Abstract 5100: Combination of κλ bispecific antibodies targeting innate (CEAxCD47, NILK-2401) and adaptive immunity (CEAxCD3, NILK-2301 and CEAxCD28, NILK-3301) for next generation immunotherapy of CEA-expressing cancers

Background: The CEAxCD3 bispecific antibody (bsAb) NILK-2301 couples CEA (CEACAM5) on cancer cells and CD3 on T-cells inducing T-cell activation (signal 1) and tumor cell killing (TDCC). T-cell activation can be boosted by CEA-targeted CD28-costimulation (NILK-3301; signal 2). NILK-2401, carrying a fully effective IgG1 Fc, induces antibody-dependent phagocytosis (ADCP) and antibody-dependent cytotoxicity (ADCC) of tumor cells by co-targeting CEA and the innate immune checkpoint CD47 (“don’t eat me” signal). We present here next generation immunotherapy to overcome limited single class activity in CEA-expressing solid cancers.

Methods: BsAbs were generated using LCB’s fully human κλ body platform. TDCC, ADCP, and ADCC with human PBMC or monocyte-derived macrophages were assessed using CEA+ colorectal (n=3), lung (n=2), and gastric (n=2) cancer lines. Combination activity of NILK-2401 + NILK-2301 (± NILK-3301) was assessed by flow cytometry. In vivo activity was tested in xenograft NOG or NSG/human PMBC-, HIS-, and hSIRPα/hCD47/hCD3/hCD28 transgenic mice. Safety data include binding to other CEACAMs, cytokine release in whole blood, erythrophagocytosis, platelet activation, exclusion of superagonism (NILK-3301), as well as PK- and tolerability in cynomolgus monkeys and Tg32-mice.

Results: NILK-2301 induced dose-dependent killing of all tested cell lines, which was also visualized by live cell imaging. Combination of NILK-2301 (1 nM) + NILK-3301 vs. NILK-2301 alone (10 nM) increased TDCC (3-8-fold), T-cell activation (CD25, CD69, HLA-DR), cytokine secretion (interferon-γ, granzyme B, perforin), and CD4+/CD8+ T-cell proliferation. NILK-2401 blocked CD47-SIRPα interaction and induced ADCP/ADCC-mediated elimination of all cell lines. NILK-2301 + NILK-2401 treatment increased maximum activity (Emax) and reduced necessary dose of the T-cell bsAb to reach Emax. E.g., Emax of 30% killing (NILK-2301 alone) was increased in combination with NILK-2401 at 0.1/1/10 µg/mL to 40%, 80%, and 80%. In vivo, NILK-2301 (10 mg/kg IV, BIW) decreased tumor progression. NILK-2301/-3301 combination induced tumor regression in 8/8 mice. NILK-2401 delayed tumor growth vs. mean of control in 100% (15/15) of mice and prevented establishment of detectable tumors (>50mm3) in 53% (8/15). Results of double and quadruple transgenic mice, including triple bsAb combinations, will be presented at the meeting. No relevant safety signals were detected.

Conclusions: NILK-2301 and NILK-2401 are active as single agents. Addition of NILK-2401 or NILK-3301 to NILK-2301 significantly increases activity, already at 10 -100x lower CEAxCD3 doses. GMP drug substance has been produced for NILK-2301 and NILK-2401. Generation of the clonal cell line for NILK-3301 clinical material production is ongoing.

Citation Format: Anja Seckinger, Lise Nouveau, Sara Majocchi, Valéry Moine, Vanessa Buatois, Bruno Daubeuf, Franck Gueneau, Ulla Ravn, Krzysztof Masternak, Yves Poitevin, Emeline Rousset, Giovanni Magistrelli, Pauline Malinge, Limin Shang, Nicolas Fischer, Klaus Strein, Walter Ferlin, Dirk Hose. Combination of κλ bispecific antibodies targeting innate (CEAxCD47, NILK-2401) and adaptive immunity (CEAxCD3, NILK-2301 and CEAxCD28, NILK-3301) for next generation immunotherapy of CEA-expressing cancers. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5100.

Abstract 2884: Optimized CD28 bispecific antibodies for targeted activation of T cells within the tumor microenvironment

Tumor-targeted CD28 bispecific antibodies (bsAbs) are designed to co-stimulate T cells specifically within the tumor microenvironment. By bridging T cells to malignant cells expressing a selected tumor-associated antigen (TAA), CD28 bsAbs deliver the so-called signal 2 to T cells unleashing their full cytotoxic potential. Contrary to bivalent CD28 monoclonal antibody (mAb) superagonists, the activation of CD28 with monovalent CD28 bispecifics requires the binding of a TAA expressed by the cancer cells to induce CD28 clustering. Preclinical studies have shown the benefit of adding costimulatory CD28 bsAbs for the treatment of solid tumors, boosting the efficacy of bispecific T cell engagers (CD3 bsAbs) or PD-(L)1 checkpoint inhibitors.

Using our proprietary fully human κλ body antibody platform, which relies on a common heavy chain and on two distinct light chains driving specificity and affinity (i.e., one kappa and one lambda), we have identified a panel of agonist anti-CD28 kappa arms. Using our existing lambda anti-TAA arms (e.g., targeting CD19, MSLN, HER2, EGFR), an array of TAA-CD28 κλ bodies targeting different tumors were generated. The capacity of these CD28 κλ bodies to provide signal 2 to T cells was assessed both in vitro and in vivo in combination with CD3 bsAbs. In the presence of cancer cells and corresponding TAA-CD3 bsAbs, the CD28 κλ bodies enabled the activation of primary human CD4 and CD8 T cells, leading to T cell proliferation and secretion of cytokines such as IL-2 and IFNγ, and granzyme B. Importantly, when used alone or in combination with an untargeted CD3 bsAb (that is, in the absence of signal 1), CD28 κλ bodies showed no sign of T cell activation, potentially limiting peripheral toxicity. The resulting change in the T cell activation status led to a potent in vitro T cell-dependent cellular cytotoxicity (TDCC) against TAA-expressing cancer cell lines. CD28 κλ bodies targeting gastrointestinal tumors were tested in combination with CD3 bsAbs in xenogeneic tumor models and synergistically improved the antitumoral activity of T cell engagers, leading to an enhanced tumor control. Thus, via the identification of optimal agonist anti CD28 arms, CD28 bsAbs targeting multiple TAAs were designed for tumor-specific activation of the immune system. The resulting TAA-CD28 κλ bodies can enhance the antitumor response induced by CD3-retargeting bsAbs via the induction of T cell proliferation and activation, increased cytokine secretion and boosted anti-tumoral cytotoxicity. Other anti-TAA arms are being explored, to expand the panel of TAAs that could be easily paired with our anti-CD28 platform arms.

Citation Format: Sara Majocchi, Pauline Lloveras, Coline Burnet-Merlin, Lise Nouveau, Nicolas Pleche, Pauline Malinge, Claudia Batista, Christelle Daviet, Maud Charreton, Guillemette Pontini, Franck Gueneau, Valery Moine, Giovanni Magistrelli, Limin Shang, Walter Ferlin, Krzysztof Masternak. Optimized CD28 bispecific antibodies for targeted activation of T cells within the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2884.

Round optimization for improved discovery of native bispecific antibodies

The assembly of bispecific antibodies (bsAb) that retain the structure of a standard IgG can be challenging as the correct pairing of the different heavy and light chains has to be ensured while unwanted side products kept to a minimum. The use of antibodies sharing a common chain facilitates assembly of such bsAb formats but requires additional efforts during the initial discovery phase. We have developed a native bsAb format called κλ body based on antibodies that, while being specific for different antigens, share the same heavy chain. Such antibodies can readily be isolated from antibody libraries incorporating a single VH combined with light chain diversity. However, in order to improve the discovery process of such fixed VH antibodies, we developed a method to optimize populations of light chains by recovering and shuffling CDRL3 sequences that have been enriched for antigen binding by phage display selection. This approach allowed for the isolation of a more diverse and potent panel of antibodies blocking the interaction between PD-1 and PD-L1 when compared to our standard in vitro selection approach, thus providing better building blocks for subsequent bsAb generation.

Antibody Neutralization of CXCL10 in Vivo Is Dependent on Binding to Free and Not Endothelial-bound Chemokine: IMPLICATIONS FOR THE DESIGN OF A NEW GENERATION OF ANTI-CHEMOKINE THERAPEUTIC ANTIBODIES

To improve our understanding of properties that confer successful inhibition of chemokines in vivo, we analyzed anti-murine CXCL10 monoclonal antibodies (mAb) having different characteristics. 1B6 displayed potent inhibition of cell recruitment in vitro with an IC50 of 0.5 nm but demonstrated little efficacy in various animal models of human disease. On the contrary, 1F11 showed efficacy in several models of inflammation yet was less potent at inhibiting chemotaxis in vitro with an IC50 of 21 nm Furthermore, we observed that 1B6 displayed a rapid dose-dependent clearance (t½ 10-60 h) in contrast to 1F11, which presented a dose-proportional pharmacokinetic profile and a half-life of 12 days. Moreover, 1B6 recognized glycosaminoglycan (GAG)-bound CXCL10, resulting in target-mediated clearance, which was corroborated using CXCL10-deficient mice. In contrast to 1B6, 1F11 inhibited the interaction of CXCL10 with GAGs, did not recognize GAG-bound CXCL10, and did not display target-mediated drug disposition. Confirming previous animal studies, 1B6 was poor at reversing glycemia in a model of type 1 diabetes, whereas 1F11 induced early and prolonged control of diabetes. Furthermore, when using 1A4, a subsequently generated anti-mCXCL10 mAb that shares the property with 1F11 of being unable to recognize CXCL10 immobilized on GAG, we observed a similar superior control of diabetes as compared with 1B6. We therefore concluded that targeting chemokines with antibodies such as 1B6 that recognize the more abundant GAG-bound form of the chemokine may not be the optimal strategy to achieve disease control.

De novo isolation of antibodies with pH-dependent binding properties

pH-dependent antibodies are engineered to release their target at a slightly acidic pH, a property making them suitable for clinical as well as biotechnological applications. Such antibodies were previously obtained by histidine scanning of pre-existing antibodies, a labor-intensive strategy resulting in antibodies that displayed residual binding to their target at pH 6.0. We report here the de novo isolation of pH-dependent antibodies selected by phage display from libraries enriched in histidines. Strongly pH-dependent clones with various affinity profiles against CXCL10 were isolated by this method. Our best candidate has nanomolar affinity for CXCL10 at pH 7.2, but no residual binding was detected at pH 6.0. We therefore propose that this new process is an efficient strategy to generate pH-dependent antibodies.

Abstract 2482: Neutralizing CD47 in cancer cells with dual targeting kappa/lambda bodies

Neutralizing CD47, the ‘don't eat me signal’ hijacked by different tumor types, is a novel generally applicable therapeutic strategy. Because of a distinct mechanism of action and the ability to stimulate the innate anti-tumor immunity, CD47-neutralizing agents are poised as attractive candidates for combination therapies in association with other immunotherapies. However, the development of general CD47 antagonists could be hindered by the ubiquitous and abundant expression of CD47 on virtually all healthy cells. To overcome potential pharmacological and clinical liabilities of a general CD47 antagonist, we have developed bispecific kappa/lambda bodies, which selectively target CD47 in cancer cells. These kappa/lambda bodies:

(i) are full-length bispecific IgGs, (ii) bind with high affinity and neutralize the CD47-SIRP alpha interaction in cancer cells expressing a tumor-associated antigen (TAA), and (iii) mediate efficient cell killing of TAA-positive cancer cells in vitro through Fc-dependent mechanisms such as ADCP (antibody mediated cellular phagocytosis) and ADCC (antibody mediated cellular cytotoxicity).

We are currently developing two molecules of this type, one targeting CD47 and CD19 (for B cell malignancies), the other targeting CD47 and mesothelin (for various mesothelin-positive solid tumors). The efficacy of the CD47/CD19 kappa/lambda body was demonstrated in vivo, using two B-cell lymphoma xenograft models in NOD/SCID mice. We also performed a pharmacokinetics study in non-human primates with the CD47/CD19 lead candidate, with the objective of assessing the potential “antigen sink” effect related to ubiquitous CD47 expression on erythrocytes, platelets and other cells. Encouragingly, the CD47/CD19 kappa/lambda body administered in a single dose to cynomolgus monkeys, at 0.5 and 10 mg/kg, showed an acceptable pharmacokinetic profile and the absence of hematological toxicities. The example of the CD47/CD19 kappa/lambda body illustrates the power of the dual-targeting approach for addressing a ubiquitous cell surface receptor such as CD47.

Citation Format: Krzysztof Masternak, Lucile Broyer, Elie Dheilly, Stefano Majocchi, Valéry Moine, Giovanni Magistrelli, François Rousseau, Ulla Ravn, Franck Gueneau, Pauline Malinge, Sébastien Calloud, Maud Charreton-Galby, Mireille Guerrier, Nessie Costes, Nicolas Bosson, Gérard Didelot, Lucie Bernard, Vanessa Buatois, Laura Cons, Laurence Chatel, Anne Papaioannou, Zoë Johnson, Walter Ferlin, Marie Kosco-Vilbois, Nicolas Fischer. Neutralizing CD47 in cancer cells with dual targeting kappa/lambda bodies. [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 2482. doi:10.1158/1538-7445.AM2015-2482

Deep sequencing of phage display libraries to support antibody discovery

The use of next generation sequencing (NGS) for the analysis of antibody sequences both in phage display libraries and during in vitro selection processes has become increasingly popular in the last few years. Here, our methods developed for DNA preparation, sequencing and data analysis are presented. A key parameter has also been to develop new software designed for high throughput antibody sequence analysis that is used in combination with publicly available tools. As an example of our methods, we provide data from the extensive analysis of five scFv libraries generated using different heavy chain CDR3 diversification strategies. The results not only confirm that the library designs were correct but also reveal differences in quality not easily identified by standard DNA sequencing approaches. The very large number of reads permits extensive sequence coverage after the selection process. Furthermore, as samples can be multiplexed, costs decrease and more information is gained per NGS run. Using examples of results obtained post phage display selections against two antigens, frequency and clustering analysis identified novel antibody fragments that were then shown to be specific for the target antigen. In summary, the methods described here demonstrate how NGS analysis enhances quality control of complex antibody libraries as well as facilitates the antibody discovery process.

Transferring the characteristics of naturally occurring and biased antibody repertoires to human antibody libraries by trapping CDRH3 sequences

Antibody repertoires are characterized by diversity as they vary not only amongst individuals and post antigen exposure but also differ significantly between vertebrate species. Such plasticity can be exploited to generate human antibody libraries featuring hallmarks of these diverse repertoires. In this study, the focus was to capture CDRH3 sequences, as this region generally accounts for most of the interaction energy with antigen. Sequences from human as well as non-human sources were successfully integrated into human antibody libraries. Next generation sequencing of these libraries proved that the CDRH3 lengths and amino acid composition corresponded to the species of origin. Specific CDRH3 sequences, biased towards the recognition of a model antigen either by immunizing mice or by selecting with phage display, were then integrated into another set of libraries. From these antigen biased libraries, highly potent antibodies were more frequently isolated, indicating that the characteristics of an immune repertoire is transferrable via CDRH3 sequences into a human antibody library. Taken together, these data demonstrate that the properties of naturally or experimentally biased repertoires can be effectively harnessed for the generation of targeted human antibody libraries, substantially increasing the probability of isolating antibodies suitable for therapeutic and diagnostic applications.

Dual specificity of anti-CXCL10-CXCL9 antibodies is governed by structural mimicry

Dual-specific antibodies are characterized by an antigen-combining site mediating specific interactions with two different antigens. We have generated five dual-specific single chain variable fragments (scFv) that neutralize the activity of the two chemokines, CXCL9 and CXCL10, to bind to their receptor CXCR3. To better understand how these dual-specific scFvs bind these two chemokines that only share a 37% sequence identity, we mapped their epitopes on human CXCL9 and CXCL10 and identified serine 13 (Ser(13)) as a critical residue. It is conserved between the two chemokines but not in the third ligand for CXCR3, CXCL11. Furthermore, Ser(13) is exposed in the tetrameric structure of CXCL10, which is consistent with our finding that the scFvs are able to bind to CXCL9 and CXCL10 immobilized on glycosaminoglycans. Overall, the data indicate that these dual-specific scFvs bind to a conserved surface involved in CXCR3 receptor interaction for CXCL10 and CXCL9. Thus, structural mimicry between the two targets is likely to be responsible for the observed dual specificity of these antibody fragments.

By-passing in vitro screening--next generation sequencing technologies applied to antibody display and in silico candidate selection

In recent years, unprecedented DNA sequencing capacity provided by next generation sequencing (NGS) has revolutionized genomic research. Combining the Illumina sequencing platform and a scFv library designed to confine diversity to both CDR3, >1.9 × 10(7) sequences have been generated. This approach allowed for in depth analysis of the library's diversity, provided sequence information on virtually all scFv during selection for binding to two targets and a global view of these enrichment processes. Using the most frequent heavy chain CDR3 sequences, primers were designed to rescue scFv from the third selection round. Identification, based on sequence frequency, retrieved the most potent scFv and valuable candidates that were missed using classical in vitro screening. Thus, by combining NGS with display technologies, laborious and time consuming upfront screening can be by-passed or complemented and valuable insights into the selection process can be obtained to improve library design and understanding of antibody repertoires.

Specificity tuning of antibody fragments to neutralize two human chemokines with a single agent

Chemokines are important mediators of the immune response that are responsible for the trafficking of immune cells between lymphoid organs and migration towards sites of inflammation.Using phage display selection and a functional screening approach, we have isolated a panel of single-chain fragment variable (scFv) capable of neutralizing the activity of the human chemokine CXCL10 (hCXCL10). One of the isolated scFv was weakly cross-reactive against another human chemokine CXCL9,but was unable to block its biological activity. We diversified the complementarity determining region 3 (CDR3) of the light chain variable domain (VL) of this scFv and combined phage display with high throughput antibody array screening to identify variants capable of neutralizing both chemokines. Using this approach it is therefore possible to engineer pan-specific antibodies that could prove very useful to antagonize redundant signaling pathways such as the chemokine signaling network.

Chemokines derived from soluble fusion proteins expressed in Escherichia coli are biologically active

Chemokines are a class of low molecular weight proteins that are involved in leukocytes trafficking. Due to their involvement in recruiting immune cells to sites of inflammation, chemokines, and chemokine receptors have become an attractive class of therapeutic targets. However, when expressed in Escherichia coli chemokines are poorly soluble and accumulate in inclusion bodies. Several purification methods have been described but involve time-consuming refolding, buffer exchange, and purification steps that complicate expression of these proteins. Here, we describe a simple and reliable method to express chemokines as fusions to the protein NusA. The fusion proteins were largely found in the soluble fraction and could be readily purified in a single step. Proteolytic cleavage was used to obtain soluble recombinant chemokines that were found to be very active in a novel in vitro chemotaxis assays. This method could be applied to several alpha and beta human chemokines, suggesting that it is generally applicable to this class of proteins.

Recombinant protein production driven by the tryptophan promoter is tightly controlled in ICONE 200, a new genetically engineered E. coli mutant

Batch processes for recombinant gene expression in prokaryotic systems should optimally comprise a growth phase with minimal promoter activity followed by a short phase favoring expression. The strong promoter of the tryptophan operon (Ptrp) gives high-level expression of recombinant proteins in E. coli. The inefficiency to control basal expression before induction is however a major obstacle towards the use of Ptrp, especially in the case of toxic proteins. To circumvent this problem, a novel E. coli strain has been generated. This mutant, named ICONE 200 (Improved Cell for Over and Non-leaky Expression), underwent replacement of tnaA, the tryptophanase encoding gene, with the trpR gene encoding the aporepressor of Ptrp. Detailed analysis of ICONE 200 showed that tryptophan, in addition to its natural role of Ptrp co-repressor, was able to induce trpR through the tryptophan-inducible tryptophanase promoter/operator. Consequently, Ptrp-dependent expression was efficiently repressed in the presence of tryptophan and was turned on, as in wild-type E. coli, as soon as tryptophan was exhausted from the medium. ICONE 200 has the capacity to express a wide range of proteins including toxic proteins such as HIV-1 protease and poliovirus 2B protein. ICONE 200 is a new host carrying stable, targeted, and marker-free genetic modifications and a candidate for large-scale applications.