Teppei Shimamura
A5009811167- Epigenetics and DNA Methylation
- Gene expression and cancer classification
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Bioinformatics and Genomic Networks
- Cancer, Hypoxia, and Metabolism
- Cancer Genomics and Diagnostics
- Neuroblastoma Research and Treatments
- Single-cell and spatial transcriptomics
- Gene Regulatory Network Analysis
- Cancer Cells and Metastasis
- Glioma Diagnosis and Treatment
- Lung Cancer Treatments and Mutations
- Genetic factors in colorectal cancer
- Cancer-related gene regulation
- RNA Research and Splicing
- Histone Deacetylase Inhibitors Research
- Pancreatic and Hepatic Oncology Research
- Genomics and Chromatin Dynamics
- Gut microbiota and health
- Lung Cancer Research Studies
- Congenital Diaphragmatic Hernia Studies
- Hedgehog Signaling Pathway Studies
- Sarcoma Diagnosis and Treatment
- CCD and CMOS Imaging Sensors
Nagoya University
2015-2024
Tokyo Medical and Dental University
2013-2024
Institute of Science Tokyo
2024
Nagoya City University
2023
Nagoya University Hospital
2022
Center for Systems Biology
2020
Tokyo University of Science
2007-2017
Waseda University
2017
The University of Tokyo
2007-2016
Kobe Children's Hospital
2014
The functional impact of recently discovered long noncoding RNAs (ncRNAs) in human cancer remains to be clarified. One ncRNA which has attracted attention is the Hox transcript antisense intergenic RNA termed HOTAIR, a expressed from developmental HOXC locus located on chromosome 12q13.13. In cooperation with Polycomb complex PRC2, HOTAIR reported reprogram chromatin organization and promote breast metastasis. this study, we examined status function patients stage IV colorectal (CRC) who...
Esophageal squamous cell carcinoma (ESCC) is the predominant form of esophageal cancer in Japan. Smoking and drinking alcohol are environmental risk factors for ESCC, whereas single nucleotide polymorphisms ADH1B ALDH2, which increase harmful intermediates produced by alcohol, genetic factors. We conducted a large-scale genomic analysis ESCCs from patients Japan to determine mutational landscape this cancer.
Diffuse lower-grade gliomas (LGGs) are genetically classified into 3 distinct subtypes based on isocitrate dehydrogenase (IDH) mutation status and codeletion of chromosome 1p 19q (1p/19q). However, the subtype-specific effects additional genetic lesions survival largely unknown.Using Cox proportional hazards regression modeling, we investigated alterations clinicopathological factors in each LGG subtype, a Japanese cohort cases fully genotyped for driver mutations copy number variations...
Cancer-associated fibroblasts (CAF) constitute a major component of the tumor microenvironment. Recent observations in genetically engineered mouse models and clinical studies have suggested that there may exist at least two functionally different populations CAFs, is, cancer-promoting CAFs (pCAF) cancer-restraining (rCAF). Although various pCAF markers been identified, identity rCAFs remains unknown because lack rCAF-specific marker(s). In this study, we found Meflin,...
Hypoxia-inducible factor 1 (HIF1) is a master regulator of adaptive gene expression under hypoxia. However, role for HIF1 in the epigenetic regulation remains unknown. Genome-wide analysis binding sites (chromatin immunoprecipitation [ChIP] with deep sequencing) endothelial cells clarified that mainly binds to intergenic regions distal from transcriptional starting both normoxia and Next, we examined temporal profile hypoxic conditions by using DNA microarrays. We early hypoxia-responsive...
Circulating tumor cells (CTC) in blood have attracted attention both as potential seeds for metastasis and biomarkers. However, most CTC detection systems might miss epithelial-mesenchymal transition (EMT)-induced metastatic because is based on epithelial markers. First, to discover novel markers capable of detecting CTCs which EMT has not been repressed, microarray analysis 132 colorectal cancers (CRC) from Japanese patients was conducted, 2,969 genes were detected that overexpressed...
Compelling evidence in Caucasian populations suggests a role for copy-number variations (CNVs) autism spectrum disorder (ASD) and schizophrenia (SCZ). We analyzed 1,108 ASD cases, 2,458 SCZ 2,095 controls Japanese population confirmed an increased burden of rare exonic CNVs both disorders. Clinically significant (or pathogenic) CNVs, including those at 29 loci common to disorders, were found about 8% which was significantly higher than controls. Phenotypic analysis revealed association...
Abstract The biological significance of micro (mi)RNAs has traditionally been evaluated according to their RNA expression levels based on the assumption that miRNAs recognize and regulate targets in an unvarying fashion. Here we show a fraction mature including miR-17-5p, -21-5p, -200c-3p let-7a-5p harbor methyl marks potentially alter stability target recognition. Importantly, methylation these was significantly increased cancer tissues as compared paired normal tissues. Furthermore,...
The cellular interactions in the tumor microenvironment of colorectal cancer (CRC) are poorly understood, hindering patient treatment. In current study, we investigate whether events occurring at invasion front particular importance for CRC treatment strategies. To this end, analyze tissues by combining spatial transcriptomics from patients with a public single-cell transcriptomic atlas to determine cell-cell front. We show that cells localized specifically These induce human leukocyte...
Abstract Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma in childhood. Here we studied 60 RMSs using whole-exome/-transcriptome sequencing, copy number (CN) and DNA methylome analyses to unravel genetic/epigenetic basis of RMS. On methylation patterns, RMS clustered into four distinct subtypes, which exhibits remarkable correlation with mutation/CN profiles, histological phenotypes clinical behaviours. A1 A2 especially A1, largely correspond alveolar histology frequent PAX3/7...
Purpose To identify stage I lung adenocarcinoma patients with a poor prognosis who will benefit from adjuvant therapy. Patients and Methods Whole gene expression profiles were obtained at 19 time points over 48-hour course human primary epithelial cells that stimulated epidermal growth factor (EGF) in the presence or absence of clinically used EGF receptor tyrosine kinase (RTK)-specific inhibitor, gefitinib. The data subjected to mathematical simulation using State Space Model (SSM)....
Conditions of the tumor microenvironment, such as hypoxia and nutrient starvation, play critical roles in cancer progression. However, role acidic extracellular pH progression is not studied extensively that hypoxia. Here, we show (pH 6.8) triggered activation sterol regulatory element-binding protein 2 (SREBP2) by stimulating nuclear translocation promoter binding to its targets, along with intracellular acidification. Interestingly, inhibition SREBP2, but SREBP1, suppressed upregulation...
Understanding intratumor heterogeneity is clinically important because it could cause therapeutic failure by fostering evolutionary adaptation. To this end, we profiled the genome and epigenome in multiple regions within each of nine colorectal tumors. Extensive intertumor observed, from which inferred history First, clonally shared alterations appeared, C>T transitions at CpG site island hypermethylation were relatively enriched. Correlation between mutation counts patients' ages suggests...
MicroRNAs (miRNAs) are key post-transcriptional regulators of gene expression and commonly deregulated in carcinogenesis. To explore functionally crucial tumor-suppressive (TS)-miRNAs hepatocellular carcinoma (HCC), we performed integrative function- expression-based screenings TS-miRNAs six HCC cell lines. The identified seven miRNAs, which showed growth-suppressive activities through the overexpression each miRNA were endogenously downregulated Further analyses using a large panel lines...
Advanced colorectal cancer harbors extensive intratumor heterogeneity shaped by neutral evolution; however, in precancerous lesions has been poorly studied. We perform multiregion whole-exome sequencing on ten early tumors, which contained adenoma and carcinoma situ. By comparing with data from advanced we show that the tumors accumulate a higher proportion of subclonal driver mutations than is highlighted KRAS APC. also demonstrate variant allele frequencies tend to be suggesting are...
Twenty studies on gut microbiota in PD have been reported, whereas only one study has reported iRBD from Germany. the highest likelihood ratio to develop PD. Our meta-analysis of Japan and Germany revealed increased mucin-layer-degrading genus Akkermansia iRBD.
An increasingly recognized component of resistance to tyrosine kinase inhibitors (TKI) involves persistence a drug-tolerant subpopulation cancer cells that survive despite effective eradication the majority cell population. Multiple groups have demonstrated these persister undergo transcriptional adaptation via an epigenetic state change promotes survival. Because this mode TKI drug tolerance appears involve addiction specific genes and pathways, we hypothesized systematic functional...
The recent development of single-cell multiomics analysis has enabled simultaneous detection multiple traits at the level, providing deeper insights into cellular phenotypes and functions in diverse tissues. However, currently, it is challenging to infer joint representations learn relationships among modalities from complex multimodal data. Here, we present scMM, a novel deep generative model-based framework for extraction interpretable crossmodal generation. scMM addresses complexity data...