Biology subjects

Hamada, N.

Publications and source records attributed to Hamada, N..

6 recordsLinked to original sources

bioRxiv2025

Dynamic ASK1 proximity networks uncover SCF-dependent and noncanonical roles in ABA and drought adaptation

Plants rely on rapid proteome remodeling to withstand fluctuating environmental conditions, yet how the ubiquitin system dynamically coordinates these multilayered responses remains unclear. Here we define the in vivo proximity interactome of ARABIDOPSIS SKP1-LIKE 1 (ASK1), the core adaptor of SCF ubiquitin ligases, under acute abscisic acid (ABA) signaling and prolonged drought. TurboID-based proximity labeling coupled with quantitative proteomics revealed that ASK1 assembles highly condition-specific protein networks, distinguishing canonical SCF modules from broader noncanonical associations with transcriptional, chromatin, translational, vesicle-trafficking, and proteostasis machinery. Acute ABA exposure rapidly recruits F-box proteins and ABA-responsive transcription factors while engaging ribosomal and chromatin modules, whereas drought drives ASK1 into expanded proteostasis and stress-signaling assemblies, including chaperone-cochaperone systems, transcriptional repressors, and autophagy-endomembrane components. Global proteomics shows that ASK1 overexpression enhances accumulation of drought-protective and ABA-responsive proteins while repressing immune and ROS-scavenging pathways, indicating a shift in resource allocation. Together, these results describe ASK1 as a multifunctional proteostasis and signaling hub that integrates SCF-dependent and SCF-independent pathways to coordinate transcriptional, translational, and proteolytic reprogramming during plant adaptation to stress.

plant biology↗

bioRxiv2022

Transfer learning of an in vivo-derived senescence signature identifies conserved and tissue-specific senescence across species and diverse pathologies

Senescent cells (SnCs) contribute to normal tissue development and repair but accumulate with aging where they are implicated in a number of pathologies and diseases. Despite their pathological role and therapeutic interest, SnC phenotype and function in vivo remains unclear due to the challenges in identifying and isolating these rare cells. Here, we developed an in vivo-derived senescence gene expression signature using a model of the foreign body response (FBR) fibrosis in a p16Ink4a-reporter mouse, a cell cycle inhibitor commonly used to identify SnCs. We identified stromal cells (CD45-CD31- CD29+) as the primary p16Ink4a expressing cell type in the FBR and collected the cells to produce a SnC transcriptomic signature with bulk RNA sequencing. To computationally identify SnCs in bulk and single-cell data sets across species and tissues, we used this signature with transfer learning to generate a SnC signature score (SenSig). We found senescent pericyte and cartilage-like fibroblasts in newly collected single cell RNAseq (scRNASeq) data sets of murine and human FBR suggesting populations associated with angiogenesis and secretion of fibrotic extracellular matrix, respectively. Application of the senescence signature to human scRNAseq data sets from idiopathic pulmonary fibrosis (IPF) and the basal cell carcinoma microenvironment identified both conserved and tissue-specific SnC phenotypes, including epithelial-derived basaloid and endothelial cells. In a wound healing model, ligand-receptor signaling prediction identified putative interactions between SnC SASP and myeloid cells that were validated by immunofluorescent staining and in vitro coculture of SnCs and macrophages. Collectively, we have found that our SenSig transfer learning strategy from an in vivo signature outperforms in vitro-derived signatures and identifies conserved and tissue-specific SnCs and their SASP, independent of p16Ink4a expression, and may be broadly applied to elucidate SnC identity and function in vivo.

bioengineering↗

bioRxiv2021

Functionalizing silica sol-gel with entrapped plant virus-based immunosorbent nanoparticles

Advancements in understanding and engineering of virus-based nanomaterials (VBNs) for biomedical applications motivate a need to explore the interfaces between VBNs and other biomedically-relevant chemistries and materials. While several strategies have been used to investigate some of these interfaces with promising initial results, including VBN-containing slow-release implants and VBN-activated bioceramic bone scaffolds, there remains a need to establish VBN-immobilized three dimensional materials that exhibit improved stability and diffusion characteristics for biosensing and other analyte-capture applications. Silica sol-gel chemistries have been researched for biomedical applications over several decades and are well understood; various cellular organisms and biomolecules (e.g., bacteria, algae, enzymes) have been immobilized in silica sol-gels to improve viability, activity, and form factor (i.e., ease of use). Here we present the immobilization of an antibody-binding VBN in silica sol-gel by pore confinement. We have shown that the resulting system is sufficiently diffuse to allow antibodies to migrate in and out of the matrix. We also show that the immobilized VBN is capable of antibody binding and elution functionality under different buffer conditions for multiple use cycles. The promising results of the VBN and silica sol-gel interface indicate a general applicability for VBN-based bioseparations and biosensing applications.

bioengineering↗

bioRxiv2021

A temporally controlled sequence of X-chromosomeinactivation and reactivation defines female mouse in vitro germ cells with meiotic potential

The early mammalian germ cell lineage is characterized by extensive epigenetic reprogramming, which is required for the maturation into functional eggs and sperm. In particular, the epigenome needs to be reset before parental marks can be established and then transmitted to the next generation. In the female germ line, reactivation of the inactive X-chromosome is one of the most prominent epigenetic reprogramming events, and despite its scale involving an entire chromosome affecting hundreds of genes, very little is known about its kinetics and biological function. Here we investigate X-chromosome inactivation and reactivation dynamics by employing a tailor-made in vitro system to visualize the X-status during differentiation of primordial germ cell-like cells (PGCLCs) from female mouse embryonic stem cells (ESCs). We find that the degree of X-inactivation in PGCLCs is moderate when compared to somatic cells and characterized by a large number of genes escaping full inactivation. Nevertheless, PGCLCs that fail to undergo X-inactivation show an abnormal gene expression signature and deficiencies in meiotic entry. Subsequent to X-inactivation we observe gradual step-wise X-reactivation, which is mostly completed by the end of meiotic prophase I. Cells deviating from these progressive kinetics and undergoing X-reactivation too rapidly fail to enter a meiotic trajectory. Our data reveals that a fine-tuned X-inactivation and -reactivation cycle is a critical feature of female germ cell developmental competence towards meiosis and oogenesis

developmental biology↗

bioRxiv2020

Contrasting beta-diversity and functional composition of aquatic insect communities across local to regional scales in Amazonian streams

We investigated how components of beta diversity (i.e., the turnover and nestedness and functional compositional) aquatic insect assemblages change among sites and are influenced by environmental and spatial drivers. For this, we analyzed beta-diversity and functional composition of Ephemeroptera, Plecoptera, and Trichoptera in 16 streams in two Amazonian basins with distinct environmental conditions (the Carajas and Tapajos regions). We performed Multiple regression on dissimilarity matrices (MRM) and Procrustes analysis to test spatial and environmental influences on the taxonomic and functional composition of communities. Community dissimilarity was most related to variations in geographic distance and topography, which highlighted the environmental distances shaping the communities. Variation in functional composition could be mostly attributed to the replacement of species by those with similar traits, indicating trait convergence among communities. Environmental predictors best-explained species replacement and trait congruence within and between the regions evaluated. In summary, among communities with different taxonomic compositions, the high species replacement observed appears to be leading them to have similar community structure, with species having the same functional composition, even in communities separated by both small and large geographic distances.

ecology↗

bioRxiv2017

Neutrophil elastase inhibitor sivelestat ameliorates gefitinib-naphthalene-induced acute pneumonitis in mice

Background and objectiveGefitinib, an epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI), is an effective therapeutic agent for non-small cell lung cancer with EGFR mutations. It can cause severe acute pneumonitis in some patients. We previously demonstrated that mice with naphthalene-induced airway epithelial injury developed severe gefitinib-induced pneumonitis and that neutrophils played important roles in the development of the disease. This study aimed to investigate the effects of the neutrophil elastase inhibitor sivelestat on gefitinib-induced pneumonitis in mice.\n\nMethodsC57BL/6J mice received naphthalene (200 mg/kg) intraperitoneally on day 0. Gefitinib (250 or 300 mg/kg) was orally administered to mice from day -1 until day 13. Sivelestat (150 mg/kg) was administered intraperitoneally from day 1 until day 13. Bronchoalveolar lavage fluid (BALF) and lung tissues were sampled on day 14.\n\nResultsSivelestat treatment significantly reduced the protein level, neutrophil count, neutrophil elastase activity in BALF, and severity of histopathologic findings on day 14 for mice administered with 250 mg/kg of gefitinib. Moreover, sivelestat treatment significantly improved the survival of mice administered with 300 mg/kg of gefitinib. Conclusions: These results indicate that sivelestat is a promising therapeutic agent for severe acute pneumonitis caused by gefitinib.\n\nSummary statementNeutrophil elastase inhibitor sivelestat is a promising therapeutic agent for severe acute pneumonitis caused by gefitinib.

pharmacology and toxicology↗