Biology subjects

Miyanari, Y.

Publications and source records attributed to Miyanari, Y..

5 recordsLinked to original sources

bioRxiv2024

Development of nanobodies against human Survivin, applicable to suppress cell proliferation.

Survivin, a member of the inhibitor of apoptosis protein (IAP) family, is overexpressed in many cancers, making it a valuable target for therapy and a biomarker for cancer diagnostics. As Survivin contributes to cancer development by inhibiting apoptosis and promoting rapid cell division, inhibiting its activity is a promising strategy to overcome cancer resistance to apoptosis and reduce tumor growth. In this study, we developed nanobodies targeting human Survivin using M13 phage display and deep sequencing to identify high-affinity binders. Seven nanobody clones were selected and evaluated through ELISA, western blotting, and immunostaining. Clones 7 and 15, which specifically bind the alpha-helix region of Survivin, effectively suppressed cell proliferation by disrupting cell cycle regulation, likely by interfering interaction with intracellular binding partners. These findings suggest that Survivin-targeting nanobodies hold potential as therapeutic agents for cancer treatment, offering a novel approach to inhibiting tumor growth through the disruption of Survivin-mediated processes.

cancer biology↗

bioRxiv2024

Efficient production of functional proaerolysin from E.coli

Proaerolysin is a bacterial toxin produced by Aeromonas hydrophila that specifically binds to GPI-anchored proteins on the plasma membrane, creating transmembrane pores that lead to cell death within a few hours. Leveraging this unique property, proaerolysin is widely used in diagnostic tests for paroxysmal nocturnal hemoglobinuria (PNH), a disease caused by somatic mutations in the PIGA gene, which is involved in the biosynthesis of GPI anchors. Additionally, proaerolysin serves as a counter-selection agent in genetic manipulations. Although bacterial expression and purification of proaerolysin have been previously reported, yields were low due to the absence of internal disulfide bonds, which are crucial for protein stability. Here, we demonstrate that using the Shuffle E. coli strain, which facilitates the formation of disulfide bonds in the cytoplasm, significantly improves the solubility and proper folding of proaerolysin. We achieved a high yield of proaerolysin, approximately 3 mg from a 50 ml bacterial culture, with a purity of over 99%. The functionality of recombinant proaerolysin was confirmed by testing in mouse embryonic stem cells (mESCs), demonstrating that this high-yield production method offers a reliable and cost-effective source of functional proaerolysin for a wide range of biotechnological applications.

biochemistry↗

bioRxiv2024

The transcription factor BATF pioneers the differentiation program of cytolytic effector CD8+ T cells through the direct interaction with IRF4

The transcription factor BATF plays critical roles in the differentiation of various immune cells, including CD8+ T cells. Here, we demonstrated that BATF controls epigenomic and transcriptomic reprogramming of CD8+ T cells at an early phase of acute viral infection, thereby promoting the differentiation of cytolytic effector CD8+ T cells. Loss of BATF drastically perturbed gene expression, chromatin accessibility, and the bindings of key transcription factors including Jun, T-bet, and IRF4. The direct interaction with IRF4 was essential for BATF-mediated effector differentiation, as the BATF mutant lacking this interaction failed to induce proper chromatin remodeling and proliferation of antigen-specific CD8+ T cells. Notably, IRF4 binding was exhaustively dependent on BATF, whereas BATF retained binding capacity even in IRF4-deficient CD8+ T cells. Furthermore, BATF initiated chromatin remodeling in the absence of IRF4, whereas subsequent dynamic epigenomic reorganization required IRF4. Our data proposed that BATF serves as a "pioneer transcription factor" spearheading the reorganization of chromatin architecture upon antigen encounter, followed by further rearrangement of epigenomic and transcriptomic landscapes through the cooperation with IRF4.

immunology↗

bioRxiv2023

S100A11 promotes focal adhesion disassembly via myosin II-driven contractility and Piezo1-mediated Ca2+ entry

S100A11 is a small Ca2+-activatable protein with an established role in different cellular processes involving actin cytoskeleton remodeling, such as cell migration, membrane protrusion formation, and plasma membrane repair. It also displays Ca2+-dependent F-actin binding activity and localizes to actin stress fibers (SFs), but its precise role in regulating these structures remains unclear. Analyzing endogenous S100A11 localization in HeLa and U2OS osteosarcoma cells confirmed SF association but in addition revealed steady localization to stable focal adhesions (FAs), typically at the end of dorsal stress fibers. In contrast, S100A11 levels at FAs increased sharply, but transiently, at the onset of peripheral FA disassembly. Elevating intracellular Ca2+ levels using the Ca2+ ionophore ionomycin reliably stimulated both S100A11 recruitment and subsequent FA disassembly. However, pre-incubation with the non-muscle myosin II (NM II) inhibitor blebbistatin, or with an inhibitor to the stretch-activatable Ca2+ channel Piezo1 effectively suppressed S100A11 recruitment, implicating S100A11 in an actomyosin contractility-driven FA disassembly mechanism involving Piezo1-dependent Ca2+ influx. Applying external mechanical forces on peripheral FAs via a micropipette likewise recruited S100A11 to FAs, even when NM II was inhibited by blebbistatin or in NM IIA knockout cells, corroborating the mechanosensitive recruitment mechanism of S100A11. However, extracellular Ca2+ and Piezo1 function was still indispensable, indicating that NM II-dependent contraction forces act upstream of Piezo1-mediated Ca2+ influx, in turn leading to S100A11 activation and FA recruitment. Moreover, S100A11 knockout cells feature enlarged FAs and display delayed FA disassembly during cell membrane retraction, consistent with impaired FA turnover in these cells. Our results thus demonstrate a novel mechano-sensitive function for S100A11 in promoting actomyosin contractility-driven FA disassembly.

cell biology↗

bioRxiv2019

Genomic profiling of PML bodies reveals transcriptional regulation by PML bodies through the DNMT3A exclusion

The promyelocytic leukaemia (PML) body is a phase-separated nuclear structure involved in various biological processes, including senescence, and tumour suppression1. PML bodies consist of various proteins, including PML proteins and several chromatin regulators2,3 and physically associate with chromatin4,5, implying their crucial roles in particular genome functions. However, their roles in transcriptional regulation are largely unknown. Here, we developed APEX-mediated chromatin labelling and purification (ALaP), to identify the genomic regions associated with PML bodies. We find that PML bodies associate with active regulatory regions across the genome and prominently with a [~]300 kb of the short arm of the Y chromosome (YS300) in mouse embryonic stem cells (mESCs). The association with YS300 is essential for the transcriptional activities of neighbouring Y-linked cluster genes. Mechanistically, we show that PML bodies play a novel role in 3D nuclear organization by providing specific nuclear spaces that the de novo DNA methyltransferase DNMT3A cannot access, which results in the robust maintenance of the hypo-methylated states at the Y-linked gene promoters. Our study underscores a new mechanism for gene regulation in the 3D-nuclear space and provides insights into the functional properties of nuclear structures for genome functions.

cell biology↗