Biology subjects

Fujibuchi, W.

Publications and source records attributed to Fujibuchi, W..

4 recordsLinked to original sources

bioRxiv2021

eSPRESSO: a spatial self-organizing-map clustering method for single-cell transcriptomes of various tissue structures using graph-based networks

Animal cells are spatially organized as tissues and cellular gene expression data contain such information that governs body structure and morphogenesis during developmental process. Although several computational tissue reconstruction methods using transcriptomic data have been proposed, those methods are insufficient with regard to arranging cells in their correct positions in tissues or organs unless spatial information is explicitly provided. Here, we propose eSPRESSO, a powerful in silico three-dimensional (3D) tissue reconstruction method using stochastic self-organizing map (stochastic-SOM) clustering, together with optimization of gene set by Markov chain Monte Carlo (MCMC) framework, to estimate the spatial domain structure of cells in any topology of tissues or organs from only their transcriptome profiles. We confirmed the performance of eSPRESSO by mouse embryo, embryonic heart, adult cortical layers, and human pancreas organoid with high reproducibility (success rate = 72.5-100%), while discovering morphologically important spatial discriminator genes (SDGs). Furthermore, we applied eSPRESSO to analysis of human adult heart diseases by virtual gene knockouts, and revealed candidate mechanisms of deformation of heart structure. The eSPRESSO may provide novel methods to analyze the mechanisms of 3D structure formation and morphology-based disease mechanisms.

bioinformatics↗

bioRxiv2020

scMontage: Fast and Robust Gene Expression Similarity Search for Massive Single-cell Data

Single-cell RNA-seq (scRNA-seq) analysis is widely used to characterize cell types or detect heterogeneity of cell states at much higher resolutions than ever before. Here we introduce scMontage (https://scmontage.stemcellinformatics.org), a gene expression similarity search server dedicated to scRNA-seq data, which can rapidly compare a query with thousands of samples within a few seconds. The scMontage search is based on Spearmans rank correlation coefficient and its robustness is ensured by introducing Fishers Z-transformation and Z-test. Furthermore, search results are linked to a human cell database SHOGoiN (http://shogoin.stemcellinformatics.org), which enable users to fast access to additional cell-type specific information. The scMontage is available not only as a web server but also as a stand-alone application for users own data, and thus it enhances the reliability and throughput of cell analysis and helps users gain new insights into their research.

bioinformatics↗

bioRxiv2020

Integrated Collection of Stem Cell Bank data, a data portal for standardized stem cell information

The last decade has witnessed an extremely rapid increase in the number of newly established stem cell lines. However, due to the lack of a standardized format, data exchange among stem cell line resources has been challenging, and no system can search all stem cell lines across resources worldwide. To solve this problem, we have developed Integrated Collection of Stem Cell Bank data (ICSCB) (http://icscb.stemcellinformatics.org/), the largest database search portal for stem cell line information, based on the standardized data items and terms of the MIACARM framework. Currently, ICSCB can retrieve >16,000 cell lines from four major data resources in Europe, Japan, and the United States. ICSCB is automatically updated to provide the latest cell line information, and its integrative search helps users collect cell line information for over 1,000 diseases including many rare diseases worldwide, which has been a formidable task, thereby distinguishing itself from other database search portals.

bioinformatics↗

bioRxiv2020

Cell Pluripotency and Its Effect on Sensitivity to Chemical Exposure

Pluripotent stem cells (PSCs) possess unique characteristics that distinguish them from other cell types. Human embryonic stem (ES) cells are recently gaining attention as a powerful tool for human toxicity assessment without the use of experimental animals, and an embryonic stem cell test (EST) was introduced for this purpose. However, human PSCs have not been thoroughly investigated in terms of drug resistance or compared with other cell types or cell states, such as naive state, to date. Aiming to close this gap in research knowledge, we assessed and compared several human PSC lines for their resistance to drug exposure. Firstly, we report that RIKEN-2A human induced pluripotent stem (iPS) cells possessed approximately the same sensitivity to selected drugs as KhES-3 human ES cells. Secondly, both ES and iPS cells were several times less resistant to drug exposure than other non-pluripotent cell types. Finally, we showed that iPS cells subjected to naive-state induction procedures exhibited a sharp increase in drug sensitivity. Upon passage of these naive-like cells in non-naive PSC culture medium, their sensitivity to drug exposure decreased. We thus revealed differences in sensitivity to drug exposure among different types or states of PSCs and, importantly, indicated that naive-state induction could increase this sensitivity.

pharmacology and toxicology↗