Biology subjects

Hirasaki, M.

Publications and source records attributed to Hirasaki, M..

12 recordsLinked to original sources

bioRxiv2026

MHC class II in dopaminergic neurons prunes GABAergic synapses in neurodevelopmental disorders

Although the brain was traditionally considered immune-privileged, recent studies show immune factors play key roles in brain function. Dysfunction of these factors is linked to neurodevelopmental disorders, but mechanisms remain unclear. Using a maternal immune activation (MIA) mouse model, we investigated immune-related genes in neurodevelopmental disorder pathogenesis. MIA mice showed increased locomotor activity and disrupted prepulse inhibition. RNA-seq and qPCR analyses revealed persistent increases in major histocompatibility complex class II (MHCII) expression and persistent decreases in GABAergic synapse-related gene expression, particularly glutamate decarboxylase (Gad) expression, in dopaminergic regions. These expressions were negatively correlated, and immunohistochemistry showed MHCII at postsynaptic GABAergic synapses on dopaminergic neurons. Patch-clamp recordings confirmed reduced mIPSC frequency in MIA mice. MHCII knockout mice showed opposite phenotypes, while MHCII overexpression in dopaminergic neurons decreased Gad expression. These results suggest MIA-induced MHCII upregulation enhances pruning of GABAergic synapses on dopaminergic neurons, leading to behavioral deficits.

neuroscience↗

bioRxiv2026

Stress Granules and FUS condensates recruit functionally distinct sets of RNAs

Cellular homeostasis relies on the organization of RNA and protein into membrane-less organelles. Stress granules (SGs) are well-known hubs for translational repression during cellular stress. Similar condensates formed by RNA-binding proteins such as FUS-- mutations in which cause amyotrophic lateral sclerosis (ALS)--remain poorly characterized relative to canonical SGs. Here, we develop Granule-seq, a microcapillary-based granule-resolved RNA sequencing approach, and demonstrate that SGs and FUS condensates are functionally distinct RNA compartments rather than variants of a unified granule class. Granules were individually aspirated, analyzed in small pooled sets, and validated through overlap with known SG components (794/2,759 genes, 28.8%, p < 0.001). Gene Ontology analysis revealed that G3BP-positive SGs sequester transcripts for stress responses and translational control, while FUS condensates are enriched for transcripts essential for synaptic function and neuronal development. Direct comparison showed that 63% of FUS-enriched and 82% of G3BP-enriched genes were granule-specific, with only 493 genes shared. Exploratory sequence analysis revealed modest contributions from compositional features, with functional identity providing primary selectivity. As a proof-of-concept study with limited biological replication, our results suggest that distinct granule identities are established through functionally specialized transcriptomes, a process that may be disrupted in ALS, and provide a framework for understanding RNA sorting. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/726389v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1378da9org.highwire.dtl.DTLVardef@35906borg.highwire.dtl.DTLVardef@9c7880org.highwire.dtl.DTLVardef@ab3b9d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic abstract.C_FLOATNO Granule-seq workflow and key findings.(Left) Individual cytoplasmic granules are isolated by microcapillary aspiration, pooled ([~]10 granules per replicate), and processed for RNA sequencing alongside total-cell input. (Middle) Venn diagram showing the overlap between FUS condensate-enriched (1,334 genes) and G3BP1 stress granule-enriched (2,759 genes) transcripts. FUS condensates preferentially recruit neuronal and synaptic transcripts; G3BP1 stress granules are enriched for stress-response and proteostasis transcripts. (Right) Two-step recruitment model: shared sequence features (long 3'UTR, GC-rich composition, stable RNA structure) provide permissiveness for granule entry (Step 1), while RBP interactome composition and functional context determine granule-type specificity (Step 2). C_FIG

molecular biology↗

bioRxiv2025

FOXM1 Expression in Invasive Ductal Breast Carcinoma of No Special Type: Insights from RNA-seq and Immunohistochemical Analysis

BackgroundInvasive ductal carcinoma of no special type (IDC-NST) is the most common subtype of breast cancer, characterized by significant clinical heterogeneity. Forkhead box M1 (FOXM1) is a key transcription factor involved in cell cycle regulation and tumor progression, but its expression profile and clinical significance in IDC-NST remain incompletely understood. MethodsWe analyzed FOXM1 expression in a cohort of 100 IDC-NST patients using RNA sequencing and immunohistochemistry (IHC). FOXM1 mRNA levels were quantified, and protein expression was scored based on the percentage of positive tumor cells. Differentially expressed genes (DEGs) between high and low FOXM1 expression groups were identified, followed by pathway enrichment and protein-protein interaction (PPI) network analyses. The prognostic value of FOXM1 was evaluated by recurrence-free survival (RFS) analysis. ResultsFOXM1 protein expression correlated significantly with mRNA abundance in 22 representative cases (p < 0.05). Receiver operating characteristic (ROC) curve analysis identified a cut-off value of 4.954 CPM for FOXM1 mRNA to predict recurrence (AUC = 0.642). High FOXM1 expression was associated with larger tumor size, higher histological grade, and negative hormone receptor status. Patients with high FOXM1 expression exhibited significantly poorer 5-year RFS (73.6% vs. 92.3%, p < 0.001). Multivariate analysis confirmed FOXM1 as an independent prognostic factor (HR 15.26; p = 0.026). Transcriptomic profiling revealed 190 upregulated and 197 downregulated genes in the FOXM1-high group, enriched in cell cycle and mitotic pathways. PPI network analysis positioned FOXM1 as a central hub coordinating genes involved in chromosomal stability and mitosis. ConclusionsFOXM1 overexpression is a strong independent predictor of poor prognosis in IDC-NST and plays a critical role in tumor proliferation and genome integrity. These findings support FOXM1 as a potential prognostic biomarker and therapeutic target, warranting further investigation into FOXM1-targeted therapies for breast cancer management.

cancer biology↗

bioRxiv2023

Transcriptome analyses of mouse cardiac myocytes and non-cardiomyocytes: postmitotic vs. proliferative cells

Adult heart mostly contains long-lived postmitotic cardiomyocytes and non-cardiomyocytes that have proliferative potential. Here, we isolated cardiomyocytes and non-cardiomyocytes from young and aged mouse heart, and performed transcriptome analyses by RNA sequencing to understand the differences of gene expression in postmitotic and proliferative cells. Gene ontology analyses revealed that genes associated with inflammatory response were upregulated in aged cardiac myocytes, whereas genes including two ATP synthases in mitochondrial respiratory complex V (Atp5l and Atp5J2) and two NADH dehydrogenases in complex I (Ndufa11 and Ndufv3) were significantly downregulated. In aged non-cardiomyocytes, genes related to inflammatory responses were also upregulated, while genes involved in cell cycle and DNA replication process were downregulated. We also found that the expression levels of some small nucleolar RNAs (snoRNAs) are decreased cardiomyocytes with aging. snoRNAs are deeply involved in RNA modification such as pseudouridylation stabilizing ribosomal RNA (rRNA) and mRNA splicing. Therefore, the age-related reduction in snoRNA expression may lead to the destabilization of rRNA, splicing dysfunction, and ultimately a decrease in protein synthesis capacity. A comparison with transcriptome results obtained for non-cardiomyocytes suggests that the decline in the expression of mitochondria-related genes and snoRNAs accompanying aging is specific to cardiomyocytes, implying their potential utility as one of novel aging markers in postmitotic cells.

physiology↗

bioRxiv2023

Transcriptome Analysis Reveals Enhancement of Cardiogenesis-Related Signaling Pathways by S-nitroso-N-pivaloyl-D-penicillamine (SNPiP): Implications for Improved Diastolic Function and Cardiac Performance

We previously reported a novel compound called S-nitroso-N-pivaloyl-D-penicillamine (SNPiP), which was screened from a group of nitric oxide (NO) donor compounds with a basic chemical structure of S-nitroso-N-acetylpenicillamine (SNAP), to activate the non-neuronal acetylcholine (NNA) system. SNPiP-treated mice exhibited improved cardiac output and enhanced diastolic function, without an increase in heart rate. The NNA-activating effects included increased resilience to ischemia, modulation of energy metabolism preference, and activation of angiogenesis. Here, we performed transcriptome analysis of SNPiP-treated mice ventricles to elucidate how SNPiP exerts beneficial effects on cardiac function. A time-course study (24 and 48 h after SNPiP administration) revealed that SNPiP initially induced Wnt and cGMP-protein kinase G (PKG) signaling pathways, along with upregulation of genes involved in cardiac muscle tissue development and oxytocin signaling pathway. We also observed enrichment of glycolysis-related genes in SNPiP-treated samples, indicating a metabolic shift from oxidative phosphorylation to glycolysis following SNPiP administration in the hearts. Additionally, SNPiP significantly upregulated atrial natriuretic peptide (ANP) and sarcolipin (SLN), which play crucial roles in calcium handling and cardiac performance. These findings suggest that SNPiP may have therapeutic potential based on the pleiotropic mechanisms elucidated in this study.

molecular biology↗

bioRxiv2023

Similarity and dissimilarity in alteration of gene expression profile associated with inhalational anesthesia between sevoflurane and desflurane

Although sevoflurane is the most commonly used inhalational anesthetic agent, the popularity of desflurane is increasing to a similar level. The main beneficial property of desflurane is the relatively fast emergence of the patient from the anesthetic state after halting its supply compared with anesthesia using other anesthetic agents. However, there has been no comprehensive comparison of the effects of these two anesthetic agents on alterations in liver gene expression profiles in animals, including humans, to assess the levels of hepatotoxicity that is induced at least in some extent by inhalational anesthesia. Thus, we compared alterations in the global gene expression profiles in the livers of rats subjected to inhalational anesthesia by sevoflurane or desflurane by a next-generation sequencing method. Our data revealed that both anesthetic agents significantly activated a similar set of genes including those related to drug metabolism and circadian rhythm. Furthermore, many genes downregulated by sevoflurane were also downregulated by desflurane. However, many of the genes related to the cholesterol biosynthetic process were specifically repressed by sevoflurane, but not by desflurane.

molecular biology↗

bioRxiv2022

PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant chemotherapy for colorectal cancer

BackgroundFluoropyrimidine-based adjuvant chemotherapy is globally recommended for postoperative stage III colon cancer and high-risk stage II patients. However, adjuvant chemotherapy is often associated with severe adverse events and is not highly effective in preventing recurrence. Therefore, a recurrence-prevention biomarker of adjuvant chemotherapy for colorectal cancer is necessary for providing such treatments to appropriate patients. Autophagy (including mitophagy) is activated under chemotherapy-induced stress and contributes to chemotherapy resistance. Expression of autophagy-related genes and their single-nucleotide polymorphisms are reported to be effective predictors of chemotherapy response in some cancers. Our goal was to evaluate the relationship between the single-nucleotide variants of autophagy-related genes and recurrence rates to identify the recurrence-prevention biomarkers of adjuvant chemotherapy in colorectal cancer. MethodsWe analyzed surgical or biopsy specimens from 84 patients who underwent radical surgery followed by fluoropyrimidine-based adjuvant chemotherapy at Saitama Medical University International Medical Center between January and December 2016. Using targeted enrichment sequencing, we identified single-nucleotide variants and insertions/deletions in 50 genes, including autophagy-related genes, and examined their association with colorectal cancer patient relapse rates. ResultsWe detected 560 single-nucleotide variants or insertions/deletions in the target region. The results of Fishers exact test indicated that the recurrence rate of colorectal cancer after adjuvant chemotherapy was significantly lower in patients with the single- nucleotide variants (c.1018G>A [p < 0.005] or c.1562A>C [p < 0.01]) of the mitophagy-related gene PTEN-induced kinase 1. ConclusionsThe two single-nucleotide variants of this mitophagy-related gene may be biomarkers of non-recurrence in colorectal cancer patients who received postoperative adjuvant chemotherapy.

cancer biology↗

bioRxiv2022

Temporal inhibition of electron transport chain attenuates stress-induced cellular senescence by prolonged disturbance of proteostasis in human fibroblasts

We previously developed a stress-induced premature senescence (SIPS) model in which normal human fibroblast MRC-5 cells were treated with either the proteasome inhibitor MG132 or the V-ATPase inhibitor bafilomycin A1 (BAFA1). To elucidate the involvement of mitochondrial function in our SIPS model, we treated cells with an inhibitor of electron transport chain (ETC) complexes I, III, or a mitochondrial uncoupler reagent along with MG132 or BAFA1 and evaluated the induction of premature senescence. SIPS induced by MG132 or BAFA1 was partially attenuated by co-treatment with antimycin A (AA) and rotenone, but not carbonyl cyanide 3-chlorophenylhydrazone (CCCP), in which intracellular reactive oxygen species (ROS) levels, acute mitochondrial unfolded protein responses, and accumulation of protein aggregates were remarkably suppressed. Co-treatment with AA also reversed the temporal depletion of SOD2 in the mitochondrial fraction on day 1 of MG132 treatment. Furthermore, co-treatment with AA suppressed the induction of mitophagy in MG132-treated cells and enhanced mitochondrial biogenesis. These findings provide evidence that the temporal inhibition of mitochondrial respiration exerts protective effects against the progression of premature senescence caused by impaired proteostasis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/515395v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@165a9eaorg.highwire.dtl.DTLVardef@1766e79org.highwire.dtl.DTLVardef@4ef4beorg.highwire.dtl.DTLVardef@1a5e827_HPS_FORMAT_FIGEXP M_FIG GRAPHICAL ABSTRACT Cellular senescence is induced by prolonged inhibition of proteasome or lysosome function using MG132 and bafilomycin A1 (BAFA1), respectively. When cells were co-treated with a mitochondrial respiration inhibitor, antimycin A, and MG132 or BAFA1, oxidative stress, mitochondrial unfolded protein response (UPRmt), accumulation of protein aggregates, and mitophagy were suppressed whereas mitochondrial biogenesis was enhanced, resulting in the attenuation of stress-induced cellular senescence (SIPS). C_FIG

cell biology↗

bioRxiv2020

Identification of germ cell-specific Mga variant mRNA that promotes meiotic entry via impediment of a non-canonical PRC1

Transition from mitosis to meiosis in cell division is a fundamental process of gametogenesis. This transition is thought to be largely controlled by the exchange of relative dominance between positive and negative regulation by the retinoic acid/Stra8 signal cascade and a non-canonical PRC1 (PRC1.6), respectively. We have previously demonstrated that germ cells have transcriptionally and/or post-translationally reduced levels of MAX, a component of PRC1.6, immediately prior to meiotic onset, leading to alleviation of the negative effect of PRC1.6 against meiotic onset. Here, we found that germ cells produced Mga variant mRNA bearing a premature termination codon (PTC) during meiosis as an additional mechanism to impede the function of PRC1.6. Our data indicated that spermatocytes and/or round spermatids produced an anomalous MGA protein lacking the bHLHZ domain from the variant mRNA and therefore functioned as a dominant negative regulator of PRC1.6 by exquisitely using their inefficient background of PTC-mediated nonsense-mediated mRNA decay. Thus, our data indicate that meiotic onset of male germ cells is controlled in a multi-layered manner in which both MAX and MGA, which constitute the core of PRC1.6 by their interaction, are at least used as targets to deteriorate the integrity of the complex to ensure initiation of meiosis. Significance StatementPRC1.6, a non-canonical PRC1, functions as a strong blocker of meiotic onset. Therefore, germ cells need to alleviate the function of the complex as a prerequisite for meiotic onset. The MGA/MAX heterodimer not only constitutes a core of PRC1.6, but also confers direct DNA-binding activity to the complex. We have previously demonstrated that germ cells reduce Max amounts prior to meiotic onset to inactivate PRC1.6. In this study, we explored the possibility of an additional molecular mechanism that promotes meiotic onset via impediment of PRC1.6 functions as a safeguard system. Here, we demonstrate that meiotic germ cells specifically generate variant Mga mRNA by alternative splicing, which leads to production of a dominant negative regulator of PRC1.6.

developmental biology↗

bioRxiv2020

Two DNA binding domains of Mga act in combination to suppress ectopic activation of meiosis-related genes in mouse embryonic stem cells

Mouse embryonic stem cells (ESCs) have high potential for meiotic entry, like germ cells. Although the physiological meaning of this potential is not known, it is certain that a rigid safeguarding system is required to prevent ectopic onset of meiosis. PRC1.6, a non-canonical PRC1, is known for its suppression of precocious and ectopic meiotic onset in germ cells and ESCs, respectively, in which MGA has important roles in DNA binding as well as in constructing the complex as a scaffolding component. As a salient feature, MGA bears two distinct DNA-binding domains termed bHLHZ and T-box. However, how these features contribute to the functions of PRC1.6, particularly in the repression of meiotic genes, remains largely obscure. Here, we demonstrated that both DNA binding domains of Mga repress distinct sets of genes in murine ESCs, and substantial numbers of meiosis-related genes are included in both gene sets. In addition, our data demonstrated that both DNA binding domains of Mga, in particular bHLHZ, are crucially involved in repressing the expression of Meiosin, which plays essential roles in meiotic entry in collaboration with Stra8, revealing at least part of the molecular mechanisms that link negative and positive regulation of meiotic onset.

cell biology↗

bioRxiv2020

Targeted disruption of Pparγ1 promotes trophoblast endoreplication in the murine placenta

In murine placentas, peroxisome proliferator-activated receptor (PPAR) {gamma}1, a nuclear receptor, is abundant at the late stage of pregnancy (E15-E16), but its functional roles are still elusive because PPAR{gamma}-full knockout embryos die early (E10). We generated mice disrupted in only Ppar{gamma}1, one of the two major mRNA splicing variants of PPAR{gamma}1. Ppar{gamma}1- knockout embryos developed normally until 15.5 dpc, but their growth was retarded thereafter and they did not survive. At 15.5 dpc, in the wild-type placentas, intense PPAR{gamma}-immunostaining was detected in sinusoidal trophoblast giant cells (sTGCs), a cell lineage that coordinates the maternal blood microcirculation in the labyrinth, whereas they were absent in the knockouts. Although Ppar{gamma}1-knockout placentas were normal in morphology, we observed severely dilated maternal blood sinuses in the labyrinth. The Ppar{gamma}1-knockout sTGCs had abnormally large nuclei, an enhanced endocycling phenotype, indicating insufficient differentiation. RNA-sequencing of the placentas showed increased expression of genes coding for nucleosome assembly factors. Labyrinthine gene expressions for atypical E2Fs and cyclin E, key drivers for endocycling, were increased >3-fold. These findings suggested that PPAR{gamma}1 plays a key role in endocycle termination.

developmental biology↗

bioRxiv2020

NPC1L1 inhibition disturbs lipid trafficking and induces large lipid droplet formation in intestinal absorptive epithelial cells

Ezetimibe inhibits Niemann-Pick C1-like 1 (NPC1L1) protein, which mediates intracellular cholesterol trafficking from the brush border membrane to the endoplasmic reticulum, where chylomicron assembly takes place in enterocytes or in the intestinal absorptive epithelial cells. Cholesterol is a minor lipid component of chylomicrons; however, whether or not a shortage of cholesterol attenuates chylomicron assembly is unknown. The aim of this study was to examine the effect of NPC1L1 inhibition on trans-epithelial lipid transport, and chylomicron assembly and secretion in enterocytes. Caco-2 cells, an absorptive epithelial model, grown onto culture inserts were given lipid micelles from the apical side, and chylomicron-like triacylglycerol-rich lipoprotein secreted basolaterally were analyzed after a 24-h incubation period in the presence of ezetimibe up to 50 M. The secretion of lipoprotein and apolipoprotein B48 were reduced by adding ezetimibe (30%, p<0.01 and 34%, p<0.05, respectively). Additionally, ezetimibe accelerated intracellular apoB protein degradation by approximately 2.8-fold and activated sterol regulatory element binding protein 2 by approximately 1.5-fold: These are indicators whether the cells are sensing cellular cholesterol shortage. Thus, ezetimibe appeared to limit cellular cholesterol mobilization required for lipoprotein assembly. In such conditions, large lipid droplet formation in Caco-2 cells and the enterocytes in mice were induced, implying that unprocessed triglyceride was sheltered in these compartments. Although ezetimibe did not reduce the post-prandial lipid surge appreciably in triolein-infused mice, the results of the present study indicated that NPC1L1-mediated supply chylomicron with cholesterol may participate in a novel regulatory mechanism for the efficient chylomicron assembly and secretion.

biochemistry↗