A5059103569- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- Immune cells in cancer
- Epigenetics and DNA Methylation
- T-cell and B-cell Immunology
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Immune Cell Function and Interaction
- Genomics and Phylogenetic Studies
- Breast Lesions and Carcinomas
- Gene expression and cancer classification
- Cancer Cells and Metastasis
- Uterine Myomas and Treatments
- Histone Deacetylase Inhibitors Research
- Head and Neck Cancer Studies
- Cell death mechanisms and regulation
- Breast Cancer Treatment Studies
- Neuroendocrine Tumor Research Advances
- Genetics, Aging, and Longevity in Model Organisms
- PARP inhibition in cancer therapy
- Renal Diseases and Glomerulopathies
- Biomedical Research and Pathophysiology
- Toxin Mechanisms and Immunotoxins
- BRCA gene mutations in cancer
- Coenzyme Q10 studies and effects
The University of Tokyo
2020-2025
National Cancer Center Hospital East
2020-2025
St. Marianna University School of Medicine
2015-2022
Tohoku University
2022
Abstract Spatial transcriptomics is an emerging technology requiring costly reagents and considerable skills, limiting the identification of transcriptional markers related to histology. Here, we show that predicted spatial gene-expression in unmeasured regions tissues can enhance biologists’ histological interpretations. We developed Deep learning model for gene Clusters Expression, DeepSpaCE, confirmed its performance using spatial-transcriptome profiles immunohistochemistry images...
LSD1, a lysine-specific histone demethylase, is overexpressed in several types of cancers and linked to poor outcomes. In breast cancer, the significance LSD1 overexpression not clear. We have performed an silico analysis assess relationship expression clinical outcome. demonstrate that prognostic factor especially basal-like subtype cancer with aggressive features. This link also observed samples triple negative cancer. Interestingly, we note correlates down-regulation BRCA1 phenomenon...
Abstract In a substantial number of patients, ductal carcinoma in situ (DCIS) the breast will never progress to invasive carcinoma, and these patients are often overtreated under current clinical criteria. Although various candidate markers available, relevant for delineating risk categories have not yet been established. this study, we analyzed characteristics 431 with DCIS performed whole-exome sequencing analysis 21-patient discovery cohort targeted deep 72-patient validation cohort. We...
Long-read whole-genome sequencing analysis of DNA methylation would provide useful information on the chromosomal context gene expression regulation. Here we describe development a method that improves read length generated by using bisulfite-sequencing-based approach. In this method, combined recently developed enzymatic base conversion, where an unmethylated cytosine (C) should be converted to thymine (T), with nanopore sequencing. After methylation-sensitive library was constructed...
Exon 2 of MED12, a subunit the transcriptional mediator complex, has been frequently mutated in uterine leiomyomas and breast fibroadenomas; however, it rarely other tumors. Although mutations were also found leiomyosarcomas, frequency was significantly lower than leiomyomas. Here, we examined MED12 mutation phyllodes tumors, another biphasic tumor with epithelial stromal components related to fibroadenomas. Mutations exon analyzed nine fibroadenomas eleven tumors via Sanger sequencing. A...
The agonistic/antagonistic biocharacter of selective estrogen receptor modulators (SERMs) can have therapeutic advantages, particularly in the case premenopausal breast cancers. Although contradictory effects these been studied terms crosstalk between α (ER) and coactivator dynamics growth factor signaling, molecular basis mechanisms is still obscure. We identify a series regulatory controlling cofactor on ER SERM function, whose activities require F-box protein 22 (Fbxo22). Skp1, Cullin1,...
Chromosomal backgrounds of cancerous mutations still remain elusive. Here, we conduct the phasing analysis non-small cell lung cancer specimens 20 Japanese patients. By combinatory use short and long read sequencing data, obtain phased blocks 834 kb in N50 length with >99% concordance rate. analyzing obtained information, reveal that several genomes harbor regions which are unevenly distributed to either two haplotypes. Large-scale chromosomal rearrangement events, resemble chromothripsis...
Single-cell spatial omics analysis requires consideration of biological functions and mechanisms in a microenvironment. However, microenvironment using bioinformatic methods is limited by the need to detect histological morphology extend it surrounding area. In this study, we developed SpatialKNifeY (SKNY), an image-processing-based toolkit that detects domains potentially reflect histology extends these Using transcriptomic data from breast cancer, applied SKNY algorithm identify tumor...
// Yuko Nakagawa 1, 2, * , Anna S. Sedukhina Naoki Okamoto 2 Satoi Nagasawa 3 Nao Suzuki Tomohiko Ohta 1 Hiroyoshi Hattori 4 Marta Roche-Molina 5 Ana J. Narváez 6 Anand D. Jeyasekharan 7 Juan A. Bernal Ko Sato Department of Translational Oncology, St. Marianna University Graduate School Medicine, Kawasaki 216–8511, Japan Obstetrics and Gynecology, Division Breast Endocrine Surgery, Laboratory Advanced Therapy, Hematology Oncology Research, Clinical Research Center, National...
Cancer genome analysis using next-generation sequencing requires adequate and high-quality DNA samples. Genomic analyses were conventionally performed formalin-fixed paraffin-embedded sections rather than cytology samples such as cell block or smear specimens. Specimens collected from liquid-based (LBC) have the potential to be sources of suitable for genetic even after long-term storage.
Immune responses are different between individuals and personal health histories unique environmental conditions should collectively determine the present state of immune cells. However, molecular systems underlying such heterogeneity remain elusive. Here, we conducted a systematic time-lapse single-cell analysis, using 171 libraries 30 mass cytometry datasets intensively for seven healthy individuals. We found substantial diversity in immune-cell profiles These patterns showed daily...
Mitochonic Acid 5 (MA-5) enhances mitochondrial ATP production, restores fibroblasts from disease patients and extends the lifespan of model “Mitomouse”. Additionally, MA-5 interacts with mitofilin modulates inner membrane organizing system (MINOS) in mammalian cultured cells. Here, we used nematode Caenorhabditis elegans to investigate whether improves Duchenne muscular dystrophy (DMD) model. Firstly, confirmed efficient penetration mitochondria C. elegans. also alleviated symptoms such as...
Abstract A substantial number of cases ductal carcinoma in situ (DCIS) the breast will never progress to invasive (IDC), indicating they are overtreated under current criteria. Although various candidate markers available, relevant for delineating risk categories have not been established. In this study, we analyzed integrated clinical features 431 DCIS followed by deep sequence analyses a 21-case discovery cohort and 72-case validation cohort. We identified five most critical aggressiveness...
Single-cell spatial omics analysis requires consideration of biological functions and mechanisms in a microenvironment. However, microenvironment using bioinformatic methods is limited by the need to detect histological morphology. In this study, we developed SpatialKNife (SKNY), an image-processing-based toolkit that detects domains potentially reflect histology extends these The SKNY algorithm identified tumour from transcriptomic data breast cancer, followed clustering domains, trajectory...
Abstract The interaction of tumor cells and their microenvironment is thought to be a key factor in development. We present spatial RNA profiles obtained from 30 lung adenocarcinoma patients at the non-invasive later invasive stages. use transcriptome sequencing data conjunction with situ profiling conduct higher resolution analyses. detailed examination each case, as well subsequent computational analyses based on observed diverse profiles, reveals that significant changes phenotypic...
Immunopositivity for neuroendocrine markers [NEs: synaptophysin (syn), chromogranin A (CGA), CD56, CD57, and neuron-specific enolase] is evidence of the presence tumor cells with cell differentiation in breast. It has been reported that a certain type breast cancer immunopositive NEs; such named carcinoma endocrine features or ductal situ (E-DCIS)．Here, we report case patient whom portion E-DCIS lesion coexisted intraductal papilloma. 38-year-old woman had an irregular hypoechoic right on...
Abstract Spatial transcriptomics is an emerging technology requiring costly reagents and considerable skills, limiting the identification of transcriptional markers related to histology. Here, we show that predicted spatial gene-expressions in unmeasured regions tissues can enhance biologists’ histological interpretations. We developed Deep learning model for Spa tial gene C lusters E xpression, DeepSpaCE confirmed its performance using spatial-transcriptome profiles immunohistochemistry...
Abstract When biologically interpretation of the data obtained from single-cell RNA sequencing (scRNA-seq) analysis is attempted, additional information on location single cells, behavior surrounding and microenvironment they generate, would be very important. We developed an inexpensive, high throughput application while preserving spatial organization, named “semibulk RNA-seq” (sbRNA-seq). utilized a microfluidic device specifically designed for experiments to encapsulate both barcoded...
ABSTRACT It is believed that immune responses are different between individuals and at times. In addition, personal health histories unique environmental conditions should collectively determine the present state of cells. However, cellular molecular system mechanisms underlying such heterogeneity remain largely elusive. this study, we conducted a systematic time-lapse single-cell analysis, using 171 libraries 30 mass cytometry datasets intensively for seven healthy individuals. We found...
In recent years, DNA methylation research has been accelerated by the advent of nanopore sequencers. However, read length limited constraints base conversion using bisulfite method, making analysis chromatin content difficult. The previous method combining and long-read sequencing was ~1.5 kb, even targeted PCR. this study, we have improved (~5 kb), converting unmethylated cytosines to uracils with APOBEC enzymes, reduce fragmentation. converted then sequenced a PromethION sequencer. We also...