Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.

Details

Serval ID
serval:BIB_F6095670EC38
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.
Journal
Cell
Author(s)
Wells D.K., van Buuren M.M., Dang K.K., Hubbard-Lucey V.M., Sheehan KCF, Campbell K.M., Lamb A., Ward J.P., Sidney J., Blazquez A.B., Rech A.J., Zaretsky J.M., Comin-Anduix B., Ng AHC, Chour W., Yu T.V., Rizvi H., Chen J.M., Manning P., Steiner G.M., Doan X.C., Merghoub T., Guinney J., Kolom A., Selinsky C., Ribas A., Hellmann M.D., Hacohen N., Sette A., Heath J.R., Bhardwaj N., Ramsdell F., Schreiber R.D., Schumacher T.N., Kvistborg P., Defranoux N.A.
Working group(s)
Tumor Neoantigen Selection Alliance
Contributor(s)
Khan A.A., Lugade A., Lazic AMM, Frentzen AAE, Tadmor A.D., Sasson A.S., Rao A.A., Pei B., Schrörs B., Berent-Maoz B., Carreno B.M., Song B., Peters B., Li B., Higgs B.W., Stevenson Brian, Iseli Christian, Miller C.A., Morehouse C.A., Melief CJM, Puig-Saus C., van Beek D., Balli D., Gfeller David, Haussler D., Jäger D., Cortes E., Esaulova E., Sherafat E., Arcila F., Bartha G., Liu G., Coukos Georges, Richard G., Chang H., Si H., Zörnig I., Xenarios Ioannis, Mandoiu I., Kooi I., Conway J.P., Kessler J.H., Greenbaum J.A., Perera J.F., Harris J., Hundal J., Shelton J.M., Wang J., Wang J., Greshock J., Blake J., Szustakowski J., Kodysh J., Forman J., Wei L., Lee L.J., Fanchi L.F., Slagter M., Lang M., Mueller M., Lower M., Vormehr M., Artyomov M.N., Kuziora M., Princiotta M., Bassani-Sternberg Michal, Macabali M., Kojicic M.R., Yang N., Raicevic NMI, Guex Nicolas, Robine N., Halama N., Skundric N.M., Milicevic O.S., Gellert P., Jongeneel P., Charoentong P., Srivastava P.K., Tanden P., Shah P., Hu Q., Gupta R., Chen R., Petit R., Ziman R., Hilker R., Shukla S.A., Al Seesi S., Boyle S.M., Qiu S., Sarkizova S., Salama S., Liu S., Wu S., Sridhar S., Ketelaars SLC, Jhunjhunwala S., Shcheglova T., Schuepbach Thierry, Creasy T.H., Josipovic V., Kovacevic V.B., Fu W., Krebber W.J., Hsu Y.H., Sebastian Y., Yalcin Z.K., Huang Z.
ISSN
1097-4172 (Electronic)
ISSN-L
0092-8674
Publication state
Published
Issued date
29/10/2020
Peer-reviewed
Oui
Volume
183
Number
3
Pages
818-834.e13
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
Abstract
Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding in patient-matched samples. By integrating peptide features associated with presentation and recognition, we developed a model of tumor epitope immunogenicity that filtered out 98% of non-immunogenic peptides with a precision above 0.70. Pipelines prioritizing model features had superior performance, and pipeline alterations leveraging them improved prediction performance. These findings were validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding. This data resource enables identification of parameters underlying effective anti-tumor immunity and is available to the research community.
Keywords
TESLA, epitope, immunogenicity, immunogenomics, immunotherapy, neoantigen
Pubmed
Web of science
Create date
18/03/2021 18:40
Last modification date
19/03/2021 7:27
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