Aquaporin-4 (AQP4) Degradome Foundation Atlas

<h2>Aquaporin-4 (AQP4) Degradome Foundation Atlas — Version 1</h2><p dir="ltr">This open-access and freely downloadable dataset introduces Version 1 of the Aquaporin-4 (AQP4) Degradome Foundation Atlas, the first comprehensive proteolytic AQP4 peptide atlas designed to accelerate translational, clinical, and biomarker research in demyelinating and neurodegenerative diseases.</p><p dir="ltr">The dataset (<code>AQP4_Degradome_Foundation_Atlas_v1.tar.gz)</code> integrates the entire proteolytic repertoire of wild-type and mutant AQP4 into a single unified resource, using high-level compression to maximize usability, optimize download speed, and ensure reproducibility.</p><h3>Clinical and Biological Context</h3><p dir="ltr">Neuromyelitis optica (NMO) and its related spectrum of inflammatory CNS disorders are characterized by autoantibodies targeting the AQP4 water channel, abundant in astrocytic foot processes. Classic clinical manifestations include optic neuritis and longitudinally extensive transverse myelitis, with additional involvement of circumventricular organs and skeletal muscle.</p><p dir="ltr">Experimental studies have demonstrated that single point mutations in AQP4 can alter the protein’s immunogenicity [1, 2]. Therefore, this dataset includes the complete degradome for all described AQP4 mutations alongside the wild-type protein.</p><h3>�� Key Features</h3><ul><li>Complete degradome profiling of wild-type and mutant AQP4 proteolytic fragments.</li><li>Inclusion of the Spanish mutation D184E [1].</li><li>Inclusion of the Chinese mutations R108T, I110N, E280R, D281R, P295R, E317M [2].</li><li>A standardized nomenclature designed for automated processing and statistical analysis.</li></ul><p dir="ltr"><b>Examples of peptide naming convention:</b></p><ul><li><code>AQP4_WT_2_16</code> → peptide <i>DRPTARRWGKCGPL </i>(wild type)</li><li><code>AQP4_D281R_4_19</code> → peptide <i>PTARRWGKCGPLCTR</i> (D281R mutation, [2])</li></ul><p dir="ltr">This structured format ensures instant interpretability, enabling researchers to filter, stratify, and analyze peptides by mutation type and cleavage position with ease.</p><h3>�� Data Format and Access</h3><ul><li>Distributed as a tab-delimited ASCII (<code>.csv</code>) file compatible with R, Python, SAS, Excel, and major bioinformatics pipelines.</li><li>Compressed into a <code>.tar.gz</code> file for efficient transfer.</li><li>Extraction command: tar -xvJf AQP4_Degradome_Foundation_Atlas_v1.tar.gz</li><li>Fully FAIR-compliant (<i>Findable, Accessible, Interoperable, Reusable</i>) and citable via DOI.</li></ul><h3>�� Reproducibility and Code Availability</h3><p dir="ltr">The dataset can be <b>fully regenerated</b> using open-source tools:</p><ul><li><b>Python</b></li></ul><p dir="ltr">All required scripts are included in the repository and extensively documented for local replication and adaptation. The computational workflow follows the methodology described in [3].</p><h3>�� Applications</h3><ul><li>Biomarker discovery and validation in demyelinating diseases.</li><li>Analysis of proteolytic cleavage patterns across AQP4 isoforms and mutations.</li><li>Autoimmunity research using degradomic signatures.</li><li>Development of diagnostic and therapeutic monitoring assays.</li><li>Integration into proteomic and machine learning workflows.</li></ul><h3>�� References</h3><ol><li>Tradtrantip L, et al. <i>Identification of Aquaporin-4 immunogenicity mechanisms.</i> <a href="https://doi.org/10.1016/j.neuroscience.2011.09.023" rel="noopener" target="_new">https://doi.org/10.1016/j.neuroscience.2011.09.023</a></li><li>Qin C, et al. <i>Molecular insights into AQP4 mutations and autoimmunity.</i> <a href="https://doi.org/10.3892/etm.2017.5267" rel="noopener" target="_new">https://doi.org/10.3892/etm.2017.5267</a></li><li>Petzold A. <i>Proteolysis-Based Biomarker Repertoire of the Neurofilament Proteome.</i> J Neurochem. 2025;169(3):e70023. <a href="https://doi.org/10.1111/jnc.70023" rel="noopener" target="_new">https://doi.org/10.1111/jnc.70023</a></li></ol><p></p>