Biology subjects

Iwamoto, Y.

Publications and source records attributed to Iwamoto, Y..

11 recordsLinked to original sources

bioRxiv2026

Decoupling Fabrication from Encoding: DNA-Addressable Template Microparticles for Large, User-Defined Optical Barcode Libraries

Optical barcodes for pooled high-throughput screening must support large libraries while remaining decodable in a single imaging step. Existing approaches often trade design control for manufacturability: deterministic barcodes often require per-code redesign of particle fabrication, whereas stochastic combinatorial barcodes are difficult to generate as predefined batches. Here we introduce a chemically programmable barcoding architecture that decouples particle fabrication from barcode assignment. Using a contact-free multilaminar flow lithography platform with all-around three-dimensional sheathing, we continuously fabricate a universal hydrogel scaffold containing five spatially segregated DNA-addressable domains at rates >106 particles/h. Chosen barcode identities are subsequently written on demand onto the same template batch by domain-selective DNA hybridization. Single-domain measurements resolved 64 candidate optical states, indicating an experimentally informed theoretical upper bound of 645 {approx} 1.1 x 109 barcodes. We further implemented a predefined 59,049-code library by split-pool labeling, achieving an 88% recovery of decoded beads at a stringent posterior threshold (>0.95). After 11 days, >7,800 beads were correctly re-identified at >0.95 accuracy in matched fields of view. This strategy provides a highly scalable, chemically programmable route to build large, user-defined optical barcode libraries with single-image optical readout and longitudinal traceability.

bioengineering↗

bioRxiv2026

High-throughput CRISPR live-cell imaging of low-frequency chromosomal events quantifies the latent efficiency of chromosome engineering

Abstract/SummaryQuantifying low-frequency chromosomal alterations in living cell populations at early stages is essential in many fields including cancer studies and chromosome engineering, yet selection-based readouts impose delays and can lose fragile positives before readout, biasing frequency estimates; CRISPR imaging rarely reports detection limits at 10^-4. Here, we developed High-throughput CRISPR Imaging (Hi-CRI), integrating engineered dCas9-sgRNA ribonucleoprotein (RNP) labeling, suppression of nonspecific aggregates via metabolic modulation and protease treatment, high-speed volumetric imaging by oblique plane microscopy, GPU-accelerated image analysis, and an explicit error-controlled detection-limit framework. Using per-cell signal-to-noise ratio calling, Hi-CRI achieves a 0.01% detection limit for target-positive cell fractions. In microcell-mediated chromosome transfer of a mouse artificial chromosome (MAC) into HT1080 recipients, Hi-CRI measured 0.03% MAC-positive cells among 184,235 recipients at day 1 post-fusion, versus 0.0007% by antibiotic-selection-based clonogenic assay at day 8 post-fusion, consistent with substantial loss before readout (pre-readout attrition). Hi-CRI enables viability-preserving, selection-independent quantification of low-frequency chromosomal states. TeaserRare chromosome events can be counted in living cells by high-throughput CRISPR imaging before selection hides them.

bioengineering↗

bioRxiv2025

Foliar application of mixed DAMP- and MAMP-oligosaccharides enhances root growth and fruit yield in okra and tomato in greenhouse experiments

Plants perceive diverse endogenous and microbial molecular patterns that shape their defense, growth, and productivity. Damage-associated molecular patterns (DAMPs) such as cello- and xylo-oligosaccharides, and microbe-associated molecular patterns (MAMPs) such as chitin-oligosaccharides, are known to promote both development and immunity. Here, we evaluated the combined application of these three oligosaccharides (Oligo-Mix) in okra and cherry tomato under greenhouse conditions. Regular foliar treatment with Oligo-Mix enhanced root elongation and biomass accumulation, and increased fruit number and yield in both crops. RNA-seq analysis of Oligo-Mix-treated tomato leaves showed coordinated induction of photosynthetic genes, components of the translational machinery, cell-wall remodeling factors, and enzymes involved in flavonoid/anthocyanin biosynthesis, indicating broad enhancement of metabolic capacity and protective secondary pathways. Together, these results demonstrate that Oligo-Mix functions as a biostimulant that supports both vegetative growth and fruit production, offering a sustainable approach to improving crop performance.

plant biology↗

bioRxiv2025

Harnessing fusion of genome-edited human stem cells to rapidly screen for novel protein functions in vivo

Genome editing has enabled the integration of fluorescent protein coding sequences into genomes, resulting in expression of in-frame fusion proteins under the control of their natural gene regulatory sequences. While this technique overcomes the well-documented artifacts associated with gene overexpression, editing genomes of metazoan cells incurs a significant time cost compared to simpler organisms, such as yeast. Editing two or more genes to express multiple fluorescent fusion proteins in a single cell line has proven to be a powerful strategy for uncovering spatio-dynamic, and therefore functional, relationships among different proteins, but it can take many months to edit each gene within the same cell line. Here, by utilizing cell fusions, we quickly generated cells expressing pairwise permutations of fluorescent fusion proteins in genome-edited human cells to reveal previously undetected protein-organelle interactions. We fused human induced pluripotent stem cells (hiPSCs) that express in-frame fusions of clathrin-mediated endocytosis (CME) and actin cytoskeleton proteins with hiPSCs that express fluorescently tagged organelle markers, uncovering novel interactions between CME proteins, branched actin filament networks, and lysosomes. Significance StatementO_LICell fusion can be used to generate new multi-colored genome-edited cell lines, which can be clonally expanded. C_LIO_LIIn combination with genome-edited fluorescent cell line libraries such as the collection from the Allen Institute for Cell Science, cell fusion can be used as a screening tool to look for novel protein localization on a variety of intracellular structures. C_LIO_LIMultiple endocytic proteins localize to the surface of lysosomes in healthy, non-stressed cells, and these proteins exhibit a broad range of behaviors on the lysosome surface. C_LI

cell biology↗

bioRxiv2024

Therapeutic Spp1 silencing in TREM2+ cardiac macrophages suppresses atrial fibrillation

Atrial fibrillation (AFib) and the risk of its lethal complications are propelled by fibrosis, which induces electrical heterogeneity and gives rise to reentry circuits. Atrial TREM2+ macrophages secrete osteopontin (encoded by Spp1), a matricellular signaling protein that engenders fibrosis and AFib. Here we show that silencing Spp1 in TREM2+ cardiac macrophages with an antibody-siRNA conjugate reduces atrial fibrosis and suppresses AFib in mice, thus offering a new immunotherapy for the most common arrhythmia.

immunology↗

bioRxiv2024

Large-scale generation of uniform sub-100 μm adipocyte spheroids in hydrogel microcapsules using a flow-focusing microfluidic device

Adipocyte spheroids are a promising three-dimensional (3D) cell culture model for obesity research because they reproduce 3D adipose tissue structures and cell-cell interactions better than 2D cultures. However, current methods fail to produce uniformly sized, small adipocyte spheroids at large scales, significantly limiting their use in analysis such as large-scale drug screening. Here, we develop a scalable method that combines simple microfluidics with templated emulsification to generate small, uniformly sized adipocyte spheroids. By encapsulating preadipocytes in numerous hollow agarose microcapsules and incubating them for two days, we reproducibly produced more than 100,000 uniform spheroids with diameters of approximately 50 {micro}m (CV: <13%); we then differentiated preadipocyte spheroids into adipocyte spheroids after an 8-day induction period. Our platform enhances large-scale 3D analysis using adipocyte spheroids for obesity research and can be adapted to generate various spheroid and organoid models, advancing biomedical research across diverse fields.

bioengineering↗

bioRxiv2024

Intersectin1 promotes clathrin-mediated endocytosis by organizing and stabilizing endocytic protein interaction networks

During clathrin-mediated endocytosis (CME), dozens of proteins are recruited to nascent CME sites on the plasma membrane. Coordination of endocytic protein recruitment in time and space is important for efficient CME. Here, we show that the multivalent scaffold protein intersectin1 (ITSN1) promotes CME by organizing and stabilizing endocytic protein interaction networks. By live-cell imaging of genome-edited cells, we observed that endogenously labeled ITSN1 is recruited to CME sites shortly after they begin to assemble. Knocking down ITSN1 impaired endocytic protein recruitment during the stabilization stage of CME site assembly. Artificially locating ITSN1 to the mitochondria surface was sufficient to assemble puncta consisting of CME initiation proteins, including EPS15, FCHO, adaptor proteins, the AP2 complex and epsin1 (EPN1), and the vesicle scission GTPase dynamin2 (DNM2). ITSN1 can form puncta and recruit DNM2 independently of EPS15/FCHO or EPN1. Our work redefines ITSN1s primary endocytic role as organizing and stabilizing the CME protein interaction networks rather than a previously suggested role in initiation and provides new insights into the multi-step and multi-zone organization of CME site assembly.

cell biology↗

bioRxiv2023

CD45-antibody-drug conjugate clears tissue resident myeloid cells from their niches enabling therapeutic adoptive cell transfer

Tissue resident myeloid cells (TRM) in adults have highly variable lifespans and may be derived from early embryonic yolk sac, fetal liver or bone marrow. Some of these TRM are known pathogenic participants in congenital and acquired diseases. Myeloablative conditioning and hematopoietic stem cell transplant can replace long-lived brain TRM resulting in clinical improvements in metabolic storage diseases. With the advent of antibody-drug-conjugate (ADC) targeted cell killing as a cell selective means of transplant conditioning, we assessed the impact of anti-CD45-ADC on TRM in multiple tissues. Replacement of TRM ranged from 40 to 95 percent efficiencies in liver, lung, and skin tissues, after a single anti-CD45-ADC dose and bone marrow hematopoietic cell transfer. Of note, the population size of TRM in tissues returned to pre-treatment levels suggesting a regulated control of TRM abundance. As expected, brain, microglia were not affected, but brain monocytes and macrophages were 50% replaced. Anti-CD45-ADC and adoptive cell transfer were then tested in the chronic acquired condition, atherosclerosis exacerbated by Tet2 mutant clonal hematopoiesis. Plaque resident myeloid cells were efficiently replaced with anti-CD45-ADC and wild-type bone marrow cells. Notably, this reduced existent atherosclerotic plaque burden. Overall, these results indicate that anti-CD45-ADC clears both HSC and TRM niches enabling cell replacement to achieve disease modification in a resident myeloid cell driven disease.

immunology↗

bioRxiv2023

Kinetic investigation reveals an HIV-1 Nef-dependent increase in AP-2 recruitment and productivity at endocytic sites

Lentiviruses express non-enzymatic accessory proteins whose function is to subvert cellular machinery in the infected host. The HIV-1 accessory protein Nef hijacks clathrin adaptors to degrade or mislocalize host proteins involved in antiviral defenses. Here, we investigate the interaction between Nef and clathrin-mediated endocytosis (CME), a major pathway for membrane protein internalization in mammalian cells, using quantitative live-cell microscopy in genome-edited Jurkat cells. Nef is recruited to CME sites on the plasma membrane, and this recruitment correlates with an increase in the recruitment and lifetime of CME coat protein AP-2 and late-arriving CME protein dynamin2. Furthermore, we find that CME sites that recruit Nef are more likely to recruit dynamin2, suggesting that Nef recruitment to CME sites promotes CME site maturation to ensure high efficiency in host protein downregulation.

cell biology↗

bioRxiv2022

Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat

The AP adaptor complexes are best known for forming the inner layer of clathrin coats on spherical vesicles. AP complexes also have many clathrin-independent roles in tubulovesicular membrane traffic, whose structural and mechanistic basis has been a mystery. HIV-1 Nef hijacks the AP-1 complex to sequester MHC-I internally, evading immune detection. We found that AP-1:Arf1:Nef:MHC-I forms a coat on tubulated membranes in the absence of clathrin, and determined its structure by cryo-ET. The coat assembles both laterally and axially via an Arf1 dimer interface not seen before. Nef recruits MHC-I, but is not essential for the underlying AP-1:Arf1 lattice. Consistent with a role for AP-1:Arf1 coated tubules as intermediates in clathrin coated vesicle formation, AP-1 positive tubules are enriched in cells upon clathrin knockdown, with or without Nef. Nef localizes preferentially to AP-1 tubules in cells, explaining how Nef can sequester MHC-I. The coat contact residues are conserved across Arf isoforms and across the Arf-dependent AP adaptors AP-1, 3, and 4. These findings reveal that AP complexes can self-assemble with Arf1 into tubular coats in the absence of clathrin or other scaffolding factors. The AP-1:Arf1 coat defines the structural basis of a broader class of tubulovesicular membrane coats, as an intermediate in clathrin vesicle formation from internal membranes, and as a MHC-I sequestration mechanism in HIV-1 infection.

cell biology↗

bioRxiv2021

Genetic Inhibition of Serum Glucocorticoid Kinase 1 Prevents Obesity-related Atrial Fibrillation

RationaleGiven its rising prevalence in both the adult and pediatric populations, obesity has become an increasingly important risk factor in the development of atrial fibrillation. However, a better mechanistic understanding of obesity-related atrial fibrillation is required. Serum glucocorticoid kinase 1 (SGK1) is a kinase positioned downstream of multiple obesity-related pathways, and prior work has shown a pathologic role for SGK1 signaling in ventricular remodeling and arrhythmias. ObjectiveTo determine the mechanistic basis of obesity associated atrial fibrillation and explore the therapeutic potential of targeting SGK1 in this context. Methods and ResultsWe utilized a mouse model of diet induced obesity to determine the atrial electrophysiologic effects of obesity using electrophysiologic studies, optical mapping, and biochemical analyses. In C57BL/6J mice fed a high fat diet, there was upregulation of SGK1 signaling along with an increase in AF inducibility determined at electrophysiology (EP) study. These changes were associated with an increase in fibrotic and inflammatory signaling. Transgenic mice expressing a cardiac specific dominant negative SGK1 (SGK1 DN) were protected from obesity-related AF as well as the fibrotic and inflammatory consequences of AF. Finally, optical mapping demonstrated a shorter action potential duration and patch clamp revealed effects on INa, with a decreased peak current as well as a depolarizing shift in activation/inactivation properties in atrial myocytes. ConclusionsDiet induced obesity leads to increased cardiac SGK1 signaling as well as an increase in AF inducibility in obese mice. Genetic SGK1 inhibition reduced AF inducibility, and this effect may be mediated by effects on inflammation, fibrosis, and cellular electrophysiology.

physiology↗