An engineered antibody fragment targeting mutant β-catenin via major histocompatibility complex I neoantigen presentation

Michelle S. Miller, Jacqueline Douglass, Michael S. Hwang, Andrew D. Skora, Michael Murphy, Nickolas Papadopoulos, Kenneth W. Kinzler, Bert Vogelstein, Shibin Zhou, Sandra B. Gabelli

Research output: Contribution to journalArticle

Abstract

Mutations in CTNNB1, the gene encoding β-catenin, are common in colon and liver cancers, the most frequent mutation affecting Ser-45 in β-catenin. Peptides derived from WT β-catenin have previously been shown to be presented on the cell surface as part of major histocompatibility complex (MHC) class I, suggesting an opportunity for targeting this common driver gene mutation with antibody-based therapies. Here, crystal structures of both the WT and S45F mutant peptide bound to HLA-A*03:01 at 2.20 and 2.45 Å resolutions, respectively, confirmed the accessibility of the phenylalanine residue for antibody recognition. Phage display was then used to identify single-chain variable fragment clones that selectively bind the S45F mutant peptide presented in HLA-A*03:01 and have minimal WT or other off-target binding. Following the initial characterization of five clones, we selected a single clone, E10, for further investigation. We developed a computational model of the binding of E10 to the mutant peptide- bound HLA-A3, incorporating data from affinity maturation as initial validation. In the future, our model may be used to design clones with maintained specificity and higher affinity. Such derivatives could be adapted into either cell-based (CAR-T) or protein-based (bispecific T-cell engagers) therapies to target cancer cells harboring the S45F mutation in CTNNB1.

Original languageEnglish (US)
Pages (from-to)19322-19334
Number of pages13
JournalJournal of Biological Chemistry
Volume294
Issue number50
DOIs
StatePublished - Jan 1 2019

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Catenins
Immunoglobulin Fragments
Major Histocompatibility Complex
Clone Cells
Peptides
Mutation
HLA-A Antigens
HLA-A3 Antigen
Single-Chain Antibodies
Bacteriophages
Gene encoding
T-cells
Antibodies
Liver Neoplasms
Cell- and Tissue-Based Therapy
Phenylalanine
Liver
Colonic Neoplasms
Genes
Crystal structure

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

An engineered antibody fragment targeting mutant β-catenin via major histocompatibility complex I neoantigen presentation. / Miller, Michelle S.; Douglass, Jacqueline; Hwang, Michael S.; Skora, Andrew D.; Murphy, Michael; Papadopoulos, Nickolas; Kinzler, Kenneth W.; Vogelstein, Bert; Zhou, Shibin; Gabelli, Sandra B.

In: Journal of Biological Chemistry, Vol. 294, No. 50, 01.01.2019, p. 19322-19334.

Research output: Contribution to journalArticle

Miller, Michelle S. ; Douglass, Jacqueline ; Hwang, Michael S. ; Skora, Andrew D. ; Murphy, Michael ; Papadopoulos, Nickolas ; Kinzler, Kenneth W. ; Vogelstein, Bert ; Zhou, Shibin ; Gabelli, Sandra B. / An engineered antibody fragment targeting mutant β-catenin via major histocompatibility complex I neoantigen presentation. In: Journal of Biological Chemistry. 2019 ; Vol. 294, No. 50. pp. 19322-19334.
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