Patent Application
20230355764
This application relates to downregulation of Membrane-Bound Proteins (MBPs), and in particular, to downregulation of Membrane-Bound Proteins by Receptor TAC Technology. The present application provides novel fusion proteins, nucleic acids encoding said proteins, vectors comprising said nucleic acids, compositions comprising said nucleic acids or vectors, host cells comprising said nucleic acids, vectors or compositions or pharmaceutical compositions. The present application also provides methods of reducing (down regulating) a target membrane-bound protein (MBP) level in a cell, methods of producing a cell having a reduced target membrane-bound protein level, or methods of treating a disease, or methods of reducing or preventing GvHD in a subject associated with the administration of one or more CAR T-cells to the subject.
The initial success of Chimeric Antigen Receptor (CAR) T cell therapy in the treatment of hematological malignancies has heralded rapid growth in a new area of immunotherapeutic treatment strategies (Seledtsov, V. I., Goncharov et al., Human Vaccines and Immunotherapeutics 11, 851-869 (2015)). CARs are designer receptors typically with modular activation domains derived from the CD3ζ ITAM motifs and a costimulatory domain, for example from 4-1BB or CD28 (Weinkove, R., George, P., et al., Clin. Transl. Immunol. 8, e1049 (2019)). Target recognition by these receptors is usually provided through a scFv domain on the extracellular terminal of the CAR, though alternative approaches have also been designed (Kuhn, N. F. et al. Cancer Cell 35, 473-488.e6 (2019)).
Two approved CD19 CAR-T drugs (Kymriah and Yescarta) as well as Abecma (BCMA CAR-T) are all autologous products. They are made from each individual patient's own T cells. While autologous CD19 CAR-T demonstrated unprecedented efficacy in refractory and relapse cancer patients, they do represent significant challenges moving forward: they require complex manufacturing; there are usually significant variations in the quality of CAR-T cells due to patient variations, and this results in variations in the quality of the product and even production failure (with failure rates up to 14%) (Bersenev, A. Transfusion (2017). doi:10.1111/trf.14110), (Dai, X., Mei, et al., Biotechnology Journal (2019)). Moreover, the lead time required to make the product is around 3-4 weeks, so patients who cannot wait this long due to disease progression will not be able to enter clinical trials; the cost is also too high to be affordable for the majority of the patient population. The cost per patient is $475,000 for Kymriah and $373,000 for Yescarta.
Allogeneic (off-the-shelf) CAR-T on the other hand will offer many advantages. The cells can be batch-prepared in advance and can supply thousands of doses; the product is frozen, stored, and distributed for off-the-shelf use; the CAR-T cells will be prepared from healthy donors with better cell quality; the cells will be of uniform quality per batch; there will be minimal lead time for patients; and the cost of goods can be significantly reduced (Rafiq, S. et, al., Nature Reviews Clinical Oncology (2020)), (Depil, S. et al., Nature Reviews Drug Discovery (2020)).
Currently there are several ways to prepare allogeneic product that will not cause Graft versus Host Disease (GvHD) in patients: they can be prepared by gene editing technology such as CRISPR (clustered regularly interspaced short palindromic repeats)-mediated TCR knockdown, or they can be prepared through siRNA down regulation of TCR, or they can be prepared with cells that naturally do not trigger GvHD such as cord blood or PBMC-derived NK cells (Li, Y et al., Cell Stem Cell (2018)), NK92 cell line, or gamma delta T cells etc. (Marcus, A. et al., Expert Opinion on Biological Therapy (2014)), (Depil, S. et al., Nature Reviews Drug Discovery (2020)), (Themeli, M., Rivière et al., Cell Stem Cell (2015)), (Rezvani, K. et al., Molecular Therapy (2017)).
The major challenge with gene editing technology is that there is always a risk of off-target modification. The rate of off-target modification can be as high as 50% (Zhang, X. H. et al., Molecular Therapy—Nucleic Acids (2015)), which can lead to unwanted mutations and would pose a significant risk for patients. Furthermore, the manufacturing process is complicated as it requires two steps of modifications: the first step is to transfect the CAR into T cells, the second step is to introduce CRISPR machinery to knockout TCR.
NK cells and gamma delta T cells on the other hand are associated with less persistence and proliferation in vivo, which will significantly affect their potency. They are also difficult to expand in vitro (Li, Y, Cell Stem Cell (2018)), (Rezvani, K., et al., Molecular Therapy (2017)), (Shimasaki, N. et al., Nature Reviews Drug Discovery (2020)).
How to downregulate Membrane-Bound Proteins (MBPs) in T cells or other cells while avoiding the above-mentioned defects is a problem that needs to be solved.
The present application provides novel fusion proteins, nucleic acids encoding said proteins, vectors comprising said nucleic acids, compositions comprising said nucleic acids or vectors, cells (e.g. host cells) comprising said nucleic acids, vectors or compositions or pharmaceutical compositions. The present application also provides methods of reducing (down regulating) a target membrane-bound protein (MBP) level in a cell, methods of producing a cell having a reduced target membrane-bound protein level, or methods of treating a disease, or methods of reducing or preventing GvHD in a subject associated with the administration of one or more CAR T-cells to the subject.
In the present application, downregulation of Membrane-Bound Proteins (MBPs) is achieved by degradation tag protein-mediated degradation, wherein the degradation tag protein comprises ubiquitin ligase and/or domains of the cell surface receptors that mediate degradation (e.g. IL2Rβ sub domain, L2Rβ jm domain). The tagging specificity or targeting specificity (or recognition specificity) of the MBPs to be degraded by the degradation tag protein (e.g. ubiquitin ligase or IL2Rβ) is mediated by an antibody (or antigen-binding fragment) of MBPs to be degraded (that is, antibody mediated substrate recognition), or mediated by subunits or structural domains of the membrane-bound protein or complex to be degraded that have a transmembrane domain (that is, transmembrane domain mediated substrate recognition). The technical solution of the present application can be applied to any targets on a cell surface, independent of cell type.
In one aspect, the fusion protein of the application comprises:
1) a first transmembrane-linking domain, which comprises a first transmembrane domain and a first linking protein;
In a specific embodiment, preferably, the MBP is a membrane-bound receptor; more preferably a mammalian origin membrane-bound receptor, most preferably a human membrane-bound receptor;
In another specific embodiment, preferably, the membrane-bound receptor is selected from one or more subunits or structural domains of CD3, TCR, CD5, CD7, PD-L1, and CD47 or a variant thereof;
In a specific embodiment, the fusion protein further comprises one or more of a hinge, or a P2A-GFP;
In another specific embodiment, the fusion protein comprises from N-terminal to C-terminal:
In a further specific embodiment, the fusion protein comprises from N-terminal to C-terminal:
In another aspect, the present application provides a nucleic acid, wherein the nucleic acid comprises a polynucleotide encoding a fusion protein of the present application.
In another aspect, the present application provides a vector, wherein the vector comprises a nucleic acid of the present application.
In a specific embodiment, preferably, an expression promoter for the fusion protein comprises CAG or EF1a;
In another aspect, the present application provides a composition, the composition comprising a nucleic acid or a vector of the present application.
In another aspect, the composition comprises a first nucleic acid and a second nucleic acid; or comprising a first vector having a first nucleic acid and a second vector having a second nucleic acid; or comprising a vector having a first nucleic acid and a second nucleic acid, wherein
In a specific embodiment, the fusion protein in the composition, which comprises a first nucleic acid and a second nucleic acid; or comprising a first vector having a first nucleic acid and a second vector having a second nucleic acid; or comprising a vector having a first nucleic acid and a second nucleic acid, is selected from one or more of the above a)-d) fusion proteins.
In a specific embodiment, the predetermined antigen is a tumor-related antigen.
In a further specific embodiment, the tumor-related antigen is selected from the following group: CEA, Claudin 18.2, GPC3, Receptor tyrosine kinase-like Orphan Receptor 1 (ROR1), CD38, CD19, CD20, CD22, BCMA, CAIX, CD446, CD133, EGFR, EGFRvIII, EpCam, GD2, EphA2, Her1, Her2, ICAM-1, IL13Ra2, Mesothelin, MUC1, MUC16, NKG2D, PSCA, NY-ESO-1, MART-1, WT1, MAGE-A10, MAGE-A3, MAGE-A4, EBV, NKG2D, PD1, PD-L1, CD25, IL-2, or CD3.
In a further specific embodiment, the tumor-related antigen is CEA.
In another aspect, the present application provides a cell (e.g. host cell), the cell comprising a nucleic acid or a vector or a composition of the present application.
In a specific embodiment, the host cell is a mammalian cell, preferably a human cell.
In a further specific embodiment, the host cell is a T cell or a primary T cell, gamma delta T cell, NK cell, NKT cell, macrophage, B cell, or non-immune cell.
In a further specific embodiment, the host cell is an allogeneic cell.
In another aspect, the present application provides a pharmaceutical composition, the pharmaceutical composition comprising the fusion protein, the nucleic acid, vector, composition or cell of the present application.
In a specific embodiment, the composition further comprises one or more pharmaceutically acceptable excipients.
In another aspect, the present application provides a method of reducing a target membrane-bound protein level in a cell, comprising introducing into a cell a nucleic acid, a vector, or a composition of the present application.
In a specific embodiment, the cell (e.g. host cell) is a mammalian cell, preferably a human cell.
In a further embodiment, the host cell is a T cell or a primary T cell, gamma delta T cell, NK cell, NKT cell, macrophage, B cell, or non-immune cell.
In a further embodiment, the host cell is an allogeneic cell.
In another aspect, the present application provides a method of producing a cell having reduced target membrane-bound protein level, comprising introducing into a cell a nucleic acid, a vector, or a composition of the present application. Preferably, the cell is a mammalian cell, more preferably a human cell; more preferably, the cell is a T cell or a primary T cell, gamma delta T cell, NK cell, NKT cell, macrophage, B cell, or non-immune cell; most preferably the cell is an allogeneic cell.
In another aspect, the present application provides a method of treating a disease, comprising administering to a subject in need thereof a therapeutically effective amount of allogeneic cells having the composition of the present application or administering to a subject in need thereof a therapeutically effective amount of cells of the present application, wherein preferably, the subject has reduced Graft-versus-Host Disease (GvHD). Preferably, the cell is a mammalian cell, more preferably a human cell; more preferably, the cell is a T cell or a primary T cell, gamma delta T cell, NK cell, NKT cell, macrophage, B cell, or non-immune cell; most preferably the cell is an allogeneic cell.
In another aspect, the present application provides a method of reducing or preventing GvHD in a subject associated with the administration of one or more CAR T-cells to the subject, comprising
In another aspect, the present application provides a method of downregulating membrane-bound protein (MBP) in a cell population, comprising adding to said cell population a host cell of the present application, wherein the host cell expresses fusion protein comprising scFv specifically binding to said MBP, and/or the host cell expresses fusion protein comprising a component of MBP or a fragment thereof that has a transmembrane domain.
In a further aspect, the host cell population is a T cell population, preferably a human primary T cell population.
In a further aspect, the MBP is CD3, preferably human CD3
The present application has the following advantages:
The novel features of the present disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure are explained in the following detailed description in the embodiments and the examples.
Unless defined otherwise, technical and scientific terms used herein have the same meaning as generally used in the art to which this application belongs. For purposes of interpreting this specification, the following definitions will apply and whenever appropriate, terms used in the singular will also include the plural and vice versa. As used herein and in the appended claims, the singular forms “a”, “an”, and “the” also refer to the plural forms unless the context clearly dictates otherwise, e.g., reference to “a host cell” includes a plurality of such host cells.
As used herein, a “T cell receptor (TCR) complex”, otherwise known as the TCR/CD3 complex, is a multimeric complex on the T-cell surface whose activation leads to the activation of the T-cell. The complex comprises (i) TCR, and (ii) CD3 T-cell co-receptor. As set forth below, the TCR comprises alpha (α) and beta (β) chains. The CD3 T-cell co-receptor comprises a CD3-gamma (CD3γ) chain, a CD3-delta (CD3δ) chain, two CD3-epsilon (CD3ε) chains and two zeta-(ζ) chains as accessory molecules.
TCRs allow for the antigen-specific activation of T-cells. Every T-cell expresses clonal TCRs which recognize a specific peptide/MHC complex during physical contact between T-cell and antigen-presenting cell-APC (via MHC class II) or any other cell type (via MHC class I). The TCR is a disulfide-linked membrane-anchored heterodimeric protein normally consisting of the highly variable alpha (a) and beta (p) chains. Each chain of the TCR comprises two extracellular domains: a variable (V) region and a constant (C) region, both of immunoglobulin superfamily (IgSF) domain forming antiparallel beta-sheets. The constant region is proximal to the cell membrane, followed by a transmembrane region and a short cytoplasmic tail, while the variable region binds to the peptide/MHC complex. The variable domain of the TCR alpha-chain and the TCR beta-chain each have three hypervariable or complementarity determining regions (CDRs) that contribute to the TCR's specificity for a particular peptide/MHC complex. The variable region of the beta-chain also has an additional area of hypervariability (HV4) that does not normally contact antigen.
A “single-chain variable fragment (scFv)” is a fusion protein of the variable regions of the heavy (VH) and light chains (VL) of an antibody, connected with a short linker peptide of ten to about 25 amino acids. The linker is usually rich in glycine for flexibility, as well as serine or threonine 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 antibody, despite removal of the constant regions and the introduction of the linker. scFv antibodies are, e.g. described in Houston, J. S., Methods in Enzymol. 203 (1991) 46-96). In addition, antibody fragments comprise single chain polypeptides having the characteristics of a VH domain, namely being able to assemble together with a VL domain, or of a VL domain, namely being able to assemble together with a VH domain into a functional antigen binding site and thereby provide the antigen binding property of full length antibodies.
As used herein, “treatment” (and grammatical variations thereof such as “treat” or “treating”) refers to clinical intervention in an attempt to alter the natural course of the individual being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include, but are not limited to, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing metastasis, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis. In some embodiments, the molecules of the application are used to delay development of a disease or to slow the progression of a disease.
The term “cancer” or “tumor” as used herein refers to proliferative diseases, such as ovarian cancer, pancreatic cancer, colon cancer, colorectal cancer, lymphomas, lymphocytic leukemias, lung cancer, non-small cell lung (NSCL) cancer, bronchioloalviolar cell lung cancer, bone cancer, pancreatic cancer, skin cancer, cancer of the head or neck, cutaneous or intraocular melanoma, uterine cancer, ovarian cancer, rectal cancer, cancer of the anal region, stomach cancer, gastric cancer, breast cancer, uterine cancer, carcinoma of the fallopian tubes, carcinoma of the endometrium, carcinoma of the cervix, carcinoma of the vagina, carcinoma of the vulva, Hodgkin's Disease, cancer of the esophagus, cancer of the small intestine, cancer of the endocrine system, cancer of the thyroid gland, cancer of the parathyroid gland, cancer of the adrenal gland, sarcoma of soft tissue, cancer of the urethra, cancer of the penis, prostate cancer, cancer of the bladder, cancer of the kidney or ureter, renal cell carcinoma, carcinoma of the renal pelvis, mesothelioma, hepatocellular cancer, biliary cancer, neoplasms of the central nervous system (CNS), spinal axis tumors, brain stem glioma, glioblastoma multiforme, astrocytomas, schwanomas, ependymonas, medulloblastomas, meningiomas, squamous cell carcinomas, pituitary adenoma and Ewings sarcoma, including refractory versions of any of the above cancers, or a combination of one or more of the above cancers.
Before the various embodiments are described, it is to be understood that the teachings of this disclosure are not limited to the particular embodiments described, and as such can, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present teachings will be limited only by the appended claims.
The present application provides novel fusion proteins with particularly advantageous properties such as reducing the membrane-bound protein (MBP) level when expressed in a host cell.
In the present application, downregulation of Membrane-Bound Proteins (MBPs) is achieved by degradation tag protein-mediated degradation, wherein the degradation tag protein comprises ubiquitin ligase and/or domains of the cell surface receptors that mediate degradation (e.g. IL2Rβ sub domain). The tagging specificity or targeting specificity (or recognition specificity) of the MBPs to be degraded by the degradation tag protein (e.g. ubiquitin ligase or IL2Rβ) is mediated by an antibody (or its antigen-binding fragment) of MBPs to be degraded (that is, antibody mediated substrate recognition), or mediated by subunits or structural domains of the membrane-bound protein or complex to be degraded that have a transmembrane domain (that is, transmembrane domain mediated substrate recognition). The technical solution of the present application can be applied to any targets on a cell surface, independent of cell type. Preferably, the MBPs to be degraded can be membrane-bound receptors or receptor complex; more preferably the membrane-bound receptors can be T-cell receptors (TCRs). Thus, preferably, this application relates to the generation of allogeneic chimeric antigen receptor T cells (CAR-T) through TCR down regulation by targeted ubiquitin-mediated degradation by Receptor TAC (receptor targeting chimera), or to the generation of a fusion protein (e.g. a fusion protein comprising a component of the membrane-bound protein to be degraded or a fragment thereof that has a transmembrane domain fused to the degradation tag protein (e.g. E3 ubiquitin ligase and/or domains of cell surface receptors that mediate degradation)), the degradation tag protein may be incorporated into the multi-subunit TCR complex during the formation of the TCR complex so as to cause downregulation of the TCR complex. Specifically, an antibody (such as an anti-CD3 antibody) or antigen-binding fragment thereof was fused extracellularly with E3 ubiquitin ligase (such as the C-terminus of Hsc70-interacting protein (CHIP)) followed by the transmembrane domain, or an E3 ubiquitin ligase or a cell surface receptor that mediates degradation was fused intracellularly to a component of the membrane-bound protein or complex to be degraded or a fragment thereof that has a transmembrane domain. When expressed in host cells (such as primary T cells), MBP (such as TCR complex) is significantly down regulated. This is a novel MBP downregulation technology that is based on protein degradation. This technology can be applied to any MBP, especially surface receptors, for therapeutic use or for research purposes.
1. Fusion Protein a):
The present application discloses a fusion protein a) comprising: the first linking protein, the degradation tag protein, the first transmembrane domain.
In some embodiments, the fusion protein comprises from N-terminal to C-terminal: the first linking protein, the degradation tag protein, the first transmembrane domain.
In some embodiments, the first linking protein comprises the antibody or antigen-binding fragment of the MBP to be degraded; more preferably, the antibody or antigen-binding fragment of the MBP to be degraded comprises antibody or antigen-binding fragment of CD3, CD5, CD7, PD-L1 or CD47; more preferably, antigen-binding fragment of CD3 comprises SP34 scFv, OKT3 scFv, UCHT1 scFv, UCHT1.Y177T scFv, L2K scFv, F6A scFv, BMA031 scFv, or BMA031.H6L12 scFv; antigen-binding fragment of CD5 comprises αCD5.14 scFv; antigen-binding fragment of CD7 comprises αCD7.TH69 scFv; antigen-binding fragment of PD-L1 comprises αPD-L1 scFv; antigen-binding fragment of CD47 comprises αCD47 scFv.
In some embodiments, the degradation tag protein comprises the E3 ubiquitin ligase; more preferably, the E3 ubiquitin ligase comprises CHIP.dTPR, FBW7.2-293, VHL.152-213, SPOP.167-374, SOCS2.143-198;
In some embodiments, the first transmembrane domain comprises CD8α transmembrane domain.
In some embodiments, the fusion protein a) further comprises a first signal peptide.
Optionally, there also may be a Linker (e.g. SEQ ID No. 91) between scFv and E3 ligase.
Optionally, there also may be a Linker (e.g. SEQ ID No. 91) between CD8α transmembrane domain (CD8 TM) and E3 ligase.
2. Fusion Protein b):
The present application discloses a fusion protein b) comprising: the first linking protein, the first transmembrane domain, the degradation tag protein.
In some embodiments, the fusion protein comprises from N-terminal to C-terminal: the first linking protein, the first transmembrane domain, the degradation tag protein.
In some embodiments, the first linking protein comprises the antibody or antigen-binding fragment of the MBP to be degraded; more preferably, the antibody or antigen-binding fragment of the MBP to be degraded comprises antibody or antigen-binding fragment of CD3; more preferably, antigen-binding fragment of CD3 comprises SP34 scFv;
In some embodiments, the degradation tag protein comprises the E3 ubiquitin ligase; more preferably, E3 ubiquitin ligase comprises GRAIL.IC;
In some embodiments, the first transmembrane domain is selected from one or more of CD3ζ transmembrane domain variant, CD8α transmembrane domain, and CD4 transmembrane domain.
In some embodiments, the fusion protein b) further comprises a first signal peptide.
Optionally, there also may be an intracellular domain (e.g. SEQ ID No. 90) attached to the C-terminal of TM domain of Fusion protein b)(e.g. LG222, LG222.1, LG222.2).
3. Fusion Protein c):
The present application discloses a fusion protein c) comprising: the second transmembrane-linking domain of the above 2), the cell surface receptors that mediate degradation.
In some embodiments, the fusion protein comprises from N-terminal to C-terminal: the second transmembrane-linking domain of the above 2), the cell surface receptors that mediate degradation.
In some embodiments, the second transmembrane-linking domain of the above 2) comprises CD3ζ.ΔIC or CD38.ΔIC;
In some embodiments, the cell surface receptors that mediate degradation comprises IL2Rβjm.
4. Fusion Protein d):
The present application discloses a fusion protein d) comprising: the second transmembrane-linking domain of the above 2), the one or more of an E3 ubiquitin ligase or a variant thereof.
In some embodiments, the fusion protein comprises from N-terminal to C-terminal: the second transmembrane-linking domain of the above 2), the one or more of an E3 ubiquitin ligase or a variant thereof.
In some embodiments, the second transmembrane-linking domain of the above 2) comprises CD3ζ.ΔIC.
In some embodiments, the one or more of an E3 ubiquitin ligase or a variant thereof comprises GRAIL.IC, CHIP.dTPR, RNF133.IC, RNF122.rIC, RNF152.rIC.
5. The Sequences Used in Fusion Proteins
In some embodiments, the SP34 scFv, OKT3 scFv, UCHT1 scFv, UCHT1.Y177T scFv, L2K scFv, F6A scFv, BMA031 scFv, BMA031.H6L12 scFv, αCD5.14 scFv, αCD7.TH69 scFv, αPD-L1 scFv or αCD47 scFv comprises an amino acid sequence at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence shown in any one of SEQ ID NOs. 2-13 respectively.
In some embodiments, the CHIP, CHIP.dTPR, FBW7.2-293, VHL.152-213, SPOP.167-374, SOCS2.143-198, GRAIL.IC, RNF133.IC, RNF122.rIC or RNF152.rIC comprises an amino acid sequence at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence shown in any one of SEQ ID NOs. 21-26, 62, 79, 81 or 83 respectively.
In some embodiments, CD3 transmembrane domain variant, CD8α transmembrane domain, or CD4 transmembrane domain comprises an amino acid sequence at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence shown in SEQ ID NO. 89, 18 or 15 respectively.
In some embodiments, the fusion protein a) further comprises a first signal peptide; preferably, the first signal peptide is selected from an amino acid sequence at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence shown in SEQ ID NO. 19 or 20 respectively.
In some embodiments, the fusion protein b) further comprises a first signal peptide; preferably, the first signal peptide is selected from an amino acid sequence at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence shown in SEQ ID NO. 19.
In some embodiments, the CD3ζ.ΔIC and CD3ε.ΔIC comprises an amino acid sequence at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence shown in SEQ ID NO. 61, 64 respectively. More preferably, the transmembrane domain (TM) of CD3ζ or CD3ε comprises an amino acid sequence at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence shown in SEQ ID NO. 67, 70 respectively; more preferably, the extracellular domain (EM) of CD3ζ or CD3ε comprises an amino acid sequence at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence shown in SEQ ID NO. 66, 69 respectively; more preferably, the second signal peptide of CD3ζ or CD3ε comprises an amino acid sequence at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence shown in SEQ ID NO. 65, 68 respectively.
In some embodiments, the L2Rβ jm domain (IL2Rβjm) comprises an amino acid sequence at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence shown in SEQ ID NO. 58.
In a non-limiting example, the fusion protein of the present application further comprises one or more of a hinge or a P2A-GFP.
In some embodiments, the hinge is selected from a CD8α hinge, or CD4 hinge; more preferably, CD8α hinge or CD4 hinge comprises an amino acid sequence at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence shown in SEQ ID NO.:16 or 14, respectively; more preferably, the hinge is adjacent to the N-terminal of the first transmembrane domain.
In some embodiments, the P2A-GFP comprises an amino acid sequence at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence shown in SEQ ID NO.:57; more preferably, the P2A-GFP sequence is at C-terminal of the fusion protein.
6. The First Transmembrane-Linking Domain Comprises a First Transmembrane Domain and a First Linking Protein
The first linking protein: An antibody of the membrane-bound protein or antigen-binding fragment thereof (e.g. scFv)
An antibody of the membrane-bound protein or antigen-binding fragment thereof (e.g. scFv) can be used as a linking protein that mediates binding (or specificity binding, specificity recognition) of the degradation tag protein to the membrane-bound protein (that is, antibody mediated substrate recognition).
Single-Chain Variable Fragment
The scFvs of the present application are those specifically binding to membrane-bound proteins (including but not limited to CD3, CD5, CD7, PD-1, PD-L1 or CD47), preferably binding to the extracellular part of those membrane-bound proteins. Preferably, the scFvs are those specifically binding to a component (or subunit) of the TCR/CD3 complex.
Thus, in some embodiments, the scFv specifically binds to CD3; for example, the CD3 is a mammalian origin CD3, preferably a human CD3.
The First Transmembrane Domain:
The first transmembrane domain is selected from transmembrane domain of one or more subunits or structural domains of CD8α, CD4, CD3, CD28, 4-1BB and IL2R or a variant thereof.
7. The Second Transmembrane-Linking Domain Comprises a Transmembrane Domain of the MBP to be Degraded or a Variant Thereof
A transmembrane domain of the MBP to be degraded or a variant thereof (Linking protein 2)
In some embodiments, one or more subunits or structural domains (or fragments) of the membrane-bound protein to be degraded or a variant thereof that has a transmembrane domain may be used as a linking protein to mediate incorporation (or specific recognition through incorporation) of the degradation tag protein to the membrane-bound protein, for example, incorporation of the degradation tag protein into the membrane-bound protein during the formation of the membrane-bound protein (that is, transmembrane domain mediated substrate recognition).
In some embodiments, the membrane-bound protein to be degraded is a membrane-bound receptor.
In some embodiments, the membrane-bound receptor is CD3, preferably a mammalian origin CD3, more preferably a human CD3.
In some embodiments, the Linking protein 2 comprises a transmembrane domain of one or more of CD3ζ, CD3γ, CD3δ, CD3ε, CD33α, CD3β or a variant thereof.
In some embodiments, the linking protein 2 comprises an extracellular domain and a transmembrane domain of one or more of CD3ζ, CD3γ, CD3δ, CD3ε, CD33α, CD3β or a variant thereof.
In some embodiments, the linking protein 2 comprises a second signal peptide, extracellular domain and a transmembrane domain of one or more of CD3ζ, CD3γ, CD3δ, CD3ε, CD33α, CD3β or a variant thereof.
8. Degradation Tag Protein 1: E3 Ubiquitin Ligase
“E3 ubiquitin ligase” or “E3 ligase” or “Ubiquitin Ligase” (UL) is used herein to describe a target enzyme(s) binding site of ubiquitin ligase moieties in the bifunctional compounds according to the present application. E3 UL is a protein that in combination with an E2 ubiquitin-conjugating enzyme causes the attachment of ubiquitin to a lysine on a target protein; the E3 ubiquitin ligase targets specific protein substrates for degradation by the proteasome. Thus, E3 ubiquitin ligase alone or in complex with an E2 ubiquitin conjugating enzyme is responsible for the transfer of ubiquitin to targeted proteins. In general, the ubiquitin ligase is involved in polyubiquitination such that a second ubiquitin is attached to the first, a third is attached to the second, and so forth. Polyubiquitination marks proteins for degradation by the proteasome. However, there are some ubiquitination events that are limited to monoubiquitination, in which only a single ubiquitin is added by the ubiquitin ligase to a substrate molecule. Mono-ubiquitinated proteins are not targeted to the proteasome for degradation, but may instead be altered in their cellular location or function, for example, via binding other proteins that have domains capable of binding ubiquitin. Further complicating matters, different lysines on ubiquitin can be targeted by an E3 to make chains. The most common lysine is Lys48 on the ubiquitin chain. This is the lysine used to make polyubiquitin, which is recognized by the proteasome.
In some embodiments, the E3 ubiquitin ligase is selected from the following proteins or the truncated forms thereof. GRAIL, C-terminus of Hsc70-interacting protein (CHIP), CHIP.dTPR, F-box WD40-containing protein 7 (FBW7), FBW7.2-293, von Hippel-Lindau (VHL), VHL.152-213, Speckle-type BTB-POZ protein (SPOP), SPOP.167-374, Ubiquitin-protein ligase E3A (UBE3A), Mouse double minute 2 homolog (MDM2), Anaphase-promoting complex (APC), UBR5, LNX, Casitas B-lineage lymphoma-transforming sequence-like protein 1 (CBLL1), HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 (HACE1), HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 (HECW1), HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 (HECW2), HECT And RLD Domain Containing E3 Ubiquitin Protein Ligase 1 (HERC1), HERC2, HERC3, HERC4, HERC5, HERC6, HUWE1, ITCH, neural precursor cell expressed developmentally down-regulated protein 4 (NEDD4), Neural precursor cell expressed developmentally downregulated gene 4-like (NEDD4L), Peptidylprolyl isomerase (cyclophilin)-like 2 (PPIL2), PIAS1, PIAS2, PIAS3, PIAS4, RANBP2, RNF4, RBX1, SMURF1, SMURF2, STUB1, TOPORS, TRIP12, UBE3A, UBE3B, UBE3C, UBE3D, UBE4A, UBE4B, UBOX5, UBR5, WWP1, WWP2, Parkin, MKRN1, GRAIL.IC, RNF133.IC, RNF122.rIC or RNF152.rIC.
In the present application, the E3 Ubiquitin ligase is used as a degradation tag protein, and the degradation of MBP mediated by E3 Ubiquitin ligase also can be achieved extracellularly and/or intracellularly.
Degradation Tag Protein 2: One or More Subunits or Structural Domains of Cell Surface Receptors that Mediate Degradation
The one or more subunits or structural domains of cell surface receptors that mediate degradation (that is, a degradation tag protein) may be a protein that mediates degradation (or endocytosis and degradation, degradation after endocytosis) of the MBP or a component thereof, and for example, the degradation of the MBP or a component thereof mediated by one or more subunits or structural domains of the cell surface receptors may be accomplished intracellularly by an E3 ubiquitin ligase, a lysosome or other degradation pathways, and possibly after endocytosis of the MBP or a component thereof.
The one or more subunits or structural domains of the cell surface receptors that mediate degradation is specifically incorporated into MBP or a component thereof by fusing to a component of the membrane-bound protein (MBP) that is used to form the MBP during the formation of the MBP. Further, the component of the MBP that is used to form the MBP can be one or more domains of the MBP, optionally, one or more domains of CD3ε or CD3ζ.
The cell surface receptors that mediate degradation are usually different from the MBP to be degraded, although the cell surface receptors may also belong to a MBP.
In some embodiments, the cell surface receptors that mediate degradation and are used as the degradation tag protein of the present application comprise Interleukin receptors, or a variant derived therefrom.
In some embodiments, the subunits or structural domains of Interleukin receptors comprises a lysosomal targeting motif of IL-2R; preferably, the lysosomal targeting motif of IL-2R comprises L2Rβ jm domain.
9. Transmembrane Domain
“Transmembrane domain” includes an amino acid sequence of about 15 amino acid residues in length which spans the plasma membrane. More preferably, a transmembrane domain includes about at least 20, 25, 30, 35, 40, or 45 amino acid residues and spans the plasma membrane. Transmembrane domains are rich in hydrophobic residues, and typically have an alpha-helical structure. In a preferred embodiment, at least 50%, 60%, 70%, 80%, 90%, 95% or more of the amino acids of a transmembrane domain are hydrophobic, e.g., leucines, isoleucines, tyrosines, or tryptophans. Transmembrane domains are described in, for example, Zagotta, W. N. et al. (1996) Annu. Rev. Neurosci. 19:235-263, the contents of which are incorporated herein by reference.
The function of transmembrane domain in the fusion protein is to anchor said fusion protein to the cell surface, and thus any transmembrane domain fulfilling that function can be used in the present application.
A transmembrane domain suitable for the present application can be selected from the following: CD8α, CD28, 4-1BB or IL2R transmembrane domain, that is, the first transmembrane domain in above 6.
A transmembrane domain suitable for the present application also can be, a transmembrane domain that is a structural domain of the linking protein itself, that is, the transmembrane domain in above 7.
The present application provides a nucleic acid encoding the fusion proteins described herein. The nucleic acid encoding the fusion proteins can be easily prepared from an amino acid sequence of the specified fusion proteins by a conventional method. A nucleotide sequence encoding an amino acid sequence can be obtained from the aforementioned NCBI RefSeq IDs or accession numbers of GenBank for an amino acid sequence of each domain, and the nucleic acid of the present disclosure can be prepared using a standard molecular biological and/or chemical procedure. For example, based on the nucleotide sequence, a nucleic acid can be synthesized, and the nucleic acid of the present disclosure can be prepared by combining DNA fragments which are obtained from a cDNA library using a polymerase chain reaction (PCR).
The nucleic acid of the present disclosure can be linked to another nucleic acid so as to be expressed under control of a suitable promoter. Examples of the promoter include a promoter that constitutively promotes the expression of a gene or operatively linked construct, a promoter that induces the expression of a gene or operatively linked construct by the action of a drug or the like (e.g. tetracycline or doxorubicin). The nucleic acid of the present disclosure can be also linked to, in order to attain efficient transcription of the nucleic acid, other regulatory elements that cooperate with a promoter or a transcription initiation site, for example, a nucleic acid comprising an enhancer sequence or a terminator sequence. In addition to the nucleic acid of the present disclosure, a gene that can be a marker for confirming expression of the nucleic acid (e.g. a drug resistance gene, a gene encoding a reporter enzyme, or a gene encoding a fluorescent protein) may be incorporated.
In an embodiment, the nucleic acid is codon-optimized nucleic acid for expression in a particular host.
The present application further provides a vector comprising nucleic acid encoding the fusion proteins described herein. The term “vector”, “expression vector”, and “expression construct” or “construct” are used interchangeably, and are both defined to be a plasmid, virus, or other nucleic acid designed for protein expression in a cell. The vector or construct is used to introduce a gene into a host cell whereby the vector will interact with polymerases in the cell to express the protein encoded in the vector/construct. The expression vector and/or expression construct may exist in a cell extrachromosomally or integrated into the chromosome. When integrated into the chromosome the nucleic acids comprising the expression vector or expression construct will be an expression vector or expression construct.
The present application further provides a composition comprising at least one nucleic acid or at least one vector described herein.
The present application further provides a composition comprising a first nucleic acid and a second nucleic acid, comprising a first vector having a first nucleic acid and a second vector having a second nucleic acid, or comprising a vector having a first nucleic acid and a second nucleic acid, wherein
In some embodiments, the predetermined antigen is a tumor-related antigen.
In some embodiments, the tumor-related antigen is selected from the following group: CEA, Claudin 18.2, GPC3, Receptor tyrosine kinase-like Orphan Receptor 1 (ROR1), CD38, CD19, CD20, CD22, BCMA, CAIX, CD446, CD133, EGFR, EGFRvIII, EpCam, GD2, EphA2, Her1, Her2, ICAM-1, IL13Ra2, Mesothelin, MUC1, MUC16, NKG2D, PSCA, NY-ESO-1, MART-1, WT1, MAGE-A10, MAGE-A3, MAGE-A4, EBV, NKG2D, PD1, PD-L1, CD25, IL-2, and CD3.
In some embodiments, the tumor-related antigen is CEA.
The present application provides a host cell comprising the nucleic acid or vector or composition described herein. Thus, when expressed, the fusion proteins described herein will be expressed on the surface of the host cells for cell therapy.
In some embodiments, the host cell is an allogeneic cell.
In some embodiments, the host cell is a mammalian cell, preferably a primate cell, more preferably a human cell.
In some embodiments, the host cell is selected from a T cell, or a primary T cell gamma delta T cell, NK cell, NKT cell, macrophage, B cell, or non-immune cell.
Pharmaceutical compositions of the present application comprise a fusion protein-expressing cell, preferably a fusion protein and a CAR-expressing cell, as described herein, in combination with one or more pharmaceutically or physiologically acceptable carriers, diluents or excipients. Such compositions may comprise buffers such as neutral-buffered saline, phosphate-buffered saline and the like; carbohydrates such as glucose, mannose, sucrose, dextrans, or mannitol; proteins, polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; adjuvants (e.g., aluminum hydroxide); and preservatives. Compositions of the present application are in one aspect formulated for intravenous administration.
Pharmaceutical compositions of the present application may be administered in a manner appropriate to the disease to be treated (or prevented). The quantity and frequency of administration will be determined by such factors as the condition of the patient, and the type and severity of the patient's disease, although appropriate dosages may be determined through clinical trials.
Suitable pharmaceutically acceptable excipients are well known to a person skilled in the art. Examples of pharmaceutically acceptable excipients include phosphate-buffered saline (e.g. 0.01 M phosphate, 0.138 M NaCl, 0.0027 M KCl, pH 7.4), an aqueous solution containing a mineral acid salt such as a hydrochloride, a hydrobromide, a phosphate, or a sulfate, saline, a solution of glycol or ethanol, and a salt of an organic acid such as an acetate, a propionate, a malonate or a benzoate. In some embodiments, an adjuvant such as a wetting agent or an emulsifier, and a pH buffering agent can also be used. In some embodiments, the pharmaceutically acceptable excipients described in Remington's Pharmaceutical Sciences (Mack Pub. Co., N.J. 1991) (which is incorporated herein by reference in its entirety for all purposes) can be appropriately used. The composition of the present application can be formulated into a known form suitable for parenteral administration, for example, injection or infusion. In some embodiments, the composition of the present application may comprise formulation additives such as a suspending agent, a preservative, a stabilizer and/or a dispersant, and a preservation agent for extending a validity term during storage.
The present application provides a method of treating disease in a subject in need thereof, comprising administering to the subject an effective amount of the pharmaceutical composition described herein.
In some embodiments, the disease is cancer.
In some embodiments, the cancer is hematological malignancy or solid tumor.
In some embodiments, the cancer is ovarian cancer, pancreatic cancer, colon cancer, colorectal cancer, lymphoma, esophageal cancer, lung cancer, ovarian cancer, hepatic cancer, head-neck cancer, or cancer of the gallbladder.
The present application provides a method of producing a cell having reduced target membrane-bound protein level, comprising introducing into a cell a nucleic acid, a vector, or a composition described herein.
The present application provides a method of reducing or preventing GvHD in a subject associated with the administration of one or more CAR T-cells to the subject, comprising:
The present application provides a method of downregulating membrane-bound protein (MBP) in a cell population, comprising adding to said cell population a host cell of the application, wherein the host cell expresses fusion protein comprising scFv specifically binding to said MBP, and/or the host cell expresses a fusion protein comprising a component of the MBP or a fragment thereof that has a transmembrane domain.
Preferably, the host cell population is a T cell population, preferably a human primary T cell population.
Preferably, the MBP is CD3, preferably human CD3.
Illustrative Sequences in this Disclosure
LS008, SP-αCD19 scFv-CD8α-hinge/TM-P2A-eGFP (
LG089, E3 ligase FBW7 fragment (2-293) linked to N-terminus of SP34 scFv (FBW7-SP34 scFv-P2A-eGFP);
LG091, E3 ligase VHL fragment (152-213) linked to C-terminus of SP34 scFv (SP34 scFv-VHL-P2A-eGFP);
LG092, E3 ligase SPOP fragment (167-374) linked to C-terminus of SP34 scFv (SP34 scFv-SPOP-P2A-eGFP);
LG085, E3 ligase CHIP fragment (128-303, CHIP.dTPR) linked to C-terminus of OKT3 scFv (OKT3 scFv-hCHTP.dTPR-P2A-eGFP);
LG021, SP34 scFv-CD8α-hinge/TM-P2A-eGFP;
LG022, membrane-anchored Signal Peptide (SP)-SP34 scFv-CD8α-hinge/TM-P2A-eGFP;
LG023, cytoplasmic OKT3 scFv-CD8α-hinge/TM-P2A-eGFP;
LG024, SP OKT3 scFv-CD8α-hinge/TM-P2A-eGFP;
LG112, SP-OKT3 scFv-CHIP.dTPR-CD8α hinge/TM-P2A-eGFP;
LG113, SP OKT3 scFv-CD8α hinge/TM CHIP.dTPR-P2A-eGFP;
LG114, SP-OKT3 scFv-FBW7-CD8α hinge/TM-P2A-eGFP;
LG115, SP-OKT3 scFv-VHL-CD8α hinge/TM-P2A-eGFP;
LG116, SP-OKT3 scFv-SPOP-CD8α hinge/TM-P2A-eGFP;
LG117, SP-OKT3 scFv-SOCS2-CD8α hinge/TM-P2A-eGFP;
LG118, SP-SP34 scFv-hCHIP.dTPR-CD8α hinge/TM-P2A-eGFP;
LG123, SP-UCHT1 scFv-hCHIP.dTPR-CD8α hinge/TM-P2A-eGFP;
LG124, SP-UCHT1.Y177T scFv-hCHIP.dTPR-CD8α hinge/TM-P2A-eGFP;
LG125, SP-L2K scFv-hCHIP.dTPR-CD8α hinge/TM-P2A-eGFP;
LG126, SP-F6A scFv-hCHIP.dTPR-CD8α hinge/TM-P2A-eGFP;
LG119, SP-BMA031.wt scFv-hCHIP.dTPR-CD8α hinge/TM-P2A-eGFP;
LG120, SP-BMA031.H6L12 scFv-hCHIP.dTPR-CD8α hinge/TM-P2A-eGFP
LG133, SP-BMA031.wt scFv-CD8α hinge/TM-P2A-eGFP
LG134, SP-BMA031.H6L12 scFv-CD8α hinge/TM-P2A-eGFP
CD5, CD7, PD-L1, CD47 Downregulation Constructs
LG137, SP-αCD5.14 scFv-hCHIP.dTPR-CD8α hinge/TM-P2A-eGFP;
LG138, SP-αCD7.TH69 scFv-hCHIP.dTPR-CD8α hinge/TM-P2A-eGFP;
MLB052, SP-αPD-L1 scFv hCHIP.dTPR-CD8α hinge/TM-P2A-eGFP;
MLB053, SP-αCD47 scFv hCHIP.dTPR-CD8α hinge/TM-P2A-eGFP;
Optionally, there also may be a Linker (e.g. SEQ ID No. 91) between scFv and E3 ligase.
Optionally, there also may be a Linker (e.g. SEQ ID No. 91) between CD8 TM and E3 ligase.
LG222, SP-SP34 CD3ζ.ΔIC-1-GRAIL.IC-P2A-eGFP
LG222.1, SP-SP34-CD8α hinge/TM-GRAIL.IC-P2A-eGFP
LG222.2, SP-SP34-CD4 hinge/TM-GRAIL.IC-P2A-Egfp
Optionally, there also may be an intracellular domain (e.g. SEQ ID No. 90) attached to the C-terminal of TM domain of LG222, LG222.1, LG222.2.
MLB014, CD3ζ.ΔIC IL2Rβjm P2A-eGFP;
MLB046, CD3ε.ΔIC IL2Rβjm P2A-eGFP;
LG171, CD3ζ.ΔIC-GRAIL.IC-P2A-eGFP
LG212, CD3ζ.ΔIC-P2A-eGFP
LG171.ZF, CD3ζ.ΔIC-GRAIL.ZF mutant P2A-GFP
LG171.H2N2, CD3ζ.ΔIC-GRAIL.IC.H2N2 mutant P2A-GFP
LG171p1, CAG-CD3ζ.ΔIC-GRAIL.IC-P2A-eGFP
LG132, CD3 CHIP.DTPR-P2A-GFP
LG213, CD3ζ.ΔIC-CHIP.DTPR-P2A-GFP
RNF133, RNF133-P2A-GFP
LG174, CD3ζ.ΔIC-RNF133.IC-P2A-GFP
RNF122, RNF122-P2A-GFP
LG180, CD3ζ.ΔIC-RNF122.rIC-P2A-GFP
RNF152, RNF152-P2A-GFP
LG183, CD3ζ.ΔIC-RNF152.rIC-P2A-GFP.
Validation of Cytoplasmic Constructs (LG089, LG091, LG092, LG085) on TCR/CD3 Complex in Human Primary T Cells
Human isolated primary T cells were activated in vitro using StemCell Immunocult-XF/Activator (StemCell Technologies) for 3 days, in the presence of human IL-2, IL-7 and IL-15. Then the activated primary T cells were collected and electroporated with pBluescript II SK(+)-PB Donor plasmid expressing one of the cytoplasmic constructs (LG089, LG091, LG092, LG085 constructs) for TCR/CD3 degradation. Two days later, the primary T cells were harvested and stained for both CD3 (PE) and TCRα/β (APC) (Biolegend). Both pmaxGFP (plasmid only express GFP) and LS008 indicated a good transfection efficiency in primary T cells, and there was no downregulation of TCRα/β and CD3 in either of these two constructs (
Validation of Membrane-Anchored Constructs (LG021, LG022, LG023, LG024) on TCR/CD3 Complex in Human Primary T Cells and Jurkat Cell Line.
Human isolated primary T cells were activated in vitro using StemCell Immunocult-XF/Activator for 3 days, in the presence of human IL-2, IL-7 and IL-15. Then the activated primary T cells were collected and electroporated with plasmid expressing one of the cytoplasmic/membrane-anchored constructs (LG021, LG022, LG023, LG024) for TCR/CD3 degradation. Two days later, the primary T cells were harvested and stained for both CD3 (PE) and TCRα/β (APC). Results showed that the usage of SP34 scFv without E3 ligase/ubiquitin could not elicit any downregulation of TCR/CD3 regardless of whether it is expressed in the cytoplasm (LG021) (
The Jurkat cells were electroporated with both PiggyBac transposase mRNA and transposon expressing the membrane-anchored OKT3 construct (LG024). The Jurkat Cells were maintained until day 57 and subjected to flow cytometry testing post staining with CD3 (PE) and TCRα/β (APC), showing a significant degradation of TCR/CD3 complex in cells with stable integration of transposon expressing the membrane-anchored OKT3 construct (LG024) (>85% in GFP positive,
Validation of E3 Ubiquitin Ligase Linkage to Membrane-Anchored OKT3 Constructs (LG112, LG113) on TCR/CD3 Complex in Jurkat Cell Line and Human Primary T Cells
1. Validation of Constructs (LG112, LG113) Using Jurkat Cells
Jurkat cells were electroporated with both PiggyBac transposase mRNA and transposon-expressing membrane-anchored OKT3 constructs linked to E3 ubiquitin ligase in different manners (LG112, LG113). The Jurkat Cells were harvested on day 3 and subjected to flow cytometry analysis post staining with CD3 (PE) and TCRα/β (APC).
2. Validation of Constructs (LG112, LG113) Using Human Isolated Primary T Cells
Human isolated primary T cells were activated in vitro using StemCell Immunocult-XF/Activator for 3 days, in the presence of human IL-2, IL-7 and IL-15. Then the primary T cells were collected and electroporated with both PiggyBac transposase mRNA and transposon expressing different membrane-anchored OKT3 constructs. Three days later, the primary T cells were harvested and stained for both CD3 (PE) and TCRα/β (APC).
A list of constructs with different E3 ligases, including FBW7, VHL, SPOP and SOCS2, linked to membrane-anchored OKT3 scFv were designed and synthesized (
A list of TCR/CD3 degradation constructs with different CD3 targeting scFv, including SP34, UCHT1, UCHT1.Y177T, L2K and F6A, were designed and synthesized (
A list of TCR degradation constructs with TCR targeting scFv, BMA031 or BMA031.H6L12, were designed and synthesized in the presence or absence of CHIP.dTPR (
Jurkat-NFAT cells were electroporated with both PiggyBac transposase mRNA and transposon expressing different membrane-anchored OKT3 constructs (LG024, LG112) or control LS008. Cells were maintained for 14 days and their activation status before and after CD3/CD28/CD2 Immunocult/Activator re-stimulation was checked. Expression of the constructs LG024, LG112 was inferred by joint GFP expression (vertical coordinates of the right panel in
A list of CD5 or CD7 degradation constructs were designed and synthesized (
Transposon-mediated delivery of E3 ligase constructs was used to modify expression of surface molecules in Jurkat cells (
To confirm that the E3 ligase construct was able to downregulate surface molecules on adjacent cells in an antigen-specific manner, we designed a co-culture experiment between Jurkat cells transduced to express LG112 and parental stock cells. To distinguish between the two populations, the parental Jurkat cells were labeled with CellTrace Violet dye.
To enhance the specific engagement between CD3 and GRAIL.IC (E3 functional domain), CD3-targeting scFv, SP34, was adopted and linked to GRAIL.IC through different hinge/transmembrane domains as listed in
1. LG222, LG222.1 and LG222.2 were Tested in Both Jurkat Cells.
At day 3 post-electroporation, Jurkat cells were harvested and stained for TCR expression using αCD3 and αTCR α/β antibodies. Cells expressing the construct were identified based on GFP co-expression on the fusion protein constructs. Results showed that both CD3ζ.ΔIC(LG222) (
2. LG222, LG222.1 and LG222.2 were Tested in Human Primary T Cells.
Pre-activated primary T cells electroporated for expressing LG222, LG222.1 or LG222.2 construct were harvested at day 3 post-electroporation and TCR/CD3 expression was evaluated using both αCD3 and αTCR α/β antibodies (
MLB014/(CD3ζ.ΔIC-IL2Rβjm) construct and MLB046/(CD3ε.ΔIC-IL2Rβjm) construct are shown in
1. Jurkat Cells Transfected with MLB014 or MLB046
At day 5 post-electroporation with either MLB014/(CD3ζ.ΔIC-IL2Rβjm) construct or MLB046/(CD3ε.ΔIC-IL2Rβjm) construct, Jurkat cells were harvested and stained for TCR expression using an αCD3 antibody (i.e. anti-CD3 antibody). Cells expressing the construct were identified based on GFP co-expression on the fusion protein constructs. Gating on the GFP positive population indicated that there was a large negative shift in detectable TCR surface expression (upper left area in the second and third panel from left to right of
2. Primary T Cells Transfected with MLB014 or MLB046
Primary T cells electroporated for expressing either MLB014/(CD3ζ.ΔIC-IL2Rβjm) construct or MLB046/(CD3ε.ΔIC-IL2Rβjm) were harvested at day 5 post-electroporation and TCR expression was evaluated using both αCD3 and αTCRα/β antibodies (
1. Jurkat Cells Transfected with LG171
LG171/(CD3ζ.ΔIC/GRAIL.IC) fusion protein construct is shown in
At day 3 post-electroporation with LG171 (i.e. CD3ζ.ΔIC-GRAIL.IC) fusion protein construct, Jurkat cells were harvested and stained for TCR expression using an αCD3 antibody and αTCR α/β antibody. Cells expressing the construct were identified based on GFP co-expression on the fusion protein constructs. Gating on the GFP positive population indicated that there was a majority shift into undetectable TCR surface expression. These data suggest that incorporation of CD3ζ.ΔIC/GRAIL.IC construct into the TCR complex promotes increased instability of the entire complex (
2. Primary T Cells Transfected with LG171
Primary T cells electroporated for expressing LG171 (i.e. CD3ζ.ΔIC-GRAIL.IC) construct were harvested at day 3 post-electroporation and TCR/CD3 expression was evaluated using both αCD3 and αTCRα/β antibodies (
3. LG212 (without E3 Ligase)
Primary T cells were electroporated with PiggyBac vector LG212 and PiggyBac Transposase. At day 3 post-electroporation, TCR expression was evaluated by staining for CD3 and TCRα/β. We could not see any TCR/CD3 downregulation when only truncated CD3ζ (i.e. CD3ζ.ΔIC) was adopted in human primary T cells (
4. Primary T Cells Transfected with Construct LG171.ZF (Contains Domain Switch) or LG171.H2N2 (Contains Point Mutation)
Two more constructs LG171.ZF, LG171.H2N2 were generated by switching zinc-finger domain (SEQ ID NO. 84) in GRAIL with CD8α hinge (SEQ ID NO. 85) or introducing point mutations into the zinc-finger domain (
5. LG171 Chimeric Proteins could not Confer Non-Specific Downregulation of CD5 or CD7
As with the Jurkat reporter cells, primary T cells were electroporated with PiggyBac vector LG171 and PiggyBac Transposase. At day 3 post-electroporation, both CD5 and CD7 expressions were evaluated by flow cytometry. The downregulation effect in primary T cells by LG171 was TCR/CD3 specific, as neither CD5 nor CD7 was affected at all (
6. T Cells Transfected with LG171p1/(CAG/CD3ζ.ΔIC/GRAIL.IC)
CAG promoter is a good alternative conferring significant and sustainable downregulation of TCR/CD3 complex in both Jurkat cells and human primary T cells
Other than EF1a promoter tested in the other examples, CAG promoter was also investigated base on LG171 design. To achieve this purpose, new construct LG171p1 was designed (
6.1 Jurkat Cells Transfected with LG171p1
At day 3 post-electroporation with LG171p1/(CAG/CD3ζ. ΔIC/GRAIL.IC) fusion protein construct (
6.2 Primary T Cells Transfected with LG171p1
Pre-activated primary T cells electroporated for expressing LG171p1 construct were harvested at day 3 post-electroporation and TCR/CD3 expression was evaluated using both αCD3 and αTCRα/β antibodies (
1. We also tested CHIP for TCR downregulation in a similar design as LG171 (
1. CD69, ppERK Levels in Jurkat Cells Transfected with Indicated Constructs
To check the impacts on activation, Jurkat cells transfected with indicated constructs were briefly stimulated by αCD3/CD28 (anti CD3/CD28 antibody) and then tested for CD69 upregulation and intracellular ERK phosphorylation (i.e. ppERK or ERK) levels. Both assays showed that LG171 significantly diminished the upregulation of CD69 and ERK phosphorylation (
2. IFN-γ Level in Primary T Cell Transfected with Indicated Constructs
We also tested the impacts on human primary T cell activation. Pre-activated primary T cells were transfected with indicated constructs. Several days later, T cells were re-stimulated with OKT3 (anti CD3 antibody) for CD69 upregulation and IFN-γ cytokine secretion. Similar to what we found in Jurkat, human primary T cells transfected with either LG171 or LG171p1 (CAG promoter) showed significant lower CD69 upregulation (
To further confirm this finding, MLR assay was employed (
To date, all CAR T cell therapies currently approved for clinical use rely on autologous T cell engineering and re-engraftment. To standardize therapies across donors and reduce the cost of CAR T cell therapies, there is a need to develop robust allogeneic T cell technologies.
1. CldnCar and LG171.CldnCar fusion protein construct are shown in
2. TCR downregulation is detected by αCD3ε (anti-CD3 antibody, for CD3 expression) and CAR expression is detected by αF(ab′)2 staining (for scFv expression); the results are shown in
T cells expressing the ReceptorTAC/CAR construct were gated on GFP expression (the first peak from top to bottom in both left and right panels of
3. To test CAR functionality in the TCR-deficient T cells, we assayed their cytotoxic potential against HEK-cldn18.2 cells, which are transduced to overexpress CLDN18.2, and HEK293T cells (i.e. parental HEK cells), which are claudin18.2-negative, the results are shown in
From the left panel of
4. Taken together, we have shown that E3 ligase fusion proteins can be used to downregulate TCR expression and prevent T cell activation, and that this effect is TCR-specific and does not affect CAR efficacy in a co-expression system. Thus, we believe that the ReceptorTAC platform represents a novel means of generating allogeneic CAR T cells through manipulation of TCR expression at the protein level.
It is to be understood that while the disclosure has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the disclosure, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.
The various embodiments described above can be combined to provide further embodiments. All of the U.S. patents, U.S. patent application publications, U.S. patent applications, foreign patents, foreign patent applications and non-patent publications referred to in this specification and/or listed in the Application Data Sheet are incorporated herein by reference, in their entirety. Aspects of the embodiments can be modified, if necessary, to employ concepts of the various patents, applications and publications to provide yet further embodiments.
These and other changes can be made to the embodiments in light of the above-detailed description. In general, in the following claims, the terms used should not be construed to limit the claims to the specific embodiments disclosed in the specification and the claims, but should be construed to include all possible embodiments along with the full scope of equivalents to which such claims are entitled. Accordingly, the claims are not limited by the disclosure.
This application claims the benefit of U.S. Provisional Patent Application No. 63/077,658, entitled “Downregulation of Membrane-Bound Proteins by Receptor TAC Technology”, filed on Sep. 13, 2020, U.S. Provisional Patent Application No. 63/144,945, entitled “Downregulation of Membrane-Bound Proteins by Receptor TAC Technology” filed on Feb. 2, 2021, and U.S. Provisional Patent Application No. 63/173,476, entitled “Downregulation of Membrane-Bound Proteins by Receptor TAC Technology” filed on Apr. 11, 2021; the contents of which are herein incorporated by reference in their entireties. This invention was made subject to a joint research agreement between SHANDONG BOAN BIOTECHNOLOGY CO., LTD. and Boan Boston LLC.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CN2021/117886 | 9/13/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63173476 | Apr 2021 | US | |
| 63144945 | Feb 2021 | US | |
| 63077658 | Sep 2020 | US |
