Biomedical subjects

Takashi Yoshida

Publications and source records attributed to Takashi Yoshida.

3 recordsLinked to original sources

PubMed2026

Draft genome sequence of a novel hydrogenogenic CO-oxidizing bacterium that is phylogenetically closely related to the family Thermicanaceae.

An anaerobic, thermophilic hydrogenogenic carbon monoxide (CO)-oxidizing Bacillota bacterium, 3446A, was isolated from freshwater pond sediments in Kyoto, Japan. The 3.11-Mbp draft genome sequence (guanine-cytosine content, 50.4%) encodes CODH-ECH genes, consistent with hydrogenogenic CO oxidation. Phylogenomic analysis suggests that Bacillota bacterium 3446A represents a novel genus-level lineage within the family Thermicanaceae.

Thermicanaceae↗

PubMed2026

Carbon monoxide-driven proton respiration enables facultative anaerobes to survive electron acceptor limitation.

Diverse microorganisms couple the oxidation of carbon monoxide gas (CO) to the reduction of protons, producing hydrogen gas (H2) using nickel-containing CO dehydrogenase/energy-converting hydrogenase (Ni-CODH/ECH). Although this process yields one of the lowest free-energy gains in biology, its physiological role at environmentally relevant CO levels remains unresolved. Here, we show that Ni-CODH/ECH functions as a survival-oriented energy conservation system that enables heterotrophic facultative anaerobes to survive electron acceptor limitation, rather than primarily supporting growth or CO detoxification. Analysis of 387 genomes of Anoxybacillaceae species revealed that Ni-CODH/ECH had a patchy distribution and, with one exception, was mutually exclusive with the oxygen-tolerant molybdenum-containing CODH, suggesting ecological specialization. Culture experiments using three isolates (Parageobacillus sp. G301, P. thermoglucosidasius NBRC 107763, and Thermolongibacillus altinsuensis B1-1) demonstrated that CO-dependent proton respiration is activated during stationary phase when exogenous electron acceptors are limiting, maintaining cell density under 25% CO, whereas no effect was observed in a Ni-CODH knockout (ΔcooCSF) strain. RNA-seq analysis of Parageobacillus sp. G301 under twelve conditions revealed that Ni-CODH/ECH genes are highly expressed (top 0.2%-1.9% of all genes) under electron acceptor-free conditions, independent of CO presence, under the predicted control of the redox-dependent transcriptional repressor Rex. ΔcooCSF cultures accumulated more CO than the wild-type (WT), suggesting trace CO scavenging by the WT. Together, our results redefine Ni-CODH/ECH as a redox-regulated auxiliary energy-conservation strategy that supports survival and maintenance in anaerobic energy-limited environments using two ubiquitous substrates. This work extends the carboxydovore paradigm of trace gas-based survival from aerobic to spatiotemporally variable anaerobic environments.

Carbon Monoxide↗

PubMed2025

HMGA2 links morphological evolution and microenvironment dynamics to systemic therapy response in clear cell renal cell carcinoma.

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) exhibits significant heterogeneity due to morphological changes and tumor microenvironment dynamics, influencing systemic therapy responses. While the role of high-mobility group AT-hook 2 (HMGA2) in tumor progression has been implicated in other cancers, its significance in ccRCC remains unclear. This study investigates the role of HMGA2 in these processes and its clinical impact. METHODS: Spatial transcriptomics (ST) was performed on primary ccRCC samples to investigate expression trajectories associated with HMGA2 expression and morphological evolution. In metastatic ccRCC cohorts treated with systemic therapy, immunohistochemistry and bulk RNA sequencing data were analyzed to evaluate molecular and clinical features in relation to HMGA2. Single-cell RNA sequencing (scRNA-seq) data were used to explore immune cell populations and their interactions. Based on these findings, multiplex immunohistochemistry (mIHC) assessed spatial distribution, cell-cell interactions, and pathological responses of key immune populations. RESULTS: HMGA2 expression was associated with aggressive morphological patterns, such as solid sheets and rhabdoid/sarcomatoid. ST revealed a progressive increase in HMGA2 expression along the morphological trajectory, marked by a shift from clear to eosinophilic cytoplasm, with eccentric nuclei and prominent nucleoli, and loss of vascular architecture. HMGA2-high tumors exhibited aggressive phenotypes driven by cell cycle, epithelial-mesenchymal transition, and inflammatory signaling pathways. Clinically, patients with high HMGA2 had worse progression-free survival but responded better to immune checkpoint inhibitor combination (Combo-ICI) therapy than to tyrosine kinase inhibitor monotherapy. To assess the immune landscape, scRNA-seq data revealed that HMGA2-high tumors were enriched with progenitor exhausted CD8+ T cells (Tpex), along with increased frequencies of conventional dendritic cell type 1 (cDC1) and inflammatory cDC type 2, which were found to interact with Tpex via ICAM-1. mIHC confirmed that Tpex were enriched among Combo-ICI responders in HMGA2-high tumors, with higher densities and closer proximity to ICAM-1+ cDC1. CONCLUSIONS: These findings suggest that dynamic HMGA2 expression contributes to morphological evolution and modulates immune responses through enhanced Tpex-cDCs engagement, serving as a potential marker for systemic therapy response in ccRCC. However, additional experimental studies are required to validate these mechanisms.

Humans↗