DNAJB1-PRKACA fusion neoantigens elicit rare endogenous T cell responses that potentiate cell therapy for fibrolamellar carcinoma

Authors: Kirk, Allison M., Crawford, Jeremy Chase, Chou, Ching-Heng, Guy, Cliff, Pandey, Kirti, Kozlik, Tanya, Shah, Ravi K., Chung, Shanzou, Nguyen, Phuong, Zhang, Xiaoyu, Wang, Jin, Bell, Matthew, Mettelman, Robert C., Allen, E. Kaitlynn, Pogorelyy, Mikhail V., Kim, Hyunjin, Minervina, Anastasia A., Awad, Walid, Bajracharya, Resha, White, Toni, Long, Donald, Jr., Gordon, Brittney, Morrison, Michelle, Glazer, Evan S., Murphy, Andrew J., Jiang, Yixing, Fitzpatrick, Elizabeth A., Yarchoan, Mark, Sethupathy, Praveen, Croft, Nathan P., Purcell, Anthony W., Federico, Sara M., Stewart, Elizabeth, Gottschalk, Stephen, Zamora, Anthony E., DeRenzo, Christopher, Strome, Scott E., Thomas, Paul G.

Source: In Cell Reports Medicine 19 March 2024 5(3)

Benchmarking Bioinformatics Pipelines in Data-Independent Acquisition Mass Spectrometry for Immunopeptidomics

Authors: Shahbazy, Mohammad, Ramarathinam, Sri H., Illing, Patricia T., Jappe, Emma C., Faridi, Pouya, Croft, Nathan P., Purcell, Anthony W.

Source: In Molecular & Cellular Proteomics April 2023 22(4)

α-Mannosylated HLA-II glycopeptide antigens dominate the immunopeptidome of immortalised cells and tumour tissues.

Authors: Goodson, Hayley, Kawahara, Rebeca, Fehring, Joshua, Purcell, Anthony W, Croft, Nathan P, Thaysen-Andersen, Morten

Source: Glycobiology; Nov2024, Vol. 34 Issue 11, p1-7, 7p

Subject Terms: DATABASES, PEPTIDES, MENINGIOMA, CELL lines, INVECTIVE

Immunopeptidomic Analysis Reveals That Deamidated HLA-bound Peptides Arise Predominantly from Deglycosylated Precursors

Authors: Mei, Shutao, Ayala, Rochelle, Ramarathinam, Sri H., Illing, Patricia T., Faridi, Pouya, Song, Jiangning, Purcell, Anthony W. ^*, Croft, Nathan P. ^*

Source: In Molecular & Cellular Proteomics July 2020 19(7):1236-1247

Most viral peptides displayed by class I MHC on infected cells are immunogenic

Authors: Croft, Nathan P., Smith, Stewart A., Pickering, Jana, Sidney, John, Peters, Bjoern, Faridi, Pouya, Witney, Matthew J., Sebastian, Prince, Flesch, Inge E. A., Heading, Sally L., Sette, Alessandro, La Gruta, Nicole L., Purcell, Anthony W., Tscharke, David C.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2019 Feb . 116(8), 3112-3117.

Access URL: https://www.jstor.org/stable/26671956

Mapping the immunopeptidome of seven SARS-CoV-2 antigens across common HLA haplotypes.

Authors: Braun, Asolina, Rowntree, Louise C., Huang, Ziyi, Pandey, Kirti, Thuesen, Nikolas, Li, Chen, Petersen, Jan, Littler, Dene R., Raji, Shabana, Nguyen, Thi H. O., Jappe Lange, Emma, Persson, Gry, Schantz Klausen, Michael, Kringelum, Jens, Chung, Shanzou, Croft, Nathan P., Faridi, Pouya, Ayala, Rochelle, Rossjohn, Jamie, Illing, Patricia T.

Source: Nature Communications; 8/30/2024, Vol. 15 Issue 1, p1-12, 12p

Subject Terms: VIRAL proteins, HLA histocompatibility antigens, GENE transfection, SARS-CoV-2, COVID-19 vaccines

Employing proteomics in the study of antigen presentation: an update

Authors: Ramarathinam, Sri H., Croft, Nathan P., Illing, Patricia T., Faridi, Pouya, Purcell, Anthony W.

Source: Expert review of proteomics. 15(8):637-645

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100103564233.0x000001&indx=1&recIds=ETOCvdc_100103564233.0x000001

Human Leukocyte Antigen (HLA) B27 Allotype-Specific Binding and Candidate Arthritogenic Peptides Revealed through Heuristic Clustering of Data-independent Acquisition Mass Spectrometry (DIA-MS) Data

Authors: Schittenhelm, Ralf B. ^‡, Sivaneswaran, Saranjah ^‡, Lim Kam Sian, Terry C.C. ^‡, Croft, Nathan P. ^‡, Purcell, Anthony W. ^{‡, ¶}

Source: In Molecular & Cellular Proteomics June 2016 15(6):1867-1876

Immunology by numbers: quantitation of antigen presentation completes the quantitative milieu of systems immunology!

Authors: Purcell, Anthony W, Croft, Nathan P, Tscharke, David C

Source: In Current Opinion in Immunology June 2016 40:88-95

MHCpLogics: an interactive machine learning-based tool for unsupervised data visualization and cluster analysis of immunopeptidomes.

Authors: Shahbazy, Mohammad¹, Ramarathinam, Sri H¹, Li, Chen¹, Illing, Patricia T¹, Faridi, Pouya^2,3, anthony.purcell@monash.edu, Croft, Nathan P¹, anthony.purcell@monash.edu, Purcell, Anthony W¹, anthony.purcell@monash.edu

Source: Briefings in Bioinformatics; Mar2024, Vol. 25 Issue 2, p1-17, 17p

Quantifying epitope presentation using mass spectrometry

Authors: Croft, Nathan P., Purcell, Anthony W., Tscharke, David C.

Source: In Molecular Immunology December 2015 68(2) Part A:77-80

Simultaneous Quantification of Viral Antigen Expression Kinetics Using Data-Independent (DIA) Mass Spectrometry

Authors: Croft, Nathan P. ^‡, de Verteuil, Danielle A. ^‡, Smith, Stewart A. ^§, Wong, Yik Chun ^§, Schittenhelm, Ralf B. ^‡, Tscharke, David C. ^§, Purcell, Anthony W. ^{¶, ‡}

Source: In Molecular & Cellular Proteomics May 2015 14(5):1361-1372

Resourcing, annotating, and analysing synthetic peptides of SARS‐CoV‐2 for immunopeptidomics and other immunological studies

Authors: Li, Chen, Revote, Jerico, Ramarathinam, Sri H., Chung, Shan Zou, Croft, Nathan P., Scull, Katherine E., Huang, Ziyi, Ayala, Rochelle, Braun, Asolina, Mifsud, Nicole A., Illing, Patricia T., Faridi, Pouya, Purcell, Anthony W.

Source: Proteomics. 21(17-18)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100132554141.0x000001&indx=1&recIds=ETOCvdc_100132554141.0x000001

The Cellular Redox Environment Alters Antigen Presentation

Authors: Trujillo, Jonathan A., Croft, Nathan P., Dudek, Nadine L., Channappanavar, Rudragouda, Theodossis, Alex, Webb, Andrew I., Dunstone, Michelle A., Illing, Patricia T., Butler, Noah S. ^**, Fett, Craig, Tscharke, David C., Rossjohn, Jamie, Perlman, Stanley, Purcell, Anthony W.

Source: In Journal of Biological Chemistry 3 October 2014 289(40):27979-27991

Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system.

Authors: Paul, Sinu¹ (AUTHOR), Croft, Nathan P.^2,3 (AUTHOR), Purcell, Anthony W.^2,3 (AUTHOR), Tscharke, David C.⁴ (AUTHOR), Sette, Alessandro^1,5 (AUTHOR), Nielsen, Morten^6,7 (AUTHOR), Peters, Bjoern^1,5 (AUTHOR) bpeters@lji.org

Source: PLoS Computational Biology. 5/26/2020, Vol. 16 Issue 5, p1-18. 18p. 3 Charts, 6 Graphs.

Subject Terms: *FORECASTING, *EPITOPES, *VACCINIA, *ARTIFICIAL neural networks, *LIGAND binding (Biochemistry), *T cell receptors

Discovery of Novel Disease-specific and Membrane-associated Candidate Markers in a Mouse Model of Multiple Sclerosis

Authors: Dagley, Laura F. ^{‡, §, ¶}, Croft, Nathan P. ^¶, Isserlin, Ruth ^§, Olsen, Jonathan B. ^{§, ‖}, Fong, Vincent ^§, Emili, Andrew ^{§, ‖}, Purcell, Anthony W. ^{¶, **}

Source: In Molecular & Cellular Proteomics March 2014 13(3):679-700

Characterization of the Antigen Processing Machinery and Endogenous Peptide Presentation of a Bat MHC Class I Molecule

Authors: Wynne, James W., Woon, Amanda P., Dudek, Nadine L., Croft, Nathan P., Ng, Justin H. J., Baker, Michelle L., Wang, Lin-Fa, Purcell, Anthony W.

Source: Journal of immunology. 196(11):4468-4476

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN606332621&indx=1&recIds=ETOCRN606332621

A Systems Approach to Understand Antigen Presentation and the Immune Response

Authors: Dudek, Nadine L., Croft, Nathan P., Schittenhelm, Ralf B., Ramarathinam, Sri H., Purcell, Anthony W.

Source: Methods in molecular biology. 1394:189-210

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN604574182&indx=1&recIds=ETOCRN604574182

Profound N-glycan remodelling accompanies MHC-II immunopeptide presentation.

Authors: Goodson, Hayley, Kawahara, Rebeca, Chatterjee, Sayantani, Goncalves, Gabriel, Fehring, Joshua, Purcell, Anthony W., Croft, Nathan P., Thaysen-Andersen, Morten

Source: Frontiers in Immunology; 2023, Vol. 14, p01-10, 10p

Subject Terms: T cell receptors, CELL surface antigens, PEPTIDES, ANTIGEN presenting cells, MAJOR histocompatibility complex, GLYCOPROTEINS, GLYCOGEN storage disease type II

Peptide Presentation to T Cells: Solving the Immunogenic Puzzle

Authors: Croft, Nathan P.

Source: BioEssays. 42(3)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100135984151.0x000001&indx=1&recIds=ETOCvdc_100135984151.0x000001