[#]
Current address: Division of Immunology and Pathogenesis, Department
of Molecular and Cell Biology, University of California Berkeley, Berkeley,
CA, USA.
AUTHOR CONTRIBUTIONS
E.A. conceived and designed the experiments, collected the data,
performed and interpreted the analyses, and wrote the manuscript. D.M.L and
A.P.M planned experiments, and collected and analyzed data. I.K. conceived
of and designed the hmMHC algorithm and performed analyses using it, and
wrote the methodological description found in this manuscript. M.D.
generated the KP9025 sarcoma cell line. A.M.L provided technical assistance
and helped plan experiments using MHC class II tetramers. W.M. and C.F.L.
planned, performed and analyzed mass spectrometry experiments. E.E. assisted
with bioinformatics analyses. A.N.V. assisted with the generation of the
CD4
+ T cell hybridomas, and helped design and perform
experiments using them. D.R. designed, collected, and analyzed data for
experiments involving multi-color flow cytometry. J.P.W. provided technical
support for MHC class I tetramer staining. M.M.G assisted in experiment
planning. R.F.V.M. collected and analyzed data for experiments involving
multi-color flow cytometry. C.D.A., K.C.F.S. and J.M.W. provided technical
assistance throughout the study. A.C. collected data. K.W.W. provided
mITGB1-MHC class II monomers and provided assistance in experimental design.
T.J. provided support in experimental design and data analysis regarding the
KP9025 sarcoma line. M.N.A. conceived and designed the hmMHC algorithm and
provided bioinformatics support. E.R.U. provided assistance in experimental
design. R.D.S. conceived experiments, interpreted data, and wrote the
manuscript. All authors contributed to manuscript revision.
R.D.S. is a cofounder, scientific advisory board member, stockholder,
and royalty recipient of Jounce Therapeutics and Neon Therapeutics and is a
scientific advisory board member for A2 Biotherapeutics, BioLegend, Codiak
Biosciences, Constellation Pharmaceuticals, NGM Biopharmaceuticals and
Sensei Biotherapeutics. K.W.W. serves on the scientific advisory board of
Tscan Therapeutics and Nextechinvest and receives sponsored research funding
from Bristol-Myers Squibb and Novartis; these activities are not related to
the findings described in this publication. T.J. is a member of the Board of
Directors of Amgen and Thermo Fisher Scientific. He is also a co-Founder of
Dragonfly Therapeutics and T2 Biosystems. T.J. serves on the Scientific
Advisory Board of Dragonfly Therapeutics, SQZ Biotech, and Skyhawk
Therapeutics. None of these affiliations represent a conflict of interest
with respect to the design or execution of this study or interpretation of
data presented in this manuscript. Dr. Jacks’s laboratory currently
also receives funding from the Johnson & Johnson Lung Cancer Initiative
and Calico, but this funding did not support the research described in this
manuscript.