PUBLISHED WORK

REVEALING THE HUMAN MUCINOME

2021

Stacy A. Malaker**ǂ, Nicholas M. Rileyǂ, D. Judy Shon, Kayvon Pedram, Venkatesh Krishnan, Oliver Dorigo, and Carolyn R. Bertozzi**. Revealing the human mucinome. bioRXiv

CLASSIFICATION, STRUCTURAL BIOLOGY, AND APPLICATIONS OF MUCIN-DEGRADING PROTEASES: A SYSTEMIC REVIEW

2021

Invited review article: D. Judy Shon, Angel Kuo, Michael J. Ferracane, and Stacy A. Malaker**. Classification, structural biology, and applications of mucin-degrading proteases: a systemic review. Under review

VECTORMOD: METHOD FOR BOTTOM-UP PROTEOMICS CHARACTERIZATION OF RAAV CAPSID PTMS AND VECTOR IMPURITIES

2021

Invited article: Neil G. Rumachik, Stacy A. Malaker**, and Nicole K. Paulk**. VectorMOD: method for bottom-up proteomics characterization of rAAV capsid PTMs and vector impurities. Under review.

GENOME-WIDE CRISPR SCREENS REVEAL A SPECIFIC LIGAND FOR GLYCAN-BINDING IMMUNE CHECKPOINT RECEPTOR SIGLEC-7

2021

Simon P. Wisnovsky, Leonhard Mockl, Stacy A. Malaker, Kayvon Pedram, Gaelen Hess, Nicholas M. Riley, Melissa A. Gray, Benhamin A.H. Smith, Michael C. Bassik, W.E. Moerner, and Carolyn R. Bertozzi. Genome-wide CRISPR screens reveal a specific ligand for glycan-binding immune checkpoint receptor Siglec-7. Proceedings of the National Academy of Sciences USA. 2021, 118(5): e2015024118. link

GENERATING ORTHOGONAL GLYCOSYLTRANSFERASE-NUCLEOTIDE SUGAR PAIRS AS NEXT GENERATION GLYCOBIOLOGY TOOLS

2021

Anna Coice, Stacy A. Malaker**, and Benjamin Schumann**. Generating Orthogonal Glycosyltransferase-Nucleotide Sugar Pairs as Next Generation Glycobiology Tools. Current Opinion in Chemical Biology. 2021, 60: 66-78. link

ON-TISSUE SPATIALLY-RESOLVED GLYCOPROTEOMICS GUIDED BY N-GLYCAN IMAGING REVEAL GLOBAL DYSREGULATION OF CANINE GLIOMA GLYCOPROTEOMIC LANDSCAPE

2020

S. A. Malakerǂ, J.Quanicoǂ, A. Raffo Romero, F. Kobeissy, S. Aboulouard, D. Tierny, C. R. Bertozzi, I. Fournier, M. Salzet. On-tissue spatially-resolved glycoproteomics guided by N-glycan imaging reveal global dysregulation of canine glioma glycoproteomic landscape. bioRXiv

ELECTRON-BASED DISSOCIATION IS NEEDED FOR O-GLYCOPEPTIDES DERIVED FROM OPERATOR PROTEOLYSIS

2020

N.M. Riley, S.A. Malaker, and C.R. Bertozzi. Electron-Based Dissociation Is Needed for O-Glycopeptides Derived from OpeRATOR Proteolysis. Analytical Chemistry. 2020, 92(22): 14878-14884. link

METABOLIC PRECISION LABELING ENABLES SELECTIVE PROBING OF O-LINKED N-ACETYLGALACTOSAMINE GLYCOSYLATION

2020

M.F. Debets, O.Y. Tastan, S.P. Wisnovsky, S.A. Malaker, N. Angelis, L.K.R. Moeckl, J. Choi, H. Flynn, L.J.S. Wagner, G. Bineva-Todd, A. Antononopoulos, A. Cioce, W.M. Browne, Z. Li, D.C. Briggs, H.L. Douglas, G.T. Hess, A.J. Agbay, C. Roustan, S. Kjaer, S.M. Haslam, A.P. Snijders, M.C. Bassik, W.E. Moerner, V.S.W. Li, C.R. Bertozzi, and B. Schumann. Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation. Proceedings of the National Academy of Sciences USA. 2020, 117(41); 25293-25301. link

AN ENZYMATIC TOOLKIT FOR SELECTIVE PROTEOLYSIS, DETECTION, AND VISUALIZATION OF MUCIN-DOMAIN GLYCOPROTEINS

2020

D.J. Shon, S.A. Malaker, K. Pedram, E. Yang, V. Krishnan, O. Dorigo, and C.R. Bertozzi. An Enzymatic Toolkit for Selective Proteolysis, Detection, and Visualization of Mucin-Domain Glycoproteins. Proceedings of the National Academy of Sciences USA. 2020, 117(5); 21299-21307. link

TARGETED GLYCAN DEGRADATION POTENTIATES THE ANTICANCER IMMUNE RESPONSE IN VIVO

2020

M.A. Gray, M.A. Stanczak, N.R. Mantuano, H. Xiao, J.F.A. Pijnenborg, S.A. Malaker, C.L. Miller, P.A. Weidenbacher, J. T. Tanzo, G. Ahn, E.C. Woods, H. Läubli, and C.R. Bertozzi. Targeted desialylation overcomes glyco-immune checkpoints and potentiates the anticancer immune response in vivo. Nature Chemical Biology. 2020, link

OPTIMAL DISSOCIATION METHODS DIFFER FOR N- AND O-GLYCOPEPTIDES

2020

N.M. Riley, S.A. Malaker, M.D. Driessen, and C.R. Bertozzi. Optimal dissociation methods differ for N- and O-glycopeptides. Journal of Proteome Research. 2020; 19(8): 3286-3301. link

BUMP-AND-HOLE ENGINEERING IDENTIFIES SPECIFIC SUBSTRATES OF GLYCOSYLTRANSFERASES IN LIVING CELLS

2020

B. Schumann, S.A. Malaker ǂ, S.P. Wisnovsky ǂ, M.F. Debets, A.J. Agbay, L.J.S. Wagner, L. Lin, Z. Li, J. Choi, D.M. Fox, J.M. Peh, M.A. Gray, K. Pedram, J.J. Kohler, M. Mrksich, and C.R. Bertozzi. Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells. Molecular Cell, 2020. 78(5): 824-834.e15. link

METHODS MATTER -- STANDARD PRODUCTION PLATFORMS FOR RECOMBINANT AAV PRODUCE CHEMICALLY AND FUNCTIONALLY DISTINCT VECTORS

2020

N.G. Rumachik, S.A. Malaker, N. Poweleit, L. Maynard, C.M. Adams, R. Leib, G. Cirolia, D. Thomas, S. Stamnes, K. Holt, P. Sinn, A.P. May, and N.K. Paulk. Methods Matter -- Standard Production Platforms for Recombinant AAV Produce Chemically and Functionally Distinct Vectors. Molecular Therapy: Methods & Clinical Development. 2020, 18: 98-118. link

ENGINEERING ORTHOGONAL POLYPEPTIDE GALNAC-TRANSFERASE AND UDP-SUGAR PAIRS

2019

J. Choi, L.J.S. Wagner, S.B.P.E. Timmermans, S.A. Malaker, B. Schumann, M.A. Gray, M.F. Debets, M.Takashima, J.Gehring, and C.R. Bertozzi. Engineering Orthogonal Polypeptide GalNAc-Transferase and UDP-Sugar Pairs. Journal of the American Chemical Society. 2019; 141(34): 13442-13453. link

THE MUCIN-SELECTIVE PROTEASE STCE ENABLES MOLECULAR AND FUNCTIONAL ANALYSIS OF HUMAN CANCER-ASSOCIATED MUCINS

2019

S.A. Malaker ǂ, K. Pedram ǂ, M.J. Ferracane, B.A. Bensing, V. Krishnan, C. Pett, J. Yu, E.C. Woods, J.R. Kramer, U. Westerlind, O. Dorigo, and C.R. Bertozzi. The mucin-selective protease StcE enables molecular and functional analysis of human cancer-associated mucins. Proceedings of the National Academy of Sciences USA. 2019, 116(15): 7278-7287. link

ISOLATION OF MAJOR HISTOCOMPATIBILITY COMPLEX (MHC)-ASSOCIATED PEPTIDES BY IMMUNOAFFINITY PURIFICATION

2019

S.A. Penny and S.A. Malaker**. Isolation of Major Histocompatibility Complex (MHC)-Associated Peptides by Immunoaffinity Purification. In: Fulton K., Twine S. (eds) Immunoproteomics. Methods in Molecular Biology, 2019, vol 2024. Humana, New York, NY. link

MASS SPECTROMETRIC IDENTIFICATION AND MOLECULAR MODELING OF GLYCOPEPTIDES PRESENTED BY MHC CLASS I AND II PROCESSING PATHWAYS

2019

S.A. Malaker**, Michael J. Ferracane. Mass Spectrometric Identification and Molecular Modeling of Glycopeptides Presented by MHC Class I and II Processing Pathways. In: Fulton K., Twine S. (eds) Immunoproteomics. Methods in Molecular Biology, 2019, vol 2024. Humana, New York, NY. link

MAMMALIAN Y-RNAS ARE GLYCOSYLATED AT DISCRETE GUANOSINE RESIDUES WITH N-TYPE GLYCANS

2019

R.A. Flynn, B.A.H. Smith, A. Johnson, K. Pedram, B.M. George, S.A. Malaker, K. Majzoub, J.E. Carette, and C.R. Bertozzi. Mammalian Y-RNAs are glycosylated at discrete guanosine residues with N-type glycans. bioRXiv

SHARED BINDING SPECIFICITIES OF HLA CLASS I AND CLASS II ALLELES ASSOCIATE WITH CUTANEOUS NEVIRAPINE HYPERSENSITIVITY AND IDENTIFY NOVEL RISK ALLELES

2017

R. Pavlos, E.J. McKinnon, D.A. Ostrov, B. Peters , S. Buus, D. Koelle, A. Chopra, R. Schutte, C. Rive, A. Redwood, S. Restrepo, A. Bracey, T. Kaever, P.T. Myers, E.H. Spears, S.A. Malaker, J. Shabanowitz, J. Yuan, S. Gaudieri, D.F. Hunt, M. Carrington, D.W. Haas, S. Mallal, and E.J. Phillips. Shared binding specificities of HLA Class I and Class II Alleles Associate with Cutaneous Nevirapine Hypersensitivity and Identify Novel Risk Alleles. Scientific Reports. 2017 Aug 17;7(1):8653. link

IDENTIFICATION OF GLYCOPEPTIDES AS POSTTRANSLATIONALLY MODIFIED NEOANTIGENS IN LEUKEMIA

2017

S.A. Malaker ǂ, S.A. Penny ǂ, L. Steadman, P.T. Myers, J.C. Loke, M. Raghavan, D. L. Bai, J. Shabanowitz, D.F. Hunt, M. Cobbold. Identification of glycopeptides as post-translationally modified neoantigens in leukemia. Cancer Immunology Research. 2017, 5(5): 376-384. link

PEPTIDE BINDING MOTIFS OF TWO COMMON EQUINE CLASS I MHC MOLECULES IN THOROUGHBRED HORSES

2017

T. Bergmann, M. Lindvall, E. Moore, E. Moore, J. Sidney, D. Miller, R. Tallmadge, P.T. Myers, S.A. Malaker, J. Shabanowitz, N. Osterrieder, B. Peters, D.F. Hunt, D.F. Antczak, and A. Sette. Peptide binding motifs of two common equine class I MHC molecules in thoroughbred horses. Immunogenetics. 2017; 69(5): 351-358. link

CANONICAL AND CROSS-REACTIVE BINDING OF NK CELL INHIBITORY RECEPTORS TO HLA-C ALLOTYPES IS DICTATED BY PEPTIDES BOUND TO HLA-C

2017

M.J.W.Sim, S.A. Malaker, A. Khan, J.M. Stowell, J. Shabanowitz, M.E. Peterson, S. Rajagopalan, D.F. Hunt, D.M. Altmann, E.O. Long, and R.J. Boyton. Canonical and Cross-reactive Binding of NK Cell Inhibitory Receptors to HLA-C Allotypes Is Dictated by Peptides Bound to HLA-C. Frontiers Immunology. 2017, 8(193). link

IDENTIFICATION AND CHARACTERIZATION OF COMPLEX GLYCOSYLATED PEPTIDES PRESENTED BY THE MHC CLASS II PROCESSING PATHWAY IN MELANOMA

2017

S.A. Malaker, M.J. Ferracane, F.R. Depontieu, A.L. Zarling, J. Shabanowitz, D.L. Bai, S. Topalian, V.H. Engelhard, and D.F. Hunt. Identification and Characterization of Complex Glycosylated Peptides Presented by the MHC Class II Processing Pathway in Melanoma. Journal of Proteome Research. 2017, 16(1): 228-237. link

MHC CLASS I–ASSOCIATED PHOSPHOPEPTIDES ARE THE TARGETS OF MEMORY-LIKE IMMUNITY IN LEUKEMIA

2013

M. Cobbold, H. De La Pena, A. Norris, J. Polefrone, J.E. Turner, J. Qian, A.M. English, Je.G. Abelin, S.A. Malaker, A.L. Zarling, H-W. Huang, S.A. Penny, S. Freeman, J. Shabanowitz, G. Pratt, C. Craddock, M.E. Williams, D.F. Hunt, and V.H. Engelhard. MHC Class I–Associated Phosphopeptides Are the Targets of Memory-like Immunity in Leukemia. Science Translational Medicine. 5(203) 203ra125 (2013). link