Biology subjects

Araki, N.

Publications and source records attributed to Araki, N..

7 recordsLinked to original sources

bioRxiv2026

Network-based integration of cross-dataset proteomic profiles using fold-change directionality

MotivationThe rapid expansion of proteomic data has created new opportunities for large-scale integrative analyses. However, substantial variability across platforms, experimental designs, and processing pipelines limits direct quantitative comparisons among studies. Differential proteomic changes between conditions are often considered to be more reproducible than absolute abundances and may therefore provide a robust basis for cross-dataset integration. However, the systematic ability of differential change-based approaches to capture biologically meaningful relationships across heterogeneous datasets remains unclear. ResultsWe developed a differential-change framework and applied it to public proteomic datasets. Pairwise contrasts were defined as differential proteomic profiles, and the concordance of up- and down-regulated proteins was quantified using odds ratios. Significant profile pairs were visualized as an integrative network. The treatment of anti-cancer drug doxorubicin vs control (MCF-7) comparison emerged as a central hub, with breast cancer proteome profiles clustering around it and associating with tumor stage (p = 0.03). Enrichment analysis revealed overrepresentation of lipid- and cholesterol-related pathways. Availability and implementationThe source code for proteome network integration is available at https://github.com/manakanishizaki/proteome-network-integration.git.

bioinformatics↗

bioRxiv2025

Design Guidelines for Dry Electrode Tip Geometry in Electroencephalography Measurements: A Proposal Based on the Scalp's Mechanical Response

In electroencephalography (EEG) measurements using dry electrodes, a trade-off between signal stability and user comfort is a critical barrier to long-term, wearable applications. While various approaches have been proposed to address this issue, the mechanical impact of electrode tip geometry has not been adequately quantified, and most existing evaluations predominantly rely on subjective assessments. To address this gap with a quantitative, mechanics-based framework, the current study aimed to identify an optimized electrode tip geometry that minimizes mechanical stress on the scalp even under tilted contact conditions. Finite element analysis was conducted using strain energy density (SED)-- a mechanical index known to correlate with neural impulse activity--as a quantitative indicator of the mechanical influence of tip geometry on the skin. Six types of electrode tip geometries, ranging from flat to hemispherical, were defined based on the ratio of fillet radius to prong radius. These geometries were analyzed under inclination angles from 0{degrees} to 5{degrees}, and their peak SED values were compared. Additionally, a geometry optimization using an iterative search algorithm was performed to minimize peak SED under the 5{degrees} tillt. The findings revealed that intermediate fillet geometries with gently rounded edges more effectively reduce peak SED under inclined conditions. Optimization further identified a geometry ratio of [Formula] as the most effective tip geometry for minimizing mechanical loading under the specified conditions. These results offer a potential geometric design guideline for dry EEG electrodes that can help maintain user comfort across varying inclination angles.

bioengineering↗

bioRxiv2024

UniScore, a unified and universal measure for peptide identification by multiple search engines

We propose UniScore as a metric for integrating and standardizing the outputs of multiple search engines in the analysis of data-dependent acquisition (DDA) data from LC/MS/MS-based bottom-up proteomics. UniScore is calculated from the annotation information attached to the product ions alone by matching the amino acid sequences of candidate peptides suggested by the search engine with the product ion spectrum. The acceptance criteria are controlled independently of the score values by using the false discovery rate based on the target-decoy approach. Compared to other rescoring methods that use deep learning-based spectral prediction, larger amounts of data can be processed using minimal computing resources. When applied to large-scale global proteome data and phosphoproteome data, the UniScore approach outperformed each of the conventional single search engines examined (Comet, X! Tandem, Mascot and MaxQuant). Furthermore, UniScore could also be directly applied to peptide matching in chimeric spectra without any additional filters.

bioinformatics↗

bioRxiv2024

Live-cell imaging and CLEM reveal the existence of ACTN4-dependent ruffle-edge lamellipodia acting as a novel mode of cell migration

-Actinin-4 (ACTN4) expression levels are correlated with the invasive and metastatic potential of cancer cells; however, the underlying mechanism remains unclear. Here, we identified ACTN4-localized ruffle-edge lamellipodia using live-cell imaging and correlative light and electron microscopy (CLEM). BSC-1 cells expressing EGFP-ACTN4 showed that ACTN4 was most abundant in the leading edges of lamellipodia, although it was also present in stress fibers and focal adhesions. ACTN4 localization in lamellipodia was markedly diminished by phosphoinositide 3-kinase inhibition, whereas its localization in stress fibers and focal adhesions remained. Furthermore, overexpression of ACTN4, but not ACTN1, promoted lamellipodial formation. Live-cell analysis demonstrated that ACTN4-enriched lamellipodia are highly dynamic and associated with cell migration. CLEM revealed that ACTN4-enriched lamellipodia exhibit a characteristic morphology of multilayered ruffle-edges that differs from canonical flat lamellipodia. Similar ruffle-edge lamellipodia were observed in A549 and MBA-MD-231 invasive cancer cells. ACTN4 knockdown suppressed the formation of ruffle-edge lamellipodia and cell migration during wound healing in A549 monolayer cultures. Additionally, membrane-type 1 matrix metalloproteinase was observed in the membrane ruffles, suggesting that ruffle-edge lamellipodia have the ability to degrade the extracellular matrix and may contribute to active cell migration/invasion in certain cancer cell types.

cell biology↗

bioRxiv2022

AT-hook DNA-binding motif-containing protein one knockdown downregulates EWS-FLI1 transcriptional activity in Ewings sarcoma cells

Ewings sarcoma is the second most common bone malignancy in children or young adults and is caused by an oncogenic transcription factor by a chromosomal translocation between the EWSR1 gene and the ETS transcription factor family. However, the transcriptional mechanism of EWS-ETS fusion proteins is still unclear. To identify the transcriptional complexes of EWS-ETS fusion transcription factors, we applied a proximal labeling system called BioID in Ewings sarcoma cells. We identified AHDC1 as a proximal protein of EWS-ETS fusion proteins. AHDC1 knockdown showed a reduced cell growth and transcriptional activity of EWS-FLI1. AHDC1 knockdown also reduced BRD4 and BRG1 protein levels, both known as interacting proteins of EWS-FLI1. In addition, AHDC1 co-localized with BRD4. Our results suggest that AHDC1 supports cell growth through EWS-FLI1.

cancer biology↗

bioRxiv2021

Water droplet-in-oil digestion method for single-cell proteomics

Recent advances in single-cell proteomics highlight the promise of sensitive analyses in limited cell populations. However, technical challenges remain for sample recovery, throughput, and versatility. Here, we first report a water droplet-in-oil digestion (WinO) method based on carboxyl-coated beads and phase transfer surfactants for proteomic analysis using limited sample amounts. This method was developed to minimize the contact area between the sample solution and the container to reduce the loss of proteins and peptides by adsorption. This method increased protein and peptide recovery 10-fold as well as the number of quantified transmembrane proteins compared to an in-solution digestion (ISD) method. The proteome profiles obtained from 100 cells using the WinO method highly correlated with those from 10000 cells using the ISD method. We successfully applied the WinO method to single-cell proteomics and quantified 462 proteins. Using the WinO method, samples can be easily prepared in a multi-well plate, making it a widely applicable and suitable method for single-cell proteomics.

systems biology↗

bioRxiv2021

Rab10-positive tubular structures represent a novel endocytic pathway that diverges from canonical macropinocytosis in RAW264 macrophages

Using the optogenetic photo-manipulation of photoactivatable (PA)-Rac1, remarkable cell surface ruffling and the formation of a macropinocytic cup (premacropinosome) could be induced in the region of RAW264 macrophages irradiated with blue light due to the activation of PA-Rac1. However, the completion of macropinosome formation did not occur until Rac1 was deactivated by the removal of the light stimulus. Following PA-Rac1 deactivation, some premacropinosomes closed into intracellular macropinosomes, whereas many others transformed into long Rab10-positive tubules without forming typical macropinosomes. These Rab10-positive tubules moved centripetally towards the Golgi region along microtubules. Surprisingly, these Rab10-positive tubules did not contain any endosome/lysosome compartment markers, such as Rab5, Rab7, or LAMP1, suggesting that the Rab10-positive tubules were not part of the degradation pathway for lysosomes. These Rab10-positive tubules were distinct from recycling endosomal compartments, which are labeled with Rab4, Rab11, or SNX1. These findings suggested that these Rab10-positive tubules belonged to a novel, non-degradative, endocytic pathway. The formation of Rab10-positive tubules from premacropinosomes was also observed in control and phorbol myristate acetate (PMA)-stimulated macrophages, although their frequencies were low. Interestingly, the formation of Rab10-positive premacropinosomes and tubules was not inhibited by phosphoinositide 3-kinase (PI3K) inhibitors, while the classical macropinosome formation requires PI3K activity. Thus, this study provides evidence to support the existence of Rab10-positive tubules as a novel, non-degradative, endocytic pathway that diverges from canonical macropinocytosis.

cell biology↗