Kosuke Ogata

Dr. Kosuke Ogata

orcid

Research Focus & Metrics

Academic Career Length

30Years (1997-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

View All Publications
20 May 2024 in Nature
Verified
Journal Article
Open access
PDF file
YMYusuke Murase
Yusuke Murase
RYRyuta Yokogawa
Ryuta Yokogawa
YYYukihiro Yabuta
Yukihiro Yabuta
MNMasahiro Nagano
Masahiro Nagano
YKYoshitaka Katou
Yoshitaka Katou
MSMitinori Saitou
Mitinori Saitou
Epigenetic reprogramming resets parental epigenetic memories and differentiates primordial germ cells (PGCs) into mitotic pro-spermatogonia or oogonia. This process ensures sexually dimorphic germ cell development for totipotency1. In vitro reconstitution of epigenetic reprogramming in humans remains a fundamental challenge. Here we establish a strategy for inducing epigenetic reprogramming and differentiation of pluripotent stem-cell-derived human PGC-like cells (hPGCLCs) into mitotic pro-spermatogonia or oogonia, coupled with their extensive amplification (about >1010-fold). Bone morphogenetic protein (BMP) signalling is a key driver of these processes. BMP-driven hPGCLC differentiation involves attenuation of the MAPK (ERK) pathway and both de novo and maintenance DNA methyltransferase activities, which probably promote replication-coupled, passive DNA demethylation. hPGCLCs deficient in TET1, an active DNA demethylase abundant in human germ cells2,3, differentiate into extraembryonic cells, including amnion, with de-repression of key genes that bear bivalent promoters. These cells fail to fully activate genes vital for spermatogenesis and oogenesis, and their promoters remain methylated. Our study provides a framework for epigenetic reprogramming in humans and an important advance in human biology. Through the generation of abundant mitotic pro-spermatogonia and oogonia-like cells, our results also represent a milestone for human in vitro gametogenesis research and its potential translation into reproductive medicine.


8 December 2022 in Journal of Proteome Research
Verified
Journal Article
Closed access
TBTaylor Battellino
Taylor Battellino
KOKosuke Ogata
Kosuke Ogata
VSVictor Spicer
Victor Spicer
YIYasushi Ishihama
Yasushi Ishihama
OKOleg Krokhin
Oleg Krokhin

16 June 2021 in Journal of Proteome Research
Verified
Journal Article
Closed access
CCChih-Hsiang Chang
Chih-Hsiang Chang
DYDarien Yeung
Darien Yeung
VSVictor Spicer
Victor Spicer
KOKosuke Ogata
Kosuke Ogata
OKOleg Krokhin
Oleg Krokhin
YIYasushi Ishihama
Yasushi Ishihama

12 October 2021 in eLife
Verified
Journal Article
Open access
KAKotaro Akaki
Kotaro Akaki
KOKosuke Ogata
Kosuke Ogata
YYYuhei Yamauchi
Yuhei Yamauchi
NINoriki Iwai
Noriki Iwai
KTKa Man Tse
Ka Man Tse
OTOsamu Takeuchi
Osamu Takeuchi
Regnase-1 is an endoribonuclease crucial for controlling inflammation by degrading mRNAs encoding cytokines and inflammatory mediators in mammals. However, it is unclear how Regnase-1-mediated mRNA decay is controlled in interleukin (IL)-1β- or Toll-like receptor (TLR) ligand-stimulated cells. Here, by analyzing the Regnase-1 interactome, we found that IL-1β or TLR stimulus dynamically induced the formation of Regnase-1-β-transducin repeat-containing protein (βTRCP) complex. Importantly, we also uncovered a novel interaction between Regnase-1 and 14-3-3 in both mouse and human cells. In IL-1R/TLR-stimulated cells, the Regnase-1-14-3-3 interaction is mediated by IRAK1 through a previously uncharacterized C-terminal structural domain. Phosphorylation of Regnase-1 at S494 and S513 is critical for Regnase-1-14-3-3 interaction, while a different set of phosphorylation sites of Regnase-1 is known to be required for the recognition by βTRCP and proteasome-mediated degradation. We found that Regnase-1-14-3-3 and Regnase-1-βTRCP interactions are not sequential events. Rather, 14-3-3 protects Regnase-1 from βTRCP-mediated degradation. On the other hand, 14-3-3 abolishes Regnase-1-mediated mRNA decay by inhibiting Regnase-1-mRNA association. In addition, nuclear-cytoplasmic shuttling of Regnase-1 is abrogated by 14-3-3 interaction. Taken together, the results suggest that a novel inflammation-induced interaction of 14-3-3 with Regnase-1 stabilizes inflammatory mRNAs by sequestering Regnase-1 in the cytoplasm to prevent mRNA recognition.

3 November 2021 in Molecular & Cellular Proteomics
Verified
Journal Article
Open access
KOKosuke Ogata
Kosuke Ogata
YIYasushi Ishihama
Yasushi Ishihama
Reversed-phase solid-phase extraction (SPE) techniques are commonly used for desalting samples before LC/MS/MS in shotgun proteomics. However, hydrophilic peptides are often lost during the desalting step under the standard SPE conditions. Here, we describe a simple protocol in which a stop-and-go extraction tip packed with a poly(styrene-divinylbenzene) copolymer disc is used at 4 °C during sample loading without any organic solvent. Using this method, which we designate as the CoolTip protocol, we identified 2.9-fold more tryptic peptides and 6.1-fold more tryptic phosphopeptides from HeLa lysates than the standard SPE protocol for hydrophilic peptides, with a mobile phase of less than 8% acetonitrile in LC/MS/MS. There was no decrease in the recovery of hydrophobic peptides. CoolTip also provided better quantitative reproducibility in LC/MS/MS analysis. We anticipate that this protocol will provide improved performance in many kinds of shotgun proteomics experiments.