Biology subjects

Imamura, M.

Publications and source records attributed to Imamura, M..

7 recordsLinked to original sources

bioRxiv2026

An iPSC-based experimental framework for investigating phenotypic variation associated with Jomon ancestry in the present-day Japanese population

Ancestry-related genomic variation may contribute to phenotypic diversity. However, its cellular consequences remain difficult to evaluate. To address this, we developed a human induced pluripotent stem cell (hiPSC)-based framework for investigating such phenotypes. We used the Japanese population as a model of Jomon-related and continental East Asian ancestry admixture. Jomon ancestry, estimated using the Jomon allele score (JAS), was associated with clinical measures, including renal-related traits and serum triglycerides in 34,152 Tohoku Medical Megabank participants. Peripheral blood mononuclear cell transcriptomics of donors from the upper and lower extremes of the JAS distribution (n = 10) suggested group-level differences in immune-related gene expression. To test whether the serum triglyceride association coincided with hepatic cellular phenotypes, we differentiated hiPSCs from these donors into hepatocyte-like cells. Neither intracellular triglycerides nor lipid-related gene expression differed between groups. These findings highlight the value of a genetically characterized hiPSC-based framework for investigating ancestry-associated phenotypes across cellular contexts.

genomics↗

bioRxiv2026

Ancient Ryukyu Jomon contributed to past and current genetic structure of Japanese populations

Characterized by the earliest use of pottery, the Jomon culture was a unique Neolithic culture that spread throughout the Japanese Archipelago. Previous archaeological evidence suggests that Jomon hunter-gatherers colonized the southernmost islands, the Ryukyu Archipelago, by approximately 7,000 years before present (YBP). However, genetic characteristics of the Ryukyu Jomon population and its contribution to the modern population have not been elucidated yet. In this study, we newly sequenced 273 modern and 25 ancient (6,700-900 YBP) whole genomes collected across the Ryukyu Archipelago. Our analysis demonstrated a genetic differentiation between the Hondo (Japanese mainland) and Ryukyu Jomon, dating back to [~]6,900 YBP. After the divergence from the Hondo Jomon, the Ryukyu Jomon experienced severe bottlenecks, with an effective population size of [~]2,000. Admixture between the Ryukyu Jomon and migrants from the historic Hondo population occurred [~]1,000 YBP, which corresponds to the widespread adoption of iron tools and agriculture in the Central Ryukyus. Different demographic histories between modern Hondo and Ryukyu populations resulted in different rates of Jomon ancestry in these populations. By providing a new perspective on the peopling of the Ryukyu Archipelago, this study significantly enhances our understanding of cultural transitions in the region.

evolutionary biology↗

bioRxiv2025

Geometric inference of cross-species transcriptome correspondence using Gromov-Wasserstein optimal transport

Sequence homology reveals evolutionary gene correspondences, but identifying functionally corresponding genes within specific cell types or during cell fate specification remains non-trivial. Here, frameworks that translate insights from model organisms into other species would accelerate wet-lab studies, so we develop Species-OT, a cross-species transcriptome analysis framework using Gromov-Wasserstein optimal transport, which quantitatively compares the geometry of transcriptome distributions. Given a pair of bulk or single-cell RNA-sequencing datasets, Species-OT returns a gene-to-gene correspondence capturing probabilistic alignments of regulatory roles, and a transcriptomic distance quantifying overall divergence. Applied pairwise, Species-OT yields a transcriptomic discrepancy array and a hierarchical clustering tree analogous to a phylogenetic tree. We validate Species-OT using bulk RNA-seq data for cell fate specification from pluripotent stem cells in mice, monkeys, and humans and scRNA-seq data from pluripotent stem cells of six mammalian species. Species-OT identifies gene correspondences within cell fate specification, while transcriptomic discrepancies recapitulate expected species relationships.

bioinformatics↗

bioRxiv2025

Concordance of claudin-18.2 expression in biopsy, resection, and recurrent specimens: implications for zolbetuximab therapy in pancreatic ductal adenocarcinoma

Claudin-18.2 is a promising therapeutic target for gastrointestinal cancer. However, its expression pattern in pancreatic ductal adenocarcinoma, especially the concordance between biopsy and resection specimens, is unknown. This study aimed to evaluate the consistency of claudin-18.2 positivity across different specimen types using the clinically validated antibody clone 43-14A employed in ongoing zolbetuximab trials. Immunohistochemical analysis for claudin-18 was conducted on 211 resected pancreatic cancer tissues, 133 matched preoperative biopsy samples, and 60 samples from recurrent lesions. Concordance rates were calculated based on a clinically relevant cutoff ([≥]75% of tumor cells with moderate-to-strong membranous staining). Receiver operating characteristic analysis was used to optimize the biopsy thresholds. Claudin-18.2 positivity was observed in 9.5% of the resection specimens. The concordance rates were 92.5% between biopsy and resection specimens and 83.3% between primary and recurrent lesions. Receiver operating characteristic analysis suggested that a lower cutoff (20%) in biopsy samples achieved 100% sensitivity for detecting positive cases. While overall claudin-18 expression levels were maintained in most recurrent lesions, decreased expression was frequently observed in cases of local recurrence and liver metastasis. Despite intrinsic heterogeneity and limited biopsy yield in pancreatic cancer, claudin-18 expression in small biopsy samples, assessed using the clinical trial-validated clone 43-14A, strongly correlated with that in resection specimens. These results suggest that claudin-18.2 is a clinically stable biomarker for zolbetuximab therapy in patients with pancreatic ductal adenocarcinoma. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/648482v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1b822e5org.highwire.dtl.DTLVardef@1fb03f0org.highwire.dtl.DTLVardef@bfa888org.highwire.dtl.DTLVardef@d1a015_HPS_FORMAT_FIGEXP M_FIG C_FIG Core TipsO_LIThis study demonstrated a high concordance (92.5%) of CLDN18.2 positivity between preoperative biopsy and resected pancreatic ductal adenocarcinoma specimens, using the clinical trial-validated antibody clone 43-14A. C_LIO_LICLDN18.2 expression in recurrent lesions generally remained consistent with that in the corresponding primary tumor, although a reduction in expression levels was observed in local recurrence and liver metastases. C_LIO_LIThese findings support the clinical utility of biopsy-based CLDN18.2 evaluation for selecting patients with pancreatic ductal adenocarcinoma who may benefit from zolbetuximab. C_LI

pathology↗

bioRxiv2024

Submolecular-scale Hairpin DNA Folding Dynamics Studied by High-Speed AFM with Optical Tweezers

Optical tweezers have contributed to elucidate the folding mechanisms associated with biomolecules. By combining single-molecule or super-resolution techniques, imaging can also be performed while measuring or inducing force coupling with biochemical reactions; however, they cannot capture structural information beyond the fluorophore spatial resolution. To overcome this problem, here, we developed a technique that combines optical tweezers with high-speed atomic force microscopy (AFM). To solve the problem of incompatible instrumental configurations, we developed a unique optical tweezers measurement system that is specialized for high-speed AFM. Upon applying an external force to a synthesized DNA secondary structure, we successfully visualized the dissociation of the duplex structure. Furthermore, we succeeded in observing spontaneous reannealing of the duplex structure upon releasing the force, which demonstrates that the folding reaction can be reversibly controlled. We also reveal that along with duplex unfolding, a metastable secondary structure is generated and its topology changes transiently over time. The results indicate that this technique provides structural insights that cannot be obtained by conventional fluorescence techniques.

biophysics↗

bioRxiv2022

Multiphasic hepatitis B virus kinetic patterns in humanized chimeric mice can be explained via stochastic agent-based modeling of intracellular virion production cycles

Serum hepatitis B virus (HBV) kinetics in urokinase-type plasminogen activator/severe combined immunodeficient (uPA-SCID) mice reconstituted with humanized livers from inoculation to steady state is highly dynamic despite the absence of an adaptive immune response. We developed a stochastic agent-based model that includes virion production cycles in individual infected human hepatocytes. The model was calibrated using a genetic algorithm approach with the serum HBV kinetics observed in mice inoculated with 108 HBV genome equivalents and fit the data well when the following viral production parameters were assumed: (1) An eclipse phase lasting 5-50 hours and (2) a post-eclipse phase production rate that is based on increasing production cycles initially starting with a long production cycle of 1 virion per 20 hours that gradually reaches 1 virion per hour after approximately 3-4 days before virion production increases dramatically to reach to a steady state production rate of 4 virions per hour per cell. The model was then validated by showing it could accurately simulate the viral kinetics observed with lower HBV inoculation doses (104-107 genome equivalents) in which similar, but delayed patterns were observed. Together, modeling suggests that it is the cyclic nature of the virus lifecycle combined with an initial slow but increasing rate of HBV production from each cell that plays a role in generating the observed multiphasic HBV kinetic patterns in humanized mice.

systems biology↗

bioRxiv2021

A hierarchical transcriptional network activates specific CDK inhibitors that regulate G2 to control cell size and number in Arabidopsis

How cell size and number are determined during organ development remains a fundamental question in cell biology. Here, we identified a GRAS family transcription factor, called SCARECROW-LIKE28 (SCL28), with a critical role in determining cell size in Arabidopsis. SCL28 is part of a transcriptional regulatory network downstream of the central MYB3Rs that regulate G2 to M phase cell cycle transition. We show that SCL28 forms a dimer with the AP2-type transcription factor, AtSMOS1, which defines the specificity for promoter binding and directly activates transcription of a specific set of SIAMESE-RELATED (SMR) family genes, encoding plant-specific inhibitors of cyclin-dependent kinases and thus inhibiting cell cycle progression at G2 and promoting the onset of endoreplication. Through this dose-dependent regulation of SMR transcription, SCL28 quantitatively sets the balance between cell size and number without dramatically changing final organ size. We propose that this hierarchical transcriptional network constitutes a cell cycle regulatory mechanism that allows to adjust cell size and number to attain robust organ growth.

plant biology↗