Publications Sjaak Neefjes

  1. Breur-Vriesendorp,B.S., Neefjes,J.J., Huis,B., van Seventer,G.A., Ploegh,H.L., and Ivanyi,P. (1986). Identification of new B27 subtypes (B27c and B27d) prevalent in oriental populations. Hum. Immunol. 16, 163-169.
  2. Neefjes,J.J., Breur-Vriesendorp,B.S., van Seventer,G.A., Ivanyi,P., and Ploegh,H.L. (1986). An improved biochemical method for the analysis of HLA-class I antigens. Definition of new HLA-class I subtypes. Hum Immunol 16, 169-181.
  3. Neefjes,J.J., Hensen,E.J., de Kroon,T.I., and Ploegh,H.L. (1986). A biochemical characterization of feline MHC products: unusually high expression of class II antigens on peripheral blood lymphocytes. Immunogenetics 23, 341-347.
  4. Neefjes,J.J., Doxiadis,I., Stam,N.J., Beckers,C.J., and Ploegh,H.L. (1986). An analysis of class I antigens of man and other species by one-dimensional IEF and immunoblotting. Immunogenetics 23, 164-171.
  5. Broxterman,H.J., van der Marel,G.A., Neefjes,J., Ploegh,H., and van Boom,J.H. (1987). Synthesis of the antibiotic 1,5-dideoxy-1,5-imino-D-glucitol; concomitant formation of the D-mannitol analogue. Recueil des Travaux Chimiques des Pays-Bas 106, 571-576.
  6. Gruters,R.A., Neefjes,J.J., Tersmette,M., de Goede,R.E., Tulp,A., Huisman,H.G., Miedema,F., and Ploegh,H.L. (1987). Interference with HIV-induced syncytium formation and viral infectivity by inhibitors of trimming glucosidase. Nature 330, 74-77.
  7. Rein,R.S., Seemann,G.H., Neefjes,J.J., Hochstenbach,F.M., Stam,N.J., and Ploegh,H.L. (1987). Association with beta 2-microglobulin controls the expression of transfected human class I genes. J. Immunol. 138, 1178-1183.
  8. Bolscher,J.G., van der Bijl,M.M., Neefjes,J.J., Hall,A., Smets,L.A., and Ploegh,H.L. (1988). Ras (proto)oncogene induces N-linked carbohydrate modification: temporal relationship with induction of invasive potential. EMBO J 7, 3361-3368.
  9. Dobbe,L.M., Stam,N.J., Neefjes,J.J., and Giphart,M.J. (1988). Biochemical complexity of serum HLA class I molecules. Immunogenetics 27, 203-210.
  10. Neefjes,J.J., Verkerk,J.M., Broxterman,H.J., van der Marel,G.A., van Boom,J.H., and Ploegh,H.L. (1988). Recycling glycoproteins do not return to the cis-Golgi. J Cell Biol 107, 79-87.
  11. Neefjes,J.J. and Ploegh,H.L. (1988). Allele and locus-specific differences in cell surface expression and the association of HLA class I heavy chain with beta 2-microglobulin: differential effects of inhibition of glycosylation on class I subunit association. Eur J Immunol 18, 801-810.
  12. Boog,C.J., Neefjes,J.J., Boes,J., Ploegh,H.L., and Melief,C.J. (1989). Specific immune responses restored by alteration in carbohydrate chains of surface molecules on antigen-presenting cells. Eur J Immunol 19, 537-542.
  13. Damoiseaux,J.G., Dopp,E.A., Neefjes,J.J., Beelen,R.H., and Dijkstra,C.D. (1989). Heterogeneity of macrophages in the rat evidenced by variability in determinants: two new anti-rat macrophage antibodies against a heterodimer of 160 and 95 kd (CD11/CD18). J Leukoc Biol 46, 556-564.
  14. Doxiadis,I., Krumbacher,K., Neefjes,J.J., Ploegh,H.L., and Grosse-Wilde,H. (1989). Biochemical evidence that the DLA-B locus codes for a class II determinant expressed on all canine peripheral blood lymphocytes. Exp Clin Immunogenet 6, 219-224.
  15. Masucci,M.G., Stam,N.J., Torsteinsdottir,S., Neefjes,J.J., Klein,G., and Ploegh,H.L. (1989). Allele-specific down-regulation of MHC class I antigens in Burkitt lymphoma lines. Cell Immunol 120, 396-400.
  16. Neefjes,J.J., Lindhout,J., Broxterman,H.J., van der Marel,G.A., van Boom,J.H., and Ploegh,H.L. (1989). Non-carrier-mediated uptake of the mannosidase I inhibitor 1- deoxymannojirimycin by K562 erythroleukemic cells. J. Biol. Chem. 264, 10271-10275.
  17. Rotteveel,F.T., Neefjes,J.J., Ploegh,H.L., and Lucas,C.J. (1989). Influenza virus changes cell-surface glycoproteins including major histocompatibility complex determinants on lymphocytes. Hum Immunol 26, 199-213.
  18. Ljunggren,H.G., Stam,N.J., Ohlen,C., Neefjes,J.J., Hoglund,P., Heemels,M.T., Bastin,J., Schumacher,T.N., Townsend,A., Karre,K., and Ploegh (1990). Empty MHC class I molecules come out in the cold. Nature 346, 476-480.
  19. Neefjes,J.J., Stollorz,V., Peters,P.J., Geuze,H.J., and Ploegh,H.L. (1990). The biosynthetic pathway of MHC class II but not class I molecules intersects the endocytic route. Cell 61, 171-183.
  20. Neefjes,J.J. and Ploegh,H.L. (1990). The role of N-linked carbohydrates in antigen presentation. TIGG 7, 364-372.
  21. Neefjes,J.J., De Bruijn,M.L., Boog,C.J., Nieland,J.D., Boes,J., Melief,C.J., and Ploegh,H.L. (1990). N-linked glycan modification on antigen-presenting cells restores an allospecific cytotoxic T cell response. J Exp Med 171, 583-588.
  22. Neefjes,J.J., Hengeveld,T., Tol,O., and Ploegh,H.L. (1990). Intracellular interactions of transferrin and its receptor during biosynthesis. J Cell Biol 111, 1383-1392.
  23. Ploegh,H. and Neefjes,J.J. (1990). Protein glycosylation. [Review] [29 refs]. Curr. Opin. Cell Biol. 2, 1125-1130.
  24. Schumacher,T.N., Heemels,M.T., Neefjes,J.J., Kast,W.M., Melief,C.J., and Ploegh,H.L. (1990). Direct binding of peptide to empty MHC class I molecules on intact cells and in vitro. Cell 62, 563-567.
  25. De Lau,W.B., Heije,K., Neefjes,J.J., Oosterwegel,M., Rozemuller,E., and Bast,B.J. (1991). Absence of preferential homologous H/L chain association in hybrid hybridomas. J Immunol 146, 906-914.
  26. Neefjes,J.J., Schumacher,T.N., and Ploegh,H.L. (1991). Assembly and intracellular transport of major histocompatibility complex molecules. Curr. Opin. Cell Biol. 3, 601-609.
  27. Peters,P.J., Neefjes,J.J., Oorschot,V., Ploegh,H.L., and Geuze,H.J. (1991). Segregation of MHC class II molecules from MHC class I molecules in the Golgi complex for transport to lysosomal compartments Nature 349, 669-676.
  28. Schumacher,T.N., De Bruijn,M.L., Vernie,L.N., Kast,W.M., Melief,C.J., Neefjes,J.J., and Ploegh,H.L. (1991). Peptide selection by MHC class I molecules. Nature 350, 703-706.
  29. Faber,E.D., Oosting,R., Neefjes,J.J., Ploegh,H.L., and Meijer,D.K. (1992). Distribution and elimination of the glycosidase inhibitors 1-deoxymannojirimycin and N-methyl-1-deoxynojirimycin in the rat in vivo. Pharm Res 9, 1442-1450.
  30. Kuijpers,K.C., van Kemenade,F.J., Hooibrink,B., Neefjes,J.J., Lucas,C.J., van Lier,R.A., and Miedema,F. (1992). HLA class I and II molecules present influenza virus antigens with different kinetics. Eur J Immunol 22, 2339-2345.
  31. Leeuwenberg,J.F., Smeets,E.F., Neefjes,J.J., Shaffer,M.A., Cinek,T., Jeunhomme,T.M., Ahern,T.J., and Buurman,W.A. (1992). E-selectin and intercellular adhesion molecule-1 are released by activated human endothelial cells in vitro. Immunology 77, 543-549.
  32. Momburg,F., Ortiz-Navarrete,V., Neefjes,J., Goulmy,E., van de Wal,Y., Spits,H., Powis,S.J., Butcher,G.W., Howard,J.C., and Walden,P. (1992). Proteasome subunits encoded by the major histocompatibility complex are not essential for antigen presentation. Nature 360, 174-177.
  33. Neefjes,J.J. and Ploegh,H.L. (1992). Inhibition of endosomal proteolytic activity by leupeptin blocks surface expression of MHC class II molecules and their conversion to SDS resistance alpha beta heterodimers in endosomes. EMBO J 11, 411-416.
  34. Neefjes,J.J. and Ploegh,H.L. (1992). Intracellular transport of MHC class II molecules. Immunol. Today 13, 179-184.
  35. Neefjes,J.J., Smit,L., Gehrmann,M., and Ploegh,H.L. (1992). The fate of the three subunits of major histocompatibility complex class I molecules. Eur J Immunol 22, 1609-1614.
  36. Bijlmakers,M.J., Neefjes,J.J., Wojcik-Jacobs,E.H., and Ploegh,H.L. (1993). The assembly of H2-Kb class I molecules translated in vitro requires oxidized glutathione and peptide. Eur J Immunol 23, 1305-1313.
  37. Neefjes,J.J., Hammerling,G.J., and Momburg,F. (1993). Folding and assembly of major histocompatibility complex class I heterodimers in the endoplasmic reticulum of intact cells precedes the binding of peptide. J Exp Med 178, 1971-1980.
  38. Neefjes,J.J., Momburg,F., and Hammerling,G.J. (1993). Selective and ATP-dependent translocation of peptides by the MHC-encoded transporter. Science 261, 769-771.
  39. Neefjes,J.J., Dierx,J., and Ploegh,H.L. (1993). The effect of anchor residue modifications on the stability of major histocompatibility complex class I-peptide interactions. Eur J Immunol 23, 840-845.
  40. Neefjes,J.J. and Momburg,F. (1993). Cell biology of antigen presentation. Curr Opin Immunol 5, 27-34.
  41. Smeets,E.F., de Vries,T., Leeuwenberg,J.F., van den Eijnden,D.H., Buurman,W.A., and  Neefjes,J.J. (1993). Phosphorylation of surface E-selectin and the effect of soluble ligand (sialyl Lewisx) on the half-life of E-selectin. Eur J Immunol 23, 147-151.
  42. Viville,S., Neefjes,J., Lotteau,V., Dierich,A., Lemeur,M., Ploegh,H., Benoist,C., and Mathis,D. (1993). Mice lacking the MHC class II-associated invariant chain. Cell 72, 635-648.
  43. Calafat,J., Nijenhuis,M., Janssen,H., Tulp,A., Dusseljee,S., Wubbolts,R., and Neefjes,J. (1994). Major histocompatibility complex class II molecules induce the formation of endocytic MIIC-like structures. J Cell Biol 126, 967-977.
  44. Momburg,F., Roelse,J., Howard,J.C., Butcher,G.W., Hammerling,G.J., and Neefjes,J.J. (1994). Selectivity of MHC-encoded peptide transporters from human, mouse and rat. Nature 367, 648-651.
  45. Momburg,F., Neefjes,J.J., and Hammerling,G.J. (1994). Peptide selection by MHC-encoded TAP transporters. Curr Opin Immunol 6, 32-37.
  46. Momburg,F., Roelse,J., Hammerling,G.J., and Neefjes,J.J. (1994). Peptide size selection by the major histocompatibility complex-encoded peptide transporter. J Exp Med 179, 1613-1623.
  47. Momburg,F., Roelse,J., Neefjes,J., and Hammerling,G.J. (1994). Peptide transporters and antigen processing. Behring Inst Mitt. 26-36.
  48. Nijenhuis,M. and Neefjes,J. (1994). Early events in the assembly of major histocompatibility complex class II heterotrimers from their free subunits. Eur J Immunol 24, 247-256.
  49. Nijenhuis,M., Calafat,J., Kuijpers,K.C., Janssen,H., de Haas,M., Nordeng,T.W., Bakke,O., and Neefjes,J.J. (1994). Targeting major histocompatibility complex class II molecules to the cell surface by invariant chain allows antigen presentation upon recycling. Eur J Immunol 24, 873-883.
  50. Roelse,J., Gromme,M., Momburg,F., Hammerling,G., and Neefjes,J. (1994). Trimming of TAP-translocated peptides in the endoplasmic reticulum and in the cytosol during recycling. J Exp Med 180, 1591-1597.
  51. Sanderson,F., Kleijmeer,M.J., Kelly,A., Verwoerd,D., Tulp,A., Neefjes,J.J., Geuze,H.J., and Trowsdale,J. (1994). Accumulation of HLA-DM, a regulator of antigen presentation, in MHC class II compartments. Science 266, 1566-1569.
  52. Benham,A., Tulp,A., and Neefjes,J. (1995). Synthesis and assembly of MHC-peptide complexes. Immunol. Today 16, 359-362.
  53. Benham,A.M. and Neefjes,J.J. (1995). Antigen processing by the class I pathway. Biochem Soc Trans 23, 664-669.
  54. Gournier,H., Pascolo,S., Siegrist,C.A., Jehan,J., Perarnau,B., Garcia,Z., Rose,T., Neefjes,J., and Lemonnier,F.A. (1995). Restriction of self-antigen presentation to cytolytic T lymphocytes by mouse peptide pumps. Eur J Immunol 25, 2019-2026.
  55. Kleijmeer,M.J., Ossevoort,M.A., van Veen,C.J., van Hellemond,J.J., Neefjes,J.J., Kast,W.M., Melief,C.J., and Geuze,H.J. (1995). MHC class II compartments and the kinetics of antigen presentation in activated mouse spleen dendritic cells. J Immunol 154, 5715-5724.
  56. Neefjes,J., Gottfried,E., Roelse,J., Gromme,M., Obst,R., Hammerling,G.J., and Momburg,F. (1995). Analysis of the fine specificity of rat, mouse and human TAP peptide transporters. Eur. J. Immunol. 25, 1133-1136.
  57. Neisig,A., Roelse,J., Sijts,A.J., Ossendorp,F., Feltkamp,M.C., Kast,W.M., Melief,C.J., and Neefjes,J.J. (1995). Major differences in transporter associated with antigen presentation (TAP)-dependent translocation of MHC class I-presentable peptides and the effect of flanking sequences. J Immunol 154, 1273-1279.
  58. Peters,P.J., Raposo,G., Neefjes,J.J., Oorschot,V., Leijendekker,R.L., Geuze,H.J., and Ploegh,H.L. (1995). Major histocompatibility complex class II compartments in human B lymphoblastoid cells are distinct from early endosomes. J Exp Med 182, 325-334.
  59. Brouns,G.S., de Vries,E., Neefjes,J.J., and Borst,J. (1996). Assembled pre-B cell receptor complexes are retained in the endoplasmic reticulum by a mechanism that is not selective for the pseudo-light chain. J Biol Chem 271, 19272-19278.
  60. Fernandez-Borja,M., Verwoerd,D., Sanderson,F., Aerts,H., Trowsdale,J., Tulp,A., and Neefjes,J. (1996). HLA-DM and MHC class II molecules co-distribute with peptidase- containing lysosomal subcompartments. Int. Immunol. 8, 625-640.
  61. Fernandez-Borja,M. and Neefjes,J.J. (1996). How cells instruct the immune system to carry out their elimination. Biochem Soc Trans 24, 1039-1043.
  62. Izquierdo,M.A., Neefjes,J.J., Mathari,A.E., Flens,M.J., Scheffer,G.L., and Scheper,R.J. (1996). Overexpression of the ABC transporter TAP in multidrug-resistant human cancer cell lines. Br. J. Cancer 74, 1961-1967.
  63. Koopmann,J.O., Post,M., Neefjes,J.J., Hammerling,G.J., and Momburg,F. (1996). Translocation of long peptides by transporters associated with antigen processing (TAP). Eur J Immunol 26, 1720-1728.
  64. Lewis,J.W., Neisig,A., Neefjes,J., and Elliott,T. (1996). Point mutations in the alpha 2 domain of HLA-A2.1 define a functionally relevant interaction with TAP. Curr. Biol. 6, 873-883.
  65. Momburg,F., Hammerling,G.J., and Neefjes,J.J. (1996). TAP Peptide Transporters and Antigen Presentation. In MHC Molecules: Expression, Assembly and Function, R.G.Urban and R.M.Chicz, eds., pp. 35-63.
  66. Neefjes,J.J. (1996). Antigen presentation by MHC class I and II molecules. Immunobiology 195, 456-460.
  67. Neisig,A., Wubbolts,R., Zang,X., Melief,C., and Neefjes,J. (1996). Allele-specific differences in the interaction of MHC class I molecules with transporters associated with antigen processing. J. Immunol. 156, 3196-3206.
  68. Ossendorp,F., Eggers,M., Neisig,A., Ruppert,T., Groettrup,M., Sijts,A., Mengede,E., Kloetzel,P.M., Neefjes,J., Koszinowski,U., and Melief,C. (1996). A single residue exchange within a viral CTL epitope alters proteasome-mediated degradation resulting in lack of antigen presentation. Immunity 5, 115-124.
  69. Sanderson,F., Thomas,C., Neefjes,J., and Trowsdale,J. (1996). Association between HLA-DM and HLA-DR in vivo. Immunity 4, 87-96.
  70. Sijts,A.J., Neisig,A., Neefjes,J., and Pamer,E.G. (1996). Two Listeria monocytogenes CTL epitopes are processed from the same antigen with different efficiencies. J Immunol 156, 683-692.
  71. Tulp,A., Verwoerd,D., Fernandez-Borja,M., Neefjes,J., and Hart,A.A. (1996). High resolution density gradient electrophoresis of cellular organelles. Electrophoresis 17, 173-178.
  72. Volkmann,A., Neefjes,J., and Stockinger,B. (1996). A conditionally immortalized dendritic cell line which differentiates in contact with T cells or T cell-derived cytokines. Eur J Immunol 26, 2565-2572.
  73. Wubbolts,R., Fernandez-Borja,M., Oomen,L., Verwoerd,D., Janssen,H., Calafat,J., Tulp,A., Dusseljee,S., and Neefjes,J. (1996). Direct vesicular transport of MHC class II molecules from lysosomal structures to the cell surface. J Cell Biol 135, 611-622.
  74. Benham,A.M. and Neefjes,J.J. (1997). Proteasome activity limits the assembly of MHC class I molecules after IFN-gamma stimulation. J Immunol 159, 5896-5904.
  75. Cerundolo,V., Benham,A., Braud,V., Mukherjee,S., Gould,K., Macino,B., Neefjes,J., and Townsend,A. (1997). The proteasome-specific inhibitor lactacystin blocks presentation of cytotoxic T lymphocyte epitopes in human and murine cells. Eur J Immunol 27, 336-341.
  76. Gromme,M., van der Valk,R., Sliedregt,K., Vernie,L., Liskamp,R., Hammerling,G., Koopmann,J.O., Momburg,F., and Neefjes,J. (1997). The rational design of TAP inhibitors using peptide substrate modifications and peptidomimetics. Eur J Immunol 27, 898-904.
  77. Khanna,R., Burrows,S.R., Neisig,A., Neefjes,J., Moss,D.J., and Silins,S.L. (1997). Hierarchy of Epstein-Barr virus-specific cytotoxic T-cell responses in individuals carrying different subtypes of an HLA allele: implications for epitope-based antiviral vaccines. J Virol 71, 7429-7435.
  78. Koppelman,B., Neefjes,J.J., de Vries,J.E., and Waal Malefyt,R. (1997). Interleukin-10 down-regulates MHC class II alphabeta peptide complexes at the plasma membrane of monocytes by affecting arrival and recycling. Immunity 7, 861-871.
  79. Neefjes,J., Momburg,F., Hammerling,G., and Roelse,J. (1997). Peptide translocation into the ER. In MHC Vol. 1 A practical approach, N.Fernandez and G.Butcher, eds. (Oxford: Oxford University Press), pp. 49-57.
  80. Neisig,A., Neefjes,J., and Gromme,M. (1997). Peptide translocation by the transporters associated with antigen processing TAP. In Immunological Methods Manual, Academic Press Ltd.), pp. 719-736.
  81. Oomen,L., Fernandez-Borja,M., Wubbolts,R., Dusseljee,S., and Neefjes,J. (1997). MHC Class II transport in living cells: Confocal analysis of the GFP-tagged protein. Biorad Application Note 20.
  82. Reits,E.A., Benham,A.M., Plougastel,B., Neefjes,J., and Trowsdale,J. (1997). Dynamics of proteasome distribution in living cells. EMBO J 16, 6087-6094.
  83. Spee,P. and Neefjes,J. (1997). TAP-translocated peptides specifically bind proteins in the endoplasmic reticulum, including gp96, protein disulfide isomerase and calreticulin. Eur. J. Immunol. 27, 2441-2449.
  84. Tan,M.C., Mommaas,A.M., Drijfhout,J.W., Jordens,R., Onderwater,J.J., Verwoerd,D., Mulder,A.A., van der Heiden,A.N., Scheidegger,D., Oomen,L.C., Ottenhoff,T.H., Tulp,A., Neefjes,J.J., and Koning,F. (1997). Mannose receptor-mediated uptake of antigens strongly enhances HLA class II-restricted antigen presentation by cultured dendritic cells. Eur. J. Immunol. 27, 2426-2435.
  85. Tulp,A., Verwoerd,D., Benham,A., and Neefjes,J. (1997). High-resolution density gradient electrophoresis of proteins and subcellular organelles. Electrophoresis 18, 2509-2515.
  86. van Ham,S.M., Tjin,E.P., Lillemeier,B.F., Gruneberg,U., van Meijgaarden,K.E., Pastoors,L., Verwoerd,D., Tulp,A., Canas,B., Rahman,D., Ottenhoff,T.H., Pappin,D.J., Trowsdale,J., and Neefjes,J. (1997). HLA-DO is a negative modulator of HLA-DM-mediated MHC class II peptide loading. Curr Biol 7, 950-957.
  87. Wubbolts,R., Fernandez-Borja,M., and Neefjes,J. (1997). MHC Class II molecules: transport pathways for antigen presentation. Trends Cell Biol 7, 115-118.
  88. Benham,A.M., Gromme,M., and Neefjes,J. (1998). Allelic differences in the relationship between proteasome activity and MHC class I peptide loading. J Immunol 161, 83-89.
  89. Dusseljee,S., Wubbolts,R., Verwoerd,D., Tulp,A., Janssen,H., Calafat,J., and Neefjes,J. (1998). Removal and degradation of the free MHC class II beta chain in the endoplasmic reticulum requires proteasomes and is accelerated by BFA. J Cell Sci 111 ( Pt 15), 2217-2226.
  90. Neisig,A., Melief,C.J., and Neefjes,J. (1998). Reduced cell surface expression of HLA-C molecules correlates with restricted peptide binding and stable TAP interaction. J. Immunol. 160, 171-179.
  91. Tulp,A., Fernandez-Borja,M., Verwoerd,D., and Neefjes,J. (1998). High-resolution density gradient electrophoresis of subcellular organelles and proteins under nondenaturing conditions. Electrophoresis 19, 1288-1293.
  92. Tulp,A., Verwoerd,D., Benham,A., Jalink,K., Sier,C., and Neefjes,J. (1998). High performance density gradient electrophoresis of subcellular organelles, protein complexes and proteins. Electrophoresis 19, 1171-1178.
  93. Vierboom,M.P., Feltkamp,M.C., Neisig,A., Drijfhout,J.W., ter Schegget,J., Neefjes,J.J., Melief,C.J., and Kast,W.M. (1998). Peptide vaccination with an anchor-replaced CTL epitope protects against human papillomavirus type 16-induced tumors expressing the wild- type epitope. J. Immunother. 21, 399-408.
  94. Andersen,M.H., Bonfill,J.E., Neisig,A., Arsequell,G., Sondergaard,I., Valencia,G., Neefjes,J., Zeuthen,J., Elliott,T., and Haurum,J.S. (1999). Phosphorylated peptides can be transported by TAP molecules, presented by class I MHC molecules, and recognized by phosphopeptide-specific CTL. J Immunol 163, 3812-3818.
  95. Fernandez-Borja,M., Wubbolts,R., Calafat,J., Janssen,H., Divecha,N., Dusseljee,S., and Neefjes,J. (1999). Multivesicular body morphogenesis requires phosphatidyl-inositol 3-kinase activity. Curr Biol 9, 55-58.
  96. Gromme,M., Uytdehaag,F.G., Janssen,H., Calafat,J., van Binnendijk,R.S., Kenter,M.J., Tulp,A., Verwoerd,D., and Neefjes,J. (1999). Recycling MHC class I molecules and endosomal peptide loading. Proc. Natl. Acad. Sci. U. S. A 96, 10326-10331.
  97. Haurum,J.S., Hoier,I.B., Arsequell,G., Neisig,A., Valencia,G., Zeuthen,J., Neefjes,J., and Elliott,T. (1999). Presentation of cytosolic glycosylated peptides by human class I major histocompatibility complex molecules in vivo. J Exp Med 190, 145-150.
  98. Neefjes,J. (1999). CIIV, MIIC and other compartments for MHC class II loading. Eur J Immunol 29, 1421-1425.
  99. Potter,P.K., Copier,J., Sacks,S.H., Calafat,J., Janssen,H., Neefjes,J.J., and Kelly,A.P. (1999). Accurate intracellular localization of HLA-DM requires correct spacing of a cytoplasmic YTPL targeting motif relative to the transmembrane domain. Eur. J. Immunol. 29, 3936-3944.
  100. Spee,P., Subjeck,J., and Neefjes,J. (1999). Identification of novel peptide binding proteins in the endoplasmic reticulum: ERp72, calnexin, and grp170. Biochemistry 38, 10559-10566.
  101. Tulp,A., Verwoerd,D., and Neefjes,J. (1999). Lectin-induced retardation of subcellular organelles during preparative density gradient electrophoresis: selective purification of plasma membranes. Electrophoresis 20, 438-444.
  102. Tulp,A., Verwoerd,D., and Neefjes,J. (1999). Electromigration for separations of protein complexes. J. Chromatogr. B Biomed. Sci. Appl. 722, 141-151.
  103. Vos,J.C., Spee,P., Momburg,F., and Neefjes,J. (1999). Membrane topology and dimerization of the two subunits of the transporter associated with antigen processing reveal a three-domain structure. J. Immunol. 163, 6679-6685.
  104. Wubbolts,R., Fernandez-Borja,M., Jordens,I., Reits,E., Dusseljee,S., Echeverri,C., Vallee,R.B., and Neefjes,J. (1999). Opposing motor activities of dynein and kinesin determine retention and transport of MHC class II-containing compartments. J Cell Sci 112 ( Pt 6), 785-795.
  105. Wubbolts,R. and Neefjes,J. (1999). Intracellular transport and peptide loading of MHC class II molecules: regulation by chaperones and motors. Immunol Rev 172, 189-208.
  106. Beekman,N.J., van Veelen,P.A., van Hall,T., Neisig,A., Sijts,A., Camps,M., Kloetzel,P.M., Neefjes,J.J., Melief,C.J., and Ossendorp,F. (2000). Abrogation of CTL epitope processing by single amino acid substitution flanking the C-terminal proteasome cleavage site. J Immunol 164, 1898-1905.
  107. Koopmann,J.O., Albring,J., Huter,E., Bulbuc,N., Spee,P., Neefjes,J., Hammerling,G.J., and Momburg,F. (2000). Export of antigenic peptides from the endoplasmic reticulum intersects with retrograde protein translocation through the Sec61p channel. Immunity. 13, 117-127.
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  198. Verweij, FJ, van Eijndhoven, MA, Hopsman, ES, Vendrig, T, Cahir-McFarland, E, Kieff, E, Geerts, D, van der Kant, R, Neefjes, J, Middeldorp, JM and Pegtel, DM (2011) LMP1 association with CD63 and secretion via exosomes limits constitutive NK-KB activation. EMBO J 30: 2115-29
  199. Neefjes J, Jongsma ML, Paul P, Bakke O. (2011) Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nat Rev Immunol. 11:823-36
  200. de Leeuw R, Neefjes J, Michalides R. (2011) A role for estrogen receptor phosphorylation in the resistance to tamoxifen. Int J Breast Cancer:232435
  201. van den Hoorn, T., Paul, P., Janssen, L.J., Janssen, J., and Neefjes, J. (2012) Dynamics within tetraspanin pairs and MHC class II expression. J Cell Sci. 15;125:328-39
  202. Spaapen, R.M., and Neefjes, J. (2012) Immuno-waste exposure and further management. Nature Immunol. 13:109-11
  203. Uusi-Rauva, K, Kyttälä, A, van der Kant, R, Vesa, J, Tanhuanpää, K, Neefjes, J, Olkkonen, VM,  Jalanko, J (2012) Neuronal ceroid lipofuscinosis protein CLN3 interacts with motor proteins and modifies location of late endosomal compartments. Cell. and Mol. Life Sciences 69:2075-89
  204. Houtman R, de Leeuw R, Rondaij M, Melchers D, Verwoerd D, Ruijtenbeek R, Martens JW, Neefjes J, Michalides R. (2012) Serine-305 phosphorylation modulates estrogen receptor alpha binding to a coregulator peptide array, with potential application in predicting responses to tamoxifen. Mol Cancer Ther. 1:805-16.
  205. Majera D, Kristan KČ, Neefjes J, Turk D, Mihelič M. (2012) Expression, purification and assembly of soluble multimeric MHC class II-invariant chain complexes. FEBS Lett. 7;586:1318-24
  206. Neefjes J, Sadaka C. (2012) Into the intracellular logistics of cross-presentation. Front Immunol. 3:31
  207. de Jong A, Merkx R, Berlin I, Rodenko B, Wijdeven RH, El Atmioui D, Yalçin Z, Robson CN, Neefjes JJ, Ovaa H. (2012). Ubiquitin-based probes prepared by total synthesis to profile the activity of deubiquitinating enzymes. Chembiochem. 15:2251-8
  208. Souwer Y, Griekspoor A, de Wit J, Martinoli C, Zagato E, Janssen H, Jorritsma T, Bar-Ephraïm YE, Rescigno M, Neefjes J, van Ham SM. (2012) Selective infection of antigen-specific B lymphocytes by Salmonella mediates bacterial survival and systemic spreading of infection. PLoS One. 7:e50667
  209. Wijdeven RH, Bakker JM, Paul P, Neefjes J. (2013) Exploring genome-wide datasets of MHC class II antigen presentation. Mol Immunol. 55:172-4
  210. Huang S, Hölzel M, Knijnenburg T, Schlicker A, Roepman P, McDermott U, Garnett M, Grernrum W, Sun C, Prahallad A, Groenendijk FH, Mittempergher L, Nijkamp W, Neefjes J, Salazar R, Ten Dijke P, Uramoto H, Tanaka F, Beijersbergen RL, Wessels LF, Bernards R. (2013) MED12 controls the response to multiple cancer drugs through regulation of TGF-β receptor signaling. Cell. 21; 15:937-50
  211. Garstka MA, Neefjes J. (2013) How to target MHC class II into the MIIC compartment. Mol Immunol. 55(2):162-5
  212. Menendez-Benito V, van Deventer SJ, Jimenez-Garcia V, Roy-Luzarraga M, van Leeuwen F, Neefjes J. (2013) Spatiotemporal analysis of organelle and macromolecular complex inheritance. Proc Natl Acad Sci U S A. 2;110:175-80
  213. Neefjes J, Unanue ER. (2013) The ever surprising field of antigen presentation. Mol Immunol. 55:105
  214. van de Kooij B, Verbrugge I, de Vries E, Gijsen M, Montserrat V, Maas C, Neefjes J, Borst J. (2013) Ubiquitination by the membrane-associated RING-CH-8 (MARCH-8) ligase controls steady-state cell surface expression of tumor necrosis factor-related apoptosis inducing ligand (TRAIL) receptor 1. J Biol Chem. 1;288:6617-28
  215. Jongsma ML, Neefjes J. (2013) Assaying peptide translocation by the peptide transporter TAP. Methods Mol Biol. 960:53-65
  216. Paul P, Neefjes J. (2013) Studying MHC class II transport in dendritic cells. Methods Mol Biol. 960:489-507
  217. Kuijl C, Pilli M, Alahari SK, Janssen H, Khoo PS, Ervin KE, Calero M, Jonnalagadda S, Scheller RH, Neefjes J, Junutula JR. (2013) Rac and Rab GTPases dual effector Nischarin regulates vesicle maturation to facilitate survival of intracellular bacteria. EMBO J. 6;32:713-27
  218. Ekkebus R, van Kasteren SI, Kulathu Y, Scholten A, Berlin I, Geurink PP, de Jong A, Goerdayal S, Neefjes J, Heck AJ, Komander D, Ovaa H. (2013) On terminal alkynes that can react with active-site cysteine nucleophiles in proteases. J Am Chem Soc. 27;135:2867-70
  219. Terweij M, van Welsem T, van Deventer S, Verzijlbergen KF, Menendez-Benito V, Ontoso D, San-Segundo P, Neefjes J, van Leeuwen F. (2013) Recombination-induced tag exchange (RITE) cassette series to monitor protein dynamics in Saccharomyces cerevisiae. G3 (Bethesda );3:1261-72
  220. van der Kant R, Zondervan I, Janssen L, Neefjes J. (2013) Cholesterol-binding molecules MLN64 and ORP1L mark distinct late endosomes with transporters ABCA3 and NPC1. J Lipid Res.54:2153-65.
  221. Pang B, Qiao X, Janssen L, Velds A, Groothuis T, Kerkhoven R, Nieuwland M, Ovaa H, Rottenberg S, van Tellingen O, Janssen J, Huijgens P, Zwart W, Neefjes J. (2013) Drug-induced histone eviction from open chromatin contributes to the chemotherapeutic effects of doxorubicin. Nat Commun. 4:1908.
  222. van der Kant R, Fish A, Janssen L, Janssen H, Krom S, Ho N, Brummelkamp T, Carette J, Rocha N, Neefjes J. (2013) Late endosomal transport and tethering are coupled processes controlled by RILP and the cholesterol sensor ORP1L. J Cell Sci.126:3462-74
  223. van Kasteren, SI, Overkleeft, H, Ovaa, H and Neefjes, J (2014) Chemical Biology of antigen presentation by MHC molecules. Curr Op Immunol 26:21-31
  224. Ovaa, H and Neefjes, J (2013). A peptide’s perspective on antigen presentation. Nature Chem Biol. 9:769-775
  225. van der Kant, R  and Neefjes, J (2014). Small regulators, major consequences- Ca2+ and cholesterol at the endosome-ER interface. J. Cell Sci 127: 929-938
  226. Albers, HM, Kuijl, C, Bakker, J, Hendrickx, L, Wekker, S, Farhou, N, Liu, N, Blasco-Moreno, B, Scanu, T, den Hertog, J, Celie, P, Ovaa, H and Neefjes, J (2014). Integrating chemical and genetic silencing strategies to identify host kinase-phosphatase inhibitor networks that control bacterial infection. ACS Chem Biol 9:414-422
  227. Neefjes, J and van der Kant, R (2014). Stuck in traffic: an emerging theme in diseases of the nervous system. Trends Neurosci 37: 66-67
  228. Verbrugge, I, Gasparini, A, Haynes, NM, Hagekyriakou, J, Galli, M, Stewart, TJ, Abrams, SI, Yagita, H, Verheij, M, Johnstone, RW, Borst, J and Neefjes, J (2014) mTOR signaling determines the outcome of radio-immunotherapy 182(2):219-29.
  229. Luteijn RD, Hoelen H, Kruse E, van Leeuwen WF, Grootens J, Horst D, Koorengevel M, Drijfhout JW, Kremmer E, Früh K, Neefjes JJ, Killian A, Lebbink RJ, Ressing ME, Wiertz EJ. (2014) Cowpox virus protein CPXV012 eludes CTLs by blocking ATP binding to TAP. J Immunol.193(4):1578-89.
  230. Wijdeven RH, Neefjes J, Ovaa H. (2014) How chemistry supports cell biology: the chemical toolbox at your service.Trends Cell Biol. 24(12):751-60.
  231. de Wit J, Jorritsma T, Makuch M, Remmerswaal EB, Klaasse Bos H, Souwer Y, Neefjes J, ten Berge IJ, van Ham SM. (2015) Human B cells promote T-cell plasticity to optimize antibody response by inducing coexpression of T(H)1/T(FH) signatures. J Allergy Clin Immunol. 135(4):1053-60.
  232. van Deventer S, Menendez-Benito V, van Leeuwen F, Neefjes J. (2015) N-terminal acetylation and replicative age affect proteasome localization and cell fitness during aging. J Cell Sci. 128(1):109-17.
  233. Jongsma ML, Berlin I, Neefjes J. (2015) On the move: organelle dynamics during mitosis. Trends Cell Biol. 25(3):112-24.
  234. Garstka MA, Fish A, Celie PH, Joosten RP, Janssen GM, Berlin I, Hoppes R, Stadnik M, Janssen L, Ovaa H, van Veelen PA, Perrakis A, Neefjes J. (2015) The first step of peptide selection in antigen presentation by MHC class I molecules. Proc Natl Acad Sci U S A. 112(5):1505-10.
  235. van Luijn MM, Kreft KL, Jongsma ML, Mes SW, Wierenga-Wolf AF, van Meurs M, Melief MJ, der Kant Rv, Janssen L, Janssen H, Tan R, Priatel JJ, Neefjes J, Laman JD, Hintzen RQ. (2015) Multiple sclerosis-associated CLEC16A controls HLA class II expression via late endosome biogenesis. Brain.138(Pt 6):1531-47.
  236. Surace L, Lysenko V, Fontana AO, Cecconi V, Janssen H, Bicvic A, Okoniewski M, Pruschy M, Dummer R, Neefjes J, Knuth A, Gupta A, van den Broek M. (2015) Complement is a central mediator of radiotherapy-induced tumor-specific immunity and clinical response. Immunity. 42(4):767-77.
  237. Pang B, de Jong J, Qiao X, Wessels LF, Neefjes J. (2015) Chemical profiling of the genome with anti-cancer drugs defines target specificities. Nat Chem Biol.11(7):472-80.
  238. Scanu T, Spaapen RM, Bakker JM, Pratap CB, Wu LE, Hofland I, Broeks A, Shukla VK, Kumar M, Janssen H, Song JY, Neefjes-Borst EA, Te Riele H, Holden DW, Nath G, Neefjes J. (2015) Salmonella Manipulation of Host Signaling Pathways Provokes Cellular Transformation Associated with Gallbladder Carcinoma. Cell Host Microbe. 17(6):763-74.
  239. Neefjes J. (2015) Expanding the peptidome for immunotherapy. Blood 126(10):1154-6
  240. Cristiane Bentin Toaldo, Karin Beelen, Marleen Kok, Michael Hauptmann, Maurice Jansen, Els Berns, Jacques Neefjes, Sabine Linn, Rob Michalides, Wilbert Zwart and Xanthippi Alexi (2015). Protein Kinase A-induced tamoxifen resistance is mediated by anchoring protein AKAP13. BMC Cancer 15:588
  241. Wijdeven RH, Pang B, van der Zanden SY, Qiao X, Blomen V, Hoogstraat M, Lips EH, Janssen L, Wessels L, Brummelkamp TR, Neefjes J.(2015) Genome-Wide Identification and Characterization of Novel Factors Conferring Resistance to Topoisomerase II Poisons in Cancer. Cancer Res 75(19)  4176-87 .
  242. van der Kant R, Jonker, CTH, Wijdeven, RH, Klumperman, J and Neefjes J. (2015) Characterization of the mammalian CORVET and HOPS complexes and their modular restructuring for endosome specificity. J. Biol Chem. 290(51):30280-90
  243. Wijdeven R, Jongsma MLM, Neefjes J and Berlin I. (2015) ER contact sites direct late endosome transport. Bioassays ;37(12):1298-302
  244. Dohmen AJ, Swartz JE, Van Den Brekel MW, Willems SM, Spijker R, Neefjes J, Zuur CL (2015) Feasibility of Primary Tumor Culture Models and Preclinical Prediction Assays for Head and Neck Cancer: A Narrative Review. Cancers (Basel). 7(3):1716-42 .
  245. Berkers CR, de Jong A, Schuurman KG, Linnemann C, Meiring HD, Janssen L, Neefjes JJ, Schumacher TN, Rodenko B, Ovaa H (2015) Definition of Proteasomal Peptide Splicing Rules for High-Efficiency Spliced Peptide Presentation by MHC Class I Molecules . J Immunol . 195(9):4085-95
  246. Unanue E, Turk V, and Neefjes J. (2016) Variation in MHC class II antigen processing and presentation in health and disease. Ann Rev Immunol. 34:265-97
  247. Schunselaar LM, Quispel-Janssen JM, Neefjes JJ, Baas P. (2016) A catalogue of treatment and technologies for malignant pleural mesothelioma. Expert Rev Anticancer Ther.16(4):455-63.
  248. Stolze SC, Liu N, Wijdeven RH, Tuin AW, van den Nieuwendijk AM, Florea BI, van der Stelt M, van der Marel GA, Neefjes JJ, Overkleeft HS. (2016) Photo-crosslinking of clinically relevant kinases using H89-derived photo-affinity probes. Mol Biosyst. 12(6):1809-17.
  249. Mulder MP, Witting K, Berlin I, Pruneda JN, Wu KP, Chang JG, Merkx R, Bialas J, Groettrup M, Vertegaal AC, Schulman BA, Komander D, Neefjes J, El Oualid F, Ovaa H. (2016) A cascading activity-based probe sequentially targets E1-E2-E3 ubiquitin enzymes Nat Chem Biol.12(7):523-30.
  250. Wijdeven RH, Janssen H, Nahidiazar L, Janssen L, Jalink K, Berlin I, Neefjes J. (2016) Cholesterol and ORP1L-mediated ER contact sites control autophagosome transport and fusion with the endocytic pathway. Nat Commun. 7:11808
  251. Jongsma MLM, Berlin I, Wijdeven, RH, Janssen H, Janssen L, Janssen GMC, Garstka MA, Mensink M, van Veelen PA, Spaapen RM and Neefjes J. (2016)  An ER-Associated Pathway Defines Endosomal Architecture for Controlled Cargo Transport. Cell 166(1):152-66
  252. Spits M, Neefjes J. (2016) Immunoproteasomes and immunotherapy-a smoking gun for lung cancer? J Thorac Dis. 8(7):E558-63.
  253. Rock KL, Reits E, Neefjes J. (2016) Present Yourself! By MHC Class I and MHC Class II Molecules. Trends Immunol. 4906(16): 30100-4
  254. Wijdeven RH, Pang B, Assaraf YG, Neefjes J. (2016) Old drugs, novel ways out: Drug resistance toward cytotoxic chemotherapeutics. Drug Resist Updat. 28:65-81.
  255. Bonifacino JS, Neefjes J. (2017) Moving and positioning the endolysosomal system. Curr Opin. Cell Biol. Aug;47-1-8
  256. Gagnaire A, Nadel B, Ranout D, Neefjes J , Gorvel JP. (2017) Collateral damage: insights into bacterial mechanisms that predispose host cells to cancer. Nat Rev Microbiol. 15(2):109-128
  257. Neefjes J, Jongsma MM, Berlin I (2017). Stop or Go? Endosome Positioning in the Establishment of Compartment Architecture, Dynamics, and Function. Trends Cell Biol. Aug;27(8):580-594
  258. Dohmen AJC, Qiao X, Duursma A, Wijdeven RH, Lieftink C, Hageman F, Morris B, Halonen P, Vens C, van den Brekel MWM, Ovaa H, Neefjes J, Zuur CL (2017) Identification of a novel ATM inhibitor with cancer cell specific radiosensization activity. Oncotarget. May 19, Epub ahead of print