A Type II-B Cas9 nuclease with minimized off-targets and reduced chromosomal translocations in vivo

Streptococcus pyogenes Cas9 (SpCas9) and derived enzymes are widely used as genome editors, but their promiscuous nuclease activity often induces undesired mutations and chromosomal rearrangements. Several strategies for mapping off-target effects have emerged, but they suffer from limited sensitivity. To increase the detection sensitivity, we develop an off-target assessment workflow that uses Duplex Sequencing. The strategy increases sensitivity by one order of magnitude, identifying previously unknown SpCas9's off-target mutations in the humanized PCSK9 mouse model. To reduce off-target risks, we perform a bioinformatic search and identify a high-fidelity Cas9 variant of the II-B subfamily from Parasutterella secunda (PsCas9). PsCas9 shows improved specificity as compared to SpCas9 across multiple tested sites, both in vitro and in vivo, including the PCSK9 site. In the future, while PsCas9 will offer an alternative to SpCas9 for research and clinical use, the Duplex Sequencing workflow will enable a more sensitive assessment of Cas9 editing outcomes.

Simultaneous inhibition of DNA-PK and Polϴ improves integration efficiency and precision of genome editing

Genome editing, specifically CRISPR/Cas9 technology, has revolutionized biomedical research and offers potential cures for genetic diseases. Despite rapid progress, low efficiency of targeted DNA integration and generation of unintended mutations represent major limitations for genome editing applications caused by the interplay with DNA double-strand break repair pathways. To address this, we conduct a large-scale compound library screen to identify targets for enhancing targeted genome insertions. Our study reveals DNA-dependent protein kinase (DNA-PK) as the most effective target to improve CRISPR/Cas9-mediated insertions, confirming previous findings. We extensively characterize AZD7648, a selective DNA-PK inhibitor, and find it to significantly enhance precise gene editing. We further improve integration efficiency and precision by inhibiting DNA polymerase theta (Polϴ). The combined treatment, named 2iHDR, boosts templated insertions to 80% efficiency with minimal unintended insertions and deletions. Notably, 2iHDR also reduces off-target effects of Cas9, greatly enhancing the fidelity and performance of CRISPR/Cas9 gene editing.

Harnessing DSB repair to promote efficient homology-dependent and -independent prime editing

Prime editing recently emerged as a next-generation approach for precise genome editing. Here we exploit DNA double-strand break (DSB) repair to develop two strategies that install precise genomic insertions using an SpCas9 nuclease-based prime editor (PEn). We first demonstrate that PEn coupled to a regular prime editing guide RNA (pegRNA) efficiently promotes short genomic insertions through a homology-dependent DSB repair mechanism. While PEn editing leads to increased levels of by-products, it can rescue pegRNAs that perform poorly with a nickase-based prime editor. We also present a small molecule approach that yields increased product purity of PEn editing. Next, we develop a homology-independent PEn editing strategy, which installs genomic insertions at DSBs through the non-homologous end joining pathway (NHEJ). Lastly, we show that PEn-mediated insertions at DSBs prevent Cas9-induced large chromosomal deletions and provide evidence that continuous Cas9-mediated cutting is one of the mechanisms by which Cas9-induced large deletions arise. Altogether, this work expands the current prime editing toolbox by leveraging distinct DNA repair mechanisms including NHEJ, which represents the primary pathway of DSB repair in mammalian cells.

Prime editing is a next-generation approach for precision genome engineering. Here the authors design a nuclease-based prime editor that leverages DNA repair pathways for targeted genomic insertions.

Universal toxin-based selection for precise genome engineering in human cells

Prokaryotic restriction enzymes, recombinases and Cas proteins are powerful DNA engineering and genome editing tools. However, in many primary cell types, the efficiency of genome editing remains low, impeding the development of gene- and cell-based therapeutic applications. A safe strategy for robust and efficient enrichment of precisely genetically engineered cells is urgently required. Here, we screen for mutations in the receptor for Diphtheria Toxin (DT) which protect human cells from DT. Selection for cells with an edited DT receptor variant enriches for simultaneously introduced, precisely targeted gene modifications at a second independent locus, such as nucleotide substitutions and DNA insertions. Our method enables the rapid generation of a homogenous cell population with bi-allelic integration of a DNA cassette at the selection locus, without clonal isolation. Toxin-based selection works in both cancer-transformed and non-transformed cells, including human induced pluripotent stem cells and human primary T-lymphocytes, as well as it is applicable also in vivo, in mice with humanized liver. This work represents a flexible, precise, and efficient selection strategy to engineer cells using CRISPR-Cas and base editing systems.

Molecular Nanomagnets as Qubits with Embedded Quantum-Error Correction

We show that molecular nanomagnets have a potential advantage in the crucial rush toward quantum computers. Indeed, the sizable number of accessible low-energy states of these systems can be exploited to define qubits with embedded quantum error correction. We derive the scheme to achieve this crucial objective and the corresponding sequence of microwave/radiofrequency pulses needed for the error correction procedure. The effectiveness of our approach is shown already with a minimal S = 3/2 unit corresponding to an existing molecule, and the scaling to larger spin systems is quantitatively analyzed.

Molecular Nanomagnets as Qubits with Embedded Quantum-Error Correction

We show that molecular nanomagnets have a potential advantage in the crucial rush toward quantum computers. Indeed, the sizable number of accessible low-energy states of these systems can be exploited to define qubits with embedded quantum error correction. We derive the scheme to achieve this crucial objective and the corresponding sequence of microwave/radiofrequency pulses needed for the error correction procedure. The effectiveness of our approach is shown already with a minimal S = 3/2 unit corresponding to an existing molecule, and the scaling to larger spin systems is quantitatively analyzed.

Development of an ObLiGaRe Doxycycline Inducible Cas9 system for pre-clinical cancer drug discovery

The CRISPR-Cas9 system has increased the speed and precision of genetic editing in cells and animals. However, model generation for drug development is still expensive and time-consuming, demanding more target flexibility and faster turnaround times with high reproducibility. The generation of a tightly controlled ObLiGaRe doxycycline inducible SpCas9 (ODInCas9) transgene and its use in targeted ObLiGaRe results in functional integration into both human and mouse cells culminating in the generation of the ODInCas9 mouse. Genomic editing can be performed in cells of various tissue origins without any detectable gene editing in the absence of doxycycline. Somatic in vivo editing can model non-small cell lung cancer (NSCLC) adenocarcinomas, enabling treatment studies to validate the efficacy of candidate drugs. The ODInCas9 mouse allows robust and tunable genome editing granting flexibility, speed and uniformity at less cost, leading to high throughput and practical preclinical in vivo therapeutic testing.

TCR Fingerprinting and Off-Target Peptide Identification

Adoptive T cell therapy using patient T cells redirected to recognize tumor-specific antigens by expressing genetically engineered high-affinity T-cell receptors (TCRs) has therapeutic potential for melanoma and other solid tumors. Clinical trials implementing genetically modified TCRs in melanoma patients have raised concerns regarding off-target toxicities resulting in lethal destruction of healthy tissue, highlighting the urgency of assessing which off-target peptides can be recognized by a TCR. As a model system we used the clinically efficacious NY-ESO-1-specific TCR C²⁵⁹, which recognizes the peptide epitope SLLMWITQC presented by HLA-A^*02:01. We investigated which amino acids at each position enable a TCR interaction by sequentially replacing every amino acid position outside of anchor positions 2 and 9 with all 19 possible alternative amino acids, resulting in 134 peptides (133 altered peptides plus epitope peptide). Each peptide was individually evaluated using three different in vitro assays: binding of the NY-ESO^c259 TCR to the peptide, peptide-dependent activation of TCR-expressing cells, and killing of peptide-presenting target cells. To represent the TCR recognition kernel, we defined Position Weight Matrices (PWMs) for each assay by assigning normalized measurements to each of the 20 amino acids in each position. To predict potential off-target peptides, we applied a novel algorithm projecting the PWM-defined kernel into the human proteome, scoring NY-ESO^c259 TCR recognition of 336,921 predicted human HLA-A^*02:01 binding 9-mer peptides. Of the 12 peptides with high predicted score, we confirmed 7 (including NY-ESO-1 antigen SLLMWITQC) strongly activate human primary NY-ESO^c259-expressing T cells. These off-target peptides include peptides with up to 7 amino acid changes (of 9 possible), which could not be predicted using the recognition motif as determined by alanine scans. Thus, this replacement scan assay determines the “TCR fingerprint” and, when coupled with the algorithm applied to the database of human 9-mer peptides binding to HLA-A^*02:01, enables the identification of potential off-target antigens and the tissues where they are expressed. This platform enables both screening of multiple TCRs to identify the best candidate for clinical development and identification of TCR-specific cross-reactive peptide recognition and constitutes an improved methodology for the identification of potential off-target peptides presented on MHC class I molecules.

Biomimetic Remineralization of Carious Lesions by Self-Assembling Peptide

Caries is the most common disease in the world. Great efforts have been undertaken for prevention and to identify a regenerative treatment solution for dental caries. Self-assembling β-sheet forming peptides have previously shown to form 3-dimensional fiber networks supporting tissue regeneration. In particular, the self-assembling peptide P₁₁-4 has shown potential in the treatment and prevention of dental caries. It has previously been shown that application of monomeric P₁₁-4 solution to early carious lesions can increase net mineral gain by forming de novo hydroxyapatite crystals. The hypothesis for the mode of action was that monomeric self-assembling peptide P₁₁-4 diffuses into the subsurface lesion body and assembles therein into higher order fibrils, facilitating mineralization of the subsurface volume by mimicking the natural biomineralization of the tooth enamel, and it remains within the lesion body as a scaffold built-in by the newly formed hydroxyapatite. The aim of the present study was to investigate the mechanism of action of the self-assembling peptide P₁₁-4 supporting mineralization of carious enamel. By various analytical methods, it could be shown that the self-assembling peptide P₁₁-4 diffuses into the subsurface lesion, assembles into higher formed aggregates throughout the whole volume of the lesion, and supports nucleation of de novo hydroxyapatite nanocrystals and consequently results in increased mineral density within the subsurface carious lesion. The results showed that the application of self-assembling peptide P₁₁-4 can facilitate the subsurface regeneration of the enamel lesion by supporting de novo mineralization in a similar mode of action as has been shown for the natural formation of dental enamel.

Dynamical tunneling of a Bose-Einstein condensate in periodically driven systems

We report measurements of dynamical tunneling rates of a Bose-Einstein condensate across a barrier in classical phase space. The atoms are initially prepared in quantum states that extend over a classically regular island region. We focus on the specific system of quantum accelerator modes of the kicked rotor in the presence of gravity. Our experimental data is supported by numerical simulations taking into account imperfections mainly from spontaneous emission. Furthermore, we predict experimentally accessible parameter ranges over which direct tunneling could be readily observed if spontaneous emission was further suppressed. Altogether, we provide a proof-of-principle for the experimental accessibility of dynamical tunneling rates in periodically driven systems.

Fidelity of the quantum δ-kicked accelerator

The sensitivity of the fidelity in the kicked rotor to an acceleration is experimentally and theoretically investigated. We used a Bose-Einstein condensate exposed to a sequence of pulses from a standing light wave followed by a single reversal pulse in which the standing wave was shifted by half a wavelength. The features of the fidelity "spectrum" as a function of acceleration are presented. This work may find applications in the measurement of temperature of an ultracold atomic sample.

Time-resolved measurement of Landau-Zener tunneling in periodic potentials

We report time-resolved measurements of Landau-Zener tunneling of Bose-Einstein condensates in accelerated optical lattices, clearly resolving the steplike time dependence of the band populations. Using different experimental protocols we were able to measure the tunneling probability both in the adiabatic and in the diabatic bases of the system. We also experimentally determine the contribution of the momentum width of the Bose condensates to the temporal width of the tunneling steps and discuss the implications for measuring the jump time in the Landau-Zener problem.

Dissipation induced coherence of a two-mode Bose-Einstein condensate

We discuss the dynamics of a Bose-Einstein condensate in a double-well trap subject to phase noise and particle loss. The phase coherence of a weakly interacting condensate as well as the response to an external driving show a pronounced stochastic resonance effect: Both quantities become maximal for a finite value of the dissipation rate matching the intrinsic time scales of the system. Even stronger effects are observed when dissipation acts in concurrence with strong interparticle interactions, restoring the purity of the condensate almost completely and increasing the phase coherence significantly.

Resonantly enhanced tunneling of Bose-Einstein condensates in periodic potentials

We report on measurements of resonantly enhanced tunneling of Bose-Einstein condensates loaded into an optical lattice. By controlling the initial conditions of our system we were able to observe resonant tunneling in the ground and the first two excited states of the lattice wells. We also investigated the effect of the intrinsic nonlinearity of the condensate on the tunneling resonances.