Biology subjects

Fukushima, T.

Publications and source records attributed to Fukushima, T..

14 recordsLinked to original sources

bioRxiv2026

Midbody inheritance predicts re-entry into quiescence, but not lineage potential, in mouse hematopoietic stem cells

Hematopoietic stem cells (HSCs) give rise to all blood cell lineages and possess long-term self-renewal potential. HSCs undergo symmetric division for their expansion and asymmetric division to generate one HSCs and one progenitor cells which contribute to production of mature blood cells. The midbody is a structure which is formed in the center of the intercellular bridge during cytokinesis. However, the midbody is either asymmetrically inherited by one daughter cell or symmetrically released after cell division, whether these distinct patterns of midbody inheritance influence HSC fate remain poorly understood. In this study, we designed a fusion protein hmKO2 and MgcRacGAP which is a component of midbody. We then traced the midbody inheritance during cell division and the future cell fates of HSC daughters after division by time-lapse imaging. As a result, we found that the midbody release correlated with the delay of the time to the next division but not to the lineage potential of HSCs, indicating the possibility that midbody remnant plays some roles in cell cycle progression. HighlightHematopoietic stem cells exhibit a low frequency of midbody inheritance. Midbody inheritance does not affect the lineage potential of daughter cells. Midbody loss is associated with delayed entry into the next cell cycle.

cell biology↗

bioRxiv2026

DNA barcoding-based paired daughter cell analysis reveals division preferences of hematopoietic stem cells

Hematopoietic stem cells(HSCs) maintain their pools by stem-stem division and produce mature blood cells through stem-progenitor or progenitor-progenitor division. A paired daughter cell(PDC) assay combined with single cell transplantation is a powerful method to compare the lineage outputs of two HSC daughter cells. However, single-cell transplantation precludes large-scale analysis of daughter-cell pairs, as only one cell can be transplanted per recipient. Here, we developed a DNA barcoding-based PDC assay to overcome this limitation, enabling simultaneous analysis of 476 daughter pairs from individual HSC divisions and revealing that daughter-cell fates are coordinated and that HSC division patterns are biased toward stem-stem and progenitor-progenitor divisions rather than stem-progenitor divisions. These findings indicate that HSC fate outcomes are directed toward symmetric division outcomes. Integration of single-cell RNA sequencing with DNA barcoding revealed a continuum of HSC states--from balanced HSCs to myeloid-biased HSCs and ultimately to a low-output HSC subset--in which progressively reduced production of mature blood cells relative to stem cell expansion, a proxy for stem-stem division bias, exhibits distinct activities of transcription factors and signaling pathways. Overall, our analysis uncovers characteristic patterns of HSC division and links stem maintenance with distinct molecular features.

cell biology↗

bioRxiv2026

ACE2 associates with insulin-responsive GLUT4 dynamics in adipocytes

Angiotensin-converting enzyme 2 (ACE2) is expressed in adipocytes, yet the mechanisms regulating its intracellular trafficking remain unclear. Here, we investigated whether ACE2 trafficking is coordinated with insulin-responsive vesicle dynamics mediated by the glucose transporter GLUT4 in 3T3L1 adipocytes. Subcellular localization analyses revealed that adipocyte differentiation promotes partial incorporation of ACE2 into insulin-responsive GLUT4-associated vesicular compartments, whereas ACE2 displayed a diffuse distribution in fibroblasts lacking a mature GLUT4 trafficking system. Reconstitution of insulin-responsive GLUT4 vesicle formation through exogenous expression of Sortilin and AS160 in fibroblasts was sufficient to partially recruit ACE2 into perinuclear GLUT4-positive compartments, indicating dependence on canonical GLUT4 vesicle machinery. NanoBiT assays demonstrated a regulated association between ACE2 and GLUT4 that was modestly enhanced by acute insulin stimulation but reduced following prolonged insulin exposure. Insulin stimulation also produced a slight increase in ACE2 surface exposure, while association with GLUT4 was accompanied by reduced ACE2 shedding, suggesting that recruitment into distinct trafficking routes may alter ACE2 accessibility to shedding machinery in adipocytes. Structural modeling further suggested that ACE2 and GLUT4 can form a membrane-compatible complex. Together, these findings indicate that ACE2 trafficking is coordinated with insulin-responsive GLUT4 vesicle dynamics, revealing a previously unrecognized association between metabolic signaling and ACE2 cellular dynamics in adipocytes, with potential implications for metabolic dysfunction and ACE2-associated disease processes.

cell biology↗

bioRxiv2025

Molecular bases for USP48 cis-activity regulation and hyperactivation by Cushing's disease-associated mutations

Ubiquitin-specific protease 48 (USP48) is a deubiquitinating enzyme involved in various pathophysiological processes, including DNA repair, tumorigenesis, and inflammation. Somatic mutations in USP48 (M415I/V) are associated with pituitary tumors in Cushings disease. These variants lead to increased USP48 enzyme activity and adrenocorticotropic hormone (ACTH) hypersecretion, a key feature of Cushings disease, indicating a direct link to the condition. Using biochemical experiments and in silico structural analyses, we identified Y414 in the catalytic USP domain as a critical residue for USP48 activity. In the wild-type USP domain, the Y414 side chain was oriented to closed, which led to catalytic triad misalignment and weak ubiquitin recognition. We also found that the C-terminal region (CTR) of USP48 is a cis-activating region. It interacts with the USP domain and ubiquitin tail, thereby facilitating the alignment of the catalytic triad and enhancing ubiquitin recognition ability. Additionally, genomic analyses of pituitary tumors in Japanese patients with Cushings disease (n=46) confirmed that USP48 M415I/V variants occurred at a frequency of 10%, which is consistent with previous reports. Our structural model suggests that M415I/V sterically interferes with and fixes the closed Y414 side chain to open, resulting in catalytic triad alignment and increased ubiquitin recognition ability. Furthermore, USP48 with M415I/V showed enhanced CTR-mediated activity, indicating that the open Y414 side chain and CTR can cause hyperactivation. This study provides a molecular basis for the novel cis-activation regulation of USP48 and its hyperactivation by Cushings disease-associated variants. Significance StatementThe regulatory mechanisms of DUB activity are not yet fully understood. This study identifies the CTR of USP48 as an activity-promoting region, a mechanism also present in USP7 and potentially other closely related DUBs such as USP40 and USP47. Despite the disease association of some DUBs, developing drugs to inhibit specific DUB members or variants remains challenging. The substitutions of USP48 M415 embedded in the USP domain to Ile/Val are associated with Cushings disease, which lacks adequate targeted therapeutics. This study reveals that these variants alter the orientation of Y414, leading to hyperactivation. These findings provide a molecular basis for developing USP48M415I/V-specific inhibitors for Cushings disease therapy.

molecular biology↗

bioRxiv2025

Differentiation stage-specific use of cap-independent and cap-dependent translation initiation in hematopoiesis

Cell stress can increase the use of m7G-cap-independent, IRES-mediated translation initiation relative to cap-dependent translation (IRES/Cap). Reporters that quantify IRES/Cap have demonstrated differential activity across cultured cell types and stress conditions. By generating an IRES/Cap reporter mouse, we were able to systematically evaluate IRES/Cap across distinct tissues and cell types during physiological stresses and lineage commitment. Caloric stress invoked the expected boost in IRES/Cap translation regardless of differentiation state, but unexpectedly IRES/Cap progressively increased during hematopoietic and epithelial (hair follicle) differentiation under normal, homeostatic conditions. This was independent of total protein output or cell cycle. Even within cells of a given differentiation state, cells with lower relative-IRES utilization had markedly higher multipotent capability in vivo. The RNA processing protein PTBP1 is a mediator of this translation initiation preference. Therefore, low IRES/Cap is a signature of high stemness and suggests modulation of translation initiation participates in cell differentiation state.

developmental biology↗

bioRxiv2025

Plcl1 Regulates Hematopoietic Stem Cell Function During Aging and Stress by Modulating Calcium Dynamics

Long-term hematopoietic stem cells (HSCs) can generate all blood lineages but typically remain quiescent, becoming activated only in response to acute stress. We previously demonstrated that quiescent HSCs exhibit heterogeneity in intracellular calcium levels. However, the mechanisms underlying this heterogeneity and its physiological relevance remain unclear. Herein, we identify phospholipase C-like 1 (Plcl1), a noncatalytic protein that binds inositol 1,4,5-trisphosphate (IP3), as being selectively enriched in the most quiescent HSC subset. Loss-of-function studies revealed that Plcl1 deficiency at steady state reduced basal intracellular calcium levels and skewed the HSC compartment toward CD41 subsets while preserving overall HSC numbers and long-term reconstitution capacity. Under acute hematopoietic stress, Plcl1 loss accelerated and amplified platelet rebound and the expansion of non-canonical megakaryocyte progenitors (ncMkPs), indicating activation of the thrombopoietic bypass pathway. In aged HSCs, Plcl1 deficiency exacerbated aging-related features, including expansion of the HSC pool, accumulation of CD41 HSCs and ncMkPs, and myeloid-skewed differentiation with impaired competitive reconstitution. These changes were accompanied by diminished induction of calcium-responsive immediate-early genes. Collectively, we identified Plcl1 as an intrinsic regulator that stabilizes calcium dynamics in HSCs, thereby restraining stress- and aging-associated megakaryocytic priming and preserving stem cell function.

cell biology↗

bioRxiv2025

Gag ubiquitination facilitates ALIX-mediated lentiviral RNA packaging, counteracted by USP8

Lentiviral Gag protein plays an integral role in viral assembly. In host cells, Gag multimerizes, recruits host budding factors, and buds from the plasma membrane. Additionally, it binds to viral genomic RNA (vRNA) and facilitates its packaging into viral particles. However, the mechanisms regulating Gag-vRNA interactions remain poorly understood. Previous studies have suggested that Gag ubiquitination influences viral infectivity. In this study, we elucidated a new mechanism by which Gag-vRNA interactions are regulated via Gag ubiquitination. Using an HIV-1-derived lentiviral vector system, we found that ubiquitin-specific protease 8 (USP8), a deubiquitinating enzyme involved in antiviral responses, reduced the vRNA content in virions through its catalytic activity. USP8 deubiquitinates Gag, and mutations at the Gag ubiquitination sites similarly impair vRNA packaging. We hypothesized that Gag ubiquitination enhances its interaction with RNA-binding proteins, thereby facilitating Gag-vRNA binding. We focused on ALG-2-interacting protein X (ALIX), which interacts with Gag, ubiquitin, and RNA. Mechanistic analyses revealed that Gag ubiquitination promotes its interaction with ALIX, which in turn binds to vRNA. In ALIX knockout (KO) cells, both Gag-vRNA binding and vRNA packaging were reduced, confirming the role of ALIX in this process. Furthermore, the deubiquitinating activity of USP8 suppressed Gag-vRNA binding, and this effect was abolished by mutation of the Gag ubiquitination site or ALIX KO. Collectively, these results reveal a new regulatory mechanism for lentiviral assembly, in which Gag ubiquitination facilitates ALIX-mediated vRNA packaging and is counteracted by USP8. Significance StatementLentiviral Gag-vRNA binding and vRNA packaging are essential for viral particle formation; however, their regulation remains unclear. We identified a USP8-Gag-ALIX axis that controls this process. USP8, a host deubiquitinating enzyme, suppresses Gag-vRNA binding by removing ubiquitin from Gag. Gag ubiquitination promotes ALIX interaction, which facilitates Gag-vRNA binding. Although ALIX is known to play a role in viral budding, we uncovered a new role for ALIX in vRNA recruitment. These findings advance our understanding of lentiviral assembly and identify USP8 and ALIX as potential targets for antiviral therapy. They may also improve lentiviral vector production by providing a molecular basis for reducing transgene-deficient particles and enhancing vector quality.

molecular biology↗

bioRxiv2025

Interrupting Elmsan1 repression of nuclear Acetyl-CoA production therapeutically reprograms cancer cells

Metabolites are essential substrates for epigenetic modifications. Although nuclear acetyl-CoA constitutes a small fraction of the whole cell pool, it regulates cell fate by locally providing histone acetylation substrate. Here, we combined phenotypic chemical screen and genome-wide CRISPR screen to demonstrate a nucleus-specific acetyl-CoA regulatory mechanism that can be modulated to achieve therapeutic cancer cell reprogramming. While previously thought that nucleus-localized pyruvate dehydrogenase complex (nPDC) is constitutively active, we found that nPDC is constitutively inhibited by the nuclear protein ELMSAN1 through direct interaction. Pharmacologic inhibition of the ELMSAN1-nPDC interaction derepressed nPDC activity, enhancing nuclear acetyl-CoA generation and reprogramming cancer cells to a postmitotic state with diminished cell-of-origin signatures. Reprogramming was synergistically enhanced by histone deacetylase 1/2 inhibition, resulting in inhibited tumor growth, durably suppressed tumor-initiating ability, and improved survival in multiple cancer types in vivo, including therapy-resistant sarcoma patient-derived xenografts and carcinoma cell line xenografts. Our findings highlight the potential of targeting ELMSAN1-nPDC as epigenetic cancer therapy.

cancer biology↗

bioRxiv2025

Hematopoietic stem cells undergo bidirectional fate transitions in vivo.

Differentiation of haematopoietic stem and progenitor cells (HSPCs) is widely considered unidirectional in vivo. Here, we developed clonal phylogenetic tracing (CP-tracer) by sequential genetic barcoding, which enabled high-resolution analysis of 181,695 subclones derived from 847 individually labelled HSPCs. This approach uncovered bidirectional fate transitions between myeloid-biased (My-) and lineage-balanced haematopoietic stem cells (HSCs). Individual HSC clones, distinguished by temporally unique serial barcodes, exhibited durable lineage bidirectionality, with dynamics favouring progressive accumulation of My-HSCs over time. CRISPR-Cas9 screening identified the homeobox gene Hhex as a suppressor of myeloid differentiation that enables pivoting toward balanced output. Hhex function is age-dependent, with its expression declining in aged HSCs. Together, these findings demonstrate unexpected plasticity in HSC differentiation, modulated in part by Hhex-mediated repression, that shifts over time to drive the myeloid bias characteristic of ageing.

cell biology↗

bioRxiv2023

The placental protein NRK promotes cell death through its plasma membrane-localizing CNH domain

Placental development is regulated by the balance between cell proliferation and death. The placental protein NRK (NIK-related kinase) plays a role in preventing excessive placenta growth. We previously demonstrated that NRK underwent rapid molecular evolution in the ancestor of placental mammals and acquired the functional regions, including the phospholipid-binding citron homology (CNH) domain, by which NRK inhibits cell proliferation. NRK is also potentially responsible for cell death; caspases cleave NRK during apoptosis, releasing the C-terminal fragment that promotes cell death. Here, we explored the molecular mechanisms underlying the cell death-promoting effects of NRK. Our experimental data using HeLa, placenta trophoblast BeWo (human), and Rcho-1 (rat) cells indicated that the CNH domain of NRK was required and sufficient to promote cell death. In vitro and in silico studies showed the NRK CNH domain bound to phospholipids via its polybasic clusters and remains at the plasma membrane (PM) during apoptosis. Evolutional analyses indicated that these clusters formed in the ancestor of placental mammals. Mutations in these clusters (CNH-18A) hindered the cell death-promoting activity of the CNH domain. We concluded that NRK promotes cell death through its plasma membrane-localizing CNH domain and suggested its active role in PM-associated events during cell death.

cell biology↗

bioRxiv2021

Placental mammals acquired the functional region and domain in NRK for regulating the CK2-PTEN-AKT pathway and placental cell proliferation

The molecular evolution processes underlying the acquisition of the placenta in eutherian ancestors are not fully understood. Mouse NCK-interacting kinase (NIK)-related kinase (NRK) is expressed highly in the placenta and plays a role in preventing placental hyperplasia. Here, we show the molecular evolution of NRK, which confers its function for inhibiting placental cell proliferation. Comparative genome analysis identified NRK orthologues across vertebrates, which share the kinase and citron homology (CNH) domains. Evolutionary analysis revealed that NRK underwent extensive amino acid substitutions in the ancestor of placental mammals and has been since conserved. Biochemical analysis of mouse NRK revealed that the CNH domain binds to phospholipids, and a region in NRK binds to and inhibits casein kinase-2 (CK2), which we named the CK2-inhibitory region (CIR). Cell culture experiments suggest the following: (1) mouse NRK is localised at the plasma membrane via the CNH domain, where the CIR inhibits CK2. (2) This mitigates CK2-dependent phosphorylation and inhibition of PTEN, and (3) leads to the inhibition of AKT signalling and cell proliferation. Nrk deficiency increased phosphorylation levels of PTEN and AKT in mouse placenta, supporting our hypothesis. Unlike mouse NRK, chicken NRK did not bind to phospholipids and CK2, decrease phosphorylation of AKT, or inhibit cell proliferation. Both the CNH domain and CIR have evolved under purifying selection in placental mammals. Taken together, our study suggests that placental mammals acquired the phospholipid-binding CNH domain and CIR in NRK for regulating the CK2-PTEN-AKT pathway and placental cell proliferation.

molecular biology↗

bioRxiv2021

The molecular basis of ubiquitin-specific protease 8 autoinhibition by the WW-like domain

Ubiquitin-specific protease 8 (USP8) is a deubiquitinating enzyme involved in multiple membrane trafficking pathways. The enzyme activity is inhibited by binding to 14-3-3 proteins, and mutations of the 14-3-3 binding motif in USP8 are related to Cushings disease. However, the molecular basis of USP8 enzyme activity regulation remains unclear. Here, we identified amino acids 645-684 of USP8 as an autoinhibitory region, which our pull-down and single-molecule FRET assay results suggested interacts with the catalytic USP domain. In silico modelling indicated that the region forms a WW-like domain structure, plugs the catalytic cleft, and narrows the entrance to the ubiquitin-binding pocket. Furthermore, 14-3-3 was found to inhibit USP8 enzyme activity partly by enhancing the interaction between the WW-like and USP domains. These findings provide the molecular basis of USP8 autoinhibition via the WW-like domain. Moreover, they suggest that the release of autoinhibition may underlie Cushings disease caused by USP8 mutations.

biochemistry↗

bioRxiv2020

A hybrid cyt c maturation system enhances the bioelectrical performance of engineered Escherichia coli by improving the rate-limiting step

Bioelectronic devices can use electron flux to enable communication between biotic components and abiotic electrodes. We have modified Escherichia coli to electrically interact with electrodes by expressing the cytochrome c from Shewanella oneidensis MR-1. However, we observe inefficient electrical performance, which we hypothesize is due to the limited compatibility of the E. coli cytochrome c maturation (Ccm) systems with MR-1 cytochrome c. Here we test whether the bioelectronic performance of E. coli can be improved by constructing hybrid Ccm systems containing protein domains from both E. coli and S. oneidensis MR-1. The hybrid CcmH increased cytochrome c expression by increasing the abundance of CymA 60%, while only slightly changing the abundance of the other cytochromes c. Electrochemical measurements showed that the overall current from the hybrid ccm strain increased 121% relative to the wildtype ccm strain, with an electron flux per cell of 12.3 {+/-} 0.3 fA{middle dot}cell-1. Additionally, the hybrid ccm strain doubled its electrical response with the addition of exogenous flavin, and quantitative analysis of this demonstrates CymA is the rate-limiting step in this electron conduit. These results demonstrate that this hybrid Ccm system can enhance the bioelectrical performance of the cyt c expressing E. coli, allowing the construction of more efficient bioelectronic devices.

bioengineering↗

bioRxiv2018

Genome-wide association meta-analysis identifies novel GP2 gene risk variants for pancreatic cancer in the Japanese population

The etiology of pancreatic cancer remains largely unknown. Here, we report the results of a meta-analysis of three genome-wide association studies (GWASs) comprising 2,039 pancreatic cancer cases and 32,592 controls, the largest sample size in the Japanese population. We identified 3 (13q12.2, 13q22.1, and 16p12.3) genome-wide significant loci (P<5.0x10-8) and 4 suggestive loci (P<1.0x10-6) for pancreatic cancer. Of these risk loci, 16p12.3 is novel; the lead SNP maps to rs78193826 (odds ratio (OR)=1.46, 95% CI=1.29-1.66, P=4.28x10-9), an Asian-specific, nonsynonymous glycoprotein 2 (GP2) gene variant predicted to be highly deleterious. Additionally, the gene-based GWAS identified a novel gene, KRT8, which is linked to exocrine pancreatic and liver diseases. The identified GP2 gene variants were pleiotropic for multiple traits, including type 2 diabetes, hemoglobin A1c (HbA1c) levels, and pancreatic cancer. Mendelian randomization analyses corroborated causality between HbA1c and pancreatic cancer. These findings suggest that GP2 gene variants are associated with pancreatic cancer susceptibility in the Japanese population, prompting further functional characterization of this locus.

genetics↗