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Author

Oleh Petriv

Bio: Oleh Petriv is an academic researcher from University of British Columbia. The author has contributed to research in topics: Stem cell & Progenitor cell. The author has an hindex of 9, co-authored 19 publications receiving 1354 citations.

Papers
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Journal ArticleDOI
TL;DR: This work presents a fully integrated microfluidic device capable of performing high-precision RT-qPCR measurements of gene expression from hundreds of single cells per run, and shows that nanoliter volume processing reduced measurement noise, increased sensitivity, and provided single nucleotide specificity.
Abstract: A long-sought milestone in microfluidics research has been the development of integrated technology for scalable analysis of transcription in single cells Here we present a fully integrated microfluidic device capable of performing high-precision RT-qPCR measurements of gene expression from hundreds of single cells per run Our device executes all steps of single-cell processing, including cell capture, cell lysis, reverse transcription, and quantitative PCR In addition to higher throughput and reduced cost, we show that nanoliter volume processing reduced measurement noise, increased sensitivity, and provided single nucleotide specificity We apply this technology to 3,300 single-cell measurements of (i) miRNA expression in K562 cells, (ii) coregulation of a miRNA and one of its target transcripts during differentiation in embryonic stem cells, and (iii) single nucleotide variant detection in primary lobular breast cancer cells The core functionality established here provides the foundation from which a variety of on-chip single-cell transcription analyses will be developed

493 citations

Journal ArticleDOI
TL;DR: A microfluidic 'megapixel' digital PCR device that uses surface tension–based sample partitioning and dehydration control to enable high-fidelity single DNA molecule amplification in 1,000,000 reactors of picoliter volume with densities up to 440,000 reactor cm−2 is presented.
Abstract: We present a microfluidic 'megapixel' digital PCR device that uses surface tension-based sample partitioning and dehydration control to enable high-fidelity single DNA molecule amplification in 1,000,000 reactors of picoliter volume with densities up to 440,000 reactors cm(-2). This device achieves a dynamic range of 10(7), single-nucleotide-variant detection below one copy per 100,000 wild-type sequences and the discrimination of a 1% difference in chromosome copy number.

281 citations

Journal ArticleDOI
TL;DR: The potential for miRNA-mediated release of oncogenes that facilitates leukemic progression from the preleukemic to leukemia inducing state is revealed and the finding of extensive sequence variations (isomiRs) for almost all miRNA and miRNA species adds additional complexity to the miRNA transcriptome.
Abstract: MicroRNAs (miRNAs) have been shown to play important roles in physiological as well as multiple malignant processes, including acute myeloid leukemia (AML). In an effort to gain further insight into the role of miRNAs in AML, we have applied the Illumina massively parallel sequencing platform to carry out an in-depth analysis of the miRNA transcriptome in a murine leukemia progression model. This model simulates the stepwise conversion of a myeloid progenitor cell by an engineered overexpression of the nucleoporin 98 (NUP98)-homeobox HOXD13 fusion gene (ND13), to aggressive AML inducing cells upon transduction with the oncogenic collaborator Meis1. From this data set, we identified 307 miRNA/miRNA species in the ND13 cells and 306 miRNA/miRNA species in ND13+Meis1 cells, corresponding to 223 and 219 miRNA genes. Sequence counts varied between two and 136,558, indicating a remarkable expression range between the detected miRNA species. The large number of miRNAs expressed and the nature of differential expression suggest that leukemic progression as modeled here is dictated by the repertoire of shared, but differentially expressed miRNAs. Our finding of extensive sequence variations (isomiRs) for almost all miRNA and miRNA species adds additional complexity to the miRNA transcriptome. A stringent target prediction analysis coupled with in vitro target validation revealed the potential for miRNA-mediated release of oncogenes that facilitates leukemic progression from the preleukemic to leukemia inducing state. Finally, 55 novel miRNAs species were identified in our data set, adding further complexity to the emerging world of small RNAs.

185 citations

Journal ArticleDOI
TL;DR: A high-throughput microfluidic real-time quantitative PCR approach for generating global miRNA profiles for 27 phenotypically distinct cell populations isolated from normal adult mouse hematopoietic tissues shows that miRNA expression is very tightly regulated within highly purified populations, underscoring the potential of single-cell miRNA profiling for assessing compartment heterogeneity.
Abstract: The hematopoietic system produces a large number of highly specialized cell types that are derived through a hierarchical differentiation process from a common stem cell population miRNAs are critical players in orchestrating this differentiation Here, we report the development and application of a high-throughput microfluidic real-time quantitative PCR (RT-qPCR) approach for generating global miRNA profiles for 27 phenotypically distinct cell populations isolated from normal adult mouse hematopoietic tissues A total of 80,000 RT-qPCR assays were used to map the landscape of miRNA expression across the hematopoietic hierarchy, including rare progenitor and stem cell populations We show that miRNA profiles allow for the direct inference of cell lineage relations and functional similarity Our analysis reveals a close relatedness of the miRNA expression patterns in multipotent progenitors and stem cells, followed by a major reprogramming upon restriction of differentiation potential to a single lineage The analysis of miRNA expression in single hematopoietic cells further demonstrates that miRNA expression is very tightly regulated within highly purified populations, underscoring the potential of single-cell miRNA profiling for assessing compartment heterogeneity

171 citations

Journal ArticleDOI
TL;DR: The results indicate that miR-146a, an LPS-induced miRNA, regulates multiple aspects of hematopoietic differentiation and survival and mimics some of the reported effects with acute LPS exposure.

101 citations


Cited by
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Journal ArticleDOI
TL;DR: A simple and effective method for performing normalization is outlined and dramatically improved results for inferring differential expression in simulated and publicly available data sets are shown.
Abstract: The fine detail provided by sequencing-based transcriptome surveys suggests that RNA-seq is likely to become the platform of choice for interrogating steady state RNA. In order to discover biologically important changes in expression, we show that normalization continues to be an essential step in the analysis. We outline a simple and effective method for performing normalization and show dramatically improved results for inferring differential expression in simulated and publicly available data sets.

6,042 citations

Journal ArticleDOI
TL;DR: This work reviews the major considerations for carrying out and interpreting results of miRNA-profiling studies and suggests several approaches that can be considered for effective use.
Abstract: MicroRNAs (miRNAs) are small RNAs that post-transcriptionally regulate the expression of thousands of genes in a broad range of organisms in both normal physiological contexts and in disease contexts. miRNA expression profiling is gaining popularity because miRNAs, as key regulators in gene expression networks, can influence many biological processes and also show promise as biomarkers for disease. Technological advances have spawned a multitude of platforms for miRNA profiling, and an understanding of the strengths and pitfalls of different approaches can aid in their effective use. Here, we review the major considerations for carrying out and interpreting results of miRNA-profiling studies.

1,465 citations

Journal ArticleDOI
Aviv Regev1, Aviv Regev2, Aviv Regev3, Sarah A. Teichmann4, Sarah A. Teichmann5, Sarah A. Teichmann6, Eric S. Lander7, Eric S. Lander2, Eric S. Lander3, Ido Amit8, Christophe Benoist7, Ewan Birney6, Bernd Bodenmiller9, Bernd Bodenmiller6, Peter J. Campbell5, Peter J. Campbell4, Piero Carninci5, Menna R. Clatworthy10, Hans Clevers11, Bart Deplancke12, Ian Dunham6, James Eberwine13, Roland Eils14, Roland Eils15, Wolfgang Enard16, Andrew Farmer, Lars Fugger17, Berthold Göttgens5, Nir Hacohen7, Nir Hacohen2, Muzlifah Haniffa18, Martin Hemberg4, Seung K. Kim19, Paul Klenerman17, Paul Klenerman20, Arnold R. Kriegstein21, Ed S. Lein22, Sten Linnarsson23, Emma Lundberg24, Emma Lundberg19, Joakim Lundeberg24, Partha P. Majumder, John C. Marioni6, John C. Marioni4, John C. Marioni5, Miriam Merad25, Musa M. Mhlanga26, Martijn C. Nawijn27, Mihai G. Netea28, Garry P. Nolan19, Dana Pe'er29, Anthony Phillipakis2, Chris P. Ponting30, Stephen R. Quake19, Wolf Reik4, Wolf Reik31, Wolf Reik5, Orit Rozenblatt-Rosen2, Joshua R. Sanes7, Rahul Satija32, Ton N. Schumacher33, Alex K. Shalek34, Alex K. Shalek3, Alex K. Shalek2, Ehud Shapiro8, Padmanee Sharma35, Jay W. Shin, Oliver Stegle6, Michael R. Stratton4, Michael J. T. Stubbington4, Fabian J. Theis36, Matthias Uhlen24, Matthias Uhlen37, Alexander van Oudenaarden11, Allon Wagner38, Fiona M. Watt39, Jonathan S. Weissman, Barbara J. Wold40, Ramnik J. Xavier, Nir Yosef34, Nir Yosef38, Human Cell Atlas Meeting Participants 
05 Dec 2017-eLife
TL;DR: An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease.
Abstract: The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.

1,391 citations

Journal ArticleDOI
TL;DR: In reviewing this new field of cancer biology, the methodological approaches of these studies are described, and recommendations for which strategies will be most informative in the future are made.
Abstract: The presence of single nucleotide polymorphisms in microRNA genes, their processing machinery and target binding sites might affect cancer risk, treatment efficacy and patient prognosis. This evolving field of cancer biology is discussed in this Review.

1,190 citations

Journal ArticleDOI
TL;DR: The unabated progress in next-generation sequencing technologies is fostering a wave of new genomics, epigenomics, transcriptomics and proteomics technologies, enabling high-throughput, multi-dimensional analyses of individual cells that will produce detailed knowledge of the cell lineage trees of higher organisms, including humans.
Abstract: The unabated progress in next-generation sequencing technologies is fostering a wave of new genomics, epigenomics, transcriptomics and proteomics technologies. These sequencing-based technologies are increasingly being targeted to individual cells, which will allow many new and longstanding questions to be addressed. For example, single-cell genomics will help to uncover cell lineage relationships; single-cell transcriptomics will supplant the coarse notion of marker-based cell types; and single-cell epigenomics and proteomics will allow the functional states of individual cells to be analysed. These technologies will become integrated within a decade or so, enabling high-throughput, multi-dimensional analyses of individual cells that will produce detailed knowledge of the cell lineage trees of higher organisms, including humans. Such studies will have important implications for both basic biological research and medicine.

1,064 citations