Publications

  1. Ahmet Ozdilek, Jiachen Huang, Rachelle Babb, Amy V. Paschall, Dustin R. Middleton, Jeremy A. Duke, Liise-anne Pirofski, Jarrod J. Mousa, Fikri Y. Avci*. A Structural model for the ligand binding of polysaccharide-specific functional antibody responses mBio (in press).
    • PDB ID: 7JVD Fab of 5.6 monoclonal mouse IgG1 co-crystallized with the trisaccharide form of serotype 3 pneumococccal capsular polysaccharide
  2. Amy V. Paschall, Dustin R. Middleton, Fikri Y. Avci*. “Glycans and Immune Regulation” in the book entitled “Encyclopedia of Cell Biology, Second Edition” by Elsevier Publishing, invited chapter (in press).
  3. Ahmet Ozdilek, Fikri Y. Avci*. Glycosylation as a key parameter in the design of nucleic acid vaccines. Current Opinion in Structural Biology invited review (in preparation for publication).
  4. Dustin R. Middleton, Fikri Y. Avci*. “Exploiting glycans in vaccine design” in the book entitled “Vaccine Development: From Concept to Clinic” by Royal Society of Chemistry Publishing, invited chapter (in press).
  5. Amy V. Paschall, Fikri Y. Avci*. “Pathogenesis of SARS-CoV-2 and vaccination programs against COVID-19” in the book entitled “Vaccine Development: From Concept to Clinic” by Royal Society of Chemistry Publishing, invited chapter (in press).
  6. Jiachen Huang, Aaron D. Gingerich, Fredejah Royer, Amy V. Paschall, Alma Pena-Briseno, Fikri Y. Avci, Jarrod J. Mousa. Human monoclonal antibodies to the pneumococcal histidine triad protein are protective, broadly reactive, and have diverse epitope specificity. Infection and Immunity DOI: 10.1128/IAI.00747-20 (2021).
  7. Dustin R. Middleton, Javid Aceil, Seema Mustafa, Amy V. Paschall, Fikri Y. Avci*. Glycosyltransferases within the psrP locus facilitate pneumococcal virulence. Journal of Bacteriology 203, JB.00389-20 (2021).
  8. Paeton L. Wantuch, Satya Jella, Jeremy A. Duke, Jarrod J. Mousa, Bernard Henrissat, John Glushka, Fikri Y. Avci*. Characterization of the β-glucuronidase Pn3Pase as the founding member of glycoside hydrolase family GH169. Glycobiology 31, 266-274 (2021).
  9. Amy V. Paschall, Dustin R. Middleton, Paeton L. Wantuch, Fikri Y. Avci*. Type 3 Streptococcus pneumoniae capsule degrading enzyme Pn3Pase shows therapeutic potential with minimal off-target effects. Pharmaceutical Research 37, 1-9 (2020).
  10. S Zhou, Z Zhen, A Paschall, L Xue, X Yang, AB Blackwell, Z Cao, W Zhang, M Wang, Y Teng, G Zhou, Z Li, Fikri Y Avci, W Tang, J Xie. FAP-targeted photodynamic therapy mediated by ferritin nanoparticles elicits an immune response against cancer cells and cancer associated fibroblasts. Advanced Functional Materials 2007017 (2020).
  11. Lina Sun, Amy V. Paschall, Dustin R. Middleton, Mayumi Ishihara, Ahmet Ozdilek, Paeton L. Wantuch, Javid Aceil, Jeremy A. Duke, Celia C. LaBranche, Michael Tiemeyer, Fikri Y. Avci*. Glycopeptide epitope facilitates HIV-1 envelope specific humoral immune responses by eliciting T cell help. Nature Communications 11, 1-14 (2020).
  12. Paeton L Wantuch, Lina Sun, Rachel K Lopilato, Jarrod J. Mousa, Robert S Haltiwanger, Fikri Y Avci*. Isolation and characterization of new human CD4+ T cell epitopes from two important vaccine immunogens. Vaccine 38, 2315-2325 (2020).
  13. Ahmet Ozdilek, Amy V. Paschall, Michelle Dookwah, Michael Tiemeyer, Fikri Y Avci*. Host protein glycosylation in viral vector-based and DNA vaccines as a major hurdle in vaccine design Proceedings of the National Academy of Sciences of the United States of America (PNAS) 117, 1280-1282 (2020).
  14. N Juge, Fikri Y. Avci, NE Scott, C Creuzenet, MA Valvano. 2020 FASEB Science Research Conference on Microbial Glycobiology, July 13-14, 2020. The FASEB Journal 34, 14069-14072 (2020).
  15. Fikri Y. Avci,  Francesco Berti, Peter Dull, John Hennesey, Olivier Marcq, Krishna Prasad, Villiam Pavliak, Willie Vann, Michael Wacker. Glycoconjugate Vaccines: What do we know and what would it take to master these well-known, yet little understood, immunogenic conjugates? mSphere 4, e00520-19 (2019).
  16. W Jiang, L Yin, H Chen, A Paschall, L Zhang, W Fu, W Zhang, T Todd, KS Yu, S Zhou, Z Zhen, M Butler, L Yao, F Zhang, Y Shen, Z Li, A Yin, H Yin, X Wang Fikri Y Avci, X Yu, J Xie. NaCl nanoparticles as a Cancer Therapeutic. Advanced Materials e1904058 (2019).
  17. Paeton Wantuch, Fikri Y. Avci*. Invasive Pneumococcal Diseases in Relation to Vaccine Serotype. Human Vaccines and Immunotherapeutics 874-875 (2019).
  18. Amy V. Paschall, Dustin R. Middleton, Fikri Y. Avci*. Opsonophagocytic Killing Assay to Assess Immunological Responses Against Bacterial Pathogens. Journal of Visualized Experiments (JoVE) 146 (2019).
  19. Shuihong Cheng, Paeton Wantuch, Megan E. Kizer, Dustin Middleton, Ruitong Wang, Mikaela DiBellow, Mingli Li, Xing Wang, Xuebing Li, Vasanti Ramachandrian, Fikri Y. Avci, Fuming Zhang,Xing Zhang,andRobert J. Linhardt. Glycoconjugate synthesis using chemoselective ligation. Organic & Biomolecular Chemistry 17, 2646-2650 (2019).
  20. Lina Sun, Mayumi Ishihara, Dustin R Middleton, Michael Tiemeyer and Fikri Y. Avci*. Metabolic labeling of HIV-1 envelope glycoprotein gp120 to elucidate the role of gp120 glycosylation on antigen uptake. Journal of Biological Chemistry 293, 15178-15194 (2018).
  21. Dustin R. Middleton, Amy V. Paschall, Jeremy A. Duke, Fikri Y. Avci*. Enzymatic hydrolysis of pneumococcal capsular polysaccharide renders the bacterium vulnerable to host defense. Infection and Immunity 86, 1-12 (2018).
    • Selected by the editors to be featured in the “Spotlight” section of Infection and Immunity that highlights research articles of significant interest.
    • Faculty of 1000 evaluated and recommended by Mattias Collin. F1000 Immunology (DOI: 10.3410/f.733387483.793547056).
  22. Paeton L. Wantuch, Fikri Y. Avci*. Clinical Manifestations of Pneumococcal Vaccine Programs. Human Vaccines and Immunotherapeutics 2303-2309 (2018).
  23. Jeremy A. Duke, Fikri Y. Avci*. “Immunological Mechanisms for Glycoconjugate Vaccines” in the book entitled “Carbohydrate-based Vaccines: From Concept to Clinic” in “ACS Symposium Series”, by Oxford University Press Chapter 3, 61-74 (2018).
  24. Dustin R Middleton, Xing Zhang, Paeton L. Wantuch, Ahmet Ozdilek, Xinyue Liu, Rachel Lopilato, Nikhil Gangasani, Robert Bridger, Lance Wells, Robert J. Linhardt, and Fikri Y. Avci* Identification and characterization of the Streptococcus pneumoniaetype 3 capsule-specific glycoside hydrolase of Paenibacillus species 32352. Glycobiology 28, 90-99 (2018).
    • Faculty of 1000 evaluated and recommended by Mattias Collin. F1000 Immunology.
  25. Dustin Middleton#, Lina Sun#, Amy Paschall, Fikri Y. Avci*. T Cell Mediated Humoral Immune Responses to Type 3 Capsular Polysaccharide of Streptococcus pneumoniaeJournal of Immunology 199, 598-603 (2017). # co-first author
  26. Dustin Middleton, Walter Lorenz, Fikri Y. Avci*. Complete Genome Sequence of the Bacterium Bacillus circulans Jordan Strain 32352. Genome Announcements 5, e00289-17 (2017).
  27. M. Osman Sheikh, Stephanie M. Halmo, Sneha Patel, Dustin Middleton, Hideyuki Takeuchi, Christopher M. Schafer, Christopher M. West, Robert S. Haltiwanger, Fikri Y. Avci, Kelley W. Moremen, Lance Wells. Rapid screening of sugar-nucleotide donor specificities of putative glycosyltransferases Glycobiology 27, 206-212 (2016).
  28. Fikri Y. Avci*. A chicken vaccine to protect humans from diarrheal disease. Glycobiology 26, 1137-1139 (2016).
  29. Lina Sun, Dustin Middleton, Paeton Wantuch, Ahmet Ozdilek, Fikri Y. Avci*. Carbohydrates as T cell Antigens with Implications to Health and Disease. Glycobiology 26, 1029-1040 (2016).
  30. Guoyun Li, Lingyun Li, Changhu Xue, Dustin Middleton, Robert J. Linhardt, Fikri Y. Avci*. Profiling pneumococcal type 3-derived oligosaccharides by liquid chromatograph-tandem mass spectrometry. Journal of Chromatography A 1397, 43-51 (2015).
  31. Dingding An, Sungwhan F. Oh, Torsten Olszak, Joana F. Neves, Fikri Y. Avci, Deniz Erturk-Hasdemir, Xi Lu, Sebastian Zeissig, Richard S. Blumberg, Dennis L. Kasper. Sphingolipids from a symbiotic microbe regulate homeostasis of host intestinal natural killer T cells. Cell 156, 123-133 (2014).
  32. Fikri Y. Avci*. Novel Strategies for Development of Next-Generation Glycoconjugate Vaccines. Current Topics in Medicinal Chemistry  13, 2535-2540 (2013).
  33. Fikri Y. Avci*, Xiangming Li, Moriya Tsuji, Dennis L. Kasper. Carbohydrates and T cells: A sweet twosome. Seminars in Immunology 25, 146-151 (2013).
  34. Vincent L. Chen, Fikri Y. Avci, Dennis L. Kasper. A Maternal Vaccine against Group B Streptococcus: Past, Present and Future. Vaccine 31, D13-D19 (2013).
  35. Fikri Y. Avci, Xiangming Li, Moriya Tsuji, Dennis L. Kasper. Isolation of carbohydrate-specific CD4+ T cell clones from mice after stimulation by two model glycoconjugate vaccines. Nature Protocols 7, 2180-2192 (2012).
  36. Fikri Y. Avci, Xiangming Li, Moriya Tsuji, Dennis L. Kasper. A mechanism for glycoconjugate vaccine activation of the adaptive immune system and its implications for vaccine design. Nature Medicine 17, 1602-1609 (2011).
    i. News and Views by Rino Rappuoli, Ennio De Gregorio. A sweet T cell response. Nature Medicine 17, 1551-1552 (2011).
    ii. The Distillery. Rational design of glycoconjugate vaccines. Science-Business eXchange 4, 1366 (2011).
    iii. Research Highlights by Laura DeFrancesco et al. Improving glycoconjugate vaccines. Nature Biotechnology 30, 158 (2012).
    iv. Research Highlights by Monica H. Flight. Enhancing glycan presentation increases vaccine efficacy. Nature Reviews Drug Discovery 11, 21-22 (2012).
    v. Faculty of 1000 evaluated and rated by Michael Kurilla. F1000 Pharmacology & Drug Discovery (2012).
    vi. Selected as “The Paper of the Month” by International Society for Vaccines, Vaccine (2012).
  37. Fikri Y. Avci*, Dennis L. Kasper. How bacterial carbohydrates influence the adaptive immune system. Annual Review of Immunology 28, 107-130 (2010).
  38. Alexis Choi, Leyla Slamti, Fikri Y. Avci, Gerald B. Pier, Tomás Maira-Litrán. The pgaABCD locus of Acinetobacter baumannii encodes the production of poly-β-1-6-N-acetyl glucosamine PNAG that is critical for biofilm formation. Journal of Bacteriology 191, 5953-5963 (2009).
  39. Jinyou Duan, Fikri Y. Avci, Dennis L. Kasper. Microbial carbohydrate depolymerization by antigen-presenting cells: Deamination prior to presentation by the MHCII pathway. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 105, 5183-5188 (2008).
  40. Fikri Y. Avci, Paul DeAngelis, Jian Liu, Robert J. Linhardt. “Chemoenzymatic sythesis of glycosaminoglycans: Improving on nature”, book entitled “Frontiers in Carbohydrate Chemistry” in “ACS Symposium Series”, by Oxford University Press  960, 253-284 (2007).
  41. Breca Tracy, Fikri Y. Avci, Paul L. DeAngelis, Robert J. Linhardt. Acceptor specificity of the Pasteurella hyaluronan and chondroitin synthases and production of chimeric glycosaminoglycans. Journal of Biological Chemistry 282, 337-344 (2007).
  42. Tatiana N. Laremore, Saravanababu Murugesan, Tae-joon Park, Fikri Y. Avci, Dmitri V. Zagorevski, Robert J. Linhardt. Matrix-assisted laser desorption/ ionization mass spectrometric analysis of uncomplexed highly sulfated oligosaccharides using ionic liquid matrices. Analytical Chemistry 78, 1774-1779 (2006).
  43. Robert J. Linhardt, Fikri Y. Avci, Toshiko Toida,Yeong Shik Kim, Miroslaw Cygler “CS Lyases: Structure, activity and applications in analysis and the treatment of diseases”, book entitled “Chondroitin Sulfate Structure, Role and Pharmacological Activity” in the series “Advanced Pharmacology” by ELSEVIER 53, 187-215 (2006).
  44. Eva Muñoz, Ding Xu, Fikri Y. Avci, Melissa Kemp, Jian Liu and Robert J. Linhardt. Enzymatic synthesis of heparin related polysaccharides on sensor chips: Rapid screening of heparin–protein interactions. Biochemical and Biophysical Research Communications 339, 597-602 (2006).
  45. Jinghua Chen, Fikri Y. Avci, Eva M. Munoz, Miao Chen, L. M. McDowell, Lars C. Pedersen, Robert J Linhardt, Jian Liu. Enzymatically Redesigning the Biologically Active Heparan Sulfate. Journal of Biological Chemistry 280, 42817-42825 (2005).
  46. Kano Hirano, Shinobu Sakai, Tsutomu Ishikawa, Fikri Y. Avci, Robert J. Linhardt, Toshihiko Toida. Preparation of hyaluronan O-methylester and its enzymatic degradation. Carbohydrate Research 340, 2297-2304 (2005).
  47. Nathalie A. Karst, Tasneem F. Islam, Fikri Y. Avci, Robert J. Linhardt. Trifluoroethylsulfonate protected monosaccharides in glycosylation reactions. Tetrahedron Letters 45, 6433-6437 (2004).
  48. Fikri Y. Avci, Nathalie A. Karst, Robert J. Linhardt. Synthetic oligosaccharides as heparin-mimetics displaying anticoagulant properties. Current Pharmaceutical Design 9, 2323-2335 (2003).
  49. Fikri Y. Avci, Toshihiko Toida, Robert J. Linhardt. Chondroitin O-methyl Ester: an unusual substrate for chondroitin AC lyase. Carbohydrate Research 338, 2101-2104 (2003).

Patents

  1. Fikri Y. Avci, Paeton Wantuch. B Glucuronidase proteins having pneumococcal capsule degrading activity and methods of use; US Patent Application Serial No: 0235.000293US60 (2020).
  2. Fikri Y. Avci, Ahmet Ozdilek. Designing nucleic acid vaccines to prevent host glycosylation; US Patent Application Serial No: 62,945,627 (2019).
  3. Fikri Y. Avci, Paeton Wantuch, Jeremy Duke. Peptide based vaccine carriers; US Patent Application Serial No: 62/939,299 (2019).
  4. Fikri Y. Avci, Lina Sun. HIV envelope glycoprotein T cell epitopes; US Patent Application Serial No: 62/909,585 (2019).
  5. Fikri Y. Avci, Dustin Middleton, Amy Paschall. Proteins having pneumococcal capsule degrading activity and methods of use; International Application No: PCT/US2018/046521 (2018).
  6. Fikri Y. Avci, Dennis L. Kasper. Glycoconjugate vaccines; PATENT NO: WO 2010110931 (2010).
  7. Jian Liu, Robert J. Linhardt, Fikri Y. Avci, Jinghua Chen, Eva M. Munoz. Enzymatic Synthesis of Sulfated Heparan Derivatives; PATENT NO: WO 2006124801 (2006).