CCG Updates and Insights
Featuring current topics in cancer genomics research and news and updates from CCG.
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EcDNAs are Extrachromosomal, Extra Active, and Extra Terrifying: Researcher Interviews with Chia-Lin Wei, Roel Verhaak, and Howard ChangExtrachromosomal DNA (ecDNA) are emerging as oncogenic elements in cancer genomes. Dr. Chia-Lin Wei, Dr. Roel Verhaak, and Dr. Howard Chang are studying the interactions ecDNAs have with chromatin and amongst each other, revealing novel mechanisms of activating oncogenes and suggesting a bigger role for ecDNAs in cancer than previously appreciated.
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Seeing Cancer Through New Lenses: A Broader Spectrum of Cancer TargetsIdentifying new targets and therapies for cancers will require thinking beyond the proverbial oncogene. Researchers from NCI’s Cancer Target Discovery and Development (CTD2) Network discuss new ways to model cancer and its potential vulnerabilities.
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The Serendipitous Off-Target Explorer – Researcher Interview with Jason SheltzerIdentifying the “targets” for targeted therapy is a major challenge in precision medicine research. Dr. Jason Sheltzer discusses how he inadvertently uncovered mischaracterized cancer targets and what his findings may mean for cancer drug development.
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Uncovering How HPV Alters the Genome in Ugandan Cervical Cancer PatientsThe molecular mechanisms by which HPV infection leads to cancer, especially in low- and middle-income countries experiencing high incidence and mortality rates, have yet to be clearly delineated. A recent genomic, epigenomic, and transcriptomic study of cervical tumors from Ugandan patients looks at specific types of HPV and the genomic alterations they cause.
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Next-Gen Technologies for Next-Gen Cancer Models, a PANACEA Database for Identifying Drug Off-Targets, and Updates to the CTD^2 and HCMI Programs: February OCG e-NewsletterA new program developing technologies facilitating next-generation cancer model usage, new features and functions from the Cancer Target Discovery and Development (CTD^2) Program, an off-target discovery DREAM Challenge, and more from the February 2021 edition of the Office of Cancer Genomics (OCG) e-Newsletter.
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NCI Genomic Data Commons: A Community Resource for Cancer ResearchA short time ago the Genomic Data Commons (GDC) was just a dream. CCG Director Lou Staudt describes what the GDC team has built so far: an interactive data system with genomic data processing pipelines for all types of researchers to use.
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An Introduction to Proteogenomics Part 2: Wielding the Proteomic ToolsIn the second guest post from the Office of Cancer Clinical Proteomics Research, our colleagues describe how proteogenomic research is done and some of the findings made so far about tumor subtypes, immune microenvironment, and other aspects of tumor biology. Many of the new insights were enabled by combining genomic and proteomic data.
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Brain Tumors Hack the Neuronal Microenvironment in Multiple Ways to Drive Tumor GrowthA glioblastoma genetic screen done in mice shows how very different pathways can be altered by different variants of the same key gene—in this case PIK3CA. Tumor cells may even act on neighboring, wild type cells to promote tumorigenesis. The work was led by Drs. Benjamin Deneen, Kenneth Scott, and Gordon Mills, researchers from NCI’s Cancer Target Discovery and Development (CTD^2) Network.
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An Introduction to Proteogenomics: Appreciating the Complexity of the Central DogmaMany layers of regulation affect the flow of information from DNA to RNA to protein. In a guest post from the Office of Cancer Clinical Proteomics Research, our colleagues describe the importance of incorporating proteomics to better understand—and potentially treat—the complexities of cancer.
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Visualizing Single-Cell RNA-Seq Data with t-SNE: Researcher Interview with Dmitry Kobak and Philipp BerensTo visualize and interpret single-cell RNA-seq data, researchers must select from endless combinations of computational methods and parameters. Dr. Dmitry Kobak and Dr. Philipp Berens discuss the pros and cons of one popular method in “The art of using t-SNE for single-cell transcriptomics.”