bioRxiv Science⌕ Search

Biology subjects

Fukumura, K.

Publications and source records attributed to Fukumura, K..

10 recordsLinked to original sources

Fat body CLOCK restrains innate immunity and maintains survival under dietary stress in Drosophila

Both aging and a high-fat diet (HFD) dampen circadian gene transcription rhythms and promote chronic inflammation. How aging and HFD interact to affect peripheral molecular clocks and circadian behavior remains unclear. Using Drosophila melanogaster, we showed that aging and HFD additively dampened circadian behavior, with their adverse effects converging on the fat body (FB), a tissue that regulates systemic metabolism and innate immunity. Applying longitudinal in vivo bioluminescence recording in small, genetically defined cell populations, we found that molecular clocks in the FB were uniquely vulnerable to aging- and HFD-induced dampening of rhythm amplitude, whereas those in the clock neurons declined with age but were resistant to dietary stress. To test the consequences of this FB clock decline, we disrupted individual components of the core molecular clock specifically in the FB. We found that only CLOCK (CLK) disruption shortened lifespan on HFD, whereas disrupting its binding partner CYCLE (CYC), or the repressors PERIOD and TIMELESS, did not. Furthermore, CLK, but not CYC, disruption upregulated antimicrobial peptide expression in the FB, dampened behavioral rhythms, and suppressed locomotor activity, even though both CLK and CYC disruption comparably dampened clock gene oscillation in the FB. Together, these results indicate that FB CLK has a unique role in suppressing pro-inflammatory signals independently of CYC. Our findings provide insight into how stressors such as aging and HFD selectively disrupt the peripheral metabolic clock, and into the distinct roles of individual clock components, with implications for age-related inflammation and metabolic disease.

molecular biology↗

Multi-Omics Study of Ancestry in Adults with Intracranial Cancers Glioma (MOSAIC)

BackgroundMost genomic studies of adult-type diffuse gliomas have focused on predominantly European ancestry populations, limiting the generalizability of molecular classifications and precision medicine approaches. We assembled a multi-institutional glioma cohort of diverse patients to investigate how germline ancestry, molecular subtypes, and mutational processes shape tumor biology and clinical outcomes. MethodsWe analyzed 1,102 adults with WHO 2021-classified diffuse gliomas (IDH-mutant, 1p/19q-codeleted oligodendroglioma; IDH-mutant astrocytoma; IDH-wildtype glioma) from seven U.S. institutions. Whole-exome sequencing (WES) of FFPE tumors identified somatic alterations and COSMIC SBS v3.2 mutational signatures. Genetic ancestry was estimated from WES using 1000 Genomes reference populations. Overall survival was assessed using Kaplan-Meier and multivariable models. ResultsThe cohort included 66.9% European (EUR), 21.1% Admixed American/Hispanic (AMR), 10.3% Admixed African (AFR), and 1.6% Asian (AS) ancestry. Survival followed expected molecular hierarchy (median overall survival: oligodendroglioma 15.7 years, astrocytoma 10.6 years, IDH-wildtype glioma 1.9 years). Within oligodendroglioma, AMR patients showed improved survival versus EUR (HR 0.67, 95% CI 0.48-0.94; p=0.011), with similar trends across subtypes. Somatic profiling confirmed canonical subtype-defining alterations and revealed higher ATRX alterations in AFR and AMR IDH-wildtype tumors compared with EUR. ATRX alterations were associated with improved survival only in AFR (p=0.003). Mutational signature analysis identified subtype-specific signatures, including therapy-associated signatures. Chemotherapy-related signatures were more frequent in EUR and AMR than in AFR. ConclusionsThis ancestrally diverse glioma cohort confirms established molecular classifications and identifies ancestry-associated differences in survival, somatic alterations, and mutational processes, indicating the critical need for broad representation to inform precision neuro-oncology. Key PointsO_LIA multi-institutional glioma cohort validates subtype and survival patterns across ancestries. C_LIO_LITherapy-associated mutational signatures differ by ancestry, suggesting distinct treatment-related mutational processes. C_LIO_LIAdmixed American patients show improved survival, particularly in oligodendroglioma. C_LI Importance of the StudyMost genomic studies of adult-type diffuse glioma have focused on populations of predominantly European ancestry which limits the ability to examine variation in tumor biology and clinical outcomes across populations. In this study, we assembled one of the largest ancestrally diverse cohorts of molecularly characterized adult diffuse gliomas, integrating germline ancestry inference with tumor whole-exome sequencing and mutational signature analysis. We confirm that established molecular classifications and survival hierarchies remain robust across ancestry groups. However, we also identified ancestry-associated differences in survival within specific tumor subtypes, higher ATRX alteration frequencies in African American and admixed American patients with IDH-wildtype tumors, and variation in therapy-associated mutational signatures across ancestry groups. These findings highlight the importance of incorporating population differences into genomic studies of glioma and provide a resource for future multi-ancestry investigations of glioma risk, tumor evolution, and treatment response, ultimately supporting more inclusive precision neuro-oncology.

bioinformatics↗

RNPS1 in PSAP complex controls cyclical pre-mRNA splicing over the cell cycle

Cell cycle progression requires periodic gene expression through splicing control. However, the splicing factor that directly controls this cell cycle-dependent splicing remain unknown. Cell cycle-dependent expression of the AURKB (aurora kinase B) gene is essential for chromosome segregation and cytokinesis. We previously reported that RNPS1 is essential to maintain precise splicing in AURKB intron 5. Here we show that RNPS1 plays this role in PSAP complex with PNN and SAP18, but not ASAP complex with ACIN1 and SAP18. Whole-transcriptome sequencing of RNPS1- and PNN-deficient cells indicated that RNPS1, either alone or as PSAP complex, is an essential splicing factor for a subset of introns. Remarkably, protein expression of RNPS1, but not PNN, is coordinated with cyclical splicing in PSAP-controlled introns including AURKB intron 5. The ubiquitin-proteasome pathway is involved in the periodic decrease of RNPS1 protein level. RNPS1 is a key factor that controls periodic splicing during the cell cycle. O_FIG O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/567984v3_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@84475dorg.highwire.dtl.DTLVardef@693637org.highwire.dtl.DTLVardef@16678feorg.highwire.dtl.DTLVardef@917ee0_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe AURKB gene encodes a protein kinase essential for cytokinesis and cell cycle C_LIO_LIPSAP complex (RNPS1, PNN, SAP18) is required for precise splicing in AURKB intron 5 C_LIO_LIRNPS1 protein in PSAP complex controls periodical splicing during the cell cycle C_LIO_LICyclical decrease of RNPS1 protein is mediated by the ubiquitin-proteasome pathway C_LI

molecular biology↗

Delineating genotypes and phenotypes of individual cells from long-read single cell transcriptomes

Single-cell nanopore sequencing of full-length mRNAs (scNanoRNAseq) is transforming singlecell multi-omics studies. However, challenges include computational complexity and dependence on short-read curation. To address this, we developed a comprehensive toolkit, scNanoGPS to calculate same-cell genotypes-phenotypes without short-read guidance. We applied scNanoGPS onto 23,587 long-read transcriptomes from 4 tumors and 2 cell lines. Standalone, scNanoGPS accurately deconvoluted error-prone long-reads into single-cells and single-molecules. Further, scNanoGPS simultaneously accessed both phenotypes (expressions/isoforms) and genotypes (mutations) of individual cells. Our analyses revealed that tumor and stroma/immune cells often expressed significantly distinct combinations of isoforms (DCIs). In a kidney tumor, we identified 924 genes with DCIs involved in cell-type-specific functions such as PDE10A in tumor cells and CCL3 in lymphocytes. Moreover, transcriptome-wide mutation analyses identified many cell-type-specific mutations including VEGFA mutations in tumor cells and HLA-A mutations in immune cells, highlighting critical roles of different populations in tumors. Together, scNanoGPS facilitates applications of single-cell long-read sequencing.

bioinformatics↗

The RBM17/SPF45-SAP30BP interaction is essential for splicing in a subset of human short introns

Human pre-mRNA splicing requires the removal of introns with highly variable lengths, from tens to over a million nucleotides. Therefore, mechanisms of intron recognition and splicing are likely not universal. Recently, we reported that splicing in a subset of human short introns with truncated polypyrimidine tracts depends on RBM17 (SPF45), instead of the canonical splicing factor U2AF heterodimer. Here, we demonstrate that SAP30BP, a factor previously implicated in transcriptional control, is an essential splicing cofactor for RBM17. In vitro binding and NMR analyses demonstrate that a U2AF-homology motif (UHM) in RBM17 binds directly to a newly identified UHM-ligand motif (ULM) in SAP30BP. We show that this RBM17-SAP30BP interaction is required to specifically recruit RBM17 to phosphorylated SF3B1 (SF3b155), a U2 snRNP component in active spliceosomes. We propose a unique mechanism for splicing in a subset of short introns, in which SAP30BP guides RBM17 in the assembly of active spliceosomes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/522300v4_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@12da1c3org.highwire.dtl.DTLVardef@d71e53org.highwire.dtl.DTLVardef@108160corg.highwire.dtl.DTLVardef@1df7275_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefFukumura et al. discover a general splicing mechanism in a subset of human short introns with truncated polypyrimidine tracts. This splicing reaction is mediated by intermediary RBM17-SAP30BP complex, instead of the known U2AF heterodimer. SAP30BP binding to RBM17 may support RBM17 association with active phosphorylated SF3B1 in U2 snRNP. HighlightsO_LIRBM17 (SPF45) is a splicing factor required for a subset of human short introns C_LIO_LISAP30BP is an essential cofactor, which interacts with RBM17 via UHM-ULM binding C_LIO_LIRBM17 forms a weak complex with SAP30BP before its binding with SF3B1 in U2 snRNP C_LIO_LIRBM17-SAP30BP complex supports RBM17 to be recruited to active phosphorylated SF3B1 C_LI

molecular biology↗

Neurosecretory protein GL-induced fat accumulation is accompanied by repressing the immune-inflammatory response in the adipose tissue of mice

We have recently identified neurosecretory protein GL (NPGL), a small secretory protein expressed in the vertebrate hypothalamus, as an orexigenic factor with remarkable fat accumulation by overexpression of the NPGL precursor gene (Npgl) for two months. In the present study, we analyzed the effects of short-term Npgl overexpression for 18 days as the early stage of obesity to address the mechanisms underlying obese-like phenotype. Similar to previous studies, short-term Npgl overexpression stimulated food intake and fat accumulation in the white adipose tissues (WAT), whereas the masses of the brown adipose tissue, testis, liver, heart, and muscle remained unchanged. In addition, we observed increased blood insulin and leptin levels due to Npgl overexpression, while little changes were induced in blood glucose, free fatty acids, triglyceride, and cholesterol levels. Furthermore, transcriptome analysis of the inguinal WAT using RNA-sequencing technique revealed that overexpression of Npgl upregulated the genes involved in cytoskeleton regulation, whereas it decreased those involved in immune-inflammatory responses. These results suggest that NPGL plays a crucial role in enlarging adipocytes and suppressing inflammation to avoid metabolic abnormalities, eventually contributing to accelerating energy storage.

physiology↗

Overexpression of the gene encoding neurosecretory protein GL precursor prevents excessive fat accumulation in the adipose tissue of mice fed a long-term high-fat diet

We previously identified a novel small hypothalamic protein, neurosecretory protein GL (NPGL), which induces feeding behavior and fat accumulation in rodents depending on their diet. In the present study, we explored the effects of NPGL on feeding behavior and energy metabolism in mice placed on a long-term high-fat diet with 60% calories from fat (HFD 60). Overexpression of the NPGL precursor gene (Npgl) over 18 weeks increased food intake and body mass. The weekly body mass gain of Npgl-overexpressing mice was higher than that of controls until 7 weeks from induction of overexpression, after which it ceased to be so. Oral glucose tolerance tests showed that Npgl overexpression maintained glucose tolerance and increased blood insulin levels, and intraperitoneal insulin tolerance tests showed that it maintained insulin sensitivity. At the experimental endpoint, Npgl overexpression was associated with increased mass of the perirenal white adipose tissue (WAT) and decreased mass of the epididymal WAT (eWAT), resulting in little effect on the total WAT mass. These results suggest that under long-term HFD 60 feeding, Npgl overexpression may play a role in avoiding metabolic disturbance both by accelerating energy storage and by suppressing excess fat accumulation in certain tissues, such as the eWAT.

physiology↗

Subcutaneous infusion of neurosecretory protein GL promotes fat accumulation in mice

We recently identified a novel small secretory protein, neurosecretory protein GL (NPGL), in the vertebrate hypothalamus. We revealed that NPGL is involved in energy homeostasis using intracerebroventricular infusion in rodents. However, the effect of NPGL through peripheral administration remains to be elucidated and may be important for therapeutic use. In this study, we performed subcutaneous infusion of NPGL in mice for 12 days and found that it accelerated fat accumulation in white adipose tissue (WAT) without increasing in body mass gain and food intake. The mass of the testis, liver, kidney, heart, and gastrocnemius muscle remained unchanged. Analysis of mRNA expression by quantitative reverse transcription-polymerase chain reaction showed that proopiomelanocortin was suppressed in the hypothalamus by the infusion of NPGL. We observed a decreasing tendency in serum triglyceride levels due to NPGL, while serum glucose, insulin, leptin, and free fatty acids levels were unchanged. These results suggest that the peripheral administration of NPGL induces fat accumulation in WAT via the hypothalamus.

physiology↗

Hypothalamic Overexpression of Neurosecretory Protein GL Leads to Obesity in Mice

IntroductionThe mechanisms underlying obesity are not fully understood, necessitating the creation of novel animal models for investigation of metabolic disorders from the cellular-molecular to behavioral levels of analysis. We have previously found that neurosecretory protein GL (NPGL), a newly-identified hypothalamic neuropeptide, is involved in feeding behavior and fat accumulation in rats. Given the broad availability of genetic tools in mice, the present investigation sought to establish a mouse model of NPGL-induced obesity. MethodsWe overexpressed the NPGL-precursor gene (Npgl) in the hypothalamus using adeno-associated virus in C57BL/6J mice fed normal chow (NC) or a high-calorie diet (HCD). After 9 weeks of Npgl overexpression, we measured adipose tissues, muscle, and several organ masses in addition to food intake and body mass. To assess the effects of Npgl overexpression on peripheral tissues, we analyzed mRNA expression of lipid metabolism-related genes by quantitative RT-PCR. ResultsNpgl overexpression increased food intake, body mass, adipose tissues and liver masses, food efficiency, and circulating insulin levels under both NC and HCD, resulting in obesity observable within 8 weeks. Furthermore, we observed fat accumulation in adipose tissues and liver. Additionally, mRNA expression of lipid metabolism-related factors was increased in white adipose tissue and the liver after Npgl overexpression. ConclusionTaken together, the present study suggests that NPGL is an endogenous obesogenic factor that acts within a short period of time in mice. As a result, this animal model can be widely applied to study the etiology of obesity from genes to behavior.

neuroscience↗

A Distinct Subset of Human Short Introns: U2AF Heterodimer Is Replaced by SPF45 (RBM17) as General Splicing Factor

Human pre-mRNA introns vary in size from under fifty to over a million nucleotides. We searched for essential factors involved in the splicing of human short introns by screening siRNAs against 154 human nuclear proteins. The splicing activity was assayed with a model HNRNPH1 pre-mRNA containing short 56-nucleotide intron. We identified a known alternative splicing regulator SPF45 (RBM17) as a constitutive splicing factor that is required to splice out this 56-nt intron. Whole-transcriptome sequencing of SPF45-deficient cells revealed that SPF45 is essential in the efficient splicing of many short introns. To initiate the spliceosome assembly on a short intron with the truncated poly-pyrimidine tract, the U2AF-homology motif (UHM) of SPF45 competes out that of U2AF65 for binding to the UHM-ligand motif (ULM) of the U2 snRNP protein SF3b155 (SF3B1). We propose that splicing in a distinct subset of human short introns depends on SPF45 but not U2AF heterodimer.

molecular biology↗