TY - JOUR
T1 - The rapid and highly parallel identification of antibodies with defined biological activities by SLISY
AU - Lu, Steve
AU - Mattox, Austin K.
AU - Aitana Azurmendi, P.
AU - Christodoulou, Ilias
AU - Wright, Katharine M.
AU - Popoli, Maria
AU - Chen, Zan
AU - Sur, Surojit
AU - Li, Yana
AU - Bonifant, Challice L.
AU - Bettegowda, Chetan
AU - Papadopoulos, Nickolas
AU - Zhou, Shibin
AU - Gabelli, Sandra B.
AU - Vogelstein, Bert
AU - Kinzler, Kenneth W.
N1 - Funding Information:
The expression of antibodies was carried out at the Eukaryotic Tissue Culture Facility of The Johns Hopkins University School of Medicine. We thank Janine Ptak, Lisa Dobbyn, Natalie Silliman and Joy Schaefer for excellent support of Next Generation sequencing. Funding for this work was supported by The Virginia and D.K. Ludwig Fund for Cancer Research, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, and NIH Cancer Center Support Grant P30 CA006973.
Funding Information:
C.L.B. and I.C. have submitted a patent application to the US PTO pertaining to the binding of the SARS-CoV-2 vial envelope by engineered NK cells (application number PCT/US2021/053042). C.L.B. has received research funding from Merck, Sharp, and Dohme, Inc., Bristol Myers Squibb, and Kiadis Pharma. B.V., K.W.K., and N.P. are founders of Thrive Earlier Detection. K.W.K. and N.P. are consultants to and were on the Board of Directors of Thrive Earlier Detection. B.V., K.W.K., N.P., and S.Z. own equity in Exact Sciences. B.V., K.W.K., N.P., and S.Z. are founders of, hold or may hold equity in, and serve or may serve as consultants to ManaT Bio. B.V., K.W.K., N.P., and S.Z. are founders of, hold equity in, and serve as consultants to Personal Genome Diagnostics. S.Z. has a research agreement with BioMed Valley Discoveries. S.B.G. is a founder and holds equity in AMS LLC. S.B.G is a consultant to Genesis. K.W.K. and B.V. are consultants to Sysmex, Eisai, and CAGE Pharma and hold equity in CAGE Pharma. B.V. is also a consultant to Catalio. K.W.K., B.V., S.Z., and N.P. are consultants to and hold equity in NeoPhore. N.P. is an advisor to and holds equity in CAGE Pharma. C.B. is a consultant to Depuy-Synthes and Bionaut Pharmaceuticals. The companies named above, as well as other companies, have licensed previously described technologies related to this paper from Johns Hopkins University. B.V., K.W.K., S.Z., N.P., and C.B. are inventors on some of these technologies. Licenses to these technologies are or will be associated with equity or royalty payments to the inventors as well as to Johns Hopkins University. The terms of all these arrangements are being managed by Johns Hopkins University in accordance with its conflict of interest policies. The remaining authors declare no competing interests.
Funding Information:
The expression of antibodies was carried out at the Eukaryotic Tissue Culture Facility of The Johns Hopkins University School of Medicine. We thank Janine Ptak, Lisa Dobbyn, Natalie Silliman and Joy Schaefer for excellent support of Next Generation sequencing. Funding for this work was supported by The Virginia and D.K. Ludwig Fund for Cancer Research, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, and NIH Cancer Center Support Grant P30 CA006973.
Publisher Copyright:
© 2023, The Author(s).
PY - 2023/12
Y1 - 2023/12
N2 - The therapeutic applications of antibodies are manifold and the emergence of SARS-CoV-2 provides a cogent example of the value of rapidly identifying biologically active antibodies. We describe an approach called SLISY (Sequencing-Linked ImmunoSorbent assaY) that in a single experiment can assess the binding specificity of millions of clones, be applied to any screen that links DNA sequence to a potential binding moiety, and requires only a single round of biopanning. We demonstrate this approach using an scFv library applied to cellular and protein targets to identify specific or broadly reacting antibodies. For a cellular target, we use paired HLA knockout cell lines to identify a panel of antibodies specific to HLA-A3. For a protein target, SLISY identifies 1279 clones that bound to the Receptor Binding Domain of the SARS-CoV-2 spike protein, with >40% of tested clones also neutralizing its interaction with ACE2 in in vitro assays. Using a multi-comparison SLISY against the Beta, Gamma, and Delta variants, we recovered clones that exhibited broad-spectrum neutralizing potential in vitro. By evaluating millions of scFvs simultaneously against multiple targets, SLISY allows the rapid identification of candidate scFvs with defined binding profiles facilitating the identification of antibodies with the desired biological activity.
AB - The therapeutic applications of antibodies are manifold and the emergence of SARS-CoV-2 provides a cogent example of the value of rapidly identifying biologically active antibodies. We describe an approach called SLISY (Sequencing-Linked ImmunoSorbent assaY) that in a single experiment can assess the binding specificity of millions of clones, be applied to any screen that links DNA sequence to a potential binding moiety, and requires only a single round of biopanning. We demonstrate this approach using an scFv library applied to cellular and protein targets to identify specific or broadly reacting antibodies. For a cellular target, we use paired HLA knockout cell lines to identify a panel of antibodies specific to HLA-A3. For a protein target, SLISY identifies 1279 clones that bound to the Receptor Binding Domain of the SARS-CoV-2 spike protein, with >40% of tested clones also neutralizing its interaction with ACE2 in in vitro assays. Using a multi-comparison SLISY against the Beta, Gamma, and Delta variants, we recovered clones that exhibited broad-spectrum neutralizing potential in vitro. By evaluating millions of scFvs simultaneously against multiple targets, SLISY allows the rapid identification of candidate scFvs with defined binding profiles facilitating the identification of antibodies with the desired biological activity.
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U2 - 10.1038/s41467-022-35668-6
DO - 10.1038/s41467-022-35668-6
M3 - Article
C2 - 36596784
AN - SCOPUS:85145429444
SN - 2041-1723
VL - 14
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 17
ER -