Shinya Tsukiji
shinyatsukiji.bsky.social
Shinya Tsukiji
@shinyatsukiji.bsky.social
Chemist | PI of the Tsukiji Lab at Nagoya Institute of Technology | Pursuing new molecular concepts and tools for chemical biology, cell biology, and synthetic biology
http://tsukijilab.web.nitech.ac.jp/index-e.html
Pinned
Our paper has been featured on the front cover of the latest issue of ChemBioChem! Huge thanks to Hiroko Uchida for the beautiful artwork—we love it! 😊
chemistry-europe.onlinelibrary.wiley.com/toc/14397633...
Reposted by Shinya Tsukiji
We are hiring! Excited about redox chemical biology? Help us discover what controls the redox state of the Golgi apparatus. Also, please help us spread the word by reposting this ad. Apply here: jobs.uzh.ch/job-vacancie...
UZH: PhD Position in Redox Chemical Biology
We are a dynamic, interdisciplinary, medium-size lab working at the interface of chemistry and biology. We work on the development of probes to visualize and control biological processes in living sys...
jobs.uzh.ch
October 31, 2025 at 4:36 PM
Reposted by Shinya Tsukiji
Do you study lipids or lipidation, but don't know where to send your newest work?

Send us your fat papers, phat papers, and even phatty acid papers. While the special issue is not saturated, it's filling up fast, and won't be unsaturated forever!

Phase separate with us and build community!
October 28, 2025 at 4:12 PM
Reposted by Shinya Tsukiji
#ACSChemBio and #Biochemistry invite submissions to a special issue on Lipids and Lipidation guest edited by @chembiobryan.bsky.social and me! Find details in the #CallforPapers and submit your exciting findings to one of these journals by May 31, 2026. axial.acs.org/chemical-bio... #lipidtime
Call for Papers: Lipids and Lipidation | ACS Publications Chemistry Blog
This Special Issue in _ACS Chemical Biology_ will highlight the latest advancements and perspectives in the chemical biology of lipids and lipidation. Submit your manuscript by May 31, 2026.
axial.acs.org
October 28, 2025 at 3:48 PM
Reposted by Shinya Tsukiji
When chemistry meets neurons! Game-changing paper on multifunctional fluorescent ligands. Luke and Pratik built the nerdy toys; we got to play! Jason Vevea nailed biotin-HTL for mito magic. My lab rocked the JQ1 HTL to shuffle chromatin in mins. 1st collab win for our Neuronal Cell Biology Division.
October 28, 2025 at 4:57 PM
Reposted by Shinya Tsukiji
A new, nerdy paper. We figured out (some) of the rules underlying cell-permeability of probes and designed ligands that light up, grab, and move proteins around. Awesome @hhmijanelia.bsky.social x @uwmadison.bsky.social x @stjuderesearch.bsky.social collaboration! www.pnas.org/doi/10.1073/...
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
October 27, 2025 at 9:43 PM
Reposted by Shinya Tsukiji
A while back we found that the lipid-binding protein PLEKHA4 boosts Wnt/β-catenin signaling and drives melanoma growth in vivo. Now, we (Nathan Frederick) identify small-molecule inhibitors of PLEKHA4 & related proteins with anticancer activity in vitro! pubs.acs.org/doi/10.1021/....
Discovery, Optimization, and Anticancer Activity of Lipid-Competitive Pleckstrin Homology Domain-Containing Family A Inhibitors
Phosphoinositide signaling is a major cellular mechanism controlling cancer cell viability, proliferation, and survival. Yet, inhibition of lipid kinases that produce oncogenic phosphoinositides has afforded only a limited number of efficacious drugs attributed in large part to on-target toxicity resulting from the pleiotropic effects of these signaling lipids. Targeting the specific phosphoinositide effector pathways via competitive inhibitors of phosphoinositide-recognizing pleckstrin homology (PH) domains represents a relatively unexplored means to achieve greater specificity. Herein, we present the discovery from in silico screening, structure–activity relationship (SAR) optimization, and cellular characterization of novel phosphoinositide-competitive inhibitors of the pleckstrin homology domain-containing A (PLEKHA) family. These compounds induce cytotoxic effects in BRAF and NRAS mutant melanoma cells, consistent with on-target inhibition, and the most potent compound is activated by endogenous esterase activity, suggesting that prodrug esters represent a viable strategy for targeting the phosphoinositide-binding pockets of the PLEKHA family of PH domains.
pubs.acs.org
October 7, 2025 at 4:06 PM
Reposted by Shinya Tsukiji
How do cells sense & respond to lipid imbalances? What happens when a disease-relevant enzyme is blocked? Shiying Huang investigates phosphoinositide lipids with the Balla lab & discovers an integrated cellular response that boosts alternate lipid synthesis pathways! www.biorxiv.org/content/10.1...
October 3, 2025 at 1:03 PM
Reposted by Shinya Tsukiji
Very excited to share new work out today in @natchembio.nature.com on a new approach - FACES - for selectively imaging of phospholipids and other biomolecules at spatial resolutions down to individual membrane leaflets (1/n) www.nature.com/articles/s41...
Leaflet-specific phospholipid imaging using genetically encoded proximity sensors - Nature Chemical Biology
An approach combining bioorthogonal chemistry with genetically encoded fluorogen-activating proteins enables subcellular imaging of phospholipids and glycans, as well as the visualization of lipid tra...
www.nature.com
September 15, 2025 at 6:03 PM
Reposted by Shinya Tsukiji
Excited to share our most recent work out in @jacs.acspublications.org today! We combined mRNA display with macrocyclic peptide chemistry to discover novel RNA-targeting molecules. This fits into our mission to target RNA regulation with novel therapeutic modalities

pubs.acs.org/doi/10.1021/...
Discovery of Macrocyclic Peptide Binders, Covalent Modifiers, and Degraders of a Structured RNA by mRNA Display
RNA targeting represents a compelling strategy for addressing challenging therapeutic targets that are otherwise intractable through traditional protein targeting. Revolutionary approaches in RNA-focused small molecule libraries have successfully identified RNA-binding ligands but generally remain limited in diversity and impeded by a dearth of structural insight into RNA and RNA complexes. Cyclic peptides are potential structural mimics of evolutionary RNA-protein interacting motifs and can be massively diversified and selected via genetically encoded libraries, offering a complementary approach. This study introduces genetically encoded thioether cyclic peptide libraries constructed through mRNA display using a dibromoxylene linker and its fluorosulfonyl derivative that can covalently engage RNA nucleophiles. Using an optimized mRNA display workflow for RNA binders, we discovered high affinity, covalent and noncovalent binders for SNCA 5′ UTR IRE, the upstream iron-responsive element that post-transcriptionally regulates the expression of α-synuclein, an intrinsically disordered protein implicated in Parkinsonism and related neurodegenerative diseases. Notably, a stringent selection strategy employing “base-paired” target analog counterselection enhanced specificity by deenriching nonspecific electrostatic interactions mediated by polycationic residues. Further engineering hit peptides with an imidazole tag yielded selective RNA degraders in which covalent degraders showed noticeably improved potency from noncovalent counterparts. This work provides a prototype framework for evolution-driven, high-throughput, RNA-targeted drug discovery using cyclic peptides.
pubs.acs.org
September 15, 2025 at 2:47 PM
Reposted by Shinya Tsukiji
Aika Toyama, Yuhei Goto, Kazuhiro Aoki and colleagues quantify cyclin–CDK dissociation constants using FCCS with green and near-infrared fluorescent proteins.
journals.biologists.com/jcs/article/...
September 15, 2025 at 8:54 AM
Reposted by Shinya Tsukiji
Congratulations to Hen (again)! Her paper, in collaboration with Jade, Juan, and the EPFL ACCESS team was just published. The paper describes a chemigenetic gene reporter tool for time-stamping and pulse-chase-type experiments.
chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/...
Two‐Color Timestamping of Gene Expression with a Chemigenetic Reporter System
A chemigenetic reporter assay is developed that enables monitoring of BiP/GRP78 expression, an important chaperone and key regulator of the unfolded protein response. The system is based on the coexp....
chemistry-europe.onlinelibrary.wiley.com
September 15, 2025 at 7:54 AM
Our paper has been featured on the front cover of the latest issue of ChemBioChem! Huge thanks to Hiroko Uchida for the beautiful artwork—we love it! 😊
chemistry-europe.onlinelibrary.wiley.com/toc/14397633...
September 13, 2025 at 12:19 PM
Reposted by Shinya Tsukiji
Dylan's study is now out in @jacs.acspublications.org! Key new experiments by Yuan-Ting Cho support a model for why a rare three-tailed lipid, NAPE, might accumulate during stroke & heart attack: as a protective response to promote lactate export as cells shift to glycolysis doi.org/10.1021/jacs...
September 5, 2025 at 12:23 PM
Welcome back, Keita! After a wonderful 3-month stay at the Neal Devaraj lab at UCSD, he’s back with exciting results and unforgettable memories👍 Huge thanks to Neal and his amazing team for hosting him!
September 1, 2025 at 9:53 PM
Exciting new paper from Shigeki Kiyonaka lab, published in Chemistry Letters! Congratulations to all authors! 🥳
academic.oup.com/chemlett/art...
A chemogenetic strategy for inhibiting G protein-coupled receptor activity using metal coordination
Abstract. G protein-coupled receptors regulate diverse physiological functions in mammalian cells. Methods enabling temporal control of individual G protei
academic.oup.com
August 29, 2025 at 3:11 AM
Reposted by Shinya Tsukiji
Our paper on the antigen fluorogenic sensor is featured as a supplementary cover in this week’s @jacs.acspublications.org
! Beautiful artwork by our co-author, Ryo Tachibana! Read it here: pubs.acs.org/doi/full/10....
#MyACSCover
August 28, 2025 at 4:54 AM
Reposted by Shinya Tsukiji
Congrats to Juan! His discovery of hemicyanines as potent activators of paraptotic cell death has just been published! With great contributions from Jade (initial observations of ER swelling) and Craig (crucial supporting experiments)!
pubs.acs.org/doi/10.1021/...
Potent Inducers of Paraptosis through Electronic Tuning of Hemicyanine Electrophiles
Paraptosis is a distinct form of programmed cell death characterized by cytoplasmic vacuolization, mitochondrial swelling, and endoplasmic reticulum (ER) dilation, offering an alternative to apoptosis...
pubs.acs.org
August 26, 2025 at 10:15 AM
Reposted by Shinya Tsukiji
Faculty opening in Cornell Chemistry at the Assistant Professor level in the area of chemical biology, broadly defined! academicjobsonline.org/ajo/jobs/30338 #chemjobs
Cornell University, Chemistry and Chemical Biology
Job #AJO30338, WDR-00054776 Assistant Professor - Chemistry and Chemical Biology, Cornell University (Ithaca, NY), Chemistry and Chemical Biology, Cornell University, Ithaca, New York, US
academicjobsonline.org
August 25, 2025 at 8:30 PM
Reposted by Shinya Tsukiji
The 4 chemically targeted Laurdan derivatives (for mitochondria, ER, lyso/endosomes, and the Golgi) that we published last year are now available (at a pretty reasonable price) from Avanti Polar Lipids (cat #880194, 880197, 880193, 880196). These have been very popular! pubs.acs.org/doi/full/10....
Organelle-Targeted Laurdans Measure Heterogeneity in Subcellular Membranes and Their Responses to Saturated Lipid Stress
Organelles feature characteristic lipid compositions that lead to differences in membrane properties. In cells, membrane ordering and fluidity are commonly measured using the solvatochromic dye Laurdan, whose fluorescence is sensitive to lipid packing. As a general lipophilic dye, Laurdan stains all hydrophobic environments in cells; therefore, it is challenging to characterize membrane properties in specific organelles or assess their responses to pharmacological treatments in intact cells. Here, we describe the synthesis and application of Laurdan-derived probes that read out the membrane packing of individual cellular organelles. The set of organelle-targeted Laurdans (OTL) localizes to the ER, mitochondria, lysosomes, and Golgi compartments with high specificity while retaining the spectral resolution needed to detect biological changes in membrane ordering. We show that ratiometric imaging with OTLs can resolve membrane heterogeneity within organelles as well as changes in lipid packing resulting from inhibition of trafficking or bioenergetic processes. We apply these probes to characterize organelle-specific responses to saturated lipid stress. While the ER and lysosomal membrane fluidity is sensitive to exogenous saturated fatty acids, that of mitochondrial membranes is protected. We then use differences in ER membrane fluidity to sort populations of cells based on their fatty acid diet, highlighting the ability of organelle-localized solvatochromic probes to distinguish between cells based on their metabolic state. These results expand the repertoire of targeted membrane probes and demonstrate their application in interrogating lipid dysregulation.
pubs.acs.org
August 15, 2025 at 3:57 PM
Reposted by Shinya Tsukiji
Excited to share our new @pubs.acs.org paper! We engineered cells with ~10% photolipids in the ER membrane. This enabled optical control of membrane viscosity to study its impact on ER→Golgi protein transport. @dirktrauner.bsky.social @noemijimenezrojo.bsky.social

pubs.acs.org/doi/10.1021/...
Optical Control of Membrane Viscosity Modulates ER-to-Golgi Trafficking
The lipid composition of cellular membranes is highly dynamic and undergoes continuous remodeling, affecting the biophysical properties critical to biological function. Here, we introduce an optical a...
pubs.acs.org
August 14, 2025 at 10:43 AM
Reposted by Shinya Tsukiji
Yuya Jikko, Shinya Tsukiji ‪@shinyatsukiji.bsky.social‬, Michiyuki Matsuda, Kenta Terai and colleagues show that a front-biased Ras-Rab5-Rac1 positive feedback loop integrates spatial cues in collective cell migration.
journals.biologists.com/jcs/article/...
#OpenAccess #ReadandPublish
August 8, 2025 at 1:38 PM
Reposted by Shinya Tsukiji
Thrilled our PANCS-binder tech is finally out in print!
www.nature.com/articles/s41...

This technology, 11-years in the making, has transformed how we do research in my lab, and was led by an amazing postdoc, Matt Styles, who is currently entering the academic job market - so look out for him! 1/n
August 6, 2025 at 5:54 PM
Reposted by Shinya Tsukiji
We are proud to be a founding contributor to lipidinteractome.org, a repository developed by @tafesselab.bsky.social & Schultz lab to increase accessibility to proteomics data from multi-functionalized lipid analogs! Check out the website & preprint: arxiv.org/abs/2507.23101 #lipidtime
The Lipid Interactome Repository – Lipid Interactome Repository
lipidinteractome.org
August 5, 2025 at 1:06 PM
Happy to see our collaborative paper with Kenta Terai and Michiyuki Matsuda published in @jcellsci.bsky.social! Many thanks and congrats to all authors! journals.biologists.com/jcs/article/...
Front-biased activation of the Ras-Rab5-Rac1 loop coordinates collective cell migration
Highlighted Article: A front-localized positive feedback loop among Ras, Rac1 and Rab5, underlies front-side identity and integrates spatial cues into EGFR-Ras-ERK signaling during collective cell mig...
journals.biologists.com
August 5, 2025 at 12:23 AM
Reposted by Shinya Tsukiji
Our latest paper is finally published in @natcomms.nature.com (doi.org/10.1038/s414...) !! We successfully constructed synthetic multinuclear metal complexes using only proteins.
August 1, 2025 at 6:16 AM