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Derek L. Stirewalt

Bio: Derek L. Stirewalt is an academic researcher from Fred Hutchinson Cancer Research Center. The author has contributed to research in topics: Myeloid leukemia & Leukemia. The author has an hindex of 42, co-authored 101 publications receiving 15718 citations. Previous affiliations of Derek L. Stirewalt include University of Washington Medical Center & University of Washington.


Papers
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Journal ArticleDOI
TL;DR: It is shown here that miRNAs are present in human plasma in a remarkably stable form that is protected from endogenous RNase activity and established the measurement of tumor-derived mi RNAs in serum or plasma as an important approach for the blood-based detection of human cancer.
Abstract: Improved approaches for the detection of common epithelial malignancies are urgently needed to reduce the worldwide morbidity and mortality caused by cancer. MicroRNAs (miRNAs) are small (≈22 nt) regulatory RNAs that are frequently dysregulated in cancer and have shown promise as tissue-based markers for cancer classification and prognostication. We show here that miRNAs are present in human plasma in a remarkably stable form that is protected from endogenous RNase activity. miRNAs originating from human prostate cancer xenografts enter the circulation, are readily measured in plasma, and can robustly distinguish xenografted mice from controls. This concept extends to cancer in humans, where serum levels of miR-141 (a miRNA expressed in prostate cancer) can distinguish patients with prostate cancer from healthy controls. Our results establish the measurement of tumor-derived miRNAs in serum or plasma as an important approach for the blood-based detection of human cancer.

7,296 citations

Journal ArticleDOI
TL;DR: Identification of extracellular Ago2–miRNA complexes in plasma raises the possibility that cells release a functional miRNA-induced silencing complex into the circulation, and reveals two populations of circulating miRNAs and suggest that circulating Ago2 complexes are a mechanism responsible for the stability of plasma mi RNAs.
Abstract: MicroRNAs (miRNAs) circulate in the bloodstream in a highly stable, extracellular form and are being developed as blood-based biomarkers for cancer and other diseases. However, the mechanism underlying their remarkable stability in the RNase-rich environment of blood is not well understood. The current model in the literature posits that circulating miRNAs are protected by encapsulation in membrane-bound vesicles such as exosomes, but this has not been systematically studied. We used differential centrifugation and size-exclusion chromatography as orthogonal approaches to characterize circulating miRNA complexes in human plasma and serum. We found, surprisingly, that the majority of circulating miRNAs cofractionated with protein complexes rather than with vesicles. miRNAs were also sensitive to protease treatment of plasma, indicating that protein complexes protect circulating miRNAs from plasma RNases. Further characterization revealed that Argonaute2 (Ago2), the key effector protein of miRNA-mediated silencing, was present in human plasma and eluted with plasma miRNAs in size-exclusion chromatography. Furthermore, immunoprecipitation of Ago2 from plasma readily recovered non–vesicle-associated plasma miRNAs. The majority of miRNAs studied copurified with the Ago2 ribonucleoprotein complex, but a minority of specific miRNAs associated predominantly with vesicles. Our results reveal two populations of circulating miRNAs and suggest that circulating Ago2 complexes are a mechanism responsible for the stability of plasma miRNAs. Our study has important implications for the development of biomarker approaches based on capture and analysis of circulating miRNAs. In addition, identification of extracellular Ago2–miRNA complexes in plasma raises the possibility that cells release a functional miRNA-induced silencing complex into the circulation.

2,900 citations

Journal ArticleDOI
TL;DR: It is shown here that most exosomes derived from standard preparations do not harbor many copies of miRNA molecules, and are, therefore, individually unlikely to be functional as vehicles for miRNA-based communication.
Abstract: Exosomes have been proposed as vehicles for microRNA (miRNA) -based intercellular communication and a source of miRNA biomarkers in bodily fluids. Although exosome preparations contain miRNAs, a quantitative analysis of their abundance and stoichiometry is lacking. In the course of studying cancer-associated extracellular miRNAs in patient blood samples, we found that exosome fractions contained a small minority of the miRNA content of plasma. This low yield prompted us to perform a more quantitative assessment of the relationship between miRNAs and exosomes using a stoichiometric approach. We quantified both the number of exosomes and the number of miRNA molecules in replicate samples that were isolated from five diverse sources (i.e., plasma, seminal fluid, dendritic cells, mast cells, and ovarian cancer cells). Regardless of the source, on average, there was far less than one molecule of a given miRNA per exosome, even for the most abundant miRNAs in exosome preparations (mean ± SD across six exosome sources: 0.00825 ± 0.02 miRNA molecules/exosome). Thus, if miRNAs were distributed homogenously across the exosome population, on average, over 100 exosomes would need to be examined to observe one copy of a given abundant miRNA. This stoichiometry of miRNAs and exosomes suggests that most individual exosomes in standard preparations do not carry biologically significant numbers of miRNAs and are, therefore, individually unlikely to be functional as vehicles for miRNA-based communication. We propose revised models to reconcile the exosome-mediated, miRNA-based intercellular communication hypothesis with the observed stoichiometry of miRNAs associated with exosomes.

852 citations

Journal ArticleDOI
TL;DR: Exploring the mechanism by which mutations in the FLT3 gene cause uncontrolled proliferation might lead to a better understanding of how cells become cancerous and provide insights for the development of new drugs.
Abstract: Normal haematopoietic cells use complex systems to control proliferation, differentiation and cell death. The control of proliferation is, in part, accomplished through the ligand-induced stimulation of receptor tyrosine kinases, which signal to downstream effectors through the RAS pathway. Recently, mutations in the FMS-like tyrosine kinase 3 (FLT3) gene, which encodes a receptor tyrosine kinase, have been found to be the most common genetic lesion in acute myeloid leukaemia (AML), occurring in approximately 25% of cases. Exploring the mechanism by which these FLT3 mutations cause uncontrolled proliferation might lead to a better understanding of how cells become cancerous and provide insights for the development of new drugs.

850 citations

Journal ArticleDOI
01 Jan 2001-Blood
TL;DR: Diagnostic bone marrow specimens from 91 pediatric patients with AML were analyzed for the presence of the Flt3/ITD and its presence was the single most significant, independent prognostic factor for poor outcome in pediatric AML.

485 citations


Cited by
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Clotilde Théry1, Kenneth W. Witwer2, Elena Aikawa3, María José Alcaraz4  +414 moreInstitutions (209)
TL;DR: The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities, and a checklist is provided with summaries of key points.
Abstract: The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.

5,988 citations

Journal ArticleDOI
TL;DR: It is demonstrated that miRNAs are present in the serum and plasma of humans and other animals such as mice, rats, bovine fetuses, calves, and horses, and can serve as potential biomarkers for the detection of various cancers and other diseases.
Abstract: Dysregulated expression of microRNAs (miRNAs) in various tissues has been associated with a variety of diseases, including cancers. Here we demonstrate that miRNAs are present in the serum and plasma of humans and other animals such as mice, rats, bovine fetuses, calves, and horses. The levels of miRNAs in serum are stable, reproducible, and consistent among individuals of the same species. Employing Solexa, we sequenced all serum miRNAs of healthy Chinese subjects and found over 100 and 91 serum miRNAs in male and female subjects, respectively. We also identified specific expression patterns of serum miRNAs for lung cancer, colorectal cancer, and diabetes, providing evidence that serum miRNAs contain fingerprints for various diseases. Two non-small cell lung cancer-specific serum miRNAs obtained by Solexa were further validated in an independent trial of 75 healthy donors and 152 cancer patients, using quantitative reverse transcription polymerase chain reaction assays. Through these analyses, we conclude that serum miRNAs can serve as potential biomarkers for the detection of various cancers and other diseases.

4,184 citations

Journal ArticleDOI
Timothy J. Ley1, Christopher A. Miller1, Li Ding1, Benjamin J. Raphael2, Andrew J. Mungall3, Gordon Robertson3, Katherine A. Hoadley4, Timothy J. Triche5, Peter W. Laird5, Jack Baty1, Lucinda Fulton1, Robert S. Fulton1, Sharon Heath1, Joelle Kalicki-Veizer1, Cyriac Kandoth1, Jeffery M. Klco1, Daniel C. Koboldt1, Krishna L. Kanchi1, Shashikant Kulkarni1, Tamara Lamprecht1, David E. Larson1, G. Lin1, Charles Lu1, Michael D. McLellan1, Joshua F. McMichael1, Jacqueline E. Payton1, Heather Schmidt1, David H. Spencer1, Michael H. Tomasson1, John W. Wallis1, Lukas D. Wartman1, Mark A. Watson1, John S. Welch1, Michael C. Wendl1, Adrian Ally3, Miruna Balasundaram3, Inanc Birol3, Yaron S.N. Butterfield3, Readman Chiu3, Andy Chu3, Eric Chuah3, Hye Jung E. Chun3, Richard Corbett3, Noreen Dhalla3, Ranabir Guin3, An He3, Carrie Hirst3, Martin Hirst3, Robert A. Holt3, Steven J.M. Jones3, Aly Karsan3, Darlene Lee3, Haiyan I. Li3, Marco A. Marra3, Michael Mayo3, Richard A. Moore3, Karen Mungall3, Jeremy Parker3, Erin Pleasance3, Patrick Plettner3, Jacquie Schein3, Dominik Stoll3, Lucas Swanson3, Angela Tam3, Nina Thiessen3, Richard Varhol3, Natasja Wye3, Yongjun Zhao3, Stacey Gabriel6, Gad Getz6, Carrie Sougnez6, Lihua Zou6, Mark D.M. Leiserson2, Fabio Vandin2, Hsin-Ta Wu2, Frederick Applebaum7, Stephen B. Baylin8, Rehan Akbani9, Bradley M. Broom9, Ken Chen9, Thomas C. Motter9, Khanh Thi-Thuy Nguyen9, John N. Weinstein9, Nianziang Zhang9, Martin L. Ferguson, Christopher Adams10, Aaron D. Black10, Jay Bowen10, Julie M. Gastier-Foster10, Thomas Grossman10, Tara M. Lichtenberg10, Lisa Wise10, Tanja Davidsen11, John A. Demchok11, Kenna R. Mills Shaw11, Margi Sheth11, Heidi J. Sofia, Liming Yang11, James R. Downing, Greg Eley, Shelley Alonso12, Brenda Ayala12, Julien Baboud12, Mark Backus12, Sean P. Barletta12, Dominique L. Berton12, Anna L. Chu12, Stanley Girshik12, Mark A. Jensen12, Ari B. Kahn12, Prachi Kothiyal12, Matthew C. Nicholls12, Todd Pihl12, David Pot12, Rohini Raman12, Rashmi N. Sanbhadti12, Eric E. Snyder12, Deepak Srinivasan12, Jessica Walton12, Yunhu Wan12, Zhining Wang12, Jean Pierre J. Issa13, Michelle M. Le Beau14, Martin Carroll15, Hagop M. Kantarjian, Steven M. Kornblau, Moiz S. Bootwalla5, Phillip H. Lai5, Hui Shen5, David Van Den Berg5, Daniel J. Weisenberger5, Daniel C. Link1, Matthew J. Walter1, Bradley A. Ozenberger11, Elaine R. Mardis1, Peter Westervelt1, Timothy A. Graubert1, John F. DiPersio1, Richard K. Wilson1 
TL;DR: It is found that a complex interplay of genetic events contributes to AML pathogenesis in individual patients and the databases from this study are widely available to serve as a foundation for further investigations of AMl pathogenesis, classification, and risk stratification.
Abstract: BACKGROUND—Many mutations that contribute to the pathogenesis of acute myeloid leukemia (AML) are undefined The relationships between patterns of mutations and epigenetic phenotypes are not yet clear METHODS—We analyzed the genomes of 200 clinically annotated adult cases of de novo AML, using either whole-genome sequencing (50 cases) or whole-exome sequencing (150 cases), along with RNA and microRNA sequencing and DNA-methylation analysis RESULTS—AML genomes have fewer mutations than most other adult cancers, with an average of only 13 mutations found in genes Of these, an average of 5 are in genes that are recurrently mutated in AML A total of 23 genes were significantly mutated, and another 237 were mutated in two or more samples Nearly all samples had at least 1 nonsynonymous mutation in one of nine categories of genes that are almost certainly relevant for pathogenesis, including transcriptionfactor fusions (18% of cases), the gene encoding nucleophosmin (NPM1) (27%), tumorsuppressor genes (16%), DNA-methylation–related genes (44%), signaling genes (59%), chromatin-modifying genes (30%), myeloid transcription-factor genes (22%), cohesin-complex genes (13%), and spliceosome-complex genes (14%) Patterns of cooperation and mutual exclusivity suggested strong biologic relationships among several of the genes and categories CONCLUSIONS—We identified at least one potential driver mutation in nearly all AML samples and found that a complex interplay of genetic events contributes to AML pathogenesis in individual patients The databases from this study are widely available to serve as a foundation for further investigations of AML pathogenesis, classification, and risk stratification (Funded by the National Institutes of Health) The molecular pathogenesis of acute myeloid leukemia (AML) has been studied with the use of cytogenetic analysis for more than three decades Recurrent chromosomal structural variations are well established as diagnostic and prognostic markers, suggesting that acquired genetic abnormalities (ie, somatic mutations) have an essential role in pathogenesis 1,2 However, nearly 50% of AML samples have a normal karyotype, and many of these genomes lack structural abnormalities, even when assessed with high-density comparative genomic hybridization or single-nucleotide polymorphism (SNP) arrays 3-5 (see Glossary) Targeted sequencing has identified recurrent mutations in FLT3, NPM1, KIT, CEBPA, and TET2 6-8 Massively parallel sequencing enabled the discovery of recurrent mutations in DNMT3A 9,10 and IDH1 11 Recent studies have shown that many patients with

3,980 citations

Journal ArticleDOI
TL;DR: Exosomes were described as vesicles of endosomal origin secreted from reticulocytes in the 1980s as discussed by the authors, and their biogenesis, their secretion, and their subsequent fate are discussed, as their functions rely on these important processes.
Abstract: In the 1980s, exosomes were described as vesicles of endosomal origin secreted from reticulocytes. Interest increased around these extracellular vesicles, as they appeared to participate in several cellular processes. Exosomes bear proteins, lipids, and RNAs, mediating intercellular communication between different cell types in the body, and thus affecting normal and pathological conditions. Only recently, scientists acknowledged the difficulty of separating exosomes from other types of extracellular vesicles, which precludes a clear attribution of a particular function to the different types of secreted vesicles. To shed light into this complex but expanding field of science, this review focuses on the definition of exosomes and other secreted extracellular vesicles. Their biogenesis, their secretion, and their subsequent fate are discussed, as their functions rely on these important processes.

3,959 citations

Journal ArticleDOI
07 Feb 2020-Science
TL;DR: The intrinsic properties of exosomes in regulating complex intracellular pathways has advanced their potential utility in the therapeutic control of many diseases, including neurodegenerative conditions and cancer.
Abstract: The study of extracellular vesicles (EVs) has the potential to identify unknown cellular and molecular mechanisms in intercellular communication and in organ homeostasis and disease. Exosomes, with an average diameter of ~100 nanometers, are a subset of EVs. The biogenesis of exosomes involves their origin in endosomes, and subsequent interactions with other intracellular vesicles and organelles generate the final content of the exosomes. Their diverse constituents include nucleic acids, proteins, lipids, amino acids, and metabolites, which can reflect their cell of origin. In various diseases, exosomes offer a window into altered cellular or tissue states, and their detection in biological fluids potentially offers a multicomponent diagnostic readout. The efficient exchange of cellular components through exosomes can inform their applied use in designing exosome-based therapeutics.

3,715 citations