Biology subjects

Adachi, J.

Publications and source records attributed to Adachi, J..

4 recordsLinked to original sources

bioRxiv2026

A comprehensive temporal proteome and phosphoproteome dataset of Y1 adrenocortical cells under FGF2 stimulation and SOS inhibition

The Y1 mouse adrenocortical tumor cell line is a classic model for cancer studies and ACTH mediated steroidogenesis. The KRAS gene amplification and SOS mediated activation sustain elevated ERK levels, which drive the tumor phenotype of this cell line. In addition, the mitogen FGF2 induces atypical cytotoxic stress and consequent cell death rather than proliferation in this system, imposing a strong perturbation on KRAS ERK signaling dynamics. Recent research from our group revealed that SOS is not solely responsible for KRAS activation in the Y1 cells, indicating a more complex regulatory landscape of GEFs and GAPs. This motivated the generation of a comprehensive time resolved proteome (DIA) and TMT phosphoproteome (DDA) in a 0 to 30 minute time course under FGF2 stimulation or combined with SOS inhibitor, with the presence or absence of FBS stimulation, in technical triplicate using Q Exactive and Thermo Lumos mass spectrometers, respectively. This dataset can enable latent mechanisms between the life and death switch caused by FGF2 signaling and the alternate stress response caused by impaired SOS dependent activation. This analysis yielded 14,512 phosphosites and 8,919 protein groups, where 10,471 phosphosites and 111 protein groups showed differential abundance with statistical significance (limma, FDR < 0.05%). This dataset provides a versatile resource for downstream applications, which includes dynamic modeling such as ordinary differential equation based frameworks, for which temporal datasets remain scarce. The data contained in this preprint will be available on JPOST Repo after the publication.

cancer biology↗

bioRxiv2024

Priming Epigenetic Landscape at Gene Promoters through Transcriptional Activation in Mammalian Germ Cells

In mammalian germ cells, a cycle of erasing and resetting epigenetic information is crucial for sex-specific gametogenesis and early embryogenesis. Specific chromatin states at promoters allow genes to be expressed at the appropriate time during germ cell development, however, the mechanism that establishes such characteristic chromatin states remains unclear. Here, we show that, in mouse male embryonic germ cells, promoters of developmental and housekeeping genes are selectively protected from de novo DNA methylation, coinciding with their transient upregulation and genome-wide erasure of H3K27me3. Importantly, a specific level of H3K4me3 density at the promoters serves as a potent probe that distinguishes between hypo- and hyper-DNA methylation states. Subsequent restoration of H3K27me3 contributes to establishing bivalent chromatin states that prime genes for activation at later developmental stages. These findings reveal a molecular framework shaping the epigenetic landscape at promoters with long-term effects beyond germ cell development.

genomics↗

bioRxiv2022

Phase-separated nuclear bodies of nucleoporin fusions, SET-NUP214 and NUP98-HOXA9, promote condensation of MLL1 and CRM1 to activate target genes

Nucleoporins NUP98 and NUP214 form chimeric fusion proteins that assemble into phase-separated nuclear bodies. However, the function and physiological significance of these nuclear bodies remain largely unknown. Previously, we reported that both NUP98-HOXA9 and SET-NUP214 are recruited to HOX cluster regions via chromatin-bound CRM1, a nuclear export receptor (Oka et al., 2019). Here, we show that these nuclear bodies promote the condensation of mixed lineage leukemia 1 (MLL1), a histone methyltransferase which is essential for the maintenance of HOX gene expression. Our analysis revealed that SET-NUP214 and CRM1 robustly associate with MLL1 to form nuclear bodies and are colocalized on chromatin. We also showed that MLL1 and CRM1 are recruited to the nuclear bodies of NUP98-HOXA9 and that the NUP98-HOXA9/CRM1/MLL1 complex accumulates on its target gene loci, including HOX clusters and MEIS1. These phenomena were not observed in phase-separation-deficient mutants or non-DNA-binding mutants of NUP98-HOXA9. Collectively, these results show that both phase separation and proper targeting of nucleoporin fusions to specific sites could enhance the activation of a wide range of target genes by promoting the condensation of MLL1 and CRM1.

cell biology↗

bioRxiv2022

Classification of Extracellular Vesicles based on Surface Glycan Structures by Spongy-like Separation Media

Extracellular vesicles (EVs) are lipid bilayer vesicles that enclose various biomolecules. EVs hold promise as sensitive biomarkers to detect and monitor various diseases. However, they have heterogenous molecular compositions. The compositions of EVs from identical donor cells obtained using the same purification methods may differ, which is a significant obstacle for elucidating objective biological functions. Herein the potential of a novel lectin-based affinity chromatography (LAC) method to classify EVs based on their glycan structures is demonstrated. The proposed method utilizes a spongy-like monolithic polymer (spongy monolith, SPM), which consists of poly(ethylene-co-glycidyl methacrylate) with continuous micropores and allows an efficient in-situ protein reaction with epoxy groups. Two distinct lectins with different specificities, Sambucus sieboldiana agglutinin and concanavalin A, are effectively immobilized on SPM without impacting the binding activity. Moreover, high recovery rates of liposomal nanoparticles as a model of EVs are achieved due to the large flow-through pores (>10 m) of SPM. Finally, lectin-immobilized SPMs are employed to classify EVs based on the surface glycan structures and demonstrate different subpopulations by proteome profiling.

biochemistry↗