51
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Understanding CML, 1 cell at a time. Blood 2017; 129:2339-2340. [PMID: 28450572 DOI: 10.1182/blood-2017-02-765578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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52
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Ellis H, Joshi MB, Lynn AJ, Walden A. Consensus-Driven Development of a Terminology for Biobanking, the Duke Experience. Biopreserv Biobank 2017; 15:126-133. [PMID: 28338350 PMCID: PMC5397220 DOI: 10.1089/bio.2016.0092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Biobanking at Duke University has existed for decades and has grown over time in silos and based on specialized needs, as is true with most biomedical research centers. These silos developed informatics systems to support their own individual requirements, with no regard for semantic or syntactic interoperability. Duke undertook an initiative to implement an enterprise-wide biobanking information system to serve its many diverse biobanking entities. A significant part of this initiative was the development of a common terminology for use in the commercial software platform. Common terminology provides the foundation for interoperability across biobanks for data and information sharing. We engaged experts in research, informatics, and biobanking through a consensus-driven process to agree on 361 terms and their definitions that encompass the lifecycle of a biospecimen. Existing standards, common terms, and data elements from published articles provided a foundation on which to build the biobanking terminology; a broader set of stakeholders then provided additional input and feedback in a secondary vetting process. The resulting standardized biobanking terminology is now available for sharing with the biobanking community to serve as a foundation for other institutions who are considering a similar initiative.
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Affiliation(s)
- Helena Ellis
- Biobanking Without Borders, LLC, Durham, North Carolina
| | - Mary-Beth Joshi
- Department of Surgery, Duke University, Durham, North Carolina
| | - Aenoch J. Lynn
- Buck Institute for Research on Aging, Novato, California
| | - Anita Walden
- University of Arkansas for Medical Sciences, Little Rock, Arkansas
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53
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Tarlock K, Alonzo TA, Loken MR, Gerbing RB, Ries RE, Aplenc R, Sung L, Raimondi SC, Hirsch BA, Kahwash SB, McKenney A, Kolb EA, Gamis AS, Meshinchi S. Disease Characteristics and Prognostic Implications of Cell-Surface FLT3 Receptor (CD135) Expression in Pediatric Acute Myeloid Leukemia: A Report from the Children's Oncology Group. Clin Cancer Res 2017; 23:3649-3656. [PMID: 28108543 DOI: 10.1158/1078-0432.ccr-16-2353] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/20/2016] [Accepted: 01/05/2017] [Indexed: 01/24/2023]
Abstract
Purpose: The FLT3 cell-surface receptor tyrosine kinase (CD135) is expressed in a majority of both acute lymphoid leukemia (ALL) and myeloid leukemia (AML). However, the prognostic significance of CD135 expression in AML remains unclear. We therefore evaluated the association between FLT3 surface expression and disease characteristics and outcomes in pediatric patients with AML.Experimental Design: We analyzed FLT3 receptor expression on AML blasts by multi-dimensional flow cytometry and its association with disease characteristics, clinical outcomes, and FLT3 transcript level in 367 children with AML treated on the Children's Oncology Group trial AAML0531.Results: There was high variability in blast CD135 cell-surface expression across specimens. CD135 expression measured by flow cytometry was not correlated with FLT3 transcript expression determined by quantitative RT-PCR. Overall, CD135 expression was not significantly different for patients with FLT3/WT, FLT3/ITD, or FLT3/ALM (P = 0.25). High cell-surface CD135 expression was associated with FAB M5 subtype (P < 0.001), KMT2A rearrangements (P = 0.009), and inversely associated with inv(16)/t(16;16) (P < 0.001). Complete remission rate, overall survival, disease-free survival, and relapse rates were not significantly different between patients with low and high CD135 expression.Conclusions: FLT3 cell-surface expression did not vary by FLT3 mutational status, but high FLT3 expression was strongly associated with KMT2A rearrangements. Our study found that there was no prognostic significance of FLT3 cell surface expression in pediatric AML. Clin Cancer Res; 23(14); 3649-56. ©2017 AACR.
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Affiliation(s)
- Katherine Tarlock
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. .,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Todd A Alonzo
- Children's Oncology Group, Monrovia, California.,Keck School of Medicine, University of Southern California, Los Angeles, California
| | | | | | - Rhonda E Ries
- Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Richard Aplenc
- Division of Hematology/Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lillian Sung
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario
| | | | - Betsy A Hirsch
- Division of Laboratory Medicine, University of Minnesota Medical School, Minneapolis, Minnesota
| | | | | | - E Anders Kolb
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Alan S Gamis
- Children's Mercy Hospitals and Clinics, Kansas City, Missouri
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
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54
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Abstract
Technology development in biological research often aims to either increase the number of cellular features that can be surveyed simultaneously or enhance the resolution at which such observations are possible. For decades, flow cytometry has balanced these goals to fill a critical need by enabling the measurement of multiple features in single cells, commonly to examine complex or hierarchical cellular systems. Recently, a format for flow cytometry has been developed that leverages the precision of mass spectrometry. This fusion of the two technologies, termed mass cytometry, provides measurement of over 40 simultaneous cellular parameters at single-cell resolution, significantly augmenting the ability of cytometry to evaluate complex cellular systems and processes. In this Primer, we review the current state of mass cytometry, providing an overview of the instrumentation, its present capabilities, and methods of data analysis, as well as thoughts on future developments and applications.
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55
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Jagannathan S, Bradley RK. Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population. Genome Res 2016; 26:1639-1650. [PMID: 27646533 PMCID: PMC5131816 DOI: 10.1101/gr.205070.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 09/16/2016] [Indexed: 01/12/2023]
Abstract
Genetic variants that disrupt protein-coding DNA are ubiquitous in the human population, with about 100 such loss-of-function variants per individual. While most loss-of-function variants are rare, a subset have risen to high frequency and occur in a homozygous state in healthy individuals. It is unknown why these common variants are well tolerated, even though some affect essential genes implicated in Mendelian disease. Here, we combine genomic, proteomic, and biochemical data to demonstrate that many common nonsense variants do not ablate protein production from their host genes. We provide computational and experimental evidence for diverse mechanisms of gene rescue, including alternative splicing, stop codon readthrough, alternative translation initiation, and C-terminal truncation. Our results suggest a molecular explanation for the mild fitness costs of many common nonsense variants and indicate that translational plasticity plays a prominent role in shaping human genetic diversity.
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Affiliation(s)
- Sujatha Jagannathan
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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56
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Highly multiplexed simultaneous detection of RNAs and proteins in single cells. Nat Methods 2016; 13:269-75. [PMID: 26808670 PMCID: PMC4767631 DOI: 10.1038/nmeth.3742] [Citation(s) in RCA: 231] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/16/2015] [Indexed: 12/20/2022]
Abstract
Precise gene expression measurement has been fundamental to developing an advanced understanding of the roles of biological networks in health and disease. To enable detection of expression signatures specific to individual cells we developed PLAYR (Proximity Ligation Assay for RNA). PLAYR enables highly multiplexed quantification of transcripts in single cells by flow- and mass-cytometry and is compatible with standard antibody staining of proteins. With mass cytometry, this currently enables simultaneous quantification of more than 40 different mRNAs and proteins. The technology was demonstrated in primary cells to be capable of quantifying multiple gene expression transcripts while the identity and the functional state of each analyzed cell was defined based on the expression of other transcripts or proteins. PLAYR now enables high throughput deep phenotyping of cells to readily expand beyond protein epitopes to include RNA expression, thereby opening a new venue on the characterization of cellular metabolism.
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57
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DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia. Nat Genet 2016; 48:253-64. [PMID: 26780610 DOI: 10.1038/ng.3488] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 12/17/2015] [Indexed: 12/14/2022]
Abstract
Charting differences between tumors and normal tissue is a mainstay of cancer research. However, clonal tumor expansion from complex normal tissue architectures potentially obscures cancer-specific events, including divergent epigenetic patterns. Using whole-genome bisulfite sequencing of normal B cell subsets, we observed broad epigenetic programming of selective transcription factor binding sites coincident with the degree of B cell maturation. By comparing normal B cells to malignant B cells from 268 patients with chronic lymphocytic leukemia (CLL), we showed that tumors derive largely from a continuum of maturation states reflected in normal developmental stages. Epigenetic maturation in CLL was associated with an indolent gene expression pattern and increasingly favorable clinical outcomes. We further uncovered that most previously reported tumor-specific methylation events are normally present in non-malignant B cells. Instead, we identified a potential pathogenic role for transcription factor dysregulation in CLL, where excess programming by EGR and NFAT with reduced EBF and AP-1 programming imbalances the normal B cell epigenetic program.
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58
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Meißner T, Seckinger A, Hemminki K, Bertsch U, Foersti A, Haenel M, Duering J, Salwender H, Goldschmidt H, Morgan GJ, Hose D, Weinhold N. Profound impact of sample processing delay on gene expression of multiple myeloma plasma cells. BMC Med Genomics 2015; 8:85. [PMID: 26714877 PMCID: PMC4696100 DOI: 10.1186/s12920-015-0161-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 12/05/2015] [Indexed: 12/18/2022] Open
Abstract
Background Gene expression profiling (GEP) has significantly contributed to the elucidation of the molecular heterogeneity of multiple myeloma plasma cells (MMPC) and only recently it has been recommended for risk stratification. Prior to GEP MMPC need to be enriched resulting in an inability to immediately freeze bone marrow aspirates or use RNA stabilization reagents. As a result in multi-center MM trials sample processing delay due to shipping may be an important confounder of molecular analyses and risk stratification based on GEP data. Results We compared GEP data of 145 in-house and 246 shipped samples and detected 3301 down-regulated and 3501 up-regulated genes in shipped samples. For 3994 genes we confirmed differential expression in an independent set of 85 in-house and 97 shipped samples. Differentially expressed genes were enriched in processes like ribosome biogenesis, cell cycle, and apoptosis. Among GEP based risk predictors the IFM-15 seemed to underestimate high risk in shipped samples, whereas the GEP70 and the EMC-92 gene signatures were more robust. In order to provide a tool to assess the “shipping effect” in public repositories, we generated a 17-gene predictor for shipped samples with a 10-fold cross validation error rate of 0.06 for the training set and an error rate of 0.15 for the validation set. Conclusion Sample processing delay significantly influences GEP of MMPC, implying it should be avoided if samples were used for risk stratification. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0161-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tobias Meißner
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany. .,Department of Molecular and Experimental Medicine, Avera Cancer Institute, 11099 North Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Anja Seckinger
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Center for Primary Health Care Ressearch, Lund University, Malmo, Sweden.
| | - Uta Bertsch
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.
| | - Asta Foersti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Center for Primary Health Care Ressearch, Lund University, Malmo, Sweden.
| | - Mathias Haenel
- Department of Internal Medicine III, Klinikum Chemnitz, Chemnitz, Germany.
| | - Jan Duering
- Department of Hematology, University Hospital Essen, Essen, Germany.
| | - Hans Salwender
- Department of Hematology and Oncology, Asklepios Hospital Hamburg Altona, Hamburg, Germany.
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany. .,National Center for Tumor Diseases, Heidelberg, Germany.
| | | | - Dirk Hose
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.,National Center for Tumor Diseases, Heidelberg, Germany
| | - Niels Weinhold
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.,Myeloma Institute, Little Rock, AR, USA
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59
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NOTCH2 missplicing can occur in relation to apoptosis. Blood 2015; 126:1731-2. [PMID: 26429967 DOI: 10.1182/blood-2015-07-657825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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60
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Grinev VV, Migas AA, Kirsanava AD, Mishkova OA, Siomava N, Ramanouskaya TV, Vaitsiankova AV, Ilyushonak IM, Nazarov PV, Vallar L, Aleinikova OV. Decoding of exon splicing patterns in the human RUNX1-RUNX1T1 fusion gene. Int J Biochem Cell Biol 2015; 68:48-58. [PMID: 26320575 DOI: 10.1016/j.biocel.2015.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/12/2015] [Accepted: 08/24/2015] [Indexed: 11/25/2022]
Abstract
The t(8;21) translocation is the most widespread genetic defect found in human acute myeloid leukemia. This translocation results in the RUNX1-RUNX1T1 fusion gene that produces a wide variety of alternative transcripts and influences the course of the disease. The rules of combinatorics and splicing of exons in the RUNX1-RUNX1T1 transcripts are not known. To address this issue, we developed an exon graph model of the fusion gene organization and evaluated its local exon combinatorics by the exon combinatorial index (ECI). Here we show that the local exon combinatorics of the RUNX1-RUNX1T1 gene follows a power-law behavior and (i) the vast majority of exons has a low ECI, (ii) only a small part is represented by "exons-hubs" of splicing with very high ECI values, and (iii) it is scale-free and very sensitive to targeted skipping of "exons-hubs". Stochasticity of the splicing machinery and preferred usage of exons in alternative splicing can explain such behavior of the system. Stochasticity may explain up to 12% of the ECI variance and results in a number of non-coding and unproductive transcripts that can be considered as a noise. Half-life of these transcripts is increased due to the deregulation of some key genes of the nonsense-mediated decay system in leukemia cells. On the other hand, preferred usage of exons may explain up to 75% of the ECI variability. Our analysis revealed a set of splicing-related cis-regulatory motifs that can explain "attractiveness" of exons in alternative splicing but only when they are considered together. Cis-regulatory motifs are guides for splicing trans-factors and we observed a leukemia-specific profile of expression of the splicing genes in t(8;21)-positive blasts. Altogether, our results show that alternative splicing of the RUNX1-RUNX1T1 transcripts follows strict rules and that the power-law component of the fusion gene organization confers a high flexibility to this process.
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Affiliation(s)
- Vasily V Grinev
- Department of Genetics, Faculty of Biology, Belarusian State University, Minsk, Belarus.
| | - Alexandr A Migas
- Laboratory of the Genetic Biotechnology, Department of Research, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Aksana D Kirsanava
- Department of Genetics, Faculty of Biology, Belarusian State University, Minsk, Belarus
| | - Olga A Mishkova
- Laboratory of the Genetic Biotechnology, Department of Research, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Natalia Siomava
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | | | - Alina V Vaitsiankova
- Department of Genetics, Faculty of Biology, Belarusian State University, Minsk, Belarus
| | - Ilia M Ilyushonak
- Department of Genetics, Faculty of Biology, Belarusian State University, Minsk, Belarus
| | - Petr V Nazarov
- Genomics Research Unit, Luxembourg Institute of Health, Luxembourg
| | - Laurent Vallar
- Genomics Research Unit, Luxembourg Institute of Health, Luxembourg
| | - Olga V Aleinikova
- Laboratory of the Genetic Biotechnology, Department of Research, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
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61
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Gloss BS, Dinger ME. The specificity of long noncoding RNA expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:16-22. [PMID: 26297315 DOI: 10.1016/j.bbagrm.2015.08.005] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/12/2015] [Accepted: 08/12/2015] [Indexed: 01/09/2023]
Abstract
Over the last decade, long noncoding RNAs (lncRNAs) have emerged as a fundamental molecular class whose members play pivotal roles in the regulation of the genome. The observation of pervasive transcription of mammalian genomes in the early 2000s sparked a revolution in the understanding of information flow in eukaryotic cells and the incredible flexibility and dynamic nature of the transcriptome. As a molecular class, distinct loci yielding lncRNAs are set to outnumber those yielding mRNAs. However, like many important discoveries, the road leading to uncovering this diverse class of molecules that act through a remarkable repertoire of mechanisms, was not a straight one. The same characteristic that most distinguishes lncRNAs from mRNAs, i.e. their developmental-stage, tissue-, and cell-specific expression, was one of the major impediments to their discovery and recognition as potentially functional regulatory molecules. With growing numbers of lncRNAs being assigned to biological functions, the specificity of lncRNA expression is now increasingly recognized as a characteristic that imbues lncRNAs with great potential as biomarkers and for the development of highly targeted therapeutics. Here we review the history of lncRNA research and how technological advances and insight into biological complexity have gone hand-in-hand in shaping this revolution. We anticipate that as increasing numbers of these molecules, often described as the dark matter of the genome, are characterized and the structure-function relationship of lncRNAs becomes better understood, it may ultimately be feasible to decipher what these non-(protein)-coding genes encode. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Brian S Gloss
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia
| | - Marcel E Dinger
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia.
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62
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Vandepoele K, Philippé J, Denys B. The YPEL5-PPP1CB fusion transcript is detected in different hematological malignancies and in normal samples. Leuk Res Rep 2015; 4:51-4. [PMID: 26605151 PMCID: PMC4621498 DOI: 10.1016/j.lrr.2015.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 06/17/2015] [Accepted: 07/07/2015] [Indexed: 11/30/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most frequent leukemia in Western adults. It was suggested that transcripts from a reciprocal trans-splicing event between YPEL5 and PPP1CB were present exclusively in CLL patients (more than 90%). Here we show that the YPEL5–PPP1CB fusion is not specific for CLL but is also detected in other hematological malignancies such as chronic myeloid leukemia, monoclonal B cell lymphocytosis or acute leukemia and also in normal samples. As such, it is unlikely that the YPEL5–PPP1CB fusion is a good drug target in CLL or a suitable target to monitor disease. YPEL5–PPP1CB is a chimeric transcript detected in CLL. We detect this transcript also in non-CLL samples. This marker is not suitable for diagnostic purposes of CLL.
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Affiliation(s)
- Karl Vandepoele
- Laboratory for Molecular Diagnostics-Hematology, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
- Corresponding author. Fax: +32 93324985.
| | - Jan Philippé
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Barbara Denys
- Laboratory for Molecular Diagnostics-Hematology, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
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63
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Amenyogbe N, Levy O, Kollmann TR. Systems vaccinology: a promise for the young and the poor. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140340. [PMID: 25964462 PMCID: PMC4527395 DOI: 10.1098/rstb.2014.0340] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2015] [Indexed: 12/15/2022] Open
Abstract
As a child, the risk of suffering and dying from infection is higher the younger you are; and higher, the less developed a region you are born in. Childhood vaccination programmes have greatly reduced mortality around the world, but least so for the very young among the very poor of the world. This appears partly owing to suboptimal vaccine effectiveness. Unfortunately, although most vaccines are administered to the newborn and very young infant (less than or equal to two months), we know the least about their host response to vaccination. We thus currently lack the knowledge to guide efforts aimed at improving vaccine effectiveness in this vulnerable population. Systems vaccinology, the study of molecular networks activated by immunization, has begun to provide unprecedented insights into mechanisms leading to vaccine-induced protection from infection or disease. However, all published reports of systems vaccinology have focused on either adults or at most children and older infants, not those most in need, i.e. newborns and very young infants. Given that the tools of systems vaccinology work perfectly well with very small sample volumes, it is time we deliver the promise that systems vaccinology holds for those most in need of vaccine-mediated protection from infection.
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Affiliation(s)
- Nelly Amenyogbe
- Department of Experimental Medicine, University of British Columbia, CFRI A5-147, 950 W28th Avenue, Vancouver, British Columbia, Canada V5Z 4H4 Department of Pediatrics, University of British Columbia, CFRI A5-147, 950 W28th Avenue, Vancouver, British Columbia, Canada V5Z 4H4
| | - Ofer Levy
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, USA Harvard Medical School, Boston, MA 02115, USA
| | - Tobias R Kollmann
- Department of Experimental Medicine, University of British Columbia, CFRI A5-147, 950 W28th Avenue, Vancouver, British Columbia, Canada V5Z 4H4 Department of Pediatrics, University of British Columbia, CFRI A5-147, 950 W28th Avenue, Vancouver, British Columbia, Canada V5Z 4H4
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64
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Dvinge H, Bradley RK. Widespread intron retention diversifies most cancer transcriptomes. Genome Med 2015; 7:45. [PMID: 26113877 PMCID: PMC4480902 DOI: 10.1186/s13073-015-0168-9] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/30/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Somatic mutations affecting components of the RNA splicing machinery occur with high frequencies across many tumor types. These mutations give rise to distinct alterations in normal splice site and exon recognition, such as unusual 3' splice site preferences, that likely contribute to tumorigenesis. METHODS We analyzed genome-wide patterns of RNA splicing across 805 matched tumor and normal control samples from 16 distinct cancer types to identify signals of abnormal cancer-associated splicing. RESULTS We found that abnormal RNA splicing, typified by widespread intron retention, is common across cancers even in the absence of mutations directly affecting the RNA splicing machinery. Almost all liquid and solid cancer types exhibited frequent retention of both alternative and constitutive introns relative to control normal tissues. The sole exception was breast cancer, where intron retention typified adjacent normal rather than cancer tissue. Different introns were preferentially retained in specific cancer types, although a small subset of introns enriched for genes encoding RNA splicing and export factors exhibited frequent retention across diverse cancers. The extent of intron retention correlated with the presence of IDH1 and IDH2 mutations in acute myeloid leukemia and across molecular subtypes in breast cancer. Many introns that were preferentially retained in primary cancers were present at high levels in the cytoplasmic mRNA pools of cancer cell lines. CONCLUSIONS Our data indicate that abnormal RNA splicing is a common characteristic of cancers even in the absence of mutational insults to the splicing machinery, and suggest that intron-containing mRNAs contribute to the transcriptional diversity of many cancers.
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Affiliation(s)
- Heidi Dvinge
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
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