A5007530779- Single-cell and spatial transcriptomics
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- RNA modifications and cancer
- Cell Image Analysis Techniques
- CRISPR and Genetic Engineering
- Lymphatic System and Diseases
- Pluripotent Stem Cells Research
- Medical Imaging Techniques and Applications
- Cell Adhesion Molecules Research
- RNA and protein synthesis mechanisms
- T-cell and B-cell Immunology
- Medical and Biological Sciences
- Immunotherapy and Immune Responses
- Angiogenesis and VEGF in Cancer
- Immune cells in cancer
- Bioinformatics and Genomic Networks
- Immune Cell Function and Interaction
- Genomics and Chromatin Dynamics
- Vascular Malformations and Hemangiomas
- DNA and Nucleic Acid Chemistry
- MicroRNA in disease regulation
- 3D Printing in Biomedical Research
- RNA Interference and Gene Delivery
- Advanced biosensing and bioanalysis techniques
RIKEN Center for Integrative Medical Sciences
2016-2025
Agency for Science, Technology and Research
2022-2025
Genome Institute of Singapore
2022-2025
National University of Singapore
2024-2025
Duke University
2019
CLS Technology (Norway)
2015-2017
Genomic Health (United States)
2017
ETH Zurich
2005-2010
École Polytechnique Fédérale de Lausanne
2007-2010
Dermatology Research Center
2008
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that time is ripe to complete 150-year-old effort identify all cell types human body. Human Cell Atlas Project an international collaborative aims define terms distinctive profiles (such as gene expression profiles) and connect this information with classical cellular descriptions location morphology). An open comprehensive reference map state cells...
Supercentenarians, people who have reached 110 y of age, are a great model healthy aging. Their characteristics delayed onset age-related diseases and compression morbidity imply that their immune system remains functional. Here we performed single-cell transcriptome analysis 61,202 peripheral blood mononuclear cells (PBMCs), derived from 7 supercentenarians 5 younger controls. We identified marked increase cytotoxic CD4 T (CD4 lymphocytes [CTLs]) as signature supercentenarians. Furthermore,...
Abstract The human brain is a complex, three‐dimensional structure. To better recapitulate complexity, recent efforts have focused on the development of human‐specific midbrain organoids. Human iPSC‐derived organoids consist differentiated and functional neurons, which contain active synapses, as well astrocytes oligodendrocytes. However, absence microglia, with their ability to remodel neuronal networks phagocytose apoptotic cells debris, represents major disadvantage for current organoid...
Fibroblast growth factors play important roles in angiogenesis, but their functions lymphangiogenesis remain poorly understood. The homeodomain transcription factor Prox1 is essential for development of the lymphatic system by specifying endothelial cell (LEC) fate. Here, we identify fibroblast (FGF) receptor (FGFR)-3 as a novel target gene. Ectopic overexpression blood vascular cells up-regulates FGFR-3. induces expression IIIc isoform, which also found to be major isoform FGFR-3 expressed...
Next-generation sequencing experiments have shown that microRNAs (miRNAs) are expressed in many different isoforms (isomiRs), whose biological relevance is often unclear. We found mature miR-21, the most widely researched miRNA because of its importance human disease, produced two prevalent isomiR forms differ by 1 nt at their 3' end, and moreover end miR-21 posttranscriptionally adenylated noncanonical poly(A) polymerase PAPD5. PAPD5 knockdown caused an increase expression level, suggesting...
CAGE (cap analysis gene expression) and RNA-seq are two major technologies used to identify transcript abundances as well structures. They measure expression by sequencing from either the 5′ end of capped molecules (CAGE) or tags randomly distributed along length a (RNA-seq). Library protocols for clonally amplified (Illumina, SOLiD, 454 Life Sciences [Roche], Ion Torrent), second-generation platforms typically employ PCR preamplification prior clonal amplification, while third-generation,...
Big leaps in science happen when scientists from different backgrounds interact. In the past 15 years, FANTOM Consortium has brought together fields to analyze and interpret genomic data produced with novel technologies, including mouse full-length cDNAs and, more recently, expression profiling at single-nucleotide resolution by cap-analysis gene expression. The provided most comprehensive cDNA collection for functional studies extensive maps of human transcriptome comprising promoters,...
Basic leucine zipper transcription factor Batf2 is poorly described, whereas Batf and Batf3 have been shown to play essential roles in dendritic cell, T B cell development regulation. was drastically induced IFN-γ-activated classical macrophages (M1) compared with unstimulated or IL-4-activated alternative (M2). knockdown experiments from subsequent expression profiling demonstrated important for regulation of immune responses, inducing inflammatory host-protective genes Tnf, Ccl5, Nos2....
Abstract Single-cell transcriptomic profiling is a powerful tool to explore cellular heterogeneity. However, most of these methods focus on the 3′-end polyadenylated transcripts and provide only partial view transcriptome. We introduce C1 CAGE, method for detection transcript 5′-ends with an original sample multiplexing strategy in TM microfluidic system. first quantifiy performance CAGE find it as accurate sensitive other then use profile promoter enhancer activities response TGF-β lung...
The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in pursuit of understanding transcriptome, and transcriptional regulation, mammalian genomes for last 20 years. To share these with research community, FANTOM web-interfaces databases are being regularly updated, enhanced expanded new data types. In recent years, Consortium's efforts have been mainly focused on creating non-coding RNA datasets resources. existing FANTOM5 human...
Abstract Single-cell omics technologies enable molecular characterization of diverse cell types and states, but how the resulting transcriptional epigenetic profiles depend on cell’s genetic background remains understudied. We describe Monopogen, a computational tool to detect single-nucleotide variants (SNVs) from single-cell sequencing data. Monopogen leverages linkage disequilibrium external reference panels identify germline SNVs detects putative somatic using allele cosegregating...
The lymphatic vascular system maintains tissue fluid homeostasis, helps mediate afferent immune responses, and promotes cancer metastasis. To address the role microRNAs (miRNAs) play in development function of system, we defined vitro miRNA expression profiles primary human endothelial cells (LECs) blood (BVECs) identified four BVEC signature two LEC miRNAs. Their lineage-specific patterns were confirmed vivo by quantitative real-time PCR situ hybridization. Functional characterization...
Abstract The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that time is ripe to complete 150-year-old effort identify all cell types human body, by undertaking Human Cell Atlas Project as an international collaborative effort. aim would be define terms distinctive profiles (e.g., gene expression) and connect this information with classical cellular descriptions location morphology). A comprehensive...
The brainstem is a posterior region of the brain, composed three parts, midbrain, pons, and medulla oblongata. It critical in controlling heartbeat, blood pressure, respiration, all which are life-sustaining functions, therefore, damages to or disorders can be lethal. Brain organoids derived from human pluripotent stem cells (hPSCs) recapitulate course brain development expected useful for medical research on central nervous system disorders. However, existing organoid models limited extent...
Summary Lack of diversity and proportionate representation in genomics datasets databases contributes to inequity healthcare outcomes globally 1,2 . The relationships human with biological biomedical phenotypes are pervasive 3 , yet remain understudied, particularly a single-cell context. Here we present the Asian Immune Diversity Atlas (AIDA), multi-national RNA-sequencing (scRNA-seq) healthy reference atlas immune cells. AIDA comprises 1,265,624 circulating cells from 619 donors 6...
Published single-cell datasets are rich resources for investigators who want to address questions not originally asked by the creators of datasets. The might be obtained different protocols and diverse analysis strategies. main challenge in utilizing such data is how we can make various large-scale comparable reusable a context. To this issue, developed centric database 'SCPortalen' (http://single-cell.clst.riken.jp/). current version covers human mouse transcriptomics that publicly...
Human stem cell-derived organoids have great potential for modelling physiological and pathological processes. They recapitulate in vitro the organization function of a respective organ or part an organ. midbrain (hMOs) been described to contain midbrain-specific dopaminergic neurons that release neurotransmitter dopamine. However, human contains also additional neuronal cell types, which are functionally interacting with each other. Here, we analysed hMOs at high-resolution by means...