Biology subjects

Matsuzaki, Y.

Publications and source records attributed to Matsuzaki, Y..

7 recordsLinked to original sources

bioRxiv2026

Megalin-mediated deterministic pseudotransduction in proximal tubules fundamentally challenges current understanding of AAV kidney transduction

Genetic kidney diseases are promising targets for gene therapy. Emerging AAV capsids that reportedly enable effective gene delivery to proximal tubules (PTs) following intravenous injection have raised hopes for treating diseases affecting renal tubules. Despite these promising developments, the scientific literature contains contradictory and non-reproducible findings, which prompted us to conduct a detailed and rigorous investigation of the mechanisms of AAV vector-mediated PT transduction. Here we provide compelling evidence that previously reported effective PT transduction following intravenous AAV-GFP or AAV-mCherry administration largely reflects megalin-mediated deterministic pseudotransduction rather than stochastic vector-mediated gene delivery. We demonstrate that this process is mediated by megalin-dependent uptake of circulating reporter proteins released from transduced organs including the liver and filtered through the glomeruli. These observations highlight the ongoing challenge of achieving true proximal tubule transduction via systemic AAV delivery and caution against relying on small reporters like GFP or mCherry, which can produce misleading signals.

bioengineering↗

bioRxiv2026

Quantitative Framework for Assessing Mesenchymal Stem Cell Quality Driven by Poised Enhancer Decommissioning

Mesenchymal stem cell (MSC) heterogeneity and conventional phenotypic criteria limitations represent major bottlenecks in therapeutic manufacturing. Here, we present a framework to prospectively identify naturally superior MSCs by shifting from superficial markers to the digital quantification of fundamental epigenetic flaws in inferior clones. We show that intrinsic MSC functional decline is driven by targeted hypermethylation of poised enhancers, causing paradoxical derepression of developmental genes. We term this process poised enhancer decommissioning (PEnD). By isolating this universal decay axis from donor-specific immunological variability, we translate this complex epigenetic state into a streamlined transcriptomic signature: the Poised Enhancer-related Gene Expression (PErGE) score. Overcoming the limitations of standard in vitro differentiation assays, our approach enables accurate, donor-independent prediction of long-term proliferative potential. Together, our findings establish a mechanism-based biomarker of cellular aging, and provide a readily applicable tool to improve the quality control of next-generation MSC-based therapies.

cell biology↗

bioRxiv2026

Molecular basis of promiscuous chemokine-engagement by the Duffy antigen receptor

The Duffy blood group antigen, encoded by a seven transmembrane protein known as Duffy Antigen Receptor for Chemokines (DARC), or Atypical Chemokine Receptor 1 (ACKR1), serves as a key receptor for the malarial parasite, Plasmodium vivax, on erythrocytes. DARC exhibits remarkable functional divergence compared to prototypical chemokine receptors and other G protein-coupled receptors (GPCRs) as it does not engage canonical signal-transducers such as G-proteins, GPCR regulatory kinases (GRKs), and {beta}-arrestins. DARC is a highly promiscuous receptor interacting with several homeostatic and inflammatory C-C and C-X-C subtype chemokines, and similar to other chemokine receptors, these interactions are modulated by post-translational tyrosine sulfation in the N-terminus. A single nucleotide polymorphism in DARC leading to Gly42Asp substitution forms the basis for Fya vs. Fyb Duffy blood group antigen classification with differential impact on Plasmodium vivax infection and cancer progression. However, the molecular basis of promiscuous chemokine-binding by DARC and the modulation by receptor sulfation and Fya/Fyb allelic variation remains unclear. Here, we design a sortase-mediated chemical-ligation strategy to generate purified DARC with naturally-occurring tyrosine sulfation at the N-terminus, and determine high-resolution cryo-EM structures in complex with a C-C type chemokine, CCL7, and a C-X-C type chemokine, CXCL8. We observe that similar to CCL7, CXCL8 engages with DARC primarily through the N-terminus of the receptor, which is in stark contrast with the two-site binding mechanism displayed by other chemokine receptors. Interestingly, the E-L-R motif in CXCL8 engages a pseudo-R-D motif in DARC leading to superficial engagement unlike CXCR2, a prototypical chemokine receptor sharing the same agonist. Moreover, tyrosine sulfation and Fyb allelic variation leads to a repositioning of the receptor N-terminus on the core domain of CXCL8, resulting in distinct interaction network imparting greater binding affinity. Taken together, our study presents novel insights into promiscuous chemokine-binding to DARC, tyrosine sulfation-mediated fine-tuning of chemokine engagement, and a generalizable sortase-mediated chemical-ligation platform applicable to other chemokine receptors.

biochemistry↗

bioRxiv2025

VCAP-102 Achieves Exceptional BBB Penetration in Marmosets After Ten Years of AAV Capsid Evaluation

Efficient passage of adenoassociated virus (AAV) vectors across the blood-brain barrier (BBB) is essential for achieving broad central nervous system transduction following systemic delivery. Since PHP.B was reported in 2016 to exhibit high BBB permeability in C57BL/6J mice, many BBB-penetrant capsids have been developed, yet their performance often varies substantially across species. From 2016 to 2025, we produced each newly reported BBB-penetrant capsid as its sequence became available and evaluated it under standardized intravenous administration conditions in marmosets. This included PHP.B, PHP.eB, AAV-F, CAP-B22, CAP-B10, CPP.16, CAP-Mac, and BR1N. Although several of these capsids have been reported to penetrate the marmoset BBB, none reproduced these effects under our unified evaluation conditions. We also pursued several directed-evolution approaches to engineer AAV9-based variants with improved BBB permeability; however, none surpassed AAV9. In 2025, VCAP-102 was reported as an AAV9-derived capsid with BBB permeability in mice and non-human primates. When evaluated using our standardized framework, VCAP-102 consistently mediated markedly stronger and more widespread whole-brain transduction than AAV9 across all three animals tested. These findings provide a decade-long, systematic assessment of BBB-penetrant AAV capsids in marmosets and identify VCAP-102 as a highly promising candidate for future systemically delivered AAV-based gene therapies.

neuroscience↗

bioRxiv2024

Light-harvesting by antenna-containing rhodopsins in pelagic Asgard archaea

Aquatic bacterial rhodopsin proton pumps have been recently reported to utilize hydroxylated carotenoids1,2. Here, by combining a marine chromophore extract with purified archaeal rhodopsins identified in marine metagenomes, we report on light energy transfer from diverse hydroxylated carotenoids (lutein, diatoxanthin, and fucoxanthin) to heimdallarchaeial rhodopsins (HeimdallRs)3,4 from uncultured marine planktonic members of the "Ca. Kariarchaeaceae" ("Ca. Asgardarchaeota")5. These light-harvesting antennas absorb in the blue-light range and transfer energy to the green-light absorbing retinal chromophore within HeimdallRs. Furthermore, antenna enhancement of proton pumping by HeimdallRs is also observed under white-light illumination along with a carotenoid-binding-induced structural change in the protein. Our results indicate that the use of light-harvesting antennas in microbial rhodopsins is observed not only in bacteria but also in marine archaea.

microbiology↗

bioRxiv2024

Optimal AAV capsid/promoter combinations to target specific cell types in the common marmoset cerebral cortex

To achieve cell type-specific gene expression, using target cell-tropic AAV capsids is advantageous. However, their tropism across brain cell types remains unexplored in non-human primates. We assessed the tropism of nine AAV serotype capsids (AAV1, 2, 5, 6, 7, 8, 9, rh.10 (rh10), and DJ) on marmoset cerebral cortical cell types. Marmoset cerebral cortex was injected with different serotype AAVs expressing enhanced GFP (EGFP) by the ubiquitous chicken {beta}-actin hybrid (CBh) promoter. After 4 weeks, all nine AAV capsid vectors, especially AAV9 and AAVrh10, caused highly neuron-selective EGFP expression. Some AAV capsids, including AAV5, caused EGFP expression in oligodendrocytes to a lesser extent, with minimal or no expression in astrocytes and microglia. Different ubiquitous CMV and CAG promoters showed similar neuron-predominant transduction. Conversely, all nine AAV capsid vectors with the astrocyte-specific hGFA(ABC1D) promoter selectively transduced astrocytes, except AAV5, which transduced oligodendrocytes modestly. Oligodendrocyte-specific mouse myeline basic protein (mMBP) promoter in AAV5 vectors transduced oligodendrocytes specifically and efficiently. Our results suggest optimal combinations of capsids and promoters for cell type-specific expression: AAV9 or AAVrh10 and ubiquitous CBh, CMV, or CAG promoter for neuron-specific transduction; AAV2 or 7 and hGFA(ABC1D) promoter for astrocyte-specific transduction; and AAV5 and mMBP promoter for oligodendrocyte-specific transduction.

neuroscience↗

bioRxiv2020

Rescoring ensembles of protein-protein docking poses using consensus approaches

Scoring is a challenging step in protein-protein docking, where typically thousands of solutions are generated. Successful scoring is more often based on physicochemical evaluation of the generated interfaces and/or statistical potentials that reproduce known interface properties. Another route is offered by consensus-based rescoring, where the set of solutions is used to build statistics in order to identify recurrent solutions. We explore several ways to perform consensus-based rescoring on the ZDOCK decoy set for Benchmark 4. We show that the information of the interface size is critical for successful rescoring. We combine consensus-based rescoring with the ZDOCK native scoring function and show that this improves the initial results.

bioinformatics↗