Application of a Spacer-nick Gene-targeting Approach to Repair Disease-causing Mutations with Increased Safety.

The CRISPR/Cas9 system is a powerful tool for gene repair that holds great potential for gene therapy to cure monogenic diseases. Despite intensive improvement, the safety of this system remains a major clinical concern. In contrast to Cas9 nuclease, Cas9 nickases with a pair of short-distance (38-68 bp) PAM-out single-guide RNAs (sgRNAs) preserve gene repair efficiency while strongly reducing off-target effects. However, this approach still leads to efficient unwanted on-target mutations that may cause tumorigenesis or abnormal hematopoiesis. We establish a precise and safe spacer-nick gene repair approach that combines Cas9D10A nickase with a pair of PAM-out sgRNAs at a distance of 200-350 bp. In combination with adeno-associated virus (AAV) serotype 6 donor templates, this approach leads to efficient gene repair with minimal unintended on- and off-target mutations in human hematopoietic stem and progenitor cells (HSPCs). Here, we provide detailed protocols to use the spacer-nick approach for gene repair and to assess the safety of this system in human HSPCs. The spacer-nick approach enables efficient gene correction for repair of disease-causing mutations with increased safety and suitability for gene therapy. Graphical overview.

The effect of temperature on specific dynamic action of juvenile fall-run Chinook salmon, Oncorhynchus tshawytscha.

Juvenile fall-run Chinook salmon (Oncorhynchus tshawytscha) in the Sacramento-San Joaquin River Basin experience temporally and spatially heterogenous temperature regimes, between cool upper tributaries and the warm channelized Delta, during freshwater rearing and outmigration. Limited water resources necessitate human management of dam releases, allowing temperature modifications. The objective of this study was to examine the effect of temperature on specific dynamic action (SDA), or the metabolic cost associated with feeding and digestion, which is thought to represent a substantial portion of fish energy budgets. Measuring SDA with respect to absolute aerobic scope (AAS), estimated by the difference between maximum metabolic rate (MMR) and standard metabolic rate (SMR), provides a snapshot of its respective energy allocation. Fish were acclimated to 16°C, raised or lowered to each acute temperature (13°C, 16°C, 19°C, 22°C or 24°C), then fed a meal of commercial pellets weighing 2% of their wet mass. We detected a significant positive effect of temperature on SMR and MMR, but not on AAS. As expected, there was no significant effect of temperature on the total O2 cost of digestion, but unlike other studies, we did not see a significant difference in duration, peak metabolic rate standardized to SMR, time to peak, percent of meal energy utilized, nor the ratio of peak O2 consumption to SMR. Peak O2 consumption represented 10.4-14.5% of AAS leaving a large amount of aerobic capacity available for other activities, and meal energy utilized for digestion ranged from 5.7% to 7.2%, leaving substantial remaining energy to potentially assimilate for growth. Our juvenile fall-run Chinook salmon exhibited thermal stability in their SDA response, which may play a role in maintaining homeostasis of digestive capability in a highly heterogeneous thermal environment where rapid growth is important for successful competition with conspecifics and for avoiding predation.

Precise CRISPR-Cas-mediated gene repair with minimal off-target and unintended on-target mutations in human hematopoietic stem cells.

While CRISPR-Cas9 is key for the development of gene therapy, its potential off-target mutations are still a major concern. Here, we establish a "spacer-nick" gene correction approach that combines the Cas9D10A nickase with a pair of PAM-out sgRNAs at a distance of 200 to 350 bp. In combination with adeno-associated virus (AAV) serotype 6 template delivery, our approach led to efficient HDR in human hematopoietic stem and progenitor cells (HSPCs including long-term HSCs) and T cells, with minimal NHEJ-mediated on-target mutations. Using spacer-nick, we developed an approach to repair disease-causing mutations occurring in the HBB, ELANE, IL7R, and PRF1 genes. We achieved gene correction efficiencies of 20 to 50% with minimal NHEJ-mediated on-target mutations. On the basis of in-depth off-target assessment, frequent unintended genetic alterations induced by classical CRISPR-Cas9 were significantly reduced or absent in the HSPCs treated with spacer-nick. Thus, the spacer-nick gene correction approach provides improved safety and suitability for gene therapy.

A homology independent sequence replacement strategy in human cells using a CRISPR nuclease.

Precision genomic alterations largely rely on homology directed repair (HDR), but targeting without homology using the non-homologous end-joining (NHEJ) pathway has gained attention as a promising alternative. Previous studies demonstrated precise insertions formed by the ligation of donor DNA into a targeted genomic double-strand break in both dividing and non-dividing cells. Here, we demonstrate the use of NHEJ repair to replace genomic segments with donor sequences; we name this method 'Replace' editing (Rational end-joining protocol delivering a targeted sequence exchange). Using CRISPR/Cas9, we create two genomic breaks and ligate a donor sequence in-between. This exchange of a genomic for a donor sequence uses neither microhomology nor homology arms. We target four loci in cell lines and show successful exchange of exons in 16-54% of human cells. Using linear amplification methods and deep sequencing, we quantify the diversity of outcomes following Replace editing and profile the ligated interfaces. The ability to replace exons or other genomic sequences in cells not efficiently modified by HDR holds promise for both basic research and medicine.

The biophysical basis of thermal tolerance in fish eggs.

A warming climate poses a fundamental problem for embryos that develop within eggs because their demand for oxygen (O2) increases much more rapidly with temperature than their capacity for supply, which is constrained by diffusion across the egg surface. Thus, as temperatures rise, eggs may experience O2 limitation due to an imbalance between O2 supply and demand. Here, we formulate a mathematical model of O2 limitation and experimentally test whether this mechanism underlies the upper thermal tolerance in large aquatic eggs. Using Chinook salmon (Oncorhynchus tshawytscha) as a model system, we show that the thermal tolerance of eggs varies systematically with features of the organism and environment. Importantly, this variation can be precisely predicted by the degree to which these features shift the balance between O2 supply and demand. Equipped with this mechanistic understanding, we predict and experimentally confirm that the thermal tolerance of these embryos in their natural habitat is substantially lower than expected from laboratory experiments performed under normoxia. More broadly, our biophysical model of O2 limitation provides a mechanistic explanation for the elevated thermal sensitivity of fish embryos relative to other life stages, global patterns in egg size and the extreme fecundity of large teleosts.

Assessment of multiple stressors on the growth of larval green sturgeon Acipenser medirostris: implications for recruitment of early life-history stages.

Early developmental stages of fishes are particularly sensitive to changes in environmental variables that affect physiological processes such as metabolism and growth. Both temperature and food availability have significant effects on the growth and survival of larval and juvenile fishes. As climate change and anthropogenic disturbances influence sensitive rearing environments of fishes it is unlikely that they will experience changes in temperature or food availability in isolation. Therefore, it is critical that we determine the effects of each of these potential stressors on larval growth and development, as well as understand the additive, synergistic or antagonistic effects of both. We reared threatened green sturgeon Acipenser medirostris (initial age ca. 32 days post hatch) at four temperatures (11, 13, 16 and 19°C) and two food availability rates (100% and 40% of optimal) to assess the effects of these stressors and their interactions on larval growth. We compared the overall size (fork length, total length and mass), growth rates (cm day-1 and g day-1 ) and relative condition factor of these larval and juvenile fish at 3 week intervals for up to 12 weeks. Our results indicated that temperature and food availability both had significant effects on growth and condition and that there was a significant interaction between the two. Fish reared with limited food availability exhibited similar patterns in growth rates to those reared with elevated food rates, but the effects of temperature were greatly attenuated when fish were food-limited. Also, the effects of temperature on condition were reversed when fish were reared with restricted food, such that fish reared at 19°C exhibited the highest relative condition when fed optimally, but the lowest relative condition when food was limited. These data are critical for the development of relevant bioenergetics models, which are needed to link the survival of larval sturgeons with historic environmental regimes, pinpoint temperature ranges for optimal survival and help target future restoration sites that will be important for the recovery of sturgeon populations.

Gene editing and clonal isolation of human induced pluripotent stem cells using CRISPR/Cas9.

Human induced pluripotent stem cells (hiPSCs) represent an ideal in vitro platform to study human genetics and biology. The recent advent of programmable nucleases makes also the human genome amenable to experimental genetics through either the correction of mutations in patient-derived iPSC lines or the de novo introduction of mutations into otherwise healthy iPSCs. The production of specific and sometimes complex genotypes in multiple cell lines requires efficient and streamlined gene editing technologies. In this article we provide protocols for gene editing in hiPSCs. We presently achieve high rates of gene editing at up to three loci using a modified iCRISPR system. This system includes a doxycycline inducible Cas9 and sgRNA/reporter plasmids for the enrichment of transfected cells by fluorescence-activated cell sorting (FACS). Here we cover the selection of target sites, vector construction, transfection, and isolation and genotyping of modified hiPSC clones.

Control of gene editing by manipulation of DNA repair mechanisms.

DNA double-strand breaks (DSBs) are produced intentionally by RNA-guided nucleases to achieve genome editing through DSB repair. These breaks are repaired by one of two main repair pathways, classic non-homologous end joining (c-NHEJ) and homology-directed repair (HDR), the latter being restricted to the S/G2 phases of the cell cycle and notably less frequent. Precise genome editing applications rely on HDR, with the abundant c-NHEJ formed mutations presenting a barrier to achieving high rates of precise sequence modifications. Here, we give an overview of HDR- and c-NHEJ-mediated DSB repair in gene editing and summarize the current efforts to promote HDR over c-NHEJ.

Integrating lipid storage into general representations of fish energetics.

Fish, even of the same species, can exhibit substantial variation in energy density (energy per unit wet weight). Most of this variation is due to differences in the amount of storage lipids. In addition to their importance as energy reserves for reproduction and for survival during unfavourable conditions, the accumulation of lipids represents a large energetic flux for many species, so figuring out how this energy flux is integrated with other major energy fluxes (growth, reproduction) is critical for any general theory of organismal energetics. Here, we synthesize data from a wide range of fish species and identify patterns of intraspecific variation in energy storage, and use these patterns to formulate a general model of energy allocation between growth, lipid storage and reproduction in fishes. From the compiled data we identified two patterns: (1) energy density increases with body size during the juvenile period, but is invariant with body size within the adult size range for most species, and (2) energy density changes across seasons, with depletion over winter, but increases fastest in periods of transition between favourable and unfavourable conditions for growth (i.e. fall). Based on these patterns we propose DEBlipid, a simple, general model of energy allocation that is closely related to a simplified version of Dynamic Energy Budget theory, DEBkiss. The crux of the model is that assimilated energy is partitioned, with κ fraction of energy allocated to pay maintenance costs first, and the surplus allocated to growth, and 1 - κ fraction of assimilated energy is allocated to accumulating storage lipids during the juvenile phase, and later to reproduction as adults. This mechanism, in addition to capturing the two patterns that motivated the model, was able to predict lipid dynamics in a novel context, the migration of anadromous fish from low-food freshwater to high-food marine environments. Furthermore, the model was used to explain intra and interspecific variation in reproductive output based on patterns of lipid accumulation as juveniles. Our results suggest that many seemingly complex, adaptive energy allocation strategies in response to ontogeny, seasonality and habitat quality can emerge from a simple physiological heuristic.

Phenomenological vs. biophysical models of thermal stress in aquatic eggs.

Predicting species responses to climate change is a central challenge in ecology. These predictions are often based on lab-derived phenomenological relationships between temperature and fitness metrics. We tested one of these relationships using the embryonic stage of a Chinook salmon population. We parameterised the model with laboratory data, applied it to predict survival in the field, and found that it significantly underestimated field-derived estimates of thermal mortality. We used a biophysical model based on mass transfer theory to show that the discrepancy was due to the differences in water flow velocities between the lab and the field. This mechanistic approach provides testable predictions for how the thermal tolerance of embryos depends on egg size and flow velocity of the surrounding water. We found support for these predictions across more than 180 fish species, suggesting that flow and temperature mediated oxygen limitation is a general mechanism underlying the thermal tolerance of embryos.

The microscopic network structure of mussel (Mytilus) adhesive plaques.

Marine mussels of the genus Mytilus live in the hostile intertidal zone, attached to rocks, bio-fouled surfaces and each other via collagen-rich threads ending in adhesive pads, the plaques. Plaques adhere in salty, alkaline seawater, withstanding waves and tidal currents. Each plaque requires a force of several newtons to detach. Although the molecular composition of the plaques has been well studied, a complete understanding of supra-molecular plaque architecture and its role in maintaining adhesive strength remains elusive. Here, electron microscopy and neutron scattering studies of plaques harvested from Mytilus californianus and Mytilus galloprovincialis reveal a complex network structure reminiscent of structural foams. Two characteristic length scales are observed characterizing a dense meshwork (approx. 100 nm) with large interpenetrating pores (approx. 1 µm). The network withstands chemical denaturation, indicating significant cross-linking. Plaques formed at lower temperatures have finer network struts, from which we hypothesize a kinetically controlled formation mechanism. When mussels are induced to create plaques, the resulting structure lacks a well-defined network architecture, showcasing the importance of processing over self-assembly. Together, these new data provide essential insight into plaque structure and formation and set the foundation to understand the role of plaque structure in stress distribution and toughening in natural and biomimetic materials.

Boronate complex formation with Dopa containing mussel adhesive protein retards ph-induced oxidation and enables adhesion to mica.

The biochemistry of mussel adhesion has inspired the design of surface primers, adhesives, coatings and gels for technological applications. These mussel-inspired systems often focus on incorporating the amino acid 3,4-dihydroxyphenyl-L-alanine (Dopa) or a catecholic analog into a polymer. Unfortunately, effective use of Dopa is compromised by its susceptibility to auto-oxidation at neutral pH. Oxidation can lead to loss of adhesive function and undesired covalent cross-linking. Mussel foot protein 5 (Mfp-5), which contains ∼ 30 mole % Dopa, is a superb adhesive under reducing conditions but becomes nonadhesive after pH-induced oxidation. Here we report that the bidentate complexation of borate by Dopa to form a catecholato-boronate can be exploited to retard oxidation. Although exposure of Mfp-5 to neutral pH typically oxidizes Dopa, resulting in a>95% decrease in adhesion, inclusion of borate retards oxidation at the same pH. Remarkably, this Dopa-boronate complex dissociates upon contact with mica to allow for a reversible Dopa-mediated adhesion. The borate protection strategy allows for Dopa redox stability and maintained adhesive function in an otherwise oxidizing environment.

Intrinsic surface-drying properties of bioadhesive proteins.

Sessile marine mussels must "dry" underwater surfaces before adhering to them. Synthetic adhesives have yet to overcome this fundamental challenge. Previous studies of bioinspired adhesion have largely been performed under applied compressive forces, but such studies are poor predictors of the ability of an adhesive to spontaneously penetrate surface hydration layers. In a force-free approach to measuring molecular-level interaction through surface-water diffusivity, different mussel foot proteins were found to have different abilities to evict hydration layers from surfaces-a necessary step for adsorption and adhesion. It was anticipated that DOPA would mediate dehydration owing to its efficacy in bioinspired wet adhesion. Instead, hydrophobic side chains were found to be a critical component for protein-surface intimacy. This direct measurement of interfacial water dynamics during force-free adsorptive interactions at solid surfaces offers guidance for the engineering of wet adhesives and coatings.

Adaptive hydrophobic and hydrophilic interactions of mussel foot proteins with organic thin films.

The adhesion of mussel foot proteins (Mfps) to a variety of specially engineered mineral and metal oxide surfaces has previously been investigated extensively, but the relevance of these studies to adhesion in biological environments remains unknown. Most solid surfaces exposed to seawater or physiological fluids become fouled by organic conditioning films and biofilms within minutes. Understanding the binding mechanisms of Mfps to organic films with known chemical and physical properties therefore is of considerable theoretical and practical interest. Using self-assembled monolayers (SAMs) on atomically smooth gold substrates and the surface forces apparatus, we explored the force-distance profiles and adhesion energies of three different Mfps, Mfp-1, Mfp-3, and Mfp-5, on (i) hydrophobic methyl (CH3)- and (ii) hydrophilic alcohol (OH)-terminated SAM surfaces between pH 3 and pH 7.5. At acidic pH, all three Mfps adhered strongly to the CH3-terminated SAM surfaces via hydrophobic interactions (range of adhesive interaction energy = -4 to -9 mJ/m(2)) but only weakly to the OH-terminated SAM surfaces through H- bonding (adhesive interaction energy ≤ -0.5 mJ/m(2)). 3, 4-Dihydroxyphenylalanine (Dopa) residues in Mfps mediate binding to both SAM surface types but do so through different interactions: typical bidentate H-bonding by Dopa is frustrated by the longer spacing of OH-SAMs; in contrast, on CH3-SAMs, Dopa in synergy with other nonpolar residues partitions to the hydrophobic surface. Asymmetry in the distribution of hydrophobic residues in intrinsically unstructured proteins, the distortion of bond geometry between H-bonding surfaces, and the manipulation of physisorbed binding lifetimes represent important concepts for the design of adhesive and nonfouling surfaces.

Adhesion of mussel foot proteins to different substrate surfaces.

Mussel foot proteins (mfps) have been investigated as a source of inspiration for the design of underwater coatings and adhesives. Recent analysis of various mfps by a surface forces apparatus (SFA) revealed that mfp-1 functions as a coating, whereas mfp-3 and mfp-5 resemble adhesive primers on mica surfaces. To further refine and elaborate the surface properties of mfps, the force-distance profiles of the interactions between thin mfp (i.e. mfp-1, mfp-3 or mfp-5) films and four different surface chemistries, namely mica, silicon dioxide, polymethylmethacrylate and polystyrene, were measured by an SFA. The results indicate that the adhesion was exquisitely dependent on the mfp tested, the substrate surface chemistry and the contact time. Such studies are essential for understanding the adhesive versatility of mfps and related/similar adhesion proteins, and for translating this versatility into a new generation of coatings and (including in vivo) adhesive materials.

Adhesion of mussel foot protein Mefp-5 to mica: an underwater superglue.

Mussels have a remarkable ability to attach their holdfast, or byssus, opportunistically to a variety of substrata that are wet, saline, corroded, and/or fouled by biofilms. Mytilus edulis foot protein-5 (Mefp-5) is one of several proteins in the byssal adhesive plaque of the mussel M. edulis. The high content of 3,4-dihydroxyphenylalanine (Dopa) (~30 mol %) and its localization near the plaque-substrate interface have often prompted speculation that Mefp-5 plays a key role in adhesion. Using the surface forces apparatus, we show that on mica surfaces Mefp-5 achieves an adhesion energy approaching E(ad) = ~-14 mJ/m(2). This exceeds the adhesion energy of another interfacial protein, Mefp-3, by a factor of 4-5 and is greater than the adhesion between highly oriented monolayers of biotin and streptavidin. The adhesion to mica is notable for its dependence on Dopa, which is most stable under reducing conditions and acidic pH. Mefp-5 also exhibits strong protein-protein interactions with itself as well as with Mefp-3 from M. edulis.

Mussel protein adhesion depends on interprotein thiol-mediated redox modulation.

Mussel adhesion is mediated by foot proteins (mfps) rich in a catecholic amino acid, 3,4-dihydroxyphenylalanine (dopa), capable of forming strong bidentate interactions with a variety of surfaces. A tendency toward facile auto-oxidation, however, often renders dopa unreliable for adhesion. We demonstrate that mussels limit dopa oxidation during adhesive plaque formation by imposing an acidic, reducing regime based on the thiol-rich mfp-6, which restores dopa by coupling the oxidation of thiols to dopaquinone reduction.