Proteomics Resource Facility

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Publications

Acknowledgment of Contributions

Publications containing data generated by the Proteomics Resource Facility (PRF) should include an acknowledgement of the PRF or include members as coauthors.  The PRF needs these acknowledgements and authorship to help demonstrate our contributions to the research community.  This in turn helps secure future funding to maintain a robust Core facility and provide professional development of its staff.  The Association of Biomolecular Resource Facilities (ABRF) has published a guideline to use when considering whether or not to include core laboratory members on publications.

 

  1. IL-17-driven intestinal fibrosis is inhibited by Itch-mediated ubiquitination of HIC-5.  Paul J, Singh AK, Kathania M, Elviche TL, Zeng M, Basrur V, Theiss AL, Venuprasak K.  Mucosal. Immunol. 2017
  2. Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas.  Rolland DCM, Basrur V, Jeon YK, McNeil-Schwalm C, Fermin D, Conlon KP, Zhou Y, Nq SY, Tsou CC, Brown NA, Thomas DG, Bailey NG, Omenn GS, Nesvizhskii AI, Root DE, Weinstock DM, Faryabi RB, Lim MS, Elenitoba-johnson KSJ.  Proc. Natl. Acad. Sci. USA 2017, 114(25):6581-6586.

  3. Protein aggregation with poly(vinyl) alcohol surfactant reduces double emulsion-encapsulated mammalian cell-free expression.  Ho KK, Lee JW, Durand G, Majumder S, Liu AP.  PLoS One 2017, 12(3):e0174689. 

  4. Pyrimidine tract-binding protein 1 mediates pyruvate kinase M2-dependent phosphorylation of signal transducer and activator of transcription 3 and oncognesis in anaplastic large cell lymphoma.  Hwang SR, Murga-Zamalloa C, Brown N, Basappa J, McDonnell SR, Mendoza-Reinoso V, Basrur V, Wilcox R, Elenitoba-Johnson K, Lim MS. Lab. Invest. 2017

  5. IL-22 controls iron-dependent nutritional immunity against sytemic bacterial infections.  Sakamoto K, Kim YF, Hara H, Kamada N, Caballero-Flores G, Tolosano E, Soares MP, Puente JL, Inohara N, Nunez G.  Sci. Immunol. 2017

  6. Targeted Degradation of BET proteins in triple-negative breast cancer.  Bai L, Zhou B, Yang CY, Ji J, McEachern D, Przybranowski S, Jiang H, Hu J, Xu F, Zhao Y, Liu L, Fernandez-Salas E, Zu J, Doy Y, Wen B, Sun D, Meagher JL, Stuckey J, Hayes DF, Li S, Ellis MJ, Wang S.  Cancer Res. 2017, 77(9):2476-2487.

  7. NPM-ALK phosphorylates WASP Y102 and contributes to oncogenesis of anaplastic large cell lymphoma.  Murga-Zamalloa CA, Mendoza-Reinoso v, Sahasrabuddhe AA, Rolland D, Hwang SR, McDonnell SR, Sciallis AP, Wilcox RA, Basrur V, Elenitoba-Johnson K, Lim MS.  Oncogene, 2017, 36(15):2085-2094.

  8. EMC1-dependent stabilization drives membrane penetration of a partially destabilized non-enveloped virus.  Bagchi P, Inoue T, Tsai B.  Elife 2016.

  9. Iron uptake via DMT1 integrates cell cycle with JAK-STAT3 signaling to promote colorectal tumorigenesis.  Xue X, Ramakrishnan SK, Weisz K, Triner D, Xie L, Attili D, Pant A, Gyorffy B, Zhan M, Carter-Su C, Hardiman KM, Wang TD, Dame MK, Varani J, Brenner D, Fearon ER, Shah YM.  Cell Metab. 2016, 24(3):447-61.

  10. NEK7 is an essential mediator of NLRP3 activation downstream of potassium efflux.  He Y, Zeng MY, Yang D, Motro B, Nunez G.  Nature, 2016, 530(7590):354-7.

  11. Loss of the ubiquitin-conjugating enzyme Ube2W results in susceptibility to early postnatal lethality and defects in skin, immune and male reproductive systems.  Wang B, Merillat SA, Vincent M, Huber AK, Basrur V, Mangelberger D, Zeng L, Elenitoba-Johnson K, Miller RA, Irani DN, Dlugosz AA, Schnell S, Scaglione KM, Paulson HL.  J. Biol. Chem. 2016, 291(6):3030-42.

  12. Aberrant expression of napsin A in a subset of malignant lymphomas.  Nam SJ, Kim S, Kim JE, Lim MS, Elenitoba-Johnson KS, Kim CW, Jeon YK.  Histol. Histopathol. 2016, 31(2):213-21.

  13. Ndfip1 regulates itch ligase activity and airway inflammation via UbcH7.  Kathania M, Zeng M, Yadav VN, Moghaddam SJ, Yang B, Venuprasad K.  J. Immunol. 2015, 194(5):2160-7.

  14. Pharmacoproteomics identifies combinatorial therapy targets for diffuse large B cell lymphoma.  Goldstein RL, Yang SN, Taldone T, Chang B, Gerecitano J, Elenitoba-Johnson K, Shaknovich R, Tam W, Leonard JP, Chiosis G, Cerchietti L, Melnick A.  J. Clin. Invest. 2015, 125(12):4559-71.

  15. The PIAS-like coactivator Zmiz1 is a direct and selective cofactor of Notch1 in T cell development and leukemia.  Pinnel N, Yan R, Cho HJ, Keeley T, Murai MJ, Liu Y, Alarcon AS, Qin J, Wang Q, Kuick R, Elenitoba-Johnson KS, Maillard I, Samuelson LC, Cierpicki T, Chiang MY.  Immunity 2015, 43(5):870-83.

  16. Tumor-selective proteotoxicity of verteporfin inhibits colon cancer progression independently of YAP1.  Zhang H, Ramakrishnan SK, Triner D, Centofanti B, Maitra D, Gyorffy B, Sebolt-Leopold JS, Dame MK, Varani J, Brenner DE, Fearon ER, Omary MB, Shah YM.  Sci. Signal. 2015, 8(397):ra98

  17. Ambient light promotes selective subcellular proteotoxicity after endogenous and exogenous porphyrinogenic stress.  Maitra D, Elenbaas JS, Whitesall SE, Basrur V, D'Alecy LG, Omary MB.  J. Biol. Chem. 2015, 290(39):23711-24

  18. The E3 ubiquitin ligase Itch inhibits p38alpha signaling and skin inflammation through the ubiquitylation of Tab1.  Theivanthiran B, Kathania M, Zeng M, Anguiano E, Basrur V, Vanderfriff T, Pascual V, Wei WZ, Massoumi R, Venuprasad K.  Sci. Signal. 2015, 8(365):ra22

  19. Conversion of the LIMA1 tumour suppressor into an oncogenic LMO-like protein by API2-MALT1 in MALT lymphoma.  Nie Z, Du MQ, McAllister-Lucas LM, Lucas PC, Bailey NG, Hogaboam CM, Lim MS, Elenitoba-Johnson KS.  Nat. Commun. 2015, 6:5908

  20. Differential proteomic analysis of endemic and sporadic Epstein-Barr virus-positive and negative Burkitt lymphoma.  El-Mallawany NK, Day N, Ayello J, Van de Ven C, Conlon K, Fermin D, Basrur V, Elenitoba-Johnson K, Lim M, Cairo MS.  Eur. J. Cancer 2015, 51(1):92-100

  21. Intrinsic disorder drives N-terminal ubiquitination by Ube2W.  Vittal V, Shi L, Wenzel DM, Scaglione KM, Duncan ED, Basrur V, Elenitoba-Johnson KS, Baker D, Paulson HL, Brzovic PS, Klevit RE.  Nat. Chem. Biol. 2015, 11(1):83-89

  22. Fbxo45 inhibits calcium-sensitive proteolysis of N-cadherin and promotes neuronal differentiation.  Chung FZ, Sahasrabuddhe AA, Ma K, Chen X, Basrur V, Lim MS, Elenitoba-Johnson KS.  J. Biol. Chem. 2014, 289(41):28448-59

  23. TRIP13 promotes error-prone nonhomologous end joining and induces chemoresistance in head and neck cancer. Banerjee R, Russo N, Liu M, Basrur V, Bellile E, Palanisamy N, Scanlon CS, van Tubergen E, Inglehart RC, Metwally T, Mani RS, Yocum A, Nyati MK, Castilho RM, Varambally S, Chinnaiyan AM, D'Silva NJ. Nat. Commun. 2014, 5:4527.

  24. Fbxo45-mediated degradation of the tumor-suppressor Par-4 regulates cancer cell survival. Chen X, Sahasrabuddhe AA, Szankasi P, Chung F, Basrur V, Rangnekar VM, Pagano M, Lim MS, Elenitoba-Johnson KS. Cell Death Differ. 2014, 21(10):1535-45.

  25. 3,4-methylenedioxy-β-nitrostyrene inhibits NLRP3 inflammasome activation by blocking assembly of the inflammasome. He Y, Varadarajan S, Munoz-Planillo R, Burberry A, Nakamura Y, Nunez G.  J. Biol. Chem. 2014, 289(2):1142-50.

  26. Global phosphoproteomic profiling reveals distinct signatures in B-cell non-hodgkin lymphomas. Rolland D, Basrur V, Conlon K, Wolfe T, Fermin D, Nesvizhskii AI, Lim MS, Elenitoba-Johnson KS. Am. J. Pathol. 2014, 184(5):1331-42.

  27. KRAS protein stability is regulated through SMURF2:UBCH5 complex-mediated b-TrCP1 degradation. Shukla S, Allam US, Ahsan A, Chen G, Krishnamurthy PM, Marsh K, Rumschlag M, Shankar S, Whitehead C, Schipper M, Basrur V, Sourthworth DR, Chinnaiyan AM, Rehemtulla A, Beer DG, Lawrence TS, Nyati MK, Ray D Neoplasia 2014, 16(2):115.

  28. Distraction-induced intestinal growth:  The role of mechanotransduction mechanisms in a mouse model of short bowel syndrome.  Sueyoshi R, Woods Ignatoski KM, Okawada M, Teitelbaum DH.  Tissue Eng. Part A. 2014, 20(3-4):830-41

  29. Involvement of ractive oxygen species in a feed-forward mechanisms of Na/K-ATPase-mediated signaling transduction.  Yan Y, Shapiro AP, Haller S, Katragadda V, Liu L, Tian J, Basrur V, Malhotra D, Xie ZJ, Abraham NG, Shapiro JI, Liu J.  J. Biol. Chem. 2013, 288(47):34249-58.

  30. Staphylococcus d-toxin induces allergic skin disease by activating mast cells.  Nakamura Y, Oscherwitz J, Cease KB, Chan SM, Munoz-Planillo R, Hasegawa M, Villaruz AE, Cheung GY, McGavin MJ, Travers JB, Otto M, Inohara N, Nunez G. Nature 2013, 503(7476):397-401.

  31. Inflammation produces catecholamine resistance in obesity via activation of PDE3B by the protein kinases IKKe and TBK1.  Mower J, Uhm M, Reilly SM, Simon J, Leto D, Chiang SH, Chang L, Saltiel AR. eLife 2013, 2:e01119.

  32. Fusion peptides from oncogenic chimeric proteins as specific biomarkers of cancer.  Conlon KP, Basrur V, Rolland D, Wolfe T, Nesvizhskii AI, Maccoss MJ, Lim MS, Elenitoba-Johnson KS.  Mol. Cell Proteomics 2013, 12(10):2714-23.

  33. Integrated phosphoproteomic and metabolomics profiling reveals NPM-ALK-mediated phosphorylation of PKM2 and metabolic reprogramming in anaplastic large cell lymphoma.  McDonnell RPS, Hwang SR, Rolland D, Murga-Zamalloa C, Basrur v, Conlon KP, Fermin D, Wolfe T, Rasking A, Ruan C, Jiang J-K, Thomas CJ, Hogaboam CM, Burant CF, Elenitoba-Johnson KSJ, Lim MS.  Blood 2013, 122(6): 959-68.

  34. Saccharomyces cerevisiae DNA ligase IV supports imprecise end joining independently of its catalytic activity.  Chiruvella KK, Liang Z, Birkeland SR, Basrur V, Wilson TE.  PLOS Genetics. 2013,9(6):e1003599.

  35. The ubiquitin conjugating enzyme (E2) Ube2w ubiquitinates the N-terminus of substrates. Scaglione KM, Basrur V, Ashraf NS, Konen JR, Elenitoba-Johnson KS, Todi SV, Paulson HL. J Biol Chem. 2013, 288(26):18784-8

  36. CGG repeat-associated translation mediates neurodegeneration in fragile X tremor ataxia syndrome.  Todd PK, Oh SY, Krans A, He F, Sellier C, Frazer M, Renoux AJ, Chen KC, Scaglione KM, Basrur V, Elenitoba-Johnson K, Vonsattel JP, Louis ED, Sutton MA, Taylor JP, Mills RE, Charlet-Berguerand N, Paulson HL.  Neuron. 2013, 78(3):440-55.

  37. RNF111-dependent neddylation activates DNA damage-induced ubiquitination.  Ma T, Chen Y, Zhang F, Yang CY, Wang S, Yu X.  Mol Cell. 2013, 49(5):897-907.

  38. Citrullinated calreticulin potentiates rheumatoid arthritis shared epitope signaling.  Ling S, Cline EN, Hauq TS, Fox DA, Holoshitz J.  Arthritis Reheum. 2013, 65(3):618-25.

  39. MMSET stimulates myeloma cell growth through microRNA-mediated modulation of c-MYC.  Min DJ, Ezponda T, Kim MK, Will CM, Martinez-Garcia E, Popovic R, Basrur V, Elenitoba-Johnson KS, Licht JD. Leukemia. 2013, 27(3):686-94. doi: 10.1038/leu.2012.269.

  40. Cysteine reactivity distinguishes redox sensing by the heat-inducible and constitutive forms of heat shock protein 70. Miyata Y, Rauch JN, Jinwal UK, Thompson AD, Srinivasan S, Dickey CA, Gestwicki JE. Chem Biol. 2012, 19(11):1391-9.

  41. Analysis of the tau-associated proteome reveals that exchange of Hsp70 for Hsp90 is involved in tau degradation. Thompson AD, Scaglione KM, Prensner J, Gillies AT, Chinnaiyan A, Paulson HL, Jinwal UK, Dickey CA, Gestwicki JE.  ACS Chem Biol. 2012, 7(10):1677-86.

  42. Fbxw7α- and GSK3-mediated degradation of p100 is a pro-survival mechanism in multiple myeloma.  Busino L, Millman SE, Scotto L, Kyratsous CA, Basrur V, O'Connor O, Hoffmann A, Elenitoba-Johnson KS, Pagano M.  Nat Cell Biol. 2012,14(4):375-85.

  43. ECSASB2 mediates MLL degration during hematopoietic differentiation.  Wang J, Muntean AG, Hess JL.  Blood. 2012,119(5):1151-61. 

  44. Site specific interaction of the polyphenol EGCG with the SEVI amyloid precursor peptide PAP(248-286).  Popovych N, Brender JR, Soong R, Vivekanandan S, Hartman K, Basrur V, Macdonald PM, Ramamoorthy A.  J Phys Chem B. 2012, 116(11):3650-8. 

  45. An N-glycosylation analysis of human alpha-2-macroglobulin using an integrated approach.  Lin Z, Lo A, Simeone DM, Ruffin MT, Lubman DM.  J Proteomics Bioinform. 2012, 5:127-34.

  46. NPM-ALK signals through glycogen synthase kinase 3β to promote oncogenesis.  McDonnell SR, Hwang SR, Basrur V, Conlon KP, Fermin D, Wey E, Murga-Zamalloa C, Zeng Z, Zu Y, Elenitoba-Johnson KS, Lim MS.  Oncogene. 2012, 31(32):3733-40.

  47. Identification and characterization of Hoxa9 binding sites in hematopoietic cells. Huang Y, Sitwala K, Bronstein J, Sanders D, Dandekar M, Collins C, Robertson G, MacDonald J, Cezard T, Bilenky M, Thissen N, Zhao Y, Zeng T, Hirst M, Hero A, Jones S, Hess JL.  Blood, 2012, 119(2):388

  48. Urine glycoprotein profile reveals novel markers for chronic kidney disease.  Vivekanandan-Giri A, Slocum JL, Buller CL, Basrur V, Ju W, Pop-Busui R, Lubman DM, Kretzler M, Pennathur S.  Int J Proteomics. 2011, 2011:214715.

  49. Ordered assembly of heat shock proteins, Hsp26, Hsp70, Hsp90, and Hsp104, on expanded polyglutamine fragments revealed by chemical probes.  Walter GM, Smith MC, Wisén S, Basrur V, Elenitoba-Johnson KS, Duennwald ML, Kumar A, Gestwicki JE.  J Biol Chem. 2011, 286(47):40486-93.

  50. Function of leukemogenic mixed lineage leukemia 1 (MLL) fusion proteins through distinct partner protein complexes.  Biswas D, Milne TA, Basrur V, Kim J, Elenitoba-Johnson KS, Allis CD, Roeder RG.Proc Natl Acad Sci U S A. 2011,108(38):15751-6.

  51. Mechanistic rationale for inhibition of poly(ADP-ribose) polymerase in ETS gene fusion-positive prostate cancer.  Brenner JC, Ateeq B, Li Y, Yocum AK, Cao Q, Asangani IA, Patel S, Wang X, Liang H, Yu J, Palanisamy N, Siddiqui J, Yan W, Cao X, Mehra R, Sabolch A, Basrur V, Lonigro RJ, Yang J, Tomlins SA, Maher CA, Elenitoba-Johnson KS, Hussain M, Navone NM, Pienta KJ, Varambally S, Feng FY, Chinnaiyan AM.  Cancer Cell. 2011,19(5):664-78.

  52. Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis.  Fermin D, Basrur V, Yocum AK, Nesvizhskii AI.  Proteomics. 2011, 11(7):1340-5.

  53. MLL-AF9 and MLL-ENL alter the dynamic association of transcriptional regulators with genes critical for leukemia.  Monroe SC, Jo SY, Sanders DS, Basrur V, Elenitoba-Johnson KS, Slany RK, Hess JL.  Exp Hematol. 2011, 39(1):77-86.

  54. An Ash2L/RbBP5 heterodimer stimulates the MLL1 methyltransferase activity through coordinated substrate interactions with the MLL1 SET domain.  Cao F, Chen Y, Cierpicki T, Liu Y, Basrur V, Lei M, Dou Y.  PLoS One. 2010, 5(11):e14102

  55. Activity and cellular functions of the deubiquitinating enzyme and polyglutamine disease protein ataxin-3 are regulated by ubiquitination at lysine 117.  Todi SV, Scaglione KM, Blount JR, Basrur V, Conlon KP, Pastore A, Elenitoba-Johnson K, Paulson HL.  J Biol Chem2010, 285(50):39303-13.

  56. A bimolecular affinity purification method under denaturing conditions for rapid isolation of a ubiquitinated protein for mass spectrometry analysis.  Maine GN, Li H, Zaidi IW, Basrur V, Elenitoba-Johnson KS, Burstein E.  Nat Protoc. 2010, 5(8):1447-59.

  57. The PAF complex synergizes with MLL fusion proteins at HOX loci to promote leukemogenesis.  Muntean AG, Tan J, Sitwala K, Huang Y, Bronstein J, Connelly JA, Basrur V, Elenitoba-Johnson KS, Hess JL.  Cancer Cell. 2010, 17(6):609-21.

  58. Multiple interactions recruit MLL1 and MLL1 fusion proteins to the HOXA9 locus in leukemogenesis.  Milne TA, Kim J, Wang GG, Stadler SC, Basrur V, Whitcomb SJ, Wang Z, Ruthenburg AJ, Elenitoba-Johnson KS, Roeder RG, Allis CD.  Mol Cell. 2010, 38(6):853-63.

  59. Regulation of the copper chaperone CCS by XIAP-mediated ubiquitination.  Brady GF, Galbán S, Liu X, Basrur V, Gitlin JD, Elenitoba-Johnson KS, Wilson TE, Duckett CS.  Mol Cell Biol. 2010, 30(8):1923-36.

  60. KDM2A represses transcription of centromeric satellite repeats and maintains the heterochromatic state.  Frescas D, Guardavaccaro D, Kuchay SM, Kato H, Poleshko A, Basrur V, Elenitoba-Johnson KS, Katz RA, Pagano M.  Cell Cycle. 2008, 7(22):3539-47.