Patent Application
20180134765
This application relates generally to the production of polypeptides having specific antigen-binding properties of Fv domains, for example, insertable variable fragments of antibodies, and modified α1-α2 domains of NKG2D ligands.
An antibody (Ab),
Antibodies are glycoproteins belonging to the immunoglobulin superfamily and are typically made of basic structural units—each with two large heavy chains and two small light chains. There are several different types of antibody heavy chains, and several different kinds of antibodies, which are grouped into different isotypes based on which heavy chain they possess. Five different antibody isotypes are known in mammals (Market E, Papavasiliou F N (October 2003). “V(D)J recombination and the evolution of the adaptive immune system”. PLoS Biol. 1 (1): E16. doi:10.1371/journal.pbio.0000016. PMC 212695. PMID 14551913). Although the general structure of all antibodies is very similar, a small region at the tip of each arm of the Y-shaped protein is extremely variable, allowing millions of antibodies with slightly different tip structures, or antigen-binding sites, to exist. This region is known as the hypervariable or variable region. Each of these natural variants can bind to a different antigen. This enormous diversity of antibodies allows the immune system to adapt and recognize an equally wide variety of antigens (Hozumi N, Tonegawa S (1976). “Evidence for somatic rearrangement of immunoglobulin genes coding for variable and constant regions”. Proc. Natl. Acad. Sci. U.S.A. 73 (10): 3628-3632. doi:10.1073/pnas.73.10.3628. PMC 431171. PMID 824647.)
The natural “Y”-shaped Ig molecule consists of four polypeptide chains; two identical heavy chains and two identical light chains connected by disulfide bonds,
Some parts of an antibody have the same functions. Each of the two arms of the Y, for example, contains the sites that can bind to antigens and, therefore, recognize specific foreign objects. This region of the antibody is called the Fv (fragment, variable) region. It is composed of one variable domain from the heavy chain (VH) and one variable region from the light chain (VL) of the antibody (Hochman J, Inbar D, Givol D (1973). An active antibody fragment (Fv) composed of the variable portions of heavy and light chains. Biochemistry 12 (6): 1130-1135. doi:10.1021/bi00730a018. PMID 4569769). The paratope is shaped at one end of the Fv and is the region for binding to antigens. It is comprised of variable loops of β-strands, three each on the VL and on the VH and is responsible for binding to the antigen,
Useful polypeptides that possess specific antigen binding function can be derived from the CDRs of the variable regions of antibodies. These two antibody variable domains, one of the light chain (VL) and one from the heavy chain (VH), each with 3 CDRs can be fused in tandem, in either order, using a single, short linker peptide of 10 to about 25 amino acids to create a linear single-chain variable fragment (scFv) polypeptide comprising one each of heavy and light chain variable domains,
The linker is usually rich in glycine for flexibility, as well as serine, threonine, or charged amino acids for solubility, and can either connect the N-terminus of the VH with the C-terminus of the VL, or vice versa. This protein retains the specificity of the original immunoglobulin, despite removal of the constant regions and the introduction of the single linker. This format enables one ordinarily skilled in the art of recombinant DNA technology to genetically fuse the linear scFv to the N- or C-terminus of a parent protein in order to impart to the parent protein the antigen binding properties of the scFv. There are numerous other proposed or created arrangements of polyvalent and tandem scFv regions, but importantly as described below, all have at least two spatially distant termini,
The present disclosure relates to modified α1-a2 domains of NKG2D ligands attached to polypeptides, in some embodiments antibodies or fragments of antibodies. In some aspects, the present disclosure relates to antigen-binding peptides derived from light and heavy chain antibody variable domains, which contain two linker regions and a split variable domain.
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
In some aspects, the present invention relates to insertable variable fragment (iFv) peptides. Because the C-terminus and N-terminus of scFv molecules including polyvalent scFv structures are far apart spatially, scFv structures cannot be inserted into a loop region embedded within a protein fold of a parent or recipient protein without disrupting or destabilizing its fold(s) and/or without disrupting the Fv framework required to properly position the CDRs or hypervariable regions to retain their antigen-binding properties.
To insert the variable fragment of an antibody containing up to 6 CDRs into one or more loop regions of a nascent parent protein molecule without disrupting structural folds of the variable fragment or of the parent protein, we invented a new class of antigen-binding peptides derived from the light and heavy chain antibody variable domains. The new structures contained two linker regions, rather than the traditional single linker of scFv structures, plus a split variable domain. Conceptually the canonical termini of the variable light (VL) and heavy (VH) domains were fused into a continuous or “circular” peptide. That circular peptide structure containing all 6 CDRs of the Fv can then conceptually be split at one of several possible novel sites to create an insertable Fv (iFv). The non-natural split site can be created within either the light or the heavy chain variable domain at or near the apex or turn of a loop to create new, unique N- and C-termini spatially positioned proximal to each other, preferably within 0.5 to 1.5 nm, so as to be insertable into loops of other (parent or recipient) proteins or polypeptides without disrupting the structure, stability, or desirable function. This new class of peptides is called an insertable variable fragment (iFv). The binding or targeting specificity conveyed by an iFv to a recipient molecule can be changed by inserting into the recipient another or different iFV based on a different antibody or scFv or by replacing 1 or more of the CDRs of an existing insertable iFv.
The insertion of one or more iFv polypeptides exhibiting specific antigen-binding properties of Fv domains into other proteins and thereby imparting novel binding properties will have multiple utilities. Such uses include but are not limited to enabling the parent protein to bind the specific antigen, target the antigen, detect the presence of antigen, remove the antigen, contact or draw near the antigen, to deliver a payload to the antigen or antigen-expressing cell, recruit the antigen, and image the presence of the antigen. A payload could be conjugated directly to one or both the amino-terminus and carboxy-terminus of an iFv or indirectly to an iFv via a parent protein or peptide. Examples of payloads include but are not limited to a chromophore, a fluorophore, a pharmacophore, an atom, a heavy or radioactive isotope, an imaging agent, a chemotherapeutic agent, or a toxin. A payloaded iFv can be used to locate or identify the presence of a target molecule to which the iFv specifically binds and as such can serve as in vitro or in vivo imaging agents or diagnostic agents that are small and stable. In addition, to one or both the amino-terminus and carboxy-terminus of an iFv peptide a chemotherapeutic agent or toxic molecule can be conjugated in order to create an iFv-drug conjugate, for example, as treatment for a malignancy or infection. A single payload may be conjugated to both the amino-terminus and the carboxy-terminus of an iFv peptide so as to span or connect the two termini; such spanning may further stabilize the iFv by blocking the termini from exopeptidase degradation or protecting the iFv from denaturation or unfolding.
Examples of parent or recipient proteins or polypeptides that are candidates for insertions of iFv peptides include but are not limited to antibodies, proteins comprised of Ig folds or Ig domains, globulins, albumens, fibronectins and fibronectin domains, integrins, fluorescent proteins, enzymes, outer membrane proteins, receptor proteins, T-cell receptors, chimeric antigen receptors, viral antigens, virus capsids, viral ligands for cell receptors, high molecular weight bacteriocins, histones, hormones, knottins, cyclic peptides or polypeptides, major histocompatibility (MHC) family proteins, MIC proteins, lectins, and ligands for lectins. It is also possible to insert iFv structures into non-protein recipient molecules such a polysaccharides, dendrimers, polyglycols, peptidoglycans, antibiotics, and polyketides.
Natural killer (NK) cells and certain (CD8+αβ and γδ) T-cells of the immunity system have important roles in humans and other mammals as first-line, innate defense against neoplastic and virus-infected cells (Cerwenka, A., and L. L. Lanier. 2001. NK cells, viruses and cancer. Nat. Rev. Immunol. 1:41-49). NK cells and certain T-cells exhibit on their surfaces NKG2D, a prominent, homodimeric, surface immunoreceptor responsible for recognizing a target cell and activating the innate defense against the pathologic cell (Lanier, L L, 1998. NK cell receptors. Ann. Rev. Immunol. 16: 359-393; Houchins J P et al. 1991. DNA sequence analysis of NKG2, a family of related cDNA clones encoding type II integral membrane proteins on human NK cells. J. Exp. Med. 173: 1017-1020; Bauer, S et al., 1999. Activation of NK cells and T cells by NKG2D, a receptor for stress-inducible MICA. Science 285: 727-730). The human NKG2D molecule possesses a C-type lectin-like extracellular domain that binds to its cognate ligands, the 84% sequence identical or homologous, monomeric MICA and MICB, polymorphic analogs of the Major Histocompatibility Complex (MHC) Class I chain-related glycoproteins (MIC) (Weis et al. 1998. The C-type lectin superfamily of the immune system. Immunol. Rev. 163: 19-34; Bahram et al. 1994. A second lineage of mammalian MHC class I genes. PNAS 91:6259-6263; Bahram et al. 1996a. Nucleotide sequence of the human MHC class I MICA gene. Immunogenetics 44: 80-81; Bahram and Spies T A. 1996. Nucleotide sequence of human MHC class I MICB cDNA. Immunogenetics 43: 230-233). Non-pathologic expression of MICA and MICB is restricted to intestinal epithelium, keratinocytes, endothelial cells and monocytes, but aberrant surface expression of these MIC proteins occurs in response to many types of cellular stress such as proliferation, oxidation and heat shock and marks the cell as pathologic (Groh et al. 1996. Cell stress-regulated human MHC class I gene expressed in GI epithelium. PNAS 93: 12445-12450; Groh et al. 1998. Recognition of stress-induced MHC molecules by intestinal γδT cells. Science 279: 1737-1740; Zwirner et al. 1999. Differential expression of MICA by endothelial cells, fibroblasts, keratinocytes and monocytes. Human Immunol. 60: 323-330). Pathologic expression of MIC proteins also seems involved in some autoimmune diseases (Ravetch, J V and Lanier L L. 2000. Immune Inhibitory Receptors. Science 290: 84-89; Burgess, S J. 2008. Immunol. Res. 40: 18-34). The differential regulation of NKG2D ligands, such as the polymorphic MICA and MICB, is important to provide the immunity system with a means to identify and respond to a broad range of emergency cues while still protecting healthy cells from unwanted attack (Stephens H A, (2001) MICA and MICB genes: can the enigma of their polymorphism be resolved? Trends Immunol. 22: 378-85; Spies, T. 2008. Regulation of NKG2D ligands: a purposeful but delicate affair. Nature Immunol. 9: 1013-1015).
Viral infection is a common inducer of MIC protein expression and identifies the viral-infected cell for NK or T-cell attack (Groh et al. 1998; Groh et al. 2001. Co-stimulation of CD8+αβT-cells by NKG2D via engagement by MIC induced on virus-infected cells. Nat. Immunol. 2: 255-260; Cerwenka, A., and L. L. Lanier. 2001). In fact, to avoid such an attack on its host cell, cytomegalovirus and other viruses have evolved mechanisms that prevent the expression of MIC proteins on the surface of the cell they infect in order to escape the wrath of the innate immunity system (Lodoen, M., K. Ogasawara, J. A. Hamerman, H. Arase, J. P. Houchins, E. S. Mocarski, and L. L. Lanier. 2003. NKG2D-mediated NK cell protection against cytomegalovirus is impaired by gp40 modulation of RAE-1 molecules. J. Exp. Med. 197:1245-1253; Stern-Ginossar et al., (2007) Host immune system gene targeting by viral miRNA. Science 317: 376-381; Stern-Ginossar et al., (2008) Human microRNAs regulate stress-induced immune responses mediated by the receptor NKG2D. Nature Immunology 9: 1065-73; Slavuljica, I A Busche, M Babic, M Mitrovic, I Gašparovic, Ð Cekinovic, E Markova Car, E P Pugel, A Cikovic, V J Lisnic, W J Britt, U Koszinowski, M Messerle, A Krmpotic and S Jonjic. 2010. Recombinant mouse cytomegalovirus expressing a ligand for the NKG2D receptor is attenuated and has improved vaccine properties. J. Clin. Invest. 120: 4532-4545).
In spite of their stress, many malignant cells, such as those of lung cancer and glioblastoma brain cancer, also avoid the expression of MIC proteins and as a result may be particularly aggressive as they too escape the innate immunity system (Busche, A et al. 2006, NK cell mediated rejection of experimental human lung cancer by genetic over expression of MHC class I chain-related gene A. Human Gene Therapy 17: 135-146; Doubrovina, E S, M M Doubrovin, E Vider, R B Sisson, R J O'Reilly, B Dupont, and Y M Vyas, 2003. Evasion from NK Cell Immunity by MHC Class I Chain-Related Molecules Expressing Colon Adenocarcinoma (2003) J. Immunology 6891-99; Friese, M. et al. 2003. MICA/NKG2D-mediated immunogene therapy of experimental gliomas. Cancer Research 63: 8996-9006; Fuertes, M B, M V Girart, L L Molinero, C I Domaica, L E Rossi, M M Barrio, J Mordoh, G A Rabinovich and N W Zwirner. (2008) Intracellular Retention of the NKG2D Ligand MHC Class I Chain-Related Gene A in Human Melanomas Confers Immune Privilege and Prevents NK Cell-Mediated Cytotoxicity. J. Immunology, 180: 4606-4614).
The high resolution structure of human MICA bound to NKG2D has been solved and demonstrates that the α3 domain of MICA has no direct interaction with the NKG2D (Li et al. 2001. Complex structure of the activating immunoreceptor NKG2D and its MHC class I-like ligand MICA. Nature Immunol. 2: 443-451; Protein Data Bank accession code 1HYR). The α3 domain of MICA, like that of MICB, is connected to the α1-α2 platform domain by a short, flexible linker peptide, and itself is positioned naturally as “spacer” between the platform and the surface of the MIC expressing cell. The 3-dimensional structures of the human MICA and MICB α3 domains are nearly identical (root-mean square distance <1 Å on 94 C-αα's) and functionally interchangeable (Holmes et al. 2001. Structural Studies of Allelic Diversity of the MHC Class I Homolog MICB, a Stress-Inducible Ligand for the Activating Immunoreceptor NKG2D. J Immunol. 169: 1395-1400).
Certain non-natural α1-α2 domains of NKG2D ligands modified to bind natural human NKG2D receptors with higher affinities than do natural α1-α2 domains have been described (Candice S. E. Lengyel, Lindsey J. Willis, Patrick Mann, David Baker, Tanja Kortemme, Roland K. Strong and Benjamin J. McFarland. Mutations Designed to Destabilize the Receptor-Bound Conformation Increase MICA-NKG2D Association Rate and Affinity. Journal of Biological Chemistry Vol. 282, no. 42, pp. 30658-30666, 2007; Samuel H. Henager, Melissa A. Hale, Nicholas J. Maurice, Erin C. Dunnington, Carter J. Swanson, Megan J. Peterson, Joseph J. Ban, David J. Culpepper, Luke D. Davies, Lisa K. Sanders, and Benjamin J. McFarland. Combining different design strategies for rational affinity maturation of the MICA-NKG2D interface. Protein Science 2012 VOL 21:1396-1402. Herein we describe non-natural α1-α2 domains of NKG2D ligands that have been modified to bind non-natural NKG2D receptors, themselves mutated at sites which consequentially result in compromised or loss of binding to natural α1-α2 domains of NKG2D ligands (David J. Culpepper, Michael K. Maddox, Andrew B. Caldwell, and Benjamin J. McFarland. Systematic mutation and thermodynamic analysis of central tyrosine pairs in polyspecific NKG2D receptor interactions. Mol Immunol. 2011 January; 48(4): 516-523; USPTO application Ser. No. 14/562,534; USPTO provisional application 62/088,456)). This invention creates bispecific molecules comprised of the specifically modified non-natural α1-α2 domains and specific targeting heterologous molecules, including but not limited to heterologous peptides or polypeptides, that bind Chimeric Antigen Receptors (CARs) wherein the receptor of the CAR is comprised of a non-natural NKG2D receptor ectodomain that binds the modified α1-α2 domains with greater affinity than it does natural α1-α2 domains. Genetically engineered cells of the immunity system comprised of such CARs can then overcome many of the disadvantages, including known severe systemic toxicities and antigen escape, of current CAR-T and CAR-NK cell therapeutics as described below (Kalos M, Levine, B L, Porter, D L, Katz, S, Grupp, S A, Bagg, A and June, C. T Cells with chimeric antigen receptors have potent antitumor effects and can establish memory in patients with advanced leukemia. Sci Transl Med 2011; 3:95ra73; Morgan R A, Yang J C, Kitano M, Dudley M E, Laurencot C M, Rosenberg S A. Case report of a serious adverse event following the administration of T cells transduced with a chimeric antigen receptor recognizing ERBB2. Mol Ther 2010, 18:843-851; Gill and June 2015).
T-cells and NK-cells can be modified using gene transfer technologies to directly and stably express on their surface binding domains of an antibody that confer novel antigen specificities (Saar Gill & Carl H. June. Going viral: chimeric antigen receptor T-cell therapy for hematological malignancies. Immunological Reviews 2015. Vol. 263: 68-89; Wolfgang Glienke, Ruth Esser, Christoph Priesner, Julia D. Suerth, Axel Schambach, Winfried S. Wels, Manuel Grez, Stephan Kloess, Lubomir Arseniev and Ulrike Koehl. 2015. Advantages and applications of CAR-expressing natural killer cells. Front. Pharmacol. doi: 10.3389/fphar.2015.00021). CAR-T cells are applications of this approach that combines an antigen recognition domain of a specific antibody with an intracellular domain of the CD3-ζ chain, which is the primary transmitter of signals from endogenous T-Cell Receptors (TCRs), into a single chimeric protein along with a co-stimulatory molecule such as CD27, CD28, ICOS, 4-1BB, or OX40,
As used herein, a “soluble MIC protein”, “soluble MICA” and “soluble MICB” refer to a MIC protein containing the α1, α2, and α3 domains of the MIC protein but without the transmembrane or intracellular domains. The NKG2D ligands, ULBP1-6, do not naturally possess an α3 domain (Cerwenka A, Lanier L L. 2004. NKG2D ligands: unconventional MHC class I-like molecules exploited by viruses and cancer. Tissue Antigens 61 (5): 335-43. doi:10.1034/j.1399-0039.2003.00070.x. PMID 12753652). An “α1-α2 domain” of an NKG2D ligand refers to the protein domain of the ligand that binds an NKG2D receptor.
In some embodiments, the α1-α2 domains of the non-natural NKG2D ligand proteins of the invention are at least 80% identical or homologous to the native or natural α1-α2 domain of an NKG2D ligand, SEQ ID NOs: 36-54. In other embodiments, the modified α1-α2 domain is 85% identical to a native or natural α1-α2 domain of an NKG2D ligand. In yet other embodiments, the modified α1-α2 domain is 90% identical to a native or natural α1-α2 domain of a natural NKG2D ligand protein and binds non-natural NKG2D.
The α1-α2 platform domain of a soluble MIC protein is tethered to the α3 domain and is diffusible in the intercellular or intravascular space of the mammal. Preferably the α1-α2 platform domains of the non-natural MIC proteins of the invention are at least 80% identical or homologous to a native or natural α1-α2 domain of a human MICA or MICB protein and bind NKG2D. In some embodiments, the α1-α2 platform domain is 85% identical to a native or natural α1-α2 platform domain of a human MICA or MICB protein and binds NKG2D. In other embodiments, the α1-α2 platform domain is 90%, 95%, 96%, 97%, 98%, or 99% identical to a native or natural α1-α2 platform domain of a human MICA or MICB protein and binds NKG2D.
In some embodiments, a heterologous peptide tag may be fused to the N-terminus or C-terminus of an α1-α2 domain or a soluble MIC protein to aid in the purification of the soluble MIC protein. Tag sequences include peptides such as a poly-histidine, myc-peptide or a FLAG tag. Such tags may be removed after isolation of the MIC molecule by methods known to one skilled in the art.
In other embodiments of the invention, specific mutations in α1-α2 domains of NKG2D ligands can be made to create non-natural α1-α2 domains that bind non-natural NKG2D receptors, themselves engineered so as to have reduced affinity for natural NKG2D ligands. This can be done, for example, through genetic engineering. A non-natural NKG2D receptor so modified can be used to create on the surface of NK- or T-cells of the immune system an NKG2D-based Chimeric Antigen Receptor (CAR) that can preferentially bind to and be activated by molecules comprised of the invented non-natural α1-α2 domains. These pairs of non-natural NKG2D receptors and their invented cognate non-natural NKG2D ligands will provide important safety, efficacy, and manufacturing advantages for treating cancer and viral infections as compared to the current CAR-T cells and CAR-NK cells, as described below.
Engineering T cells with CARs has emerged as a promising approach to adoptive T cell therapy for cancer, and CARs targeting many different molecules have been tested in CAR-T cells as therapeutics for malignancies (Porter D L, Levine B L, Kalos M, Bagg A, June C H. Chimeric antigen receptor-modified T cells in chronic lymphoid leukemia. N Engl J Med. 365:725-733.). While remarkable clinical efficacy has been observed in hundreds of patients receiving adoptive transfer of T cells expressing CD19-specific chimeric antigen receptors, the processes of custom engineering a CAR to target a specific antigen, isolating autologous T-cells from the patient, genetically engineering the autologous T-cells to express the personalized CAR, expanding the modified cells in vitro, and controlling the quality their production have all been onerous and expensive. Currently this is feasible only in the context of large academic centers with extensive expertise and resources (Gill & June, 2015).
Once the autologous CAR-T cells are infused back into the donor patient, their expansion in vivo cannot be controlled—“living therapy”, and there is not a dose-response relationship with efficacy (Gill & June, 2015). Furthermore, tumor escape from the CAR T-cell can occur through antigen loss escape (Stephan A. Grupp, M.D., Ph.D., Michael Kalos, Ph.D., David Barrett, M.D., Ph.D., Richard Aplenc, M.D., Ph.D., David L. Porter, M.D., Susan R. Rheingold, M.D., David T. Teachey, M.D., Anne Chew, Ph.D., Bernd Hauck, Ph.D., J. Fraser Wright, Ph.D., Michael C. Milone, M.D., Ph.D., Bruce L. Levine, Ph.D., and Carl H. June, M.D. Chimeric Antigen Receptor-Modified T Cells for Acute Lymphoid Leukemia. N Engl J Med 2013; 368:1509-1518), and this escape pathway can most readily be addressed by sequential therapy with a differently targeted CAR-T cell or by an initial infusion of a T-cell product that contains CARs of two or more specificities, further complicating the manufacturing processes and quality control.
In addition to CAR-T cells targeting tumors with single chain antibody binding domains (scFv), CAR-T cells that employ the ligand-binding domain of the NKG2D receptor have been studied in animals and recently in humans (Sentman C L, Meehan K R. NKG2D CARs as cell therapy for cancer. Cancer J. 2014 March-April; 20(2):156-9. doi: 10.1097/PPO.0000000000000029; Manfred Lehner, Gabriel Götz, Julia Proff, Niels Schaft, Jan Dörrie, Florian Full, Armin Ensser, Yves A. Muller, Adelheid Cerwenka, Hinrich Abken, Ornella Parolini, Peter F. Ambros, Heinrich Kovar, Wolfgang Holter. Redirecting T Cells to Ewing's Sarcoma Family of Tumors by a Chimeric NKG2D Receptor Expressed by Lentiviral Transduction or mRNA Transfection Research Article I published 15 Feb. 2012 | PLOS ONE 10.1371/journal.pone.0031210; www.clinicaltrials.gov NCT02203825). Since NKG2D ligand expression is increased on the surface of stressed cells, such as tumor cells, this family of natural NKG2D ligands is of significant interest as targets for cancer immunotherapies (Spear P, Wu M R, Sentman M L, Sentman C L. NKG2D ligands as therapeutic targets. Cancer Immun. 2013 May 1; 13:8.; Song D G, Ye Q, Santoro S, Fang C, Best A, Powell D J Jr., Chimeric NKG2D CAR-expressing T cell-mediated attack of human ovarian cancer is enhanced by histone deacetylase inhibition. Hum Gene Ther. 2013 March; 24(3):295-305). One NKG2D CAR was a fusion of the full-length NKG2D receptor and CD3ζ (NKG2Dζ); another was with only the ectodomain of NKG2D fused in opposite orientation to a second-generation CAR scaffold composed of transmembrane and intracellular domains from CD28 and the signaling domain of CD3ζ (NKG2D28ζ). Since activation of NKG2D is dependent upon the presence of DAP10, a CAR-T cell was also constructed wherein DAP10 was co-expressed with NKG2Dζ (NKG2Dζ10). T cells expressing any of the above NKG2D CARs produced IFNγ and TNFα in response to NKG2D ligand stimulation and in vitro efficiently killed tumor targets expressing NKG2D ligands (Heather VanSeggelen, Joanne A. Hammill, Anna Dvorkin-Gheva, Daniela G. M. Tantalo, Jacek M. Kwiecien, Galina F. Denisova, Brian Rabinovich, Yonghong Wan, Jonathan L. Bramson, T cells engineered with chimeric antigen receptors targeting NKG2D ligands display lethal toxicity in mice, Molecular Therapy accepted article preview online 30 Jun. 2015; doi:10.1038/mt.2015.119). The cytotoxic potential of NK cells against a wide spectrum of tumor subtypes could also be markedly enhanced by expression of a CAR based on NKG2D-DAP10-CD3ζ (Yu-Hsiang Chang, John Connolly, Noriko Shimasaki, Kousaku Mimura, Koji Kono, and Dario Campana. Chimeric Receptor with NKG2D Specificity Enhances Natural Killer Cell Activation and Killing of Tumor Cells. Cancer Res; 73(6) Mar. 15, 2013).
However, following infusion into syngeneic murine hosts, significant toxicity occurred with these CAR-T constructs that bind and are activated by natural ligands of the natural NKG2D receptor. Signs of toxicity, including poor body condition, hunched posture, labored breathing, and decreased core body temperature were observed in tumor-bearing and tumor-free mice treated with NKG2D-based CAR-T cells as compared to untreated control mice. The severity of NKG2D CAR-T cell toxicity varied, with NKG2Dζ10 being severely toxic, NKG2D28ζ showing intermediate toxicity, and NKG2Dζ being tolerable. Clinical symptoms of toxicity and mortality rates were exacerbated when mice received chemotherapy prior to adoptive transfer of T cells expressing any of the NKG2D CARs (VanSeggelen et al. 2015). Chemotherapy and radiation are known to induce NKG2D ligands on otherwise healthy tissues (Xiulong Xu, Geetha S Rao, Veronika Groh, Thomas Spies, Paolo Gattuso, Howard L Kaufman, Janet Plate and Richard A Prinz. Major histocompatibility complex class I-related chain A/B (MICA/B) expression in tumor tissue and serum of pancreatic cancer: Role of uric acid accumulation in gemcitabine-induced MICA/B expression. BMC Cancer 2011, 11:194 doi:10.1186/1471-2407-11-194; Gannagé M, Buzyn A, Bogiatzi S I, Lambert M, Soumelis V, Dal Cortivo L, Cavazzana-Calvo M, Brousse N, Caillat-Zucman Induction of NKG2D ligands by gamma radiation and tumor necrosis factor-alpha may participate in the tissue damage during acute graft-versus-host disease. Transplantation. 2008 Mar. 27; 85(6):911-5. doi: 10.1097/TP.0b013e31816691ef.). Further characterization revealed that the toxicity coincided with a systemic cytokine storm and lethal levels of inflammation within the lungs. These data warn that extreme caution must be taken when using natural NKG2D ligands for targeted immunotherapy and demonstrate that enhancing T cell expression of strongly activating CARs can be detrimental in vivo (VanSeggelen et al. 2015).
CAR-T or CAR-NK cells comprised of ectodomains of non-natural NKG2D receptors that do not or only poorly bind natural NKG2D ligands will not be subject to the above form of activation and thus will not be toxigenic as a cell expressing CAR based on a natural NKG2D receptor. Furthermore, ectodomains of non-natural NKG2D receptors on cells will not be subject to down-regulation by natural NKG2D ligands in a soluble format or on Myeloid Derived Suppressor Cells (MDSC) (Deng W, Gowen B G, Zhang L, Wang L, Lau S, Iannello A, Xu J, Rovis T L, Xiong N, Raulet D H, 2015. Antitumor immunity. A shed NKG2D ligand that promotes natural killer cell activation and tumor rejection. Science. 2015 Apr. 3; 348(6230):136-9. doi: 10.1126/science.1258867. Epub 2015 Mar. 5). However, when such CAR cells bearing ectodomains of non-natural NKG2D receptors are engaged by bispecific molecules with the cognate non-natural α1-α2 domains of the instant invention and its heterologous targeting motif which has found and bound its intended target, the CAR will be activated and the CAR-cell's effector functions expressed.
Because the CAR-T or CAR-NK cells comprised of non-natural NKG2D receptor ectodomains are not activated except in the presence of an engaged bispecific molecule comprised of a cognate non-natural α1-α2 domains, their activation can be controlled by the administered bispecific molecules, which as biopharmaceuticals will exhibit pharmacokinetics and pharmacodynamics well known in the field. In the event that an adverse event develops, the physician can simply modify the dosing regimen of the administered bispecific molecule rather than having to deploy an induced suicide mechanism to destroy the infused CAR cells as currently done (Monica Casucci and Attilio Bondanza. Suicide Gene Therapy to Increase the Safety of Chimeric Antigen Receptor-Redirected T Lymphocytes. J Cancer. 2011; 2: 378-382). Furthermore, such bispecific molecules with different specific targeting motifs can be administered simultaneously or sequentially to help address tumor resistance and escape as a results of target antigen loss without having to create, expand and infuse multiple different autologous CAR cells (Gill & June, 2015). Since all CAR constructions can be identical for all CAR cells and the targeting specificity determined simply by the targeting motif of the produced bispecific molecule of the instant invention, manufacturing processes will be simplified and less expensive.
Thus, the instant invention expands the diversity and practicality of this remarkable, very promising immunologic approach to managing cancer with CAR-T cells and CAR-NK cells while overcoming many of these current, recognized difficulties.
As used herein “peptide”, “polypeptide”, and “protein” are used interchangeably; and a “heterologous molecule”, “heterologous peptide”, “heterologous sequence” or “heterologous atom” is a molecule, peptide, nucleic acid or amino acid sequence, or atom, respectively, that is not naturally or normally found in physical conjunction with the subject molecule. As used herein, “non-natural” and “modified” are used interchangeably. As used herein, “natural” and “native” are used interchangeably and “NKG2D” and “NKG2D receptor” are used interchangeably. The term “antibody” herein is used in the broadest sense and specifically covers monoclonal antibodies, multispecific antibodies (e.g. bispecific antibodies), and antibody fragments, so long as they exhibit the desired biological activity. “Antibody fragments” comprise a portion of an intact antibody, preferably comprising the antigen binding region thereof. Examples of antibody fragments include Fab, Fab′, F(ab′)2, and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules; and multi-specific antibodies formed from antibody fragment(s).
The term “comprising,” which is used interchangeably with “including,” “containing,” or “characterized by,” is inclusive or open-ended language and does not exclude additional, unrecited elements or method steps. The phrase “consisting of” excludes any element, step, or ingredient not specified in the claim. The phrase “consisting essentially of” limits the scope of a claim to the specified materials or steps and those that do not materially affect the basic and novel characteristics of the claimed invention. The present disclosure contemplates embodiments of the invention compositions and methods corresponding to the scope of each of these phrases. Thus, a composition or method comprising recited elements or steps contemplates particular embodiments in which the composition or method consists essentially of or consists of those elements or steps.
All references cited herein are hereby incorporated by reference in their entireties, whether previously specifically incorporated or not. As used herein, the terms “a”, “an”, and “any” are each intended to include both the singular and plural forms.
Having now fully described the invention, it will be appreciated by those skilled in the art that the same can be performed within a wide range of equivalent parameters, concentrations, and conditions without departing from the spirit and scope of the invention and without undue experimentation. While this invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications. This application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and may be applied to the essential features hereinbefore set forth.
As specific examples, we synthesized a 1126 bp and a 1144 bp DNA fragment (SEQ ID NO:1 and 2, respectively) encoding in the following order: the α3 domain of human MICA (as a parent peptide) amino acid 182 to amino acid 194 (the beginning of loop 1 of the α3 domain), no spacer or a GGS amino acid spacer region (SR), an iFv peptide based on the structure of a Fibroblast Growth Factor Receptor 3 (FGFR3)-binding antibody (MAbR3; Qing, J., Du, X., Chen, Y., Chan, P., Li, H., Wu, P., Marsters, S., Stawicki, S., Tien, J., Totpal, K., Ross, S., Stinson, S., Dornan, D., French, D., Wang, Q. R., Stephan, J. P., Wu, Y., Wiesmann, C., and Ashkenazi, A. (2009) Antibody-based targeting of FGFR3 in bladder carcinoma and t(4;14)-positive multiple myeloma in mice, The Journal of clinical investigation 119, 1216-1229.), no spacer or another GGS spacer region, the distal portion of loop 1 of the α3 domain starting at amino acid 196 and including the remaining carboxy-terminal portion of the α3 domain to amino acid 276 of a soluble MICA molecule. Each synthetic, double stranded DNA polynucleotide then encoded a polypeptide that contained 6 CDRs in the form of an iFv inserted into loop 1 of the α3 domain of MICA.
This iFv peptide itself (SEQ ID NO.:3), encoded by SEQ ID NO.:4, contained two identical, typical linker regions (LR) corresponding to residues GGSSRSSSSGGGGSGGGG (SEQ ID NO.:5) (Andris-Widhopf, J., Steinberger, P., Fuller, R., Rader, C., and Barbas, C. F., 3rd. (2011) Generation of human Fab antibody libraries: PCR amplification and assembly of light- and heavy-chain coding sequences, Cold Spring Harbor protocols 2011). One LR joined the C-terminus of VL to the N-terminus of the VH domain, and the second LR joined the C-terminus of the VH domain to the N-terminus of VL. Conceptually this new structure is the continuous or “circular” peptide referred to above and contained 6 CDRs of the starting Fv. The variable VL chain of the antibody was effectively split within the loop region between beta-strands 1 and 2 (S1 and S2) and thereby created a new N-terminal segment (VLN) and a new C-terminal segment (VLC) with an accompanying pair of new, non-natural C- and N-termini, respectively,
To produce the soluble MICA proteins with a heterologous iFv peptide inserted into the α3 domain we generated a baculoviral expression vector to accommodate the DNA sequences (SEQ ID NOs:1 and 2) encoding the α3-iFv.1 (SEQ ID NO.:6) and α3-iFv.2 (SEQ ID NO.:7), respectively. The DNA fragments were amplified by PCR, digested using NcoI and EcoRI restriction enzymes, and subcloned into the baculoviral expression vector, SW403, replacing the wild-type α3 domain. SW403 is a baculoviral expression vector derived from pVL1393 (Invitrogen, Inc.) into which wild-type sMICA (residues 1-276) had previously been cloned using 5′ BamHI and 3′ EcoRI sites. The new expression vector was co-transfected with baculoviral DNA into SF9 insect cells, and baculovirus was grown for two amplification cycles and used to express the His-tagged MICA-α3-iFv proteins in T.ni insect cells according to manufacturer's protocol (Invitrogen). The expression was carried out in a 100 mL volume for three days and the growth medium was harvested for purification of the secreted soluble protein using Ni-affinity chromatography. Monomeric MICA-α3-iFv was purified to >90% purity with the expected molecular weight of 60.9 kDa as determined by SDS-PAGE. Functional characterization was carried out using binding ELISAs and in vitro target cell killing assays.
The purified MICA-α3-iFv proteins were tested in a FGFR3-binding ELISA to confirm simultaneous binding to the FGFR3 target and the NKG2D receptor. FGFR3 in phosphate buffered saline (PBS) was coated onto Maxisorp plates at 2 ug/ml concentration. Each MICA protein was titrated, allowed to bind FGFR3 for 1 hour, and washed to remove unbound sMICA protein. Bound MICA-α3-iFv protein was detected using NKG2D-Fc and anti-Fc-HRP conjugate.
We tested and compared the thermal stability of sMICA-α3-iFv.2 to that of sMICA-scFv. Both proteins were subjected for 1 hr to increasing temperatures from 60-90° C. and then allowed to equilibrate to room temperature for 1 hour before being assayed for binding properties by ELISA. The results in
The ability of MICA-α3-iFv to redirect NK cell-mediated lysis of FGFR3-expressing target cells was demonstrated in vitro in a calcein-release assay. The Natural Killer (NK) cell line, NKL, was co-cultured with calcein-loaded P815 target cells ectopically expressing FGFR3. The results in
The applicability of the iFv format to other antibody variable domains was demonstrated by similarly constructing an α3-iFv.3 (SEQ ID NO.:8), which contained an iFv derived from a CD20-specific antibody (Du, J., Wang, H., Zhong, C., Peng, B., Zhang, M., Li, B., Huo, S., Guo, Y., and Ding, J. (2007) Structural basis for recognition of CD20 by therapeutic antibody Rituximab, The Journal of biological chemistry 282, 15073-15080).
Human proteins designated ULBP-1 through ULBP-6 are, like MICA and MICB, naturally occurring, stress-induced, cell surface ligands that bind NKG2D receptors on and activate human NK cells and certain T-cells (15; Cerwenka A, Lanier L L (2004). NKG2D ligands: unconventional MHC class I-like molecules exploited by viruses and cancer. Tissue Antigens 61 (5): 335-43. doi:10.1034/j.1399-0039.2003.00070.x. PMID 12753652). In addition, the cowpox virus protein OMCP is a secreted domain that like the α1-α2 domain of MIC proteins binds NKG2D. OMCP exhibits a very high affinity for NKG2D, apparently in order to block NKG2D's recognition of the natural stress ligands induced by the virus on its infected host cell (Eric Lazear, Lance W. Peterson, Chris A. Nelson, David H. Fremont. J Virol. 2013 January; 87(2): 840-850. doi: 10.1128/JVI.01948-12). While the ULBPs and OMCP are considered NKG2D ligands (NKG2DLs) that share the canonical α1-α2 domain structure, the sequence homology with MICA α1-α2 is less than 27%, and they all naturally lack an α3 domain for tethering targeting domains. We constructed a series of non-natural ULB and OMCP proteins by attaching the heterologous polypeptides that specifically targeted and killed FGFR3-expressing cells as the result of fusing to each of ULBP-1, ULBP-2, ULBP-3, ULBP-4, ULBP-6 and OMCP, a modified α3 domain of MICA into which a targeting iFv had been inserted. In addition, we modified the α1-α2 domain of MICA to enhance the affinity of α1-α2 domain for NKG2D and then attached to the modified α1-α2 domains heterologous molecules such as polypeptides. To produce the proteins consisting of ULBP and OMCP α1-α2 domains attached to modified α3-iFv domains we generated a baculoviral expression vector to accommodate the DNA fragments (SEQ ID NOs:9-14) that encoded the different α1-α2 domains of ULBP-1, ULBP-2, ULBP-3, ULBP-4, ULBP-6, and OMCP (SEQ ID NOs:15-20, respectively). The DNA fragments were amplified by PCR, digested using BlpI and NcoI restriction enzymes, and individually subcloned into the baculoviral expression vector, KLM44, replacing the MICA α1-α2 domain. KLM44 was a baculoviral expression vector derived from SW403 into which MICA-α3-iFv.2 had previously been cloned (example 1). The new NKG2DL-α3-iFv.2 constructs, containing the ULBPs and OMCP α1-α2 domain fusions to α3-iFv.2 (ULBP1-α3-iFv.2, ULBP2-α3-iFv.2, ULBP3-α3-iFv.2, ULBP4-α3-iFv.2, ULBP6-α3-iFv.2, and OMCP-α3-iFv.2; SEQ ID NO.:21-26, respectively), were co-transfected with baculoviral DNA into SF9 insect cells. Baculovirus was grown for two amplification cycles and used to express these His-tagged NKG2DL-α3-iFv.2 proteins in T.ni insect cells according to manufacturer's protocol (Invitrogen). The expression was carried out in a 100 mL volume for three days and the growth medium was harvested for purification of the secreted soluble protein using Ni-affinity chromatography. Monomeric proteins of correct molecular weight were purified to >90% purity as determined by SDS-PAGE. Functional characterization was carried out using binding ELISAs and in vitro target cell killing assays.
The 6 purified NKG2DL-α3-iFv.2 proteins were tested in a FGFR3-binding ELISA to confirm simultaneous binding to the FGFR3 target and the NKG2D receptor. FGFR3 in phosphate buffered saline (PBS) was coated onto Maxisorp plates at 2 ug/ml concentration. Each NKG2DL-α3-iFv.2 protein was titrated, allowed to bind FGFR3 for 1 hour, and washed to remove unbound protein. The bound NKG2DL-α3-iFv.2 protein was detected using NKG2D-Fc and anti-Fc-HRP conjugate.
The ability of the NKG2DL-α3-iFv.2 proteins to redirect NK cell-mediated lysis of FGFR3-expressing target cells was demonstrated in vitro in a calcein-release assay. The Natural Killer (NK) cell line, NKL, was co-cultured with calcein-loaded P815 target cells ectopically expressing FGFR3. The results in
These are examples of attaching polypeptides to NKG2DLs which were modified to significantly enhance their binding affinity to the human NKG2D receptor. The α1-α2 domain of MIC proteins is an NKG2DL for the NKG2D receptor. This affinity is sufficient for physiologic activation of NK cells and stimulating lysis of cells expressing native full-length MIC proteins irreversibly tethered to the two-dimensional plasma membrane surface of a “target cell” (Bauer S, Groh V, Wu J, Steinle A, Phillips J H, Lanier L L, Spies T., Science. 1999 Jul. 30; 285(5428):727-9.). However, because engineered soluble MIC proteins of the instant invention reversibly bind specific target antigens on the surface of a target cell, the binding affinity of the engineered soluble MIC protein to NKG2D will directly affect the stability of the soluble MIC-dependent complex formed between NK cells and cells expressing target antigens. Especially if the affinity between sMICA and NKG2D is increased by a substantially slower dissociation rate or off-rate of the modified sMICA from NKG2D, the NK cell-based killing would be expected to be greater at lower densities of soluble MIC molecules bound to a target cell. Prior to the instant invention there had not been identified any α1-α2 mutations that alter the killing activity of soluble MIC proteins or significantly reduce the binding off-rate to enhance affinity of MIC proteins to NKG2D. A computational design effort showed that three mutations in the α1-α2 domain of wild-type MICA: N69W, K152E, and K154D (WED-MICA) in combination can moderately affect NKG2D binding affinity by affecting the stability of unbound MICA and thereby its association rate or on-rate of binding to NKG2D (Lengyel C S, Willis L J, Mann P, Baker D, Kortemme T, Strong R K, McFarland B J. J Biol Chem. 2007 Oct. 19; 282(42):30658-66. Epub 2007 Aug. 8); Subsequent extensive computational design work by the same group scanning by iterative calculations 22 amino acid positions of MICA theoretically in contact with NKG2D, according to the published structural descriptions (Li P, Morris D L, Willcox B E, Steinle A, Spies T, Strong R K., Nat Immunol. 2001 May; 2(5):443-451), showed experimentally that when combined with the earlier designed 3 changes, further rational, iterative computational design of MICA qualitatively changed its affinity for NKG2D from weak (Kd ˜2.5 μM) to moderately tight (Kd=51 nM) with a total of seven combined mutations (Henager, Samuel H., Melissa A. Hale, Nicholas J. Maurice, Erin C. Dunnington, Carter J. Swanson, Megan J. Peterson, Joseph J. Ban, David J. Culpepper, Luke D. Davies, Lisa K. Sanders, and Benjamin J. McFarland, 2102, Combining different design strategies for rational affinity maturation of the MICA-NKG2D interface. Protein Science 21:1396-1402). In contrast, the experimental approach described in the instant invention experimentally selected amino acid modifications of MICA that slowed the off-rate between the α1-α2 domain of MICA and NKG2D, commencing with a MICA stabilized by the 3 WED changes of Lengyel et al (Lengyel C S, Willis L J, Mann P, Baker D, Kortemme T, Strong R K, McFarland B J., J Biol Chem. 2007 Oct. 19; 282(42):30658-66. Epub 2007 Aug. 8).
This example of the instant invention relates to modifying the NKG2D binding affinity of soluble MIC proteins through engineering specific mutations at selected amino acid positions within the α1-α2 domain that influence the off-rate binding kinetics and thereby alter the NK cell-mediated killing activity of the invented non-natural, targeted MIC molecules.
To engineer soluble non-natural α1-α2 domains with altered affinity to NKG2D 57 residues in the α1-α2 domain were chosen for extensive mutagenesis (
We synthesized DNA polynucleotides (SEQ ID NOs. 27-30) encoding the α1-α2 domains of 4 representative variants 15, 16, 17, 18 that contained different combinations of specific discovered mutations (Table 2).
To the NKG2DLs in the above example, we directly attached heterologous molecules such as a polypeptide to each of these 4 modified α1-α2 NKG2DLs using a linker peptide. Four His-tagged proteins (SEQ ID NOs.: 31-34) consisting of modified NKG2DLs with attached heterologous molecules were expressed in insect cells and purified to characterize their NKG2D binding affinities and kinetic binding parameters. Using a competitive binding ELISA, we determined the relative NKG2D binding affinities of the 4 modified α1-α2 variants. A soluble wild type (WT) NKG2DL, sMICA protein, was coated in all wells of a maxisorp ELISA plate to provide a binding partner for the human NKG2D-Fc reagent. Solutions of the four α1-α2 variants as well as WT and WED-α1-α2 domains (SEQ ID NO.: 35) were titrated in the ELISA wells and allowed to competitively inhibit 2 nM human NKG2D-Fc binding to the WT sMICA coated on the plate. The level of human NKG2D-Fc that bound to the WT NKG2DL on the plate was detected using an anti-Fc-HRP antibody.
Importantly, the relative IC50 differences also translated to better binding to murine NKG2D-Fc (
In order to understand the kinetic basis for the altered affinities, both the on-rates and off-rates for the α1-α2 variant NKG2DLs binding to surface coated biotinylated human NKG2D were measured using biolayer interferometry (Octet) at 100 nM of each of the modified α1-α2 proteins. Consistent with results from the IC50 ELISAs, variants 16, 17 and 18 each displayed significant reductions in the off-rate (18-fold relative to WT), which is largely responsible for the affinity increase (˜30-fold relative to WT α1-α2)(
The ability of the α1-α2 affinity variants to redirect NK cell-mediated lysis of FGFR3-expressing target cells was demonstrated in vitro in a calcein-release assay. The human Natural Killer (NK) cell line, NKL, was co-cultured with calcein-loaded P815 target cells ectopically expressing FGFR3 and titrated with soluble modified MIC proteins. The results in
These α1-α2 NKG2DL affinity variants 15, 16, 17, and 18 enhanced the binding affinity of the attached polypeptide to the NKG2D receptor and thereby enhanced NK cell-mediated lysis of targeted cells,
The α1-α2 domain of MICA and other NKG2D ligands bind the NKG2D receptor at a known specific site (Li et al 2001; Benjamin J. McFarland, Tanja Kortemme, Shuyuarn F. Yu, David Baker, and Roland K. Strong. Symmetry Recognizing Asymmetry: Analysis of the Interactions between the C-Type Lectin-like Immunoreceptor NKG2D and MHC Class I-like Ligands. Structure, Vol. 11, 411-422, April, 2003) and drive activation of the NKG2D receptor-bearing immune cell, which consequentially kills target cells displaying MICA or other ligands. We utilized phage display to engineer non-natural α1-α2 domains of MICA by extensive mutagenesis at 57 specific sites likely to be involved in binding to NKG2D (
Table 4. The non-natural α1-α2 domain variants selected for increased affinity to natural NKG2D receptor and the MICwed variant described previously (McFarland et al., 2003). The positions of the indicated amino acid changes referenced to the residue positions in SEQ ID NO.: 42 and the common names of the variants and their SEQ ID NOs are provided.
The DNA polynucleotides encoding the 8 variant α1-α2 domains were amplified with PCR primers (SEQ ID NO.s: 63-64). Using Blp1 and Sap1 restriction enzymes, each was subcloned into a His-tagged α1-α2-α3-Fv fusion expression construct (SEQ ID NO.:65) to replace the sequence encoding the natural (wt) α1-α2 sequences with the mutated α1-α2 sequences. The 9 fusion proteins (SEQ ID NO.s: 66-74) were expressed in 293 cells (Expi293™ Expression System, Life Technologies, Thermo Fisher, Inc.) and affinity purified using Ni-affinity chromatography (HisTrap HP, GE Healthcare Life Sciences).
To construct NKG2D receptor proteins, we synthesized DNA encoding the extracellular domain (“ectodomain”) of the wild type receptor (SEQ ID No.:75) and used PCR primers (SEQ ID NO.s: 76-77) and XbaI and BamHI sites to clone the synthetic DNA into an N-terminal His-avitag expression vector (SEQ ID NO.: 78). The His-avitag-natural NKG2D (SEQ ID NO.:79) was expressed transiently in 293 cells and purified using Ni-affinity chromatography. Following purification, the NKG2D proteins were site-specifically biotinylated using BirA to attach a biotin group onto the avitag sequence (BirA biotin-protein ligase standard reaction kit, Avidity, LLC, Aurora, Colo.).
In order to characterize and compare the kinetic binding parameters of the natural and 8 variant α1-α2 domains to natural NKG2D, we measured their binding to surface coated biotinylated natural NKG2D ectodomain using biolayer interferometry (Octet) at 100 nM of each of the α1-α2-α3-Fv fusion proteins. Results are displayed in Table 5.
Table 5: Kinetic parameters of the wild type (wt or natural) and 8 variant α1-α2 domain α3-Fv fusion proteins binding to the natural NKG2D. MICwed-Fv was here studied in 2 separate Octet analyses, once comparing to the wt α1-α2 domain α3-Fv fusion and the other compared to 7 other non-natural α1-α2 domain α3-Fv fusions. The common names of each α1-α2 domain variants and the SEQ ID NO.s of their α3-Fv fusion proteins are provided along with their affinity (Kd) values in molar (M), on rates (kon) in inverse molar-seconds (1/Ms), and dissociation- or off-rates (kdis) in inverse seconds.
As shown in Table 5, the selected α1-α2 domain mutations as fusions to heterologous polypeptides α3-Fv of SEQ ID NO.s: 68-74 increased the α1-α2 domain affinity for natural NKG2D through significant reduction of the off-rate. The off-rates ranged from 20- to more than 100-fold slower than those of wt (SEQ ID NO.:66) and the previously described MICwed α1-α2 domain variant (SEQ ID NO.:67).
In this example of the instant invention, we further demonstrated as described below, that a non-natural α1-α2 domain (DSM25, SEQ ID NO.:57, Table 4) that as an α1-α2-α3-Fv fusion had high affinity for and very slow off-rate from natural NKG2D (Table 2; SEQ ID NO.:69), exhibited tight binding affinity to a non-natural NKG2D receptor containing a specific mutation that abolished its binding to natural NKG2D ligands. It had been demonstrated by others that mutations at tyrosine 152 and tyrosine 199 in human NKG2D, the equivalent of positions 73 and 120 of the NKG2D ectodomain (SEQ ID NO.:75 and
To construct the non-natural NKG2D receptor proteins, we used PCR primers (SEQ ID NO.s:76-77) to clone the DNA encoding the natural NKG2D ectodomain (SEQ ID NO.:75) and insert it into the N-terminal His-avitag expression vector SEQ ID NO.:78 to produce His-avitag-NKG2D (SEQ ID NO.:79). Site-directed mutagenesis was performed on the natural NKG2D ectodomain DNA construct to introduce Y152A, Y199A, or Y152A plus Y199A mutations and created three non-natural variants of human NKG2D (SEQ ID NO.s: 80-82, respectively). The natural NKG2D and 3 non-natural NKG2D mutants with His-avitags were expressed transiently in 293 cells and purified using Ni-affinity chromatography. Following purification, the NKG2D proteins were site-specifically biotinylated using BirA to attach a biotin group onto the avitag sequence (BirA biotin-protein ligase standard reaction kit, Avidity, LLC, Aurora, Colo.).
To generate fusions of α3-Fc heterologous polypeptides to α1-α2 domain of MICwed (SEQ ID NO.:55) and DSM25 α1-α2 domain (SEQ ID NO.: 57) the DNA polynucleotides encoding the α1-α2 domains were amplified using PCR primers (SEQ ID NO.s: 63-64). Using XbaI and NcoI restriction enzymes, each was subcloned into a α1-α2-α3-Fc fusion expression construct (SEQ ID NO.:83) to replace the sequence encoding the natural (wt) α1-α2 sequences with the mutated α1-α2 sequences. The 3 fusion proteins, MICA-Fc (SEQ ID NO.: 84), MICwed-Fc (SEQ ID NO.: 85), and MICv25-Fc (SEQ ID NO.: 86) were expressed in 293 cells (Expi293™ Expression System, Life Technologies, Thermo Fisher, Inc.) and affinity purified using Protein A affinity chromatography (cat. no. 20334, Pierce Biotechnology, Rockford, Ill.).
In addition to purifying the above 3 Fc-fusion proteins NKG2D ligand-Fc fusion proteins MICB-Fc, ULBP1-Fc, ULBP2-Fc, ULBP3-Fc, and ULBP4-Fc were purchased from R&D Systems, Inc. (Minneapolis, Minn.). Binding of the different α1-α2 domain-Fc fusions to both natural and non-natural NKG2D ectodomain proteins was analyzed using a plate-based ELISA method. All of the natural and non-natural α1-α2 domain-Fc fusions were coated overnight at 4° C. onto separate wells of Maxisorp 96 well plates using a coating concentration of 2 μg/ml in phosphate-buffered saline (PBS). The plates were washed 3-times in PBS/0.05% Tween20 at 20-22° C., and blocked with 0.5% bovine serum albumin for 2 hours. The biotinylated natural and non-natural NKG2D receptor proteins were titrated against the plate-bound NKG2D ligands for 2 hours at 20-22° C., washed 3 times with PBS/0.05% Tween20 at 20-22° C., and the bound NKG2D proteins subsequently detected using a streptavidin-HRP secondary detection step and developed with 1-Step Ultra TMB Elisa. The natural form of the ectodomain of NKG2D (SEQ ID NO.:75) was capable of binding all α1-α2 domain-Fc fusions tested (
While the binding specificity of natural NKG2D shows preference for the high affinity non-natural ligands, its potent binding to the natural NKG2D ligands, which are present on certain healthy tissues and many stressed tissues, creates an extreme risk for toxicity using current NKG2D CAR approaches (VanSeggelen et al. 2015). The Y152A non-natural NKG2D receptor specifically bound to only the protein comprised of the high affinity non-natural α1-α2 domain engineered for a markedly decreased off-rate. This prototypical example highlighted the ability of non-natural α1-α2 domains to bind non-natural NKG2D receptors, thus provided for selective control of non-natural NKG2D CARs using bispecific proteins containing the invented non-natural α1-α2 domain of NKG2D ligands.
This embodiment relates to additional α1-α2 NKG2DL affinity variants derived through engineering the α1-α2 domains of ULBP proteins. ULBP proteins contain α1-α2 domains, which are NKG2D ligands capable of binding to the NKG2D receptor (Cerwenka A, Lanier L L (2004). NKG2D ligands: unconventional MHC class I-like molecules exploited by viruses and cancer. Tissue Antigens 61 (5): 335-43. doi:10.1034/j.1399-0039.2003.00070.x. PMID 12753652). This affinity of NKG2D binding is sufficient for physiologic activation of NK cells and stimulating lysis of cells expressing native full-length ULBP proteins naturally and irreversibly tethered to the two-dimensional plasma membrane surface of a “target cell” (Cerwenka A, Lanier L L (2004). NKG2D ligands: unconventional MHC class I-like molecules exploited by viruses and cancer. Tissue Antigens 61 (5): 335-43. doi:10.1034/j.1399-0039.2003.00070.x. PMID 12753652). However, because engineered soluble α1-α2 domains fused to heterologous polypeptides in certain embodiments of the instant invention reversibly bind specific target antigens on the surface of a target cell, the binding affinity of the engineered ULBP α1-α2 domains to NKG2D will directly affect the stability of the artificial synapse formed between NK cells and cells expressing target antigens, as already shown by engineered soluble MIC proteins (Examples 2-4). In order to diversify the repertoire of engineered non-natural α1-α2 domains as NKG2D ligands, ULBP proteins were used as a substrate or starting point for phage display-based engineering of their NKG2D binding affinity. Despite the structural homology observed between ULBPs and MICA (Radaev, S., Rostro, B., Brooks, A G., Colonna, M., Sun, P D. (2001) Conformational plasticity revealed by the cocrystal structure of NKG2D and its class I MHC-like Ligand ULBP3. Immunity 15, 1039-49.), the sequence homology is <50% for the ULBP α1-α2 domains relative to MICA. Thus, we sought the identities of codon positions in ULBP α1-α2 domains that improve NKG2D binding affinity.
To engineer soluble, non-natural α1-α2 domains from ULBP proteins, ULBP2 and ULBP3 were chosen for phage display and selection of mutants with high affinity NKG2D binding. Sixty amino acid positions in the α1-α2 domain of ULBP2 (SEQ ID NO: 16), and thirty-six amino acid positions in the α1-α2 domain of ULBP3 (SEQ ID NO: 17), were chosen for extensive mutagenesis. In addition, conservative cysteine-to-serine mutations were made at C8S in ULBP2 (SEQ ID NO: 16) and C103S in ULBP3 (SEQ ID NO: 17) eliminating unpaired free cysteines in order to increase stability and function of the NKG2D ligands with attached polypeptides as well as to improve phage panning processes. Synthetic DNA libraries coding for these cysteine to serine modified α1-α2 domains, and containing NNK mutagenic codons at each of the selected amino acid positions, were synthesized, individually; cloned as fusions to the pIII minor coat protein of M13 phage; and phage particles displaying the mutagenized α1-α2 ULBP2 or ULBP3 variants were produced in SS320 E. coli cells according to standard methodologies (Andris-Widhopf, J., Steinberger, P., Fuller, R., Rader, C., and Barbas, C. F., 3rd. (2011). Generation of human Fab antibody libraries: PCR amplification and assembly of light- and heavy-chain coding sequences, Cold Spring Harbor protocols 2011). The α1-α2 phage display libraries were sorted for increased binding affinity to NKG2D using human NKG2D-Fc as the target protein, and cycled through iterative rounds of intentionally prolonged binding, prolonged washing, and eluting of the phage clones in order to select high affinity variants enriched for slow dissociation- or off-rates. For ULBP2, specific amino acid mutations were found at high frequencies at positions R80, V151, V152, and A153 in α1-α2, and were identified as preferred amino acid substitutions with enhanced NKG2D-binding affinity (
For ULBP3, specific amino acid mutations were found at high frequencies in different locations relative to ULBP2. Positions R162 and K165 in the α1-α2 domain of ULBP3 contained specific mutations that were identified as preferred amino acid substitutions with enhanced NKG2D-binding affinity (
The following example relates to attaching antibody polypeptides to NKG2DLs which were modified to significantly enhance their binding affinity to the human and murine NKG2D receptor. The α1-α2 domain of each ULBP protein is a natural ligand for the NKG2D receptor, i.e. an NKG2DL. Antibodies are highly stable glycoproteins made up of two large heavy chains and two small light chains (
To generate engineered α1-α2 domain fusions to antibodies, the DNA sequences encoding the C8S modified α1-α2 domains of ULBP2 (SEQ ID NO.: 16) variants R80W and V151D (SEQ ID NO.s: 87 and 88, respectively) and the C103S modified α1-α2 domain of ULBP3 (SEQ ID NO.: 17) variant R162G (SEQ ID NO.: 89) were synthesized and cloned as C-terminal fusions to the heavy chain sequence from the Her2-specific antibody (Carter, P., Presta, L., Gorman, C M., Ridgway, J B., Henner, D., Wong, W L., Rowland, A M., Kotts, C., Carver, M E., Shepard, H M. (1992) Proc Natl Acad Sci 15, 4285-9.). The resulting fusions were cloned into the mammalian expression vector pD2509 and expressed with the light chain of the parent antibody as paired full IgG antibodies. Transient expressions were carried out in HEK293 cells using the Expi293 expression system according to the manufacturer's protocol (Life Technologies), and purified using standard protein A affinity chromatography. Binding ELISAs performed on the ULBP2 and ULBP3 α1-α2 antibody heavy chain fusions demonstrated the modified ULBP2 fusions (HC_R80W and HC_V151D) and UBLP3 fusion (HC_R162G) bound with higher affinity to human NKG2D relative to their respective natural α1-α2 domains fused to the same heavy chain (
To characterize the target cell killing properties of the modified ULBP antibody fusions, the human Natural Killer (NK) cell line, NKL, was co-cultured with calcein-loaded SKBR3 target cells expressing Her2 and titrated with the engineered antibody fusion proteins. The results in
Means to selectively control CAR-T cell therapies are highly sought after to mitigate toxicity and improve efficacy against tumors (Gill and June, op cit). Previous attempts have been made to develop CARs using the ectodomain of CD16 which can then be engaged through the Fc domain of therapeutic monoclonal antibodies, allowing for antibody-based control of CAR-T targeting (Chang et al., op cit. However, CD16-based CAR-T cells can recognize all endogenous antibody molecules in blood and tissues, and the therapeutic antibodies used to control these cells will encounter interference from endogenous CD16 receptors on NK cells. Both of these features create problems with off-tumor toxicity and poor pharmacokinetics, respectively.
To address these issues we have engineered non-natural NKG2D CAR-T cells which lack binding to all natural NKG2D ligands and can be controlled through the binding of high-affinity non-natural α1-α2 domains as demonstrated in Example 4. An additional requirement is for the non-natural α1-α2 domains to retain high affinity for non-natural NKG2D, and avoid binding to natural NKG2D domains. Thus, engineered α1-α2 domains that exhibit strong selectivity for non-natural NKG2D receptors over natural NKG2D represent an ideal system for selective control of non-natural NKG2D CAR receptors, or any receptor or protein fused to non-natural NKG2D ectodomains that can be selectively engaged by non-natural α1-α2 domains.
We employed phage display to engineer orthogonal non-natural α1-α2 domains that exhibit selective binding to the Y152A NKG2D receptor. As a starting point, three non-natural α1-α2 domains with high affinity for natural NKG2D were selected as parent domains for further mutagenesis and screening by phage display. Synthetic DNA libraries were generated for the individual α1-α2 domain variants DSM25, ULBP2 R80W, and ULBP3 R162G (SEQ ID NO.s: 57, 87, and 89), whereby codons of amino acid residues that in the bound state are positioned in close proximity to the Y152 position on the NKG2D receptor were replaced with NNK codons. DSM 25 libraries consisted of NNK positions at residues 71-75 and 155-159, ULBP2 R80W libraries with NNK codons at positions 154-159, and ULBP3 R162G libraries with NNK codons at positions 155-159. Libraries were cloned as fusions to the pIII minor coat protein of M13 phage; and phage particles displaying the mutagenized α1-α2 domain variants were produced in SS320 E. coli cells according to standard methodologies (Andris-Widhopf, J., Steinberger, P., Fuller, R., Rader, C., and Barbas, C. F., 3rd. (2011). Generation of human Fab antibody libraries: PCR amplification and assembly of light- and heavy-chain coding sequences, Cold Spring Harbor protocols 2011). The α1-α2 phage display libraries were sorted for high binding affinity to the non-natural Y152A NKG2D receptor by selectively capturing phage clones bound to biotinylated Y152A NKG2D-Fc protein in the presence of non-biotinylated natural NKG2D-Fc competitor protein. Selective clones were enriched by cycling through multiple rounds of competitive selection with increasing concentrations of non-biotinylated natural NKG2D-Fc.
After four rounds of selection, phage clones were sequenced to identify specific mutations within the NNK mutagenic regions. Tables 8, 9, and 10 show the selected amino acid residues that were found to be prevalent for each α1-α2 domain resulting from the Y152A NKG2D selective screening.
To confirm the phage clones displayed proper selective binding, phages were produced for the individual clones: MICA25.17, MICA25.18, ULBP2.S1, ULBP2.S2, ULBP2.S3, ULBP3.S1 and ULBP3.S2 (SEQ ID NOs: 90, 91, 92, 93, 94, 95, and 96 respectively) and titrated against Y152A or natural NKG2D in binding ELISAs.
To confirm the Y152A-selective α1-α2 domain variants retain specific binding properties within the context of antibody fusions, we cloned MICA25.17 and ULBP2.S3 as C-terminal fusions to the heavy chain of an FGFR3 specific antibody previously described (Qing et al, 2009. op cit; SEQ ID NO.s: 97 and 98, respectively). The resulting fusions were cloned into the mammalian expression vector pD2509 and co-expressed with the light chain of the parent antibody as paired full IgG antibodies (R3 HC25.17 and R3 HC.U2S3). Transient expressions were carried out in HEK293 cells using the Expi293 expression system according to the manufacturer's protocol (Life Technologies), and purified using standard protein-A affinity chromatography. ELISAs measuring the binding of R3 HC25.17 and R3 HC.U2S3 α1-α2 antibody heavy chain fusions to non-natural Y152A NKG2D and to natural NKG2D demonstrated their significantly greater binding affinity toward Y152A NKG2D relative to the natural NKG2D (
To demonstrate selective control of CAR-T cells constructed with a chimeric receptor deploying the non-natural NKG2D ectodomain, we constructed CARs with either the natural NKG2D or the non-natural Y152A NKG2D ectodomains based on previous work using 4-1BB/CD3zeta CAR constructs (Campana U.S. Pat. No. 8,399,645) fusing the respective NKG2D ectodomains to the CD8 hinge region (
| Number | Date | Country | |
|---|---|---|---|
| 62200949 | Aug 2015 | US |
