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Author Rush, J.S. url  openurl
  Title Role of Flippases in Protein Glycosylation in the Endoplasmic Reticulum Type Journal Article
  Year 2015 Publication Abbreviated Journal Lipid Insights  
  Volume 8 Issue Suppl 1 Pages 45-53  
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  Abstract Glycosylation is essential to the synthesis, folding, and function of glycoproteins in eukaryotes. Proteins are co- and posttranslationally modified by a variety of glycans in the endoplasmic reticulum (ER); modifications include C- and O-mannosylation, N-glycosylation, and the addition of glycosylphosphatidylinositol membrane anchors. Protein glycosylation in the ER of eukaryotes involves enzymatic steps on both the cytosolic and lumenal surfaces of the ER membrane. The glycans are first assembled as precursor glycolipids, on the cytosolic surface of the ER, which are tethered to the membrane by attachment to a long-chain polyisoprenyl phosphate (dolichol) containing a reduced α-isoprene. The lipid-anchored building blocks then migrate transversely (flip) across the ER membrane to the lumenal surface, where final assembly of the glycan is completed. This strategy allows the cell to export high-energy biosynthetic intermediates as lipid-bound glycans, while constraining the glycosyl donors to the site of assembly on the membrane surface. This review focuses on the flippases that participate in protein glycosylation in the ER.  
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  Call Number UofT @ ankit.sinha @ Serial 45207  
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Author Stowell, S.R.; Ju, T.; Cummings, R.D. url  openurl
  Title Protein glycosylation in cancer Type Journal Article
  Year 2015 Publication Abbreviated Journal Annu Rev Pathol  
  Volume 10 Issue Pages 473-510  
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  Abstract Neoplastic transformation results in a wide variety of cellular alterations that impact the growth, survival, and general behavior of affected tissue. Although genetic alterations underpin the development of neoplastic disease, epigenetic changes can exert an equally significant effect on neoplastic transformation. Among neoplasia-associated epigenetic alterations, changes in cellular glycosylation have recently received attention as a key component of neoplastic progression. Alterations in glycosylation appear to not only directly impact cell growth and survival but also facilitate tumor-induced immunomodulation and eventual metastasis. Many of these changes may support neoplastic progression, and unique alterations in tumor-associated glycosylation may also serve as a distinct feature of cancer cells and therefore provide novel diagnostic and even therapeutic targets.  
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  Call Number UofT @ ankit.sinha @ Serial 45212  
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Author Sowers, J.L.; Mirfattah, B.; Xu, P.; Tang, H.; Park, I.Y.; Walker, C.; Wu, P.; Laezza, F.; Sowers, L.C.; Zhang, K. url  openurl
  Title Quantification of histone modifications by parallel-reaction monitoring: a method validation Type Journal Article
  Year 2015 Publication Abbreviated Journal Anal Chem  
  Volume 87 Issue 19 Pages 10006-10014  
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  Abstract Abnormal epigenetic reprogramming is one of the major causes leading to irregular gene expression and regulatory pathway perturbations, in the cells, resulting in unhealthy cell development or diseases. Accurate measurements of these changes of epigenetic modifications, especially the complex histone modifications, are very important, and the methods for these measurements are not trivial. By following our previous introduction of PRM to targeting histone modifications (Tang, H.; Fang, H.; Yin, E.; Brasier, A. R.; Sowers, L. C.; Zhang, K. Multiplexed parallel reaction monitoring targeting histone modifications on the QExactive mass spectrometer. Anal. Chem. 2014, 86 (11), 5526-34), herein we validated this method by varying the protein/trypsin ratios via serial dilutions. Our data demonstrated that PRM with SILAC histones as the internal standards allowed reproducible measurements of histone H3/H4 acetylation and methylation in the samples whose histone contents differ at least one-order of magnitude. The method was further validated by histones isolated from histone H3 K36 trimethyltransferase SETD2 knockout mouse embryonic fibroblasts (MEF) cells. Furthermore, histone acetylation and methylation in human neural stem cells (hNSC) treated with ascorbic acid phosphate (AAP) were measured by this method, revealing that H3 K36 trimethylation was significantly down-regulated by 6 days of treatment with vitamin C.  
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  Call Number UofT @ ankit.sinha @ Serial 45227  
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Author Robertson, I.B.; Horiguchi, M.; Zilberberg, L.; Dabovic, B.; Hadjiolova, K.; Rifkin, D.B. url  openurl
  Title Latent TGF-β-binding proteins Type Journal Article
  Year 2015 Publication Abbreviated Journal Matrix Biol  
  Volume 47 Issue Pages 44-53  
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  Abstract The LTBPs (or latent transforming growth factor β binding proteins) are important components of the extracellular matrix (ECM) that interact with fibrillin microfibrils and have a number of different roles in microfibril biology. There are four LTBPs isoforms in the human genome (LTBP-1, -2, -3, and -4), all of which appear to associate with fibrillin and the biology of each isoform is reviewed here. The LTBPs were first identified as forming latent complexes with TGFβ by covalently binding the TGFβ propeptide (LAP) via disulfide bonds in the endoplasmic reticulum. LAP in turn is cleaved from the mature TGFβ precursor in the trans-golgi network but LAP and TGFβ remain strongly bound through non-covalent interactions. LAP, TGFβ, and LTBP together form the large latent complex (LLC). LTBPs were originally thought to primarily play a role in maintaining TGFβ latency and targeting the latent growth factor to the extracellular matrix (ECM), but it has also been shown that LTBP-1 participates in TGFβ activation by integrins and may also regulate activation by proteases and other factors. LTBP-3 appears to have a role in skeletal formation including tooth development. As well as having important functions in TGFβ regulation, TGFβ-independent activities have recently been identified for LTBP-2 and LTBP-4 in stabilizing microfibril bundles and regulating elastic fiber assembly.  
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  Call Number UofT @ ankit.sinha @ Serial 45253  
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Author Blume-Jensen, P.; Berman, D.M.; Rimm, D.L.; Shipitsin, M.; Putzi, M.; Nifong, T.P.; Small, C.; Choudhury, S.; Capela, T.; Coupal, L.; Ernst, C.; Hurley, A.; Kaprelyants, A.; Chang, H.; Giladi, E.; Nardone, J.; Dunyak, J.; Loda, M.; Klein, E.A.; Magi-Galluzzi, C.; Latour, M.; Epstein, J.I.; Kantoff, P.; Saad, F. url  openurl
  Title Development and clinical validation of an in situ biopsy-based multimarker assay for risk stratification in prostate cancer Type Journal Article
  Year 2015 Publication Abbreviated Journal Clin Cancer Res  
  Volume 21 Issue 11 Pages 2591-2600  
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  Abstract PURPOSE: Prostate cancer aggressiveness and appropriate therapy are routinely determined following biopsy sampling. Current clinical and pathologic parameters are insufficient for accurate risk prediction leading primarily to overtreatment and also missed opportunities for curative therapy. EXPERIMENTAL DESIGN: An 8-biomarker proteomic assay for intact tissue biopsies predictive of prostate pathology was defined in a study of 381 patient biopsies with matched prostatectomy specimens. A second blinded study of 276 cases validated this assay’s ability to distinguish “favorable” versus “nonfavorable” pathology independently and relative to current risk classification systems National Comprehensive Cancer Network (NCCN and D’Amico). RESULTS: A favorable biomarker risk score of ≤0.33, and a nonfavorable risk score of >0.80 (possible range between 0 and 1) were defined on “false-negative” and “false-positive” rates of 10% and 5%, respectively. At a risk score ≤0.33, predictive values for favorable pathology in very low-risk and low-risk NCCN and low-risk D’Amico groups were 95%, 81.5%, and 87.2%, respectively, higher than for these current risk classification groups themselves (80.3%, 63.8%, and 70.6%, respectively). The predictive value for nonfavorable pathology was 76.9% at biomarker risk scores >0.8 across all risk groups. Increased biomarker risk scores correlated with decreased frequency of favorable cases across all risk groups. The validation study met its two coprimary endpoints, separating favorable from nonfavorable pathology (AUC, 0.68; P < 0.0001; OR, 20.9) and GS-6 versus non-GS-6 pathology (AUC, 0.65; P < 0.0001; OR, 12.95). CONCLUSIONS: The 8-biomarker assay provided individualized, independent prognostic information relative to current risk stratification systems, and may improve the precision of clinical decision making following prostate biopsy.  
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  Call Number UofT @ ankit.sinha @ Serial 45258  
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Author Ignatchenko, V.; Ignatchenko, A.; Sinha, A.; Boutros, P.C.; Kislinger, T. url  openurl
  Title VennDIS: a JavaFX-based Venn and Euler diagram software to generate publication quality figures Type Journal Article
  Year 2015 Publication Abbreviated Journal Proteomics  
  Volume 15 Issue 7 Pages 1239-1244  
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  Abstract Venn diagrams are graphical representations of the relationships among multiple sets of objects and are often used to illustrate similarities and differences among genomic and proteomic datasets. All currently existing tools for producing Venn diagrams evince one of two traits; they require expertise in specific statistical software packages (such as R), or lack the flexibility required to produce publication-quality figures. We describe a simple tool that addresses both shortcomings, Venn Diagram Interactive Software (VennDIS), a JavaFX-based solution for producing highly customizable, publication-quality Venn, and Euler diagrams of up to five sets. The strengths of VennDIS are its simple graphical user interface and its large array of customization options, including the ability to modify attributes such as font, style and position of the labels, background color, size of the circle/ellipse, and outline color. It is platform independent and provides real-time visualization of figure modifications. The created figures can be saved as XML files for future modification or exported as high-resolution images for direct use in publications.  
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  Call Number UofT @ ankit.sinha @ Serial 45271  
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Author Schölz, C.; Lyon, D.; Refsgaard, J.C.; Jensen, L.J.; Choudhary, C.; Weinert, B.T. url  openurl
  Title Avoiding abundance bias in the functional annotation of post-translationally modified proteins Type Journal Article
  Year 2015 Publication Abbreviated Journal Nat Methods  
  Volume 12 Issue 11 Pages 1003-1004  
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  Call Number UofT @ ankit.sinha @ Serial 45272  
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Author Van Gool, B.; Dedieu, S.; Emonard, H.; Roebroek, A.J. url  openurl
  Title The Matricellular Receptor LRP1 Forms an Interface for Signaling and Endocytosis in Modulation of the Extracellular Tumor Environment Type Journal Article
  Year 2015 Publication Abbreviated Journal Front Pharmacol  
  Volume 6 Issue Pages 271  
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  Abstract The membrane protein low-density lipoprotein receptor related-protein 1 (LRP1) has been attributed a role in cancer. However, its presumably often indirect involvement is far from understood. LRP1 has both endocytic and signaling activities. As a matricellular receptor it is involved in regulation, mostly by clearing, of various extracellular matrix degrading enzymes including matrix metalloproteinases, serine proteases, protease inhibitor complexes, and the endoglycosidase heparanase. Furthermore, by binding extracellular ligands including growth factors and subsequent intracellular interaction with scaffolding and adaptor proteins it is involved in regulation of various signaling cascades. LRP1 expression levels are often downregulated in cancer and some studies consider low LRP1 levels a poor prognostic factor. On the contrary, upregulation in brain cancers has been noted and clinical trials explore the use of LRP1 as cargo receptor to deliver cytotoxic agents. This mini-review focuses on LRP1’s role in tumor growth and metastasis especially by modulation of the extracellular tumor environment. In relation to this role its diagnostic, prognostic and therapeutic potential will be discussed.  
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  Call Number UofT @ ankit.sinha @ Serial 45275  
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Author Pinho, S.S.; Reis, C.A. url  openurl
  Title Glycosylation in cancer: mechanisms and clinical implications Type Journal Article
  Year 2015 Publication Abbreviated Journal Nat Rev Cancer  
  Volume 15 Issue 9 Pages 540-555  
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  Abstract Despite recent progress in understanding the cancer genome, there is still a relative delay in understanding the full aspects of the glycome and glycoproteome of cancer. Glycobiology has been instrumental in relevant discoveries in various biological and medical fields, and has contributed to the deciphering of several human diseases. Glycans are involved in fundamental molecular and cell biology processes occurring in cancer, such as cell signalling and communication, tumour cell dissociation and invasion, cell-matrix interactions, tumour angiogenesis, immune modulation and metastasis formation. The roles of glycans in cancer have been highlighted by the fact that alterations in glycosylation regulate the development and progression of cancer, serving as important biomarkers and providing a set of specific targets for therapeutic intervention. This Review discusses the role of glycans in fundamental mechanisms controlling cancer development and progression, and their applications in oncology.  
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  Call Number UofT @ ankit.sinha @ Serial 45283  
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Author Ferlay, J.; Soerjomataram, I.; Dikshit, R.; Eser, S.; Mathers, C.; Rebelo, M.; Parkin, D.M.; Forman, D.; Bray, F. url  openurl
  Title Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012 Type Journal Article
  Year 2015 Publication Abbreviated Journal Int J Cancer  
  Volume 136 Issue 5 Pages E359-86  
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  Abstract Estimates of the worldwide incidence and mortality from 27 major cancers and for all cancers combined for 2012 are now available in the GLOBOCAN series of the International Agency for Research on Cancer. We review the sources and methods used in compiling the national cancer incidence and mortality estimates, and briefly describe the key results by cancer site and in 20 large “areas” of the world. Overall, there were 14.1 million new cases and 8.2 million deaths in 2012. The most commonly diagnosed cancers were lung (1.82 million), breast (1.67 million), and colorectal (1.36 million); the most common causes of cancer death were lung cancer (1.6 million deaths), liver cancer (745,000 deaths), and stomach cancer (723,000 deaths).  
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  Call Number UofT @ ankit.sinha @ Serial 45319  
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