Honors & Awards

  • CGS/ProQuest Distinguished Dissertation Nominee, University of Virginia (2015)
  • Post Doc Symposium Oral Presentation; Third Place, University of Virginia (2015)
  • 3 Minute Thesis; First Place, University of Virginia (2014)
  • Huskey Research Symposium Oral Presentation; First Place, University of Virginia (2014)
  • Robert J. Huskey Travel Fellowship, University of Virginia (2014)
  • Washington-Baltimore Mass Spectrometry Discussion Group Travel Award, Washington-Baltimore Mass Spectrometry Discussion Group (2014)
  • Achievement Rewards for College Scientists (ARCS) Fellowship, Danaher Scholar, Achievement Rewards for College Scientists (2013-2014)
  • Huskey Research Symposium Poster; First Place, University of Virginia (2013)
  • Pratt Fellowship, University of Virginia (2013)
  • Alpha Chi Sigma Presidential Award, Alpha Chi Sigma (2010)
  • Angell Scholar, University of Michigan (2009)
  • University of Michigan Honors, University of Michigan (2007-2009)

Boards, Advisory Committees, Professional Organizations

  • Member, American Chemical Society (2016 - Present)
  • Member, American Society for Mass Spectrometry (2014 - Present)
  • Member, Alpha Chi Sigma (2007 - Present)

Professional Education

  • Bachelor of Science, University of Michigan Ann Arbor (2009)
  • Doctor of Philosophy, University of Virginia (2014)

Stanford Advisors


  • Donald F. Hunt, Jeffrey Shabanowitz, Stacy A. Malaker, Sarah Penny, and Mark Cobbold. "United States Patent 14/424,702 Target Peptides for Esophageal Cancer Immunotherapy and Diagnostics", University of Virginia
  • Donald F. Hunt, Jeffrey Shabanowitz, Stacy A. Malaker, Victor H. Engelhard, Angela Zarling, Kara L. Cummings, Rebecca C. Obeng, and Mark Cobbold. "United States Patent 61/696,787 Target Peptides for Immunotherapy and Diagnostics", University of Virginia
  • Donald F. Hunt, Jeffrey Shabanowitz, Stacy A. Malaker, Mark Cobbold, and Sarah Penny. "United States Patent 62/202,359 Identification of Class I MHC Associated Glycopeptides as Targets for Cancer Immunotherapy", University of Virginia

Current Research and Scholarly Interests

Aberrant glycosylation is a universal feature of cancer and contributes to the ability of malignant cells to evade the immune system. Elucidating how glycosylation can downregulate the immune system is key to designing cancer immunotherapies that would serve to re-activate the immune system to specifically target and kill cancer cells. My research research uses glycobiology and mass spectrometry to identify glycosylated targets on tumor cells that contribute to immune suppression.

All Publications

  • Peptide-binding motifs of two common equine class I MHC molecules in Thoroughbred horses. Immunogenetics Bergmann, T., Lindvall, M., Moore, E., Moore, E., Sidney, J., Miller, D., Tallmadge, R. L., Myers, P. T., Malaker, S. A., Shabanowitz, J., Osterrieder, N., Peters, B., Hunt, D. F., Antczak, D. F., Sette, A. 2017


    Quantitative peptide-binding motifs of MHC class I alleles provide a valuable tool to efficiently identify putative T cell epitopes. Detailed information on equine MHC class I alleles is still very limited, and to date, only a single equine MHC class I allele, Eqca-1*00101 (ELA-A3 haplotype), has been characterized. The present study extends the number of characterized ELA class I specificities in two additional haplotypes found commonly in the Thoroughbred breed. Accordingly, we here report quantitative binding motifs for the ELA-A2 allele Eqca-16*00101 and the ELA-A9 allele Eqca-1*00201. Utilizing analyses of endogenously bound and eluted ligands and the screening of positional scanning combinatorial libraries, detailed and quantitative peptide-binding motifs were derived for both alleles. Eqca-16*00101 preferentially binds peptides with aliphatic/hydrophobic residues in position 2 and at the C-terminus, and Eqca-1*00201 has a preference for peptides with arginine in position 2 and hydrophobic/aliphatic residues at the C-terminus. Interestingly, the Eqca-16*00101 motif resembles that of the human HLA A02-supertype, while the Eqca-1*00201 motif resembles that of the HLA B27-supertype and two macaque class I alleles. It is expected that the identified motifs will facilitate the selection of candidate epitopes for the study of immune responses in horses.

    View details for DOI 10.1007/s00251-017-0978-6

    View details for PubMedID 28315936

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


    Human natural killer (NK) cell activity is regulated by a family of killer cell immunoglobulin-like receptors (KIRs) that bind human leukocyte antigen (HLA) class I. Combinations of KIR and HLA genotypes are associated with disease, including susceptibility to viral infection and disorders of pregnancy. KIR2DL1 binds HLA-C alleles of group C2 (Lys(80)). KIR2DL2 and KIR2DL3 bind HLA-C alleles of group C1 (Asn(80)). However, this model cannot explain HLA-C allelic effects in disease or the impact of HLA-bound peptides. The goal of this study was to determine the extent to which the endogenous HLA-C peptide repertoire can influence the specific binding of inhibitory KIR to HLA-C allotypes.The impact of HLA-C bound peptide on inhibitory KIR binding was investigated taking advantage of the fact that HLA-C*05:01 (HLA-C group 2, C2) and HLA-C*08:02 (HLA-C group 1, C1) have identical sequences apart from the key KIR specificity determining epitope at residues 77 and 80. Endogenous peptides were eluted from HLA-C*05:01 and used to test the peptide dependence of KIR2DL1 and KIR2DL2/3 binding to HLA-C*05:01 and HLA-C*08:02 and subsequent impact on NK cell function. Specific binding of KIR2DL1 to the C2 allotype occurred with the majority of peptides tested. In contrast, KIR2DL2/3 binding to the C1 allotype occurred with only a subset of peptides. Cross-reactive binding of KIR2DL2/3 with the C2 allotype was restricted to even fewer peptides. Unexpectedly, two peptides promoted binding of the C2 allotype-specific KIR2DL1 to the C1 allotype. We showed that presentation of endogenous peptides or HIV Gag peptides by HLA-C can promote KIR cross-reactive binding.KIR2DL2/3 binding to C1 is more peptide selective than that of KIR2DL1 binding to C2, providing an explanation for KIR2DL3-C1 interactions appearing weaker than KIR2DL1-C2. In addition, cross-reactive binding of KIR is characterized by even higher peptide selectivity. We demonstrate a hierarchy of functional peptide selectivity of KIR-HLA-C interactions with relevance to NK cell biology and human disease associations. This selective peptide sequence-driven binding of KIR provides a potential mechanism for pathogen as well as self-peptide to modulate NK cell activation through altering levels of inhibition.

    View details for DOI 10.3389/fimmu.2017.00193

    View details for PubMedID 28352266

  • Identification of glycopeptides as post-translationally modified neoantigens in leukemia. Cancer immunology research Malaker, S. A., Penny, S. A., Steadman, L. G., Myers, P. T., Loke, J., Raghavan, M., Bai, D. L., Shabanowitz, J., Hunt, D., Cobbold, M. 2017


    Leukemias are highly immunogenic but have a low mutational load, providing few mutated peptide targets. Thus, the identification of alternative neoantigens is a pressing need. Here, we identify 36 MHC class I-associated peptide antigens with O-linked β-N-acetylglucosamine (O-GlcNAc) modifications as candidate neoantigens, using three experimental approaches. Thirteen of these peptides were also detected with disaccharide units on the same residues and two contain either mono- and/or di-methylated arginine residues. A subset were linked with key cancer pathways, and these peptides were shared across all of the leukemia patient samples tested (5/5). Seven of the O-GlcNAc peptides were synthesized and five (71%) were shown to be associated with multifunctional memory T-cell responses in healthy donors. An O-GlcNAc-specific T-cell line specifically killed autologous cells pulsed with the modified peptide, but not the equivalent unmodified peptide. Therefore, these post-translationally modified neoantigens provide logical targets for cancer immunotherapy.

    View details for DOI 10.1158/2326-6066.CIR-16-0280

    View details for PubMedID 28314751

  • Identification and Characterization of Complex Glycosylated Peptides Presented by the MHC Class II Processing Pathway in Melanoma. Journal of proteome research Malaker, S. A., Ferracane, M. J., Depontieu, F. R., Zarling, A. L., Shabanowitz, J., Bai, D. L., Topalian, S. L., Engelhard, V. H., Hunt, D. F. 2016


    The MHC class II (MHCII) processing pathway presents peptides derived from exogenous or membrane-bound proteins to CD4+ T cells. Several studies have shown that glycopeptides are necessary to modulate CD4+ T cell recognition, though glycopeptide structures in these cases are generally unknown. Here, we present a total of 93 glycopeptides from three melanoma cell lines and one matched EBV-transformed line with most found only in the melanoma cell lines. The glycosylation we detected was diverse and comprised 17 different glycoforms. We then used molecular modeling to demonstrate that complex glycopeptides are capable of binding the MHC and may interact with complementarity determining regions. Finally, we present the first evidence of disulfide-bonded peptides presented by MHCII. This is the first large scale study to sequence glyco- and disulfide bonded MHCII peptides from the surface of cancer cells and could represent a novel avenue of tumor activation and/or immunoevasion.

    View details for DOI 10.1021/acs.jproteome.6b00496

    View details for PubMedID 27550523

  • MHC Class I-Associated Phosphopeptides Are the Targets of Memory-like Immunity in Leukemia SCIENCE TRANSLATIONAL MEDICINE Cobbold, M., De la Pena, H., Norris, A., Polefrone, J. M., Qian, J., English, A. M., Cummings, K. L., Penny, S., Turner, J. E., Cottine, J., Abelin, J. G., Malaker, S. A., Zarling, A. L., Huang, H., Goodyear, O., Freeman, S. D., Shabanowitz, J., Pratt, G., Craddock, C., Williams, M. E., Hunt, D. F., Engelhard, V. H. 2013; 5 (203)


    Deregulation of signaling pathways is a hallmark of malignant transformation. Signaling-associated phosphoproteins can be degraded to generate cancer-specific phosphopeptides that are presented by major histocompatibility complex (MHC) class I and II molecules and recognized by T cells; however, the contribution of these phosphoprotein-specific T cells to immune surveillance is unclear. We identified 95 phosphopeptides presented on the surface of primary hematological tumors and normal tissues, including 61 that were tumor-specific. Phosphopeptides were more prevalent on more aggressive and malignant samples. CD8(+) T cell lines specific for these phosphopeptides recognized and killed both leukemia cell lines and human leukocyte antigen-matched primary leukemia cells ex vivo. Notably, healthy individuals showed robust CD8(+) T cell responses against many of these phosphopeptides within the circulating memory compartment. This immunity was significantly reduced or absent in some leukemia patients. This reduction correlated with clinical outcome; however, immunity was restored after allogeneic stem cell transplantation. These results suggest that phosphopeptides may be targets of cancer immune surveillance in humans, and point to their importance for development of vaccine-based and T cell adoptive transfer immunotherapies.

    View details for DOI 10.1126/scitranslmed.3006061

    View details for Web of Science ID 000324589900004

    View details for PubMedID 24048523