1
|
Farthing DE, Buxbaum NP, Lucas PJ, Maglakelidze N, Oliver B, Wang J, Hu K, Castro E, Bare CV, Gress RE. Comparing DNA enrichment of proliferating cells following administration of different stable isotopes of heavy water. Sci Rep 2017. [PMID: 28642474 PMCID: PMC5481421 DOI: 10.1038/s41598-017-04404-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Deuterated water (2H2O) is a label commonly used for safe quantitative measurement of deuterium enrichment into DNA of proliferating cells. More recently, it has been used for labeling proteins and other biomolecules. Our in vitro - in vivo research reports important stable isotopic labeling enrichment differences into the DNA nucleosides and their isotopologues (e.g. deoxyadenosine (dA) M + 1, dA M + 2, dA M + 3), as well as tumor cell proliferation effects for various forms of commercially available stable heavy water (2H2O, H218O, and 2H218O). Using an in vitro mouse thymus tumor cell line, we determined that H218O provides superior DNA labeling enrichment quantitation, as measured by GC-positive chemical ionization (PCI)-MS/MS. In addition, at higher but physiologically relevant doses, both 2H218O and 2H2O down modulated mouse thymus tumor cell proliferation, whereas H218O water had no observable effects on cell proliferation. The in vivo labeling studies, where normal mouse bone marrow cells (i.e. high turnover) were evaluated post labeling, demonstrated DNA enrichments concordant with measurements from the in vitro studies. Our research also reports a headspace-GC-NCI-MS method, which rapidly and quantitatively measures stable heavy water levels in total body water.
Collapse
Affiliation(s)
- Don E Farthing
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States.
| | - Nataliya P Buxbaum
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Philip J Lucas
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Natella Maglakelidze
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Brittany Oliver
- OCRT&ME, 10 Center Drive, Bethesda, MD, 20814, United States
| | - Jiun Wang
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Kevin Hu
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Ehydel Castro
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Catherine V Bare
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Ronald E Gress
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| |
Collapse
|
2
|
Sbarrato T, Horvilleur E, Pöyry T, Hill K, Chaplin LC, Spriggs RV, Stoneley M, Wilson L, Jayne S, Vulliamy T, Beck D, Dokal I, Dyer MJS, Yeomans AM, Packham G, Bushell M, Wagner SD, Willis AE. A ribosome-related signature in peripheral blood CLL B cells is linked to reduced survival following treatment. Cell Death Dis 2016; 7:e2249. [PMID: 27253413 PMCID: PMC5143378 DOI: 10.1038/cddis.2016.148] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 04/18/2016] [Accepted: 05/02/2016] [Indexed: 01/14/2023]
Abstract
We have used polysome profiling coupled to microarray analysis to examine the translatome of a panel of peripheral blood (PB) B cells isolated from 34 chronic lymphocytic leukaemia (CLL) patients. We have identified a ‘ribosome-related' signature in CLL patients with mRNAs encoding for ribosomal proteins and factors that modify ribosomal RNA, e.g. DKC1 (which encodes dyskerin, a pseudouridine synthase), showing reduced polysomal association and decreased expression of the corresponding proteins. Our data suggest a general impact of dyskerin dysregulation on the translational apparatus in CLL and importantly patients with low dyskerin levels have a significantly shorter period of overall survival following treatment. Thus, translational dysregulation of dyskerin could constitute a mechanism by which the CLL PB B cells acquire an aggressive phenotype and thus have a major role in oncogenesis.
Collapse
Affiliation(s)
- T Sbarrato
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - E Horvilleur
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - T Pöyry
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - K Hill
- The Babraham Institute, Babraham, Cambridge, UK
| | - L C Chaplin
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - R V Spriggs
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - M Stoneley
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - L Wilson
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - S Jayne
- Department of Cancer Studies, Ernest and Helen Scott Haematology Research Institute, University of Leicester, Lancaster Road, Leicester LE1 7H, UK
| | - T Vulliamy
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, Whitechapel, London E1 2AT, UK
| | - D Beck
- Department of Cancer Studies, Ernest and Helen Scott Haematology Research Institute, University of Leicester, Lancaster Road, Leicester LE1 7H, UK
| | - I Dokal
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, Whitechapel, London E1 2AT, UK
| | - M J S Dyer
- Department of Cancer Studies, Ernest and Helen Scott Haematology Research Institute, University of Leicester, Lancaster Road, Leicester LE1 7H, UK
| | - A M Yeomans
- Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton, UK
| | - G Packham
- Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton, UK
| | - M Bushell
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - S D Wagner
- Department of Cancer Studies, Ernest and Helen Scott Haematology Research Institute, University of Leicester, Lancaster Road, Leicester LE1 7H, UK
| | - A E Willis
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| |
Collapse
|
3
|
Schaefer MH, Serrano L, Andrade-Navarro MA. Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions from different cancer types. Front Genet 2015; 6:260. [PMID: 26300911 PMCID: PMC4523822 DOI: 10.3389/fgene.2015.00260] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/21/2015] [Indexed: 01/17/2023] Open
Abstract
Protein-protein interaction (PPI) networks are associated with multiple types of biases partly rooted in technical limitations of the experimental techniques. Another source of bias are the different frequencies with which proteins have been studied for interaction partners. It is generally believed that proteins with a large number of interaction partners tend to be essential, evolutionarily conserved, and involved in disease. It has been repeatedly reported that proteins driving tumor formation have a higher number of PPI partners. However, it has been noticed before that the degree distribution of PPI networks is biased toward disease proteins, which tend to have been studied more often than non-disease proteins. At the same time, for many poorly characterized proteins no interactions have been reported yet. It is unclear to which extent this study bias affects the observation that cancer proteins tend to have more PPI partners. Here, we show that the degree of a protein is a function of the number of times it has been screened for interaction partners. We present a randomization-based method that controls for this bias to decide whether a group of proteins is associated with significantly more PPI partners than the proteomic background. We apply our method to cancer proteins and observe, in contrast to previous studies, no conclusive evidence for a significantly higher degree distribution associated with cancer proteins as compared to non-cancer proteins when we compare them to proteins that have been equally often studied as bait proteins. Comparing proteins from different tumor types, a more complex picture emerges in which proteins of certain cancer classes have significantly more interaction partners while others are associated with a smaller degree. For example, proteins of several hematological cancers tend to be associated with a higher number of interaction partners as expected by chance. Solid tumors, in contrast, are usually associated with a degree distribution similar to those of equally often studied random protein sets. We discuss the biological implications of these findings. Our work shows that accounting for biases in the PPI network is possible and increases the value of PPI data.
Collapse
Affiliation(s)
- Martin H Schaefer
- Systems Biology Research Unit, Centre for Genomic Regulation - European Molecular Biology Laboratory, Barcelona Spain ; Universitat Pompeu Fabra, Barcelona Spain
| | - Luis Serrano
- Systems Biology Research Unit, Centre for Genomic Regulation - European Molecular Biology Laboratory, Barcelona Spain ; Universitat Pompeu Fabra, Barcelona Spain ; Institució Catalana de Recerca i Estudis Avançats, Barcelona Spain
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg University of Mainz Mainz, Germany ; Institute of Molecular Biology, Mainz Germany
| |
Collapse
|
4
|
Bollyky JB, Long SA, Fitch M, Bollyky PL, Rieck M, Rogers R, Samuels PL, Sanda S, Buckner JH, Hellerstein MK, Greenbaum CJ. Evaluation of in vivo T cell kinetics: use of heavy isotope labelling in type 1 diabetes. Clin Exp Immunol 2013; 172:363-74. [PMID: 23600824 DOI: 10.1111/cei.12064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2013] [Indexed: 01/27/2023] Open
Abstract
CD4(+) memory cell development is dependent upon T cell receptor (TCR) signal strength, antigen dose and the cytokine milieu, all of which are altered in type 1 diabetes (T1D). We hypothesized that CD4(+) T cell turnover would be greater in type 1 diabetes subjects compared to controls. In vitro studies of T cell function are unable to evaluate dynamic aspects of immune cell homoeostasis. Therefore, we used deuterium oxide ((2) H(2)O) to assess in vivo turnover of CD4(+) T cell subsets in T1D (n = 10) and control subjects (n = 10). Serial samples of naive, memory and regulatory (T(reg)) CD4(+) T cell subsets were collected and enrichment of deoxyribose was determined by gas chromatography-mass spectrometry (GC-MS). Quantification of T cell turnover was performed using mathematical models to estimate fractional enrichment (f, n = 20), turnover rate (k, n = 20), proliferation (p, n = 10) and disappearance (d*, n = 10). Although turnover of T(regs) was greater than memory and naive cells in both controls and T1D subjects, no differences were seen between T1D and controls in T(reg) or naive kinetics. However, turnover of CD4(+) memory T cells was faster in those with T1D compared to control subjects. Measurement and modelling of incorporated deuterium is useful for evaluating the in vivo kinetics of immune cells in T1D and could be incorporated into studies of the natural history of disease or clinical trials designed to alter the disease course. The enhanced CD4(+) memory T cell turnover in T1D may be important in understanding the pathophysiology and potential treatments of autoimmune diabetes.
Collapse
Affiliation(s)
- J B Bollyky
- Benaroya Research Institute, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|