PCDH15 Dual-AAV Gene Therapy for Deafness and Blindness in Usher Syndrome Type 1F

Usher syndrome type 1F (USH1F), resulting from mutations in the protocadherin-15 (PCDH15) gene, is characterized by congenital lack of hearing and balance, and progressive blindness in the form of retinitis pigmentosa. In this study, we explore a novel approach for USH1F gene therapy, exceeding the single AAV packaging limit by employing a dual adeno-associated virus (AAV) strategy to deliver the full-length PCDH15 coding sequence. We demonstrate the efficacy of this strategy in mouse USH1F models, effectively restoring hearing and balance in these mice. Importantly, our approach also proves successful in expressing PCDH15 in clinically relevant retinal models, including human retinal organoids and non-human primate retina, showing efficient targeting of photoreceptors and proper protein expression in the calyceal processes. This research represents a major step toward advancing gene therapy for USH1F and the multiple challenges of hearing, balance, and vision impairment.

Rescue of hearing by adenine base editing in a humanized mouse model of Usher syndrome type 1F

Usher syndrome type 1F (USH1F), characterized by congenital lack of hearing and balance and progressive loss of vision, is caused by mutations in the PCDH15 gene. In the Ashkenazi population, a recessive truncation mutation accounts for a large proportion of USH1F cases. The truncation is caused by a single C→T mutation, which converts an arginine codon to a stop (R245X). To test the potential for base editors to revert this mutation, we developed a humanized Pcdh15R245X mouse model for USH1F. Mice homozygous for the R245X mutation were deaf and exhibited profound balance deficits, while heterozygous mice were unaffected. Here we show that an adenine base editor (ABE) is capable of reversing the R245X mutation to restore the PCDH15 sequence and function. We packaged a split-intein ABE into dual adeno-associated virus (AAV) vectors and delivered them into cochleas of neonatal USH1F mice. Hearing was not restored in a Pcdh15 constitutive null mouse despite base editing, perhaps because of early disorganization of cochlear hair cells. However, injection of vectors encoding the split ABE into a late-deletion conditional Pcdh15 knockout rescued hearing. This study demonstrates the ability of an ABE to correct the PCDH15 R245X mutation in the cochlea and restore hearing.

Mini-PCDH15 gene therapy rescues hearing in a mouse model of Usher syndrome type 1F

Usher syndrome type 1 F (USH1F), caused by mutations in the protocadherin-15 gene (PCDH15), is characterized by congenital deafness, lack of balance, and progressive blindness. In hair cells, the receptor cells of the inner ear, PCDH15 is a component of tip links, fine filaments which pull open mechanosensory transduction channels. A simple gene addition therapy for USH1F is challenging because the PCDH15 coding sequence is too large for adeno-associated virus (AAV) vectors. We use rational, structure-based design to engineer mini-PCDH15s in which 3-5 of the 11 extracellular cadherin repeats are deleted, but which still bind a partner protein. Some mini-PCDH15s can fit in an AAV. An AAV encoding one of these, injected into the inner ears of mouse models of USH1F, produces a mini-PCDH15 which properly forms tip links, prevents the degeneration of hair cell bundles, and rescues hearing. Mini-PCDH15s may be a useful therapy for the deafness of USH1F.

Quantum Lyapunov exponents and complex spacing ratios: Two measures of dissipative quantum chaos

The agenda of dissipative quantum chaos is to create a toolbox that would allow us to categorize open quantum systems into "chaotic" and "regular" ones. Two approaches to this categorization have been proposed recently. One of them is based on the spectral properties of generators of open quantum evolution. The other one utilizes the concept of Lyapunov exponents to analyze quantum trajectories obtained by unraveling this evolution. By using two quantum models, we relate the two approaches and try to understand whether there is an agreement between the corresponding categorizations. Our answer is affirmative.

Electron Microscopy Techniques for Investigating Structure and Composition of Hair-Cell Stereociliary Bundles

Hair cells—the sensory cells of the vertebrate inner ear—bear at their apical surfaces a bundle of actin-filled protrusions called stereocilia, which mediate the cells’ mechanosensitivity. Hereditary deafness is often associated with morphological disorganization of stereocilia bundles, with the absence or mislocalization within stereocilia of specific proteins. Thus, stereocilia bundles are closely examined to understand most animal models of hereditary hearing loss. Because stereocilia have a diameter less than a wavelength of light, light microscopy is not adequate to reveal subtle changes in morphology or protein localization. Instead, electron microscopy (EM) has proven essential for understanding stereocilia bundle development, maintenance, normal function, and dysfunction in disease. Here we review a set of EM imaging techniques commonly used to study stereocilia, including optimal sample preparation and best imaging practices. These include conventional and immunogold transmission electron microscopy (TEM) and scanning electron microscopy (SEM), as well as focused-ion-beam scanning electron microscopy (FIB-SEM), which enables 3-D serial reconstruction of resin-embedded biological structures at a resolution of a few nanometers. Parameters for optimal sample preparation, fixation, immunogold labeling, metal coating and imaging are discussed. Special attention is given to protein localization in stereocilia using immunogold labeling. Finally, we describe the advantages and limitations of these EM techniques and their suitability for different types of studies.

Sex-Specific Age-Related Changes in Methylation of Certain Genes

The aim of the study was to conduct a functional analysis of sex-specific age-related changes in DNA methylation.

AAV-S: A versatile capsid variant for transduction of mouse and primate inner ear

Gene therapy strategies using adeno-associated virus (AAV) vectors to treat hereditary deafnesses have shown remarkable efficacy in some mouse models of hearing loss. Even so, there are few AAV capsids that transduce both inner and outer hair cells-the cells that express most deafness genes-and fewer still shown to transduce hair cells efficiently in primates. AAV capsids with robust transduction of inner and outer hair cells in primate cochlea will be needed for most clinical trials. Here, we test a capsid that we previously isolated from a random capsid library, AAV-S, for transduction in mouse and non-human primate inner ear. In both mice and cynomolgus macaques, AAV-S mediates highly efficient reporter gene expression in a variety of cochlear cells, including inner and outer hair cells, fibrocytes, and supporting cells. In a mouse model of Usher syndrome type 3A, AAV-S encoding CLRN1 robustly and durably rescues hearing. Overall, our data indicate that AAV-S is a promising candidate for therapeutic gene delivery to the human inner ear.

Nrf2 overexpression rescues the RPE in mouse models of retinitis pigmentosa

Nrf2, a transcription factor that regulates the response to oxidative stress, has been shown to rescue cone photoreceptors and slow vision loss in mouse models of retinal degeneration (rd). The retinal pigment epithelium (RPE) is damaged in these models, but whether it also could be rescued by Nrf2 has not been previously examined. We used an adeno-associated virus (AAV) with an RPE-specific (Best1) promoter to overexpress Nrf2 in the RPE of rd mice. Control rd mice showed disruption of the regular array of the RPE, as well as loss of RPE cells. Cones were lost in circumscribed regions within the cone photoreceptor layer. Overexpression of Nrf2 specifically in the RPE was sufficient to rescue the RPE, as well as the disruptions in the cone photoreceptor layer. Electron microscopy showed compromised apical microvilli in control rd mice but showed preserved microvilli in Best1-Nrf2–treated mice. The rd mice treated with Best1-Nrf2 had slightly better visual acuity. Transcriptome profiling showed that Nrf2 upregulates multiple oxidative defense pathways, reversing declines seen in the glutathione pathway in control rd mice. In summary, Nrf2 overexpression in the RPE preserves RPE morphology and survival in rd mice, and it is a potential therapeutic for diseases involving RPE degeneration, including age-related macular degeneration (AMD).

Chaotic spin-photonic quantum states in an open periodically modulated cavity

When applied to dynamical systems, both classical and quantum, time periodic modulations can produce complex non-equilibrium states which are often termed "chaotic." Being well understood within the unitary Hamiltonian framework, this phenomenon is less explored in open quantum systems. Here, we consider quantum chaotic states emerging in a leaky cavity when the intracavity photonic mode is coherently pumped with the pumping intensity varying periodically in time. We show that a single spin when placed inside the cavity and coupled to the mode can moderate transitions between regular and chaotic regimes-that are identified by using quantum Lyapunov exponents or features of photon emission statistics-and thus can be used to control the degree of chaos.

Serial scanning electron microscopy of anti-PKHD1L1 immuno-gold labeled mouse hair cell stereocilia bundles

Serial electron microscopy techniques have proven to be a powerful tool in biology. Unfortunately, the data sets they generate lack robust and accurate automated segmentation algorithms. In this data descriptor publication, we introduce a serial focused ion beam scanning electron microscopy (FIB-SEM) dataset consisting of six outer hair cell (OHC) stereocilia bundles, and the supranuclear part of the hair cell bodies. Also presented are the manual segmentations of stereocilia bundles and the gold bead labeling of PKHD1L1, a coat protein of hair cell stereocilia important for hearing in mice. This depository includes all original data and several intermediate steps of the manual analysis, as well as the MATLAB algorithm used to generate a three-dimensional distribution map of gold labels. They serve as a reference dataset, and they enable reproduction of our analysis, evaluation and improvement of current methods of protein localization, and training of algorithms for accurate automated segmentation.

Preclinical testing of AAV9-PHP.B for transgene expression in the non-human primate cochlea

In a number of mouse models of hereditary deafness, therapeutic transgene delivery to the cochlea and vestibular organs using adeno-associated viral vectors (AAVs) has shown striking rescue of hearing and balance. However, only a subset of AAV capsids have shown efficacy in transducing both inner hair cells and outer hair cells, and it is also not clear which of these can be translated to treatment of human inner ear. We recently reported efficient transgene expression of a GFP reporter in a non-human primate cochlea, in both inner and outer hair cells, following injection of the AAV9 capsid variant PHP.B via the round window membrane (RWM). However efficiency was poor at a lower dose. To further define the transduction potential of AAV9-PHP.B, we have performed a dosing study in the cynomolgus monkey and assessed vector-encoded GFP expression. Three animals were injected in both ears and four doses were tested. We describe a transmastoid surgical approach needed to access the RWM of this common primate model. We found that AAV9-PHP.B transduced nearly 100% of both IHCs and OHCs, from base to apex, at the higher doses (3.5 × 10¹¹ and 7 × 10¹¹ vector genomes). However, at lower doses there was a steep reduction in viral transduction. Thus, AAV9-PHP.B efficiently transduces the IHCs and OHCs of nonhuman primates, and should be considered as an AAV capsid for inner ear gene therapy in humans.

Photon waiting-time distributions: A keyhole into dissipative quantum chaos

Open quantum systems can exhibit complex states, for which classification and quantification are still not well resolved. The Kerr-nonlinear cavity, periodically modulated in time by coherent pumping of the intracavity photonic mode, is one of the examples. Unraveling the corresponding Markovian master equation into an ensemble of quantum trajectories and employing the recently proposed calculation of quantum Lyapunov exponents [I. I. Yusipov et al., Chaos 29, 063130 (2019)], we identify "chaotic" and "regular" regimes there. In particular, we show that chaotic regimes manifest an intermediate power-law asymptotics in the distribution of photon waiting times. This distribution can be retrieved by monitoring photon emission with a single-photon detector so that chaotic and regular states can be discriminated without disturbing the intracavity dynamics.

Quantum Neimark-Sacker bifurcation

Recently, it has been demonstrated that asymptotic states of open quantum system can undergo qualitative changes resembling pitchfork, saddle-node, and period doubling classical bifurcations. Here, making use of the periodically modulated open quantum dimer model, we report and investigate a quantum Neimark-Sacker bifurcation. Its classical counterpart is the birth of a torus (an invariant curve in the Poincaré section) due to instability of a limit cycle (fixed point of the Poincaré map). The quantum system exhibits a transition from unimodal to bagel shaped stroboscopic distributions, as for Husimi representation, as for observables. The spectral properties of Floquet map experience changes reminiscent of the classical case, a pair of complex conjugated eigenvalues approaching a unit circle. Quantum Monte-Carlo wave function unraveling of the Lindblad master equation yields dynamics of single trajectories on “quantumtorus” and allows for quantifying it by rotation number. The bifurcation is sensitive to the number of quantum particles that can also be regarded as a control parameter.

Quantum Lyapunov exponents beyond continuous measurements

Quantum systems, when interacting with their environments, may exhibit nonequilibrium states that are tempting to be interpreted as quantum analogs of chaotic attractors. However, different from the Hamiltonian case, the toolbox for quantifying dissipative quantum chaos remains limited. In particular, quantum generalizations of Lyapunov exponents, the main quantifiers of classical chaos, are established only within the framework of continuous measurements. We propose an alternative generalization based on the unraveling of quantum master equation into an ensemble of "quantum trajectories," by using the so-called Monte Carlo wave-function method. We illustrate the idea with a periodically modulated open quantum dimer and demonstrate that the transition to quantum chaos matches the period-doubling route to chaos in the corresponding mean-field system.

Gene Transfer with AAV9-PHP.B Rescues Hearing in a Mouse Model of Usher Syndrome 3A and Transduces Hair Cells in a Non-human Primate

Hereditary hearing loss often results from mutation of genes expressed by cochlear hair cells. Gene addition using AAV vectors has shown some efficacy in mouse models, but clinical application requires two additional advances. First, new AAV capsids must mediate efficient transgene expression in both inner and outer hair cells of the cochlea. Second, to have the best chance of clinical translation, these new vectors must also transduce hair cells in non-human primates. Here, we show that an AAV9 capsid variant, PHP.B, produces efficient transgene expression of a GFP reporter in both inner and outer hair cells of neonatal mice. We show also that AAV9-PHP.B mediates almost complete transduction of inner and outer HCs in a non-human primate. In a mouse model of Usher syndrome type 3A deafness (gene CLRN1), we use AAV9-PHP.B encoding Clrn1 to partially rescue hearing. Thus, we have identified a vector with promise for clinical treatment of hereditary hearing disorders, and we demonstrate, for the first time, viral transduction of the inner ear of a primate with an AAV vector.

Anderson localization or nonlinear waves: a matter of probability

In linear disordered systems Anderson localization makes any wave packet stay localized for all times. Its fate in nonlinear disordered systems (localization versus propagation) is under intense theoretical debate and experimental study. We resolve this dispute showing that, unlike in the common hypotheses, the answer is probabilistic rather than exclusive. At any small but finite nonlinearity (energy) value there is a finite probability for Anderson localization to break up and propagating nonlinear waves to take over. It increases with nonlinearity (energy) and reaches unity at a certain threshold, determined by the initial wave packet size. Moreover, the spreading probability stays finite also in the limit of infinite packet size at fixed total energy. These results generalize to higher dimensions as well.

q Breathers in finite lattices: nonlinearity and weak disorder

Nonlinearity and disorder are the recognized ingredients of the lattice vibrational dynamics, the factors that could be diminished, but never excluded. We generalize the concept of q breathers-periodic orbits in nonlinear lattices, exponentially localized in the linear mode space-to the case of weak disorder, taking the Fermi-Pasta-Ulan chain as an example. We show that these nonlinear vibrational modes remain exponentially localized near the central mode and stable, provided the disorder is sufficiently small. The instability threshold depends sensitively on a particular realization of disorder and can be modified by specifically designed impurities. Based on this sensitivity, an approach to controlling the energy flow between the modes is proposed. The relevance to other model lattices and experimental miniature arrays is discussed.

q-Breathers in finite two- and three-dimensional nonlinear acoustic lattices

In their celebrated experiment, Fermi, Pasta, and Ulam (FPU) [Los Alamos Report No. LA-1940, 1955] observed that in simple one-dimensional nonlinear atomic chains the energy must not always be equally shared among the modes. Recently, it was shown that exact and stable time-periodic orbits, coined q-breathers (QBs), localize the mode energy in normal mode space in an exponential way, and account for many aspects of the FPU problem. Here we take the problem into more physically important cases of two- and three-dimensional acoustic lattices to find existence and principally different features of QBs. By use of perturbation theory and numerical calculations we obtain that the localization and stability of QBs are enhanced with increasing system size in higher lattice dimensions opposite to their one-dimensional analogues.

q-breathers in Fermi-Pasta-Ulam chains: existence, localization, and stability

The Fermi-Pasta-Ulam (FPU) problem consists of the nonequipartition of energy among normal modes of a weakly anharmonic atomic chain model. In the harmonic limit, each normal mode corresponds to a periodic orbit in phase space and is characterized by its wave number q. We continue normal modes from the harmonic limit into the FPU parameter regime and obtain persistence of these periodic orbits, termed here q-breathers (QB). They are characterized by time periodicity, exponential localization in the q-space of normal modes, and linear stability up to a size-dependent threshold amplitude. Trajectories computed in the original FPU setting are perturbations around these exact QB solutions. The QB concept is applicable to other nonlinear lattices as well.

q-Breathers and the Fermi-Pasta-Ulam problem

The Fermi-Pasta-Ulam (FPU) paradox consists of the non-equipartition of energy among normal modes of a weakly anharmonic atomic chain model. In the harmonic limit each normal mode corresponds to a periodic orbit in phase space and is characterized by its wave number q. We continue normal modes from the harmonic limit into the FPU parameter regime and obtain persistence of these periodic orbits, termed here q-breathers (QB). They are characterized by time periodicity, exponential localization in the q-space of normal modes and linear stability up to a size-dependent threshold amplitude. Trajectories computed in the original FPU setting are perturbations around these exact QB solutions. The QB concept is applicable to other nonlinear lattices as well.