Biology subjects

Suga, S.

Publications and source records attributed to Suga, S..

7 recordsLinked to original sources

bioRxiv2026

Quantum Dot-Based Non-invasive Monitoring of Sinusoidal Endothelial Scavenger Function in Steatohepatitis

Metabolic dysfunction-associated steatotic liver disease (MASLD) and its progressive form, metabolic dysfunction-associated steatohepatitis (MASH), represent urgent medical challenges. Current non-invasive assessments rely on serum indices or tissue stiffness, and none visualizes functional changes within the liver, hindering drug discovery and patient management. In this study, we developed a non-invasive technique using semiconductor quantum dots, as blood-borne foreign particle mimics, to evaluate the scavenger function of liver sinusoidal endothelial cells (LSECs) via near-infrared optical imaging. Progression from MASLD to MASH induced a significant decline in the scavenger capability of LSECs, resulting in a marked reduction of intrahepatic quantum dot retention. Mechanistically, we demonstrated that quantum dots are recognized and internalized by scavenger receptor class A (SR-A) on LSECs, and that SR-A-mediated uptake progressively diminishes with increasing MASH severity. Crucially, quantum dot retention levels significantly correlated with both the progression and regression of MASH pathology. These findings demonstrate that quantum dot-based optical evaluation of LSEC scavenger function offers a highly sensitive, non-invasive diagnostic platform for staging MASH and assessing therapeutic efficacy.

bioengineering↗

bioRxiv2026

Ultrastructurally planar growth cones during neocortical axon navigation

Neurons extend axons toward spatially defined but often distant targets to establish brain circuits. Callosal projection neurons exemplify this organization, linking corresponding cortical territories between the two hemispheres. Growing axons rely on growth cones to regulate direction and speed through densely packed tissues. Although growth cone morphology and dynamics have been extensively characterized in cultured neurons and invertebrate models, how growth cones navigate the three-dimensional environment of the developing mammalian brain remains poorly explored. Here, we combined a genetically encoded electron microscopy (EM)-labeling strategy and zero-shot deep-learning-based tracing with high-resolution volume EM to reconstruct growth cones of identified callosal projection neurons in the developing mouse brain. Mediolaterally extending growth cones exhibited a planar, fan-shaped morphology, preferentially expanded along the dorsoventral axis. Filopodia extended from the edges of this plane and aligned predominantly with the same axis but showed no directional bias toward the growing direction. Longitudinal in vivo imaging revealed that increased growth cone complexity associated with filopodial extension coincided with lower instantaneous velocity but preceded accelerated extension. Together, these findings reveal a dorsoventrally oriented planar growth cone architecture in which filopodial extension precedes accelerated axon growth, suggesting a structural constraint that may restrict axon navigation to the callosal plane.

neuroscience↗

bioRxiv2024

Optimization of an adeno-associated viral vector for keratinocytes in vitro and in vivo

BackgroundLocal gene therapies, including in vivo genome editing, are highly anticipated for the treatment of genetic diseases in skin, especially the epidermis. While the adeno-associated virus (AAV) is a potent vector for in vivo gene delivery, the lack of efficient gene delivery methods has limited its clinical applications. ObjectiveTo optimize the AAV gene delivery system with higher gene delivery efficiency and specificity for epidermis and keratinocytes (KCs), using AAV capsid and promoter engineering technologies. MethodsAAV variants with mutations in residues reported to be critical to determine the tropism of AAV2 for KCs were generated by site-directed mutagenesis of AAVDJ. The infection efficiency and specificity for KCs of these variants were compared with those of previously reported AAVs considered to be suitable for gene delivery to KCs in vitro and in vivo. Additionally, we generated an epidermis-specific promoter using the most recent short-core promoter and compared its specificity with existing promoters. ResultsA novel AAVDJ variant capsid termed AAVDJK2 was superior to the existing AAVs in terms of gene transduction efficiency and specificity for epidermis and KCs in vitro and in vivo. A novel tissue-specific promoter, termed the K14 SCP3 promoter, was superior to the existing promoters in terms of gene transduction efficiency and specificity for KCs. ConclusionThe combination of the AAVDJK2 capsid and K14 SCP3 promoter improves gene delivery to epidermis in vivo and KCs in vitro. The novel AAV system may benefit experimental research and development of new epidermis-targeted gene therapies.

bioengineering↗

bioRxiv2023

Mitochondrial protein FKBP8 captures PDZD8 to form mitochondria-ER contacts

Mitochondria-ER membrane contact sites (MERCS) represent a fundamental ultrastructural feature underlying unique biochemistry and physiology in eukaryotic cells. The ER protein PDZD8 is required for the formation of MERCS in many cell types, however, its tethering partner on the outer mitochondrial membrane (OMM) is currently unknown. Here we identified the OMM protein FKBP8 as the tethering partner of PDZD8 using a combination of unbiased proximity proteomics, CRISPR-Cas9 endogenous protein tagging, Cryo-Electron Microscopy (Cryo-EM) tomography, and correlative light-EM (CLEM). Single molecule tracking revealed highly dynamic diffusion properties of PDZD8 along the ER membrane with significant pauses and capture at MERCS. Overexpression of FKBP8 was sufficient to narrow the ER-OMM distance, whereas independent versus combined deletions of these two proteins demonstrated their interdependence for MERCS formation. Furthermore, PDZD8 enhances mitochondrial complexity in a FKBP8-dependent manner. Our results identify a novel ER-mitochondria tethering complex that regulates mitochondrial morphology in mammalian cells.

cell biology↗

bioRxiv2023

In vivo reprogramming of wound-resident cells generates skin with hair

Summary ParagraphMammalian skin appendages, such as hair follicles and sweat glands, are complex mini-organs formed during skin development1, 2. As wounds heal, the resulting scar tissue lacks skin appendages. The clinical regeneration of skin appendages is an ongoing challenge3, 4. Skin epithelial tissues have been regenerated in vivo by cellular reprogramming5, 6, but the de novo generation of skin appendages has not previously been achieved. Here, we show that transplantation of a type of epithelial cell and two types of mesenchymal cells, reprogrammed from adult mouse subcutaneous mesenchymal cells to mimic developing skin cells, resulted in the generation of skin-appendage-like structures. Furthermore, with the development of a new AAV serotype, in vivo reprogramming of wound-resident cells with the same reprogramming factors generates skin with de novo appendages in adult mice. These findings may provide new therapeutic avenues for skin regeneration and frequent aging-associated skin appendage disorders, such as hair loss and dry skin, and may extend to other tissues and organs. This study also provides the potential for de novo generation of complex organs in vivo.

cell biology↗

bioRxiv2022

Horizontal transmission of penicillin binding protein 1A caused a nationwide spread of β-lactam resistance in pneumococci

The emergence and spread of drug-resistant bacteria continue to be a global crisis. The mechanism of the resistance spread via mobile genetic elements such as plasmids is well known, however, the impact of the natural transformation on the spread remains unclear. Streptococcus pneumoniae is well known to be a transformable pathogen by natural competence and they become {beta}-lactam resistance by the acquisition of chromosomal genetic elements including mutated PBPs by natural transformation. To trace the transmission of pneumococcal PBPs among nationwide pediatric population and analyze the impact of transformed PBPs to {beta}-lactam resistance, we collected and analyzed more than 1300 isolates of S. pneumoniae through nationwide surveillance study for pediatric pneumococcal diseases between 2012-2017 in Japan. We discovered a high prevalence of a specific PBP1A type (pbp1a-13) in {beta}-lactam resistant pneumococci that had a 370SSMK substitution in their {beta}-lactam binding SXXK motif, suggesting that this pbp1a-13 transferred horizontally between different clones resulting in emergence and spread of {beta}-lactam resistant pneumococcal clones. Divergence dating analysis suggested that pbp1a-13 was inserted into major resistant lineages in the early 1990s through the 2000s, before introduction of pneumococcal conjugate vaccines in Japan. Our additional analysis for pneumococcal isolates that were recovered in the 90s in Japan suggested that pbp1a-13 in GPSC1 (serotype 19F-CC236) and GPSC14 (serotype 23F-CC242) isolates were the origin of the currently spread pbp1a-13. We provide evidence of pbp1a horizontal transmission at a nationwide scale and highlight the importance of PBP profile monitoring for identifying the emergence and spread of resistant pneumococci lineages.

microbiology↗

bioRxiv2021

An interactive deep learning-based approach reveals mitochondrial cristae topologies

Outer and inner mitochondrial membranes are highly specialized structures with distinct functional properties. Reconstructing complex 3D ultrastructural features of mitochondrial membranes at the nanoscale requires analysis of large volumes of serial scanning electron tomography data. While deep-learning-based methods improved in sophistication recently, time-consuming human intervention processes remain major roadblocks for efficient and accurate analysis of organelle ultrastructure. In order to overcome this limitation, we developed a deep-learning image analysis platform called Python-based Human-In-the-LOop Workflows (PHILOW). Our implementation of an iterative segmentation algorithm and Three-Axis-Prediction method not only improved segmentation speed, but also provided unprecedented ultrastructural detail of whole mitochondria and cristae. Using PHILOW, we found that 42% of cristae surface exhibits tubular structures that are not recognizable in light microscopy and 2D electron microscopy. Furthermore, we unraveled a fundamental new regulatory function for the dynamin-related GTPase Optic Atrophy 1 (OPA1) in controlling the balance between lamellar versus tubular cristae subdomains.

cell biology↗