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      Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS

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          Summary

          Lenalidomide is a highly effective treatment for myelodysplastic syndrome (MDS) with deletion of chromosome 5q (del(5q)). Here, we demonstrate that lenalidomide induces the ubiquitination of casein kinase 1A1 (CK1α) by the CRL4 CRBN E3 ubiquitin ligase, resulting in CK1α degradation. CK1α is encoded by a gene within the common deleted region for del(5q) MDS and haploinsufficient expression sensitizes cells to lenalidomide therapy, providing a mechanistic basis for lenalidomide's therapeutic window in del(5q) MDS. We found that mouse cells are resistant to lenalidomide but that changing a single amino acid in mouse Crbn to the corresponding human residue enables lenalidomide-dependent degradation of CK1α. We further demonstrate that minor side chain modifications in thalidomide and a novel analogue, CC-122, can modulate the spectrum of substrates targeted by CRL4 CRBN. These findings have implications for the clinical activity of lenalidomide and related compounds and demonstrate the therapeutic potential of novel modulators of E3 ubiquitin ligases.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Statistical methods for assessing agreement between two methods of clinical measurement.

            In clinical measurement comparison of a new measurement technique with an established one is often needed to see whether they agree sufficiently for the new to replace the old. Such investigations are often analysed inappropriately, notably by using correlation coefficients. The use of correlation is misleading. An alternative approach, based on graphical techniques and simple calculations, is described, together with the relation between this analysis and the assessment of repeatability.
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              Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.

              Quantitative proteomics has traditionally been performed by two-dimensional gel electrophoresis, but recently, mass spectrometric methods based on stable isotope quantitation have shown great promise for the simultaneous and automated identification and quantitation of complex protein mixtures. Here we describe a method, termed SILAC, for stable isotope labeling by amino acids in cell culture, for the in vivo incorporation of specific amino acids into all mammalian proteins. Mammalian cell lines are grown in media lacking a standard essential amino acid but supplemented with a non-radioactive, isotopically labeled form of that amino acid, in this case deuterated leucine (Leu-d3). We find that growth of cells maintained in these media is no different from growth in normal media as evidenced by cell morphology, doubling time, and ability to differentiate. Complete incorporation of Leu-d3 occurred after five doublings in the cell lines and proteins studied. Protein populations from experimental and control samples are mixed directly after harvesting, and mass spectrometric identification is straightforward as every leucine-containing peptide incorporates either all normal leucine or all Leu-d3. We have applied this technique to the relative quantitation of changes in protein expression during the process of muscle cell differentiation. Proteins that were found to be up-regulated during this process include glyceraldehyde-3-phosphate dehydrogenase, fibronectin, and pyruvate kinase M2. SILAC is a simple, inexpensive, and accurate procedure that can be used as a quantitative proteomic approach in any cell culture system.
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                6 June 2015
                01 July 2015
                9 July 2015
                03 May 2016
                : 523
                : 7559
                : 183-188
                Affiliations
                [1 ] Brigham and Women's Hospital, Division of Hematology, Boston, Massachusetts, USA.
                [2 ] University Hospital of Ulm, Department of Internal Medicine III, Ulm, Germany.
                [3 ] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
                [4 ] Celgene Corporation, San Diego, California, USA.
                [5 ] Roswell Park Cancer Center, Buffalo, New York, USA.
                Author notes
                Correspondence: Benjamin L. Ebert, Brigham and Women's Hospital, 1 Blackfan Circle – Karp CHRB 5.210, Boston, MA 02115, bebert@ 123456partners.org
                Article
                NIHMS697379
                10.1038/nature14610
                4853910
                26131937
                24c02026-6874-42ed-8cdd-22972e3dabeb

                Reprints and permissions information is available at www.nature.com/reprints.

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