Biology subjects

Saeki, K.

Publications and source records attributed to Saeki, K..

12 recordsLinked to original sources

bioRxiv2026

DVT-primed neutrophils reshape the brain microenvironment to promote brain metastasis

Brain metastasis (BrM) is a devastating complication of triple-negative breast cancer (TNBC), yet how host macroenvironmental conditions influence brain metastatic susceptibility remains poorly understood. Here, we investigated the impact of deep vein thrombosis (DVT), a common complication in patients with cancer, on TNBC brain metastasis. Analysis of a large clinical cohort identified DVT as an independent risk factor for BrM in patients with metastatic breast cancer. Using two syngeneic TNBC models, we demonstrated that DVT selectively enhanced brain metastasis without significantly affecting primary tumor growth or lung metastasis. Mechanistically, DVT increased neutrophil accumulation in the brain metastatic microenvironment, and neutrophil depletion completely abrogated the metastasis-promoting effect of DVT. Single-cell RNA sequencing of CD45+ cells in peripheral blood revealed that DVT reprogrammed circulating neutrophils toward migratory and inflammatory transcriptomic profiles characterized by neutrophil extracellular trap (NET) formation. DVT increased CXCR2 expression on circulating neutrophils and enhanced neutrophil recruitment in brain. Moreover, DVT significantly increased circulating NETs. Collectively, our findings identify DVT as a systemic driver of TNBC brain metastasis and reveal that DVT primes circulating neutrophils toward enhanced vascular recruitment and NET formation, providing a mechanistic link between cancer-associated thrombosis and brain metastatic susceptibility.

molecular biology↗

bioRxiv2026

A red-eye mutant in Nesidiocoris tenuis (Hemiptera: Miridae) is caused by exon skipping due to an indel mutation in the scarlet gene

Nesidiocoris tenuis is an important zoophytophagous mirid bug used as a biological control agent in agriculture, and breeding efforts based on genomic information aim to increase its utility. Visible eye-color mutants are useful genetic markers because they are easily distinguishable and are therefore widely used in insect genetics and genome editing studies. Here, we investigated the genetic basis of a spontaneous red-eye mutant identified in a laboratory strain of N. tenuis. Classical crossing experiments suggested that the red-eye phenotype is controlled by a single recessive locus. RNA-seq and RNA interference (RNAi) analyses identified scarlet and cinnabar as the primary candidate genes associated with the phenotype. Further genomic analysis revealed a large deletion and insertion within exon 5 of the mutant scarlet allele, potentially causing exon skipping and disrupting transporter structure. The insertion pattern is consistent with a microhomology-mediated break-induced replication (MMBIR)/fork stalling and template switching (FoSTeS)-like event that may have been generated through polymerase{theta} -mediated repair. Together, these findings identify the causative mutation underlying the red-eye phenotype and provide a useful visible marker for future functional genetic studies and genome-assisted breeding in N. tenuis.

genetics↗

bioRxiv2026

B cell-intrinsic IRF8 transcriptionally reprograms antigen presentation to sustain CD8⁺ T cell antitumor immunity

Interferon regulatory factor 8 (IRF8) is a master transcription factor of myeloid differentiation, but whether IRF8 intrinsically controls B cell function in tumors remains unknown. Using paired single-cell transcriptomic and chromatin accessibility profiling of tumors from wild-type and Irf8-deficient mice, we identify a B cell-intrinsic IRF8 axis regulating antigen presentation and sustaining anti-tumor CD8 T cell immunity. IRF8 establishes conserved chromatin accessibility programs across myeloid cells and plasmablasts centered on antigen processing and MHC class I presentation, but engages distinct motifs by lineage: myeloid cells preferentially utilize ISRE and ETS-composite elements, whereas plasmablasts are selectively enriched for EICE elements, reflecting B lineage-specific IRF8-IRF4 cooperation. Loss of IRF8 disrupts these programs, skews B cells toward plasmablast differentiation and reduces antigen presentation machinery. B cell depletion accelerated tumor growth, while CD40 agonism activated B cells, expanded T cells, and enhanced anti-tumor immunity. B cell-specific IRF8 deletion alone accelerated tumor growth, establishing a cell-intrinsic requirement independent of myeloid IRF8 function. The IRF8-regulated B cell signature was enriched in PD-1 blockade cancer patient responders, and plasmablast abundance correlated with response in pembrolizumab-treated cancer patients. These findings establish IRF8 as a lineage-adapted regulator of antigen presentation and define the IRF8-B cell axis as a determinant of anti-tumor immunity. HighlightsIRF8 establishes a conserved chromatin accessibility across tumor-infiltrating myeloid and B cells Myeloid cells engage ISRE motifs, whereas plasmablasts rely on EICE motifs as IRF8 lineage-specific cis-regulation IRF8 regulates an antigen presentation in B cells to sustain anti-tumor T cell immunity B cell-intrinsic IRF8 transcription signature predicts patient response to PD-1 blockade immunotherapy

immunology↗

bioRxiv2025

geneSCOPE: gene Spatial Co-Occurrence of Pairwise Expression

Spatial transcriptomics captures neighborhood-dependent gene expression, but existing workflows do not always fully account for measurement scale and often treat space implicitly. We present geneSCOPE, a framework that integrates ecology-inspired statistics with network analysis. Molecules are binned on a grid whose width is chosen near the mode of the per-gene unit-invariant knee (UIK) distribution derived from Morisitas I{delta} -width curves. Pairwise adjacency-weighted spatial association is quantified with Lees L. We then assemble a spatial gene network and identify gene modules by consensus clustering. To identify cell-cell interactions between different cell types, high Lees L and low Pearsons r is examined. Applied to human colorectal cancer (three Xenium sections) and a lymph node, geneSCOPE recovered spatial gene modules that map to microanatomy such as invasive margins, luminal epithelium, fibroblast-rich territories and germinal-center subdomains, and highlights intercellular neighborhood patterns at tumor-stroma interfaces between LGR5-marked stem-like tumor programs and C3-centered fibroblast/complement-associated niches. geneSCOPE thus provides a scalable, interpretable analytical foundation that generalizes across spatial omics and supports a wide range of applications.

bioinformatics↗

bioRxiv2025

IRF8 deficiency causes anxiety-like behavior in a sex-dependent manner

Anxiety disorder is a serious psychiatric disease that affects women twice more than men and disrupts patients daily lives. It is often comorbid with major depression and other mental diseases. Various underlying mechanisms have been proposed, such as neurotransmitters and neuroanatomical disruptions, and more recently, oxidative stress; however, much remained unclear, including the role of glial cells. Here, we investigated the role of IRF8 in anxiety disorders in the mouse model. IRF8 is a transcription factor expressed primarily in microglia in the brain. A battery of behavioral tests revealed that female IRF8 knockout (IRF8KO) mice show increased anxiety relative to male IRF8KO and wild-type mice. Female IRF8KO mice also exhibited a higher tendency for obsessive-compulsive disorder. However, these behavioral abnormalities were not observed when IRF8 was deleted postnatally, indicating that it acts during the fetal stage to control anxiety. Transcriptome analysis revealed that IRF8 deficiency leads to redox dysregulation. Further, 2,7-dichlorofluorescin diacetate (DCFDA) staining for microglia demonstrated that female IRF8KO microglia produce higher levels of reactive oxygen species (ROS) compared to WT and male IRF8KO counterparts. Detailed RNA-seq analysis, however, did not reveal specific genes that cause high ROS production in female cells. In sum, this work demonstrates that IRF8 in microglia plays a major role in controlling anxiety in a sex dependent manner.

neuroscience↗

bioRxiv2024

Clonal evolution of hematopoietic stem cells after cancer chemotherapy

Normal hematopoietic stem and progenitor cells (HSPCs) inherently accumulate somatic mutations and lose clonal diversity with age, processes implicated in the development of myeloid malignancies1. The impact of exogenous stressors, such as cancer chemotherapies, on the genomic integrity and clonal dynamics of normal HSPCs is not well defined. We conducted whole-genome sequencing on 1,032 single-cell-derived HSPC colonies from 10 patients with multiple myeloma (MM), who had undergone various chemotherapy regimens. Our findings reveal that melphalan treatment distinctly increases mutational burden with a unique mutation signature, whereas other MM chemotherapies do not significantly affect the normal mutation rate of HSPCs. Among these therapy-induced mutations were several oncogenic drivers such as TET2 and PPM1D. Phylogenetic analysis showed a clonal architecture in post-treatment HSPCs characterized by extensive convergent evolution of mutations in genes such as TP53 and PPM1D. Consequently, the clonal diversity and structure of post-treatment HSPCs mirror those observed in normal elderly individuals, suggesting an accelerated clonal aging due to chemotherapy. Furthermore, analysis of matched therapy-related myeloid neoplasm (t-MN) samples, which occurred 1-8 years later, enabled us to trace the clonal origin of t-MNs to a single HSPC clone among a group of clones with competing malignant potential, indicating the critical role of secondary mutations in dictating clonal dominance and malignant transformation. Our findings suggest that cancer chemotherapy promotes an oligoclonal architecture with multiple HSPC clones possessing competing leukemic potentials, setting the stage for the selective emergence of a singular clone that evolves into t-MNs after acquiring secondary mutations. These results underscore the importance of further systematic research to elucidate the long-term hematological consequences of cancer chemotherapy.

cancer biology↗

bioRxiv2023

IRF8 configures enhancer landscape in postnatal microglia and directs microglia specific transcriptional programs

Microglia are innate immune cells in the brain. Transcription factor IRF8 is highly expressed in microglia. However, its role in postnatal microglia development is unknown. We demonstrate that IRF8 binds stepwise to enhancer regions of postnatal microglia along with Sall1 and PU.1, reaching a maximum after day 14. IRF8 binding correlated with a stepwise increase in chromatin accessibility, which preceded the initiation of microglia-specific transcriptome. Constitutive and postnatal Irf8 deletion led to a loss of microglia identity and gain of disease-associated microglia-like genes. Combined analysis of scRNA-seq and scATAC-seq revealed a correlation between chromatin accessibility and transcriptome at a single-cell level. IRF8 was also required for microglia-specific DNA methylation patterns. Lastly, in the 5xFAD model, constitutive and postnatal Irf8 deletion reduced the interaction of microglia with A{beta} plaques and the size of plaques, lessening neuronal loss. Together, IRF8 sets the epigenetic landscape, which is required for postnatal microglia gene expression.

immunology↗

bioRxiv2023

Acvr1b loss promotes formation of precancerous lesions from acinar and ductal cells of origin

Background & AimsPancreatic ductal adenocarcinoma (PDAC) can develop from precursor lesions, including pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasm (IPMN). Previous studies indicated that loss of Acvr1b accelerates the Kras-mediated development of papillary IPMN in the mouse pancreas, however, the cell type predominantly affected by these genetic changes remains unclear. MethodsWe investigated the contribution of cellular origin by inducing IPMN associated mutations-KRASG12D expression and Acvr1b loss - specifically in acinar (Ptf1aCreER;KrasLSL-G12D;Acvr1bfl/flmice) or ductal (Sox9CreER;KrasLSL- G12D;Acvr1bfl/flmice) cells in mice. We then performed MRI imaging and a thorough histopathological analysis of their pancreatic tissues. ResultsThe loss of Acvr1b increased the development of PanIN and IPMN-like lesions when either acinar and ductal cells expressed a Kras mutation. MRI, immunohistochemistry and histology revealed large IPMN-like lesions in these mice that exhibited features of flat, gastric epithelium. In addition, cyst formation in both mouse models was accompanied by chronic pancreatitis. Experimental acute pancreatitis accelerated the development of large mucinous cysts and PanIN when acinar, but not ductal, cells expressed mutant Kras and lost Acvr1b. ConclusionThese findings indicate that loss of Acvr1b in the presence of the Kras oncogene promotes the development of large and small precancerous lesions from both ductal and acinar cells. However, the IPMN-like phenotype was not equivalent to that observed when these mutations were made in all pancreatic cells during development. Our study underscores the significance of the cellular context in the initiation and progression of precursor lesions from exocrine cells.

cancer biology↗

bioRxiv2023

Identification and characterization of a proliferative cell population in estrogen receptor-positive metastatic breast cancer through spatial and single-cell transcriptomics

BackgroundIntratumor heterogeneity is a hallmark of most solid tumors, including breast cancers. We applied spatial transcriptomics and single-cell RNA-sequencing technologies to profile spatially resolved cell populations within estrogen receptor-positive (ER+) metastatic breast cancers and elucidate their importance in estrogen-dependent tumor growth. MethodsSpatial transcriptomics and single-cell RNA-sequencing were performed on two patient-derived xenografts (PDXs) of "ER-high" metastatic breast cancers with opposite estrogen-mediated growth responses: estrogen-suppressed GS3 (80-100% ER) and estrogen-stimulated SC31 (30-75% ER) models. The analyses included samples treated with and without 17{beta}-estradiol. The findings were validated via scRNA-seq analyses on "ER-low" estrogen-accelerating PDX, GS1 (5% ER). The results from our spatial and single-cell analyses were further supported by the analysis of a publicly available single cell dataset and a protein-based dual immunohistochemical (IHC) evaluation using three important clinical markers [i.e., ER, progesterone receptor (PR), and Ki67]. The translational implication of these results was assessed by clinical outcome analyses on public breast cancer cohorts. ResultsOur novel space-gene-function study revealed a "proliferative" cell population in addition to three major spatially distinct compartments within ER+ metastatic breast cancers. These compartments showed functional diversity (i.e., estrogen-responsive, proliferative, hypoxia-induced, and inflammation-related). The "proliferative (MKI67+)" population, not "estrogen-responsive" compartment, was crucial for estrogen-dependent tumor growth, leading to the acquisition of luminal B features. The cells with induction of typical estrogen-responsive genes such as PGR were not directly linked to estrogen-dependent proliferation. Additionally, the dual IHC analyses demonstrated the distinct contribution of the Ki67+ proliferative cells toward estrogen-mediated growth and their response to palbociclib, a CDK4/6 inhibitor. The gene signatures developed from the proliferative, hypoxia-induced, and inflammation-related compartments were significantly correlated with worse clinical outcomes, while patients with the high estrogen-responsive scores showed better prognosis, confirming that the estrogen-responsive compartment would not be directly associated with estrogen-dependent tumor progression. ConclusionsFor the first time, our study elucidated a "proliferative" cell population distinctly distributed in ER+ metastatic breast cancers. They contribute differently toward progression of these cancers, and the gene signature in the "proliferative" compartment is an important determinant of luminal cancer subtypes.

cancer biology↗

bioRxiv2021

Inactivation of SARS-CoV-2 and influenza A virus by spraying hypochlorous acid solution and hydrogen peroxide solution in the form of Dry Fog

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is transmitted by droplet and contact infection. SARS-CoV-2 that adheres to environmental surfaces remains infectious for several days. We herein attempted to inactivate SARS-CoV-2 and influenza A virus adhering to an environmental surface by spraying aerosolized hypochlorous acid solution and hydrogen peroxide solution in the form of Dry Fog (fog that does not wet objects even if touched). SARS-CoV-2 and influenza virus were dried on plastic plates and placed into a test chamber for inactivation by the Dry Fog spraying of disinfectants. The results obtained showed that Dry Fog spraying inactivated SARS-CoV-2 and influenza A virus in time- and exposed disinfectant amount-dependent manners. SARS-CoV-2 was more resistant to the virucidal effects of aerosolized hypochlorous acid solution and hydrogen peroxide solution than influenza A virus; therefore, higher concentrations of spray solutions were required to inactivate SARS-CoV-2 than influenza A virus. The present results provide important information for the development of a strategy that inactivates SARS-CoV-2 and influenza A virus on environmental surfaces by spatial spraying.

microbiology↗

bioRxiv2019

Aberrant expression of the COX2/PGE2 axis is induced by activation of the RAF/MEK/ERK pathway in BRAFV595E canine urothelial carcinoma

Cancer-promoting inflammation is an important event in cancer development. The cyclooxygenase 2 (COX2)/prostaglandin E2 (PGE2) axis is a prominent inducer of inflammation. Canine urothelial carcinoma (cUC) uniquely overexpresses PGE2 and is often managed well with COX inhibitor monotherapy. In most cases, cUC tissue harbours homologous human BRAFV600E mutation, which causes aberrant activation of the RAF/MEK/ERK pathway in human cancer. However, mechanisms underlying aberrant PGE2 production and the importance of the BRAF mutation remain unclear. We show that activation of the RAF/MEK/ERK pathway in BRAF mutant cUC cells leads to COX2 overexpression and PGE2 production. Drug screening revealed that treatment with inhibitors of the arachidonic acid cascade (FDR<0.086), RAF/MEK/ERK pathway (FDR<0.067), and p38/JNK pathway (FDR<0.067) significantly reduced PGE2 production in cUC cells. We also validated the association between RAF/MEK/ERK pathway activation and COX2/PGE2 overexpression in BRAF mutant cUC cells using protein detection techniques. In histochemical analysis, BRAF mutant cUC tissue showed higher COX2 expression. Therefore, the driver mutation in the BRAF gene probably promotes tumour-promoting inflammation. These findings would benefit dogs suffering from cUC and can be extrapolated to human cancer. Finally, cUC can serve as a valuable model to elucidate the association between driver mutations and tumour-promoting inflammation.

cancer biology↗

bioRxiv2018

miR-10b Deficiency Affords Atherosclerosis Resistance

Human vascular endothelial cells (ECs) are categorized into two groups; pro-stenotic (Type-I) and anti-stenotic (Type-II) ECs, and one of the master genes for a stress-induced \"Type-II-to-Type-I\" degeneration is Regulator of G-protein signaling 5 (RGS5). Here we show that miR-10b is a crucial downstream mediator in RGS5-dependent degeneration. We also demonstrated the miR-10bhigh Type-I EC exosome has a trans effect which suppresses anti-proliferative abilities of Type-II ECs. Moreover, we found miR-10b-deficient mice showed a resistance to experimental atherosclerosis, where high-fat-high-cholesterol-diet-fed mice were subjected to partial carotid ligation. Furthermore, we determined the key target of miR-10b was Latent transforming growth factor-{beta} binding protein 1 (LTBP1), which is a regulator of TGF-{beta} signaling. Compatible with a commonly accepted view that TGF-{beta} creates the major growth-inhibitory signal against vascular smooth muscle cells, TGF-{beta} inhibitor treatments abolished anti-proliferative functions of Type-II ECs. Therefore, RGS5/miR-10b/LTBP1/TGF-{beta} axis plays a leading role in quality control of ECs.

cell biology↗