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Biology subjects

Saito, R.

Publications and source records attributed to Saito, R..

At least 19 recordsLinked to original sources

Spatial transcriptomic analysis reveals coordinated gene expression in ovarian clear cell carcinoma and adjacent endometriosis in UK and Japanese patients

PurposeOvarian clear cell carcinoma (OCCC) is strongly associated with endometriosis and shows geographic variation in incidence. We investigated whether OCCC and adjacent endometriosis exhibit distinct transcriptional states and whether these patterns differ between United Kingdom (UK) and Japanese cohorts. Experimental DesignWe performed whole-transcriptome spatial profiling on specimens from 16 OCCC cases (8 UK, 8 Japan) in which tumor and endometriosis were both present. Gene expression was analyzed in tumor, endometriosis and stroma. ARID1A status was assessed by immunohistochemistry. ResultsMedian age was 59 years (range 26-82). 13/16 cases (81.3%) had early-stage disease. Tissue compartment rather than cohort of origin was the dominant source of variation across endometriosis and tumor regions. Endometriosis was enriched for inflammatory and immune-related pathways compared to tumor, whilst there was greater representation of chromatin and protein-DNA complex assembly pathways in tumor regions. These patterns were conserved across both cohorts and after stratification by ARID1A status. Mesenchymal-associated gene expression scores also significantly differed across stroma, endometriosis and tumor with clear compartmental separation. Cell type deconvolution analyses showed clear compositional differences between stromal and epithelial disease compartments. ConclusionsOCCC and coexisting endometriosis are transcriptionally distinct, with the dominant contrast being compartmental rather than geographic. ARID1A alone is unlikely to account for the principal spatial transcriptional states identified here. Further analyses will be required to ascertain whether these differences reflect genuine biological differences between OCCC and coexisting endometriosis or represent different stages of endometriosis-associated tumorigenesis. Translational RelevanceOvarian clear cell carcinoma often arises in association with endometriosis, yet the biological transition between these lesions remains poorly understood. Using spatial transcriptomics in matched tumor and adjacent endometriosis from Japanese and UK cohorts, we showed that endometriosis is characterized by inflammatory and antigen-presentation features, whereas tumor regions showed chromatin-organization and oncogenic transcriptional states. These patterns were largely maintained irrespective of ARID1A status and geographic background. In addition, spatial deconvolution suggested differences in local immune composition, with tumor regions showing relatively greater neutrophil- and T cell-associated signals. Together, our data suggest that OCCC and coexisting endometriosis share a spatially linked tissue context, but that tumor regions have distinct transcriptional profile and microenvironment that may be involved in the malignant transformation and inform interpretation of molecular classification in endometriosis-associated OCCC.

pathology↗

Modular mRNA platform for in vivo antigen-specific immune tolerance

Immune-mediated diseases such as autoimmunity and allergy arise from dysregulated antigen-specific responses, yet current therapies largely rely on broad immunosuppression and rarely re-establish durable, antigen-selective tolerance. Here we introduce Tol-mRNA, a modular tolerogenic mRNA platform designed to deliver multiple immune-regulatory signals in vivo to program antigen-specific tolerance. Tol-mRNA co-encodes an antigen together with two complementary regulatory cues, PD-L1 and TGF-{beta}, enabling coordinated antigen presentation and tolerogenic signaling that robustly induces antigen-specific Tregs and suppresses pathogenic effector responses. In murine disease models, Tol-mRNA conferred therapeutic benefit across distinct immune pathologies. In experimental autoimmune encephalomyelitis, Tol-mRNA ameliorated clinical disease and reduced inflammatory immune activation. In an ovalbumin-driven food allergy model, Tol-mRNA prevented allergic symptoms and dampened type 2 inflammation. Extending these findings to humans, Tol-mRNA demonstrated potent, antigen-dependent immunosuppressive activity and a strong capacity to promote antigen-specific Treg induction in human immune settings. Collectively, these results establish Tol-mRNA as a scalable and versatile approach to reprogram antigen-specific immunity and support its development as a next-generation therapeutic modality for immune-mediated diseases.

immunology↗

A Novel Slow-Progressive Knee Osteoarthritis Murine Model Induced by Non-Invasive Posterior Cruciate Ligament Rupture in Mice

ObjectiveRecently, alternatives to animal testing, such as new approach methodologies, are being developed in the orthopedic research field; animal models still provide valuable insights into the pathogenesis of knee osteoarthritis (OA). However, commonly used models develop OA much more rapidly and severely than those observed in human patients. We aimed to develop a novel murine model that closely mimics the slow progression of human OA with posterior Cruciate ligament (PCL) rupture. Design12-week-old C57BL/6 mice were induced to PCL-rupture (PCL-R) by manually applying an external tibial posterior translation force. We analyzed joint kinematics, histological observations, and bone structure to confirm the absence of concurrent injury on day 0. Then, joint stability and the pathophysiological progression of knee OA were analyzed at 8, 16, and 34 weeks post-PCL-R. The destabilized medial meniscus (DMM) model was also analyzed to compare the OA progression. ResultsNon-invasive PCL-R intervention induced the complete rupture in the central region of PCL without concurrent injury. The PCL-R group showed larger posterior tibial deviation than the INTACT (P=0.008). Regarding the range of motion in the PCL-R group, there was no limitation in range of motion on day 0, but extension limitations occurred at weeks 16 and 34 weeks. Histologically, articular cartilage degeneration in PCL-R was milder than DMM. In the subchondral bone, micro-CT reconstruction images indicated that, compared with the INTACT group, the DMM group observed progressive subchondral bone formation from 16 weeks post-surgery. In contrast, the PCLR group maintained the subchondral bone structure even at 34 weeks. ConclusionsPCL-R model induced mild abnormal mechanical stress depending on posterior instability, and cartilage degeneration occurred more slowly in this model than in DMM models.

pathology↗

Mechanochemical coupling tunes robustness of PAR polarity across developmental contexts in the C. elegans embryo

Proper establishment of cell polarity is essential for reliable asymmetric divisions during embryonic development. In the Caenorhabditis elegans zygote, polarity is established through mechanochemical coupling between advective transport driven by cortical flows and mutually antagonistic PAR protein interactions. How these mechanisms are integrated across developmental contexts to establish cell polarity in the early embryo remains unexplored. Here we show that P1 polarization relies primarily on sustained antagonistic activity of anterior PAR proteins mediated by CDC-42 and PKC-3. Cortical contractility is regulated by CDC-42 through MRCK-1 to drive cortical flow, and is largely independent of the RHO-1 - LET-502 pathway that is crucial in zygotic polarity establishment. We find that these flows contribute only weakly to P1 polarity and primarily during the late phase. P1 polarization is sensitive to CDC-42 dosage, as indicated by reduced cytoplasmic asymmetry of MEX-5 and loss of division asynchrony between daughter cells. In contrast, zygotic polarization remains robust to comparable perturbations in CDC-42 expression when cortical flow is intact, but becomes sensitized when cortical flow is suppressed. Together, these findings show that cortical flow acts as a transport-mediated reinforcement that buffers PAR polarity against perturbations in CDC-42 expression, and that weakening this reinforcement sensitizes polarity establishment across developmental contexts.

biophysics↗

Vicious circle of amyloid and leptomeningeal macrophages evokes vascular dysfunction in CAA

The subarachnoid space contains leptomeningeal arteries and resident immune cells known as subarachnoid macrophages (SAMs). In Alzheimers disease (AD) and related cerebral amyloid angiopathy, amyloid-{beta} (A{beta}) frequently accumulates around the leptomeningeal arteries. Nevertheless, the local immune responses and their functional consequences remain poorly understood. Using longitudinal intravital imaging in a mouse model of AD, we tracked A{beta} deposition and identified a distinct SAM population that migrates to and phagocytoses these arterial A{beta} deposits. SAM recruitment correlated with vascular remodeling, including smooth muscle loss, aneurysm formation, and reduced cerebral perfusion. Transcriptomic profiling revealed a distinct SAM population in AD with upregulated CD39 expression. Pharmacological inhibition of CD39 attenuated arterial A{beta} deposition, identifying SAMs as a potential therapeutic target in AD.

neuroscience↗

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↗

Decoding Spine Nanostructure in Mental Disorders Reveals a Schizophrenia-Linked Role for Ecrg4

Dendritic spine dysfunction may contribute to the etiology and symptom expression of neuropsychiatric disorders. The intimate relationship between spine morphology and function suggests that decoding disease-related abnormalities from spine morphology can aid in developing synapse-targeted interventions. Here, we describe a population analysis of dendritic spine nanostructure applied to the objective grouping of multiple mouse models of neuropsychiatric disorders. This method has identified two major groups of spine phenotypes linked to schizophrenia and autism spectrum disorder (ASD). An increase in spine subpopulation with small volumes characterized the spines of schizophrenia-associated mouse models, whereas a spine subset with large volumes increased in ASD models. Schizophrenia-associated mouse models showed higher similarity in spine morphology, driven by reduced size and growth of nascent spines. The expression of Ecrg4, a gene encoding small secretory peptides, was increased in schizophrenia-associated mouse models, and functional studies confirmed its critical involvement in impaired spine dynamics and shape. These results suggest that population-level spine analysis provides rich insights into heterogeneous spine pathology, facilitating the identification of new molecular targets related to core synaptic dysfunction.

neuroscience↗

G3BP1 Maintains Lysosomal Homeostasis to Limit Tau Aggregate Accumulation

Tau aggregation is a pathological hallmark of a group of neurodegenerative diseases collectively termed tauopathies. While impaired proteostasis is known to drive the accumulation of abnormal proteins, the molecular factors influencing Tau aggregate clearance remain incompletely understood. In this study, we employed a cell-based Tau reporter assay combined with a lentivirus-based pooled CRISPR-Cas9 loss-of-function library to identify genes that regulate Tau aggregation. Genome-wide screening revealed that candidate genes were significantly enriched in categories related to mRNA metabolic processes and autophagy. Among them, we focused on the RNA-binding protein G3BP1, which is functionally associated with both processes. Detailed analyses showed that G3BP1 deficiency promoted the accumulation of Tau aggregates without affecting stress granule formation or autophagic flux. Instead, G3BP1 dysfunction resulted in impaired lysosomal homeostasis, as evidenced by reduced lysosomal abundance and acidification. Furthermore, lysosomal damage induced by L-leucyl-L-leucine methyl ester (LLOMe) enhanced Tau aggregation, particularly in G3BP1-deficient cells. Conversely, pharmacological activation of TFEB by the curcumin analog C1 restored lysosomal function and suppressed Tau aggregate accumulation to wild-type levels. These findings highlight a role of G3BP1 in maintaining lysosomal homeostasis and promoting Tau clearance. Our results further suggest that therapeutic strategies aimed at enhancing lysosomal biogenesis, such as TFEB activation, may hold promise for the treatment of tauopathies.

cell biology↗

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↗

Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocations

Centromeres are among the most diverse and dynamically evolving regions of the human genome and are commonly affected in various human cancers. However, organized into highly repetitive -satellite higher-order repeats (HORs), human centromere sequences have long resisted detailed genomic analysis. Although the development of long-read sequencing platforms has enabled the analysis of complete centromere sequences, their application to a large set of samples is still largely limited, preventing our understanding of centromere variation and haplotype structures across large human populations and the structural basis of centromere-involving translocations in cancer. Here we show that rare k-mers present in centromeric regions can serve as effective markers for dissecting the complexity of centromere structure, particularly that of active -satellite HOR arrays (aHOR arrays), across human populations and for understanding centromere-involving abnormalities in cancer. Based on rare k-mer-based clustering, centromere aHOR arrays are clustered into discrete haplogroups (aHOR-HGs) with distinct structural features. These k-mers were also used to develop a framework that enables the inference of haplogroups in a given sample based on short-read whole genome sequencing (WGS) data (ascairn). By applying ascairn to large-scale human population datasets (n > 3,300), we revealed the diversity of aHOR-HGs and their geographic histories across populations. The rare k-mer-based approach was also applied to investigate the structure of 1p/19q co-deletion, a highly recurrent centromere-involving translocation in IDH-mutated oligodendrogliomas. Analyzing short-read WGS data from 142 cases with 1p/19q co-deletion using rare k-mers, we showed that breakpoints of 1p/19q co-deletion were mapped to aHOR arrays in chromosomes 1 (D1Z7) and 19 (D19Z3), which was validated by long-read sequencing of two 1p/19q co-deletion-positive cases. Notably, the translocation preferentially involved haplogroups composed of haplotypes containing larger regions susceptible to rearrangement. These results highlight the role of rare k-mers in dissecting the complexity of centromere sequences and their evolutionary history as well as understanding centromere-involving abnormalities associated with human diseases.

genomics↗

Decoding the molecular logic of rapidly evolving ZAD zinc-finger proteins in Drosophila

The zinc-finger associated domain (ZAD)-containing C2H2 zinc-finger proteins (ZAD-ZnFs) represent the most abundant class of transcription factors that emerged during insect evolution, yet their molecular diversity and biological functions remain largely unclear. Here, we established a systematic CRISPR-based protein-tagging approach that enables direct, unambiguous comparison of nuclear localization and genome-wide binding profiles of endogenous ZAD-ZnFs in developing Drosophila embryos. Evidence is provided that a subset of ZAD-ZnFs forms nuclear condensates through the stacking of the N-terminal ZAD dimerization surface. Disruption of condensation activity leads to misregulation of genome-wide binding profiles and lethality, underscoring its functional and physiological significance in development. Importantly, integrative ChIP-seq and Micro-C data analyses reveal that many ZAD-ZnFs colocalize with core insulator proteins such as CTCF and CP190 to strengthen the formation of topological boundaries. We suggest that the diverse molecular functions of ZAD-ZnFs have evolutionally arisen from their ancestral role as insulator-binding proteins.

molecular biology↗

Establishment of a second-generation transgenic marmoset model of polyglutamine disease recapitulating neurological symptoms and pathology

Neurodegenerative diseases, including polyglutamine diseases, remain a major clinical challenge, partly because of limited animal models that recapitulate human disease. Here, we describe a second-generation transgenic marmoset model of spinocerebellar ataxia 3 (SCA3), a polyglutamine disease, which stably expresses expanded CAG repeats in ATXN3. All five offspring of the founder marmoset harbored the transgene with reduced transgene integration sites and without repeat instability or genetic mosaicism, offering improved construct validity. Three of the five marmosets developed progressive motor impairments that segregated into two distinct phenotypes: early onset with rapid progression and late onset with mild progression, accompanied by corresponding patterns in body weight gain and grip strength. Pathological analysis revealed cerebellar Purkinje cell loss, spinal cord neurodegeneration, and widespread intranuclear inclusions. The severity of motor phenotypes correlated with transgene expression levels in disease-relevant brain regions, including the cerebellum, spinal cord, and striatum. By overcoming the common translational limitations of rodent systems, our second-generation model offers a powerful platform for investigating disease mechanisms and testing potential therapeutic interventions. Our results advance the utility of transgenic marmosets as clinically relevant models of neurodegenerative diseases. Summary StatementSecond-generation transgenic marmoset models of spinocerebellar ataxia 3 replicated the progressive motor deficits and neuropathology of the founder marmoset, providing a powerful platform for studying disease mechanisms and developing therapies.

neuroscience↗

Successive failure triggered by motor exploration in a reinforcement-based reaching task

Motor exploration, a key process in reinforcement-based motor learning, is triggered by suboptimal performance and leads to increased movement variability. Consequently, failure in one trial may increase the likelihood of failure in subsequent trials. If this pattern emerges, successive failures (SFs) are not merely events to be avoided but part of the trial-and-error process of identifying optimal movements, which can facilitate motor learning. This study investigated whether and how SFs occur above chance levels during a motor learning task with binary success/failure feedback and explored the relationship between SFs and motor learning outcomes. Thirty-three healthy young adults participated in the study, performing a reaching task to pass through a target without visual feedback of their hand position. Binary feedback was provided after each trial, indicating whether the hand trajectory overlapped with the target. The results showed that the probability of two SFs was significantly higher than the square of the overall failure probability, indicating that failure streaks occurred above chance levels. A computational model, in which motor variability comprised constant motor noise and exploratory variability regulated by recent reward history (where variability increased following failure), successfully explained SF emergence. However, the learning index, defined as the difference in failure probability between the first and latter halves of the experiment, was unrelated to SF emergence. Additionally, failure streaks disappeared when participants were asked to reach one of seven randomly selected targets in each trial, suggesting that introducing environmental variability can help alleviate SFs.

neuroscience↗

The braking force to Control the Abnormal Tibial Translation Affects the Spontaneous Healing Response for Complete Ruptured Anterior Cruciate Ligament in Mice Model

Purpose of this studyThe anterior cruciate ligament (ACL) has been believed to have a low spontaneous healing capacity; growing evidence has suggested that ACL could heal spontaneously. While the healed ACL has reduced mechanical properties and incomplete tissue maturation, the mechanisms underlying these problems remain unknown. We aimed to elucidate the effect of mechanical stresses during the early phase of spontaneous ACL healing. Materials and MethodsMale and female C57BL/6 mice were subjected to ACL rupture and randomly classified into three groups: Tight-CATT; tightly controlled anterior tibial translation (ATT), Loose-CATT; loosely controlled ATT and mild increasing mechanical stress compared to Tight-CATT, and ACL-Rupture (ACL-R) group; not controlled ATT. Mice were sacrificed and analyzed immediately after injury and at 4 and 8 weeks. We evaluated the effect of controlling the braking force of the ATT of each knee, the success rate of the ACL healing, collagen maturation, COL1A1 expression in the healed ACL, and the mechanical properties of the healed ACL. ResultsThe Tight-CATT group showed a higher success rate of ACL healing than the Loose-CATT group at 4 and 8 weeks. However, collagen maturation and the mechanical properties of healed ACL did not differ between the Tight-CATT and Loose-CATT groups. ConclusionOur results suggested that loose ATT braking immediately after injury is a negative factor for the healing of the completely ruptured ACL, and that it may be necessary to apply higher mechanical stress in the later stages to achieve greater healing.

physiology↗

Downstream metabolites of (+)-cis-12-oxo-phytodienoic acid function as noncanonical bioactive jasmonates in Arabidopsis thaliana.

(+)-cis-12-oxo-phytodienoic acid (cis-OPDA) is a biosynthetic precursor of the plant hormone (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile). It functions as an endogenous chemical signal independent of the JA-Ile receptor COI1-JAZ in Arabidopsis thaliana. The bioactive form of cis-OPDA that induces COI1-JAZ-independent gene expression remains unknown. In this study, we hypothesized that the genuine bioactive forms of cis-OPDA are the downstream metabolites, which upregulate the expression of the OPDA marker genes such as ZAT10/ERF5 in a JA-Ile-independent manner. These downstream metabolites function independently of the JA-Ile-COI1-JAZ-MYCs canonical jasmonate signaling module, and its electrophilic nature is essential for its bioactivity.

plant biology↗

ADMA-histones define genomic loading of Rhino at the initial step of piRNA cluster formation

In Drosophila germ cells, piRNAs arise from dual-strand piRNA clusters, which are marked by a repressive histone mark H3K9me3, but are transcribed from internal sites in a manner dependent on the HP1 homolog Rhino. Rhino binds to H3K9me3 on these clusters, yet the mechanism controlling its binding to clusters remains unclear. Here, we used cultured ovarian somatic cells (OSCs), which lack endogenous Rhino and its stabilizer Kipferl, whose absence renders the dual-strand clusters inert, and found that exogenous Rhino tends to bind to the ends of dual-strand clusters with asymmetric dimethylarginine histones (ADMA-histones). Depletion of the arginine methyltransferases responsible for ADMA modifications, such as DART4, affected the genomic localization of Rhino in both OSCs and ovaries. We also identified primitive, cluster-like genomic regions, termed DART4 piSL, where Rhino propagates in an DART4-dependent but unstable manner. Our study proposes that ADMA-histones play a crucial role in the initial genome loading of Rhino and may establish the potential sites of its propagation, which are subsequently stabilized to support piRNA production.

molecular biology↗

STRESS GRANULE-RELATED GENES DURING EMBRYOGENESIS OF AN INVERTEBRATE CHORDATE

Control of global protein synthesis through the assembly of stress granules (SGs) represents a strategy adopted by eukaryotic cells to face various stress conditions. TIAR, TTP and G3BP are key components of SGs, allowing the regulation of mRNA stability and thus controlling not only stress responses but also cell proliferation and differentiation. In the present work we aimed to investigate the role of tiar, ttp and g3bp during embryogenesis of the solitary ascidian Ciona robusta, both in physiological and stress conditions. We carried out CRISPR/Cas9 knockout to evaluate the effects on normal embryonic development, and gene reporter assays to study time and tissue specificity of gene expression, together with whole mount ISH and qRT-PCR. To induce acute stress conditions, we used iron and cadmium as "essential" and "non-essential" metals, respectively. Our results highlight, for the first time, the importance of tiar, ttp and g3bp in the control of development of mesendodermal tissue derivatives during embryogenesis of an invertebrate chordate. HIGHLIGHTS- Mesenchyme, nervous cells, and endoderm are the embryonic regions mainly transcribing cr-tiarx1, cr-ttp and cr-g3bp2 during metal stress conditions. - Only cr-ttp transcription is regulated at mid gastrula stage. - The highest transcription levels are reached in hatching larvae after iron exposure. - cr-tiarx1, cr-ttp and cr-g3bp2 knockouts resulted in impaired embryogenesis.

developmental biology↗

Can Colpoda travel across oceans? Salinity tolerance of resting cysts may enable global dispersal of the species.

Protist species are distributed worldwide. The processes that enabled this global distribution are unclear. One possible means is through the oceanic dispersal of freshwater protists, although this has not been investigated in detail to date. Here, the ability of resting cysts to tolerate saline conditions is examined as a possible mechanism that enables the oceanic dispersal of protists. Resting cysts of Colpoda cucullus, a freshwater soil protist, can tolerate saline conditions of at least 3.5% NaCl for more than one week. A transcriptome analysis showed that the relative levels of expression of genes associated with membrane function are increased in resting cysts, indicating that salinity tolerance is associated with reconstruction of the cell membrane. Additionally, the outer layer of the cyst wall, a shell-like ectocyst, includes chitin. This may function as a form of "biological armor" that protects the cell from physical stress during oceanic dispersal. Teaser: Fresh water protists may be dispersed across oceans by formation of resting cysts that can tolerate saline conditions.

zoology↗