Program Official

Principal Investigator

Carolyn
Bertozzi
Awardee Organization

Stanford University
United States

Fiscal Year
2024
Activity Code
R01
Early Stage Investigator Grants (ESI)
Not Applicable
Project End Date

Chemical glycoproteomics

Mucins are heavily glycosylated proteins that have been known to play roles in inflammation and cancer with potential to be therapeutic targets for future treatments1. Probing the mucinome is something that the Bertozzi lab has worked towards since 2002 in the form of mucin-type O-glycoproteomics technology development. To build upon these accomplishments, I will work towards the development of a new mucin-selective enrichment strategy for mass spectrometry analysis of the “mucinome” by utilizing a novel proximity labeling approach6. To do this, I will develop a StcE[E447D] mucinase with an iridium photocatalyst conjugate which will catalyze the labeling of mucin domain containing proteins with a biotin probe which can then be enriched. The conjugated StcE[E447D] mucinase will be validated utilizing mass spectrometry glycoproteomics in prostate cancer cell models. Finally, I will also expand upon the existing library of inactive mucinases by adding inactive mucinases with photocatalyst conjugates.

Publications

  • Wei W, Riley NM, Lyu X, Shen X, Guo J, Raun SH, Zhao M, Moya-Garzon MD, Basu H, Sheng-Hwa Tung A, Li VL, Huang W, Wiggenhorn AL, Svensson KJ, Snyder MP, Bertozzi CR, Long JZ. Organism-wide, cell-type-specific secretome mapping of exercise training in mice. Cell metabolism. 2023 Jul 11;35(7):1261-1279.e11. Epub 2023 May 3. PMID: 37141889
  • Malaker SA, Quanico J, Raffo-Romero A, Kobeissy F, Aboulouard S, Tierny D, Bertozzi CR, Fournier I, Salzet M. On-tissue spatially resolved glycoproteomics guided by N-glycan imaging reveal global dysregulation of canine glioma glycoproteomic landscape. Cell chemical biology. 2022 Jan 20;29(1):30-42.e4. Epub 2021 Jun 7. PMID: 34102146
  • Cioce A, Bineva-Todd G, Agbay AJ, Choi J, Wood TM, Debets MF, Browne WM, Douglas HL, Roustan C, Tastan OY, Kjaer S, Bush JT, Bertozzi CR, Schumann B. Optimization of Metabolic Oligosaccharide Engineering with Ac4GalNAlk and Ac4GlcNAlk by an Engineered Pyrophosphorylase. ACS chemical biology. 2021 Oct 15;16(10):1961-1967. Epub 2021 Apr 9. PMID: 33835779
  • Yang AC, Stevens MY, Chen MB, Lee DP, Stähli D, Gate D, Contrepois K, Chen W, Iram T, Zhang L, Vest RT, Chaney A, Lehallier B, Olsson N, du Bois H, Hsieh R, Cropper HC, Berdnik D, Li L, Wang EY, Traber GM, Bertozzi CR, Luo J, Snyder MP, Elias JE, Quake SR, James ML, Wyss-Coray T. Physiological blood-brain transport is impaired with age by a shift in transcytosis. Nature. 2020 Jul;583(7816):425-430. Epub 2020 Jul 1. PMID: 32612231
  • Spiciarich DR, Oh ST, Foley A, Hughes SB, Mauro MJ, Abdel-Wahab O, Press RD, Viner R, Thompson SL, Chen Q, Azadi P, Bertozzi CR, Maxson JE. A Novel Germline Variant in CSF3R Reduces N-Glycosylation and Exerts Potent Oncogenic Effects in Leukemia. Cancer research. 2018 Dec 15;78(24):6762-6770. Epub 2018 Oct 22. PMID: 30348809
  • Malaker SA, Riley NM, Shon DJ, Pedram K, Krishnan V, Dorigo O, Bertozzi CR. Revealing the human mucinome. Nature communications. 2022 Jun 20;13(1):3542. PMID: 35725833
  • Woo CM, Felix A, Byrd WE, Zuegel DK, Ishihara M, Azadi P, Iavarone AT, Pitteri SJ, Bertozzi CR. Development of IsoTaG, a Chemical Glycoproteomics Technique for Profiling Intact N- and O-Glycopeptides from Whole Cell Proteomes. Journal of proteome research. 2017 Apr 7;16(4):1706-1718. Epub 2017 Feb 28. PMID: 28244757
  • Shon DJ, Malaker SA, Pedram K, Yang E, Krishnan V, Dorigo O, Bertozzi CR. An enzymatic toolkit for selective proteolysis, detection, and visualization of mucin-domain glycoproteins. Proceedings of the National Academy of Sciences of the United States of America. 2020 Sep 1;117(35):21299-21307. Epub 2020 Aug 17. PMID: 32817557
  • Woo CM, Bertozzi CR. Isotope Targeted Glycoproteomics (IsoTaG) to Characterize Intact, Metabolically Labeled Glycopeptides from Complex Proteomes. Current protocols in chemical biology. 2016 Mar 16;8(1):59-82. PMID: 26995354
  • Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Molecular & cellular proteomics : MCP. 2021;20:100029. Epub 2020 Dec 20. PMID: 33583771
  • Chongsaritsinsuk J, Steigmeyer AD, Mahoney KE, Rosenfeld MA, Lucas TM, Ince D, Kearns FL, Battison AS, Hollenhorst MA, Shon DJ, Tiemeyer KH, Attah V, Kwon C, Bertozzi CR, Ferracane MJ, Amaro RE, Malaker SA. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. bioRxiv : the preprint server for biology. 2023 Feb 3. PMID: 36778266
  • Woo CM, Iavarone AT, Spiciarich DR, Palaniappan KK, Bertozzi CR. Isotope-targeted glycoproteomics (IsoTaG): a mass-independent platform for intact N- and O-glycopeptide discovery and analysis. Nature methods. 2015 Jun;12(6):561-7. Epub 2015 Apr 20. PMID: 25894945
  • Hollander MJ, Malaker SA, Riley NM, Perez I, Abney NM, Gray MA, Maxson JE, Cochran JR, Bertozzi CR. Mutational screens highlight glycosylation as a modulator of colony-stimulating factor 3 receptor (CSF3R) activity. The Journal of biological chemistry. 2023 Jun;299(6):104755. Epub 2023 Apr 26. PMID: 37116708
  • Goyette MA, Stevens LE, DePinho CR, Seehawer M, Nishida J, Li Z, Wilde CM, Li R, Qiu X, Pyke AL, Zhao S, Lim K, Tender GS, Northey JJ, Riley NM, Long HW, Bertozzi CR, Weaver VM, Polyak K. Cancer-stromal cell interactions in breast cancer brain metastases induce glycocalyx-mediated resistance to HER2-targeting therapies. Proceedings of the National Academy of Sciences of the United States of America. 2024 May 14;121(20):e2322688121. Epub 2024 May 6. PMID: 38709925
  • Schumann B, Malaker SA, Wisnovsky SP, Debets MF, Agbay AJ, Fernandez D, Wagner LJS, Lin L, Li Z, Choi J, Fox DM, Peh J, Gray MA, Pedram K, Kohler JJ, Mrksich M, Bertozzi CR. Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells. Molecular cell. 2020 Jun 4;78(5):824-834.e15. Epub 2020 Apr 22. PMID: 32325029
  • Shon DJ, Fernandez D, Riley NM, Ferracane MJ, Bertozzi CR. Structure-guided mutagenesis of a mucin-selective metalloprotease from Akkermansia muciniphila alters substrate preferences. The Journal of biological chemistry. 2022 May;298(5):101917. Epub 2022 Apr 9. PMID: 35405095
  • Sheta R, Roux-Dalvai F, Woo CM, Fournier F, Bourassa S, Bertozzi CR, Droit A, Bachvarov D. Proteomic dataset for altered glycoprotein expression upon GALNT3 knockdown in ovarian cancer cells. Data in brief. 2016 May 30;8:342-9. doi: 10.1016/j.dib.2016.05.060. eCollection 2016 Sep. PMID: 27331112
  • Sheta R, Woo CM, Roux-Dalvai F, Fournier F, Bourassa S, Droit A, Bertozzi CR, Bachvarov D. A metabolic labeling approach for glycoproteomic analysis reveals altered glycoprotein expression upon GALNT3 knockdown in ovarian cancer cells. Journal of proteomics. 2016 Aug 11;145:91-102. Epub 2016 Apr 17. PMID: 27095597
  • Flynn RA, Pedram K, Malaker SA, Batista PJ, Smith BAH, Johnson AG, George BM, Majzoub K, Villalta PW, Carette JE, Bertozzi CR. Small RNAs are modified with N-glycans and displayed on the surface of living cells. Cell. 2021 Jun 10;184(12):3109-3124.e22. Epub 2021 May 17. PMID: 34004145
  • Hollenhorst MA, Tiemeyer KH, Mahoney KE, Aoki K, Ishihara M, Lowery SC, Rangel-Angarita V, Bertozzi CR, Malaker SA. Comprehensive analysis of platelet glycoprotein Ibα ectodomain glycosylation. Journal of thrombosis and haemostasis : JTH. 2023 Apr;21(4):995-1009. Epub 2023 Jan 14. PMID: 36740532
  • Tender GS, Bertozzi CR. Bringing enzymes to the proximity party. RSC chemical biology. 2023 Sep 29;4(12):986-1002. doi: 10.1039/d3cb00084b. eCollection 2023 Nov 29. PMID: 38033727
  • Palaniappan KK, Bertozzi CR. Chemical Glycoproteomics. Chemical reviews. 2016 Dec 14;116(23):14277-14306. Epub 2016 Nov 18. PMID: 27960262
  • Debets MF, Tastan OY, Wisnovsky SP, Malaker SA, Angelis N, Moeckl LKR, Choi J, Flynn H, Wagner LJS, Bineva-Todd G, Antonopoulos A, Cioce A, Browne WM, Li Z, Briggs DC, Douglas HL, Hess GT, Agbay AJ, Roustan C, Kjaer S, Haslam SM, Snijders AP, Bassik MC, Moerner WE, Li VSW, Bertozzi CR, Schumann B. Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation. Proceedings of the National Academy of Sciences of the United States of America. 2020 Oct 13;117(41):25293-25301. Epub 2020 Sep 28. PMID: 32989128
  • Cioce A, Calle B, Rizou T, Lowery SC, Bridgeman VL, Mahoney KE, Marchesi A, Bineva-Todd G, Flynn H, Li Z, Tastan OY, Roustan C, Soro-Barrio P, Rafiee MR, Garza-Garcia A, Antonopoulos A, Wood TM, Keenan T, Both P, Huang K, Parmeggian F, Snijders AP, Skehel M, Kjær S, Fascione MA, Bertozzi CR, Haslam SM, Flitsch SL, Malaker SA, Malanchi I, Schumann B. Cell-specific bioorthogonal tagging of glycoproteins. Nature communications. 2022 Oct 25;13(1):6237. PMID: 36284108
  • Bouchard G, Garcia-Marques FJ, Karacosta LG, Zhang W, Bermudez A, Riley NM, Varma S, Mehl LC, Benson JA, Shrager JB, Bertozzi CR, Pitteri SJ, Giaccia AJ, Plevritis SK. Multiomics Analysis of Spatially Distinct Stromal Cells Reveals Tumor-Induced O-Glycosylation of the CDK4-pRB Axis in Fibroblasts at the Invasive Tumor Edge. Cancer research. 2022 Feb 15;82(4):648-664. PMID: 34853070
  • Pensinger DA, Fisher AT, Dobrila HA, Van Treuren W, Gardner JO, Higginbottom SK, Carter MM, Schumann B, Bertozzi CR, Anikst V, Martin C, Robilotti EV, Chow JM, Buck RH, Tompkins LS, Sonnenburg JL, Hryckowian AJ. Butyrate Differentiates Permissiveness to Clostridioides difficile Infection and Influences Growth of Diverse C. difficile Isolates. Infection and immunity. 2023 Feb 16;91(2):e0057022. Epub 2023 Jan 24. PMID: 36692308
  • Andres LM, Blong IW, Evans AC, Rumachik NG, Yamaguchi T, Pham ND, Thompson P, Kohler JJ, Bertozzi CR. Chemical Modulation of Protein O-GlcNAcylation via OGT Inhibition Promotes Human Neural Cell Differentiation. ACS chemical biology. 2017 Aug 18;12(8):2030-2039. Epub 2017 Jun 19. PMID: 28541657
  • Woo CM, Felix A, Zhang L, Elias JE, Bertozzi CR. Isotope-targeted glycoproteomics (IsoTaG) analysis of sialylated N- and O-glycopeptides on an Orbitrap Fusion Tribrid using azido and alkynyl sugars. Analytical and bioanalytical chemistry. 2017 Jan;409(2):579-588. Epub 2016 Sep 30. PMID: 27695962
  • Calle B, Gonzalez-Rodriguez E, Mahoney KE, Cioce A, Bineva-Todd G, Tastan OY, Roustan C, Flynn H, Malaker SA, Schumann B. Bump-and-hole engineering of human polypeptide N-acetylgalactosamine transferases to dissect their protein substrates and glycosylation sites in cells. STAR protocols. 2023 Mar 17;4(1):101974. Epub 2023 Jan 11. PMID: 36633947
  • Tomlin FM, Gerling-Driessen UIM, Liu YC, Flynn RA, Vangala JR, Lentz CS, Clauder-Muenster S, Jakob P, Mueller WF, Ordoñez-Rueda D, Paulsen M, Matsui N, Foley D, Rafalko A, Suzuki T, Bogyo M, Steinmetz LM, Radhakrishnan SK, Bertozzi CR. Inhibition of NGLY1 Inactivates the Transcription Factor Nrf1 and Potentiates Proteasome Inhibitor Cytotoxicity. ACS central science. 2017 Nov 22;3(11):1143-1155. Epub 2017 Oct 25. PMID: 29202016
  • Spiciarich DR, Nolley R, Maund SL, Purcell SC, Herschel J, Iavarone AT, Peehl DM, Bertozzi CR. Bioorthogonal Labeling of Human Prostate Cancer Tissue Slice Cultures for Glycoproteomics. Angewandte Chemie (International ed. in English). 2017 Jul 24;56(31):8992-8997. Epub 2017 Jun 26. PMID: 28649697
  • Jolly AL, Agarwal P, Metruccio MME, Spiciarich DR, Evans DJ, Bertozzi CR, Fleiszig SMJ. Corneal surface glycosylation is modulated by IL-1R and Pseudomonas aeruginosa challenge but is insufficient for inhibiting bacterial binding. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 2017 Jun;31(6):2393-2404. Epub 2017 Feb 21. PMID: 28223334
  • Choi J, Wagner LJS, Timmermans SBPE, Malaker SA, Schumann B, Gray MA, Debets MF, Takashima M, Gehring J, Bertozzi CR. Engineering Orthogonal Polypeptide GalNAc-Transferase and UDP-Sugar Pairs. Journal of the American Chemical Society. 2019 Aug 28;141(34):13442-13453. Epub 2019 Aug 16. PMID: 31373799
  • Riley NM, Malaker SA, Driessen MD, Bertozzi CR. Optimal Dissociation Methods Differ for N- and O-Glycopeptides. Journal of proteome research. 2020 Aug 7;19(8):3286-3301. Epub 2020 Jun 28. PMID: 32500713
  • Riley NM, Malaker SA, Bertozzi CR. Electron-Based Dissociation Is Needed for O-Glycopeptides Derived from OpeRATOR Proteolysis. Analytical chemistry. 2020 Nov 17;92(22):14878-14884. Epub 2020 Oct 30. PMID: 33125225
  • Riley NM, Bertozzi CR. Deciphering O-glycoprotease substrate preferences with O-Pair Search. Molecular omics. 2022 Dec 5;18(10):908-922. PMID: 36373229
  • Bule P, Chuzel L, Blagova E, Wu L, Gray MA, Henrissat B, Rapp E, Bertozzi CR, Taron CH, Davies GJ. Inverting family GH156 sialidases define an unusual catalytic motif for glycosidase action. Nature communications. 2019 Oct 23;10(1):4816. PMID: 31645552
  • Chongsaritsinsuk J, Steigmeyer AD, Mahoney KE, Rosenfeld MA, Lucas TM, Smith CM, Li A, Ince D, Kearns FL, Battison AS, Hollenhorst MA, Judy Shon D, Tiemeyer KH, Attah V, Kwon C, Bertozzi CR, Ferracane MJ, Lemmon MA, Amaro RE, Malaker SA. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. Nature communications. 2023 Oct 4;14(1):6169. PMID: 37794035
  • Lu L, Riley NM, Shortreed MR, Bertozzi CR, Smith LM. O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Nature methods. 2020 Nov;17(11):1133-1138. Epub 2020 Oct 26. PMID: 33106676
  • Biering SB, Sarnik SA, Wang E, Zengel JR, Leist SR, Schäfer A, Sathyan V, Hawkins P, Okuda K, Tau C, Jangid AR, Duffy CV, Wei J, Gilmore RC, Alfajaro MM, Strine MS, Nguyenla X, Van Dis E, Catamura C, Yamashiro LH, Belk JA, Begeman A, Stark JC, Shon DJ, Fox DM, Ezzatpour S, Huang E, Olegario N, Rustagi A, Volmer AS, Livraghi-Butrico A, Wehri E, Behringer RR, Cheon DJ, Schaletzky J, Aguilar HC, Puschnik AS, Button B, Pinsky BA, Blish CA, Baric RS, O'Neal WK, Bertozzi CR, Wilen CB, Boucher RC, Carette JE, Stanley SA, Harris E, Konermann S, Hsu PD. Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection. Nature genetics. 2022 Aug;54(8):1078-1089. Epub 2022 Jul 25. PMID: 35879412
  • Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ. Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag). Molecular & cellular proteomics : MCP. 2018 Apr;17(4):764-775. Epub 2018 Jan 19. PMID: 29351928
  • Riley NM, Wen RM, Bertozzi CR, Brooks JD, Pitteri SJ. Measuring the multifaceted roles of mucin-domain glycoproteins in cancer. Advances in cancer research. 2023;157:83-121. Epub 2022 Oct 8. PMID: 36725114
  • Yao Y, Kim G, Shafer S, Chen Z, Kubo S, Ji Y, Luo J, Yang W, Perner SP, Kanellopoulou C, Park AY, Jiang P, Li J, Baris S, Aydiner EK, Ertem D, Mulder DJ, Warner N, Griffiths AM, Topf-Olivestone C, Kori M, Werner L, Ouahed J, Field M, Liu C, Schwarz B, Bosio CM, Ganesan S, Song J, Urlaub H, Oellerich T, Malaker SA, Zheng L, Bertozzi CR, Zhang Y, Matthews H, Montgomery W, Shih HY, Jiang J, Jones M, Baras A, Shuldiner A, Gonzaga-Jauregui C, Snapper SB, Muise AM, Shouval DS, Ozen A, Pan KT, Wu C, Lenardo MJ. Mucus sialylation determines intestinal host-commensal homeostasis. Cell. 2022 Mar 31;185(7):1172-1188.e28. Epub 2022 Mar 17. PMID: 35303419
  • Scott E, Hodgson K, Calle B, Turner H, Cheung K, Bermudez A, Marques FJG, Pye H, Yo EC, Islam K, Oo HZ, McClurg UL, Wilson L, Thomas H, Frame FM, Orozco-Moreno M, Bastian K, Arredondo HM, Roustan C, Gray MA, Kelly L, Tolson A, Mellor E, Hysenaj G, Goode EA, Garnham R, Duxfield A, Heavey S, Stopka-Farooqui U, Haider A, Freeman A, Singh S, Johnston EW, Punwani S, Knight B, McCullagh P, McGrath J, Crundwell M, Harries L, Bogdan D, Westaby D, Fowler G, Flohr P, Yuan W, Sharp A, de Bono J, Maitland NJ, Wisnovsky S, Bertozzi CR, Heer R, Guerrero RH, Daugaard M, Leivo J, Whitaker H, Pitteri S, Wang N, Elliott DJ, Schumann B, Munkley J. Upregulation of GALNT7 in prostate cancer modifies O-glycosylation and promotes tumour growth. Oncogene. 2023 Mar;42(12):926-937. Epub 2023 Feb 1. PMID: 36725887