Biology subjects

Aoyama, J.

Publications and source records attributed to Aoyama, J..

3 recordsLinked to original sources

bioRxiv2025

In Situ Graphene-Seq: Spatial Transcriptomics and Chronic Electrophysiological Characterization of Tissue Microenvironments

Biological systems are composed of diverse, interconnected cell types, yet capturing both their functional dynamics and molecular identities at high spatiotemporal resolution remains challenging. While electrophysiological measurements provide real-time insights into cellular activities, they cannot fully describe the molecular architecture and states of the measured cells. Conversely, transcriptomics reveals cell gene expression patterns but does not capture functional states. Bridging these modalities is essential for a holistic understanding of the molecular mechanisms driving functional changes. In this study, we introduce in situ graphene-sequencing (graphene-seq), a unique platform that seamlessly integrates chronic electrophysiology with imaging-based, spatially resolved 3D transcriptomics, overcoming longstanding limitations of current multimodal approaches. This system leverages stretchable mesh nanoelectronics for long-term, single-cell-level interfacing and incorporates transparent graphene/PEDOT:PSS electrodes, enabling seamless integration of electrical recordings and optical imaging. By combining electrophysiology with high-throughput, imaging-based in situ sequencing, this platform allows comprehensive multimodal, spatially resolved analysis of cell microenvironment within spatially heterogeneous tissues. We validate in situ graphene-seq by charting multimodal profiles of human-induced pluripotent stem cell-derived cardiomyocyte and endothelial cell co-cultures, examining how spatial heterogeneity in cell composition influences both electrophysiological activity and gene expression. This scalable, integrated approach offers a powerful tool for studying the complex interplay between cellular function and molecular identity. It also provides insights into how tissue microenvironments shape cell behavior and molecular states, advancing applications in regenerative medicine, stem cell therapy, and disease modeling.

bioengineering↗

bioRxiv2024

Disruption of the PGE2 synthesis / response pathway restrains atherogenesis in programmed cell death-1 (Pd-1) deficient hyperlipidemic mice

Immune checkpoint inhibitors (ICIs) that target programmed cell death 1 (PD-1) have revolutionized cancer treatment by enabling the restoration of suppressed T-cell cytotoxic responses. However, resistance to single-agent ICIs limits their clinical utility. Combinatorial strategies enhance their antitumor effects, but may also enhance the risk of immune related adverse effects of ICIs. Prostaglandin (PG) E2, formed by the sequential action of the cyclooxygenase (COX) and microsomal PGE synthase (mPGES-1) enzymes, acting via its E prostanoid (EP) receptors, EPr2 and EPr4, promotes lymphocyte exhaustion, revealing an additional target for ICIs. Thus, COX inhibitors and EPr4 antagonists are currently being combined with ICIs potentially to enhance antitumor efficacy in clinical trials. However, given the cardiovascular (CV) toxicity of COX inhibitors, such combinations may increase the risk particularly of CV AEs. Here, we compared the impact of distinct approaches to disruption of the PGE2 synthesis /response pathway - global or myeloid cell specific depletion of mPges-1 or global depletion of Epr4 - on the accelerated atherogenesis in Pd-1 deficient hyperlipidemic (Ldlr-/-) mice. All strategies restrained the atherogenesis. While depletion of mPGES-1 suppresses PGE2 biosynthesis, reflected by its major urinary metabolite, PGE2 biosynthesis was increased in mice lacking EPr4, consistent with enhanced expression of aortic Cox-1 and mPges-1. Deletions of mPges-1 and Epr4 differed in their effects on immune cell populations in atherosclerotic plaques; the former reduced neutrophil infiltration, while the latter restrained macrophages and increased the infiltration of T-cells. Consistent with these findings, chemotaxis by bone-marrow derived macrophages from Epr4-/- mice was impaired. Epr4 depletion also resulted in extramedullary lymphoid hematopoiesis and inhibition of lipoprotein lipase activity (LPL) with coincident spelenomegaly, leukocytosis and dyslipidemia. Targeting either mPGES-1 or EPr4 may restrain lymphocyte exhaustion while mitigating CV irAEs consequent to PD-1 blockade.

pharmacology and toxicology↗

bioRxiv2021

AzuCR RNA modulates carbon metabolism as a dual-function RNA in Escherichia coli

Bacteria have evolved small RNAs (sRNAs) to regulate numerous biological processes and stress responses. While sRNAs generally are considered to be "noncoding", a few have been found to also encode a small protein. Here we describe one such dual-function RNA that modulates carbon utilization in Escherichia coli. The 164 nucleotide RNA was previously shown to encode a 28 amino acid protein (denoted AzuC). We discovered the membrane-associated AzuC protein interacts with GlpD, the aerobic glycerol-3-phosphate dehydrogenase, leading to increased GlpD activity. Overexpression of the RNA encoding AzuC results in a growth defect in glycerol and galactose medium. The defect in galactose medium was still observed for a stop codon mutant derivative, suggesting a potential regulatory role for the RNA. Consistent with this observation, we found that cadA and galE are repressed by base pairing with the RNA (denoted AzuCR). Interestingly, translation of AzuC interferes with the observed repression of cadA and galE by AzuCR and base pairing interferes with AzuC translation, demonstrating that the translation and base pairing functions compete.

microbiology↗