Takafumi N. Yamaguchi
A5029886406- Prostate Cancer Treatment and Research
- Cancer Genomics and Diagnostics
- Advanced Proteomics Techniques and Applications
- Genomics and Rare Diseases
- Prostate Cancer Diagnosis and Treatment
- Radiomics and Machine Learning in Medical Imaging
- Genomics and Phylogenetic Studies
- Cancer, Lipids, and Metabolism
- Molecular Biology Techniques and Applications
- Genetics, Bioinformatics, and Biomedical Research
- Health Systems, Economic Evaluations, Quality of Life
- Epigenetics and DNA Methylation
- Probabilistic and Robust Engineering Design
- Electronic Packaging and Soldering Technologies
- Genetic factors in colorectal cancer
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Integrated Circuits and Semiconductor Failure Analysis
- Bioinformatics and Genomic Networks
- Cancer, Hypoxia, and Metabolism
- Gene expression and cancer classification
- Genomics and Chromatin Dynamics
- Evolution and Genetic Dynamics
- Chromosomal and Genetic Variations
- PARP inhibition in cancer therapy
University of California, Los Angeles
2020-2025
Aichi Cancer Center
2025
Nagoya University
2025
Ontario Institute for Cancer Research
2014-2024
University of Tsukuba
2023-2024
Precision Research (United States)
2021-2024
Institute of Livestock and Grassland Science
2024
Sumitomo Chemical (Japan)
2019-2024
Takara (Japan)
2024
APLA Health
2023
The first report of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge introduces BAMSurgeon tool for accurate tumor simulation and reports performance 248 submissions in calling single-nucleotide variants from three pairs synthetic tumor–normal genome benchmarks. detection somatic mutations cancer sequences is key to understanding genetic basis disease progression, patient survival response therapy. Benchmarking needed assessment improvement but complicated by a lack gold standards,...
Abstract As whole-genome sequencing for cancer genome analysis becomes a clinical tool, full understanding of the variables affecting output is required. Here using tumour-normal sample pairs from two different types cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct benchmarking exercise within context International Cancer Genome Consortium. We compare methods, pipelines validation methods. show that PCR-free methods increasing depth to ∼100 × shows benefits, as long...
Abstract Germline mutations in the BRCA2 tumour suppressor are associated with both an increased lifetime risk of developing prostate cancer (PCa) and aggressive disease. To understand this aggression, here we profile genomes methylomes localized PCa from 14 carriers deleterious germline ( -mutant PCa). We show that harbour genomic instability a mutational more closely resembles metastastic than shows epigenomic dysregulation MED12L / MED12 axis, which is frequently dysregulated metastatic...
A global genetic suppression network The background of an organism can influence the overall effects new variants. Some mutations amplify a deleterious phenotype, whereas others suppress it. Starting with literature survey and expanding into genomewide assay, van Leeuwen et al. generated large-scale in yeast. data set reveals general properties that be used to predict interactions. Furthermore, study provides template for extending studies other genes or more complex organisms. Science ,...
Metastatic castration-resistant prostate cancer (mCRPC) has a highly complex genomic landscape. With the recent development of novel treatments, accurate stratification strategies are needed. Here we present whole-genome sequencing (WGS) analysis fresh-frozen metastatic biopsies from 197 mCRPC patients. Using unsupervised clustering based on features, define eight distinct clusters. We observe potentially clinically relevant genotypes, including microsatellite instability (MSI), homologous...
Abstract Immune-mediated anti-tumoral responses, elicited by oncolytic viruses and augmented with checkpoint inhibition, may be an effective treatment approach for glioblastoma. Here in this multicenter phase 1/2 study we evaluated the combination of intratumoral delivery virus DNX-2401 followed intravenous anti-PD-1 antibody pembrolizumab recurrent glioblastoma, first a dose-escalation then dose-expansion phase, 49 patients. The primary endpoints were overall safety objective response rate....
Anaplastic thyroid carcinoma is arguably the most lethal human malignancy. It often co-occurs with differentiated cancers, yet molecular origins of its aggressivity are unknown. We sequenced tumor DNA from 329 regions cancer, including 213 patients primary anaplastic carcinomas. also whole genome 9 using multi-region sequencing both and cancer components. Using these data, we demonstrate thatanaplastic carcinomas have a higher burden mutations than other distinct mutational signatures...
Signaling via the epidermal growth factor receptor (EGFR), which has critical roles in development and diseases such as cancer, is regulated by proteolytic shedding of its membrane-tethered ligands. Sheddases for EGFR-ligands are therefore key signaling switches EGFR pathway. Here, we determined ADAMs (a disintegrin metalloprotease) can shed various EGFR-ligands, analyzed regulation EGFR-ligand two commonly used stimuli, phorbol esters calcium influx. Phorbol predominantly activate ADAM17,...
Abstract Background Patients with human papillomavirus–related oropharyngeal cancers have excellent outcomes but experience clinically significant toxicities when treated standard chemoradiotherapy (70 Gy). We hypothesized that functional imaging could identify patients who be safely deescalated to 30 Gy of radiotherapy. Methods In 19 patients, pre- and intratreatment dynamic fluorine-18-labeled fluoromisonidazole positron emission tomography (PET) was used assess tumor hypoxia. without...
Invasive cribriform and intraductal carcinoma (CR/IDC) is associated with adverse outcome of prostate cancer patients. The aim this study was to determine the molecular aberrations CR/IDC in primary cancer, focusing on genomic instability somatic copy number alterations (CNA). Whole-slide images Cancer Genome Atlas Project (TCGA, N = 260) Canadian Prostate Network (CPC-GENE, 199) radical prostatectomy datasets were reviewed for Gleason score (GS) presence CR/IDC. Genomic assessed by...
The tumor microenvironment can be classified into immunologically active "inflamed" tumors and inactive "non-inflamed" based on the infiltration of cytotoxic immune cells. Previous studies liver cancer have reported a superior prognosis for inflamed compared to non-inflamed tumors. However, is highly heterogeneous genetically, finer classification may improve our understanding its immunological diversity response therapy.We characterized gene signatures 234 primary cancers, mainly...
Host genetics is a key determinant of COVID-19 outcomes. Previously, the Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with However, largest impact on outcomes are expected be rare in population. Hence, studying may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome whole-genome sequencing from 21 cohorts across 12 countries performed...
Abstract Motivation The ongoing expansion in the volume of biomedical data has contributed to a growing complexity tools and technologies used research with an increased reliance on complex workflows written orchestration languages such as Nextflow integrate algorithms into processing pipelines. use involving various led scrutiny software development practices avoid errors individual connections between them. Results To facilitate test-driven pipelines, we created NFTest, framework for...
Abstract Newly diagnosed prostate cancers differ dramatically in mutational composition and lethality. The most accurate clinical predictor of lethality is tumor tissue architecture, quantified as grade. To interrogate the evolutionary origins cancer heterogeneity, we analyzed 666 whole genomes. We identified a compendium 223 recurrently mutated driver regions, influencing downstream processes gene expression. validated individual germline variants that predispose tumors to acquire specific...
Each Drosophila ovariole has three independent sets of stem cells: germ-line cells (GSCs) and escort cells, located at the anterior tip germarium, somatic (SSCs), adjacent to newly formed 16-cell cysts. Decapentaplegic (Dpp) is required maintain whereas Hedgehog for maintenance cell division SCCs. In an effort establish a new in vitro system analyze intrinsic extrinsic factors regulating differentiation GSCs , we tested various culture conditions growing GSCs, derived from bag marbles ( bam...
Abstract Prostate cancer is the second most commonly diagnosed malignancy among men worldwide. Recurrently mutated in primary and metastatic prostate tumors, FOXA1 encodes a pioneer transcription factor involved disease onset progression through both androgen receptor-dependent receptor-independent mechanisms. Despite its oncogenic properties however, regulation of expression remains unknown. Here, we identify set six cis -regulatory elements regulatory plexus harboring somatic...
Abstract Recent advances in cancer therapeutics clearly demonstrate the need for innovative multiplex therapies that attack tumour on multiple fronts. Oncolytic or “cancer-killing” viruses (OVs) represent up-and-coming multi-mechanistic immunotherapeutic drugs treatment of cancer. In this study, we perform an in-vitro screen based virus-encoded artificial microRNAs (amiRNAs) and find a unique amiRNA, herein termed amiR-4, confers replicative advantage to VSVΔ51 OV platform. Target validation...