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      A combination treatment based on drug repurposing demonstrates mutation-agnostic efficacy in pre-clinical retinopathy models

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          Abstract

          Inherited retinopathies are devastating diseases that in most cases lack treatment options. Disease-modifying therapies that mitigate pathophysiology regardless of the underlying genetic lesion are desirable due to the diversity of mutations found in such diseases. We tested a systems pharmacology-based strategy that suppresses intracellular cAMP and Ca2+ activity via G protein-coupled receptor (GPCR) modulation using tamsulosin, metoprolol, and bromocriptine coadministration. The treatment improves cone photoreceptor function and slows degeneration in Pde6βrd10 and RhoP23H/WT retinitis pigmentosa mice. Cone degeneration is modestly mitigated after a 7-month-long drug infusion in PDE6A-/- dogs. The treatment also improves rod pathway function in an Rpe65-/- mouse model of Leber congenital amaurosis but does not protect from cone degeneration. RNA-sequencing analyses indicate improved metabolic function in drug-treated Rpe65-/- and rd10 mice. Our data show that catecholaminergic GPCR drug combinations that modify second messenger levels via multiple receptor actions provide a potential disease-modifying therapy against retinal degeneration.

          Abstract

          This preclinical study demonstrates the potential of a drug repurposing strategy using the coadministration of tamsulosin, metoprolol, and bromocriptine to provide a mutation-agnostic therapy for inherited retinal degeneration.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            Trimmomatic: a flexible trimmer for Illumina sequence data

            Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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              STAR: ultrafast universal RNA-seq aligner.

              Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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                Author and article information

                Contributors
                henri.leinonen@uef.fi
                kpalczew@uci.edu
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                15 July 2024
                15 July 2024
                2024
                : 15
                : 5943
                Affiliations
                [1 ]School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, ( https://ror.org/00cyydd11) Yliopistonranta 1C, 70211 Kuopio, Finland
                [2 ]GRID grid.266093.8, ISNI 0000 0001 0668 7243, Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, , University of California, ; Irvine, CA 92697 USA
                [3 ]Small Animal Clinical Sciences, Michigan State University, ( https://ror.org/05hs6h993) East Lansing, MI 48824 USA
                [4 ]International Centre for Translational Eye Research, Warsaw, Poland
                [5 ]GRID grid.413454.3, ISNI 0000 0001 1958 0162, Institute of Physical Chemistry, , Polish Academy of Sciences, ; Warsaw, Poland
                [6 ]Department of Ophthalmology, Department of Cell & Developmental Biology, Ann Arbor, MI 48105 USA
                [7 ]GRID grid.266093.8, ISNI 0000 0001 0668 7243, Department of Physiology and Biophysics, School of Medicine, , University of California - Irvine, ; Irvine, CA 92697 USA
                [8 ]Department of Clinical Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University of California - Irvine, ( https://ror.org/04gyf1771) Irvine, CA 92697 USA
                [9 ]Research Service, VA Long Beach Healthcare System, ( https://ror.org/058p1kn93) Long Beach, California 90822 USA
                [10 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Department of Ophthalmology, , Johns Hopkins University School of Medicine, ; Baltimore, MD 21205 USA
                [11 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Department of Neurology, , Johns Hopkins University School of Medicine, ; Baltimore, MD 21205 USA
                [12 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Institute for Cell Engineering, , Johns Hopkins University School of Medicine, ; Baltimore, MD 21205 USA
                [13 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Kavli Neuroscience Discovery Institute, , Johns Hopkins University School of Medicine, ; Baltimore, MD 21205 USA
                [14 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Solomon H. Snyder Department of Neuroscience, , Johns Hopkins University School of Medicine, ; Baltimore, MD 21205 USA
                [15 ]Department of Chemistry, University of California-Irvine, ( https://ror.org/04gyf1771) Irvine, CA 92697 USA
                [16 ]Department of Molecular Biology and Biochemistry, University of California-Irvine, ( https://ror.org/04gyf1771) Irvine, CA 92697 USA
                [17 ]GRID grid.266093.8, ISNI 0000 0001 0668 7243, Present Address: Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, , University of California, ; Irvine, CA 92697 USA
                Author information
                http://orcid.org/0000-0002-0388-832X
                http://orcid.org/0000-0003-4570-0425
                http://orcid.org/0000-0002-2233-5501
                http://orcid.org/0009-0009-7759-1519
                http://orcid.org/0000-0003-1184-9539
                http://orcid.org/0000-0002-1338-8476
                http://orcid.org/0000-0002-6166-2820
                http://orcid.org/0000-0003-1110-9223
                http://orcid.org/0000-0002-7410-2304
                http://orcid.org/0000-0002-0788-545X
                Article
                50033
                10.1038/s41467-024-50033-5
                11251169
                39009597
                59c42f3f-66ce-4dff-8156-577d75e7125c
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 11 August 2023
                : 21 June 2024
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100002341, Academy of Finland (Suomen Akatemia);
                Award ID: 346295
                Award Recipient :
                Funded by: H.L. was also supported by the Knights Templar Eye Foundation Career-Starter Research Grant, Fight for Sight Postdoctoral Award, Finnish Cultural Foundation, The Osk. Huttunen Foundation, Orion Research Foundation, Finnish Eye and Tissue Bank Foundation, Finnish Retina Registered Association, and Sokeain Ystävät/De Blindas Vänner Registered Association.
                Categories
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                © Springer Nature Limited 2024

                Uncategorized
                retina,molecular medicine,preclinical research,pharmacodynamics
                Uncategorized
                retina, molecular medicine, preclinical research, pharmacodynamics

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