Biology subjects

Okazaki, T.

Publications and source records attributed to Okazaki, T..

7 recordsLinked to original sources

bioRxiv2026

Temporal Mechanisms of T-Cell Fate Decisions under Immune Checkpoint Blockade Resolved by CanonicalTockySeq

In cancer immunotherapy, T-cell functional states change dynamically, and no single marker or gene fully defines them. Static molecular profiles may therefore be insufficient to resolve these states. Capturing signalling history together with ongoing activity could provide a temporal framework for their dissection. Here, we developed CanonicalTockySeq, which integrates a molecular clock of T-cell receptor (TCR) signalling based on the Fluorescent Timer reporter Nr4a3-Tocky (Timer-of-cell-kinetics-and-activity) with scRNA-seq to establish an experimentally anchored temporal reference. Using landmark Tocky fractions as biological ground truths, CanonicalTockySeq constructs a transcriptomic manifold in canonical space with conical geometry. In a murine melanoma model treated with combination anti-PD-L1 and anti-CTLA-4, this framework separates temporal progression (geodesic angle) from signalling strength (radial intensity), enabling time-resolved analysis of gene-expression programmes at single-cell resolution. Application to scRNA-seq data from patients with melanoma further identifies distinct temporal programmes associated with clinical response. These analyses indicate that effective combination immunotherapy is associated with decreased persistence of antigen engagement, suppression of exhaustion-associated TCR signalling programmes, and maintenance of progenitor-like features linked to durable antitumour responses. Collectively, our findings identify temporal-state control as a key component of immunotherapy outcome and establish CanonicalTockySeq as a framework for resolving T-cell response states in vivo.

immunology↗

bioRxiv2026

Type I IFN dynamics define an early checkpoint for survival and orchestrate systemic neutrophil heterogeneity in lethal viral infection

The early host response is critical for protection against viral infections, yet the systemic events that dictate individual differences in outcomes remain poorly defined. Here, we leveraged variability in survival following intranasal vesicular stomatitis virus (VSV) challenge in genetically identical mice to retrospectively profile systemic immune responses associated with survival or lethality. Survival was strongly associated with a robust systemic type I interferon (IFN) surge within 24 hours of infection, and blockade of type I IFN signaling during this narrow early window markedly reduced survival, establishing early IFN induction as a key determinant of outcome. This protective IFN surge rapidly remodeled the systemic immune landscape. Single-cell profiling revealed a transcriptionally and functionally distinct ICAM1 neutrophil subset as the strongest early correlate of survival, primed within the bone marrow. ICAM1 neutrophils exhibited a pro-inflammatory signature and enhanced phagocytic activity compared with ICAM1- neutrophils, which predominated in lethal outcomes. Together, these findings define a type I IFN-driven early checkpoint that governs survival in lethal viral infection and identify ICAM1 neutrophils as a blood-accessible biomarker of protective immunity, highlighting the critical role of early innate immune dynamics in shaping disease trajectories and providing a framework for early prognostic markers and host-directed therapies.

immunology↗

bioRxiv2025

Local niche-derived immunosuppressive CXCR2+ cells impair antiviral immunity

Symptom severity after viral infection varies among individuals, yet its mechanism remains poorly understood. We categorized mice into recovering and non-recovering groups based on body weight after infection of the same titer of vesicular stomatitis virus (VSV). We revealed that in the olfactory bulb (OB) where VSV initially expands, non-recovering mice exhibited an anti-inflammatory environment, suggesting its detrimental effect. Importantly, CXCR2+ cells resembling immunosuppressive myeloid-derived suppressor cells (MDSCs) were more abundant in the OB of non-recovering mice than in that of recovering mice after VSV infection. Depleting CXCR2+ MDSC-like cells from the brain increased inflammatory responses and the animals survival after infection. Furthermore, site-specific labeling indicated that a significant fraction of these cells in the OB originate from the skull-bone marrow (skull-BM) as well as circulation. This study reveals the lethal effects of CXCR2+ MDSC-like cells on local immune responses to viral infection, highlighting their therapeutic potential for antiviral defense.

immunology↗

bioRxiv2022

Single-cell level temporal profiling of tumour-reactive T cells under immune checkpoint blockade

The blockade of the immune checkpoints PD-1 and CTLA-4 enhances T cell response. However, it is largely unknown how antigen-reactive T cells regulate their checkpoint expression in vivo and whether and how the checkpoint blockade can change activation dynamics of tumour-reactive T cells. To address this, here we used Nr4a3-Timer-of-cell-kinetics-and-activity (Tocky), which allows analysis of temporal changes of activated T cells following TCR signalling in vivo. By analysing melanoma-bearing Nr4a3 Tocky mice, we elucidate hidden dynamics of tumour-reactive T cells in the steady-state. Checkpoint blockade depleted highly activated effector Treg, while promoting unique effector T cell populations, and thus differentially modulating activation of tumour-reactive T cell populations. Furthermore, multidimensional analysis and seamless analysis of Tocky and scRNA-seq revealed a full spectrum of T cell dynamics in response to tumour burden and treatment with checkpoint blockade. Lastly, we propose a rational design of combinatorial therapy to further enhance T cell activities.

immunology↗

bioRxiv2020

Waves out of the Korean Peninsula and inter- and intra-species replacements in freshwater fishes in Japan

The Japanese archipelago is located at the periphery of the continent of Asia. Rivers in the Japanese archipelago, separated from the continent of Asia about 17 Ma, have experienced an intermittent exchange of freshwater fish taxa through a narrow land bridge generated by lowered sea level. As the Korean Peninsula and Japanese archipelago were not covered by an ice sheet during glacial periods, phylogeographical analyses in this region can trace the history of biota for a long time beyond the last glacial maximum. In this study, we analyzed the phylogeography of four freshwater fish taxa, Hemibarbus longirostris, dark chub Nipponocypris temminckii, Tanakia ssp. and Carassius ssp., whose distributions include both the Korean Peninsula and western Japan. We found for each taxon that a small component of diverse Korean clades of freshwater fishes migrated in waves into the Japanese archipelago to form the current phylogeographic structure of biota. Indigenous populations were replaced by succeeding migrants. We refer to this phenomenon as "waves out of the Korean Peninsula," with parallels to "out of Africa" in humans.

zoology↗

bioRxiv2020

NUDT21 links mitochondrial IPS-1 to RLR-containing stress granules and activates host antiviral defense

Viral RNA in the cytoplasm of mammalian host cells is recognized by retinoic acid- inducible protein-I (RIG-I)-like receptors (RLRs), which localize to cytoplasmic stress granules (SGs). Activated RLRs associate with the mitochondrial adaptor protein IPS-1, which activates antiviral host defense mechanisms including type I interferon (IFN) induction. It has remained unclear, however, how RLRs in SGs and IPS-1 in the mitochondrial outer membrane associate physically and engage in information transfer. Here we show that NUDT21, an RNA binding protein that regulates alternative transcript polyadenylation, physically associates with IPS-1 and mediates its localization to SGs in response to transfection with poly(I:C), a mimic of viral double-stranded RNA. We found that, despite its well-established function in the nucleus, a fraction of NUDT21 localizes to mitochondria in resting cells and becomes localized to SGs in response to poly(I:C) transfection. NUDT21 was also found to be required for efficient type I IFN induction in response to viral infection. Our results together indicate that NUDT21 links RLRs in SGs to mitochondrial IPS-1 and thereby activates host defense responses to viral infection.

immunology↗

bioRxiv2018

Peroxisomes control mitochondrial dynamics and the mitochondrion-dependent pathway of apoptosis

Summary StatementsWe unveil a previously unrecognized role of peroxisomes in the regulation of mitochondrial fission-fusion dynamics, mitochondrion-dependent caspase activation, and cellular apoptosis.\n\nAbstractPeroxisomes cooperate with mitochondria in the performance of cellular metabolic functions such as fatty acid oxidation and maintenance of redox homeostasis. Whether peroxisomes also regulate mitochondrial fission-fusion dynamics or mitochondrion-dependent apoptosis has remained unclear, however. We now show that genetic ablation of the peroxins Pex3 or Pex5, which are essential for peroxisome biogenesis, resulted in mitochondrial fragmentation in mouse embryonic fibroblasts (MEFs) in a manner dependent on dynamin-related protein 1 (Drp1). Conversely, treatment with 4-phenylbutyric acid, an inducer of peroxisome proliferation, resulted in mitochondrial elongation in wild-type MEFs, but not in Pex3-deficient MEFs. We further found that peroxisome deficiency increased the levels of cytosolic cytochrome c and caspase activity under basal conditions without inducing apoptosis. It also greatly enhanced etoposide-induced caspase activation and apoptosis, indicative of an enhanced cellular sensitivity to death signals. Together, our data unveil a previously unrecognized role of peroxisomes in the regulation of mitochondrial dynamics and mitochondrion-dependent apoptosis. Given that mutations of peroxin genes are responsible for lethal disorders such as Zellweger syndrome, effects of such mutations on mitochondrion-dependent apoptosis may contribute to disease pathogenesis.

cell biology↗