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BackgroundThe continued discovery of therapeutic antibodies, which address unmet medical needs, requires the continued discovery of tractable antibody targets. Multiple protein-level target discovery approaches are available and these can be used in combination to extensively survey relevant cell membranomes. In this study, the MDA-MB-231 cell line was selected for membranome survey as it is a ‘triple negative’ breast cancer cell line, which represents a cancer subtype that is aggressive and has few treatment options.MethodsThe MDA-MB-231 breast carcinoma cell line was used to explore three membranome target discovery approaches, which were used in parallel to cross-validate the significance of identified antigens. A proteomic approach, which used membrane protein enrichment followed by protein identification by mass spectrometry, was used alongside two phenotypic antibody screening approaches. The first phenotypic screening approach was based on hybridoma technology and the second was based on phage display technology. Antibodies isolated by the phenotypic approaches were tested for cell specificity as well as internalisation and the targets identified were compared to each other as well as those identified by the proteomic approach. An anti-CD73 antibody derived from the phage display-based phenotypic approach was tested for binding to other ‘triple negative’ breast cancer cell lines and tested for tumour growth inhibitory activity in a MDA-MB-231 xenograft model.ResultsAll of the approaches identified multiple cell surface markers, including integrins, CD44, EGFR, CD71, galectin-3, CD73 and BCAM, some of which had been previously confirmed as being tractable to antibody therapy. In total, 40 cell surface markers were identified for further study. In addition to cell surface marker identification, the phenotypic antibody screening approaches provided reagent antibodies for target validation studies. This is illustrated using the anti-CD73 antibody, which bound other ‘triple negative’ breast cancer cell lines and produced significant tumour growth inhibitory activity in a MDA-MB-231 xenograft model.ConclusionsThis study has demonstrated that multiple methods are required to successfully analyse the membranome of a desired cell type. It has also successfully demonstrated that phenotypic antibody screening provides a mechanism for rapidly discovering and evaluating antibody tractable targets, which can significantly accelerate the therapeutic discovery process.

BackgroundMonolayer cultures of immortalised cell lines are a popular screening tool for novel anti-cancer therapeutics, but these methods can be a poor surrogate for disease states, and there is a need for drug screening platforms which are more predictive of clinical outcome. In this study, we describe a phenotypic antibody screen using three-dimensional cultures of primary cells, and image-based multi-parametric profiling in PC-3 cells, to identify anti-cancer biologics against new therapeutic targets.MethodsScFv Antibodies and designed ankyrin repeat proteins (DARPins) were isolated using phage display selections against primary non-small cell lung carcinoma cells. The selected molecules were screened for anti-proliferative and pro-apoptotic activity against primary cells grown in three-dimensional culture, and in an ultra-high content screen on a 3-D cultured cell line using multi-parametric profiling to detect treatment-induced phenotypic changes. The targets of molecules of interest were identified using a cell-surface membrane protein array. An anti-CUB domain containing protein 1 (CDCP1) antibody was tested for tumour growth inhibition in a patient-derived xenograft model, generated from a stage-IV non-small cell lung carcinoma, with and without cisplatin.ResultsTwo primary non-small cell lung carcinoma cell models were established for antibody isolation and primary screening in anti-proliferative and apoptosis assays. These assays identified multiple antibodies demonstrating activity in specific culture formats. A subset of the DARPins was profiled in an ultra-high content multi-parametric screen, where 300 morphological features were measured per sample. Machine learning was used to select features to classify treatment responses, then antibodies were characterised based on the phenotypes that they induced. This method co-classified several DARPins that targeted CDCP1 into two sets with different phenotypes. Finally, an anti-CDCP1 antibody significantly enhanced the efficacy of cisplatin in a patient-derived NSCLC xenograft model.ConclusionsPhenotypic profiling using complex 3-D cell cultures steers hit selection towards more relevant in vivo phenotypes, and may shed light on subtle mechanistic variations in drug candidates, enabling data-driven decisions for oncology target validation. CDCP1 was identified as a potential target for cisplatin combination therapy.Electronic supplementary materialThe online version of this article (doi:10.1186/s12943-015-0415-0) contains supplementary material, which is available to authorized users.

The neutral amino acid transporter, ASCT2, is frequently overexpressed in several cancers to sustain "glutamine addiction" of cancer cells. High expression of ASCT2 is often associated with poor disease prognosis. Immuno-histochemistry (IHC) on formalin-fixed paraffin embedded (FFPE) tissue samples revealed high prevalence of membranous ASCT2 expression in several hematological cancers, including MM, AML, and DLBCL summarized in Table1. ASCT2 expression was predominantly on the plasma membrane of the carcinoma cells. ASCT2 staining was observed in almost all the samples with high positivity (>2+ and in >50% of tumor cells) in 98, 74 and 55% of MM, AML and DLBCL samples respectively. Additionally, flow cytometry analyses suggest significantly high expression of ASCT2 in bone marrow (BM) samples from AML and MM patients in comparison to BM from healthy donors. Also, our data suggest relatively less expression of ASCT2 in LT-HSC (long term hematopoietic stem cells) in comparison to prominent myeloid-associated marker CD33. In contrast, we found similar expression profile of ASCT2 and CD33 in downstream lineage-committed progenitor cells, such as MPP (multi potent progenitors) and CP (common progenitors). Furthermore, IHC evaluated across normal tissues suggest restricted ASCT2 expression in the normal tissues of vital organs. Broad expression across various unmet cancers and restricted expression in normal tissues warrant ASCT2 as an attractive candidate for an antibody drug conjugate. MEDI7247 is a novel investigational antibody-drug conjugate (ADC) comprising an anti-ASCT2 human monoclonal antibody site-specifically conjugated to pyrrolobenzodiazepine (PBD) dimer via a protease-cleavable linker, with a drug to antibody ratio (DAR) of 2. MEDI7247 specifically binds to the cell surface ASCT2 while exhibiting no affinity to the other members of the family, including ASCT1. Following binding to the extracellular region of ASCT2 antigen, MEDI7247 is internalized and trafficked to the lysosomes to subsequently release the PBD warhead. The release of PBD induces DNA damage and results in tumor cell death. MEDI7247 shows potent in vitro cytotoxic killing in several heme cancer cell lines (IC50 range of 0.05 ng/ml to ~65 ng/ml) with variable levels of ASCT2 expression (e.g. H929 (high) ~ 1.1 X106 copies/cell; Nomo (low) ~ 1.3 X105 copies/cell). In vivo anti-tumor activity of MEDI7247 was evaluated in a panel of hematological tumor models (CDx) representing AML, MM, DLBCL, cALL, and Burkitt's lymphoma. Briefly, MEDI7247 (dosed: single dose or Q1Wx4) demonstrated a significant survival advantage in disseminated or subcutaneous tumor models, when compared to the untreated control or standard of care (SOC) at the various dose levels examined: 0.05, 0.1 and 0.4 mg/kg, respectively. Likewise, MEDI7247 was also tested in disseminated AML PDX (ASCT2-low) models. Significant improvement in survival was observed at both 0.1 and 0.4 mg/kg with the higher dose level extending survival by >80 days and PDX models showed robust antitumor effect and significant survival benefit compared to standard of care (SOC). We used flow cytometry sorting of CD34+ and CD38+ populations from AML BM and ran colony forming assays in methocult culture conditions to confirm that CD34+CD38+ cells are leukemic stem cells (LSC) of AML BM samples. Furthermore, we confirmed high expression of ASCT2 in LSC and in the bulk population of AML BM. Similar analyses suggest relatively high expression of ASCT2 in MM plasma cells (CD138+CD19-) and modest to low expression in MM stem cells (CD19+ CD138-). This may yield opportunity for more durable clinical response in AML, genetically heterogeneous diseases. Furthermore, MEDI7247 demonstrated acceptable safety profile in toxicity studies with non-human primates to support first in human trials. In conclusion, based on its combined efficacy and safety, MEDI7247, a first-in class ADC is currently being evaluated in clinic for the treatment of ASCT2 positive hematological malignancies (NCT03106428). Disclosures Pore: Medimmune: Employment. Schifferli:Medimmune: Employment. Monks:Medimmune: Employment. Tammali:Medimmune: Employment. Borrok:Medimmune: Employment. Hurt:Medimmune: Employment. Flynn:Medimmune: Employment. Rebelatto:Medimmune: Employment. Townsley:Medimmue: Employment. Hinrichs:Medimmune: Employment. Dixit:Medimmune: Employment. Coats:Medimmune: Employment. Herbst:Medimmune: Employment. Tice:Medimmune: Employment.

Discovery of therapeutic antibodies requires the continued identification of tractable targets, and we have employed a phenotypic screening strategy to this end. In this study, antibodies from phage display libraries were screened for their abilities to inhibit MDA-MB-231 (‘triple negative’) breast cancer cells. The screening cascade included tests for specific cell binding, antibody internalization, and cytotoxicity as an antibody-drug conjugate. Targets of these antibodies then were identified using immunoprecipitation and mass spectrometry, and confirmed by showing diminished antibody binding after siRNA-mediated knockdown of the putative target gene. One target was identified as NT5E (also known as CD73), a 5’-ectonucleotidase. NT5E catalyzes the conversion of adenosine monophosphate to adenosine, and its function has been linked with immunity, angiogenesis, and cancer. To screen for additional inhibitors of this target, a novel, high-throughput ectonucleotidase assay was developed. NT5E activity is typically assayed either by high performance liquid chromatography or by quantification of free phosphate using malachite green, and neither of these methods is suitable for high-throughput screening. One inhibitory antibody was found to significantly slow growth of MDA-MB-231 xenograft tumors in mice. In summary, our phenotypic screening approach provides a mechanism for rapidly discovering and evaluating new antibody targets and is being used to accelerate the discovery of new cancer drugs. Citation Format: Carl Hay, Steven Rust, Erin Sult, Lori Clarke, Kim Rosenthal, Sandrine Guillard, David Lowne, Matt Flynn, Lutz Jermutus, Ralph Minter, Robert Hollingsworth, Kris Sachsenmeier. Phenotypic selection for identification of functional antibodies and development of high throughput screening assays. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4328. doi:10.1158/1538-7445.AM2013-4328

Cancer stem cells (CSCs) represent an important clinical entity given their role in tumor initiation, metastasis and patient relapse. Phenotypic selection allows for identification of novel antigens important in biological processes. Therefore, we undertook a phenotypic selection campaign using a designed ankyrin-repeat (DARPin) library to identify new cancer stem cell (CSC) targets. CSCs generated from late-stage pancreatic cancer patient-derived xenograft (PDX) models were used to pan a designed Ankyrin repeat (DARPin) library. The most prevalent target identified in this screen was Annexin A2 (ANXA2). ANXA2 is a member of the Annexin family that has diverse roles in cancer including proliferation and invasion and is widely expressed in cancer. Furthermore, expression of ANXA2 is linked to poor prognosis in pancreatic cancer. Targeting of Annexin A2 on the surface of pancreatic cancer cells using DARPins resulted in decreased frequency of CSCs both in vitro and in vivo in several pancreatic patient-derived xenografts. ANXA2 DARPins also reduced proliferation and tumor growth of HPAC cells both in vitro and in vivo. Mechanistically, we found that blocking ANXA2 resulted in decreased IL6 and IL8 secretion, two cytokines that have been linked to CSC expansion and survival. Additionally, we found that pharmacological blockade of ANXA2 resulted in decreased plasmin activation, a pathway that has been linked to dissemination of cancer cells. Together our data suggests that targeting of cell surface ANXA2 is effective at reducing CSCs and could be a novel target for the treatment of pancreatic cancer. Citation Format: Elaine M. Hurt, Matt Flynn, Paul Hynes, M. Carla Cabrera, Suneetha B. Thomas, Lilian van Vlerken-Ysla, Louise Slater, Alan Sandercock, Steven Rust, Ralph Minter, Ronald Herbst. Phenotypic selection screening reveals Annexin A2 as a pancreatic cancer stem cell target [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 151.

Cancer stem cells (CSCs) represent an important subpopulation of tumor cells that are untouched and perhaps even expanded after chemotherapy and radiation. This population has been shown in murine models of cancer to be solely responsible for the regrowth of tumors following chemotherapy, underscoring the importance of therapeutically targeting this population. Therefore, we sought to find novel targets against CSCs using a phenotypic selection screen. Using a designed ankyrin repeat (DARpin) library, we panned cells disaggregated from tumor spheres from three patient-derived xenograft models of late stage pancreatic cancer to enrich for DARPins that bind CSCs. Once released from the cells, the DARPins were further analyzed for binding to both normal, pancreatic cancer total tumor cells and pancreatic CSCs in order to choose targets that showed either pancreatic cancer-specific or pancreatic CSC-specific binding. These DARPins were then tested in a sphere formation assay, an EZH2-based high content imaging screen, and a standard proliferation assay. Those DARPins showing good cancer-specific binding profiles were also tested for internalization and killing using a saporin-conjugated secondary antibody. Using this approach, we identified 30 DARPins of interest for either direct inhibitory antibody approaches or for potential antibody drug conjugate or nanoparticle delivery approaches. Identification of the proteins bound by each of the DARPins was done using either immunopreciptation followed by liquid chromatography tandem-mass spectrometry or through Retrogenix's cell expression microarray technology. Identified targets included known CSC antigens such as integrin alpha6 (CD49f) as well as other potentially novel targets. These results highlight the possibilities of finding therapeutic targets for CSCs and opens up an exciting possibility for novel therapies. Citation Format: Elaine M. Hurt, Matt Flynn, Suneetha Thomas, Lilian van Vlerken-Ysla, Alan Sandercock, Steven Rust, Minter Ralph, Robert Hollingsworth. Phenotypic selection screening reveals cancer stem cell therapeutic targets. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4218. doi:10.1158/1538-7445.AM2015-4218