Compact zinc finger architecture utilizing toxin-derived cytidine deaminases for highly efficient base editing in human cells

Nucleobase editors represent an emerging technology that enables precise single-base edits to the genomes of eukaryotic cells. Most nucleobase editors use deaminase domains that act upon single-stranded DNA and require RNA-guided proteins such as Cas9 to unwind the DNA prior to editing. However, the most recent class of base editors utilizes a deaminase domain, DddAtox, that can act upon double-stranded DNA. Here, we target DddAtox fragments and a FokI-based nickase to the human CIITA gene by fusing these domains to arrays of engineered zinc fingers (ZFs). We also identify a broad variety of Toxin-Derived Deaminases (TDDs) orthologous to DddAtox that allow us to fine-tune properties such as targeting density and specificity. TDD-derived ZF base editors enable up to 73% base editing in T cells with good cell viability and favorable specificity.

Dosimetric Impact of Seed Segmentation in GammaTile Surgically Targeted Radiation Therapy for Gliomas and Brain Metastases Cases

PURPOSE/OBJECTIVE(S)

To assess the variability of dose reporting variability due to uncertainty in segmentation of Cs-131 seeds in GammaTile therapy for gliomas and brain metastases.

MATERIALS/METHODS

Ten patients with either glioma or brain metastases had 4-11 GammaTiles placed along resection bed during craniotomy. A dose of 60 Gy is prescribed to 5 mm depth. Each GammaTile has four Cs-131 seeds imbedded in a biodegradable collagen sponge. GammaTile Post-Op workflow in MIM Symphony software is used for post-implant dose evaluation and reporting. This workflow requires a post-surgery CT to identify seeds, and a post-surgery MR for residual disease and OAR contours. Seeds are segmented using a threshold tool. Threshold levels may change depending on the CT used, thus users need to manually change the HU threshold value in each data set. Since GammaTiles are lined along the resection bed, PTVs are generated automatically by adding 8 mm expansion on the seed contours and later combined with residual disease contours. We simulate the seed contour uncertainty by applying -0.5 mm, -1.0 mm, +0.5 mm & +1.0 mm concentric margins to the current seed contours to create 4 new seed contours per patient. New PTVs are generated by adding 8 mm expansion on the new seed contours combined with residual disease contours. PTV volume, PTV volume receiving 100% and 150% of prescription dose (V100, V150), and percentage of the prescription dose received by 90% of the PTV (D90) are calculated to evaluate dose reporting variability due to seed segmentation uncertainty.

RESULTS

Mean PTV volume decreases by 8.4 cc & 10.2 cc for PTVs generated from seed contours with -0.5 mm & -1.0 mm margin, respectively, and increases by 5.8 cc & 8.2 cc, respectively, when +0.5 mm & +1 mm margins are applied to the original seed contours. We observe up to 10% change in V100 due to seed segmentation uncertainty. Mean V100 increases by 4.0% (range: 0.2% - 8.9%) & 4.9% (range: 0.5% - 11.0%) for cases with -0.5 m & -1.0 mm seed margin, respectively, and reduces by 4.2% (range: 0.5% - 6.7%) & 5.9% (range: 0.6% - 10.4%) for cases with +0.5 mm and +1.0 mm seed margin, respectively. Mean D90 increases by 7.7% (range: 4.0% - 12.6%) & 9.9% (range: 4.0% - 17.4%) for cases with -0.5 m & -1.0 mm seed margin, respectively, and reduces by 5.5% (range: 3.6% - 7.8%) & 7.4% (range: 5.2% - 9.6%) for cases with +0.5 mm and +1.0 mm seed margin, respectively. We also observe up to 8.0% changes in mean V150 when margins are applied to the seed contours.

CONCLUSION

Our results show significant impact of seed segmentation uncertainty on dose reporting in GammaTile therapy. Variability in dose reporting parameters highlight the need for a more standardized and automated approach to seed segmentation to ensure consistent and accurate dose reporting. The current manual threshold adjustment method is subject to user dependence and therefore unreliable. Development of a more robust tool could help to minimize variability and improve reliability of dose reporting.

Persistent repression of tau in the brain using engineered zinc finger protein transcription factors

Neuronal tau reduction confers resilience against β-amyloid and tau-related neurotoxicity in vitro and in vivo. Here, we introduce a novel translational approach to lower expression of the tau gene MAPT at the transcriptional level using gene-silencing zinc finger protein transcription factors (ZFP-TFs). Following a single administration of adeno-associated virus (AAV), either locally into the hippocampus or intravenously to enable whole-brain transduction, we selectively reduced tau messenger RNA and protein by 50 to 80% out to 11 months, the longest time point studied. Sustained tau lowering was achieved without detectable off-target effects, overt histopathological changes, or molecular alterations. Tau reduction with AAV ZFP-TFs was able to rescue neuronal damage around amyloid plaques in a mouse model of Alzheimer's disease (APP/PS1 line). The highly specific, durable, and controlled knockdown of endogenous tau makes AAV-delivered ZFP-TFs a promising approach for the treatment of tau-related human brain diseases.

Prey with hidden colour defences benefit from their similarity to aposematic signals

Some camouflaged animals hide colour signals and display them only transiently. These hidden colour signals are often conspicuous and are used as a secondary defence to warn or startle predators (deimatic displays) and/or to confuse them (flash displays). The hidden signals used in these displays frequently resemble typical aposematic signals, so it is possible that prey with hidden signals have evolved to employ colour patterns of a form that predators have previously learned to associate with unprofitability. Here, we tested this hypothesis by conducting two experiments that examined the effect of predator avoidance learning on the efficacy of deimatic and flash displays. We found that the survival benefits of both deimatic and flash displays were substantially higher against predators that had previously learned to associate the hidden colours with unprofitability than against naive predators. These findings help explain the phenological patterns we found in 1568 macro-lepidopteran species on three continents: species with hidden signals tend to occur later in the season than species without hidden signals.

Enhancing gene editing specificity by attenuating DNA cleavage kinetics

Engineered nucleases have gained broad appeal for their ability to mediate highly efficient genome editing. However the specificity of these reagents remains a concern, especially for therapeutic applications, given the potential mutagenic consequences of off-target cleavage. Here we have developed an approach for improving the specificity of zinc finger nucleases (ZFNs) that engineers the FokI catalytic domain with the aim of slowing cleavage, which should selectively reduce activity at low-affinity off-target sites. For three ZFN pairs, we engineered single-residue substitutions in the FokI domain that preserved full on-target activity but showed a reduction in off-target indels of up to 3,000-fold. By combining this approach with substitutions that reduced the affinity of zinc fingers, we developed ZFNs specific for the TRAC locus that mediated 98% knockout in T cells with no detectable off-target activity at an assay background of ~0.01%. We anticipate that this approach, and the FokI variants we report, will enable routine generation of nucleases for gene editing with no detectable off-target activity.

Allele-selective transcriptional repression of mutant HTT for the treatment of Huntington's disease

Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder caused by a CAG trinucleotide expansion in the huntingtin gene (HTT), which codes for the pathologic mutant HTT (mHTT) protein. Since normal HTT is thought to be important for brain function, we engineered zinc finger protein transcription factors (ZFP-TFs) to target the pathogenic CAG repeat and selectively lower mHTT as a therapeutic strategy. Using patient-derived fibroblasts and neurons, we demonstrate that ZFP-TFs selectively repress >99% of HD-causing alleles over a wide dose range while preserving expression of >86% of normal alleles. Other CAG-containing genes are minimally affected, and virally delivered ZFP-TFs are active and well tolerated in HD neurons beyond 100 days in culture and for at least nine months in the mouse brain. Using three HD mouse models, we demonstrate improvements in a range of molecular, histopathological, electrophysiological and functional endpoints. Our findings support the continued development of an allele-selective ZFP-TF for the treatment of HD.

Diversifying the structure of zinc finger nucleases for high-precision genome editing

Genome editing for therapeutic applications often requires cleavage within a narrow sequence window. Here, to enable such high-precision targeting with zinc-finger nucleases (ZFNs), we have developed an expanded set of architectures that collectively increase the configurational options available for design by a factor of 64. These new architectures feature the functional attachment of the FokI cleavage domain to the amino terminus of one or both zinc-finger proteins (ZFPs) in the ZFN dimer, as well as the option to skip bases between the target triplets of otherwise adjacent fingers in each zinc-finger array. Using our new architectures, we demonstrate targeting of an arbitrarily chosen 28 bp genomic locus at a density that approaches 1.0 (i.e., efficient ZFNs available for targeting almost every base step). We show that these new architectures may be used for targeting three loci of therapeutic significance with a high degree of precision, efficiency, and specificity.

Engineering altered protein-DNA recognition specificity

Protein engineering is used to generate novel protein folds and assemblages, to impart new properties and functions onto existing proteins, and to enhance our understanding of principles that govern protein structure. While such approaches can be employed to reprogram protein-protein interactions, modifying protein-DNA interactions is more difficult. This may be related to the structural features of protein-DNA interfaces, which display more charged groups, directional hydrogen bonds, ordered solvent molecules and counterions than comparable protein interfaces. Nevertheless, progress has been made in the redesign of protein-DNA specificity, much of it driven by the development of engineered enzymes for genome modification. Here, we summarize the creation of novel DNA specificities for zinc finger proteins, meganucleases, TAL effectors, recombinases and restriction endonucleases. The ease of re-engineering each system is related both to the modularity of the protein and the extent to which the proteins have evolved to be capable of readily modifying their recognition specificities in response to natural selection. The development of engineered DNA binding proteins that display an ideal combination of activity, specificity, deliverability, and outcomes is not a fully solved problem, however each of the current platforms offers unique advantages, offset by behaviors and properties requiring further study and development.

Objective model using only gender, age and medication list predicts in-hospital morbidity after elective surgery

Background.

Most current surgical risk models contain many variables: some of which may be esoteric, require a physician's assessment or must be obtained intraoperatively. Early preoperative risk stratification is essential to identify high risk, elective surgical patients for medical optimization and care coordination across the perioperative period. We sought to create a simple, patient-driven scoring system using: gender, age and list of medications to predict in-hospital postoperative morbidity. We hypothesized that certain medications would elevate risk, as indices of underlying conditions.

Methods.

Two Logistic regression models were created based on patient's gender, age, and medications: GAMMA (Gender, age and type of medications to predict in-hospital morbidity) and GAMMA-N (Gender, age and number of medications to predict in-hospital morbidity). A logistic regression models predicting in-hospital morbidity based on ASA score alone was also created (ASA-M). The predictive performance of these models was tested in a large surgical patient database.

Results.

Our GAMMA model predicts postoperative morbidity after perioperative care with high accuracy (c-statistic 0.819, Brier score 0.034). This result is similar to a model using only the ASA score (c-statistic 0.827, Brier score 0.033) and better than our GAMMA-N model (c-statistic 0.795, Brier score 0.050).

Conclusions.

The combination of a patient's gender, age, and medication list provided reliable prediction of postoperative morbidity. Our model has the added benefit of increased objectivity, can be conducted preoperatively, and is amenable to patient-use as it requires only limited medical knowledge.

Abstract TP168: Risk of Stroke and Hemorrhage in Patients Treated With Warfarin Versus Dabigatran Requiring Surgery

Introduction: Patients with atrial fibrillation (AF) cease anticoagulants prior to surgery to minimize bleeding risk. Patients requiring emergency surgery may be particularly vulnerable to bleeding if anticoagulants remain in the blood. This may be especially problematic with dabigatran (DAB) use given its lack of reversal agent.

Objective: This study compares stroke or bleeding risk in patients with AF taking DAB or warfarin (WARF) that undergo elective, urgent, or emergent inpatient surgery.

Methods: Medicare inpatient claims were used to identify patients with AF who underwent elective (n=20,535) and urgent or emergent (n=24,665) surgery from 11/2010 -12/2012, and had received DAB or WARF within 90 days prior to admission. Outcomes included stroke and major bleeding within 30 days of surgery, and blood units used during the admission. Other patient characteristics included demographics, operation type, and comorbid conditions. Risk adjusted differences in outcomes between patients taking DAB or WARF were estimated within admission category using multivariable regression.

Results: DAB was used by 5,495 (12%) of patients prior to admission. Overall, 1.0% of patients had stroke within 30 days of surgery, 1.2% had a major bleeding event, and patients received an average 0.12 units of blood. Stroke and bleeding rates did not differ for patients taking WARF or DAB, overall or within admission category. Among elective admissions, blood units used also did not differ between WARF or DAB patients. Among urgent and emergent admissions, patients taking DAB used significantly fewer blood units than patients taking WARF (0.09 vs 0.18, respectively; p<.001). Results were consistent after controlling for other patient factors in multivariable models.

Conclusions: Stroke and bleeding risk in patients taking either DAB or WARF were comparable, while patients taking DAB required significantly fewer blood units than patients taking WARF when undergoing emergency surgery. The lack of a reversal agent for DAB does not appear to increase the risk of complications even for emergency surgery.

Obesity and the extent of liver damage among adult New Zealanders: findings from a national survey

Objective

Non‐alcoholic fatty liver disease (NAFLD), defined as excessive fat accumulation in hepatocytes when no other pathologic causes are present, is an increasingly common obesity‐related disorder. We sought to describe the prevalence of elevated liver enzymes, a marker of liver damage, among New Zealand adults, and high‐risk subgroups including those with an elevated body mass index and those with pre‐diabetes or diabetes, to gain a better understanding of the burden of liver disease.

Methods

A total of 4,721 New Zealanders aged 15+ years participated in a nationally representative nutrition survey. Liver enzymes, alanine transaminase (ALT) and gamma glutamyl transpeptidase (GGT) were measured in serum. Results were available for 3,035 participants, of whom 10.8% were Māori and 4.5% Pacific.

Results

Overall, the prevalence of elevated ALT and elevated GGT was 13.1% (95% confidence interval [CI]: 11.2 – 15.0) and 13.7% (95% CI: 12.0 – 15.4), respectively. Odds ratios for an elevated ALT or GGT markedly increased with increasing body mass index. Men with obesity had the highest elevated ALT prevalence (28.5%; 95% CI: 21.7–35.4), and women with diabetes had the highest elevated GGT prevalence (36.5%; 95% CI: 26.0–47.0). Adding alcohol consumption categories to each of the adjusted models did not meaningfully change any results, although for women, heavy alcohol consumption was associated with an elevated GGT (overall p = 0.03).

Conclusions

Obesity‐related liver disease is likely to increasingly burden the New Zealand health sector and contribute to health disparities unless effective obesity treatment and prevention measures are given high priority. © 2015 The Authors. Obesity Science & Practice published by John Wiley & Sons Ltd, World Obesity and The Obesity Society.

Improved specificity of TALE-based genome editing using an expanded RVD repertoire

Transcription activator-like effector (TALE) proteins have gained broad appeal as a platform for targeted DNA recognition, largely owing to their simple rules for design. These rules relate the base specified by a single TALE repeat to the identity of two key residues (the repeat variable diresidue, or RVD) and enable design for new sequence targets via modular shuffling of these units. A key limitation of these rules is that their simplicity precludes options for improving designs that are insufficiently active or specific. Here we address this limitation by developing an expanded set of RVDs and applying them to improve the performance of previously described TALEs. As an extreme example, total conversion of a TALE nuclease to new RVDs substantially reduced off-target cleavage in cellular studies. By providing new RVDs and design strategies, these studies establish options for developing improved TALEs for broader application across medicine and biotechnology.

The Effects of Kernel Feeding by Halyomorpha halys (Hemiptera: Pentatomidae) on Commercial Hazelnuts

Halyomorpha halys Stål, the brown marmorated stink bug (Hemiptera: Pentatomidae), is an invasive pest with established populations in Oregon. The generalist feeding habits of H. halys suggest it has the potential to be a pest of many specialty crops grown in Oregon, including hazelnuts, Corylus avellana L. The objectives of this study were to: 1) characterize the damage to developing hazelnut kernels resulting from feeding by H. halys adults, 2) determine how the timing of feeding during kernel development influences damage to kernels, and 3) determine if hazelnut shell thickness has an effect on feeding frequency on kernels. Adult brown marmorated stink bugs were allowed to feed on developing nuts for 1-wk periods from initial kernel development (spring) until harvest (fall). Developing nuts not exposed to feeding by H. halys served as a control treatment. The degree of damage and diagnostic symptoms corresponded with the hazelnut kernels' physiological development. Our results demonstrated that when H. halys fed on hazelnuts before kernel expansion, development of the kernels could cease, resulting in empty shells. When stink bugs fed during kernel expansion, kernels appeared malformed. When stink bugs fed on mature nuts the kernels exhibited corky, necrotic areas. Although significant differences in shell thickness were observed among the cultivars, no significant differences occurred in the proportions of damaged kernels based on field tests and laboratory choice tests. The results of these studies demonstrated that commercial hazelnuts are susceptible to damage caused by the feeding of H. halys throughout the entire period of kernel development.

Perspective: follow the money: the implications of medical schools' funds flow models

Medical schools conduct research, provide clinical care, and educate future physicians and scientists. Each school has its own unique mix of revenue sources and expense sharing among the medical school, faculty practice plan(s), parent university, and affiliated hospital(s). Despite these differences, revenues from clinical care subsidize the money-losing research and education missions at every medical school.In this perspective, the authors discuss the flow of funds among a medical school, its faculty practice plan(s), parent university, and affiliated hospital(s). They summarize where medical school revenues come from, how revenues and expenses flow within a medical school and between a medical school and its partners, and why understanding this process is crucial to leading and managing such an enterprise. They conclude with recommendations for medical schools to consider in developing funds flow models that meet their individual needs and circumstances: (1) understand economic drivers, (2) reward desired behaviors, (3) enable every unit to generate a positive margin, (4) communicate budget priorities, financial performance, and the use of institutional resources, and (5) establish principles for sharing resources and allocating expenses among entities within the institution.Medical schools should develop funds flow models that are transparent, aligned with their strategic priorities, and reward the behaviors necessary to produce effective collaboration within and across mission areas.

Transcriptional activation of Brassica napus β-ketoacyl-ACP synthase II with an engineered zinc finger protein transcription factor

Targeted gene regulation via designed transcription factors has great potential for precise phenotypic modification and acceleration of novel crop trait development. Canola seed oil composition is dictated largely by the expression of genes encoding enzymes in the fatty acid biosynthetic pathway. In the present study, zinc finger proteins (ZFPs) were designed to bind DNA sequences common to two canola β-ketoacyl-ACP Synthase II (KASII) genes downstream of their transcription start site. Transcriptional activators (ZFP-TFs) were constructed by fusing these ZFP DNA-binding domains to the VP16 transcriptional activation domain. Following transformation using Agrobacterium, transgenic events expressing ZFP-TFs were generated and shown to have elevated KASII transcript levels in the leaves of transgenic T(0) plants when compared to 'selectable marker only' controls as well as of T(1) progeny plants when compared to null segregants. In addition, leaves of ZFP-TF-expressing T(1) plants contained statistically significant decreases in palmitic acid (consistent with increased KASII activity) and increased total C18. Similarly, T(2) seed displayed statistically significant decreases in palmitic acid, increased total C18 and reduced total saturated fatty acid contents. These results demonstrate that designed ZFP-TFs can be used to regulate the expression of endogenous genes to elicit specific phenotypic modifications of agronomically relevant traits in a crop species.

Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme

Zinc-finger nucleases (ZFNs) drive highly efficient genome editing by generating a site-specific DNA double-strand break (DSB) at a predetermined site in the genome. Subsequent repair of this break via the nonhomologous end-joining (NHEJ) or homology-directed repair (HDR) pathways results in targeted gene disruption or gene addition, respectively. Here, we report that ZFNs can be engineered to induce a site-specific DNA single-strand break (SSB) or nick. Using the CCR5-specific ZFNs as a model system, we show that introduction of a nick at this target site stimulates gene addition using a homologous donor template but fails to induce significant levels of the small insertions and deletions (indels) characteristic of repair via NHEJ. Gene addition by these CCR5-targeted zinc finger nickases (ZFNickases) occurs in both transformed and primary human cells at efficiencies of up to ∼1%–8%. Interestingly, ZFNickases targeting the AAVS1 “safe harbor” locus revealed similar in vitro nicking activity, a marked reduction of indels characteristic of NHEJ, but stimulated far lower levels of gene addition—suggesting that other, yet to be identified mediators of nick-induced gene targeting exist. Introduction of site-specific nicks at distinct endogenous loci provide an important tool for the study of DNA repair. Moreover, the potential for a SSB to direct repair pathway choice (i.e., HDR but not NHEJ) may prove advantageous for certain therapeutic applications such as the targeted correction of human disease-causing mutations.

Absolute stability of axisymmetric perturbations in strongly magnetized collisionless axisymmetric accretion disk plasmas

This Letter presents a kinetic description of low-frequency and long-wavelength axisymmetric electromagnetic perturbations in nonrelativistic, strongly magnetized, and gravitationally bound axisymmetric accretion-disk plasmas in the collisionless regime. The analysis, carried out within the framework of the Vlasov-Maxwell description, relies on stationary kinetic solutions which allow for the simultaneous treatment of nonuniform fluid fields, stationary accretion flows, and temperature anisotropies. It is demonstrated that these stationary configurations are actually stable against axisymmetric kinetic instabilities of this type. As a fundamental consequence, this rules out the possibility of having the axisymmetric magnetorotational or thermal instabilities to arise in these systems.

An unbiased genome-wide analysis of zinc-finger nuclease specificity

Zinc-finger nucleases (ZFNs) allow gene editing in live cells by inducing a targeted DNA double-strand break (DSB) at a specific genomic locus. However, strategies for characterizing the genome-wide specificity of ZFNs remain limited. We show that nonhomologous end-joining captures integrase-defective lentiviral vectors at DSBs, tagging these transient events. Genome-wide integration site analysis mapped the actual in vivo cleavage activity of four ZFN pairs targeting CCR5 or IL2RG. Ranking loci with repeatedly detectable nuclease activity by deep-sequencing allowed us to monitor the degree of ZFN specificity in vivo at these positions. Cleavage required binding of ZFNs in specific spatial arrangements on DNA bearing high homology to the intended target site and only tolerated mismatches at individual positions of the ZFN binding sites. Whereas the consensus binding sequence derived in vivo closely matched that obtained in biochemical experiments, the ranking of in vivo cleavage sites could not be predicted in silico. Comprehensive mapping of ZFN activity in vivo will facilitate the broad application of these reagents in translational research.

Targeted genome editing across species using ZFNs and TALENs

Evolutionary studies necessary to dissect diverse biological processes have been limited by the lack of reverse genetic approaches in most organisms with sequenced genomes. We established a broadly applicable strategy using zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) for targeted disruption of endogenous genes and cis-acting regulatory elements in diverged nematode species.

Engineering HIV-resistant human CD4+ T cells with CXCR4-specific zinc-finger nucleases

HIV-1 entry requires the cell surface expression of CD4 and either the CCR5 or CXCR4 coreceptors on host cells. Individuals homozygous for the ccr5Δ32 polymorphism do not express CCR5 and are protected from infection by CCR5-tropic (R5) virus strains. As an approach to inactivating CCR5, we introduced CCR5-specific zinc-finger nucleases into human CD4+ T cells prior to adoptive transfer, but the need to protect cells from virus strains that use CXCR4 (X4) in place of or in addition to CCR5 (R5X4) remains. Here we describe engineering a pair of zinc finger nucleases that, when introduced into human T cells, efficiently disrupt cxcr4 by cleavage and error-prone non-homologous DNA end-joining. The resulting cells proliferated normally and were resistant to infection by X4-tropic HIV-1 strains. CXCR4 could also be inactivated in ccr5Δ32 CD4+ T cells, and we show that such cells were resistant to all strains of HIV-1 tested. Loss of CXCR4 also provided protection from X4 HIV-1 in a humanized mouse model, though this protection was lost over time due to the emergence of R5-tropic viral mutants. These data suggest that CXCR4-specific ZFNs may prove useful in establishing resistance to CXCR4-tropic HIV for autologous transplant in HIV-infected individuals.

Rapid and efficient clathrin-mediated endocytosis revealed in genome-edited mammalian cells

Clathrin-mediated endocytosis (CME) is the best-studied pathway by which cells selectively internalize molecules from the plasma membrane and surrounding environment. Previous live-cell imaging studies using ectopically overexpressed fluorescent fusions of endocytic proteins indicated that mammalian CME is a highly dynamic but inefficient and heterogeneous process. In contrast, studies of endocytosis in budding yeast using fluorescent protein fusions expressed at physiological levels from native genomic loci have revealed a process that is very regular and efficient. To analyse endocytic dynamics in mammalian cells in which endogenous protein stoichiometry is preserved, we targeted zinc finger nucleases (ZFNs) to the clathrin light chain A and dynamin-2 genomic loci and generated cell lines expressing fluorescent protein fusions from each locus. The genome-edited cells exhibited enhanced endocytic function, dynamics and efficiency when compared with previously studied cells, indicating that CME is highly sensitive to the levels of its protein components. Our study establishes that ZFN-mediated genome editing is a robust tool for expressing protein fusions at endogenous levels to faithfully report subcellular localization and dynamics.

A rapid and general assay for monitoring endogenous gene modification

The development of zinc finger nucleases for targeted gene modification can benefit from rapid functional assays that directly quantify activity at the endogenous target. Here we describe a simple procedure for quantifying mutations that result from DNA double-strand break repair via non-homologous end joining. The assay is based on the ability of the Surveyor nuclease to selectively cleave distorted duplex DNA formed via cross-annealing of mutated and wild-type sequence.

Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures

Zinc-finger nucleases (ZFNs) drive efficient genome editing by introducing a double-strand break into the targeted gene. Cleavage is induced when two custom-designed ZFNs heterodimerize upon binding DNA to form a catalytically active nuclease complex. The importance of this dimerization event for subsequent cleavage activity has stimulated efforts to engineer the nuclease interface to prevent undesired homodimerization. Here we report the development and application of a yeast-based selection system designed to functionally interrogate the ZFN dimer interface. We identified critical residues involved in dimerization through the isolation of cold-sensitive nuclease domains. We used these residues to engineer ZFNs that have superior cleavage activity while suppressing homodimerization. The improvements were portable to orthogonal domains, allowing the concomitant and independent cleavage of two loci using two different ZFN pairs. These ZFN architectures provide a general means for obtaining highly efficient and specific genome modification.

Highly efficient deletion of FUT8 in CHO cell lines using zinc-finger nucleases yields cells that produce completely nonfucosylated antibodies

IgG1 antibodies produced in Chinese hamster ovary (CHO) cells are heavily alpha1,6-fucosylated, a modification that reduces antibody-dependent cellular cytotoxicity (ADCC) and can inhibit therapeutic antibody function in vivo. Addition of fucose is catalyzed by Fut8, a alpha1,6-fucosyltransferase. FUT8(-/-) CHO cell lines produce completely nonfucosylated antibodies, but the difficulty of recapitulating the knockout in protein-production cell lines has prevented the widespread adoption of FUT8(-/-) cells as hosts for antibody production. We have created zinc-finger nucleases (ZFNs) that cleave the FUT8 gene in a region encoding the catalytic core of the enzyme, allowing the functional disruption of FUT8 in any CHO cell line. These reagents produce FUT8(-/-) CHO cells in 3 weeks at a frequency of 5% in the absence of any selection. Alternately, populations of ZFN-treated cells can be directly selected to give FUT8(-/-) cell pools in as few as 3 days. To demonstrate the utility of this method in bioprocess, FUT8 was disrupted in a CHO cell line used for stable protein production. ZFN-derived FUT8(-/-) cell lines were as transfectable as wild-type, had similar or better growth profiles, and produced equivalent amounts of antibody during transient transfection. Antibodies made in these lines completely lacked core fucosylation but had an otherwise normal glycosylation pattern. Cell lines stably expressing a model antibody were made from wild-type and ZFN-generated FUT8(-/-) cells. Clones from both lines had equivalent titer, specific productivity distributions, and integrated viable cell counts. Antibody titer in the best ZFN-generated FUT8(-/-) cell lines was fourfold higher than in the best-producing clones of FUT8(-/-) cells made by standard homologous recombination in a different CHO subtype. These data demonstrate the straightforward, ZFN-mediated transfer of the Fut8- phenotype to a production CHO cell line without adverse phenotypic effects. This process will speed the production of highly active, completely nonfucosylated therapeutic antibodies.

Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology

We previously demonstrated high-frequency, targeted DNA addition mediated by the homology-directed DNA repair pathway. This method uses a zinc-finger nuclease (ZFN) to create a site-specific double-strand break (DSB) that facilitates copying of genetic information into the chromosome from an exogenous donor molecule. Such donors typically contain two approximately 750 bp regions of chromosomal sequence required for homology-directed DNA repair. Here, we demonstrate that easily-generated linear donors with extremely short (50 bp) homology regions drive transgene integration into 5-10% of chromosomes. Moreover, we measure the overhangs produced by ZFN cleavage and find that oligonucleotide donors with single-stranded 5' overhangs complementary to those made by ZFNs are efficiently ligated in vivo to the DSB. Greater than 10% of all chromosomes directly incorporate this exogenous DNA via a process that is dependent upon and guided by complementary 5' overhangs on the donor DNA. Finally, we extend this non-homologous end-joining (NHEJ)-based technique by directly inserting donor DNA comprising recombinase sites into large deletions created by the simultaneous action of two separate ZFN pairs. Up to 50% of deletions contained a donor insertion. Targeted DNA addition via NHEJ complements our homology-directed targeted integration approaches, adding versatility to the manipulation of mammalian genomes.

Generation of a triple-gene knockout mammalian cell line using engineered zinc-finger nucleases

Mammalian cells with multi-gene knockouts could be of considerable utility in research, drug discovery, and cell-based therapeutics. However, existing methods for targeted gene deletion require sequential rounds of homologous recombination and drug selection to isolate rare desired events--a process sufficiently laborious to limit application to individual loci. Here we present a solution to this problem. Firstly, we report the development of zinc-finger nucleases (ZFNs) targeted to cleave three independent genes with known null phenotypes. Mammalian cells exposed to each ZFN pair in turn resulted in the generation of cell lines harboring single, double, and triple gene knockouts, that is, the successful disruption of two, four, and six alleles. All three biallelic knockout events were obtained at frequencies of >1% without the use of selection, displayed the expected knockout phenotype(s), and harbored DNA mutations centered at the ZFN binding sites. These data demonstrate the utility of ZFNs in multi-locus genome engineering.

Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome

Isogenic settings are routine in model organisms, yet remain elusive for genetic experiments on human cells. We describe the use of designed zinc finger nucleases (ZFNs) for efficient transgenesis without drug selection into the PPP1R12C gene, a "safe harbor" locus known as AAVS1. ZFNs enable targeted transgenesis at a frequency of up to 15% following transient transfection of both transformed and primary human cells, including fibroblasts and hES cells. When added to this locus, transgenes such as expression cassettes for shRNAs, small-molecule-responsive cDNA expression cassettes, and reporter constructs, exhibit consistent expression and sustained function over 50 cell generations. By avoiding random integration and drug selection, this method allows bona fide isogenic settings for high-throughput functional genomics, proteomics, and regulatory DNA analysis in essentially any transformed human cell type and in primary cells.

BAK and BAX deletion using zinc-finger nucleases yields apoptosis-resistant CHO cells

Anoxic and metabolic stresses in large-scale cell culture during biopharmaceutical production can induce apoptosis. Strategies designed to ameliorate the problem of apoptosis in cell culture have focused on mRNA knockdown of pro-apoptotic proteins and over-expression of anti-apoptotic ones. Apoptosis in cell culture involves mitochondrial permeabilization by the pro-apoptotic Bak and Bax proteins; activity of either protein is sufficient to permit apoptosis. We demonstrate here the complete and permanent elimination of both the Bak and Bax proteins in combination in Chinese hamster ovary (CHO) cells using zinc-finger nuclease-mediated gene disruption. Zinc-finger nuclease cleavage of BAX and BAK followed by inaccurate DNA repair resulted in knockout of both genes. Cells lacking Bax and Bak grow normally but fail to activate caspases in response to apoptotic stimuli. When grown using scale-down systems under conditions that mimic growth in large-scale bioreactors they are significantly more resistant to apoptosis induced by starvation, staurosporine, and sodium butyrate. When grown under starvation conditions, BAX- and BAK-deleted cells produce two- to fivefold more IgG than wild-type CHO cells. Under normal growth conditions in suspension culture in shake flasks, double-knockout cultures achieve equal or higher cell densities than unmodified wild-type cultures and reach viable cell densities relevant for large-scale industrial protein production.

Wishful Thinking in the 2008 U.S. Presidential Election

In elections, political preferences are strongly linked to the expectations of the electoral winner—people usually expect their favorite candidate to win. This link could be driven by wishful thinking (a biasing influence of preferences), driven by a biasing influence of expectations on one’s wishes, or produced spuriously. To examine these competing possibilities in the 2008 U.S. presidential election, a longitudinal study assessed uncommitted young voters’ electoral expectations and preferences over four time points during the month before the election. The findings indicated clear support for wishful thinking: Over time, people’s preferences shaped their expectations, but the reverse was not the case. Moreover, these relations were larger among those more strongly identified with their political party and held even when perceptions of general candidate popularity were taken into account. Finally, changes in electoral expectations were consequential, as they shaped disappointment in the electoral results even after taking candidate preferences into account.

Distribution of vaccine/antivirals and the 'least spread line' in a stratified population

We describe a prioritization scheme for an allocation of a sizeable quantity of vaccine or antivirals in a stratified population. The scheme builds on an optimal strategy for reducing the epidemic's initial growth rate in a stratified mass-action model. The strategy is tested on the EpiSims network describing interactions and influenza dynamics in the population of Utah, where the stratification we have chosen is by age (0-6, 7-13, 14-18, adults). No prior immunity information is available, thus everyone is assumed to be susceptible-this may be relevant, possibly with the exception of persons over 50, to the 2009 H1N1 influenza outbreak. We have found that the top priority in an allocation of a sizeable quantity of seasonal influenza vaccinations goes to young children (0-6), followed by teens (14-18), then children (7-13), with the adult share being quite low. These results, which rely on the structure of the EpiSims network, are compared with the current influenza vaccination coverage levels in the US population.

Knockout rats via embryo microinjection of zinc-finger nucleases

The toolbox of rat genetics currently lacks the ability to introduce site-directed, heritable mutations into the genome to create knockout animals. By using engineered zinc-finger nucleases (ZFNs) designed to target an integrated reporter and two endogenous rat genes, Immunoglobulin M (IgM) and Rab38, we demonstrate that a single injection of DNA or messenger RNA encoding ZFNs into the one-cell rat embryo leads to a high frequency of animals carrying 25 to 100% disruption at the target locus. These mutations are faithfully and efficiently transmitted through the germline. Our data demonstrate the feasibility of targeted gene disruption in multiple rat strains within 4 months time, paving the way to a humanized monoclonal antibody platform and additional human disease models.

Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases

Realizing the full potential of human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) requires efficient methods for genetic modification. However, techniques to generate cell type-specific lineage reporters, as well as reliable tools to disrupt, repair or overexpress genes by gene targeting, are inefficient at best and thus are not routinely used. Here we report the highly efficient targeting of three genes in human pluripotent cells using zinc-finger nuclease (ZFN)-mediated genome editing. First, using ZFNs specific for the OCT4 (POU5F1) locus, we generated OCT4-eGFP reporter cells to monitor the pluripotent state of hESCs. Second, we inserted a transgene into the AAVS1 locus to generate a robust drug-inducible overexpression system in hESCs. Finally, we targeted the PITX3 gene, demonstrating that ZFNs can be used to generate reporter cells by targeting non-expressed genes in hESCs and hiPSCs.

Precise genome modification in the crop species Zea mays using zinc-finger nucleases

Agricultural biotechnology is limited by the inefficiencies of conventional random mutagenesis and transgenesis. Because targeted genome modification in plants has been intractable, plant trait engineering remains a laborious, time-consuming and unpredictable undertaking. Here we report a broadly applicable, versatile solution to this problem: the use of designed zinc-finger nucleases (ZFNs) that induce a double-stranded break at their target locus. We describe the use of ZFNs to modify endogenous loci in plants of the crop species Zea mays. We show that simultaneous expression of ZFNs and delivery of a simple heterologous donor molecule leads to precise targeted addition of an herbicide-tolerance gene at the intended locus in a significant number of isolated events. ZFN-modified maize plants faithfully transmit these genetic changes to the next generation. Insertional disruption of one target locus, IPK1, results in both herbicide tolerance and the expected alteration of the inositol phosphate profile in developing seeds. ZFNs can be used in any plant species amenable to DNA delivery; our results therefore establish a new strategy for plant genetic manipulation in basic science and agricultural applications.

Targeted transgene integration in plant cells using designed zinc finger nucleases

Targeted transgene integration in plants remains a significant technical challenge for both basic and applied research. Here it is reported that designed zinc finger nucleases (ZFNs) can drive site-directed DNA integration into transgenic and native gene loci. A dimer of designed 4-finger ZFNs enabled intra-chromosomal reconstitution of a disabled gfp reporter gene and site-specific transgene integration into chromosomal reporter loci following co-transformation of tobacco cell cultures with a donor construct comprised of sequences necessary to complement a non-functional pat herbicide resistance gene. In addition, a yeast-based assay was used to identify ZFNs capable of cleaving a native endochitinase gene. Agrobacterium delivery of a Ti plasmid harboring both the ZFNs and a donor DNA construct comprising a pat herbicide resistance gene cassette flanked by short stretches of homology to the endochitinase locus yielded up to 10% targeted, homology-directed transgene integration precisely into the ZFN cleavage site. Given that ZFNs can be designed to recognize a wide range of target sequences, these data point toward a novel approach for targeted gene addition, replacement and trait stacking in plants.

Development of a single-chain, quasi-dimeric zinc-finger nuclease for the selective degradation of mutated human mitochondrial DNA

The selective degradation of mutated mitochondrial DNA (mtDNA) molecules is a potential strategy to re-populate cells with wild-type (wt) mtDNA molecules and thereby alleviate the defective mitochondrial function that underlies mtDNA diseases. Zinc finger nucleases (ZFNs), which are nucleases conjugated to a zinc-finger peptide (ZFP) engineered to bind a specific DNA sequence, could be useful for the selective degradation of particular mtDNA sequences. Typically, pairs of complementary ZFNs are used that heterodimerize on the target DNA sequence; however, conventional ZFNs were ineffective in our system. To overcome this, we created single-chain ZFNs by conjugating two FokI nuclease domains, connected by a flexible linker, to a ZFP with an N-terminal mitochondrial targeting sequence. Here we show that these ZFNs are efficiently transported into mitochondria in cells and bind mtDNA in a sequence-specific manner discriminating between two 12-bp long sequences that differ by a single base pair. Due to their selective binding they cleave dsDNA at predicted sites adjacent to the mutation. When expressed in heteroplasmic cells containing a mixture of mutated and wt mtDNA these ZFNs selectively degrade mutated mtDNA, thereby increasing the proportion of wt mtDNA molecules in the cell. Therefore, mitochondria-targeted single-chain ZFNs are a promising candidate approach for the treatment of mtDNA diseases.

Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases

Homozygosity for the naturally occurring Delta32 deletion in the HIV co-receptor CCR5 confers resistance to HIV-1 infection. We generated an HIV-resistant genotype de novo using engineered zinc-finger nucleases (ZFNs) to disrupt endogenous CCR5. Transient expression of CCR5 ZFNs permanently and specifically disrupted approximately 50% of CCR5 alleles in a pool of primary human CD4(+) T cells. Genetic disruption of CCR5 provided robust, stable and heritable protection against HIV-1 infection in vitro and in vivo in a NOG model of HIV infection. HIV-1-infected mice engrafted with ZFN-modified CD4(+) T cells had lower viral loads and higher CD4(+) T-cell counts than mice engrafted with wild-type CD4(+) T cells, consistent with the potential to reconstitute immune function in individuals with HIV/AIDS by maintenance of an HIV-resistant CD4(+) T-cell population. Thus adoptive transfer of ex vivo expanded CCR5 ZFN-modified autologous CD4(+) T cells in HIV patients is an attractive approach for the treatment of HIV-1 infection.

Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases

We describe here the use of zinc finger nucleases (ZFNs) for somatic and germline disruption of genes in zebrafish (Danio rerio), where targeted mutagenesis was previously intractable. ZFNs induce a targeted double-strand break in the genome that is repaired to generate small insertions and deletions. We designed ZFNs targeting the zebrafish golden and no tail/Brachyury genes. In both cases, injection of ZFN-encoding mRNA into 1-cell embryos yielded a high percentage of animals carrying distinct mutations at the ZFN-specified position and exhibiting expected loss-of-function phenotypes. Disrupted ntl alleles were transmitted from ZFN mRNA-injected founder animals in over half the adults tested at frequencies averaging 20%. The frequency and precision of gene disruption events observed, in combination with the ability to design ZFNs against any locus, open fundamentally novel avenues of experimentation, and suggest that ZFN technology may be widely applied to many organisms that allow mRNA delivery into the fertilized egg.

Estimation of the reproduction number of dengue fever from spatial epidemic data

Dengue, a vector-borne disease, thrives in tropical and subtropical regions worldwide. A retrospective analysis of the 2002 dengue epidemic in Colima located on the Mexican central Pacific coast is carried out. We estimate the reproduction number from spatial epidemic data at the level of municipalities using two different methods: (1) Using a standard dengue epidemic model and assuming pure exponential initial epidemic growth and (2) Fitting a more realistic epidemic model to the initial phase of the dengue epidemic curve. Using Method I, we estimate an overall mean reproduction number of 3.09 (95% CI: 2.34,3.84) as well as local reproduction numbers whose values range from 1.24 (1.15,1.33) to 4.22 (2.90,5.54). Using Method II, the overall mean reproduction number is estimated to be 2.0 (1.75,2.23) and local reproduction numbers ranging from 0.49 (0.0,1.0) to 3.30 (1.63,4.97). Method I systematically overestimates the reproduction number relative to the refined Method II, and hence it would overestimate the intensity of interventions required for containment. Moreover, optimal intervention with defined resources demands different levels of locally tailored mitigation. Local epidemic peaks occur between the 24th and 35th week of the year, and correlate positively with the final local epidemic sizes (rho=0.92, P-value<0.001). Moreover, final local epidemic sizes are found to be linearly related to the local population size (P-value<0.001). This observation supports a roughly constant number of female mosquitoes per person across urban and rural regions.

An improved zinc-finger nuclease architecture for highly specific genome editing

Genome editing driven by zinc-finger nucleases (ZFNs) yields high gene-modification efficiencies (>10%) by introducing a recombinogenic double-strand break into the targeted gene. The cleavage event is induced using two custom-designed ZFNs that heterodimerize upon binding DNA to form a catalytically active nuclease complex. Using the current ZFN architecture, however, cleavage-competent homodimers may also form that can limit safety or efficacy via off-target cleavage. Here we develop an improved ZFN architecture that eliminates this problem. Using structure-based design, we engineer two variant ZFNs that efficiently cleave DNA only when paired as a heterodimer. These ZFNs modify a native endogenous locus as efficiently as the parental architecture, but with a >40-fold reduction in homodimer function and much lower levels of genome-wide cleavage. This architecture provides a general means for improving the specificity of ZFNs as gene modification reagents.

Submarine watch schedules: underway evaluation of rotating (contemporary) and compressed (alternative) schedules

INTRODUCTION

With a desire to increase health, cognitive performance effectiveness, and quality of life for submarine watch-standers underway, we performed an evaluation comparing an alternative, compressed-work (ALT) schedule, designed to enhance circadian rhythm entrainment and sleep hygiene, to the contemporary submarine (SUB) forward rotating schedule, aboard the ballistic-missile submarine, USS Henry M. Jackson (SSBN-730 Gold).

METHODS

We assessed a compressed close-6 watch-schedule ("ALT") relative to the existing backward rotating 6-hr on, 12-hr off 18-hr watch schedule ("SUB") employed underway aboard submarines. We monitored 40 subjects' sleep, and temperature and salivary cortisol from 10 of the 40 for approximately two weeks on each respective schedule underway.

RESULTS

The cortisol cosinor mesors (midline estimating statistic of rhythm), and amplitudes did not differ significantly between conditions. The temperature cosinor mesors, and the cosinor amplitude were not significantly different, while the cosine curve fit accounted for significantly more variance in the ALT condition than in the SUB condition. The SUB schedule garnered significantly more sleep (7.1 +/- 0.2 hours) than that of the ALTMID schedule (6.3 +/- 0.3 hours). Surveys revealed that 52% of respondents preferred the SUB schedule, 15% preferred the ALT, and 33% were either indifferent or submitted uninterpretable surveys.

CONCLUSIONS

The ALT schedule was not superior to the existing SUB schedule by physiological or subjective measures and was incompatible to accommodating operational constraints.