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Nano-scale protein quantification in multiple myeloma
References
1. Broyl A, Hose D, Lokhorst H, et al. Gene expression profiling for molecular classifica- tion of multiple myeloma in newly diag- nosed patients. Blood. 2010;116(14):2543– 2553.
2. Tian Q, Stepaniants SB, Mao M, et al. Integrated genomic and proteomic analyses of gene expression in mammalian cells. Mol Cell Proteomics. 2004;3(10):960–969.
3. Chen J-Q, Wakefield LM, Goldstein DJ. Capillary nano-immunoassays: advancing quantitative proteomics analysis, biomarker assessment, and molecular diagnostics. J Transl Med. 2015;13:182.
4. Chen J-Q, Heldman MR, Herrmann MA, et al. Absolute quantitation of endogenous proteins with precision and accuracy using a capillary western system. Anal Biochem. 2013;442(1):97–103.
5. GhoshR,GildaJE,GomesAV.Thenecessity of and strategies for improving confidence in the accuracy of western blots. Expert Rev Proteomics. 2014;11(5):549–560.
6. Gassmann M, Grenacher B, Rohde B, Vogel J. Quantifying western blots: pitfalls of den- sitometry. Electrophoresis. 2009;30(11): 1845–1855.
7. Fan AC, Deb-Basu D, Orban MW, et al. Nanofluidic proteomic assay for serial analy- sis of oncoprotein activation in clinical spec- imens. Nat Med. 2009;15(5):566–571.
8. Technicalguidefortheeleborationofmono- graphs.
9. Bergsagel PL, Kuehl WM, Zhan F, Sawyer J, Barlogie B, Shaughnessy J. Cyclin D dysreg- ulation: an early and unifying pathogenic event in multiple myeloma. Blood. 2005;106(1):296–303.
10. ChesiM,BergsagelPL.Molecularpathogen- esis of multiple myeloma: basic and clinical updates. Int J Hematol. 2013;97(3):313–323.
11. Misiewicz-Krzeminska I, Sarasquete ME, Vicente-Dueñas C, et al. Post-transcriptional modifications contribute to the upregulation of Cyclin D2 in multiple myeloma. Clin Cancer Res. 2016;22(1):207–217.
12. Chiecchio L, Dagrada GP, Protheroe RKM, et al. Loss of 1p and rearrangement of MYC are associated with progression of smoulder- ing myeloma to myeloma: sequential analy- sis of a single case. Haematologica. 2009;94(7):1024–1028.
13. Chng W-J, Huang GF, Chung TH, et al. Clinical and biological implications of MYC activation: a common difference between MGUS and newly diagnosed multiple myeloma. Leukemia 2011;25(6):1026–1035.
14. Zhang L, Fok JHL, Davies FE. Heat shock proteins in multiple myeloma. Oncotarget. 2014;5(5):1132–1148.
15. MunshiNC,HideshimaT,CarrascoD,etal. Identification of genes modulated in multi- ple myeloma using genetically identical twin samples. Blood. 2004;103(5):1799–1806.
16. Cimino D, Fuso L, Sfiligoi C, et al. Identification of new genes associated with breast cancer progression by gene expres- sion analysis of predefined sets of neoplastic tissues. Int J Cancer. 2008;123(6):1327–1338.
17. Schneider AT, Gautheron J, Feoktistova M, et al. RIPK1 suppresses a TRAF2-dependent pathway to liver cancer. Cancer Cell. 2017;31(1):94–109.
18. YooJY,Jaime-RamirezAC,BolyardC,etal.
Bortezomib treatment sensitizes oncolytic HSV-1-treated tumors to NK cell immunotherapy. Clin Cancer Res. 2016;22 (21):5265–5276.
19. Bjorklund CC, Lu L, Kang J, et al. Rate of CRL4(CRBN) substrate Ikaros and Aiolos degradation underlies differential activity of lenalidomide and pomalidomide in multiple myeloma cells by regulation of c-Myc and IRF4. Blood Cancer J. 2015;5e354.
20. Kortüm KM, Zhu YX, Shi CX, Jedlowski P, Stewart AK. Cereblon binding molecules in multiple myeloma. Blood Rev. 2015;29(5):329–334.
21. Park GB, Kim Y-S, Kim D, et al. Melphalan- induced apoptosis of EBV-transformed B cells through upregulation of TAp73 and XAF1 and nuclear import of XPA. J Immunol. 2013;191(12):6281–6291.
22. Dytfeld D, Luczak M, Wrobel T, et al. Comparative proteomic profiling of refrac- tory/relapsed multiple myeloma reveals bio- markers involved in resistance to borte- zomib-based therapy. Oncotarget. 2016;7(35):56726-56736.
23. Chomczynski P. A reagent for the single- step simultaneous isolation of RNA, DNA and proteins from cell and tissue samples. BioTechniques. 1993;15(3):532–534, 536– 537.
24. Vorreiter F, Richter S, Peter M, Baumann S, von Bergen M, Tomm JM. Comparison and optimization of methods for the simultane- ous extraction of DNA, RNA, proteins, and metabolites. Anal Biochem. 2016;50825–33.
25. Mathieson W, Thomas GA. Simultaneously extracting DNA, RNA, and protein using kits: is sample quantity or quality preju- diced? Anal Biochem. 2013;433(1):10–18.
26. Pace CN, Treviño S, Prabhakaran E, Scholtz JM. Protein structure, stability and solubility in water and other solvents. Philos Trans R Soc Lond B Biol Sci. 2004;359(1448):1225- 1234; discussion 1234-1235.
27. Race J. The determination of blood-proteins by acid-acetone. Biochem J. 1932;26(5):1571–1584.
28. Crowell AMJ, Wall MJ, Doucette AA. Maximizing recovery of water-soluble pro- teins through acetone precipitation. Anal Chim Acta. 2013;79648–54.
29. Cutler P, editor. Protein Purification Protocols. 2nd. Totowa, NJ: Humana Press; 2004. 484 p.
30. Rustandi RR, Loughney JW, Hamm M, et al. Qualitative and quantitative evaluation of SimonTM, a new CE-based automated Western blot system as applied to vaccine development. Electrophoresis. 2012;33(17): 2790–2797.
31. Copeland RA. Methods for Protein Analysis. Boston, MA: Springer US.
32. Strupat K. Molecular weight determination of peptides and proteins by ESI and MALDI. Meth Enzymol. 2005;405:1–36.
33. McDonough AA, Veiras LC, Minas JN, Ralph DL. Considerations when quantitating pro- tein abundance by immunoblot. Am J Physiol Cell Physiol. 2015;308(6):C426-433.
34. Vogel C, Marcotte EM. Insights into the reg- ulation of protein abundance from proteom- ic and transcriptomic analyses. Nat Rev Genet. 2012;13(4):227–232.
35. Liu Y, Beyer A, Aebersold R. On the Dependency of cellular protein levels on mRNA abundance. Cell. 2016;165(3):535– 550.
36. 37.
38.
39.
40.
41.
42.
43.
44.
45.
46.
47.
48.
49.
50.
Payne SH. The utility of protein and mRNA correlation. Trends Biochem Sci. 2015;40 (1):1–3.
Mitchell JL, Yankee TM. Variations in mRNA and protein levels of Ikaros family members in pediatric T cell acute lym- phoblastic leukemia. Ann Transl Med. 2016;4(19):363–363.
Ito T, Ando H, Suzuki T, et al. Identification of a primary target of thalidomide terato- genicity. Science. 2010;327(5971):1345– 1350.
Ito T, Ando H, Handa H. Discovery of the target for immunomodulatory drugs (IMiDs). Rinsho Ketsueki. 2016;57(5):556– 562.
Gandhi AK, Mendy D, Waldman M, et al. Measuring cereblon as a biomarker of response or resistance to lenalidomide and pomalidomide requires use of standardized reagents and understanding of gene com- plexity. Br J Haematol. 2014;164(2):233–244. Lu G, Middleton RE, Sun H, et al. The myeloma drug lenalidomide promotes the cereblon-dependent destruction of Ikaros proteins. Science. 2014;343(6168):305–309. Krönke J, Udeshi ND, Narla A, et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science. 2014;343(6168):301–305.
Zhu YX, Braggio E, Shi C-X, et al. Cereblon expression is required for the antimyeloma activity of lenalidomide and pomalidomide. Blood. 2011;118(18):4771–4779.
Krönke J, Kuchenbauer F, Kull M, et al. IKZF1 expression is a prognostic marker in newly diagnosed standard-risk multiple myeloma treated with lenalidomide and intensive chemotherapy: a study of the German Myeloma Study Group (DSMM). Leukemia. 2017;31(6):1363-1367.
Zhu YX, Braggio E, Shi C-X, et al. Identification of cereblon-binding proteins and relationship with response and survival after IMiDs in multiple myeloma. Blood. 2014;124(4):536–545.
Pourabdollah M, Bahmanyar M, Atenafu EG, Reece D, Hou J, Chang H. High IKZF1/3 protein expression is a favorable prognostic factor for survival of relapsed/refractory multiple myeloma patients treated with lenalidomide. J Hematol Oncol. 2016;9 (1):123.
Bila J, Sretenovic A, Jelicic J, et al. Prognostic significance of cereblon expression in patients with multiple myeloma. Clin Lymphoma Myeloma Leuk. 2016;16(11): 610–615.
Jung S-H, Choi H-J, Shin M-G, et al. Thalidomide-based induction regimens are as effective as bortezomib-based regimens in elderly patients with multiple myeloma with cereblon expression. Ann Hematol. 2016;95(10):1645–1651.
Huang S-Y, Lin C-W, Lin H-H, et al. Expression of cereblon protein assessed by immunohistochemicalstaining in myeloma cells is associated with superior response of thalidomide- and lenalidomide-based treat- ment, but not bortezomib-based treatment, in patients with multiple myeloma. Ann Hematol. 2014;93(8):1371–1380.
Broyl A, Kuiper R, van Duin M, et al. High cereblon expression is associated with better survival in patients with newly diagnosed multiple myeloma treated with thalidomide maintenance. Blood. 2013;121(4):624–627.
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