Biology subjects

Suga, K.

Publications and source records attributed to Suga, K..

6 recordsLinked to original sources

bioRxiv2025

Sox4 in Treg Cells Suppresses IL-10 Production via c-Maf Degradation and Exacerbates Type 2 Inflammation

The anti-inflammatory cytokine interleukin-10 (IL-10) produced by regulatory T (Treg) cells plays a crucial role in regulating allergic airway inflammation. However, the mechanisms governing IL-10 production in Treg cells remain unclear. In this study, we first identified Sox4 as a gene whose expression is down-regulated in IL-10-producing Treg cells. Comprehensive gene expression profiling of Sox4-deficient Treg cells and Sox4-overexpressing Treg cells revealed specific downregulation of Il10 and Ctla4 by Sox4. Sox4-deficient Treg cells exhibited increased IL-10 production and CTLA-4 expression both in vitro and in vivo and strongly suppressed Th2 cell proliferation compared with Sox4-expressing Treg cells. In a house dust mite (HDM)-induced asthma model, Treg-specific Sox4-deficient (Sox4-cKO) mice exhibited IL-10-dependent reductions in eosinophilic inflammation and Th2 cell infiltration in the airways. A comparison of Sox4-cKO and wild-type Treg cells in the same inflamed environment in mixed bone marrow chimeric mice with HDM-induced asthma revealed that Sox4-mediated suppression of c-Maf is cell-intrinsic. In addition, overexpression of Sox4 in Treg cells repressed the activation of c-Maf-regulated chromatin regions, including those around the Il10 and Ctla4 loci. Moreover, Sox4-induced suppression of IL-10 and CTLA-4 in Treg cells was rescued by forced expression of c-Maf. While Sox4 did not significantly affect Maf mRNA levels, Sox4 degraded c-Maf proteins in Treg cells through its 33 C-terminal residues. Via a domain distinct from its C-terminus, Sox4 physically interacted with c-Maf, subsequently facilitating its degradation through a ubiquitin-proteasome pathway. These findings elucidate a mechanism by which Sox4 influences the asthmatic responses by regulating the c-Maf/IL-10 axis in lung Treg cells.

immunology↗

bioRxiv2025

Deciphering the comprehensive relationship between 5'UTR and 3'UTR sequences with deep learning

MotivationRecent advances in mRNA therapeutics have driven further research on untranslated region (UTR) of mRNA. However, prior studies have mainly focused on either the 5' or 3' UTR individually. Increasing evidence suggests potential cooperative effects between these two regions, which remain largely unexplored in computational studies. ResultsWe present a deep learning-based approach to predicting relationships between 5' and 3' UTRs by leveraging latent representations from a pre-trained RNA language model and contrastive learning. Our method effectively identifies highly related UTR pairs, uncovering sequence and expression characteristics that suggest functional interplay. Our analysis revealed that Highly Related UTR pairs (HRUs) are significantly enriched in genes associated with neural development, exhibit distinctive UTR length and secondary structure characteristics, and are involved in cell type-specific regulation of translation efficiency. These findings provide new insights into UTR co-optimization for mRNA therapeutics. AvailabilityThe source code is available for free at https://github.com/hmdlab/utr_pairpred.git. The data and intermediate files used in our analysis are available at https://waseda.box.com/v/utr-pairpred-data.

bioinformatics↗

bioRxiv2024

Multi-objective computational optimization of human 5' UTR sequences

The computational design of mRNA sequences is a critical technology for both scientific research and industrial applications. Recent advances in prediction and optimization models have enabled the automatic scoring and optimization of 5' UTR sequences, key upstream elements of mRNA. However, fully automated design of 5' UTR sequences with more than two objective scores has not yet been explored. In this study, we present a computational pipeline that optimizes human 5' UTR sequences in a multi-objective framework, addressing up to four distinct and conflicting objectives. Our work represents an important advancement in the multi-objective computational design of mRNA sequences, paving the way for more sophisticated mRNA engineering.

bioinformatics↗

bioRxiv2023

Reactive blue dye detects male reproductive toxicity

BackgroundReactive blue 2 (RB2) dye specifically binds to the nuclei of human spermatozoa under weakly alkaline conditions, thus providing a new method to assess sperm quality. However, this technique has not yet been applied to other mammalian species, such as well-established rodent models, which could enable evaluation of the male reproductive toxicity of drug candidates in non-clinical studies. ObjectivesWe aimed to evaluate the usefulness of RB2 staining in assessing testicular and epididymal sperm toxicity in mice using a busulfan-induced infertility model. MethodsMale C57BL/6J mice were intraperitoneally administered 40 mg/kg of busulfan. After 28 days, the testes and epididymis were collected and stained with RB2 at pH 10. In vitro evaluations were conducted on uncoated glass slides with RB2 mixed with either protamines extracted from the spermatozoa or intracellular protein components from somatic cells without protamines. ResultsFollowing peanut agglutinin (PNA) lectin histochemistry, RB2-positive cells were observed in elongating and elongated spermatids at all stages except for stages IX-XI of the seminiferous epithelium. After busulfan administration, the proportion of RB2-positive germ cells in the seminiferous tubules decreased significantly, and no RB2-positive spermatozoa were found in the caput epididymis of treated mice. Aggregates were observed in the mixture of RB2 dye (pH 10) with protamines but not in the mixture of intracellular protein components without protamines, and this specificity was lost at neutral pH. Discussion and ConclusionOur study demonstrates that RB2 specifically stains steps 12-16 spermatids, indicating specific binding to protamine expressed in these spermatids. The RB2 staining technique has potential as a biomarker for male reproductive toxicity, allowing for the rapid visualization of protamination.

pharmacology and toxicology↗

bioRxiv2022

Development of a non-invasive method for testicular toxicity evaluation using a novel compact magnetic resonance imaging system

In non-clinical animal studies for drug discovery, histopathological evaluation is the most powerful tool to assess testicular toxicity. However, histological analysis is extremely invasive; many experimental animals are needed to evaluate changes in the pathology and anatomy of the testes over time. As an alternative, small animal magnetic resonance imaging (MRI) offers a non-invasive methodology to examine testicular toxicity without radiation. The present study demonstrated the suitability of a new, ready-to-use compact MRI platform using a high-field permanent magnet to assist with the evaluation of testicular toxicity. To validate the utility of the MRI platform, male mice were treated with busulfan (40 mg/kg, intraperitoneal injection). Tenty-eight days after treatment, both testes in busulfan-treated and control mice (n = 3/group) were non-invasively scanned in situ by MRI at 1 tesla. On a T1-weighted, 3D gradient-echo MRI sequences (voxel size: 0.23 x 0.23 x 0.50 mm), the total testicular volume in busulfan-treated mice was significantly smaller than in controls. On T1-weighted images, the signal intensity of the testes was significantly higher in busulfan-treated mice than in controls. The mice were sacrificed, and the testes were isolated for histopathological analysis. The weight of the testes in busulfan-treated mice significantly decreased, similar to the results of the non-invasive analysis. Additionally, periodic acid-Schiff stain-positive effusions were observed in the interstitium of the busulfan-treated mouse testes, potentially explaining T1 shortening due to a high concentration of glycoproteinaceous content. The present data demonstrated a rapid evaluation of testicular toxicity in vivo by compact MRI.

pharmacology and toxicology↗

bioRxiv2018

Multiple interfacial hydration of dihydro-sphingomyelin bilayer reported by the Laurdan fluorescence

The hydration properties of the lipid bilayer interface are important for determining membrane characteristics. The hydration properties of different lipid bilayer species were evaluated using the solvent sensitive fluorescence probe, 6-lauroyl-2-dimethylamino naphthalene (Laurdan). Sphingolipids, D-erythro-N-palmitoyl-sphingosylphosphorylcholine (PSM) and D-erythro-N-palmitoyl-dihydrosphingomyelin (DHPSM) showed specific, interfacial hydration properties stemming from their intra- and intermolecular hydrogen bonds. As control, the bilayers of glycerophospholipids, such as 1-palmitoyl-2-palmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1-oleoyl-2-oleoyl-sn-glycero-3-phosphocholine (DOPC), were also evaluated. The fluorescence properties of Laurdan in sphingolipids indicated multiple excited states according to the results obtained from the emission spectra, fluorescence anisotropy, and the center of mass spectra during the decay time. Deconvolution of the Laurdan emission spectra into four components enabled us to identify the variety of hydration and the configurational states derived from intermolecular hydrogen bonding in sphingolipids. Particularly, the Laurdan in DHPSM revealed more hydrated properties compared to the case in PSM, even though DHPSM has a higher Tm than PSM. Since DHPSM forms hydrogen bonds with water molecules (in 2NH configurational functional groups) and the different flexibility among the head groups compared with PSM, which could modulate space to retain a high amount of water molecules. The careful analysis of Laurdan such as the deconvolution of emission spectra into four components performed in this study gives the important view for understanding the membrane hydration property.

biophysics↗