV8) vector encoding the human low-density lipoprotein receptor (LDLR) cDNA results in significant correction of hypercholesterolemia in humanized mouse models of homozygous and heterozygous familial hypercholesterolemia (FH).
doi:10.1089/hum.2012.108
PMCID: PMC3555111  PMID: 22985273
17.  Human Treg responses allow sustained recombinant adeno-associated virus–mediated transgene expression 
The Journal of Clinical Investigation  2013;123(12):5310-5318.
Recombinant adeno-associated virus (rAAV) vectors have shown promise for the treatment of several diseases; however, immune-mediated elimination of transduced cells has been suggested to limit and account for a loss of efficacy. To determine whether rAAV vector expression can persist long term, we administered rAAV vectors expressing normal, M-type α-1 antitrypsin (M-AAT) to AAT-deficient subjects at various doses by multiple i.m. injections. M-specific AAT expression was observed in all subjects in a dose-dependent manner and was sustained for more than 1 year in the absence of immune suppression. Muscle biopsies at 1 year had sustained AAT expression and a reduction of inflammatory cells compared with 3 month biopsies. Deep sequencing of the TCR Vβ region from muscle biopsies demonstrated a limited number of T cell clones that emerged at 3 months after vector administration and persisted for 1 year. In situ immunophenotyping revealed a substantial Treg population in muscle biopsy samples containing AAT-expressing myofibers. Approximately 10% of all T cells in muscle were natural Tregs, which were activated in response to AAV capsid. These results suggest that i.m. delivery of rAAV type 1–AAT (rAAV1-AAT) induces a T regulatory response that allows ongoing transgene expression and indicates that immunomodulatory treatments may not be necessary for rAAV-mediated gene therapy.
doi:10.1172/JCI70314
PMCID: PMC3859421  PMID: 24231351
18.  Muscle-directed Gene Therapy for Hemophilia B with More Efficient and Less Immunogenic AAV Vectors 
Summary
Background
Adeno-associated viral vector (AAV)-mediated and muscle-directed gene therapy is a safe and noninvasive approach to treat hemophilia B and other genetic diseases. However, low efficiency of transduction, inhibitor formation and high prevalence of pre-existing immunity to the AAV capsid in humans remain as main challenges for AAV2-based vectors using this strategy. Vectors packaged with AAV7, 8, and 9 serotypes have improved gene transfer efficiencies and may provide potential alternatives to overcome these problems.
Objective
To compare the long-term expression of canine factor IX (cFIX) levels and anti-cFIX antibody responses following intramuscular injection of vectors packaged with AAV1, 2, 5, 7, 8, and 9 capsid in immunocompetent hemophilia B mice.
Methods and results
Highest expression was detected in mice injected with AAV2/8 vector (28% of normal), followed by AAV2/9 (15%) and AAV2/7 (10%). cFIX expression by AAV2/1 only ranged from 0–5% of normal levels. High incidences of anti-cFIX inhibitor (IgG) were detected in mice injected with AAV2 and 2/5 vectors, followed by AAV2/1. None of the mice treated with AAV2/7, 2/8, and 2/9 developed inhibitors or capsid T cells.
Conclusions
AAV7, 8, and 9 are more efficient and safer vectors for muscle-directed gene therapy with high levels of transgene expression and absence of inhibitor formation. The absence of antibody response to transgene by AAV7, 8, and 9 is independent of vector dose but may be due to the fact that these three serotypes are associated with high level distribution to, and transduction of, hepatocytes following i.m. injection.
doi:10.1111/j.1538-7836.2011.04491.x
PMCID: PMC3393098  PMID: 21883883
Hemophilia B; gene therapy; adeno-associated viruses (AAV); factor IX; muscle
19.  CpG-depleted adeno-associated virus vectors evade immune detection 
The Journal of Clinical Investigation  2013;123(7):2994-3001.
Due to their efficient transduction potential, adeno-associated virus (AAV) vectors are leading candidates for gene therapy in skeletal muscle diseases. However, immune responses toward the vector or transgene product have been observed in preclinical and clinical studies. TLR9 has been implicated in promoting AAV-directed immune responses, but vectors have not been developed to circumvent this barrier. To assess the requirement of TLR9 in promoting immunity toward AAV-associated antigens following skeletal muscle gene transfer in mice, we compared immunological responses in WT and Tlr9-deficient mice that received an AAV vector with an immunogenic capsid, AAVrh32.33. In Tlr9-deficient mice, IFN-γ T cell responses toward capsid and transgene antigen were suppressed, resulting in minimal cellular infiltrate and stable transgene expression in target muscles. These findings suggest that AAV-directed immune responses may be circumvented by depleting the ligand for TLR9 (CpG sequences) from the vector genome. Indeed, we found that CpG-depleted AAVrh32.33 vectors could establish persistent transgene expression, evade immunity, and minimize infiltration of effector cells. Thus, CpG-depleted AAV vectors could improve outcome of clinical trials of gene therapy for skeletal muscle disease.
doi:10.1172/JCI68205
PMCID: PMC3696560  PMID: 23778142
20.  Widespread gene transfer in the central nervous system of cynomolgus macaques following delivery of AAV9 into the cisterna magna 
Adeno-associated virus serotype 9 (AAV9) vectors have recently been shown to transduce cells throughout the central nervous system of nonhuman primates when injected into the cerebrospinal fluid (CSF), a finding which could lead to a minimally invasive approach to treat genetic and acquired diseases affecting the entire CNS. We characterized the transduction efficiency of two routes of vector administration into the CSF of cynomolgus macaques—lumbar puncture, which is typically used in clinical practice, and suboccipital puncture, which is more commonly used in veterinary medicine. We found that delivery of vector into the cisterna magna via suboccipital puncture is up to 100-fold more efficient for achieving gene transfer to the brain. In addition, we evaluated the inflammatory response to AAV9-mediated GFP expression in the nonhuman primate CNS. We found that while CSF lymphocyte counts increased following gene transfer, there were no clinical or histological signs of immune toxicity. Together these data indicate that delivery of AAV9 into the cisterna magna is an effective method for achieving gene transfer in the CNS, and suggest that adapting this uncommon injection method for human trials could vastly increase the efficiency of gene delivery.
doi:10.1038/mtm.2014.51
PMCID: PMC4448732  PMID: 26052519
21.  Hepatic Gene Transfer in Neonatal Mice by Adeno-Associated Virus Serotype 8 Vector 
Human Gene Therapy  2011;23(5):533-539.
Abstract
For genetic diseases that manifest at a young age with irreversible consequences, early treatment is critical and essential. Neonatal gene therapy has the advantages of achieving therapeutic effects before disease manifestation, a low vector requirement and high vector-to-cell ratio, and a relatively immature immune system. Therapeutic effects or long-term rescue of neonatal lethality have been demonstrated in several animal models. However, vigorous cell proliferation in the newborn stage is a significant challenge for nonintegrating vectors, such as adeno-associated viral (AAV) vector. Slightly delaying the injection age, and readministration at a later time, are two of the alternative strategies to solve this problem. In this study, we demonstrated robust and efficient hepatic gene transfer by self-complementary AAV8 vector in neonatal mice. However, transduction quickly decreased over a few weeks because of vector dilution caused by fast proliferation. Delaying the injection age improved sustained expression, although it also increased neutralizing antibody (NAb) responses to AAV capsid. This approach can be used to treat genetic diseases with slow progression. For genetic diseases with early onset and severe consequences, early treatment is essential. A second injection of vector of a different serotype at a later time may overcome preexisting NAb and achieve sustained therapeutic effects.
Wang and colleagues conduct a series of preclinical animal studies examining the kinetics of AAV gene transfer. They demonstrate that self-complementary AAV8 results in robust and efficient hepatic gene transfer in neonatal mice. Yet, this transduction quickly decreases over a few weeks because of vector dilution caused by rapid cell proliferation in the liver of growing young mice.
doi:10.1089/hum.2011.183
PMCID: PMC3360497  PMID: 22098408
22.  The Black Canyon Forecast Station: Experiences And Lessons Learned 
Objective
To evaluate the sociological effect on indigenous biological event signature recognition and community resilience due to the operational activities of an infectious disease forecast station.
Introduction
The nation’s first operational infectious disease forecast station, modeled after warning protocols developed in the meteorology community, was activated in 2011. The approach was originally pioneered in Haiti following the 2010 earthquake.
Methods
We assembled global event signature and forecast libraries that reflected locally diagnosed infectious disease activity and infrastructure impact in a rural community from a public health, veterinary, and human clinical medicine perspective. The deployment site is home to a variety of infectious disease including hantavirus, plague, tularemia, and West Nile in the context of high wildlife-livestock-human interfacing. Information derived from the issuance of forecasts coupled to situational awareness was shared with the public, local officials, public health officers, veterinarians, healthcare providers, and patients through various social media methods.
Results
Provision of 30-60-90 day forecasts for routine and non-routine endemic infectious disease activity and impact facilitated better coordination of public health messaging and daily conversation with patients in the inpatient and outpatient settings. The signature of an unusual, infrastructure-disruptive outbreak of metapneumovirus and respiratory syncytial virus was recognized and communicated with enough time to activate effective clinical mitigation protocols. Cost estimates demonstrated financial benefit at a local level to anticipating surges of infectious disease activity with enough time to mitigate patient demand. Community-wide engagement with infectious disease forecasts and live event advisories included the promotion of proactive infection control and public health surveillance and response, healthcare provider recognition of non-routine infectious disease, clinical sampling and diagnostic testing protocols, clinician and patient education, and synchronization of proactive disease reporting both in the routine daily clinical setting and in times of crisis. Collateral benefit of consistent messaging delivered to the public by the participating entities was noted. Community awareness of the repertoire of indigenous infectious disease activity was expanded beyond the official public health notification list. Neither issuance of infectious disease forecasts nor advisories issued during crises triggered an influx of anxious well phone calls or visits to the medical system that was deemed operationally relevant.
Conclusions
Activation of a local infectious disease forecast station modeled after a local weather station promotes routine communication of a broader array of infectious disease activity than that monitored by public health; facilitates proactive, cost effective healthcare; and enabled recognition of unusual, disruptive infectious activity with enough time to enable mitigation of clinical, infrastructure, and financial impact to the community. Routine communication of comprehensive infectious disease forecast and situational awareness information promotes community adaptive fitness to a wide variety of infectious hazards. The results suggest it is possible to transform the traditional public health model of data collection and analysis to one of transparent and open data availability to support innovative reduction in morbidity and mortality.
PMCID: PMC3692870
biosurveillance; forecast; meteorology
23.  Intramuscular Injection of AAV8 in Mice and Macaques Is Associated with Substantial Hepatic Targeting and Transgene Expression 
PLoS ONE  2014;9(11):e112268.
Intramuscular (IM) administration of adeno-associated viral (AAV) vectors has entered the early stages of clinical development with some success, including the first approved gene therapy product in the West called Glybera. In preparation for broader clinical development of IM AAV vector gene therapy, we conducted detailed pre-clinical studies in mice and macaques evaluating aspects of delivery that could affect performance. We found that following IM administration of AAV8 vectors in mice, a portion of the vector reached the liver and hepatic gene expression contributed significantly to total expression of secreted transgenes. The contribution from liver could be controlled by altering injection volume and by the use of traditional (promoter) and non-traditional (tissue-specific microRNA target sites) expression control elements. Hepatic distribution of vector following IM injection was also noted in rhesus macaques. These pre-clinical data on AAV delivery should inform safe and efficient development of future AAV products.
doi:10.1371/journal.pone.0112268
PMCID: PMC4230988  PMID: 25393537
24.  In Memory of Sonia Skarlatos, PhD (1953–2013) 
Human Gene Therapy  2013;24(11):895.
doi:10.1089/hum.2013.2519
PMCID: PMC3814981  PMID: 24164235
25.  Analyzing the cancer methylome through targeted bisulfite sequencing 
Cancer letters  2012;340(2):10.1016/j.canlet.2012.10.040.
Bisulfite conversion of genomic DNA combined with next-generation sequencing (NGS) has become a very effective approach for mapping the whole-genome and sub-genome wide DNA methylation landscapes. However, whole methylome shotgun bisulfite sequencing is still expensive and not suitable for analyzing large numbers of human cancer specimens. Recent advances in the development of targeted bisulfite sequencing approaches offer several attractive alternatives. The characteristics and applications of these methods are discussed in this review article. In addition, the bioinformatic tools that can be used for sequence capture probe design as well as downstream sequence analyses are also addressed.
doi:10.1016/j.canlet.2012.10.040
PMCID: PMC3616138  PMID: 23200671

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