Optogenetic control of Neisseria meningitidis Cas9 genome editing using an engineered, light-switchable anti-CRISPR protein.

Optogenetic control of CRISPR-Cas9 systems has significantly improved our ability to perform genome perturbations in living cells with high precision in time and space. As new Cas orthologues with advantageous properties are rapidly being discovered and engineered, the need for straightforward strategies to control their activity via exogenous stimuli persists. The Cas9 from Neisseria meningitidis (Nme) is a particularly small and target-specific Cas9 orthologue, and thus of high interest for in vivo genome editing applications. Here, we report the first optogenetic tool to control NmeCas9 activity in mammalian cells via an engineered, light-dependent anti-CRISPR (Acr) protein. Building on our previous Acr engineering work, we created hybrids between the NmeCas9 inhibitor AcrIIC3 and the LOV2 blue light sensory domain from Avena sativa. Two AcrIIC3-LOV2 hybrids from our collection potently blocked NmeCas9 activity in the dark, while permitting robust genome editing at various endogenous loci upon blue light irradiation. Structural analysis revealed that, within these hybrids, the LOV2 domain is located in striking proximity to the Cas9 binding surface. Together, our work demonstrates optogenetic regulation of a type II-C CRISPR effector and might suggest a new route for the design of optogenetic Acrs.

Computational design of anti-CRISPR proteins with improved inhibition potency.

Anti-CRISPR (Acr) proteins are powerful tools to control CRISPR-Cas technologies. However, the available Acr repertoire is limited to naturally occurring variants. Here, we applied structure-based design on AcrIIC1, a broad-spectrum CRISPR-Cas9 inhibitor, to improve its efficacy on different targets. We first show that inserting exogenous protein domains into a selected AcrIIC1 surface site dramatically enhances inhibition of Neisseria meningitidis (Nme)Cas9. Then, applying structure-guided design to the Cas9-binding surface, we converted AcrIIC1 into AcrIIC1X, a potent inhibitor of the Staphylococcus aureus (Sau)Cas9, an orthologue widely applied for in vivo genome editing. Finally, to demonstrate the utility of AcrIIC1X for genome engineering applications, we implemented a hepatocyte-specific SauCas9 ON-switch by placing AcrIIC1X expression under regulation of microRNA-122. Our work introduces designer Acrs as important biotechnological tools and provides an innovative strategy to safeguard CRISPR technologies.

Are some effector systems harder to switch to? In search of cost asymmetries when switching between manual, vocal, and oculomotor tasks.

In task-switching studies, performance is typically worse in task-switch trials than in task-repetition trials. These switch costs are often asymmetrical, a phenomenon that has been explained by referring to a dominance of one task over the other. Previous studies also indicated that response modalities associated with two tasks may be considered as integral components for defining a task set. However, a systematic assessment of the role of response modalities in task switching is still lacking: Are some response modalities harder to switch to than others? The present study systematically examined switch costs when combining tasks that differ only with respect to their associated effector systems. In Experiment 1, 16 participants switched (in unpredictable sequence) between oculomotor and vocal tasks. In Experiment 2, 72 participants switched (in pairwise combinations) between oculomotor, vocal, and manual tasks. We observed systematic performance costs when switching between response modalities under otherwise constant task features and could thereby replicate previous observations of response modality switch costs. However, we did not observe any substantial switch-cost asymmetries. As previous studies using temporally overlapping dual-task paradigms found substantial prioritization effects (in terms of asymmetric costs) especially for oculomotor tasks, the present results suggest different underlying processes in sequential task switching than in simultaneous multitasking. While more research is needed to further substantiate a lack of response modality switch-cost asymmetries in a broader range of task switching situations, we suggest that task-set representations related to specific response modalities may exhibit rapid decay.

Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9.

Anti-CRISPR proteins are powerful tools for CRISPR-Cas9 regulation; the ability to precisely modulate their activity could facilitate spatiotemporally confined genome perturbations and uncover fundamental aspects of CRISPR biology. We engineered optogenetic anti-CRISPR variants comprising hybrids of AcrIIA4, a potent Streptococcus pyogenes Cas9 inhibitor, and the LOV2 photosensor from Avena sativa. Coexpression of these proteins with CRISPR-Cas9 effectors enabled light-mediated genome and epigenome editing, and revealed rapid Cas9 genome targeting in human cells.

Cell-specific CRISPR-Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins.

The rapid development of CRISPR-Cas technologies brought a personalized and targeted treatment of genetic disorders into closer reach. To render CRISPR-based therapies precise and safe, strategies to confine the activity of Cas(9) to selected cells and tissues are highly desired. Here, we developed a cell type-specific Cas-ON switch based on miRNA-regulated expression of anti-CRISPR (Acr) proteins. We inserted target sites for miR-122 or miR-1, which are abundant specifically in liver and cardiac muscle cells, respectively, into the 3'UTR of Acr transgenes. Co-expressing these with Cas9 and sgRNAs resulted in Acr knockdown and released Cas9 activity solely in hepatocytes or cardiomyocytes, while Cas9 was efficiently inhibited in off-target cells. We demonstrate control of genome editing and gene activation using a miR-dependent AcrIIA4 in combination with different Streptococcus pyogenes (Spy)Cas9 variants (full-length Cas9, split-Cas9, dCas9-VP64). Finally, to showcase its modularity, we adapted our Cas-ON system to the smaller and more target-specific Neisseria meningitidis (Nme)Cas9 orthologue and its cognate inhibitors AcrIIC1 and AcrIIC3. Our Cas-ON switch should facilitate cell-specific activity of any CRISPR-Cas orthologue, for which a potent anti-CRISPR protein is known.

Optical analysis of cellular oxygen sensing.

Molecular imaging of the assembly of hypoxia inducible factor (HIF) complexes in living cells may lead to a deeper understanding of cellular oxygen sensing. Sophisticated live cell imaging has extended the toolbox to study the molecular response to changes in oxygen supply. In this respect fluorescence resonance energy transfer (FRET) as a technique to investigate protein-protein interaction in the nanoscale range gets increasing interest. Herein, we review FRET studies related to hypoxia research, emphasizing on recent progress, but also demonstrating how FRET studies are complementary or potentially superior to conventional biochemical as well as histochemical techniques. Technical advances in the application of FRET in living cells will overcome restrictions to end-point analysis on the population rather than single cell level and will thereby provide progress in understanding the cellular hypoxic response by HIF.

Unlocking precision gene therapy: harnessing AAV tropism with nanobody swapping at capsid hotspots.

Adeno-associated virus (AAV) has been remarkably successful in the clinic, but its broad tropism is a practical limitation of precision gene therapy. A promising path to engineer AAV tropism is the addition of binding domains to the AAV capsid that recognize cell surface markers present on a targeted cell type. We have recently identified two previously unexplored capsid regions near the 2/5-fold wall and 5-fold pore of the AAV capsid that are amenable to insertion of larger protein domains, including nanobodies. Here, we demonstrate that these hotspots facilitate AAV tropism switching through simple nanobody replacement without extensive optimization in both VP1 and VP2. Our data suggest that engineering VP2 is the preferred path for maintaining both virus production yield and infectivity. We demonstrate highly specific targeting of human cancer cells expressing fibroblast activating protein (FAP). Furthermore, we found that the combination of FAP nanobody insertion plus ablation of the heparin binding domain can reduce off-target infection to a minimum, while maintaining a strong infection of FAP receptor-positive cells. Taken together, our study shows that nanobody swapping at multiple capsid locations is a viable strategy for nanobody-directed cell-specific AAV targeting.

Unlocking Precision Gene Therapy: Harnessing AAV Tropism with Nanobody Swapping at Capsid Hotspots.

Adeno-associated virus has been remarkably successful in the clinic, but its broad tropism is a practical limitation of precision gene therapy. A promising path to engineer AAV tropism is the addition of binding domains to the AAV capsid that recognize cell surface markers present on a targeted cell type. We have recently identified two previously unexplored capsid regions near the 2-fold valley and 5-fold pore of the AAV capsid that are amenable to insertion of larger protein domains including nanobodies. Here, we demonstrate that these hotspots facilitate AAV tropism switching through simple nanobody replacement without extensive optimization in both VP1 and VP2. We demonstrate highly specific targeting of human cancer cells expressing fibroblast activating protein (FAP). Our data suggest that engineering VP2 is the preferred path for maintaining both virus production yield and infectivity. Our study shows that nanobody swapping at multiple capsid location is a viable strategy for nanobody-directed cell-specific AAV targeting.

Multiparametric domain insertional profiling of Adeno-Associated Virus VP1.

Evolved properties of Adeno-Associated Virus (AAV), such as broad tropism and immunogenicity in humans, are barriers to AAV-based gene therapy. Previous efforts to re-engineer these properties have focused on variable regions near AAV’s 3-fold protrusions and capsid protein termini. To comprehensively survey AAV capsids for engineerable hotspots, we determined multiple AAV fitness phenotypes upon insertion of large, structured protein domains into the entire AAV-DJ capsid protein VP1. This is the largest and most comprehensive AAV domain insertion dataset to date. Our data revealed a surprising robustness of AAV capsids to accommodate large domain insertions. There was strong positional, domain-type, and fitness phenotype dependence of insertion permissibility, which clustered into correlated structural units that we could link to distinct roles in AAV assembly, stability, and infectivity. We also identified new engineerable hotspots of AAV that facilitate the covalent attachment of binding scaffolds, which may represent an alternative approach to re-direct AAV tropism.

Multiparametric domain insertional profiling of adeno-associated virus VP1.

Several evolved properties of adeno-associated virus (AAV), such as broad tropism and immunogenicity in humans, are barriers to AAV-based gene therapy. Most efforts to re-engineer these properties have focused on variable regions near AAV's 3-fold protrusions and capsid protein termini. To comprehensively survey AAV capsids for engineerable hotspots, we determined multiple AAV fitness phenotypes upon insertion of six structured protein domains into the entire AAV-DJ capsid protein VP1. This is the largest and most comprehensive AAV domain insertion dataset to date. Our data revealed a surprising robustness of AAV capsids to accommodate large domain insertions. Insertion permissibility depended strongly on insertion position, domain type, and measured fitness phenotype, which clustered into contiguous structural units that we could link to distinct roles in AAV assembly, stability, and infectivity. We also identified engineerable hotspots of AAV that facilitate the covalent attachment of binding scaffolds, which may represent an alternative approach to re-direct AAV tropism.

Task-order representations in dual tasks: Separate or integrated with component task sets?

In situations requiring the execution of two tasks at around the same time, we need to decide which of the tasks should be executed first. Previous research has revealed several factors that affect the outcome of such response order control processes, including bottom-up factors (e.g., the temporal order of the stimuli associated with the two tasks) and top-down factors (e.g., instructions). In addition, it has been shown that tasks associated with certain response modalities are preferably executed first (e.g., temporal prioritisation of tasks involving oculomotor responses). In this study, we focused on a situation in which task order has to be unpredictably switched from trial to trial and asked whether task-order representations are coded separately or integrated with the component task sets (i.e., in a task-specific manner). Across three experiments, we combined two tasks known to differ in prioritisation, namely an oculomotor and a manual (or pedal) task. The results indicated robust task-order switch costs (i.e., longer RTs when task order was switched vs. repeated). Importantly, the data demonstrate that it is possible to show an asymmetry of task-order switch costs: While these costs were of similar size for both task orders in one particular experimental setting with specific spatial task characteristics, two experiments consistently indicated that it was easier for participants to switch to their prioritised task order (i.e., to execute the dominant oculomotor task first). This suggests that in a situation requiring frequent task-order switches (indicated by unpredictable changes in stimulus order), task order is represented in an integrated, task-specific manner, bound to characteristics (here, associated effector systems) of the component tasks.

Light-Inducible CRISPR Labeling.

CRISPR labeling is a powerful technique to study the chromatin architecture in live cells. In CRISPR labeling, a catalytically dead CRISPR-Cas9 mutant is employed as programmable DNA-binding domain to recruit fluorescent proteins to selected genomic loci. The fluorescently labeled loci can then be identified as fluorescent spots and tracked over time by microscopy. A limitation of this approach is the lack of temporal control of the labeling process itself: Cas9 binds to the g(uide)RNA-complementary target loci as soon as it is expressed. The decoration of the genome with Cas9 molecules will, however, interfere with gene regulation and-possibly-affect the genome architecture itself. The ability to switch on and off Cas9 DNA binding in CRISPR labeling experiments would thus be important to enable more precise interrogations of the chromatin spatial organization and dynamics and could further be used to study Cas9 DNA binding kinetics directly in living human cells.Here, we describe a detailed protocol for light-inducible CRISPR labeling. Our method employs CASANOVA, an engineered, optogenetic anti-CRISPR protein, which efficiently traps the Streptococcus pyogenes (Spy)Cas9 in the dark, but permits Cas9 DNA targeting upon illumination with blue light. Using telomeres as exemplary target loci, we detail the experimental steps required for inducible CRISPR labeling with CASANOVA. We also provide instructions on how to analyze the resulting microscopy data in a fully automated fashion.

Optogenetics and CRISPR: A New Relationship Built to Last.

Since the breakthrough discoveries that CRISPR-Cas9 nucleases can be easily programmed and employed to induce targeted double-strand breaks in mammalian cells, the gene editing field has grown exponentially. Today, CRISPR technologies based on engineered class II CRISPR effectors facilitate targeted modification of genes and RNA transcripts. Moreover, catalytically impaired CRISPR-Cas variants can be employed as programmable DNA binding domains and used to recruit effector proteins, such as transcriptional regulators, epigenetic modifiers or base-modifying enzymes, to selected genomic loci. The juxtaposition of CRISPR and optogenetics enables spatiotemporally confined and highly dynamic genome perturbations in living cells and animals and holds unprecedented potential for biology and biomedicine.Here, we provide an overview of the state-of-the-art methods for light-control of CRISPR effectors. We will detail the plethora of exciting applications enabled by these systems, including spatially confined genome editing, timed activation of endogenous genes, as well as remote control of chromatin-chromatin interactions. Finally, we will discuss limitations of current optogenetic CRISPR tools and point out routes for future innovation in this emerging field.

Effects of Input Modality on Vocal Effector Prioritization in Manual-Vocal Dual Tasks.

Doing two things at once (vs. one in isolation) usually yields performance costs. Such decrements are often distributed asymmetrically between the two actions involved, reflecting different processing priorities. A previous study (Huestegge & Koch, 2013) demonstrated that the particular effector systems associated with the two actions can determine the pattern of processing priorities: Vocal responses were prioritized over manual responses, as indicated by smaller performance costs (associated with dual-action demands) for the former. However, this previous study only involved auditory stimulation (for both actions). Given that previous research on input-output modality compatibility in dual tasks suggested that pairing auditory input with vocal output represents a particularly advantageous mapping, the question arises whether the observed vocal-over-manual prioritization was merely a consequence of auditory stimulation. To resolve this issue, we conducted a manual-vocal dual task study using either only auditory or only visual stimuli for both responses. We observed vocal-over-manual prioritization in both stimulus modality conditions. This suggests that input-output modality mappings can (to some extent) attenuate, but not abolish/reverse effector-based prioritization. Taken together, effector system pairings appear to have a more substantial impact on capacity allocation policies in dual-task control than input-output modality combinations.

Two sources of task prioritization: The interplay of effector-based and task order-based capacity allocation in the PRP paradigm.

When processing of two tasks overlaps, performance is known to suffer. In the well-established psychological refractory period (PRP) paradigm, tasks are triggered by two stimuli with a short temporal delay (stimulus onset asynchrony; SOA), thereby allowing control of the degree of task overlap. A decrease of the SOA reliably yields longer RTs of the task associated with the second stimulus (Task 2) while performance in the other task (Task 1) remains largely unaffected. This Task 2-specific SOA effect is usually interpreted in terms of central capacity limitations. Particularly, it has been assumed that response selection in Task 2 is delayed due to the allocation of less capacity until this process has been completed in Task 1. Recently, another important factor determining task prioritization has been proposed-namely, the particular effector systems associated with tasks. Here, we study both sources of task prioritization simultaneously by systematically combining three different effector systems (pairwise combinations of oculomotor, vocal, and manual responses) in the PRP paradigm. Specifically, we asked whether task order-based task prioritization (SOA effect) is modulated as a function of Task 2 effector system. The results indicate a modulation of SOA effects when the same (oculomotor) Task 1 is combined with a vocal versus a manual Task 2. This is incompatible with the assumption that SOA effects are solely determined by Task 1 response selection duration. Instead, they support the view that dual-task processing bottlenecks are resolved by establishing a capacity allocation scheme fed by multiple input factors, including attentional weights associated with particular effector systems.

Coupling Cas9 to artificial inhibitory domains enhances CRISPR-Cas9 target specificity.

The limited target specificity of CRISPR-Cas nucleases poses a challenge with respect to their application in research and therapy. Here, we present a simple and original strategy to enhance the specificity of CRISPR-Cas9 genome editing by coupling Cas9 to artificial inhibitory domains. Applying a combination of mathematical modeling and experiments, we first determined how CRISPR-Cas9 activity profiles relate to Cas9 specificity. We then used artificially weakened anti-CRISPR (Acr) proteins either coexpressed with or directly fused to Cas9 to fine-tune its activity toward selected levels, thereby achieving an effective kinetic insulation of ON- and OFF-target editing events. We demonstrate highly specific genome editing in mammalian cells using diverse single-guide RNAs prone to potent OFF-targeting. Last, we show that our strategy is compatible with different modes of delivery, including transient transfection and adeno-associated viral vectors. Together, we provide a highly versatile approach to reduce CRISPR-Cas OFF-target effects via kinetic insulation.

Motor sources of dual-task interference: Evidence for effector-based prioritization in dual-task control.

Dual tasking is known to yield performance costs. Corresponding research has often focused on early or central task processing stages, that is, on features related to stimulus processing or response selection. Here, we demonstrate the important role of the final (late) stage of task processing by studying effects of effector system combinations. We used pairwise combinations of tasks requiring oculomotor, manual, vocal, and pedal responses, triggered by visual/auditory stimuli. Across task combinations, we compared dual-task costs among effector systems (e.g., oculomotor, vocal, and pedal) under controlled conditions, that is, when combined with the same "context effector" (e.g., manual) in the other task. The dual-task cost pattern was strongly determined by the particular combination of effector systems in line with the assumption of an ordinal effector-based prioritization pattern (oculomotor > pedal > vocal > manual), and could not be explained by classic "first-come, first-served" accounts of central processing. Stimulus modality and its mapping to effector systems affected reaction times (RTs), but the impact on the general prioritization scheme was negligible, suggesting a more substantial influence of output (compared with input) system characteristics on dual-task capacity scheduling. The results call for a distinct effector system weighting mechanism in models of dual-task control. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Determination of content and fatty acid composition of unlabeled phosphoinositide species by thin-layer chromatography and gas chromatography.

Recent advances in research on the physiological roles of phosphoinositides in eukaryotic organisms indicate a need to distinguish molecular phosphoinositide species on the basis of their characteristic head groups as well as their glycerolipid moieties. Accurate identification of phosphoinositide species in biological samples poses an analytical challenge, because structurally similar inositol phosphate head groups must be resolved, as must lipid-associated fatty acids. Although intact phosphoinositide species have been successfully analyzed, such analyses employ state-of-the-art liquid chromatography/mass spectrometry and require expensive equipment not accessible to many researchers. Described here is a cost-efficient and reliable alternative developed by adaptation of a combination of classic methods for lipid analysis, thin-layer chromatography and gas chromatography.

Essential role of EBF1 in the generation and function of distinct mature B cell types.

The transcription factor EBF1 is essential for lineage specification in early B cell development. In this study, we demonstrate by conditional mutagenesis that EBF1 is required for B cell commitment, pro-B cell development, and subsequent transition to the pre-B cell stage. Later in B cell development, EBF1 was essential for the generation and maintenance of several mature B cell types. Marginal zone and B-1 B cells were lost, whereas follicular (FO) and germinal center (GC) B cells were reduced in the absence of EBF1. Activation of the B cell receptor resulted in impaired intracellular signaling, proliferation and survival of EBF1-deficient FO B cells. Immune responses were severely reduced upon Ebf1 inactivation, as GCs were formed but not maintained. ChIP- and RNA-sequencing of FO B cells identified EBF1-activated genes that encode receptors, signal transducers, and transcriptional regulators implicated in B cell signaling. Notably, ectopic expression of EBF1 efficiently induced the development of B-1 cells at the expense of conventional B cells. These gain- and loss-of-function analyses uncovered novel important functions of EBF1 in controlling B cell immunity.

Metabolic engineering of omega3-very long chain polyunsaturated fatty acid production by an exclusively acyl-CoA-dependent pathway.

omega3-Very long chain polyunsaturated fatty acids (VLCPUFA) are essential for human development and brain function and, thus, are indispensable components of the human diet. The current main source of VLCPUFAs is represented by ocean fish stocks, which are in severe decline, and the development of alternative, sustainable sources of VLCPUFAs is urgently required. Our research aims at exploiting the powerful infrastructure available for the large scale culture of oilseed crops, such as rapeseed, to produce VLCPUFAs such as eicosapentaenoic acid in transgenic plants. VLCPUFA biosynthesis requires repeated desaturation and repeated elongation of long chain fatty acid substrates. In previous experiments the production of eicosapentaenoic acid in transgenic plants was found to be limited by an unexpected bottleneck represented by the acyl exchange between the site of desaturation, endoplasmic reticulum-associated phospholipids, and the site of elongation, the cytosolic acyl-CoA pool. Here we report on the establishment of a coordinated, exclusively acyl-CoA-dependent pathway, which avoids the rate-limiting transesterification steps between the acyl lipids and the acyl-CoA pool during VLCPUFA biosynthesis. The pathway is defined by previously uncharacterized enzymes, encoded by cDNAs isolated from the microalga Mantoniella squamata. The conceptual enzymatic pathway was established and characterized first in yeast to provide proof-of-concept data for its feasibility and subsequently in seeds of Arabidopsis thaliana. The comparison of the acyl-CoA-dependent pathway with the known lipid-linked pathway for VLCPUFA biosynthesis showed that the acyl-CoA-dependent pathway circumvents the bottleneck of switching the Delta6-desaturated fatty acids between lipids and acyl-CoA in Arabidopsis seeds.