Biology subjects

Shimada, M.

Publications and source records attributed to Shimada, M..

14 recordsLinked to original sources

bioRxiv2025

Passive and active demethylation in immune diseases with proliferation driving global hypomethylation

Global DNA hypomethylation is a hallmark of immune-mediated diseases, yet its regulatory significance remains unclear. Replication-associated loss of DNA methylation at solo-WCGW (W = A/T) CpGs has recently been proposed as a consequence of cell division. Here we systematically investigated genome-wide hypomethylation patterns across seven immune-mediated diseases. Most diseases exhibited global hypomethylation, particularly at solo-WCGW CpGs in transcriptionally repressed regions, potentially reflecting increased immune cell proliferation. By contrast, CpG sites whose methylation levels were associated with cytokine exposure or SNP genotypes were predominantly located in transcriptionally active regions. To investigate whether immunological events driving immune cell proliferation may also be imprinted in transcriptionally active regions, we searched for differentially methylated regions (DMRs) correlated with an index reflecting the extent of solo-WCGW hypomethylation. In narcolepsy, we identified a DMR within the T-cell receptor alpha (TRA) locus, and greater hypomethylation was associated with increased clonality of both TRA and TRB repertoires, with a similar pattern in an independent cohort. In multiple sclerosis, a DMR was also detected within the IGH locus encoding the B-cell receptor. Together, these findings suggest that the hypomethylation index captures the impact of disease-specific immune dynamics, while reflecting a shared epigenetic signature of immune cell proliferation across diseases.

genomics↗

bioRxiv2024

Multiomics analysis of narcolepsy T cells: global hypomethylation in solo-WCGW motif linked to T cell proliferation

Narcolepsy type 1 (NT1) is a chronic sleep disorder caused by a loss of orexin-producing cells in the brain and involves autoimmune mechanisms, including the presence of autoreactive T cells. We performed a genome-wide DNA methylation analysis using CD4+ and CD8+ T cells of NT1 patients. Analysis of differentially methylated regions as well as multiomics analysis with genomic and transcriptomic data obtained from the same samples indicated that cell chemotaxis pathways are implicated as a cause in the pathogenesis of NT1. Additionally, we found global hypomethylation in both the T cells of NT1 cases (CD4+: P = 1.69E-67; CD8+: P = 4.83E-12). These NT1-associated hypomethylated sites were significantly more abundant in solo-WCGW (sequences without neighboring CpGs, where W is an A or T base; P = 9.87E-194). Solo-WCGW tends to lose DNA methylation over the course of cell divisions, suggesting enhanced T cell proliferation in NT1.

genomics↗

bioRxiv2024

Testosterone-Induced Metabolic Changes in Seminal Vesicle Epithelial cells Alter Plasma Components to Enhance Sperm Fertility

Male factors account for almost half of the causes of infertility. In rodents and humans, most of the components of semen are supplied by the seminal vesicles, and they support male reproductive ability, but there are many unknown details. In this study, the metabolic changes in the seminal vesicle epithelial cells were focused on, and the mechanisms by which testosterone affected the seminal plasma composition were investigated. A factor improving the linear motility of sperm was secreted from the seminal vesicles, and it was produced in an androgen-dependent manner. Bioassays, gene expression, and flux analysis studies demonstrated that testosterone promotes glucose uptake in seminal vesicle epithelial cells via GLUT4, resulting in fatty acid synthesis. ACLY was a critical factor in this metabolic change, which produced fatty acid, especially oleic acid. In conclusion, the critical role of testosterone-induced metabolic changes in the seminal vesicles is to ensure the synthesis of fatty acid. These findings suggest that testosterone-dependent lipid remodeling may contribute to sperm straight-line motility, and further functional verification is required. One Sentence Summary Testosterone promotes the conversion of glucose to fatty acid by increasing the expression of ACLY in seminal vesicle epithelial cells, thereby regulating the seminal plasma components.

cell biology↗

bioRxiv2023

Identification of Region-Specific Gene Isoforms in the Human Brain Using Long-Read Transcriptome Sequencing and Their Correlation with DNA Methylation

BackgroundSite specificity is known in neuropsychiatric disorders, and differences in gene expression patterns could potentially explain this mechanism. However, studies using long-read transcriptome sequencing to analyze gene expression in different regions of the human brain have been limited, and none have focused on the hypothalamus, which plays a crucial role in regulating autonomic functions. ResultsWe performed long-read RNA sequencing on 12 samples derived from three different brain regions of the same individuals; the cerebellum, hypothalamus, and temporal cortex. We found that, compared to other regions, many genes with higher expression levels in the cerebellum and temporal cortex were associated with neuronal pathways, whereas those with higher expression levels in the hypothalamus were primarily linked to immune pathways. In addition, we investigated genes with different major isoforms in each brain region, even with similar overall expression levels among regions, and identified several genes, such as GAS7, that express different major isoforms in different regions. Many of these genes are involved in "actin filament-based process" and "cell projection organization" pathways, suggesting that region-dependent isoforms may have distinct roles in dendritic spine and neuronal formation in each region. Furthermore, we investigated the involvement of DNA methylation in these isoforms and found that DNA methylation may be associated with isoforms that have different first exons. ConclusionsOur results provide potentially valuable findings for future research on brain disorders and shed light on the mechanisms underlying isoform diversity in the human brain.

genomics↗

bioRxiv2022

Tetraploidy-linked sensitization to CENP-E inhibition in human cells

Tetraploidy caused by whole-genome duplication is a hallmark of cancer cells, and tetraploidy-selective cell growth suppression is a potential strategy for targeted cancer therapy. However, how tetraploid cells differ from normal diploids in their sensitivity to anti-proliferative treatments remains largely unknown. In this study, we found that tetraploid cells are significantly more susceptible to inhibitors of a mitotic kinesin CENP-E than diploids. CENP-E inhibitor preferentially diminished the tetraploid cell population in diploid-tetraploid co-culture at optimum conditions. Live imaging revealed that tetraploidy-linked increase in unsolvable polar chromosome misalignment caused substantially longer mitotic delay in tetraploids than in diploids upon moderate CENP-E inhibition. This time gap of mitotic arrest resulted in cohesion fatigue and subsequent cell death, specifically in tetraploids, leading to tetraploidy-selective cell growth suppression. In contrast, the microtubule-stabilizing compound paclitaxel caused tetraploidy-selective growth suppression through the aggravation of spindle multipolarization. We also found that CENP-E inhibitor had superior generality to paclitaxel in its tetraploidy selectivity across a broader spectrum of cell lines. Our results highlight the unique properties of CENP-E inhibitors in tetraploidy-selective suppression, giving us clues on the further development of tetraploidy-targeting interventions in cancer.

cell biology↗

bioRxiv2022

Evolutionary stability of social commitment

Conflict resolution between individual cells and a group is essential for multicellularity. The social amoeba Dictyostelium discoideum switches between solitary growth and social fruitification depending on nutrient availability. Under starvation, cells form fruiting bodies consisting of spores and non-viable altruistic stalk cells. Once cells socially committed, they complete fruitification even with a renewed source of nutrients. This social commitment is puzzling because it deprives individual cells of benefits of quickly resuming solitary growth. One idea posits that traits that facilitate premature de-commitment are somehow hindered from being selected. We studied outcomes of premature de-commitment by forced refeeding. We show that when refed cells resume sociality together with non-refed cells, besides some becoming solitary outside of fruiting bodies, a large fraction was redirected to a sub-region of altruistic stalk regardless of their original fate. The refed cells exhibited reduced cohesivity and were sorted out to the altruistic positions in morphogenesis. Furthermore, a theoretical model considering evolution of cell-cell association revealed a valley in the fitness landscape that prevents invasion of de-committing mutants. Our results provide a general scheme that naturally penalizes withdrawal from a society by evolving a specific division of labor that less cohesive individuals become altruists. Significance StatementEvolution of unicellular to multicellular organisms must resolve conflicts of reproductive interests between individual cells and the group. In the social amoeba Dictyostelium, a transition from a solitary to multicellular group occurs under starvation. Once cells commit themselves to multicellular organization, the process continues even when shifting to an environment that favors solitary growth. Our study revealed that cells forced to partially revert to a de-committed state take an altruistic role through interaction with socially committed cells. The de-committed cells exhibited reduced cohesivity and were sorted out to altruistic positions in morphogenesis. This inevitably penalizes selfish cells that revert to solitary growth too quickly. Our results explain group-level behavior that is apparently difficult to understand from an individual-level fitness.

evolutionary biology↗

bioRxiv2021

Phosphorylation of PNKP mediated by CDKs promotes end-processing of Okazaki fragments during DNA replication

Polynucleotide kinase phosphatase (PNKP) has enzymatic activities as 3' -phosphatase and 5' - kinase of DNA ends to promote DNA ligation and repair. Here, we show that cyclin-dependent kinases (CDKs) regulate the phosphorylation of threonine 118 (T118) in PNKP. This phosphorylation allows recruitment to the gapped DNA structure found in single-strand DNA nicks and/or gaps between Okazaki fragments (OFs) during DNA replication. T118A (alanine)-substituted PNKP-expressing cells exhibited accumulation of single-strand DNA gaps in S phase and accelerated replication fork progression. Furthermore, PNKP is involved in poly (ADP-ribose) polymerase 1 (PARP1)-dependent replication gap filling as a backup pathway in the absence of OFs ligation. Altogether, our data suggest that CDK-mediated PNKP phosphorylation at T118 is important for its recruitment to single-strand DNA gaps to proceed with OFs ligation and its backup errors via the gap-filling pathway to maintain genome stability.

molecular biology↗

bioRxiv2021

Comprehensive analysis of full-length transcripts reveal aberrations of splicing variants in liver cancer

Genes generate various transcripts by alternative splicing, and these transcripts can have diverse functions. However, in most transcriptome studies, short-reads sequencing technologies (next-generation sequencers) have been used and full-length transcripts have not been observed directly. Although long-reads sequencing technologies would enable us to sequence full-length transcripts, analysis of the data is a difficult task. In the present study, we developed an analysis pipeline named SPLICE to analyze full-length cDNA sequences. Using this method, we analyzed cDNA sequences from 42 pairs of hepatocellular carcinoma (HCC) and matched non-cancerous liver with Oxford Nanopore technology. Our analysis detected 46,663 transcripts from the protein-coding genes in the HCCs and the matched non-cancerous livers, of which 5,366 (11.5 %) were novel. Comparison of expression levels identified 9,933 differentially expressed transcripts (DETs) in 4,744 genes. Importantly, 746 genes with DET were not found by the gene-level analysis. We also identified novel exons derived from transposable elements (TEs). In the analysis of transcripts from hepatitis B virus (HBV), HBx-human TE fusions were found to be overexpressed in the HCCs. Furthermore, fusion gene detection showed novel recurrent fusion events. These results suggest that long-reads sequencing technologies allow us to analyze full-length transcripts, and show the importance of splicing variants in carcinogenesis.

cancer biology↗

bioRxiv2021

Sumoylation of the human histone H4 tail inhibits p300-mediated transcription by RNA polymerase II in cellular extracts

Post-translational modification of histone H4 by the small ubiquitin-like modifier (SUMO) protein was associated with gene repression. However, this could not be proven due to the challenge of site-specifically sumoylating H4 in cells. Biochemical crosstalk between SUMO and other histone modifications, such as H4 acetylation and H3 methylation, that are associated with active genes also remains unclear. We addressed these challenges in mechanistic studies using H4 chemically modified at Lys12 by SUMO-3 (H4K12su) that was incorporated into mononucleosomes and chromatinized plasmids. Mononucleosome-based assays revealed that H4K12su inhibits transcription-activating H4 tail acetylation by the histone acetyltransferase p300, and transcription-associated H3K4 methylation by the extended catalytic module of the Set1/COMPASS histone methyltransferase complex. Activator- and p300-dependent in vitro transcription assays with chromatinized plasmids revealed H4K12su inhibits RNA polymerase II-mediated transcription and H4 tail acetylation. Thus, we have uncovered negative biochemical crosstalk with acetylation/methylation and the direct inhibition of RNAPII-mediated transcription by H4K12su.

biochemistry↗

bioRxiv2020

Novel candidates of pathogenic variants of the BRCA1 and BRCA2 genes in a 3,552 Japanese whole-genome sequence dataset (3.5KJPNv2)

Identification of pathogenic germline variants yet no clinical evidence in BRCA genes has become important in patient care of hereditary breast and ovarian cancer syndrome (HBOC). Computational scoring and prospective cohort studies may help to identify such pathogenic variants. We annotated the variants in the BRCA1 and BRCA2 genes from a dataset of 3,552 whole-genome sequences obtained from members of the genome cohorts by Tohoku Medical Megabank Project (TMM) with the InterVar software. Computational impact scores (CADD_phred and Eigen_raw) and minor allele frequencies (MAF) of pathogenic (P) and likely pathogenic (LP) variants in ClinVar are used for filtration criteria. Familial predispositions in cancers among the 35,000 TMM genome cohort participants are analyzed to verify the pathogenicity. Seven potentially pathogenic variants were newly identified. Carriers of these potential pathogenic variants and definite P and LP variants among participants of the TMM prospective cohort show a statistically significant preponderance in cancer onset in sisters in the self-reported cancer history. Filtering by computational scoring and MAF is useful to identify potential pathogenic variants in BRCA genes for Japanese population. These results will be helpful to follow up the carriers of variants of uncertain significance in the HBOC genes.

genetics↗

bioRxiv2019

Polyandry and Paternity influence disease resistance in a eusocial wasp - support for the pathogen parasite hypothesis

Polyandry (multiple mating by females) is a central challenge for understanding the evolution of eusociality. Several hypotheses have been proposed to explain its observed benefits in eusocial Hymenoptera, and one, the parasite-pathogen hypothesis, proposes that high genotypic variance among workers for disease resistance prevents catastrophic colony collapse. We tested the parasite-pathogen hypothesis in the polyandrous wasp Vespula shidai. We infected isolated workers with the entomopathogenic fungus Beauveria bassiana and quantified their survival in the laboratory. Additionally, we conducted paternity analysis of the workers using nine microsatellite loci to investigate the relationship between survival and matriline/patriline of the workers. As predicted by the parasite-pathogen hypothesis, nestmate workers of different patrilines showed differential resistance to B. bassiana. We also demonstrated variations in virulence among strains of B. bassiana. Our results are the first to directly support the parasite-pathogen hypothesis in eusocial wasps and suggest that similar evolutionary pressures drove the convergent origin and maintenance of polyandry in ants, bees, and wasps.

animal behavior and cognition↗

bioRxiv2019

Liposomes Under Real Cell Conditions Behave Like Real Cells with a Single Pulsed Electric Field

Liposomes are widely assumed to present a straightforward physical model of cells. However, almost all previous liposome experiments with pulsed electric fields (PEFs) have been conducted in low-conductivity liquids, a condition that differs significantly from that of cells in medium. Here, we prepared liposomes consisting of soy bean lecithin and cholesterol, at a molar ratio of 1:1, in higher-conductivity liquid that approximated the conditions of red blood cells in phosphate-buffered saline, with inner and outer liquid conductivities of 0.6 and 1.6 S/m, respectively. We found that a single 1.1 kV/cm, 400 s PEF promoted cell-like spontaneous division of liposomes.

biophysics↗

bioRxiv2018

Genetic distance and social compatibility in the aggregation behavior of Japanese toad tadpoles

From microorganism to vertebrates, living things often exhibit social aggregation. One of anuran larvae, dark-bodied toad tadpoles (genus Bufo) are known to aggregate against predators. When individuals share genes from a common ancestor for whom social aggregation was a functional trait, they are also likely to share common recognition cues regarding association preferences, while greater genetic distances make cohesive aggregation difficult. In this study, we conducted quantitative analyses to examine aggregation behavior among three lineages of toad tadpoles: Bufo japonicus japonicus, B. japonicus formosus, and B. gargarizans miyakonis. To determine whether there is a correlation between cohesiveness and genetic similarity among group members, we conducted an aggregation test using 42 cohorts consisting of combinations drawn from a laboratory-reared set belonging to distinct clutches. As genetic indices, we used mitochondrial DNA (mtDNA) and major histocompatibility complex (MHC) class II alleles. The results clearly indicated that aggregation behavior in toad tadpoles is directly influenced by genetic distances based on mtDNA sequences and not on MHC haplotypes. Cohesiveness among heterogeneous tadpoles is negatively correlated with the geographic dispersal of groups. Our findings suggest that social incompatibility among toad tadpoles reflects phylogenetic relationships.

animal behavior and cognition↗

bioRxiv2018

Cyclic dominance emerges from the evolution of two cooperative behaviors in the social amoeba

Evolution of cooperation has been one of the most important problems in sociobiology, and many researchers have revealed mechanisms that can facilitate the evolution of cooperation. However, most studies deal only with one cooperative behaviour, even though some organisms perform two or more cooperative behaviours. The social amoeba Dictyostelium discoideum performs two cooperative behaviours in starvation: fruiting body formation and macrocyst formation. Here, we constructed a model that couples these two behaviours, and we found that the two behaviours are maintained due to the emergence of cyclic dominance, although cooperation cannot evolve if only either of the two behaviours is performed. The common chemoattractant cyclic AMP is used in both fruiting body formation and macrocyst formation, providing a biological context for this coupling. Cyclic dominance emerges regardless of the existence of mating types or spatial structure in the model. In addition, cooperation can re-emerge in the population even after it goes extinct. These results indicate that the two cooperative behaviours of the social amoeba are maintained due to the common chemical signal that underlies both fruiting body formation and macrocyst formation. We demonstrate the importance of coupling multiple games when the underlying behaviours are associated with one another.

evolutionary biology↗