John N. Weinstein
A5026079862- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
- Renal cell carcinoma treatment
- Monoclonal and Polyclonal Antibodies Research
- Lung Cancer Treatments and Mutations
- Cancer-related molecular mechanisms research
- Renal and related cancers
- Computational Drug Discovery Methods
- Molecular Biology Techniques and Applications
- Ferroptosis and cancer prognosis
- Pancreatic and Hepatic Oncology Research
- Cancer-related Molecular Pathways
- Radiomics and Machine Learning in Medical Imaging
- Bladder and Urothelial Cancer Treatments
- Cancer therapeutics and mechanisms
- Lung Cancer Research Studies
- Drug Transport and Resistance Mechanisms
- RNA Research and Splicing
- Lipid Membrane Structure and Behavior
- Phagocytosis and Immune Regulation
- Peptidase Inhibition and Analysis
- Genetics, Bioinformatics, and Biomedical Research
The University of Texas MD Anderson Cancer Center
2016-2025
Scripps MD Anderson Cancer Center
2015-2025
Comer Children's Hospital
2024
Lurie Children's Hospital
2024
National Institutes of Health
2005-2023
National Cancer Institute
2004-2023
Center for Cancer Research
2004-2023
Laboratory of Molecular Genetics
2006-2023
Center for Information Technology
2003-2023
Center for Systems Biology
2023
Current clinical practice is organized according to tissue or organ of origin tumors. Now, The Cancer Genome Atlas (TCGA) Research Network has started identify genomic and other molecular commonalities among a dozen different types cancer. Emerging similarities contrasts will form the basis for targeted therapies future repurposing existing by rather than histological diseases. profiled analyzed large numbers human tumors discover aberrations at DNA, RNA, protein epigenetic levels. resulting...
Many mutations that contribute to the pathogenesis of acute myeloid leukemia (AML) are undefined. The relationships between patterns and epigenetic phenotypes not yet clear. We analyzed genomes 200 clinically annotated adult cases de novo AML, using either whole-genome sequencing (50 cases) or whole-exome (150 cases), along with RNA microRNA DNA-methylation analysis. AML have fewer than most other cancers, an average only 13 found in genes. Of these, 5 genes recurrently mutated AML. A total...
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled TCGA. Across types, we identified six immune subtypes—wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant—characterized differences in macrophage or signatures, Th1:Th2 cell ratio, extent intratumoral heterogeneity, aneuploidy, neoantigen load, overall proliferation, expression immunomodulatory genes,...
The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations. Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations the oncogene PIK3CA, novel alterations involving loss TRAF3, amplification cycle gene E2F1. Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 CDKN2A inactivation with frequent copy number including 3q26/28 11q13/22. A...
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical contain key features representing the democratized nature collection process. To ensure proper use this large dataset associated genomic features, we developed standardized named Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major outcome endpoints. In...
Urothelial carcinoma of the bladder is a common malignancy that causes approximately 150,000 deaths per year worldwide. So far, no molecularly targeted agents have been approved for treatment disease. As part The Cancer Genome Atlas project, we report here an integrated analysis 131 urothelial carcinomas to provide comprehensive landscape molecular alterations. There were statistically significant recurrent mutations in 32 genes, including multiple genes involved cell-cycle regulation,...
We conducted comprehensive integrative molecular analyses of the complete set tumors in The Cancer Genome Atlas (TCGA), consisting approximately 10,000 specimens and representing 33 types cancer. performed clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, miRNA expression levels reverse-phase protein arrays, which all, except for revealed primarily organized by histology, tissue type, or anatomic origin. influence cell type was evident...
Cancer progression involves the gradual loss of a differentiated phenotype and acquisition progenitor stem-cell-like features. Here, we provide novel stemness indices for assessing degree oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic epigenetic feature sets derived from non-transformed pluripotent stem cells their progeny. Using OCLR, were able identify previously undiscovered biological mechanisms...
The mutational profile of head and neck cancer is complex may pose challenges to the development targeted therapies.
Abstract We have developed GoMiner, a program package that organizes lists of 'interesting' genes (for example, under- and overexpressed from microarray experiment) for biological interpretation in the context Gene Ontology. GoMiner provides quantitative statistical output files two useful visualizations. The first is tree-like structure analogous to AmiGO browser second compact, dynamically interactive 'directed acyclic graph'. Genes displayed are linked major public bioinformatics resources.
Since 1990, the National Cancer Institute (NCI) has screened more than 60,000 compounds against a panel of 60 human cancer cell lines. The 50-percent growth-inhibitory concentration (GI 50 ) for any single line is simply an index cytotoxicity or cytostasis, but patterns such GI values encode unexpectedly rich, detailed information on mechanisms drug action and resistance. Each compound's pattern like fingerprint, essentially unique among many billions distinguishable possibilities. These...
Cancer chromatin accessibility landscape The Genome Atlas (TCGA) provides a high-quality resource of molecular data on large variety human cancers. Corces et al. used recently modified assay to profile determine the accessible in 410 TCGA samples from 23 cancer types (see Perspective by Taipale). When were integrated with other omics available for same tumor samples, inherited risk loci predisposition revealed, transcription factors and enhancers driving subtypes patient survival differences...
Muscle-invasive bladder cancer (MIBC) is a molecularly diverse disease with heterogeneous clinical outcomes. Several molecular classifications have been proposed, but the diversity of their subtype sets impedes application. To achieve an international consensus on MIBC subtypes that reconciles published classification schemes. We used 1750 transcriptomic profiles from 16 datasets and two additional cohorts. performed network-based analysis six independent systems to identify set classes....
Epithelial-mesenchymal transition (EMT) has been associated with metastatic spread and EGF receptor (EGFR) inhibitor resistance. We developed validated a robust 76-gene EMT signature using gene expression profiles from four platforms non-small cell lung carcinoma (NSCLC) lines patients treated in the Biomarker-Integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE) study.We conducted an integrated expression, proteomic, drug response analysis tumors NSCLC. A was...
Aneuploidy, whole chromosome or arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression proliferation genes. Aneuploidy anti-correlated immune signaling genes, due to decreased leukocyte infiltrates in high-aneuploidy samples. Chromosome arm-level alterations show cancer-specific patterns, including loss 3p squamous We applied genome...
<h2>Summary</h2> DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 types. Mutations with accompanying loss heterozygosity were observed in over 1/3 genes, including <i>TP53</i> <i>BRCA1/2</i>. Other prevalent included epigenetic silencing the direct genes <i>EXO5</i>, <i>MGMT</i>, <i>ALKBH3</i> ∼20% samples. Homologous recombination (HRD) was...