Engineered Fn3 Protein has Targeted Therapeutic Effect on Mesothelin-Expressing Cancer Cells and Increases Tumor Cell Sensitivity to Chemotherapy

Mesothelin is a protein expressed at high levels on the cell surface in a variety of cancers, with limited expression in healthy tissues. The presence of mesothelin on tumor tissue correlates with increased invasion and metastasis, and resistance to traditional chemotherapies, through mechanisms that remain poorly understood. Molecules that specifically recognize mesothelin and interrupt its contribution to tumor progression have significant potential for targeted therapy and targeted drug delivery applications. A number of mesothelin-targeting therapies are in preclinical and clinical development, although none are currently approved for routine clinical use. In this work, we report the development of a mesothelin-targeting protein based on the fibronectin type-III non-antibody protein scaffold, which offers opportunities for applications where antibodies have limitations. We engineered protein variants that bind mesothelin with high affinity and selectively initiate apoptosis in tumor cells expressing mesothelin. Interestingly, apoptosis does not occur through a caspase-mediated pathway and does not require downregulation of cell-surface mesothelin, suggesting a currently unknown pathway through which mesothelin contributes to cancer progression. Importantly, simultaneous treatment with mesothelin-binding protein and chemotherapeutic mitomycin C had a greater cytotoxic effect on mesothelin-positive cells compared to either molecule alone, underscoring the potential for combination therapy including biologics targeting mesothelin

Fn3 Proteins Engineered to Recognize Tumor Biomarker Mesothelin Internalize Upon Binding

Mesothelin is a cell surface protein that is overexpressed in numerous cancers, including breast, ovarian, lung, liver, and pancreatic tumors. Aberrant expression of mesothelin has been shown to promote tumor progression and metastasis through interaction with established tumor biomarker CA125. Therefore, molecules that specifically bind to mesothelin have potential therapeutic and diagnostic applications. However, no mesothelin-targeting molecules are currently approved for routine clinical use. While antibodies that target mesothelin are in development, some clinical applications may require a targeting molecule with an alternative protein fold. For example, non-antibody proteins are more suitable for molecular imaging and may facilitate diverse chemical conjugation strategies to create drug delivery complexes. In this work, we engineered variants of the fibronectin type III domain (Fn3) non-antibody protein scaffold to bind to mesothelin with high affinity, using directed evolution and yeast surface display. Lead engineered Fn3 variants were solubly produced and purified from bacterial culture at high yield. Upon specific binding to mesothelin on human cancer cell lines, the engineered Fn3 proteins internalized and co-localized to early endosomes. To our knowledge, this is the first report of non-antibody proteins engineered to bind mesothelin. The results validate that non-antibody proteins can be engineered to bind to tumor biomarker mesothelin, and encourage the continued development of engineered variants for applications such as targeted diagnostics and therapeutics

Fn3 Proteins Engineered to Recognize Tumor Biomarker Mesothelin Internalize Upon Binding

Mesothelin is a cell surface protein that is overexpressed in numerous cancers, including breast, ovarian, lung, liver, and pancreatic tumors. Aberrant expression of mesothelin has been shown to promote tumor progression and metastasis through interaction with established tumor biomarker CA125. Therefore, molecules that specifically bind to mesothelin have potential therapeutic and diagnostic applications. However, no mesothelin-targeting molecules are currently approved for routine clinical use. While antibodies that target mesothelin are in development, some clinical applications may require a targeting molecule with an alternative protein fold. For example, non-antibody proteins are more suitable for molecular imaging and may facilitate diverse chemical conjugation strategies to create drug delivery complexes. In this work, we engineered variants of the fibronectin type III domain (Fn3) non-antibody protein scaffold to bind to mesothelin with high affinity, using directed evolution and yeast surface display. Lead engineered Fn3 variants were solubly produced and purified from bacterial culture at high yield. Upon specific binding to mesothelin on human cancer cell lines, the engineered Fn3 proteins internalized and co-localized to early endosomes. To our knowledge, this is the first report of non-antibody proteins engineered to bind mesothelin. The results validate that non-antibody proteins can be engineered to bind to tumor biomarker mesothelin, and encourage the continued development of engineered variants for applications such as targeted diagnostics and therapeutics

Production and characterization of selected Fn3 variants.

<p>Engineered Fn3 clones 1.4.1 and 2.4.1 were expressed in bacteria with a C-terminal hexahistidine tag and a short peptide tag containing GKSK residues for later bioconjugation chemistry. (A) Fn3 protein 1.4.1 was purified by nickel affinity chromatography followed by SEC, demonstrating desired product with retention time of ~ 42 min. (B) Fn3 protein 2.4.1 was purified by nickel affinity chromatography followed by HPLC, demonstrating desired product with retention time of ~30 min. (C) Proteins were purified to high purity > 99% as analyzed by SDS-PAGE. Yields of Fn3 protein production were routinely ~ 10 mg/L.</p

Directed evolution of a naïve yeast surface display library yielded Fn3 variants that bind soluble MSLN.

<p>We started with a naïve yeast surface display library with 2.8 x 10⁹ variants of the Fn3 non-antibody scaffold. The library was sorted for full-length protein expression, detected by an antibody to a terminal c-myc epitope tag, and binding to MSLN using MACS and FACS. Red polygon indicates example cell population collected for further enrichment and analysis. Additional diversity was introduced into the enriched library through a single round of mutagenic PCR and sorting of this second generation library resulted in further enrichment for MSLN binding variants. A double-negative population of yeast cells is characteristic of yeast surface display.</p

Approach to engineering Fn3 proteins to recognize tumor biomarker MSLN for diagnostic and therapeutic applications.

<p>(A) The tenth domain of human fibronectin type III (Fn3) (PDB 1TTG) is a highly stable protein structure with three loops (BC, DE, and FG) broadly tolerant of mutation to confer novel binding properties. Structure was rendered in PyMOL. (B) We employed a previously developed hydrophilic Fn3 yeast surface display library [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197029#pone.0197029.ref056" target="_blank">56</a>] that incorporates a range of loop lengths and biased amino acid composition to mimic the diversity of naturally occurring antibody complementarity-determining regions. (C) Fn3 proteins that bind cell surface protein MSLN have numerous potential clinical applications, such as through diagnostic imaging, internalization for drug delivery, and metastatic reduction by blocking MSLN-MUC16 interactions. Stars represent conjugated imaging or therapeutic molecules.</p

Yeast displayed Fn3 variants 1.4.1 and 2.4.1 bound specifically to tumor biomarker MSLN.

<p>(A) Two dominant Fn3 variants, 1.4.1 and 2.4.1, were recovered from a first generation and second generation Fn3 library, respectively. (B) Individual clones and Fn3 WT were displayed on the surface of yeast and incubated with a range of concentrations of soluble MSLN. Experimental triplicate data were collected, and the dissociation constant is reported as the mean and standard deviation of the K_D values calculated for each replicate. A representative binding curve is shown for each variant. (C) Individual clones were displayed on the surface of yeast and incubated with a range of concentrations of a biotinylated, Fc fragment. Experimental triplicate data were collected. A representative curve is shown for each variant.</p

Engineered Fn3 protein variants bound cancer cells expressing MSLN.

<p>A431/H9 cells, epidermoid carcinoma cells transfected to express high levels of MSLN, and MCF-7 cells, breast cancer cells lacking surface MSLN, were used in all binding assays. (A) Analysis by flow cytometry confirms MSLN presence on the surface of A431/H9 cells as detected by an anti-MLSN antibody. The MCF-7 cell line does not express MSLN. (B) Fn3 variants 1.4.1 and 2.4.1 were isolated and binding to MSLN was measured using equilibrium binding assays. A431/H9 and MCF-7 cells were incubated with a range of concentrations of soluble fluorescently labeled 1.4.1 or 2.4.1. The assays were performed in experimental triplicate. Data from each replicate were fit to a sigmoidal curve, and a K_D value was calculated for each replicate. The K_D is reported as the mean +/- standard deviation. A representative binding curve of each clone for both cell lines is shown.</p

Engineered Fn3 protein variants 1.4.1 and 2.4.1 localized to early endosomes upon binding MSLN.

<p>Analysis by (A) flow cytometry and (B) imaging flow cytometry confirms MSLN presence on the surface of KB-3-1 cells compared to the MSLN-negative MCF-7 cells, as detected by an anti-MSLN antibody. (C, D) KB-3-1 cells (<i>top</i>) internalize AF488-labeled 1.4.1 (C) and AF488-labeled 2.4.1 (D), while MCF-7 cells show no specific binding or internalization (C <i>bottom</i>, D <i>bottom</i>). Endosomes are detected by an AF647-conjuated antibody recognizing the EAA1 early endosomal marker. Yellow in the merged images indicate co-localization between AF488-1.4.1 or AF488-2.4.1 anti-MSLN engineered proteins (green) and EEA1 (red). Original magnification 40X. Co-localization is quantified by the Bright Detail Similarity (BDS) metric, with values near 1 indicating co-localization. KB-3-1 BDS = 1.31 and 0.919 for AF488-1.4.1 and AF488-2.4.1, respectively. BDS values are not quantifiable for the negative control cell line, due to insufficient fraction of negative control cell population staining for binding or internalization of engineered protein variants.</p