Biology subjects

Maruyama, R.

Publications and source records attributed to Maruyama, R..

10 recordsLinked to original sources

bioRxiv2026

Integrating spatial and single-cell multi-omics analysis of induced pluripotent stem cell-derived cervical adenocarcinoma model

Human papillomavirus 18 (HPV18) preferentially infects cervical stem cell-like cells and is strongly associated with adenocarcinoma. However, the mechanisms underlying differentiation into cervical adenocarcinoma remain unclear due to the lack of appropriate experimental models. We aimed to establish a model of HPV18-associated cervical adenocarcinoma and elucidate its molecular and cellular differentiation mechanisms. HPV18 E6/E7 were introduced into induced pluripotent stem cell-derived reserve cell-like cells (iRCs) to generate tumor models. Spatial transcriptomics and single-cell multi-omics analyses were performed to integrate histological and molecular data. A distinct component (Gland_A) exhibited morphological and immunohistochemical features of cervical adenocarcinoma and was efficiently induced in iRC-18 tumors. Gland_A showed increased chromatin accessibility and elevated expression of FOXA1, FOXA2, and ALDH1A1. Analysis of clinical samples confirmed enrichment of ALDH1A1 in HPV-associated adenocarcinomas. This model recapitulates key features of HPV18-associated cervical adenocarcinoma and provides insights into its differentiation mechanisms.

cancer biology↗

bioRxiv2025

Plasticity of extrachromosomal DNA segregation during drug adaptation

Uneven segregation during mitosis is a striking feature of extrachromosomal DNA (ecDNA). Because ecDNA lacks a centromere, it is thought to segregate stochastically and randomly during cell division, thereby generating extensive intratumoral heterogeneity in genomic copy number. Several studies have reported that ecDNA copy numbers can readily change in response to drug treatment, which enables the cells to acquire drug resistance. However, the mechanisms underlying these dynamic changes remain poorly understood --particularly whether such copy-number changes result from static selection of pre-existing clones or from active reconfiguration under drug-induced stress. This key question remains unresolved, mainly due to the absence of technologies capable of tracking ecDNA copy number simultaneously across clones. To overcome this limitation, we developed a high-throughput framework that combines single-cell DNA sequencing with cellular barcoding for clonal tracking of ecDNA copy-number dynamics. The results of single-cell cloning experiments revealed that not all clones exhibit identical segregation modes even under drug-free conditions. Clonal tracking under drug treatment showed that resistant populations do not simply emerge from pre-existing clones with favorable ecDNA states; instead, some clones seemed capable of actively reconfiguring their segregation behavior, possibly involving neuron-like alternation in microtubule organization and intracellular transport pathways, to generate drug-resistant cells. These findings suggest that, although ecDNA might segregate stochastically, it may undergo nonrandom, actively regulated segregation under drug stress. This discovery allows the therapeutically targeting of ecDNA segregation mechanisms to counteract adaptive drug resistance.

cell biology↗

bioRxiv2025

Breast cancer identity is defined by specialized enhancer sets via lysine deacetylation

Breast cancer subtypes are defined by distinct transcriptional programs, yet the epigenetic mechanisms underlying subtype-specific gene regulation remain unclear. Enhancers, key regulators of gene expression and cell identity, are well positioned to define breast cancer subtypes. Here, we identify a previously unrecognized class of enhancers, termed hypoacetylation-defined (HD) enhancers, that regulate cancer-related genes in a luminal breast cancer cell line. HD enhancers are defined by RNA polymerase II dissociation upon lysine deacetylase inhibition, and bidirectional eRNA transcription. They are distinct from super-enhancers, require a specific Mediator subunit for gene-specific transcription, and form extensive chromatin interactions suggestive of a hub-like architecture. Analyses of clinical datasets further identified a subset of HD enhancers, termed HD cluster 1 enhancers, which classify patients into breast cancer subtypes and are associated with expression quantitative trait loci linked to subtype-specific gene expression. This study identifies the lysine deacetylation-regulated cell identity enhancers, which are potential therapeutic targets.

cancer biology↗

bioRxiv2025

Clonal lineage tracing and parallel multiomics profiling reveal transcriptional diversification induced by ARID1A deficiency

Phenotypic heterogeneity among genetically identical cancer cells underpins tumor progression and therapy resistance. However, the mechanism of epigenetic dysregulation that drives such divergence remains unclear. This study introduces integrated multimodal experimental platform specialized in analyzing inter/intraclonal heterogeneity (IMPACH), a scalable platform that integrates lineage tracing, genetic perturbation, and multimodal single-cell analysis. Utilizing IMPACH, results revealed that loss of epigenetic regulators--particularly ARID1A--enhances transcriptomic and epigenetic heterogeneity under controlled conditions. ARID1A deficiency promotes stochastic chromatin opening and induces an atypical gene expression program associated with poor clinical outcomes. Despite increased epigenetic randomness, chromatin changes remain localized to regulatory elements, partially linked to SMARCA4 binding sites. These findings revealed that chromatin remodeling defects promote clonal diversification through both stochastic and constrained mechanisms. Thus, owing to its scalability and versatility, IMPACH provides a robust framework for elucidating how epigenetic perturbations shape cellular heterogeneity in cancer.

cancer biology↗

bioRxiv2025

Human TIMELESS, a potential circadian clock regulator, plays an essential role in survival and reawakening of metastasis-initiating cells in bone

Bone metastasis is becoming increasingly common globally. In such cases, cancer cells disseminate from the primary site to bone, subsequently entering a dormant state. Following a certain incubation period, the cells reawaken and grow, forming a metastatic mass. These dormant cells are called metastasis-initiating cells (MICs), but their survival and reawakening are poorly understood. Here, we established an in vivo MIC-reawakening mouse model in bone. Microarray analysis demonstrated enrichment for mitochondrial oxidative phosphorylation (OXPHOS) and fatty acid synthesis in isolated MICs. In addition, transcriptional regulator TIMELESS was identified as an independent poor prognostic factor by using clinical transcriptomic datasets, which was validated by immunostaining on 209 breast cancer cases. TIMELESS-deficient breast, prostate, and bladder cancer cell lines exhibited reduced viability and MIC reawakening in bone. Single-cell analysis on the epigenetic landscape of MICs revealed that motif activities of CLOCK and BMAL1/ARNTL were enhanced in a cluster with increased TIMELESS accessibility scores. As TIMELESS regulates stemness through the OXPHOS metabolic state, an inhibitor targeting the metabolic pathway, MP-A08, was identified to suppress MIC reawakening and growth in bone more efficiently than cisplatin. These results suggest that TIMELESS regulates survival and reawakening in MICs and MP-A08 could contribute to adjuvant therapeutic strategies.

cancer biology↗

bioRxiv2024

Arc controls organ architecture through modulation of Crb and MyoII

Precise orchestration of morphogenetic processes is required to generate organs that are optimally situated within the organism, and that are of the right size and shape to fit and maximize functionality. Here, we describe the role of Arc, a large apical membrane-associated PDZ domain-containing protein, that works through the apical determinant Crumb (Crb) to limit MyoII activity during tissue invagination in the forming Drosophila salivary gland (SG). We show that loss of Arc, attenuation of Crb function, as well as increased activation of non-muscle Myosin II (MyoII) leads to the simultaneous internalization of more precursor cells than normal. Consequently, mature SGs are significantly shorter with more cells surrounding the lumen at all positions along the tube. Correspondingly, overexpression of Arc or SG-specific knockdown of MyoII leads to the formation of longer SGs with fewer cells surrounding the lumen. We show that both Arc PDZ domains are required for Arc function and that they have distinct activities. Finally, we show that Arc facilitates Crb plasma membrane (PM) localization and suggests a model wherein PM-associated Crb stabilizes cellular junctions countering the destabilizing effects of apical medial and junctional pools of activated MyoII, thus limiting the number of primordial cells internalizing at any given time.

developmental biology↗

bioRxiv2024

A single microRNA miR-195 rescues the arrested B cell development induced by EBF1 deficiency

Accumulated studies have reported that hematopoietic differentiation was primarily regulated by transcription factors. Early B cell factor 1 (EBF1) is an essential transcription factor for B lymphopoiesis. Contrary to the canonical notion, we found that a single miRNA, miRNA-195 (miR-195) transduction let EBF1 deficient hematopoietic progenitor cells (HPCs) express CD19, carry out V(D)J recombination and class switch recombination, which implied that B cell matured without EBF1. A part of the mechanism was caused by FOXO1 accumulation via inhibition of FOXO1 phosphorylation pathways in which targets of miR-195 are enriched. These results suggested that some miRNA transductions could function as alternatives to transcription factors.

immunology↗

bioRxiv2022

Herbarium records provide reliable phenology estimates in the understudied tropics

Plant phenology has been shifting dramatically in response to climate change, a shift that may have significant and widespread ecological consequences. Of particular concern are tropical biomes, which represent the most biodiverse and imperiled regions of the world. However, compared to temperate floras, we know little about phenological responses of tropical plants because long-term observational datasets from the tropics are sparse. Herbarium specimens have greatly increased our phenological knowledge in temperate regions, but similar data have been underutilized in the tropics and their suitability for this purpose has not been broadly validated. Here, we compare phenological estimates derived from field observational data (i.e., plot surveys) and herbarium specimens at various spatial and taxonomic scales to determine whether specimens can provide accurate estimations of reproductive timing and its spatial variation. Here we demonstrate that phenological estimates from field observations and herbarium specimens coincide well. Fewer than 5% of the species exhibited significant differences between flowering periods inferred from field observations versus specimens regardless of spatial aggregation. In contrast to studies based on field records, herbarium specimens sampled much larger geographic and climatic ranges, as has been documented previously for temperate plants, and effectively captured phenological responses across varied environments. Herbarium specimens are verified to be a vital resource for closing the gap in our phenological knowledge of tropical systems. Tropical plant reproductive phenology inferred from herbarium records are widely congruent with field observations, suggesting that they can (and should) be used to investigate phenological variation and their associated environmental cues more broadly across tropical biomes.

ecology↗

bioRxiv2018

HERC2 promotes BLM and WRN to suppress G-quadruplex DNA

BLM and WRN are RecQ DNA helicases essential for genomic stability. Here we demonstrate that HERC2, a HECT E3 ligase, is critical for their functions to suppress G-quadruplex (G4) DNA. HERC2 interacts with BLM, WRN, and replication protein A (RPA) complexes during S-phase of the cell cycle. Depletion of HERC2 dissociates RPA from BLM and WRN complexes and significantly increases G4 formation. Triple depletion revealed that HERC2 has an epistatic relationship with BLM and WRN in their G4- suppressing function. In vitro, HERC2 releases RPA onto single-stranded DNA (ssDNA), rather than anchoring onto RPA-coated ssDNA. CRISPR/Cas9-mediated deletion of the catalytic ubiquitin-binding site of HERC2 causes RPA accumulation in the helicase complexes and increases G4, indicating an essential role for E3 activity in G4 suppression. Both HERC2 depletion and E3 inactivation sensitize cells to the G4-interacting compounds, telomestatin and pyridostatin. Overall, HERC2 is a master regulator of G4 suppression and affects the sensitivity of cells to G4 stabilizers.

molecular biology↗

bioRxiv2018

Soil nutrient stoichiometry affects the initial response of microbial community to trophic perturbation.

Soil microbes are drivers of global ecosystem functionality and are continuously subjected to external perturbations. It is fundamental for ecologists and environmental scientists to understand and further predict the microbes responses to these perturbations. A major and ubiquitous perturbation is the addition of chemical nutrients, including fertilizers and animal urine, to soil. Recent biogeographical studies suggest that soil nutrient stoichiometry (i.e., nutritional balance) determines microbial community structure and its functions with regard to material circulation. Given this information, here, we show that soil nutrient stoichiometry, or the bioavailable C:P ratio, determines the impact of nutrient addition on the soils microbial communities. We sampled two soils with similar carbon and nitrogen concentrations but with a 20-fold difference in phosphorus bioavailability. Soil microcosms with carbon and nitrogen amendments were constructed for both the soils. The phosphorus-depleted soil received prolonged effect from carbon and nitrogen amendments: the phosphatase activity gradually increased over a 24-day incubation period and the microbial community structure did not present recovery to its initial state. In contrast, in the other soil, both phosphatase activity and microbial community structure gradually returned to those of the control samples. Phosphorus depletion mitigated carbon and nitrogen intake; therefore, the effects of carbon and nitrogen amendment lasted longer. Our results demonstrate that nutritional stoichiometry is a strong predictor of microbial community dynamics in response to trophic perturbation, particularly when considering the length of time the trait of perturbation persists in the soil.

ecology↗