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      Systemic administration of novel engineered AAV capsids facilitates enhanced transgene expression in the macaque CNS

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          Abstract

          Background

          Adeno-associated virus (AAV) vectors are a promising vehicle for noninvasive gene delivery to the central nervous system via intravenous infusion. However, naturally occurring serotypes have a limited ability to transduce the brain, and translating engineered capsids from mice to nonhuman primates has proved challenging.

          Methods

          In this study, we use an mRNA-based directed evolution strategy in multiple strains of mice as well as in a de novo selection in cynomolgus macaques to identify families of engineered vectors with increased potency in the brain and decreased tropism for the liver.

          Findings

          We compare the transgene expression capabilities of several engineered vectors and show that while some of our novel macaque-derived variants significantly outperform AAV9 in transducing the macaque brain following systemic administration, mouse-derived variants—both those identified in this study and those reported by other groups—universally did not.

          Conclusions

          Together, this work introduces a class of primate-derived engineered AAV capsids with increased therapeutic potential and underscores the critical need for using appropriate animal models to both identify and evaluate novel AAVs intended for delivery to the human central nervous system.

          Funding

          This work was funded primarily through an anonymous philanthropic gift to the P.C.S. lab at the Broad Institute of MIT and Harvard and by a grant from the Howard Hughes Medical Institute to P.C.S.

          Graphical Abstract

          eTOC blurb

          Stanton et al. use a directed evolution strategy in mice and macaques to find AAV capsids with increased tropism for the brain after systemic administration. A resulting family of capsids show increased brain transduction and reduced tropism for the liver and other peripheral organs in juvenile macaques compared to AAV9.

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          Most cited references71

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          SWISS-MODEL: homology modelling of protein structures and complexes

          Abstract Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. Here, we present an update to the SWISS-MODEL server, which pioneered the field of automated modelling 25 years ago and been continuously further developed. Recently, its functionality has been extended to the modelling of homo- and heteromeric complexes. Starting from the amino acid sequences of the interacting proteins, both the stoichiometry and the overall structure of the complex are inferred by homology modelling. Other major improvements include the implementation of a new modelling engine, ProMod3 and the introduction a new local model quality estimation method, QMEANDisCo. SWISS-MODEL is freely available at https://swissmodel.expasy.org.
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            Single-Dose Gene-Replacement Therapy for Spinal Muscular Atrophy

            Spinal muscular atrophy type 1 (SMA1) is a progressive, monogenic motor neuron disease with an onset during infancy that results in failure to achieve motor milestones and in death or the need for mechanical ventilation by 2 years of age. We studied functional replacement of the mutated gene encoding survival motor neuron 1 (SMN1) in this disease.
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              CellProfiler 4: improvements in speed, utility and usability

              Background Imaging data contains a substantial amount of information which can be difficult to evaluate by eye. With the expansion of high throughput microscopy methodologies producing increasingly large datasets, automated and objective analysis of the resulting images is essential to effectively extract biological information from this data. CellProfiler is a free, open source image analysis program which enables researchers to generate modular pipelines with which to process microscopy images into interpretable measurements. Results Herein we describe CellProfiler 4, a new version of this software with expanded functionality. Based on user feedback, we have made several user interface refinements to improve the usability of the software. We introduced new modules to expand the capabilities of the software. We also evaluated performance and made targeted optimizations to reduce the time and cost associated with running common large-scale analysis pipelines. Conclusions CellProfiler 4 provides significantly improved performance in complex workflows compared to previous versions. This release will ensure that researchers will have continued access to CellProfiler’s powerful computational tools in the coming years. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04344-9.
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                Author and article information

                Journal
                101769215
                49734
                Med (N Y)
                Med (N Y)
                Med (New York, N.Y.)
                2666-6359
                2666-6340
                14 December 2022
                13 January 2023
                22 November 2022
                15 January 2023
                : 4
                : 1
                : 31-50.e8
                Affiliations
                [1 ]Broad Institute of MIT and Harvard, Cambridge, MA, USA 02142
                [2 ]Harvard Program in Virology, Harvard Medical School, Boston, MA, USA 02115
                [3 ]Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA 02115
                [4 ]Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA 02142
                [5 ]Harvard Medical School, Boston, MA, USA 02115
                [6 ]Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA 02115
                [7 ]Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA 02138
                [8 ]Lead Contact
                Author notes
                [*]

                These authors contributed equally

                Author Contributions.

                A.C.S. and K.A.L. designed and performed experiments and in vivo studies. A.C.S. collected, interpreted, and visualized all data and performed all statistical analyses. L.T., A.K., and E.M.K. prepared virus for experiments and performed in vivo studies. S.Y. analyzed NGS data. I.H.S. supervised and interpreted histopathology experiments. M.T. designed in vivo studies. A.C.S., K.A.L., and P.C.S. had unrestricted access to all data and wrote the manuscript. M.T. and P.C.S. conceived of the research strategy and supervised the study. All authors read and approved the final manuscript and take responsibility for its content.

                Article
                NIHMS1852296
                10.1016/j.medj.2022.11.002
                9840684
                36417917
                69f19853-c30e-4339-b1eb-c0e415d34b0f

                This work is licensed under a Creative Commons Attribution 4.0 International License, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.

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