Biology subjects

Hamada, K.

Publications and source records attributed to Hamada, K..

11 recordsLinked to original sources

bioRxiv2026

Deficiency of CD239 increases susceptibility to chronic kidney disease

CD239, also known as Lutheran blood group glycoprotein (Lu) or basal cell adhesion molecule (B-CAM), is a transmembrane protein belonging to the immunoglobulin superfamily (IgSF). CD239 serves as a specific receptor for laminin 5, a subunit of laminin-511/-521, which are major components of renal basement membranes. A previous study of another group demonstrated that CD239-null mice are healthy and develop normally. Although no alteration in renal function was observed, most glomeruli in the mutant kidneys exhibited morphological abnormalities. In this study, we investigated the role of CD239 in renal tubules. We examined the distribution of CD239 using renal tubule-specific markers. CD239 was localized to the Henle's loop, distal tubule, and collecting duct, but not to the proximal tubule. Next, we analyzed the localization of renal tubular molecules in CD239-null mice. The localization of uromodulin (UMOD) and Na-K-Cl cotransporter (NKCC2) was disrupted in the distal tubules lacking CD239, suggesting that CD239 plays a role in maintaining the polarity of renal epithelial cells. Furthermore, to examine the stability of the distal tubules, CD239-null mice were subjected to chronic kidney disease (CKD) using an adenine-rich diet. Blood analysis revealed that CD239-null mice fed an adenine diet readily developed CKD. Adenine-fed null mice exhibited more marked histological injury along the distal tubules compared to that by controls. These results indicate that CD239 is essential not only for maintaining cellular polarity but also for ensuring the stability of the distal tubules. Although CD239-null humans exhibit no obvious associated pathology, it could be a predisposition to CKD.

pathology↗

bioRxiv2025

Chemotherapy Induces an IL1β-dependent Neutrophil Recruitment that Promotes Chemoresistance in Metastatic Ovarian Cancer

High-grade serous carcinoma (HGSC) of the ovary acquires chemoresistance through diverse cancer cell-intrinsic and-extrinsic mechanisms, culminating in treatment-refractory intraperitoneal metastasis. How chemotherapy-induced remodeling of the tumor microenvironment modulates drug sensitivity remains unclear. In this study, we demonstrate that chemotherapy induced IL1{beta}-dependent neutrophil accumulation in tumors, driving chemoresistance in HGSC. Using patient samples, bulk transcriptomic profiling before and after chemotherapy revealed post-treatment upregulation of IL1B, and single-cell RNA sequencing identified myeloid cells as its principal source. In a chemoresistant murine metastatic ovarian cancer model, chemotherapy increased neutrophils and neutrophil extracellular traps (NETs) in omentum tumors; these increases were abrogated in IL1{beta}-deficient mice, with expansion of activated CD8+ T cells and tumor control. Neutrophil depletion in wild-type mice recapitulated the chemosensitive phenotype of IL1{beta}-deficient mice. In vitro, IL1{beta} did not alter cancer cell-intrinsic chemosensitivity, whereas NETs reduced the chemosensitivity of cancer cells. Additionally, the dominant IL1{beta} receptor (IL1R1) was predominantly expressed in tumor-associated fibroblasts in humans and mice. Consistently, IL1R1-deficient mice exhibited chemosensitivity with decreased neutrophil accumulation and increased IFN{gamma}TNFCD8 T cells. We also found that chemotherapy upregulated CXCL2 in patients and that ablating IL1{beta}-IL1R1 axis decreased CXCL2 expression in tumor-associated fibroblasts in mice. Finally, residual human HGSC tumor after chemotherapy showed increased neutrophils and a trend toward more NETs. Collectively, these findings illuminate a paradoxical, cancer cell-extrinsic mechanism in HGSC whereby chemotherapy itself amplifies chemoresistance and suggest that targeting chemotherapy-induced inflammation may help overcome treatment resistance.

immunology↗

bioRxiv2025

Structure and inhibition mechanism of the helicase-primase complex from human herpesvirus 1

Human herpesviruses (HHVs) are widespread pathogens causing severe diseases, especially in immunocompromised individuals, and are linked to neurodegenerative and autoimmune disorders. Current antiviral therapies primarily target the -subfamily, with limited options for {beta}- and {gamma}-subfamilies. The helicase-primase complex (HPC) is essential for viral DNA replication and represents a key antiviral target, but its structure and inhibition mechanisms were previously unclear. Here, cryo-EM structures of the HHV1 (-subfamily) HPC bound to single-stranded DNA and two clinical inhibitors, amenamevir and pritelivir, are reported. The HPC features flexible helicase and primase modules, with both inhibitors binding a shared allosteric pocket in the helicase module. Structural, biochemical, and molecular dynamics analyses indicate that these inhibitors lock the helicase in an open, inactive conformation. Combined molecular dynamics and fragment molecular orbital analyses explain the -subfamily selectivity and distinct antiviral spectra of these drugs. These findings provide a structural framework to guide the development of novel inhibitors targeting {beta}- and {gamma}-subfamily herpesviruses. SignificanceHerpesviruses are ubiquitous human pathogens responsible for a wide spectrum of diseases, including severe infections in immunocompromised individuals and associations with neurodegenerative and autoimmune disorders. Despite the clinical importance of these viruses, current antiviral therapies are largely limited to the -subfamily, with few effective options for {beta}- and {gamma}-subfamilies. The helicase-primase complex (HPC) is a critical enzyme for viral DNA replication and a validated antiviral target, yet its structural basis and inhibition mechanisms have remained elusive, hindering the rational development of next-generation therapeutics. This study provides the first high-resolution cryo-EM structures of the human herpesvirus 1 (HHV1) HPC bound to single-stranded DNA and two clinically relevant inhibitors, amenamevir and pritelivir. These structures reveal the modular organization of the HPC and identify a shared allosteric pocket where both inhibitors bind. Structural, biochemical, and molecular dynamics analyses demonstrate that these inhibitors lock the helicase in an open, catalytically inactive conformation, thereby blocking ATP binding and halting DNA unwinding. Fragment molecular orbital (FMO) calculations further elucidate the molecular determinants of inhibitor binding, explaining the -subfamily specificity and the distinct antiviral spectra of amenamevir and pritelivir. The integrated approach combining cryo-EM, molecular dynamics, and quantum chemical calculations not only clarifies the mechanism of action of current clinical inhibitors but also establishes a robust framework for the rational design of novel antivirals. By providing detailed insights into the structural and dynamic properties of the HPC and its inhibition, this work paves the way for the development of new drugs with tailored specificity and improved pharmacokinetic properties, potentially expanding therapeutic options to currently untreatable herpesvirus infections. These findings have broad implications for antiviral drug discovery and for understanding the molecular mechanisms underlying DNA replication in herpesviruses.

biochemistry↗

bioRxiv2025

Organo-metal coprecipitation contributes to stable organic carbon fraction in mangrove soil

Prediction of the impact of anthropogenic disturbances and global change on organic carbon (OC) pools in mangrove soils requires a detailed understanding of the mechanisms underlying OC stabilization. Using density fractionation to physically separate OC fractions with varying degrees of mineral association and protection, this study aimed to assess distributions of these fractions and the geochemical factors influencing the most dominant and refractory mineral-associated, high-density fraction (HF) in mangrove soil. We conducted forest-wide soil sampling in the Gaburumata mangrove forest on Ishigaki Island, Japan, along three transects (upstream, midstream, downstream) and at five depths (until 100 cm). The OC in HF (OCHF) was the oldest (median {Delta}14C value of -13.81{per thousand}) and contributed most significantly to total soil OC (43%-63%) and nitrogen (64%-85%). Among the extractable metals analyzed (aluminum [Al], iron [Fe], calcium [Ca], and magnesium [Mg]) with different crystallinity, only organically complexed Al and Fe showed strong positive correlations with OCHF. Together with high OCHF:Fe ratios that surpassed the maximum sorptive capacity of Fe oxides, these results indicate that co-precipitation of OC and Fe was the dominant mode of organo-mineral associations. The low clay content reduced the importance of Ca and Mg on OCHF, as these divalent cations typically facilitate OC stabilization through cation bridging between negatively charged clay surfaces and organic matter. Furthermore, the {Delta}14C-OC relationship suggested efficient incorporation of mangrove-derived modern C into HF, in addition to the pre-existing old C. Thus, mangrove expansion is likely to enhance stable soil OC pools in addition to increasing plant biomass and litter. Overall, this study proposes a biogeochemical mechanism for how stable mangrove OC is newly formed, as well as maintained, with ramifications for global mangrove expansion and plantation efforts.

ecology↗

bioRxiv2024

Intraperitoneal activation of myeloid cells clears ascites and reveals IL27-dependent regression of metastatic ovarian cancer

Patients with metastatic ovarian cancer (OvCa) have a 5-year survival rate of less than 30% due to persisting dissemination of chemoresistant cells in the peritoneal fluid and the immunosuppressive microenvironment in the peritoneal cavity. Here, we report that intraperitoneal administration of {beta}-glucan and IFN{gamma} (BI) induced robust tumor regression in clinically relevant models of metastatic OvCa. BI induced tumor regression by controlling fluid tumor burden and activating localized antitumor immunity. {beta}-glucan alone cleared ascites and eliminated fluid tumor cells by inducing intraperitoneal clotting in the fluid and Dectin-1-Syk-dependent NETosis in the omentum. In omentum tumors, BI expanded a novel subset of immunostimulatory IL27+ macrophages and neutralizing IL27 impaired BI efficacy in vivo. Moreover, BI directly induced IL27 secretion in macrophages where single agent treatment did not. Finally, BI extended mouse survival in a chemoresistant model and significantly improved chemotherapy response in a chemo-sensitive model. In summary, we propose a new therapeutic strategy for the treatment of metastatic OvCa.

immunology↗

bioRxiv2022

Pharmacometabolomics reveals urinary diacetylspermine as a biomarker of doxorubicin effectiveness in triple negative breast cancer

Triple-negative breast cancer (TNBC) patients receive chemotherapy treatment, including doxorubicin, due to the lack of targeted therapies. Drug resistance is a major cause of treatment failure in TNBC and therefore, there is a need to identify biomarkers that determine effective drug response. Here, a pharmacometabolomics study was performed using TNBC patient-derived xenograft models to detect urinary metabolic biomarkers of doxorubicin effectiveness. Diacetylspermine was identified as a urine metabolite that robustly changed in response to effective doxorubicin treatment, which persisted after the final dose. Diacetylspermine was directly traced back to the tumor and correlated with tumor volume. Ex vivo tumor slices revealed that doxorubicin directly increases diacetylspermine production by increasing tumor spermidine/spermine N1-acetyltransferase 1 expression and activity, which was corroborated by elevated polyamine flux. In breast cancer patients, tumor diacetylspermine was elevated compared to matched non-cancerous tissue and increased in HER2+ and TNBC compared to ER+ subtypes. In addition, 12-hour urine diacetylspermine was associated with breast cancer tumor volume and poor tumor grade. This study describes a pharmacometabolomics strategy for identifying cancer metabolic biomarkers that indicate drug response. Our findings characterize urine diacetylspermine as a non-invasive biomarker of doxorubicin effectiveness in TNBC.

cancer biology↗

bioRxiv2021

A triple-negative matrix-producing breast carcinoma is arrested by tumor-targeting Salmonella typhimurium A1-R in a PDOX model

Background/AimMatrix-producing breast carcinoma (MPBC), is a rare, recalcitrant and highly aggressive. The present study aimed to determine the efficacy of tumor-targeting Salmonella typhimurium (S. typhimurium) A1-R on a triple-negative MPBC in a patient-derived orthotopic xenograft (PDOX) model. MethodsThe PDOX model was established in the left second mammary gland of a nude mouse by surgical orthotopic implantation (SOI) of the patient triple-negative MPBC PDOX models were randomized into two groups: G1, control group (n=6); G2, tumor-targeting S. typhimurium A1-R group (n=7, intravenous (i.v.) injection via tail vein, weekly, for two weeks). All mice were sacrificed on day 15. Tumor volume and body weight were measured one time per week. ResultsS. typhimurium A1-R arrested tumor growth compared to the control group (P = 0.016). ConclusionThe results of the present study suggest that S. typhimurium A1-R has future clinical potential in triple-negative MPBC patients.

cancer biology↗

bioRxiv2021

Histone H3K4me3 and H3K9me3 are super over-methylated in soft tissue sarcoma compared to normal muscle in patient-derived xenograft (PDX) mouse models: an indicator of cancer methionine addiction

Methionine addiction is a fundamental and general hallmark of cancer discovered by us almost a half-century ago [Proc Natl Acad Sci U S A 73 (1976) 1523-1527]. Methionine addiction is defined as the requirement, specific for cancer cells of all types, for exogenous methionine despite the normal ability to synthesize methionine from homocysteine. The methionine addiction of cancer is termed the Hoffman-effect, analogous to the Warburg-effect of the high glucose requirement of cancer cells. Methionine addiction is due to excess transmethylation reactions resulting in high methionine flux in cancer cells, which causes them to selectively arrest under methionine restriction due to depletion of free methionine and S-adenosyl methionine. Recently we have shown methionine-addicted cancer cells over-methylate histone H3 lysine marks which are not over-methylated in normal cells or in low-malignancy methionine-independent revertants derived from methionine-addicted cancer cells. In the present report, we show that in patient-derived xenograft (PDX) mouse models of the most common soft tissue sarcomas: myxofibrosarcoma, undifferentiated pleomorphic sarcoma (UPS) and liposarcoma, histone H3K4me3 and H3K9me3 are super over-methylated compared to normal muscle tissue. This new result is discussed along with our previous reports, regarding the potential of histone H3 over-methylation as a basis of malignancy.

cancer biology↗

bioRxiv2020

Cancer-specific overmethylation of histone H3 lysines is necessary for methionine addiction and malignancy

Methionine addiction is a fundamental and general hallmark of cancer and is an area of current intense interest. Methionine addiction results from the overuse of methionine by cancer cells for excess transmethylation reactions. In order to identify excess transmethylation reactions in cancer and further understand the basis of methionine addiction, we compared the histone H3 lysine-methylation status and malignancy between methionine-addicted cancer cells and their methionine-independent revertants which have regained the ability to grow on low levels of methionine or independently of exogenous methionine. The levels of trimethylated histone H3 lysine marks were reduced in methionine-independent revertants compared to parental cancer cells in vitro. Tumorigenicity and experimental metastatic potential in nude mice were also highly reduced in the methionine-independent revertants compared to the parental cells. Our present results demonstrate that overmethylation of histone H3 lysines is linked with methionine addiction of cancer and to malignancy which suggests a possible causal relationship.

cancer biology↗

bioRxiv2020

Structural basis of the regulation of normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2

Dimethylated histone H3 Lys36 (H3K36me2) regulates gene expression by antagonizing the repressive effect of polycomb-group proteins. Aberrant upregulation of H3K36me2, either by overexpression or point mutations of NSD2/MMSET, an H3K36 dimethyltransferase, is found in various cancers, including multiple myeloma. To understand the mechanism underlying its regulation, here we report the cryo-electron microscopy structure of the catalytic fragment of NSD2 bound to the nucleosome at 2.8 [A] resolution. The nucleosomal DNA is partially unwrapped at superhelix location +5.5, facilitating the access of NSD2 to H3K36. NSD2 interacts with DNA and H2A along with H3. The autoinhibitory loop of NSD2 changes its conformation upon nucleosome binding to accommodate H3 in its substrate-binding cleft. Kinetic analysis revealed two oncogenic mutations, E1099K and T1150A, to aberrantly activate NSD2 by increasing its catalytic turnover but not the nucleosome affinity. Molecular dynamics simulations suggested that in both mutants, the autoinhibitory loop adopts an open state that can accommodate H3 more often than the wild type. We propose that E1099K and T1150A destabilize the interactions that keep the autoinhibitory loop closed, thereby enhancing the catalytic turnover. Our analyses would guide the development of specific inhibitors of NSD2 for the treatment of various cancers.

biochemistry↗

bioRxiv2020

Removal of repressive histone marks creates epigenetic memory of recurring heat in Arabidopsis

Acclimation to high temperature increases plants tolerance of subsequent lethal high temperatures1-3. Although epigenetic regulation of plant gene expression is well studied, how plants maintain a memory of environmental changes over time remains unclear. Here, we show that JUMONJI (JMJ) proteins4-8, demethylases involved in histone H3 lysine 27 trimethylation (H3K27me3), are necessary for Arabidopsis thaliana heat acclimation. Acclimation induces sustained H3K27me3 demethylation at key HEAT SHOCK PROTEIN (HSP) loci by JMJs, poising the HSP genes for subsequent activation. Upon sensing heat after a 3-day interval, JMJs directly reactivate HSP genes. Finally, jmj mutants fail to maintain heat memory under fluctuating field temperature conditions. Our findings of an epigenetic memory mechanism involving histone demethylases may have implications for environmental adaptation of field plants.

plant biology↗